@article {pmid39629059,
year = {2024},
author = {Pecsi, EL and Forbes, S and Guillemette, F},
title = {Organic Matter Composition as a Driver of Soil Bacterial Responses to Pig Carcass Decomposition in a Canadian Continental Climate.},
journal = {Journal of geophysical research. Biogeosciences},
volume = {129},
number = {12},
pages = {e2024JG008355},
pmid = {39629059},
issn = {2169-8953},
abstract = {Organic by-products are released into the surrounding soil during the terrestrial decomposition of animal remains. The affected area, known as the Cadaver Decomposition Island (CDI), can undergo biochemical changes that contribute to landscape heterogeneity. Soil bacteria are highly sensitive to labile inputs, but it is unknown how they respond to shifts in dissolved organic matter (DOM) quantity and quality resulting from animal decomposition. We aimed to evaluate the relationship between soil DOM composition and bacterial activity/function in CDIs under a Canadian temperate continental climate. This was studied in soils surrounding adult pig carcasses (n = 3) that were surface deposited within a mixed forested environment (Trois-Rivières, Québec) in June 2019. Using fluorescence spectroscopy and dissolved organic carbon analyses, we detected a pulse of labile protein-like DOM during the summer season (day 55). This was found to be an important driver of heightened soil bacterial respiration, cell abundance and potential carbohydrate metabolism. These bacterial disturbances persisted into the cooler autumn season (day 156) and led to the gradual transformation of labile DOM inputs into microbially sourced humic-like compounds. By the spring (day 324), DOM quantities and bacterial measures almost recovered, but DOM quality remained distinct from surrounding vegetal humic signals. All observed effects were spatially constrained to the topsoil (A-horizon) and within 20 cm laterally from the carcasses. These findings provide valuable insight into CDI organic matter cycling within a cold-climate ecosystem. Repeated CDI studies will however be required to capture the changing dynamics resulting from increasing global temperatures.},
}

@article {pmid39628456,
year = {2024},
author = {Sinclair, JS and Buchner, D and Gessner, MO and Müller, J and Pauls, SU and Stoll, S and Welti, EAR and Bässler, C and Buse, J and Dziock, F and Enss, J and Hörren, T and Künast, R and Li, Y and Marten, A and Morkel, C and Richter, R and Seibold, S and Sorg, M and Twietmeyer, S and Weis, D and Weisser, W and Wiggering, B and Wilmking, M and Zotz, G and Frenzel, M and Leese, F and Haase, P},
title = {Effects of land cover and protected areas on flying insect diversity.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e14425},
doi = {10.1111/cobi.14425},
pmid = {39628456},
issn = {1523-1739},
support = {//Hessisches Landesamt für Umwelt und Geologie/ ; //LOEWE Centre for Translational Biodiversity Genomics/ ; 871128//EU Horizon project eLTER PLUS/ ; },
abstract = {Widespread insect losses are a critical global problem. Mitigating this problem requires identifying the principal drivers across different taxa and determining which insects are covered by protected areas. However, doing so is hindered by missing information on most species owing to extremely high insect diversity and difficulties in morphological identification. To address this knowledge gap, we used one of the most comprehensive insect DNA metabarcoding data sets assembled (encompassing 31,846 flying insect species) in which data were collected from a network of 75 Malaise traps distributed across Germany. Collection sites encompass gradients of land cover, weather, and climate, along with differences in site protection status, which allowed us to gain broader insights into how insects respond to these factors. We examined changes in total insect biomass, species richness, temporal turnover, and shifts in the composition of taxa, key functional groups (pollinators, threatened species, and invasive species), and feeding traits. Lower insect biomass generally equated to lower richness of all insects and higher temporal turnover, suggesting that biomass loss translates to biodiversity loss and less stable communities. Spatial variability in insect biomass and composition was primarily driven by land cover, rather than weather or climate change. As vegetation and land-cover heterogeneity increased, insect biomass increased by 50% in 2019 and 56% in 2020 and total species richness by 58% and 33%, respectively. Similarly, areas with low-vegetation habitats exhibited the highest richness of key taxa, including pollinators and threatened species, and the widest variety of feeding traits. However, these habitats tended to be less protected despite their higher diversity. Our results highlight the value of heterogeneous low vegetation for promoting overall insect biomass and diversity and that better protection of insects requires improved protection and management of unforested areas, where many biodiversity hotspots and key taxa occur.},
}

@article {pmid39624182,
year = {2024},
author = {Wirth, JS and Katz, LS and Williams, GM and Chen, JC},
title = {primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.},
journal = {Journal of open source software},
volume = {9},
number = {101},
pages = {},
pmid = {39624182},
issn = {2475-9066},
abstract = {In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives. An "ingroup" refers to a group of microbes that are the primary focus of study or interest. Conversely, an "outgroup" consists of microbes that are closely-related to, but have evolved separately from, the ingroup. While whole genome sequencing and downstream phylogenetic analyses can be employed to do this, these techniques are often slow and can be resource intensive. Additionally, the laboratory would have to sequence the whole genome to use these tools to determine whether or not a new sample is part of the ingroup or outgroup. Alternatively, polymerase chain reaction (PCR) can be used to amplify regions of genetic material that are specific to the strain(s) of interest. PCR is faster, less expensive, and more accessible than whole genome sequencing, so having a PCR-based approach can accelerate the detection of specific strain(s) of microbes and facilitate diagnoses and/or population studies.},
}

@article {pmid39621250,
year = {2024},
author = {Lin, X and Lin, C and Li, X and Yao, F and Guo, X and Wang, M and Zeng, M and Yuan, Y and Xie, Q and Huang, X and Jiao, X},
title = {Gut Microbiota Dysbiosis Facilitates Susceptibility to Bloodstream Infection.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39621250},
issn = {1976-3794},
support = {201224106490150//Shantou Science and Technology Project/ ; },
abstract = {To study the role of intestinal flora in the development of bloodstream infections (BSIs). 42 patients and 19 healthy controls (HCs) were screened into the study and their intestinal flora was measured by 16S rRNA gene sequencing. The bacterial diversity was significantly lower in the BSI group compared with that in the HCs (P < 0.001), and beta diversity was significantly differentiated between the two groups (PERMANOVA, P = 0.001). The four keystone species [Roseburia, Faecalibacterium, Prevotella, and Enterococcus (LDA > 4)] differed significantly between the two groups. Dysbiosis of fecal microbial ecology is a common condition present in patients with BSI. The proliferation of certain pathogens or reduction of SCFA-producing bacteria would cause susceptibility to BSI.},
}

@article {pmid39619625,
year = {2024},
author = {Sakarika, M and Matassa, S and Carvajal-Arroyo, JM and Ganigué, R},
title = {Editorial: Microbial biorefineries for a more sustainable, circular economy.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1512756},
doi = {10.3389/fbioe.2024.1512756},
pmid = {39619625},
issn = {2296-4185},
}

@article {pmid39612478,
year = {2024},
author = {Zhao, Y and Ran, W and Xu, W and Song, Y},
title = {ITS amplicon sequencing revealed that rare taxa of tea rhizosphere fungi are closely related to the environment and provide feedback on tea tree diseases.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0188924},
doi = {10.1128/spectrum.01889-24},
pmid = {39612478},
issn = {2165-0497},
abstract = {The rhizospheres of plants and soil microorganisms are intricately interconnected. Tea trees are cultivated extensively on the karst plateau of Guizhou Province, China; however, the understanding of the interactions among fungal communities, community taxa, and diseases impacting tea tree in the soil rhizosphere is limited. Our aim is to offer insights for the advancement of modern agriculture in ecologically fragile karst tea gardens, as well as microbiomics concepts for green and sustainable environmental development. This study utilized the internal transcribed spacer high-throughput sequencing technology to explore the symbiotic relationship between rhizosphere fungi and plant disease feedback in multiple tea estates across the Guizhou Plateau. The ecological preferences and environmental thresholds of fungi were investigated via environmental variables. Furthermore, a correlation was established between different taxa and individual soil functions. Research has indicated that tea leaf blight disrupts symbiotic connections among fungal groups. For various taxa, we found that numerous taxa consistently maintained core positions within the community, whereas rare taxa were able to stabilize due to a high proportion of positive effects. Additionally, abundant taxa presented a wider range of environmental feedback, whereas the rare taxon diversity presented a stronger positive association with the soil Z score. This study contributes to our understanding of the importance of rare taxa in plant rhizosphere soil processes. Emphasis should be placed on the role of rare taxa in pest and disease control within green agriculture while also strengthening systematic development and biogeographical research related to rare taxa in this region.IMPORTANCEIn this study, based on internal transcribed spacer high-throughput sequencing, fungal communities in the rhizosphere soil of tea trees and their interactions with the environment in karst areas were reported, and the symbiotic relationships of different fungal taxa and their feedback to the environment were described in detail by using the knowledge of microbial ecology. On this basis, it was found that tea tree diseases affect the symbiotic relationships of fungal taxa. At the same time, we found that rare taxa have stronger cooperative relationships in response to environmental changes and explored their participation in soil processes based on fungal trait sets. This study will provide basic data for the development of modern agriculture in tea gardens and theoretical basis for the sustainable prevention and control of tea tree diseases.},
}

@article {pmid39611982,
year = {2024},
author = {Kou, Z and Liu, J and Tohti, G and Zhu, X and Zheng, B and Zhu, Y and Zhang, W},
title = {Distinct Bacterial Communities Within the Nonrhizosphere, Rhizosphere, and Endosphere of Ammodendron bifolium Under Winter Condition in the Takeermohuer Desert.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {151},
pmid = {39611982},
issn = {1432-184X},
support = {2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; },
mesh = {*Rhizosphere ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; *Desert Climate ; *Seasons ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; },
abstract = {Due to human activities and severe climatic conditions, the population of Ammodendron bifolium, an excellent sand-fixing plant, has gradually decreased in the Takeermohuer Desert. The plant-associated bacteria community can enhance its survival in harsh environments. However, the understanding of A. bifolium-associated bacterial community is still unclear during the harsh winter. We investigated the bacterial community structure from the A. bifolium rhizosphere and nonrhizosphere at different depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) and from endosphere (i.e., root endosphere and stem endosphere) in winter. At the same time, we analyzed the impact of different compartments and soil factors on the bacterial community structure. Studies have shown that the A. bifolium rhizosphere exhibits higher levels of SOM (soil organic matter), SOC (soil organic carbon), SAN (soil alkaline nitrogen), and SAK (soil available potassium) compared with the nonrhizosphere. The dominant bacterial phyla were Proteobacteria (19.6%), Cyanobacteria (15.9%), Actinobacteria (13.6%), Acidobacteria (9.0%), and Planctomycetota (5.7%) in the desert. Proteobacteria (24.0-30.2%) had the highest relative abundance in rhizosphere, Actinobacteria (18.3-22.6%) had the highest relative abundance in nonrhizosphere, and Cyanobacteria had the highest relative abundance in endosphere. At the genus level, the relative abundance of Pseudomonas (1.2%) in the root endosphere was the highest and the other genera were mostly unclassified. The Chao1 and PD_whole_tree indices showed that the diversity of the bacterial communities decreased from nonrhizosphere, rhizosphere, root endosphere to stem endosphere. Co-occurrence network analyses identified Proteobacteria and Actinobacteria as key species across the three compartments. Additionally, unique keystone species like Cyanobacteria, Verrucomicrobiota, and Desulfobacterota were found only in the endosphere. The bacterial community in the rhizosphere was influenced by factors such as EC (electrical conductivity), STC (soil total carbon), SOM, SOC, STN (soil total nitrogen), SAN, STP (soil total phosphorus), and SAK, while that of the nonrhizosphere was mainly influenced by pH, C/N (STC/STN), SAP, and distance. The study highlighted differences in bacterial community composition, diversity, and influencing factors across the three compartments, which can provide a better understanding of the association/interactions between A. bifolium and bacterial communities and lay a foundation for revealing its adaptability in winter.},
}

*Rhizosphere
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
*Desert Climate
*Seasons
Plant Roots/microbiology
Soil/chemistry
Microbiota

@article {pmid39611949,
year = {2024},
author = {Makumbi, JP and Leareng, SK and Pierneef, RE and Makhalanyane, TP},
title = {Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {150},
pmid = {39611949},
issn = {1432-184X},
support = {UID 110717//National Research Foundation of South Africa/ ; UID 110717//National Research Foundation of South Africa/ ; },
mesh = {*Microbiota/drug effects ; Humans ; *Ecotoxicology ; Animals ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Public Health ; Drug Resistance, Microbial ; },
abstract = {The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.},
}

*Microbiota/drug effects
Humans
*Ecotoxicology
Animals
Risk Assessment
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial
Public Health
Drug Resistance, Microbial

@article {pmid39611829,
year = {2024},
author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K},
title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0137624},
doi = {10.1128/spectrum.01376-24},
pmid = {39611829},
issn = {2165-0497},
abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.

IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.},
}

@article {pmid39611809,
year = {2024},
author = {Mermans, F and Chatzigiannidou, I and Teughels, W and Boon, N},
title = {Quantifying synthetic bacterial community composition with flow cytometry: efficacy in mock communities and challenges in co-cultures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100924},
doi = {10.1128/msystems.01009-24},
pmid = {39611809},
issn = {2379-5077},
abstract = {Determination of bacterial community composition in synthetic communities is critical for understanding microbial systems. The community composition is typically determined through bacterial plating or through PCR-based methods, which can be labor-intensive, expensive, or prone to bias. Simultaneously, flow cytometry has been suggested as a cheap and fast alternative. However, since the technique captures the phenotypic state of bacterial cells, accurate determination of community composition could be affected when bacteria are co-cultured. We investigated the performance of flow cytometry for quantifying oral synthetic communities and compared it to the performance of strain specific qPCR and 16S rRNA gene amplicon sequencing. Therefore, axenic cultures, mock communities and co-cultures of oral bacteria were prepared. Random forest classifiers trained on flow cytometry data of axenic cultures were used to determine the composition of the synthetic communities, as well as strain specific qPCR and 16S rRNA gene amplicon sequencing. Flow cytometry was shown to have a lower average root mean squared error and outperformed the PCR-based methods in even mock communities (flow cytometry: 0.11 ± 0.04; qPCR: 0.26 ± 0.09; amplicon sequencing: 0.15 ± 0.01). When bacteria were co-cultured, neither flow cytometry, strain-specific qPCR, nor 16S rRNA gene amplicon sequencing resulted in similar community composition. Performance of flow cytometry was decreased compared with mock communities due to changing phenotypes. Finally, discrepancies between flow cytometry and strain-specific qPCR were found. These findings highlight the challenges ahead for quantifying community composition in co-cultures by flow cytometry.IMPORTANCEQuantification of bacterial composition in synthetic communities is crucial for understanding and steering microbial interactions. Traditional approaches like plating, strain-specific qPCR, and amplicon sequencing are often labor-intensive and expensive and limit high-throughput experiments. Recently, flow cytometry has been suggested as a swift and cheap alternative for quantifying communities and has been successfully demonstrated on simple bacterial mock communities. However, since flow cytometry measures the phenotypic state of cells, measurements can be affected by differing phenotypes. Especially, changing phenotypes resulting from co-culturing bacteria can have a profound effect on the applicability of the technique in this context. This research illustrates the feasibility and challenges of flow cytometry for the determination of community structure in synthetic mock communities and co-cultures.},
}

@article {pmid39609949,
year = {2024},
author = {Almela, P and Elser, JJ and Giersch, JJ and Hotaling, S and Rebbeck, V and Hamilton, TL},
title = {Laboratory Experiments Suggest a Limited Impact of Increased Nitrogen Deposition on Snow Algae Blooms.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70052},
doi = {10.1111/1758-2229.70052},
pmid = {39609949},
issn = {1758-2229},
support = {2113783//National Science Foundation/ ; 2113784//National Science Foundation/ ; },
mesh = {*Nitrogen/metabolism/analysis ; *Snow/chemistry ; *Phosphorus/metabolism/analysis ; *Eutrophication ; *Biomass ; },
abstract = {Snow algal blooms decrease snow albedo and increase local melt rates. However, the causes behind the size and frequency of these blooms are still not well understood. One factor likely contributing is nutrient availability, specifically nitrogen and phosphorus. The nutrient requirements of the taxa responsible for these blooms are not known. Here, we assessed the growth of three commercial strains of snow algae under 24 different nutrient treatments that varied in both absolute and relative concentrations of nitrogen and phosphorus. After 38 days of incubation, we measured total biomass and cell size and estimated their effective albedo reduction surface. Snow algal strains tended to respond similarly and achieved bloom-like cell densities over a wide range of nutrient conditions. However, the molar ratio of nitrogen to phosphorus at which maximum biomass was achieved was between 4 and 7. Our data indicate a high requirement for phosphorus for snow algae and highlights phosphorus availability as a critical factor influencing the frequency and extent of snow algae blooms and their potential contribution to snow melt through altered albedo. Snow algae can thrive across a range of nitrogen (N) and phosphorus (P) conditions, with a higher P requirement for optimal growth. Our study suggests that increased N deposition may have a limited impact on snow algae bloom occurrence and size, emphasising P as a key factor influencing these blooms and their potential to accelerate snow melt by lowering albedo.},
}

*Nitrogen/metabolism/analysis
*Snow/chemistry
*Phosphorus/metabolism/analysis
*Eutrophication
*Biomass

@article {pmid39609930,
year = {2024},
author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE},
title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {98},
pmid = {39609930},
issn = {2524-6372},
abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.

RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.

CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.},
}

@article {pmid39608606,
year = {2024},
author = {Young Lee, J and Hyeon Jo, Y and Hee Kim, T and Eun Lee, S and Seo Hong, E and Sun Kang, T},
title = {Microbial and Sensory Characteristics of Traditional Watery Kimchi (Dongchimi) Fortified with Probiotics.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100422},
doi = {10.1016/j.jfp.2024.100422},
pmid = {39608606},
issn = {1944-9097},
abstract = {Dongchimi, a traditional Korean watery kimchi, relies on complex interactions among diverse lactic acid bacteria (LAB) to maintain its freshness and quality. Recently, dongchimi has gained attention as a health-promoting food due to its content of probiotics and prebiotics. In this study, six probiotic strains were employed into dongchimi fermentation, and its sensory and microbial characteristics were evaluated. The LAB-enriched dongchimi demonstrated superior sensory preference (63%) and significantly higher LAB counts (average 5.2 × 10[7] CFU/ml) compared to traditional dongchimi. Furthermore, microbial diversity between the LAB-enriched and traditional dongchimi was analyzed during the fermentation process using both culture-dependent Sanger sequencing and culture-independent metabarcoding techniques, employing 16S ribosomal RNA gene sequences. Lactiplantibacillus plantarum was identified as the dominant probiotic strain in both types of dongchimi, while other probiotics, including Bifidobacterium bifidum, B. animalis, Limosilactobacillus Fermentum, and Heyndrickxia coagulans, were exclusively detected in the LAB-enriched dongchimi. In conclusion, Lactiplanti. plantarum and Limosi. Fermentum were identified as the most effective probiotics for dongchimi fermentation. These results offer critical insights into the microbial ecology and probiotic strains essential for optimizing synbiotic dongchimi, thereby reinforcing health claims related to probiotics and prebiotics.},
}

@article {pmid39605469,
year = {2024},
author = {Woodruff, GC and Moser, KA and Wang, J},
title = {The Bacteria of a Fig Microcommunity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.22.624729},
pmid = {39605469},
issn = {2692-8205},
abstract = {UNLABELLED: Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach towards tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata such as foundress wasp number and nematode occupancy were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 3,000 OTUs were detected, and microbial communities were dominated by members of Proteobacteria , Bacteroidota , and Actinobacteriota . Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. Nematodes likewise had no detectable impact on microbial alpha diversity, although nematodes were associated with a modest change in microbial community composition. A handful of OTUs (associated with the genera Kosokonia , Ochobactrum , and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.

IMPORTANCE: Unraveling why different species live in different places is a longstanding open question in ecology, and it is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata , a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Likewise, we found that nematode occupancy impacts microbial composition but not alpha diversity. Moreover, we show that as the number of foundress wasps increases, the microbial alpha diversity decreases. Finally, we identified OTUs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a microcommunity wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.},
}

@article {pmid39604741,
year = {2024},
author = {de Freitas, AS and Carlos, FS and Martins, GL and Monteiro, GGTN and Roesch, LFW},
title = {Bacterial Resilience and Community Shifts Under 11 Draining-Flooding Cycles in Rice Soils.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {149},
pmid = {39604741},
issn = {1432-184X},
mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Floods ; *Soil/chemistry ; Brazil ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Ecosystem ; },
abstract = {Flooded rice cultivation, accounting for 75% of global rice production, significantly influences soil redox potential, element speciation, pH, and nutrient availability, presenting challenges such as extensive water usage and altered soil properties. This study investigates bacterial community dynamics in rice soils subjected to repeated draining and flooding in Rio Grande do Sul, Brazil. We demonstrate that bacterial communities exhibit remarkable resilience (the capacity to recover after being altered by a disturbance) but cannot remain stable after long-term exposure to environmental changes. The beta diversity analysis revealed four distinct community states after 11 draining/flooding cycles, indicating resilience over successive environment changes. However, the consistent environmental disturbance reduced microbial resilience, causing the bacterial community structure to shift over time. Those differences were driven by substitutions of taxa and functions and not by the loss of diversity. Notable shifts included a decline in Acidobacteria and an increase in Proteobacteria and Chloroflexi. Increased Verrucomicrobia abundance corresponded with lower pH levels. Functional predictions suggested dynamic metabolic responses, with increased nitrification during drained cycles and a surge in fermenters after the sixth cycle. Despite cyclic disturbances, bacterial communities exhibit resilience, contributing to stable ecosystem functioning in flooded rice soils. These findings enhance our understanding of microbial adaptation, providing insights into sustainable rice cultivation and soil management practices.},
}

*Oryza/microbiology
*Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Floods
*Soil/chemistry
Brazil
Microbiota
RNA, Ribosomal, 16S/genetics
Hydrogen-Ion Concentration
Ecosystem

@article {pmid39603473,
year = {2024},
author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T},
title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131878},
doi = {10.1016/j.biortech.2024.131878},
pmid = {39603473},
issn = {1873-2976},
abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %∼74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.},
}

@article {pmid39601575,
year = {2024},
author = {Maguire, M and Serna, C and Montero Serra, N and Kovarova, A and O'Connor, L and Cahill, N and Hooban, B and DeLappe, N and Brennan, W and Devane, G and Cormican, M and Morris, D and Coughlan, SC and Miliotis, G and Gonzalez-Zorn, B and Burke, LP},
title = {Spatiotemporal and genomic analysis of carbapenem resistance elements in Enterobacterales from hospital inpatients and natural water ecosystems of an Irish city.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0090424},
doi = {10.1128/spectrum.00904-24},
pmid = {39601575},
issn = {2165-0497},
abstract = {Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosystems represent a known reservoir of CPE. However, the dynamics of carbapenemase-bearing MGE dissemination between Enterobacterales in humans and environmental waters are poorly understood. We carried out whole-genome sequencing, combining short- and long-sequencing reads to enable complete characterization of CPE isolated from patients, wastewaters, and natural waters between 2018 and 2020 in Galway, Ireland. Isolates were selected based on their carriage of Class A blaKPC-2 (n = 6), Class B blaNDM-5 (n = 12), and Class D blaOXA-48 (n = 21) CEGs. CEGs were plasmid-borne in all but two isolates. OXA-48 dissemination was associated with a 64 kb IncL plasmid (62%), in a broad range of Enterobacterales isolates from both niches. Conversely, blaKPC-2 and blaNDM-5 genes were usually carried on larger and more variable multireplicon IncF plasmids in Klebsiella pneumoniae and Escherichia coli, respectively. In every isolate, each CEG was surrounded by a gene-specific common genetic environment which constituted part, or all, of a transposable element that was present in both plasmids and the bacterial chromosome. Transposons Tn1999 and Tn4401 were associated with blaOXA-48 and blaKPC-2, respectively, while blaNDM-5 was associated with variable IS26 bound composite transposons, usually containing a class 1 integron.IMPORTANCESince 2018, the Irish National Carbapenemase-Producing Enterobacterales (CPE) Reference Laboratory Service at University Hospital Galway has performed whole-genome sequencing on suspected and confirmed CPE from clinical specimens as well as patient and environmental screening isolates. Understanding the dynamics of CPE and carbapenemase-encoding gene encoding mobile genetic element (MGE) flux between human and environmental reservoirs is important for One Health surveillance of these priority organisms. We employed hybrid assembly approaches for improved resolution of CPE genomic surveillance, typing, and plasmid characterization. We analyzed a diverse collection of human (n = 17) and environmental isolates (n = 22) and found common MGE across multiple species and in different ecological niches. The conjugation ability and frequency of a subset of these plasmids were demonstrated to be affected by the presence or absence of necessary conjugation genes and by plasmid size. We characterize several MGE at play in the local dissemination of carbapenemase genes. This may facilitate their future detection in the clinical laboratory.},
}

@article {pmid39601521,
year = {2024},
author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS},
title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0063724},
doi = {10.1128/mra.00637-24},
pmid = {39601521},
issn = {2576-098X},
abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.},
}

@article {pmid39597739,
year = {2024},
author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H},
title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112350},
pmid = {39597739},
issn = {2076-2607},
support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; },
abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.},
}

@article {pmid39597685,
year = {2024},
author = {Zhang, K and Chen, X and Shi, X and Yang, Z and Yang, L and Liu, D and Yu, F},
title = {Endophytic Bacterial Community, Core Taxa, and Functional Variations Within the Fruiting Bodies of Laccaria.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112296},
pmid = {39597685},
issn = {2076-2607},
support = {202205AD160036//the Yunnan Technology Innovation/ ; 42077072//the National Natural Science Foundation of Management Practices China/ ; },
abstract = {Macrofungi do not exist in isolation but establish symbiotic relationships with microorganisms, particularly bacteria, within their fruiting bodies. Herein, we examined the fruiting bodies' bacteriome of seven species of the genus Laccaria collected from four locations in Yunnan, China. By analyzing bacterial diversity, community structure, and function through 16S rRNA sequencing, we observed the following: (1) In total, 4,840,291 high-quality bacterial sequences obtained from the fruiting bodies were grouped into 16,577 amplicon sequence variants (ASVs), and all samples comprised 23 shared bacterial ASVs. (2) The Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex was found to be the most abundant and presumably coexisting bacterium. (3) A network analysis revealed that endophytic bacteria formed functional groups, which were dominated by the genera Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Novosphingobium, and Variovorax. (4) The diversity, community structure, and dominance of ecological functions (chemoheterotrophy and nitrogen cycling) among endophytic bacteria were significantly shaped by geographic location, habitat, and fungal genotype, rather than fruiting body type. (5) A large number of the endophytic bacteria within Laccaria are bacteria that promote plant growth; however, some pathogenic bacteria that pose a threat to human health might also be present. This research advances our understanding of the microbial ecology of Laccaria and the factors shaping its endophytic bacterial communities.},
}

@article {pmid39597671,
year = {2024},
author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E},
title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112281},
pmid = {39597671},
issn = {2076-2607},
support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; },
abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.},
}

@article {pmid39597543,
year = {2024},
author = {Wu, D and He, X and Lu, Y and Gao, Z and Chong, Y and Hong, J and Wu, J and Deng, W and Xi, D},
title = {Effects of Different Dietary Combinations on Blood Biochemical Indicators and Rumen Microbial Ecology in Wenshan Cattle.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112154},
pmid = {39597543},
issn = {2076-2607},
abstract = {With the continuous optimization of feed ingredients in livestock production, barley has garnered significant attention as a potential substitute for corn in feed. This study aims to investigate the effects of replacing part of the corn and soybean meal with barley, wheat bran, and rapeseed meal on Wenshan cattle, focusing on the rumen microbial community, blood physiological and biochemical indicators, and growth traits. Through an intensive feeding experiment with two different dietary ratios, we found that adding barley to the diet significantly reduced the host's blood lipid concentration and significantly increased the height, body length, heart girth, and average daily weight gain of Wenshan cattle. Analysis of the rumen microbial community structure showed that the addition of barley significantly affected the relative abundance of Firmicutes, Proteobacteria, and Bacteroidetes, with the relative abundance of Spirochaetes being significantly lower than that of the control group (p < 0.05). The dominant bacterial groups mainly included Acinetobacter, Solibacillus, and Lysinibacillus. In summary, this study reveals the potential of different feed ingredient ratios involving barley, wheat bran, and rapeseed meal in the production performance of Wenshan cattle. By regulating blood physiology and improving the rumen micro-ecological structure, it provides new scientific evidence for optimizing livestock and poultry feeding management strategies. Future research will further explore the optimal application ratio of barley under different feeding conditions and its long-term impact on animal health and production performance.},
}

@article {pmid39597512,
year = {2024},
author = {Banerji, A and Brinkman, NE and Davis, B and Franklin, A and Jahne, M and Keely, SP},
title = {Food Webs and Feedbacks: The Untold Ecological Relevance of Antimicrobial Resistance as Seen in Harmful Algal Blooms.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112121},
pmid = {39597512},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) has long been framed as an epidemiological and public health concern. Its impacts on the environment are unclear. Yet, the basis for AMR is altered cell physiology. Just as this affects how microbes interact with antimicrobials, it can also affect how they interact with their own species, other species, and their non-living environment. Moreover, if the microbes are globally notorious for causing landscape-level environmental issues, then these effects could alter biodiversity and ecosystem function on a grand scale. To investigate these possibilities, we compiled peer-reviewed literature from the past 20 years regarding AMR in toxic freshwater cyanobacterial harmful algal blooms (HABs). We examined it for evidence of AMR affecting HAB frequency, severity, or persistence. Although no study within our scope was explicitly designed to address the question, multiple studies reported AMR-associated changes in HAB-forming cyanobacteria (and co-occurring microbes) that pertained directly to HAB timing, toxicity, and phase, as well as to the dynamics of HAB-afflicted aquatic food webs. These findings highlight the potential for AMR to have far-reaching environmental impacts (including the loss of biodiversity and ecosystem function) and bring into focus the importance of confronting complex interrelated issues such as AMR and HABs in concert, with interdisciplinary tools and perspectives.},
}

@article {pmid39596705,
year = {2024},
author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF},
title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111010},
pmid = {39596705},
issn = {2079-6382},
support = {FAPESP//001/ ; },
abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.},
}

@article {pmid39592542,
year = {2024},
author = {Kaur, T and Devi, R and Negi, R and Kour, H and Singh, S and Khan, SS and Kumari, C and Kour, D and Chowdhury, S and Kapoor, M and Rai, AK and Rustagi, S and Shreaz, S and Yadav, AN},
title = {Macronutrients-availing microbiomes: biodiversity, mechanisms, and biotechnological applications for agricultural sustainability.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39592542},
issn = {1874-9356},
abstract = {Nitrogen, phosphorus, and potassium are the three most essential micronutrients which play major roles in plant survivability by being a structural or non-structural component of the cell. Plants acquire these nutrients from soil in the fixed (NO3[¯], NH4[+]) and solubilized forms (K[+], H2PO4[-] and HPO4[2-]). In soil, the fixed and solubilized forms of nutrients are unavailable or available in bare minimum amounts; therefore, agrochemicals were introduced. Agrochemicals, mined from the deposits or chemically prepared, have been widely used in the agricultural farms over the decades for the sake of higher production of the crops. The excessive use of agrochemicals has been found to be deleterious for humans, as well as the environment. In the environment, agrochemical usage resulted in soil acidification, disturbance of microbial ecology, and eutrophication of aquatic and terrestrial ecosystems. A solution to such devastating agro-input was found to be substituted by macronutrients-availing microbiomes. Macronutrients-availing microbiomes solubilize and fix the insoluble form of nutrients and convert them into soluble forms without causing any significant harm to the environment. Microbes convert the insoluble form to the soluble form of macronutrients (nitrogen, phosphorus, and potassium) through different mechanisms such as fixation, solubilization, and chelation. The microbiomes having capability of fixing and solubilizing nutrients contain some specific genes which have been reported in diverse microbial species surviving in different niches. In the present review, the biodiversity, mechanism of action, and genomics of different macronutrients-availing microbiomes are presented.},
}

@article {pmid39587399,
year = {2024},
author = {Trevathan-Tackett, SM and Kepfer-Rojas, S and Malerba, M and Macreadie, PI and Djukic, I and Zhao, J and Young, EB and York, PH and Yeh, SC and Xiong, Y and Winters, G and Whitlock, D and Weaver, CA and Watson, A and Visby, I and Tylkowski, J and Trethowan, A and Tiegs, S and Taylor, B and Szpikowski, J and Szpikowska, G and Strickland, VL and Stivrins, N and Sousa, AI and Sinutok, S and Scheffel, WA and Santos, R and Sanderman, J and Sánchez-Carrillo, S and Sanchez-Cabeza, JA and Rymer, KG and Ruiz-Fernandez, AC and Robroek, BJM and Roberts, T and Ricart, AM and Reynolds, LK and Rachlewicz, G and Prathep, A and Pinsonneault, AJ and Pendall, E and Payne, R and Ozola, I and Onufrock, C and Ola, A and Oberbauer, SF and Numbere, AO and Novak, AB and Norkko, J and Norkko, A and Mozdzer, TJ and Morgan, P and Montemayor, DI and Martin, CW and Malone, SL and Major, M and Majewski, M and Lundquist, CJ and Lovelock, CE and Liu, S and Lin, HJ and Lillebo, A and Li, J and Kominoski, JS and Khuroo, AA and Kelleway, JJ and Jinks, KI and Jerónimo, D and Janousek, C and Jackson, EL and Iribarne, O and Hanley, T and Hamid, M and Gupta, A and Guariento, RD and Grudzinska, I and da Rocha Gripp, A and González Sagrario, MA and Garrison, LM and Gagnon, K and Gacia, E and Fusi, M and Farrington, L and Farmer, J and de Assis Esteves, F and Escapa, M and Domańska, M and Dias, ATC and de Los Santos, CB and Daffonchio, D and Czyryca, PM and Connolly, RM and Cobb, A and Chudzińska, M and Christiaen, B and Chifflard, P and Castelar, S and Carneiro, LS and Cardoso-Mohedano, JG and Camden, M and Caliman, A and Bulmer, RH and Bowen, J and Boström, C and Bernal, S and Berges, JA and Benavides, JC and Barry, SC and Alatalo, JM and Al-Haj, AN and Adame, MF},
title = {Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02116},
pmid = {39587399},
issn = {1520-5851},
abstract = {Patchy global data on belowground litter decomposition dynamics limit our capacity to discern the drivers of carbon preservation and storage across inland and coastal wetlands. We performed a global, multiyear study in over 180 wetlands across 28 countries and 8 macroclimates using standardized litter as measures of "recalcitrant" (rooibos tea) and "labile" (green tea) organic matter (OM) decomposition. Freshwater wetlands and tidal marshes had the highest tea mass remaining, indicating a greater potential for carbon preservation in these ecosystems. Recalcitrant OM decomposition increased with elevated temperatures throughout the decay period, e.g., increase from 10 to 20 °C corresponded to a 1.46-fold increase in the recalcitrant OM decay rate constant. The effect of elevated temperature on labile OM breakdown was ecosystem-dependent, with tidally influenced wetlands showing limited effects of temperature compared with freshwater wetlands. Based on climatic projections, by 2050 wetland decay constants will increase by 1.8% for labile and 3.1% for recalcitrant OM. Our study highlights the potential for reduction in belowground OM in coastal and inland wetlands under increased warming, but the extent and direction of this effect at a large scale is dependent on ecosystem and OM characteristics. Understanding local versus global drivers is necessary to resolve ecosystem influences on carbon preservation in wetlands.},
}

@article {pmid39586934,
year = {2024},
author = {Rong, X and Liu, X and Du, F and Aanderud, ZT and Zhang, Y},
title = {Biocrusts Mediate the Niche Distribution and Diversity of Ammonia-Oxidizing Microorganisms in the Gurbantunggut Desert, Northwestern China.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {148},
pmid = {39586934},
issn = {1432-184X},
support = {2022TSYCCX0007//the Xinjiang Tianshan Youth Talent Top Project/ ; 2022D01D083//the Key Fund Projects of the Natural Science Foundation of Xinjiang/ ; U2003214//the National Natural Science Foundation of China/ ; },
mesh = {*Archaea/genetics/metabolism/classification ; *Desert Climate ; *Ammonia/metabolism ; *Soil Microbiology ; China ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Oxidation-Reduction ; Soil/chemistry ; Biodiversity ; Ecosystem ; Seasons ; Microbiota ; Nitrification ; },
abstract = {Biological soil crusts (biocrusts) play pivotal ecological roles in regulating nitrogen cycling within desert ecosystems. While acknowledging the essential role played by ammonia-oxidizing microorganisms in nitrogen transformation, there remains a paucity of understanding concerning how disturbances to biocrusts impact the diversity and spatial distribution patterns among ammonia oxidizer communities within temperate deserts. This investigation delved into assessing how 4 years' worth of removing biocrust influenced niche differentiation between nitrifying archaea and bacteria while also examining its effects on shaping community structures of predominant ammonia-oxidizing archaea (AOA) within the Gurbantunggut Desert soils. Despite notable variations in abundance of ammonia-oxidizing microbes across distinct soil depths throughout different seasons, it became apparent that removing biocrust significantly altered both the abundance and niche pattern for AOA alongside their bacterial counterparts during winter and summer periods. Notably dominating over their bacterial counterparts within desert soils, AOA displayed their highest archaeal to bacterial amoA gene copy ratio (6549-fold higher) at a soil depth of 5-10 cm during summer. Moreover, substantial impacts were observed upon AOA diversity along with compositional changes following such perturbation events. The aftermath saw an emergence of more diffuse yet dynamic AOA communities, especially noticeable amidst winter when nitrogen and water limitations were relatively alleviated. In summary, our findings underscore how interactions between biocrust coverages alongside factors like soil temperature, total carbon content, or NO3[-]_N concentrations govern niches occupied by ammoxidation communities whilst influencing assemblage processes too. The sensitivity shown by dominant AOAs towards biocrust removal further underscores how biocrust coverage influences nitrogen transformation processes while potentially involving other communities and functions in desert ecosystems.},
}

*Archaea/genetics/metabolism/classification
*Desert Climate
*Ammonia/metabolism
*Soil Microbiology
China
*Bacteria/metabolism/genetics/classification/isolation & purification
*Oxidation-Reduction
Soil/chemistry
Biodiversity
Ecosystem
Seasons
Microbiota
Nitrification

@article {pmid39587087,
year = {2024},
author = {Whalen, ED and Grandy, AS and Geyer, KM and Morrison, EW and Frey, SD},
title = {Microbial trait multifunctionality drives soil organic matter formation potential.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10209},
pmid = {39587087},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism ; *Carbon/metabolism ; Biomass ; Organic Chemicals/metabolism ; },
abstract = {Soil microbes are a major source of organic residues that accumulate as soil organic matter, the largest terrestrial reservoir of carbon on Earth. As such, there is growing interest in determining the microbial traits that drive soil organic matter formation and stabilization; however, whether certain microbial traits consistently predict soil organic matter accumulation across different functional pools (e.g., total vs. stable soil organic matter) is unresolved. To address these uncertainties, we incubated individual species of fungi in soil organic matter-free model soils, allowing us to directly relate the physiological, morphological, and biochemical traits of fungi to their soil organic matter formation potentials. We find that the formation of different soil organic matter functional pools is associated with distinct fungal traits, and that 'multifunctional' species with intermediate investment across this key grouping of traits (namely, carbon use efficiency, growth rate, turnover rate, and biomass protein and phenol contents) promote soil organic matter formation, functional complexity, and stability. Our results highlight the limitations of categorical trait-based frameworks that describe binary trade-offs between microbial traits, instead emphasizing the importance of synergies among microbial traits for the formation of functionally complex soil organic matter.},
}

*Soil Microbiology
*Soil/chemistry
*Fungi/metabolism
*Carbon/metabolism
Biomass
Organic Chemicals/metabolism

@article {pmid39585925,
year = {2024},
author = {Richards, TA and Eme, L and Archibald, JM and Leonard, G and Coelho, SM and de Mendoza, A and Dessimoz, C and Dolezal, P and Fritz-Laylin, LK and Gabaldón, T and Hampl, V and Kops, GJPL and Leger, MM and Lopez-Garcia, P and McInerney, JO and Moreira, D and Muñoz-Gómez, SA and Richter, DJ and Ruiz-Trillo, I and Santoro, AE and Sebé-Pedrós, A and Snel, B and Stairs, CW and Tromer, EC and van Hooff, JJE and Wickstead, B and Williams, TA and Roger, AJ and Dacks, JB and Wideman, JG},
title = {Reconstructing the last common ancestor of all eukaryotes.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002917},
doi = {10.1371/journal.pbio.3002917},
pmid = {39585925},
issn = {1545-7885},
abstract = {Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.},
}

@article {pmid39583547,
year = {2024},
author = {Yang, X and Gänzle, M and Wang, R},
title = {Editorial: How the application of antimicrobial hurdles in meat processing facilities shapes microbial ecology.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501925},
pmid = {39583547},
issn = {1664-302X},
}

@article {pmid39348267,
year = {2024},
author = {Clegg, T and Pawar, S},
title = {Variation in thermal physiology can drive the temperature-dependence of microbial community richness.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.84662},
pmid = {39348267},
issn = {2050-084X},
support = {NERC QMEE Centre for Doctoral Training NE/P012345/1//Natural Environment Research Council/ ; RF-2020-653\2//Leverhulme Trust/ ; NE/M020843/1//NERC Natural Environment Research Council/ ; NE/S000348/1//NERC Natural Environment Research Council/ ; },
mesh = {*Temperature ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism ; Biodiversity ; Bacterial Physiological Phenomena ; },
abstract = {Predicting how species diversity changes along environmental gradients is an enduring problem in ecology. In microbes, current theories tend to invoke energy availability and enzyme kinetics as the main drivers of temperature-richness relationships. Here, we derive a general empirically-grounded theory that can explain this phenomenon by linking microbial species richness in competitive communities to variation in the temperature-dependence of their interaction and growth rates. Specifically, the shape of the microbial community temperature-richness relationship depends on how rapidly the strength of effective competition between species pairs changes with temperature relative to the variance of their growth rates. Furthermore, it predicts that a thermal specialist-generalist tradeoff in growth rates alters coexistence by shifting this balance, causing richness to peak at relatively higher temperatures. Finally, we show that the observed patterns of variation in thermal performance curves of metabolic traits across extant bacterial taxa is indeed sufficient to generate the variety of community-level temperature-richness responses observed in the real world. Our results provide a new and general mechanism that can help explain temperature-diversity gradients in microbial communities, and provide a quantitative framework for interlinking variation in the thermal physiology of microbial species to their community-level diversity.},
}

*Temperature
*Microbiota/physiology
Bacteria/classification/genetics/metabolism
Biodiversity
Bacterial Physiological Phenomena

@article {pmid39578630,
year = {2024},
author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK},
title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28934},
pmid = {39578630},
issn = {2045-2322},
support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; },
mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.},
}

*Metagenomics/methods
*Soil Microbiology
Soil/chemistry
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Metagenome

@article {pmid39572704,
year = {2024},
author = {Li, J and Göbel, F and Hsu, HY and Koch, JN and Hager, N and Flegler, WA and Tanabe, TS and Dahl, C},
title = {YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1548},
pmid = {39572704},
issn = {2399-3642},
support = {Da 351/8-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Da 351/14-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Sulfur/metabolism ; *Oxidation-Reduction ; *Signal Transduction ; *Bacterial Proteins/metabolism/genetics ; *Gene Expression Regulation, Bacterial ; Biological Transport ; },
abstract = {Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.},
}

*Sulfur/metabolism
*Oxidation-Reduction
*Signal Transduction
*Bacterial Proteins/metabolism/genetics
*Gene Expression Regulation, Bacterial
Biological Transport

@article {pmid39572621,
year = {2024},
author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM},
title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28890},
pmid = {39572621},
issn = {2045-2322},
support = {07939716/2020//Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; },
abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.},
}

Humans
*Helicobacter pylori/pathogenicity/genetics
*Helicobacter Infections/microbiology/pathology
*Stomach Neoplasms/microbiology/pathology
*Gastritis/microbiology/pathology
Virulence
*Gastric Mucosa/microbiology/pathology
Male
Female
RNA, Ribosomal, 16S/genetics
Middle Aged
Aged
Metaplasia/microbiology
Adult
Gastrointestinal Microbiome

@article {pmid39572453,
year = {2024},
author = {Méndez, A and Sanmartín, P and Balboa, S and Trueba-Santiso, A},
title = {Environmental Proteomics Elucidates Phototrophic Biofilm Responses to Ornamental Lighting on Stone-built Heritage.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {147},
pmid = {39572453},
issn = {1432-184X},
support = {04_IN606D_2021_2598528//Programa de Doutoramento Industrial - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431F 2022/14//FONTES project - Xunta de Galicia/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; ED431C 2022/09//Competitive Reference Group (GRC) grant - GEMAP/ ; RYC2020-029987-I//Ramón y Cajal contract - Spanish State Research Agency (AEI)/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; ED431C-2021/37//Competitive Reference Group (GRC) - Biogroup/ ; },
mesh = {*Biofilms/radiation effects/growth & development ; *Proteomics ; Light ; Phototrophic Processes ; Cyanobacteria/metabolism/radiation effects/physiology ; Chlorophyta/radiation effects/metabolism/physiology ; Proteome ; Lighting ; },
abstract = {Recent studies are showing that some lights suitable for illuminating the urban fabric (i.e. that do not include the red, green and blue sets of primary colours) may halt biological colonisation on monuments, mainly that caused by phototrophic subaerial biofilms (SABs), which may exacerbate the biodeterioration of substrates. However, the light-triggered mechanisms that cause changes in the growth of the phototrophs remain unknown. Environmental proteomics could be used to provide information about the changes in the SAB metabolism under stress inflicted by nocturnal lighting. Here, laboratory-produced SABs, composed of Chlorophyta, Streptophyta and Cyanobacteriota, were subjected to three types of lighting used for monuments: cool white, warm white and amber + green (potentially with a biostatic effect). A control without light (i.e. darkness) was also included for comparison. The nocturnal lighting impaired the capacity of the SABs to decompose superoxide radicals and thus protect themselves from oxidative stress. Cool white and warm white light both strongly affected the proteomes of the SABs and reduced the total peptide content, with the extent of the reduction depending on the genera of the organisms involved. Analysis of the photo-damaging effect of amber + green light on the biofilm metabolism revealed a negative impact on photosystems I and II and production of photosystem antenna protein-like, as well as a triggering effect on protein metabolism (synthesis, folding and degradation). This research provides, for the first-time, a description of the proteomic changes induced by lighting on SABs colonising illuminated monuments in urban areas.},
}

*Biofilms/radiation effects/growth & development
*Proteomics
Light
Phototrophic Processes
Cyanobacteria/metabolism/radiation effects/physiology
Chlorophyta/radiation effects/metabolism/physiology
Proteome
Lighting

@article {pmid39571806,
year = {2024},
author = {Graham, A and Thorn, C and McDonagh, M and O'Donnell, C and Nolan, S and Kirwan, SF and O'Connor, S and Nzeteu, CO and Montoya, ACV and Bartle, A and Hall, A and Abberton, C and Friel, R and Waters, SM and O'Flaherty, V},
title = {Development and in-vitro assessment of novel oxygen-releasing feed additives to reduce enteric ruminant methane emissions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177598},
doi = {10.1016/j.scitotenv.2024.177598},
pmid = {39571806},
issn = {1879-1026},
abstract = {Ruminant livestock contribute significantly to global methane production and mitigation of which is of utmost importance. Feed additives represent a cost-effective means of achieving this. A potential target for such additives is rumen Oxidative Reduction Potential (ORP), a parameter which influences CH4 production rates, with methanogenesis occurring optimally at ORPs below -300 mV. Thus, a controlled elevation of rumen ORP represents a potentially benign means of methanogen suppression. This research involved assessing a range of oxygen-releasing compounds for their ability to increase rumen ORP and inhibit methanogenesis, using the in-vitro rumen simulation technique (RUSITEC). Seven potential CH4 inhibitors were tested in a 21-day trial monitoring biogas volume, CH4 content, ORP, digestibility, ammonia, and volatile fatty acids concentration. The additives evaluated included: liquid peroxide (H2O2) and urea hydrogen peroxide (UHP), as well as slower reacting species (calcium and magnesium peroxide), in addition to encapsulated liquid H2O2 for controlled, slow release. Consistent CH4 reductions of >50 % were observed from all additives. Reduced neutral detergent fibre (NDF) digestibility and a reduction in total volatile fatty acids (VFAs) was observed for some treatments, but MgO2 and encapsulated H2O2 reduced CH4 volume by 62 % and 58 %, respectively, and had no detrimental effects on digestibility (p > 0.05) or on VFA production. Ex-situ ORP measurements demonstrated significant increases in ORP upon addition of the additives, with MgO2 and encapsulated H2O2 inducing a more moderate effect suggesting a controlled additive release was achieved with the slow-release format of encapsulated liquid H2O2. Thus, potential slow-release forms deemed suitable to progress to bolus or pellet format in-vivo were identified and could enable a longer-lasting suppression of methanogens within the rumen, facilitating application in both intensive and pasture-based production systems.},
}

@article {pmid39571521,
year = {2024},
author = {Zuo, J and Yang, S and Grossart, HP and Xiao, P and Zhang, H and Sun, R and Li, G and Jiang, H and Zhao, Q and Jiao, M and Cheng, Y and Wang, Z and Geng, R and Ma, Z and Li, R},
title = {Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu.},
journal = {Water research},
volume = {269},
number = {},
pages = {122784},
doi = {10.1016/j.watres.2024.122784},
pmid = {39571521},
issn = {1879-2448},
abstract = {River ecosystems face escalating challenges due to altered flow regimes from human activities, such as urbanization with hydrological modifications. Understanding the role of microbial communities for ecosystems with changing flow regimes is still incomplete and remains at the frontier of aquatic microbial ecology. In particular, influences of riverine backward flow on the aquatic biota remain largely unknown. Therefore, we examined the impact of backward flow on the cyanobacterial, total prokaryotic, and eukaryotic communities in the Changdougang River, which naturally flows into Lake Taihu, through environmental DNA metabarcoding. We analyzed the differences in community diversity, assembly, and ecological network stability among groups under backward, weak, and forward flow direction conditions. Non-metric multidimensional scaling showed higher variations in communities of groups across flow direction conditions than seasonal groups. Variations in alpha and beta diversity showed that cyanobacterial and total prokaryotic communities experienced strong homogenization under backward flow conditions, whereas the ecological uniqueness of the eukaryotic community decreased. Assembly of the three flow-related communities was primarily governed by drift and dispersal limitation in stochastic processes. However, in the cyanobacterial community, homogeneous selection in deterministic processes increased from 22.79 % to 42.86 % under backward flow, aligning with trends observed in the checkerboard score (C-score). More importantly, the topological properties of ecological networks and the degree of average variation revealed higher stability in the cyanobacterial community compared to total prokaryotic and eukaryotic communities. Considering the variations in cohesion, the network stability in the cyanobacterial community decreased under backward flow. Our findings emphasize the distinct and sequentially diminishing responses of cyanobacterial, total prokaryotic, and eukaryotic communities to backward flowing rivers. This knowledge is crucial for maintaining ecological health of rivers, assessing the complex ecological impacts on hydrological engineering, and formulating sustainable water management strategies.},
}

@article {pmid39570409,
year = {2024},
author = {Xu, H and Zhang, Y and Fan, D and Meng, S and Fan, L and Song, C and Qiu, L and Li, D and Fang, L and Liu, Z and Bing, X},
title = {Influences of Community Coalescence on the Assembly of Bacterial Communities of the Small-Scale Complex Aquatic System from the Perspective of Bacterial Transmission, Core Taxa, and Co-occurrence Patterns.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {145},
pmid = {39570409},
issn = {1432-184X},
support = {2023JBFR01//Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; CARS-46//the earmarked fund for CARS/ ; 2023TD18//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
mesh = {*Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Aquaculture ; *Rhizosphere ; *Feces/microbiology ; Animals ; Biofilms ; Fishes/microbiology ; Water Microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recirculating aquaculture and aquaponics are considered sustainable aquaculture models playing important roles in animal-derived protein supply. In these aquaculture systems, microorganisms are crucial for the system stability. The community coalescence by mixing substances and microorganisms from various microhabitats under hydraulic forces is important for shaping the bacterial communities in these small-scale complex systems. However, the influences of community coalescence on bacterial communities remain rarely revealed in these systems. In this study, aquaponics (APS) and recirculating aquaculture (RAS) systems were set up to explore the bacterial community coalescence across different microhabitats, including water, fish feces, biofilter biofilms, and plant rhizosphere environment. Our results showed that diversity and compositions varied across different microhabitats in both systems. However, bacterial transmissions across these microhabitats differed between systems. The core microbiome of the RAS and APS were formed under community coalescence with the highest contribution of bacterial taxa derived from the fish feces. Nevertheless, the plant rhizosphere bacterial community also contributed to the core microbiome of the APS. Furthermore, the core taxa showed a higher average degree than the other nodes in the bacterial community networks in all microhabitats except for the plant rhizosphere environment, implying the important roles of core taxa in maintaining these bacterial community networks. Our results provide new insights into the assembly of bacterial communities under community coalescence in the artificial aquatic ecosystems comprising complex microhabitats, which is vital for developing microbial solutions for regulating the microbial communities to improve system performance in the future.},
}

*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Aquaculture
*Rhizosphere
*Feces/microbiology
Animals
Biofilms
Fishes/microbiology
Water Microbiology
Ecosystem
RNA, Ribosomal, 16S/genetics

@article {pmid39570377,
year = {2024},
author = {Jensen, IC and Schramm, A and Offenberg, J},
title = {Fungus Fighters: Wood Ants (Formica polyctena) and Their Associated Microbes Inhibit Plant Pathogenic Fungi.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {146},
pmid = {39570377},
issn = {1432-184X},
support = {NNF21OC0071665//Novo Nordisk Fonden/ ; NNF21OC0071665//Novo Nordisk Fonden/ ; 34009-19-1562//Internationalt Center for Forskning i Økologisk Jordbrug og Fødevaresystemer/ ; },
mesh = {*Ants/microbiology/physiology ; Animals ; *Plant Diseases/microbiology/prevention & control ; Malus/microbiology ; Fungi/physiology/classification ; Antibiosis ; Bacteria/classification/drug effects/isolation & purification ; Ascomycota/physiology/drug effects ; },
abstract = {Plant diseases cost the global economy billions of US dollars every year. The problem has mainly been addressed by using chemical pesticides, but recently, the use of ants has shown promising effects against plant pathogens. However, the mechanisms accounting for these effects have not yet been determined. One possible explanation is antimicrobial microorganisms associated with ants. Through controlled laboratory experiments, we investigated the inhibitory effects of wood ants (Formica polyctena) and their associated microorganisms against economically important plant pathogenic fungi. All live ants, extracts from crushed ants, and extracts from washed ants significantly inhibited the apple brown rot (Monilinia fructigena) while yielding the growth of other microbes. Furthermore, all investigated wood ants transferred microorganisms to their surroundings within 10 s when walking across a surface. We isolated the most dominant microorganisms deposited by walking ants and from washed ant extracts (i.e., strains likely found on the surface of ants), resulting in four bacterial cultures and one yeast. Two of these isolates, strain I3 (most closely related to Pseudomonas sichuanensis and P. entomophila) and strain I1b (most closely related to Bacillus mycoides), showed inhibitory effects against apple brown rot and apple scab (Venturia inaequalis), while strain I3 also inhibited gray mold (Botrytis cinerea) and Fusarium head blight (Fusarium graminearum). These results suggest that wood ants have potential as biological control agents against commercially relevant plant pathogens, and that their inhibitory effect might be at least partially caused by antibiotic compounds produced by their associated microorganisms.},
}

*Ants/microbiology/physiology
Animals
*Plant Diseases/microbiology/prevention & control
Malus/microbiology
Fungi/physiology/classification
Antibiosis
Bacteria/classification/drug effects/isolation & purification
Ascomycota/physiology/drug effects

@article {pmid39568064,
year = {2024},
author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB},
title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on Southern African dryland soil microbial communities.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae157},
pmid = {39568064},
issn = {1574-6941},
abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggest that they are functionally stable, and that they could be functional even under harsher conditions, such as those expected with climate change.},
}

@article {pmid39567391,
year = {2024},
author = {Vezina, B and Cooper, HB and Wisniewski, JA and Parker, MH and Jenney, AWJ and Holt, KE and Wyres, KL},
title = {Wild-Type Domestication: Loss of Intrinsic Metabolic Traits Concealed by Culture in Rich Media.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {144},
pmid = {39567391},
issn = {1432-184X},
support = {DP200103364//Australian Research Council/ ; DP200103364//Australian Research Council/ ; APP1176192//National Health and Medical Research Council/ ; },
mesh = {*Klebsiella pneumoniae/genetics/metabolism/growth & development ; *Culture Media/chemistry ; *Genome, Bacterial ; Histidine/metabolism ; Mutation ; Whole Genome Sequencing ; },
abstract = {Bacteria are typically isolated on rich media to maximise isolation success, removing them from their native evolutionary context. This eliminates selection pressures, enabling otherwise deleterious genomic events to accumulate. Here, we present a cautionary tale of these 'quiet mutations' which can persist unnoticed in bacterial culture lines. We used a combination of microbiological culture (standard and minimal media conditions), whole genome sequencing and metabolic modelling to investigate putative Klebsiella pneumoniae L-histidine auxotrophs. Additionally, we used genome-scale metabolic modelling to predict auxotrophies among completed public genomes (n = 2637). Two sub-populations were identified within a K. pneumoniae frozen stock, differing in their ability to grow in the absence of L-histidine. These sub-populations were the same 'strain', separated by eight single nucleotide variants and an insertion sequence-mediated deletion of the L-histidine biosynthetic operon. The His[-] sub-population remained undetected for > 10 years despite its inclusion in independent laboratory experiments. Genome-scale metabolic models predicted 0.8% public genomes contained ≥ 1 auxotrophy, with purine/pyrimidine biosynthesis and amino acid metabolism most frequently implicated. We provide a definitive example of the role of standard rich media culture conditions in obscuring biologically relevant mutations (i.e. nutrient auxotrophies) and estimate the prevalence of such auxotrophies using public genome collections. While the prevalence is low, it is not insignificant given the thousands of K. pneumoniae that are isolated for global surveillance and research studies each year. Our data serve as a pertinent reminder that rich-media culturing can cause unnoticed wild-type domestication.},
}

*Klebsiella pneumoniae/genetics/metabolism/growth & development
*Culture Media/chemistry
*Genome, Bacterial
Histidine/metabolism
Mutation
Whole Genome Sequencing

@article {pmid39567372,
year = {2024},
author = {Issifu, S and Acharya, P and Kaur-Bhambra, J and Gubry-Rangin, C and Rasche, F},
title = {Biological Nitrification Inhibitors with Antagonistic and Synergistic Effects on Growth of Ammonia Oxidisers and Soil Nitrification.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {143},
pmid = {39567372},
issn = {1432-184X},
support = {RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; RA 1717/8-1//2019-2020 Bio-divERsA joint call for research proposals, under the BiodivClim ERA-Net COFUND programme, and with the funding organisations German Research Foundation/ ; URF150571//Royal Society University Research Fellowship/ ; },
mesh = {*Nitrification ; *Soil Microbiology ; *Ammonia/metabolism ; *Soil/chemistry ; Archaea/metabolism/drug effects/growth & development ; Oxidation-Reduction ; Rhizosphere ; Bacteria/metabolism/drug effects/growth & development ; },
abstract = {Biological nitrification inhibition (BNI) refers to the plant-mediated process in which nitrification is inhibited through rhizospheric release of diverse metabolites. While it has been assumed that interactive effects of these metabolites shape rhizosphere processes, including BNI, there is scant evidence supporting this claim. Hence, it was a primary objective to assess the interactive effects of selected metabolites, including caffeic acid (CA), vanillic acid (VA), vanillin (VAN), syringic acid (SA), and phenylalanine (PHE), applied as single and combined compounds, against pure cultures of various ammonia-oxidising bacteria (AOB, Nitrosomonas europaea, Nitrosospira multiformis, Nitrosospira tenuis, Nitrosospira briensis) and archaea (AOA, Nitrososphaera viennensis), as well as soil nitrification. Additionally, benzoic acid (BA) was examined as a novel biological nitrification inhibitor. All metabolites, except SA, tested as single compounds, achieved varied levels of inhibition of microbial growth, with CA exhibiting the highest inhibitory potential. Similarly, all metabolites applied as single compounds, except PHE, inhibited soil nitrification by up to 62%, with BA being the most potent. Inhibition of tested nitrifying microbes was also observed when compounds were assessed in combination. The combinations VA + PH, VA + CA, and VA + VAN exhibited synergism against N. tenuis and N. briensis, while others showed antagonism against N. europaea, N. multiformis, and N. viennensis. Although all combinations suppressed soil nitrification, their interactions against soil nitrification revealed antagonism. Our findings indicate that both antagonism and synergism are possible in rhizospheric interactions involving BNI metabolites, resulting in growth inhibition of nitrifiers and suppression of soil nitrification.},
}

*Nitrification
*Soil Microbiology
*Ammonia/metabolism
*Soil/chemistry
Archaea/metabolism/drug effects/growth & development
Oxidation-Reduction
Rhizosphere
Bacteria/metabolism/drug effects/growth & development

@article {pmid39565130,
year = {2024},
author = {Yu, C and Yu, M and Ma, R and Wei, S and Jin, M and Jiao, N and Zheng, Q and Zhang, R and Feng, X},
title = {A novel Alteromonas phage with tail fiber containing six potential iron-binding domains.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0093424},
doi = {10.1128/spectrum.00934-24},
pmid = {39565130},
issn = {2165-0497},
abstract = {Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. Alteromonas is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of Alteromonas and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects Alteromonas marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the Schitoviridae family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using Alteromonas, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.},
}

@article {pmid39563404,
year = {2024},
author = {Chari, NR and Muratore, TJ and Frey, SD and Winters, CL and Martinez, G and Taylor, BN},
title = {Long-Term Soil Warming Drives Different Belowground Responses in Arbuscular Mycorrhizal and Ectomycorrhizal Trees.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17550},
doi = {10.1111/gcb.17550},
pmid = {39563404},
issn = {1365-2486},
support = {DEB-1456610//National Science Foundation/ ; DEB-1832110//National Science Foundation/ ; },
mesh = {*Mycorrhizae/physiology ; *Trees/microbiology/physiology/growth & development ; *Soil/chemistry ; *Plant Roots/microbiology ; *Global Warming ; Biomass ; Soil Microbiology ; Carbon/metabolism/analysis ; Nitrogen/metabolism/analysis ; Climate Change ; Temperature ; },
abstract = {The ability of trees to acquire soil nutrients under future climate conditions will influence forest composition and function in a warmer world. Rarely are multiple belowground carbon allocation pathways measured simultaneously in large global change experiments, restricting our understanding of how trees may shift their allocation of resources to different nutrient acquisition mechanisms under future climates. Leveraging a 20-year soil warming experiment, we show that ectomycorrhizal (EM) trees reduce mycorrhizal colonization and root exudation while increasing fine root biomass, while arbuscular mycorrhizal (AM) trees largely maintained their belowground carbon allocation patterns in warmer soils. We suggest that AM trees may be better adapted to thrive under global warming due to higher rates of nitrogen mineralization in warmer soils and the ability of their mycorrhizal symbiont to acquire mineralized inorganic nutrients, whereas EM trees may need to alter their belowground carbon allocation patterns to remain competitive as global temperatures rise.},
}

*Mycorrhizae/physiology
*Trees/microbiology/physiology/growth & development
*Soil/chemistry
*Plant Roots/microbiology
*Global Warming
Biomass
Soil Microbiology
Carbon/metabolism/analysis
Nitrogen/metabolism/analysis
Climate Change
Temperature

@article {pmid39561700,
year = {2024},
author = {Partida-Martínez, LP},
title = {Laila P. Partida-Martínez.},
journal = {Current biology : CB},
volume = {34},
number = {22},
pages = {R1121-R1122},
doi = {10.1016/j.cub.2024.09.085},
pmid = {39561700},
issn = {1879-0445},
mesh = {*Symbiosis ; Fungi/physiology ; Plants/microbiology ; History, 21st Century ; History, 20th Century ; },
abstract = {Interview with Laila Partida-Martínez, who studies microbial ecology, fungal-bacterial symbioses and plant-microbe interactions at the Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav).},
}

*Symbiosis
Fungi/physiology
Plants/microbiology
History, 21st Century
History, 20th Century

@article {pmid39561304,
year = {2024},
author = {Vargas Ribera, PR and Kim, N and Venbrux, M and Álvarez-Pérez, S and Rediers, H},
title = {Evaluation of sequence-based tools to gather more insight into the positioning of rhizogenic agrobacteria within the Agrobacterium tumefaciens species complex.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0302954},
pmid = {39561304},
issn = {1932-6203},
mesh = {*Agrobacterium tumefaciens/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Agrobacterium/genetics ; Genome, Bacterial ; DNA, Bacterial/genetics ; },
abstract = {Rhizogenic Agrobacterium, the causative agent of hairy root disease (HRD), is known for its high phenotypic and genetic diversity. The taxonomy of rhizogenic agrobacteria has undergone several changes in the past and is still somewhat controversial. While the classification of Agrobacterium strains was initially mainly based on phenotypic properties and the symptoms they induced on plants, more and more genetic information has been used along the years to infer Agrobacterium taxonomy. This has led to the definition of the so-called Agrobacterium tumefaciens species complex (Atsc), which comprises several genomospecies. Interestingly, the rhizogenic Agrobacterium strains are found in several of these genomospecies. Nevertheless, even up until today Agrobacterium strains, and in particular rhizogenic agrobacteria, are prone to misclassification and considerable confusion in literature. In this study, we evaluated different phylogenetic analysis approaches for their use to improve Agrobacterium taxonomy and tried to gain more insight in the classification of strains into this complex genus, with a particular focus on rhizogenic agrobacteria. The genome sequence analysis of 580 assemblies, comprising Agrobacterium, Allorhizobium and Rhizobium strains demonstrated that phylogenies based on single marker genes, such as the commonly used 16S rRNA and recA gene, do not provide sufficient resolution for proper delineation of the different genomospecies within the Atsc. Our results revealed that (in silico) multi-locus sequences analysis (MLSA) in combination with average nucleotide identity (ANIb) at a 94.0% threshold delineates genomospecies accurately and efficiently. Additionally, this latter approach permitted the identification of two new candidate genomospecies.},
}

*Agrobacterium tumefaciens/genetics
*Phylogeny
RNA, Ribosomal, 16S/genetics
Agrobacterium/genetics
Genome, Bacterial
DNA, Bacterial/genetics

@article {pmid39560406,
year = {2024},
author = {Ye, Y-Q and Ye, M-Q and Zhang, X-Y and Huang, Y-Z and Zhou, Z-Y and Feng, Y-J and Du, Z-J},
title = {Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0053524},
doi = {10.1128/msystems.00535-24},
pmid = {39560406},
issn = {2379-5077},
abstract = {The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.},
}

@article {pmid39558480,
year = {2024},
author = {Zechner, EL and Kienesberger, S},
title = {Microbiota-derived small molecule genotoxins: host interactions and ecological impact in the gut ecosystem.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2430423},
pmid = {39558480},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/genetics/classification/drug effects ; Animals ; *Host Microbial Interactions ; Mutagens/metabolism ; Polyketides/metabolism/pharmacology ; Enterotoxins/metabolism ; Peptides ; },
abstract = {The human intestinal tract is densely colonized by a microbial community that is subject to intense competition. Bacteria in this complex habitat seek to outcompete their neighbors for nutrients and eliminate competitors with antibacterial toxins. Antagonism can be mediated by diverse effectors including toxic proteins and small molecule inhibitors that are released extracellularly or delivered by specialized secretion systems to targeted cells. Two prototypical microbiota-derived enterotoxins, colibactin and tilimycin, and the newly discovered family of indolimines represent an expanding group of non-proteinaceous small molecules which specifically target DNA. In addition to cell killing, they generate mutations and genome instability in intoxicated microbes and host cells alike. They have been studied in detail because of their direct toxicity to human cells and important etiological roles in intestinal pathologies. Increasing evidence, however, reveals that these commensal genotoxins are also mediators of interbacterial antagonism, which impacts gut microbial ecology. In this review, we illustrate the functional versatility of commensal genotoxins in the gut ecosystem.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Bacteria/metabolism/genetics/classification/drug effects
Animals
*Host Microbial Interactions
Mutagens/metabolism
Polyketides/metabolism/pharmacology
Enterotoxins/metabolism
Peptides

@article {pmid39557685,
year = {2024},
author = {Mai, N and Foysal, MJ and Timms, VJ and Pearson, LA and Romanis, CS and Mills, TJT and Powell, JR and Neilan, BA},
title = {Seasonal and Spatial Dynamics of Fungal Leaf Endophytes in Eucalyptus crebra (Narrow-Leaved Ironbark).},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {142},
pmid = {39557685},
issn = {1432-184X},
support = {CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; CE200100029//Australian Research Council/ ; FF0883440//Australian Research Council/ ; },
mesh = {*Eucalyptus/microbiology ; *Seasons ; *Endophytes/isolation & purification/classification/genetics ; *Plant Leaves/microbiology ; *Fungi/classification/isolation & purification/genetics ; Biodiversity ; Ascomycota/genetics/isolation & purification ; Basidiomycota/isolation & purification/genetics/classification ; },
abstract = {Fungal endophytes play an important role in improving the health and productivity of native and cultivated plant species. Despite their ecological and industrial importance, few eucalypt species have been studied in terms of their endophyte communities. We examined the seasonal and spatial dynamics of fungal leaf endophytes in the model species, Eucalyptus crebra (narrow-leaved ironbark), using ITS-based amplicon sequencing. Alpha and beta diversity analyses revealed significantly higher species richness in summer compared to autumn and spring. Similarly, two-way ANOVA analysis showed significantly higher species diversity in summer compared to autumn (observed p < 0.001, Chao1 p < 0.005) and spring (observed p < 0.005, Chao1 p < 0.005). No difference in Shannon index was observed among different canopy levels across the season. Beta-diversity showed differences in fungal composition across the seasons and at various canopy levels based on unweighted UniFrac distance metric (PERMANOVA season p < 0.001, canopy p < 0.05), signifying distinct separation of fungi based on presence-absence. Ascomycota was the most abundant and diverse phylum and was present throughout the year. In contrast, Basidiomycota was only observed during cooler and drier seasons. Neofusicoccum was the most abundant genus, but distribution fluctuated significantly across the seasons. Pestalotiopsis and Neopestalotiopsis were most abundant in the low leaf canopy, whereas Pseudosydowia was most abundant in the high canopy. This study indicates that the diversity and abundance of endophytic fungi in the leaves of healthy E. crebra trees fluctuate seasonally and across canopy levels. The data generated can be used as a baseline for assessing and potentially modulating the health of E. crebra and other important Eucalyptus spp.},
}

*Eucalyptus/microbiology
*Seasons
*Endophytes/isolation & purification/classification/genetics
*Plant Leaves/microbiology
*Fungi/classification/isolation & purification/genetics
Biodiversity
Ascomycota/genetics/isolation & purification
Basidiomycota/isolation & purification/genetics/classification

@article {pmid39551884,
year = {2024},
author = {Mamo, Z and Abera, S and Tafesse, M},
title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {12},
pages = {384},
pmid = {39551884},
issn = {1573-0972},
support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; },
mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; },
abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.},
}

*Solid Waste
*Bacteria/classification/genetics/metabolism
*Waste Disposal Facilities
*Microbiota
*Metagenomics
Phylogeny
Refuse Disposal
Biodegradation, Environmental
Drug Resistance, Microbial/genetics
Soil Microbiology

@article {pmid39551202,
year = {2024},
author = {Duran, C and Bouchard, A and Agogué, H and Dupuy, C and Duran, R and Cravo-Laureau, C},
title = {Importance of eukaryotes in shaping microbial benthic communities in Charente-maritime marshes, France.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177523},
doi = {10.1016/j.scitotenv.2024.177523},
pmid = {39551202},
issn = {1879-1026},
abstract = {Marshes are wetlands known for providing major ecosystem services in terms of water quality and human activities. These ecosystem services are mainly provided by marshes' benthic community, composed of prokaryotes (bacteria and archaea) but also of eukaryotes (micro-eukaryotes and meiofauna). The aim of this study is to (1) assess the environmental parameters affecting benthic community composition in marshes, (2) highlight the associations between organisms from the three domains of life, and (3) determine the parameters controlling these associations. Hence, benthic communities of eight different marshes from three typologies (salted, brackish and freshwater) and four seasons (autumn 2020, spring 2021, summer 2021 and autumn 2021) were assessed. This study revealed three main drivers of community composition. First, salinity drives the community composition illustrated by the differences observed between the three typologies of marshes. Relative abundance of Nitrososphaeria, Halobacteria, Bacillariophyceae, Conoidasida and nematodes increased with salinity while methanogenic archaea, Chlorophyceae and copepod's relative abundance decreased. The second driver is the physical-chemistry of the site, particularly nutrients. The season is the last driver of community composition, seasonal pattern varying for each site within a typology. LEfSe analyses defined biomarkers of typology and season, among which many prokaryotes involved in the nitrogen cycle and photosynthetic micro-eukaryotes where present in different co-occurrence networks, highlighting the importance of nitrogen cycle in marshes. Co-occurrence networks revealed several connections between organisms of the three domains of life, particularly between prokaryotes and photosynthetic eukaryotes. This study illustrates thus the importance of holistic approaches in microbial ecology for revealing a comprehensive view of the whole microbial interactions occurring in complex ecosystems.},
}

@article {pmid39549623,
year = {2024},
author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L},
title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122727},
doi = {10.1016/j.watres.2024.122727},
pmid = {39549623},
issn = {1879-2448},
abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.},
}

@article {pmid39549075,
year = {2024},
author = {de la Sovera, V and Bovio-Winkler, P and Zinola, G and Etchebehere, C},
title = {Microbial community evolution in a lab-scale reactor operated to obtain biomass for biochemical methane potential assays.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {519},
pmid = {39549075},
issn = {1432-0614},
support = {SNI//ANII/ ; SNI//ANII/ ; SNI//ANII/ ; (II/FVF/2019/121).//Carlos Vaz Ferreira/ ; },
mesh = {*Methane/metabolism ; *Biomass ; *Bioreactors/microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Archaea/genetics/metabolism/classification ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Microbiota ; Biodegradation, Environmental ; },
abstract = {Biochemical methane potential (BMP) test is an important tool to evaluate the methane production biodegradability and toxicity of different wastes or wastewaters. This is a key parameter for assessing design and feasibility issues in the full-scale implementation of anaerobic digestion processes. A standardized and storable inoculum is the key to obtain reproducible results. In Uruguay, a local enterprise dedicated to design and install anaerobic digesters operated a lab-scale bioreactor as a source of biomass for BMP tests, using a protocol previously described. This reactor was controlled and fed with a mixture of varied organic compounds (lipids, cellulolytic wastes, proteins). Biomass was reintroduced into the reactor after BMP assays to maintain a constant volume and biomass concentration. The aim of this work was to evaluate how the microbial community evolved during this operation and the effect of storing biomass in the refrigerator. The composition of the microbial communities was analyzed by 16S rRNA amplicon sequencing using primers for Bacteria and Archaea. The methanogenic activity was determined, and the methanogens were quantified by mcrA qPCR. One sample was stored for a 5-month period in the refrigerator (4 °C); the activity and the microbial community composition were analyzed before and after storage. Results showed that applying the reported methodology, a reliable methanogenic sludge with an acceptable SMA was obtained even though the reactor suffered biomass alterations along the evaluated period. Refrigerating the acclimatized biomass for 5 months did not affect its activity nor its microbial composition according to the 16S rRNA gene sequence analysis, even though changes in the mcrA abundance were observed. KEY POINTS: • The applied methodology was successful to obtain biomass suitable to perform BMP assays. • The microbial community was resilient to external biomass addition. • Biomass storage at 4 °C for 5 months did not alter the methanogenic activity.},
}

*Methane/metabolism
*Biomass
*Bioreactors/microbiology
*Bacteria/genetics/metabolism/classification/isolation & purification
*Archaea/genetics/metabolism/classification
Anaerobiosis
*RNA, Ribosomal, 16S/genetics
*Sewage/microbiology
Microbiota
Biodegradation, Environmental

@article {pmid39546027,
year = {2024},
author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M},
title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {141},
pmid = {39546027},
issn = {1432-184X},
mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; },
abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.},
}

*Carbon-Sulfur Lyases/genetics/metabolism
*Metagenomics
*Phylogeny
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
Archaea/genetics/enzymology/classification
Groundwater/microbiology
Metagenome
Seawater/microbiology

@article {pmid39545996,
year = {2024},
author = {Scheelings, TF and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Location Matters: Variations in Cloacal Microbiota Composition of Spatially Separated Freshwater Turtles.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {140},
pmid = {39545996},
issn = {1432-184X},
mesh = {Animals ; *Turtles/microbiology ; *Cloaca/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Fresh Water/microbiology ; Australia ; Gastrointestinal Microbiome ; Biodiversity ; },
abstract = {The gut microbiota of vertebrates is malleable and may be shaped by both intrinsic and extrinsic factors. Here, the effect that geography has on the cloacal microbiota of two species of Australian freshwater chelonians, eastern longneck turtle (Chelodina longicollis) and Macquarie River turtle (Emydura macquarii), captured from waterbodies with different levels of anthropogenic pressure was investigated. We analysed the microbiota composition, structure and diversity through 16S rRNA gene amplicon sequencing. It was hypothesised that animals from less disturbed environments would harbour a more diverse cloacal microbial population. The cloacal microbiotas from 93 turtles (C. longicollis n = 78; E. macquarii n = 15), from five locations, were analysed. For both species, the most predominant phylum was Proteobacteria. Cloacal microbiota alpha diversity varied significantly between the C. longicollis from all locations, but no differences were found for E. macquarii. In C. longicollis, turtles from wetlands within the centre of Melbourne had the lowest alpha diversity metrics, while the highest alpha diversity values were seen in turtles captured from an undisturbed rural waterbody. Beta diversity, obtained by weighted UniFrac distance, showed significant differences between locations of capture for both species of turtles in this investigation. For C. longicollis, 87 biomarkers were identified responsible for explaining differences between locations, and in E. macquarii, 42 biomarkers were found. This is the first study to explore the cloacal microbiota composition of the eastern longneck turtle and gives greater insight into microbial community structures in Macquarie River turtles. Our study demonstrated that cloacal microbiota composition of freshwater turtles was significantly influenced by locality and that disrupted environments may reduce microbial diversity in C. longicollis. Interestingly, we discovered that the effects of location contrasted significantly between species for alpha diversity with differences discovered for C. longicollis but not E. macquarii. However, for both species, beta diversity was notably influenced by habitat type. These results highlight the need to interpret chelonian microbiota data in the context of geography and human disturbance of the environment.},
}

Animals
*Turtles/microbiology
*Cloaca/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Fresh Water/microbiology
Australia
Gastrointestinal Microbiome
Biodiversity

@article {pmid39545729,
year = {2024},
author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC},
title = {Enriching the future of public health microbiology with hybridization bait capture.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0006822},
doi = {10.1128/cmr.00068-22},
pmid = {39545729},
issn = {1098-6618},
abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.},
}

@article {pmid39544963,
year = {2024},
author = {Wong, HL and Bulzu, PA and Ghai, R and Chiriac, MC and Salcher, MM},
title = {Ubiquitous genome streamlined Acidobacteriota in freshwater environments.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae124},
pmid = {39544963},
issn = {2730-6151},
abstract = {Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named "A. lacustris" and "A. fluvialis". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.},
}

@article {pmid39543974,
year = {2024},
author = {Gonsiorczyk, T and Hupfer, M and Hilt, S and Gessner, MO},
title = {Rapid Eutrophication of a Clearwater Lake: Trends and Potential Causes Inferred From Phosphorus Mass Balance Analyses.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17575},
doi = {10.1111/gcb.17575},
pmid = {39543974},
issn = {1365-2486},
mesh = {*Eutrophication ; *Lakes/chemistry ; *Phosphorus/analysis ; *Geologic Sediments/analysis/chemistry ; *Seasons ; Environmental Monitoring/methods ; },
abstract = {Many clearwater lakes increasingly show symptoms of eutrophication, but the underlying causes are largely unknown. We combined long-term water chemistry data, multi-year sediment trap measurements, sediment analyses and simple mass balance models to elucidate potential causes of eutrophication of a deep temperate clearwater lake, where total phosphorus (TP) concentrations quadrupled within a decade, accompanied by expanding hypolimnetic anoxia. Discrepancies between modeled and empirically determined P inputs suggest that the observed sharp rise in TP was driven by internal processes. The magnitude of seasonal variation in TP greatly increased at the same time, both in surface and deep water, partly decoupled from deep water oxygen conditions. A positive correlation between annual P loss from the upper water column and hypolimnetic P accumulation could hint at a short-circuited P cycle involving lateral TP transport from shallow-water zones and deposition and release from sediments in deep water. This hypothesis is also supported by P budgets for the upper 20 m during stable summer stratification, suggesting that sediments in shallow lake areas acted as a P net source until 2018. These changes are potentially related to shifts in submerged macrophytes from wintergreen charophyte meadows (Nitellopsis obtusa) to annual free-floating hornwort (Ceratophyllum demersum) and to increased sulfide formation, promoting iron fixation in the sediments. Iron bound to sulfur is unavailable for binding P, resulting in a positive feedback between P release in shallow lake areas, primary productivity, macrophyte community structure and redox-dependent sediment biogeochemistry. Overall, our results suggest that relationships more complex than the commonly invoked increase in internal P release under increasingly anoxic conditions can drive rapid lake eutrophication. Since the proportion of littoral areas is typically large even in deep stratified lakes, littoral processes may contribute more frequently to the rapid lake eutrophication trends observed around the world than is currently recognized.},
}

*Eutrophication
*Lakes/chemistry
*Phosphorus/analysis
*Geologic Sediments/analysis/chemistry
*Seasons
Environmental Monitoring/methods

@article {pmid39541983,
year = {2024},
author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH},
title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.},
journal = {Cell systems},
volume = {15},
number = {11},
pages = {1002-1017.e4},
doi = {10.1016/j.cels.2024.10.007},
pmid = {39541983},
issn = {2405-4720},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Mammals/microbiology ; Feces/microbiology ; },
abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Fecal Microbiota Transplantation/methods
Mice, Inbred C57BL
Gastrointestinal Tract/microbiology
Dysbiosis/microbiology
Mammals/microbiology
Feces/microbiology

@article {pmid39541852,
year = {2024},
author = {Wang, Q and Wang, M and Yang, Q and Feng, L and Zhang, H and Wang, R and Wang, R},
title = {The role of bacteriophages in facilitating the horizontal transfer of antibiotic resistance genes in municipal wastewater treatment plants.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122776},
doi = {10.1016/j.watres.2024.122776},
pmid = {39541852},
issn = {1879-2448},
abstract = {Bacteriophages play integral roles in the ecosystem; however, their precise involvement in horizontal gene transfer and the spread of antibiotic resistance genes (ARGs) are not fully understood. In this study, a coculture system involving consortia of bacteriophages and multidrug-resistant bacteria from an aerobic tank in a municipal wastewater treatment plant (WWTP) was established to investigate the functions of bacteriophages in ARG transfer and spread. The results of the cocultivation of the MRB and bacteriophage consortia indicated that the bacterial community remained stable throughout the whole process, but the addition of bacteriophages significantly increased ARG abundance, especially in bacteriophage DNA. Nine out of the 11 identified ARGs significantly increased, indicating that more bacteriophage particles carried ARGs in the system after cocultivation. In addition, 686 plasmids were detected during cocultivation, of which only 3.36 % were identified as conjugative plasmids, which is significantly lower than the proportion found among previously published plasmids (25.2 %, totaling 14,029 plasmids). Our findings revealed that bacteriophages may play important roles in the horizontal transfer of ARGs through both bacteriophage-mediated conduction and an increase in extracellular ARGs; however, conjugative transfer may not be the main mechanism by which multidrug-resistant bacteria acquire and spread ARGs. Unlike in most previous reports, a coculture system of diverse bacteria and bacteriophages was established in this study to assess bacteriophage functions in ARG transfer and dissemination in the environment, overcoming the limitations associated with the isolation of bacteria and bacteriophages, as well as the specificity of bacteriophage hosts.},
}

@article {pmid39540979,
year = {2024},
author = {Frew, A and Aguilar-Trigueros, CA},
title = {Increasing Phylogenetic Clustering of Arbuscular Mycorrhizal Fungal Communities in Roots Explains Enhanced Plant Growth and Phosphorus Uptake.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {139},
pmid = {39540979},
issn = {1432-184X},
support = {DE220100479//Australian Research Council/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Phosphorus/metabolism ; *Plant Roots/microbiology/growth & development ; *Phylogeny ; *Symbiosis ; *Sorghum/microbiology/growth & development ; Soil Microbiology ; Mycobiome ; Biomass ; Plant Development ; },
abstract = {Temporal variation during the assembly of arbuscular mycorrhizal (AM) fungal communities within plant roots have been posited as critical drivers of the plant-fungal symbiotic outcomes. However, functional implications of these dynamics for the host plant remain poorly understood. We conducted a controlled pot experiment with Sorghum bicolor to investigate how temporal shifts in AM fungal community composition and phylogenetic diversity influence plant growth and phosphorus responses to the symbiosis. We characterised the root-colonising AM fungal communities across three time points and explored their community assembly processes by analysing their phylogenetic diversity and employing joint species distribution modelling with the Hierarchical Modelling of Species Communities (HMSC) framework. We found strong AM fungal turnover through time with a high phylogenetic signal, indicating recruitment of phylogenetically clustered AM fungal species in the host. This temporal phylogenetic clustering of communities coincided with marked increases in plant biomass and phosphorus responses to the AM fungal symbiosis, suggesting that host selection for specific fungi may be a key determinant of these benefits.},
}

*Mycorrhizae/genetics/physiology
*Phosphorus/metabolism
*Plant Roots/microbiology/growth & development
*Phylogeny
*Symbiosis
*Sorghum/microbiology/growth & development
Soil Microbiology
Mycobiome
Biomass
Plant Development

@article {pmid39537004,
year = {2024},
author = {Bernetti, A and Barili, S and Sannino, C and Mugnai, G and Borruso, L and Pinchuk, I and Pezzolla, D and Turchetti, B and Gigliotti, G and Buzzini, P},
title = {Selective response of soil bacterial and fungal taxa to biodegradable polymers.},
journal = {Environmental research},
volume = {264},
number = {Pt 1},
pages = {120344},
doi = {10.1016/j.envres.2024.120344},
pmid = {39537004},
issn = {1096-0953},
abstract = {Biodegradable mulching films offer an eco-friendly alternative to petroleum-based plastics in agriculture, but their effects on soil parameters are not well understood. A microcosm experiment (20 °C, 75% field capacity) investigated the impact of two doses (0.021% and 1% w/w) of a biodegradable polymer on soil chemical and microbiological properties over a year. The 1% dose significantly (p < 0.05) increased CO2 emissions, water-extractable organic C, and hydrolytic activity. A significant (p < 0.05) effect on microbial alpha- and beta-diversity was noted only during short- and medium-term incubations. In contrast, a taxon-related response was found for both bacterial and fungal taxa affecting the abundance of the genera Aquicella, Cellvibrio, Bacillus, Ramlibacter, and Saccharibacteria genera incertae sedis among bacteria, and Malassezia, Orbilia, and Rhodotorula among fungi (including both yeast and filamentous lifestyles). Microbial functions revealed a greater impact on fungal communities compared to bacterial ones. However, after one year of exposition, only a marginal effect on the abundance of both bacterial and fungal functional groups was found in the microcosms. A significantly higher concentration of tightly bound exopolysaccharides in the presence of 1% biodegradable polymer at the start of the experiment suggested their key role in microbial degradation of bioplastics via biofilm formation.},
}

@article {pmid39536049,
year = {2024},
author = {Zhao, Y and Cordero, OX and Tikhonov, M},
title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.},
journal = {PLoS computational biology},
volume = {20},
number = {11},
pages = {e1012590},
doi = {10.1371/journal.pcbi.1012590},
pmid = {39536049},
issn = {1553-7358},
abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.},
}

@article {pmid39524341,
year = {2024},
author = {Dzialo, MC and Arumugam, S and Piampongsant, S and Cool, L and Vanderaa, C and Herrera-Malaver, B and Opsomer, T and Dehaen, W and Wenseleers, T and Roncoroni, M and Alawamleh, A and Wäckers, F and Lievens, B and Hansson, BS and Voordeckers, K and Sachse, S and Verstrepen, KJ},
title = {Drosophila suzukii and Drosophila melanogaster prefer distinct microbial and plant aroma compounds in a complex fermented matrix.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111141},
pmid = {39524341},
issn = {2589-0042},
abstract = {Volatile aroma compounds are important chemical cues for insects. Behavioral responses to specific odors differ strongly between insect species, and the exact causative molecules are often unknown. Beer is frequently used in insect traps because it combines hundreds of plant and microbial aromas that attract many insects. Here, we analyzed responses of the pest fruit fly Drosophila suzukii and benign Drosophila melanogaster to beers with different chemical compositions. Using extensive chemical and behavioral assays, we identified ecologically relevant chemicals that influence drosophilid behavior and that induce different odor-evoked activity patterns in the antennal lobe of the two species obtained by functional imaging. Specific mixes of compounds increased the species-specificity and sex-specificity of lures in both laboratory and greenhouse settings. Together, our study shows how examining insect responses to highly complex natural mixtures of aroma compounds provides insight into insect-specific behavioral responses and also opens avenues for improved pest control.},
}

@article {pmid39535358,
year = {2024},
author = {Tidimalo, C and Maximiliano, O and Karen, J and Lebre, PH and Bernard, O and Michelle, G and Oagile, D and Cowan, DA},
title = {Microbial diversity in the arid and semi-arid soils of Botswana.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70044},
pmid = {39535358},
issn = {1758-2229},
support = {//PhD bursary for Tidimalo Coetzee from the University of Botswana/ ; //Oppenheimer Foundation/ ; 674-AA-2010-A1//United States Agency for International Development/ ; //University of Pretoria for postdoctoral support/ ; },
mesh = {*Soil Microbiology ; Botswana ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Soil/chemistry ; *Biodiversity ; Microbiota/genetics ; Phylogeny ; Hydrogen-Ion Concentration ; DNA, Bacterial/genetics ; },
abstract = {To date, little research has been conducted on the landscape-scale distribution of soil microbial communities and the factors driving their community structures in the drylands of Africa. We investigated the influence of landscape-scale variables on microbial community structure and diversity across different ecological zones in Botswana. We used amplicon sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacers (ITS) and a suite of environmental parameters to determine drivers of microbial community structure. Bacterial communities were dominated by Actinomycetota (21.1%), Pseudomonadota (15.9%), and Acidobacteriota (10.9%). The dominant fungal communities were Ascomycota (57.3%) and Basidiomycota (7.5%). Soil pH, mean annual precipitation, total organic carbon, and soil ions (calcium and magnesium) were the major predictors of microbial community diversity and structure. The co-occurrence patterns of bacterial and fungal communities were influenced by soil pH, with network-specific fungi-bacteria interactions observed. Potential keystone taxa were identified for communities in the different networks. Most of these interactions were between microbial families potentially involved in carbon cycling, suggesting functional redundancy in these soils. Our findings highlight the significance of soil pH in determining the landscape-scale structure of microbial communities in Botswana's dryland soils.},
}

*Soil Microbiology
Botswana
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Soil/chemistry
*Biodiversity
Microbiota/genetics
Phylogeny
Hydrogen-Ion Concentration
DNA, Bacterial/genetics

@article {pmid39532738,
year = {2024},
author = {Fu, M and Liu, Y and Li, S and Yan, D and Liu, P and Liu, Y and Ji, M},
title = {The Spatial Dynamics of Diazotrophs in the Forefield of Three Tibetan Glaciers.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {138},
pmid = {39532738},
issn = {1432-184X},
support = {42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 32161123004//National Natural Science Foundation of China/ ; },
mesh = {*Ice Cover/microbiology ; Tibet ; *Soil Microbiology ; *Nitrogen Fixation ; Soil/chemistry ; Nitrogen/metabolism ; Ecosystem ; Bacteria/classification/metabolism/genetics/isolation & purification/enzymology ; Nitrogen-Fixing Bacteria/metabolism/classification/isolation & purification/genetics ; Phylogeny ; Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Nitrogen is often a limiting nutrient for microbial communities and plants in glacier forefields. Nitrogen-fixing microorganisms (diazotrophs) play an important role in providing bioavailable nitrogen, with their composition determining the nitrogen-fixating capacities. This study investigates the spatial and temporal dynamics of diazotrophs in the forefields of three Tibetan glaciers: Qiangyong, Kuoqionggangri, and Longxiazailongba. We collected soil samples from recently deglaciated barren grounds, and also along an ecosystem succession transect at Kuoqionggangri glacier, encompassing barren ground, herb steppe, legume steppe, and alpine meadow ecosystems. Our finding revealed abundant and diverse diazotrophs in the recently deglaciated barren ground. They are taxonomically affiliated with anaerobic Bradyrhizobium, Desulfobulbus, and Pelobacter, which may be relics from subglacial sediments. The vegetated soils (herb steppe, legume steppe, and alpine meadow) were dominated by phototrophic Nostoc and Anabaena, as well as symbiotic Sinorhizobium. Soil physicochemical parameters, such as soil organic carbon, pH, and nitrate ion, significantly influenced diazotroph community structure. This study highlights the critical role of diazotrophs in mitigating nitrogen limitation during early ecosystem development in glacier forefields. Understanding the distribution and ecological drivers of diazotrophs in these rapidly changing environments provides insights into biogeochemical cycling and ecosystem resilience under climate change.},
}

*Ice Cover/microbiology
Tibet
*Soil Microbiology
*Nitrogen Fixation
Soil/chemistry
Nitrogen/metabolism
Ecosystem
Bacteria/classification/metabolism/genetics/isolation & purification/enzymology
Nitrogen-Fixing Bacteria/metabolism/classification/isolation & purification/genetics
Phylogeny
Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid39528791,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39528791},
issn = {1740-1534},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
}

@article {pmid39528727,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39528727},
issn = {2058-5276},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
}

@article {pmid39528652,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {34},
pmid = {39528652},
issn = {2731-4243},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}

@article {pmid39528617,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1466},
pmid = {39528617},
issn = {2399-3642},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}

@article {pmid39528577,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {122},
pmid = {39528577},
issn = {2055-5008},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}

@article {pmid39528441,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9637},
pmid = {39528441},
issn = {2041-1723},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {This paper is a call to action. By publishing concurrently across journals like an emergency bulletin, we are not merely making a plea for awareness about climate change. Instead, we are demanding immediate, tangible steps that harness the power of microbiology and the expertise of researchers and policymakers to safeguard the planet for future generations.},
}

@article {pmid39528211,
year = {2024},
author = {Jang, J and Park, J and Hwang, CY and Gim, Y and Park, KT and Yoon, YJ and Seo, M and Lee, BY},
title = {Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177462},
doi = {10.1016/j.scitotenv.2024.177462},
pmid = {39528211},
issn = {1879-1026},
abstract = {This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.},
}

@article {pmid39527614,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39527614},
issn = {1751-7370},
}

@article {pmid39527081,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Adoukè Agbodjato, N and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {11},
pages = {},
pmid = {39527081},
issn = {1574-6941},
abstract = {Injecting H2 in deep underground to store this energy carrier will produce artificial subsurface lithoautotrophic microbial ecosystems that modify the taxonomic diversity of indigenous microbial communities and their metabolic activities.},
}

@article {pmid39526991,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Falcao Salles, J and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0141624},
doi = {10.1128/msystems.01416-24},
pmid = {39526991},
issn = {2379-5077},
}

@article {pmid39526896,
year = {2024},
author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L},
title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo02704c},
pmid = {39526896},
issn = {2042-650X},
abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.},
}

@article {pmid39526802,
year = {2024},
author = {Schiml, VC and Walter, JM and Hagen, LH and Varnai, A and Bergaust, LL and De Leon, AVP and Elsgaard, L and Bakken, LR and Arntzen, MØ},
title = {Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0174224},
doi = {10.1128/aem.01742-24},
pmid = {39526802},
issn = {1098-5336},
abstract = {UNLABELLED: Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.

IMPORTANCE: Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.},
}

@article {pmid39520764,
year = {2025},
author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS},
title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.},
journal = {International journal of food microbiology},
volume = {427},
number = {},
pages = {110955},
doi = {10.1016/j.ijfoodmicro.2024.110955},
pmid = {39520764},
issn = {1879-3460},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth & development/classification/genetics/isolation & purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; },
abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.},
}

*Volatile Organic Compounds/analysis/metabolism
Hydrogen-Ion Concentration
Vacuum
Cattle
Animals
*Red Meat/microbiology
*Food Packaging/methods
*Food Microbiology
*Food Storage
Bacteria/metabolism/growth & development/classification/genetics/isolation & purification
Metabolome
Brazil
RNA, Ribosomal, 16S/genetics

@article {pmid39520558,
year = {2024},
author = {Boadella, J and Butturini, A and Doménech-Pascual, A and Freixinos, Z and Perujo, N and Urmeneta, J and Vidal, A and Romaní, AM},
title = {Microbial Life in Playa-Lake Sediments: Adapted Structure, Plastic Function to Extreme Water Activity Variations.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {137},
pmid = {39520558},
issn = {1432-184X},
support = {PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-123735OB-C21//Spanish Ministry of Science, Innovation and Universities/ ; 2020 FISDU 00465//Catalan Government Ministry of Business and Knowledge, Area of Universities and Research/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Biofilms/growth & development ; *Salinity ; *Bacteria/classification/genetics/metabolism ; Biomass ; Droughts ; Water ; },
abstract = {Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (aw, the availability of water for microbial use) from 0.99 to 0.72. aw reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high aw, while phenol oxidase activity and prokaryote biomass increased at lower aw. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 aw). The increased levels of extracellular polymeric substances and carotenoids developed at low aw may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.},
}

*Lakes/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
*Biofilms/growth & development
*Salinity
*Bacteria/classification/genetics/metabolism
Biomass
Droughts
Water

@article {pmid39516195,
year = {2024},
author = {Speth, DR and Zeller, LM and Graf, JS and Overholt, WA and Küsel, K and Milucka, J},
title = {Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9682},
pmid = {39516195},
issn = {2041-1723},
mesh = {*Symbiosis ; *Phylogeny ; *Denitrification ; Metagenome ; Aerobiosis ; Ciliophora/genetics/metabolism ; Groundwater/microbiology ; Gammaproteobacteria/genetics/metabolism ; Germany ; Electron Transport Complex IV/genetics/metabolism ; California ; Genome, Bacterial ; },
abstract = {The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.},
}

*Symbiosis
*Phylogeny
*Denitrification
Metagenome
Aerobiosis
Ciliophora/genetics/metabolism
Groundwater/microbiology
Gammaproteobacteria/genetics/metabolism
Germany
Electron Transport Complex IV/genetics/metabolism
California
Genome, Bacterial

@article {pmid39513042,
year = {2024},
author = {Park, KJ and Gao, Y},
title = {Gut-brain axis and neurodegeneration: mechanisms and therapeutic potentials.},
journal = {Frontiers in neuroscience},
volume = {18},
number = {},
pages = {1481390},
pmid = {39513042},
issn = {1662-4548},
abstract = {This paper reviews the effects of gut microbiota in regulating neurodegenerative diseases through controlling gut-brain axis. Specific microbial populations and their metabolites (short-chain fatty acids and tryptophan derivatives) regulate neuroinflammation, neurogenesis and neural barrier integrity. We then discuss ways by which these insights lead to possible interventions - probiotics, prebiotics, dietary modification, and fecal microbiota transplantation (FMT). We also describe what epidemiological and clinical studies have related certain microbiota profiles with the courses of neurodegenerative diseases and how these impact the establishment of microbiome-based diagnostics and individualized treatment options. We aim to guide microbial ecology research on this key link to neurodegenerative disorders and also to highlight collaborative approaches to manage neurological health by targeting microbiome-related factors.},
}

@article {pmid39511174,
year = {2024},
author = {Chen, SC and Chen, S and Musat, N and Kümmel, S and Ji, J and Lund, MB and Gilbert, A and Lechtenfeld, OJ and Richnow, HH and Musat, F},
title = {Back flux during anaerobic oxidation of butane support archaea-mediated alkanogenesis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9628},
pmid = {39511174},
issn = {2041-1723},
support = {NNF22OC0071609//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; ERC-RA-0020//Helmholtz Association/ ; 101059607//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 12471341//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Oxidation-Reduction ; Anaerobiosis ; *Archaea/metabolism/genetics ; *Butanes/metabolism ; *Carbon Dioxide/metabolism ; Oxidoreductases/metabolism/genetics ; Kinetics ; Alkanes/metabolism ; Thermodynamics ; },
abstract = {Microbial formation and oxidation of volatile alkanes in anoxic environments significantly impacts biogeochemical cycles on Earth. The discovery of archaea oxidizing volatile alkanes via deeply branching methyl-coenzyme M reductase variants, dubbed alkyl-CoM reductases (ACR), prompted the hypothesis of archaea-catalysed alkane formation in nature (alkanogenesis). A combination of metabolic modelling, anaerobic physiology assays, and isotope labeling of Candidatus Syntrophoarchaeum archaea catalyzing the anaerobic oxidation of butane (AOB) show a back flux of CO2 to butane, demonstrating reversibility of the entire AOB pathway. Back fluxes correlate with thermodynamics and kinetics of the archaeal catabolic system. AOB reversibility supports a biological formation of butane, and generally of higher volatile alkanes, helping to explain the presence of isotopically light alkanes and deeply branching ACR genes in sedimentary basins isolated from gas reservoirs.},
}

*Oxidation-Reduction
Anaerobiosis
*Archaea/metabolism/genetics
*Butanes/metabolism
*Carbon Dioxide/metabolism
Oxidoreductases/metabolism/genetics
Kinetics
Alkanes/metabolism
Thermodynamics

@article {pmid39509969,
year = {2024},
author = {Aparicio, S and Ríos-Mejía, A and Gallardo-Mejías, JP and Robles, Á and Borrás, L},
title = {Microalgae-bacteria consortia dynamics in a long term operated membrane-coupled high-rate algal pond (MHRAP).},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123186},
doi = {10.1016/j.jenvman.2024.123186},
pmid = {39509969},
issn = {1095-8630},
abstract = {Traditional activated sludge-based technologies have significant drawbacks, including high energy requirements and greenhouse gas emissions. Microalgae-based processes offer a promising, low-cost, and environmentally friendly alternative. However, the knowledge of treatment systems based on microalgae-bacteria consortia is limited, and even more so is their microbial composition and its relationship with operational parameters. Thus, this study explores the dynamics of microalgae-bacteria consortia in a long-term operated membrane-coupled high-rate algal pond (MHRAP) for wastewater treatment. For this, a pilot-scale MHRAP plant, located in a wastewater treatment plant in Valencia (Spain), was monitored under various hydraulic retention times (HRT) and wastewater influents: i) effluent from a primary settler and ii) effluent form pre-treatment. The biomass retention time was kept constant at 6 days. The composition of the bacterial community was studied through 16S rDNA sequencing, while 18S rDNA sequencing was used to study the microalgae. The results indicate that shorter HRTs significantly increased bacterial diversity, but not eukarya. Principal Co-ordinates Analysis (PCoA) revealed that the HRT and the incoming wastewater quality control the type of the bacterial populations. However, this effect was not observed in eukaryotic organisms. The dominant microalgae genera identified were Desmodesmus and Coelastrella, with Coelastrella becoming more prevalent at shorter HRTs. For bacteria, Verrumicrobiota dominated (18-56%) at high HRT while Proteobacteria was dominant (28-44%) at HRTs below 6 days. The changes observed in the bacterial composition, including the ammonia oxidizing bacteria (AOB) community (mainly Nitrosomonas), suggest that photo-inhibition could be taking place. The nitrite oxidizing bacteria (NOB) community was dominated by Nitrospira and Candidatus Nitrotoga. Operational parameters such as light intensity, pH, and nitrite concentration were found to significantly influence the microbial community structure. Higher light intensity and alkaline pH favored the growth of Desmodesmus, while Coelastrella thrived under lower HRTs. Bacterial diversity plays a crucial role in the treatment process, while microalgae primarily support aerobic bacterial processes by providing oxygen. These findings contribute to a deeper understanding of the complex biological processes in microalgae-bacteria consortia and offer insights into improving wastewater treatment technologies.},
}

@article {pmid39508609,
year = {2024},
author = {Xue, S-J and Liu, J and Zhao, F-Y and Zhang, X-T and Zhu, Z-Q and Zhang, J-Y},
title = {Spatio-temporal distribution and biotechnological potential of culturable yeasts in the intertidal sediments and seawater of Aoshan Bay, China.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0157024},
doi = {10.1128/aem.01570-24},
pmid = {39508609},
issn = {1098-5336},
abstract = {Marine yeasts play a crucial role in marine microbial ecology, facilitating the biogeochemical cycling of carbon and nitrogen in marine ecosystems, while also serving as important reservoirs of bioactive compounds with extensive applications in pharmaceuticals, agriculture, and various industries. Intertidal flats, characterized by their complex ecological dynamics, are postulated to harbor a wealth of yeast resources. This study employed a culture-dependent approach to assess the diversity, spatio-temporal distribution, and biotechnological potential of yeast communities residing within the intertidal sediments and seawater of Aoshan Bay. A total of 392 yeast strains were identified from 20 distinct genera, encompassing 43 recognized species and four candidate novel species. Notably, 17 of these species were identified as novel occurrences in marine environments, underscoring the rich yeast biodiversity of the Aoshan Bay ecosystem, with Candida emerging as the dominant genus in both sedimentary and aqueous habitats. Yeast community composition exhibited significant spatial and temporal variation, with peak diversity and abundance observed in autumn, the subtidal zone, and the surface soil layer. No clear pattern, however, emerged linking these shifts to specific changes in community composition, highlighting the complex interactions between microbial communities, environmental variables, and anthropogenic disturbance. Although several yeast species isolated here have been previously recognized for their biotechnological potential, their diverse and abundant extracellular enzyme profiles were characterized, further highlighting their crucial role in organic matter decomposition and nutrient cycling within the tidal ecosystem, as well as their potential applicability in the food, fine chemical, textile, and pharmaceutical industries.IMPORTANCEThis study presents groundbreaking insights into the yeast diversity of Aoshan Bay, offering invaluable information on their spatial and temporal distribution patterns, as well as their biotechnological potential in the tidal environment. The findings reveal that the eutrophic intertidal flat is a rich repository of yeasts with abundant extracellular enzymatic activity and an important role in nutrient cycling and decomposition processes. Also, these yeasts serve as crucial indicators of ecosystem health and function and are excellent candidates for biotechnological and industrial applications. Collectively, this study not only expands our knowledge of the diversity and distribution of intertidal yeasts but also highlights their promising potential for biotechnological applications.},
}

@article {pmid39505133,
year = {2024},
author = {Hu, Y and Song, Y and Cai, J and Chao, J and Gong, Y and Jiang, X and Shao, K and Tang, X and Gao, G},
title = {Stronger biogeographical pattern of bacterioplankton communities than biofilm communities along a riverine ecosystem: A local scale study of the Kaidu river in the arid and semi-arid northwest of China.},
journal = {Environmental research},
volume = {264},
number = {Pt 1},
pages = {120294},
doi = {10.1016/j.envres.2024.120294},
pmid = {39505133},
issn = {1096-0953},
abstract = {Although the biogeographical pattern and mechanisms underlying microbial assembly have been well-explored in lentic ecosystems, the relevant scenarios in lotic ecosystems remain poorly understood. By sequencing the bacterial communities in bacterioplankton and biofilm, our study detected their distance-decay relationship (DDR), and the balance between deterministic and stochastic processes, along the Kaidu river in an arid and semi-arid region of northwest China. Our results revealed that bacterioplankton and biofilm had significantly contrasting community structures. The bacterioplankton communities showed a gradually decreasing trend in alpha-diversity from the headwater to the river mouth, contrasting with the alpha-diversity of biofilm communities which was constant along the river length. Both bacterioplankton and biofilm showed significant DDRs along the 500-km river corridor with the slope of the bacterioplankton DDR being steeper than that of the biofilm DDR, which implies a stronger biogeography of bacterioplankton than biofilm. Relative to biofilm communities, the species interactions formed a denser and more complex network in the bacterioplankton communities than in the biofilm communities. Our results also revealed that there was a transition of community assembly from deterministic to stochastic processes upstream to downstream, although both the bacterioplankton and biofilm communities were mainly regulated by deterministic processes within the entire river. All these empirical results expand our knowledge of microbial ecology in an arid and semi-arid lotic ecosystem.},
}

@article {pmid39503489,
year = {2024},
author = {Teixeira, GM and Cordeiro Montanari, GC and Nicoletto, MLA and da Silva, DV and Noriler, SA and de Oliveira, JP and da Silva Rodrigues, MV and Sipoli Sanches, D and de Padua Pereira, U and Nunes da Rocha, U and Oliveira, AGd},
title = {Draft genome of Bacillus velezensis CMRP6330, a suitable biocontrol agent for disease management in crops.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0065724},
doi = {10.1128/mra.00657-24},
pmid = {39503489},
issn = {2576-098X},
abstract = {As a biological alternative to managing diseases in crop production, we highlight the Bacillus velezensis strain LABIM41 (CMRP6330). Its genome, composed of 3,970,959 bp, possesses a rich metabolic machinery and a wide range of molecules with different biological activities and roles in its symbiotic relationship with its plant hosts.},
}

@article {pmid39502209,
year = {2024},
author = {Kipkoech, R and Takase, M and Ahogle, AMA and Ocholla, G},
title = {Analysis of properties of biodiesel and its development and promotion in Ghana.},
journal = {Heliyon},
volume = {10},
number = {20},
pages = {e39078},
pmid = {39502209},
issn = {2405-8440},
abstract = {The increasing global population and the challenges associated with fossil fuel has led to a surge in energy demand, necessitating research on renewable and environmentally friendly energy sources. Biodiesel, is produced from biomass materials like vegetable oil and fats, is a promising alternative. Transesterification is a principal method used in biodiesel production, as it is simple, versatile, and efficient. Biodiesel offers several advantages, including emissions, lubricity, and safety, making it a sustainable fuel option and its properties conforms to the international standards. However, it has lower energy content, cold weather performance issues, and slightly reduced engine power compared to petroleum diesel. The choice of biodiesel feedstock depends on its properties, with jatropha oil and other feedstocks being potential in Ghana. Research on biodiesel in Ghana is still in early stages and the Ghanaian government's policy aims to replace 10 % of petroleum fuel with biofuel by 2020 and 20 % by 2030, but these goals have not been achieved due to barriers. Despite these challenges, the government and stakeholders in the biofuel industry are working to optimize the biodiesel sector for sustainability, efficiency, and scalability. Innovative cultivation techniques and low-cost oil extraction methods are required, necessitating interdisciplinary research collaborations. By capitalizing on these opportunities and implementing targeted interventions, Ghana can become a regional leader in sustainable biodiesel production.},
}

@article {pmid39501667,
year = {2024},
author = {You, Z and Zhang, X and Huang, S and Chen, D and Zhu, Y and Li, G and Chen, X},
title = {The Influence of Skin Microbial Ecology on γδ T Cell Immune Pathways in Allergic Dermatitis Models in Mice.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiae244},
pmid = {39501667},
issn = {1938-3673},
abstract = {Atopic dermatitis (AD) is a complex disease influenced by alterations in the skin microbiome and immune dysregulation. Despite the recognized role of these factors, the specific pathways by which distinct microbial populations affect skin immunity remain insufficiently understood. On a molecular level, the pathogenesis of AD involves critical cytokines such as IL-4, IL-17, interferon-γ (IFN-γ), and IL-10, which contribute to the imbalance in T helper (Th) cell responses. Importantly, gamma-delta (γδ) T cells, which produce these cytokines and infiltrate affected epithelial cells in AD, have been underexplored. This study seeks to alleviate AD symptoms in mice by adjusting both peripheral and local immune environments through the transplantation of skin microbiota. By employing 16S rRNA sequencing, we characterized the skin microbiome of the mouse model. Our results demonstrate that microbiota intervention significantly reduces skin thickening and serum IgE levels in DNFB-induced AD mice. Additionally, changes in skin microbiota modulated immune cell dynamics, restoring the Th1/Th2 balance and leading to clinical improvement. These findings highlight the critical role of skin microbiota in shaping immune responses, positioning microbiota-based therapies as a potential treatment for AD.},
}

@article {pmid39501615,
year = {2024},
author = {Prost-Boxoen, L and Bafort, Q and Van de Vloet, A and Almeida-Silva, F and Paing, YT and Casteleyn, G and D'hondt, S and De Clerck, O and Van de Peer, Y},
title = {Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
pmid = {39501615},
issn = {1469-8137},
support = {833522//H2020 European Research Council/ ; 833522/ERC_/European Research Council/International ; I001621N//European Marine Biological Resource Centre Belgium/ ; 11H0426N//Fonds Wetenschappelijk Onderzoek/ ; G0C0116N//Fonds Wetenschappelijk Onderzoek/ ; BOF.MET.2021.0005.01//Bijzonder Onderzoeksfonds UGent/ ; 1168420N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of 'functional dominance' from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.},
}

@article {pmid39500284,
year = {2024},
author = {Arrigan, D and Kothe, CI and Oliverio, A and Evans, JD and Wolfe, BE},
title = {Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes.},
journal = {Current biology : CB},
volume = {34},
number = {21},
pages = {R1094-R1108},
doi = {10.1016/j.cub.2024.09.047},
pmid = {39500284},
issn = {1879-0445},
mesh = {*Fermented Foods/microbiology ; *Fermentation ; *Microbiota ; *Food Microbiology/methods ; Humans ; },
abstract = {Fermented foods and beverages have been produced around the world for millennia, providing humans with a range of gastronomic, cultural, health, and scientific benefits. Building on these traditional forms, a convergence of factors, including culinary innovation, globalization, shifts in consumer preferences, and advances in microbiome sciences, has led to the emergence of so-called 'novel fermentations'. In this review, we define novel fermentation as the confluence of traditional food practices and rational microbiome design. Using principles of microbial ecology and evolution, we develop a microbiological framework that outlines several strategies for producing and characterizing novel fermentations, including switching substrates, engrafting target species, assembling whole-community chimeras, and generating novel phenotypes. A subsequent analysis of existing traditional ferments points to gaps in 'fermentation space' where novel ferments could potentially be produced using new combinations of microbes and food substrates. We highlight some important safety and sociocultural issues presented by the repurposing and modification of microbes from traditional ferments that fermented-food producers and microbiologists need to address.},
}

*Fermented Foods/microbiology
*Fermentation
*Microbiota
*Food Microbiology/methods
Humans

@article {pmid39499580,
year = {2024},
author = {Zhang, X and Zhang, XX and Ma, L},
title = {New Horizons in Micro/Nanoplastic-Induced Oxidative Stress: Overlooked Free Radical Contributions and Microbial Metabolic Dysregulations in Anaerobic Digestion.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c08865},
pmid = {39499580},
issn = {1520-5851},
abstract = {Excessive production of reactive oxygen species (ROS) induced by micro/nanoplastics (MPs/NPs) is highly toxic to microbes. However, the mechanisms underlying ROS generation and metabolic regulation within anaerobic guilds remain poorly understood. In this study, we investigated the effects of environmentally relevant levels of polypropylene (PP)-MPs/NPs on oxidative stress and microbial ecology during anaerobic digestion (AD). Electron paramagnetic resonance spectroscopy revealed that PP-MPs/NPs elevated the concentrations of environmentally persistent free radicals (EPFRs) and derived hydroxyl radicals ([•]OH). EPFRs were identified as the primary contributors to [•]OH generation, as evidenced by a high Spearman correlation coefficient (r = 0.884, p < 0.001) and free radical-quenching studies. The formation of [•]OH enhanced ROS production by 86.2-100.9%, resulting in decreased cellular viability and methane production (by 37.5-50.5%) at 100 mg/g TS PP-MPs/NPs. Genome-centric metagenomic and metatranscriptomic analyses suggested that PP-MPs/NPs induced the reassembly of community structures, re-evolution of functional traits, and remodeling of interspecies interactions. Specifically, PP-MPs/NPs induced a shift in methanogen consortia from hydrogenotrophic Methanofollis sp. to acetoclastic and hydrogenotrophic Methanothrix soehngenii, primarily because of the latter's diverse ingestion patterns, electron bifurcation complexes, and ROS-scavenging abilities. Downregulation of genes associated with antioxidative defense systems (i.e., sodN, katA, and osmC) and ROS-driven redox signal transduction pathways (c-di-AMP and phosphorylation signaling pathways) provided insights into the mechanisms underlying ROS-induced microbial metabolic dysregulation. Our findings enhance the understanding of microbial ecological and metabolic traits under MPs/NPs stressors, facilitating the control of MPs/NPs toxicity and the stabilization of AD processes.},
}

@article {pmid39498487,
year = {2024},
author = {Dooley, KD and Henry, LP and Bergelson, J},
title = {Impact of timing on the invasion of synthetic bacterial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae220},
pmid = {39498487},
issn = {1751-7370},
abstract = {Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process. Fifteen distinct communities were subjected to each of three bacterial invaders at the initial assembly of the community ("initial invasion"), 24 hours into community assembly ("early invasion"), when the community was still undergoing transient dynamics, and 7 days into community assembly ("late invasion"), once the community had settled into its final composition. Communities were passaged daily and characterized through sequencing after reaching a stable composition. Invasions often failed to persist over time, particularly in higher richness communities. However, invasions had their largest effect on composition when they occurred before a community had settled into a stable composition. We found instances where an invader was ultimately excluded yet had profound and long-lasting effects on invaded communities. Invasion outcome was positively associated with lower community richness and resource use efficiency by the community, which varied throughout assembly. Our results demonstrate that microbial communities experiencing transient community dynamics are more affected by, and in some instances prone to, invasion, a finding relevant to efforts to modify the composition of microbial communities.},
}

@article {pmid39498135,
year = {2024},
author = {Gu, Y and Meng, D and Liu, Z and Zhang, M and Yang, Z and Yin, H and Liang, Y and Xiao, N},
title = {Biotic and abiotic properties mediating sediment microbial diversity and function in a river-lake continuum.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479670},
pmid = {39498135},
issn = {1664-302X},
abstract = {A river-lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river-lake ecosystem.},
}

@article {pmid39497067,
year = {2024},
author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD},
title = {Removal of sequencing adapter contamination improves microbial genome databases.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1033},
pmid = {39497067},
issn = {1471-2164},
mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; },
abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.},
}

Animals
*Databases, Genetic
DNA Contamination
Genome, Microbial
Humans
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Cattle
Mice
Swine

@article {pmid39496952,
year = {2024},
author = {Djotan, AKG and Matsushita, N and Fukuda, K},
title = {Within-Site Variations in Soil Physicochemical Properties Explained the Spatiality and Cohabitation of Arbuscular Mycorrhizal Fungi in the Roots of Cryptomeria Japonica.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {136},
pmid = {39496952},
issn = {1432-184X},
support = {JP22H02382//Japan Society for the Promotion of Science/ ; },
mesh = {*Mycorrhizae/classification ; *Soil/chemistry ; *Soil Microbiology ; *Cryptomeria/microbiology ; *Plant Roots/microbiology ; Japan ; Phosphorus/analysis ; Forests ; Hydrogen-Ion Concentration ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) live in a community in the roots of host plants. Still, the patterns and factors that drive their spatiality and cohabitation remain uncovered, particularly that of trees in planted forests, which we aimed to clarify in Cryptomeria japonica, a major plantation tree in Japan. We analyzed 65 paired root and soil samples of Cryptomeria japonica trees collected from 11 microsite (MS) plots at two environmentally different forest sites in central Japan and measured soil pH, total phosphorus (TP), C, N, and the carbon-to-nitrogen ratio. Root AMF communities were recovered using Illumina's next-generation amplicon sequencing targeting the small subunit of ribosomal DNA. We detected more than 500 AMF OTUs at each site but only three belonging to Dominikia, Rhizophagus, and Sclerocystis were dominant in the roots of C. japonica, detected each at an average relative abundance higher than 20%. Two showed negatively correlated spatial distributions and different associations with soil pH. Similarly, the physicochemical properties at MSs significantly determined the AMF assemblages in the roots of C. japonica. Dominikia, Rhizophagus, and Sclerocystis coexist in the roots of C. japonica where soil physicochemical properties, particularly pH, determine their spatial dynamic, turnovers, and cohabitation patterns. These findings highlight the importance of simultaneous colonization of plants by multiple AMF.},
}

*Mycorrhizae/classification
*Soil/chemistry
*Soil Microbiology
*Cryptomeria/microbiology
*Plant Roots/microbiology
Japan
Phosphorus/analysis
Forests
Hydrogen-Ion Concentration
Nitrogen/analysis/metabolism
Carbon/analysis/metabolism

@article {pmid39496518,
year = {2024},
author = {Khaleque, HN and Fathollahzadeh, H and Kaksonen, AH and Valdés, J and Vergara, E and Holmes, DS and Watkin, ELJ},
title = {Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {12},
pages = {},
pmid = {39496518},
issn = {1574-6941},
support = {//Curtin University/ ; //CSIRO/ ; },
mesh = {*Phosphates/metabolism ; *Carbon/metabolism ; *Nitrogen/metabolism ; *Genome, Bacterial ; Citric Acid Cycle/genetics ; Genomics ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; },
abstract = {In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only A. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only A. prosperus DSM 5130T and A. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while A. ferrooxydans DSM 14175T and A. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.},
}

*Phosphates/metabolism
*Carbon/metabolism
*Nitrogen/metabolism
*Genome, Bacterial
Citric Acid Cycle/genetics
Genomics
Phylogeny
Bacterial Proteins/genetics/metabolism

@article {pmid39494810,
year = {2024},
author = {Malik, M and Das, S and Paul, P and Chakraborty, P and Roy, R and Maity, A and Das, A and Dasgupta, M and Trivedi, S and Tribedi, P},
title = {Cuminaldehyde in combination with tetracycline shows promising antibiofilm activity against drug-resistant Pseudomonas aeruginosa.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/08927014.2024.2422874},
pmid = {39494810},
issn = {1029-2454},
abstract = {Pseudomonas aeruginosa, an opportunistic pathogen often causes biofilm-linked infections. A combinatorial approach involving tetracycline (antibiotic) and cuminaldehyde (phytochemical) was explored to combat this infectious pathogen. The results showed that both tetracycline and cuminaldehyde individually demonstrated antibacterial effects. However, when the compounds were applied together, there was a significant increase in their antimicrobial potential. The determined fractional inhibitory concentration index of 0.43 indicated a synergistic interaction between the two compounds. Furthermore, a series of experiments demonstrated that the combined application of cuminaldehyde and tetracycline could lead to a significant enhancement of their antibiofilm potential. This enhanced antibiofilm potential was attributed to the accumulation of reactive oxygen species and increased cell membrane permeability. Besides, this combinatorial application reduced the secretion of various virulence factors from P. aeruginosa. Therefore, this combined approach holds promise for effectively treating P. aeruginosa biofilms.},
}

@article {pmid39493671,
year = {2024},
author = {Kleikamp, HBC and van der Zwaan, R and van Valderen, R and van Ede, JM and Pronk, M and Schaasberg, P and Allaart, MT and van Loosdrecht, MCM and Pabst, M},
title = {NovoLign: metaproteomics by sequence alignment.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae121},
pmid = {39493671},
issn = {2730-6151},
abstract = {Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.},
}

@article {pmid39491387,
year = {2023},
author = {González-Alonso, V and Pradal, I and Wardhana, YR and Cnockaert, M and Wieme, AD and Vandamme, P and De Vuyst, L},
title = {Microbial ecology and metabolite dynamics of backslopped triticale sourdough productions and the impact of scale.},
journal = {International journal of food microbiology},
volume = {408},
number = {},
pages = {110445},
doi = {10.1016/j.ijfoodmicro.2023.110445},
pmid = {39491387},
issn = {1879-3460},
abstract = {Triticale (X Triticosecale Wittmack) is a hybrid of wheat (Triticum aestivum L.) and rye (Secale cereale L.), combining the positive attributes of both cereals. However, it has not been exploited for sourdough production yet. Further, the effect of scale on sourdough production has not been investigated systematically up to now. The aims of the present study were to assess the microbial ecology and metabolomic output of eleven spontaneously fermented, backslopped sourdough productions made with triticale flour on a scale of 100, 200, 500, and 1000 g. The acidification profile [pH and total titratable acidity (TTA)], microbial diversity (culture-dependent and culture-independent), metabolite dynamics, and appropriate correlations were determined. After ten fermentation steps, different species of Lactobacillaceae were prevalent in the mature sourdoughs, in particular Latilactobacillus curvatus, Limosilactobacillus fermentum, and Pediococcus pentosaceus. The microbial diversity could be traced back to the grains and was also present in the milling fractions (flour, bran, and shorts). Furthermore, thanks to the use of Illumina-based high-throughput sequencing and an amplicon sequence variant (ASV) approach, the presence of undesirable bacterial groups (bacilli, clostridia, and enterobacteria) during the initial steps of the backslopping cycle was revealed, as well as a finetuned taxonomic diversity of the LAB genera involved. Small sourdough productions (100 and 200 g) selected for a lower species diversity and reached a stable consortium faster than large ones (500 and 1000 g). Although a comparable final pH of 3.6-4.0 was obtained, the TTA of small sourdoughs was lower than that of large ones. Regarding the metabolic output, the simultaneous production of mannitol and erythritol, beyond ethanol and glycerol, could be linked to sourdoughs in which Liml. fermentum was the sole LAB species present. Further, the use of the arginine deiminase pathway by P. pentosaceus and Liml. fermentum was obvious. An appropriate extraction method followed by liquid injection gas chromatography coupled to triple quadrupole tandem mass spectrometry allowed the quantification of interesting volatile organic compounds, such as ethyl lactate. These findings support the inclusion of triticale as a viable alternative to wheat or rye for the production of sourdoughs that can be integrated into bread-making production schemes.},
}