@article {pmid37286586,
year = {2023},
author = {Leung, H and Xiong, L and Ni, Y and Busch, A and Bauer, M and Press, AT and Panagiotou, G},
title = {Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {35},
pmid = {37286586},
issn = {2055-5008},
abstract = {Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.},
}

@article {pmid37285121,
year = {2023},
author = {Tran, PQ and Bachand, SC and Hotvedt, JC and Kieft, K and McDaniel, EA and McMahon, KD and Anantharaman, K},
title = {Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0020123},
doi = {10.1128/msystems.00201-23},
pmid = {37285121},
issn = {2379-5077},
abstract = {The sulfur-containing amino acid cysteine is abundant in the environment, including in freshwater lakes. Biological cysteine degradation can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments. Here, we investigated the ecological significance of cysteine in oxic freshwater, using isolated cultures, controlled experiments, and multiomics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. We identified 29 isolates (Bacteroidota, Proteobacteria, and Actinobacteria) that produced H2S. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized three isolates using whole-genome sequencing (using a combination of short-read and long-read sequencing) and tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophilia (Gammaproteobacteria), S. bentonitica (Gammaproteobacteria), and Chryseobacterium piscium (Bacteroidota). Cysteine decreased and H2S increased, and all three genomes had genes involved in cysteine degradation. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a 5-year time series of metagenomic data from the same isolation source (Lake Mendota, Madison, WI, USA) and identified their presence throughout the time series. Overall, our study shows that diverse isolated bacterial strains can use cysteine and produce H2S under oxic conditions, and we show evidence using metagenomic data that this process may occur more broadly in natural freshwater lakes. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from the degradation of organosulfur compounds.IMPORTANCEHydrogen sulfide (H2S), a naturally occurring gas with both biological and abiotic origins, can be toxic to living organisms. In aquatic environments, H2S production typically originates from anoxic (lacking oxygen) environments, such as sediments, or the bottom layers of thermally stratified lakes. However, the degradation of sulfur-containing amino acids such as cysteine, which all cells and life forms rely on, can be a source of ammonia and H2S in the environment. Unlike other approaches for biological H2S production such as dissimilatory sulfate reduction, cysteine degradation can occur in the presence of oxygen. Yet, little is known about how cysteine degradation influences sulfur availability and cycling in freshwater lakes. In our study, we identified diverse bacteria from a freshwater lake that can produce H2S in the presence of O2. Our study highlights the ecological importance of oxic H2S production in natural ecosystems and necessitates a change in our outlook on sulfur biogeochemistry.},
}

@article {pmid37283549,
year = {2023},
author = {Oba, PM and Carroll, MQ and Sieja, KM and Yang, X and Epp, TY and Warzecha, CM and Varney, JL and Fowler, JW and Coon, CN and Swanson, KS},
title = {Effects of a Saccharomyces cerevisiae fermentation product on fecal characteristics, metabolite concentrations, and microbiota populations of dogs undergoing transport stress.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skad191},
pmid = {37283549},
issn = {1525-3163},
abstract = {Previously, a Saccharomyces cerevisiae fermentation product (SCFP) positively altered fecal microbiota, fecal metabolites, and immune cell function of adult dogs. Our objective was to determine the fecal characteristics, microbiota, and metabolites of SCFP-supplemented dogs subjected to transport stress. All procedures were approved by the Four Rivers Kennel IACUC prior to experimentation. Thirty-six adult dogs (18 male, 18 female; age: 7.1 ± 0.77 y; body weight: 28.97 ± 3.67 kg) were randomly assigned to be controls or receive SCFP supplementation (250 mg/dog/d) (n=18/group) for 11 wk. At that time, fresh fecal samples were collected before and after transport in a hunting dog trailer with individual kennels. The trailer was driven 40 miles round trip for about 45 min. Fecal microbiota data were evaluated using Quantitative Insights Into Microbial Ecology 2, while all other data were analyzed using the Mixed Models procedure of Statistical Analysis System. Effects of treatment, transport, and treatment*transport were tested, with P<0.05 being considered significant. Transport stress increased fecal indole concentrations and relative abundances of fecal Actinobacteria, Collinsella, Slackia, Ruminococcus, and Eubacterium. In contrast, relative abundances of fecal Fusobacteria, Streptococcus, and Fusobacterium were reduced by transport. Fecal characteristics, metabolites, and bacterial alpha and beta diversity measures were not affected by diet alone. Several diet*transport interactions were significant, however. Following transport, relative abundance of fecal Turicibacter increased in SCFP-supplemented dogs, but decreased in controls. Following transport, relative abundances of fecal Proteobacteria, Bacteroidetes, Prevotella, and Sutterella increased in controls, but not in SCFP-supplemented dogs. In contrast, relative abundances of fecal Firmicutes, Clostridium, Faecalibacterium, and Allobaculum increased and fecal Parabacteroides and Phascolarctobacterium decreased after transport stress in SCFP-supplemented dogs, but not in controls. Our data demonstrate that both transport stress and SCFP alter fecal microbiota in dogs, with transport being the primary cause for shifts. SCFP supplementation may provide benefits to dogs undergoing transport stress, but more research is necessary to determine proper dosages. More research is also necessary to determine if and how transport stress impacts gastrointestinal microbiota and other indicators of health.},
}

@article {pmid37280438,
year = {2023},
author = {Ndour, PMS and Bargaz, A and Rchiad, Z and Pawlett, M and Clark, IM and Mauchline, TH and Harris, J and Lyamlouli, K},
title = {Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37280438},
issn = {1432-184X},
abstract = {Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.},
}

@article {pmid37280212,
year = {2023},
author = {Weyhenmeyer, GA and Obertegger, U and Rudebeck, H and Jakobsson, E and Jansen, J and Zdorovennova, G and Bansal, S and Block, BD and Carey, CC and Doubek, JP and Dugan, H and Erina, O and Fedorova, I and Fischer, JM and Grinberga, L and Grossart, HP and Kangur, K and Knoll, LB and Laas, A and Lepori, F and Meier, J and Palshin, N and Peternell, M and Pulkkanen, M and Rusak, JA and Sharma, S and Wain, D and Zdorovennov, R},
title = {Author Correction: Towards critical white ice conditions in lakes under global warming.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3283},
doi = {10.1038/s41467-023-39005-3},
pmid = {37280212},
issn = {2041-1723},
}

@article {pmid37280177,
year = {2023},
author = {Gralka, M},
title = {Searching for principles of microbial ecology across levels of biological organization.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icad060},
pmid = {37280177},
issn = {1557-7023},
abstract = {Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems.},
}

@article {pmid37279442,
year = {2023},
author = {Suzzi, AL and Stat, M and Gaston, TF and Huggett, MJ},
title = {Spatial patterns in host-associated and free-living bacterial communities across six temperate estuaries.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad061},
pmid = {37279442},
issn = {1574-6941},
abstract = {A major goal of microbial ecology is to establish the importance of spatial and environmental factors in driving community variation. Their relative importance likely varies across spatial scales, but focus has primarily been on free-living communities within well-connected aquatic environments rather than less connected island-like habitats such as estuaries, and key host-associated communities within these systems. Here we sampled both free-living (seawater and sediment) and host-associated (estuarine fish hindgut microbiome, Pelates sexlineatus) communities across six temperate Australian estuaries spanning ∼500 km. We find that spatial and environmental factors have different influences on these communities, with seawater demonstrating strong distance-decay relationships (R = -0.69) and significant associations with a range of environmental variables. Distance-decay relationships were weak for sediment communities but became stronger over smaller spatial scales (within estuaries, R = -0.5) potentially reflecting environmental filtering across biogeochemical gradients or stochastic processes within estuary sediments. Finally, P. sexlineatus hindgut microbiome communities displayed weak distance-decay relationships (R = -0.36) and limited variation explained by environmental variables, indicating the significance of host-related factors in driving community variation. Our findings provide important ecological insights into the spatial distributions and driving forces of both free-living and host-associated bacterial patterns across temperate estuarine systems.},
}

@article {pmid37278908,
year = {2023},
author = {Gao, H and Wu, M and Liu, H and Ou, Y and Zhang, T and Duan, X},
title = {Unraveling the Positive Effect of Soil Moisture on the Bioaugmentation of Petroleum-Contaminated Soil Using Bioinformatics.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37278908},
issn = {1432-184X},
abstract = {Petroleum contamination is a severe threat to the soil environment. Previous studies have demonstrated that petroleum degradation efficiency is promoted by enhancing soil moisture content (MC). However, the effects of MC on soil microbial ecological functions during bioremediation remain unclear. Here, we investigated the impacts of 5% and 15% of moisture contents on petroleum degradation, soil microbial structures and functions, and the related genes using high-throughput sequencing and gene function prediction. Results indicated that petroleum biodegradation efficiency was increased by 8.06% in the soils with 15% MC when compared to that with 5% of MC. The complexity and stability of soil microbial community structures with 15% MC were higher than those in the soils with 5% MC when hydrocarbon-degrading bacterial flora (HDBF) were inoculated into the soils. Fifteen percent of moisture content strengthened the interaction of the bacterial community network and reduced the loss of some key bacteria species including Mycobacterium, Sphingomonas, and Gemmatimonas. Some downregulated gene pathways relating to bioaugmentation were enhanced in the soils with 15% MC. The results suggested that the dynamic balances of microbial communities and the metabolic interactions by 15% MC treatment are the driving forces for the enhancement of bioremediation in petroleum-contaminated soil.},
}

@article {pmid37278524,
year = {2023},
author = {Dedrick, S and Warrier, V and Lemon, KP and Momeni, B},
title = {When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0075722},
doi = {10.1128/msystems.00757-22},
pmid = {37278524},
issn = {2379-5077},
abstract = {To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities.IMPORTANCEAlthough mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.},
}

@article {pmid37278360,
year = {2023},
author = {Zayed, N and Ghesquière, J and Kamarudin, NHN and Bernaerts, K and Boon, N and Braem, A and Van Holm, W and Teughels, W},
title = {Oral Biofilm Cryotherapy as a Novel Ecological Modulation Approach.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345231172688},
doi = {10.1177/00220345231172688},
pmid = {37278360},
issn = {1544-0591},
abstract = {Oral cryotherapy is used in dentistry as a safe, simple, and low-cost treatment for a variety of oral lesions. It is well known for its ability to aid in the healing process. However, its effect on oral biofilms is unknown. As a result, the purpose of this study was to assess the effects of cryotherapy on in vitro oral biofilms. In vitro multispecies oral biofilms were grown on the surface of hydroxyapatite discs in symbiotic or dysbiotic states. CryoPen X+ was used to treat the biofilms, whereas untreated biofilms served as control. One set of biofilms was collected for study immediately after cryotherapy, whereas another group was reincubated for 24 h to permit biofilm recovery. Changes in biofilm structure were analyzed with a confocal laser scanning microscope (CLSM) and a scanning electron microscope (SEM), while biofilm ecology and community compositional changes were analyzed with viability DNA extraction and quantitative polymerase chain reaction (v-qPCR) analysis. One cryo-cycle immediately reduced biofilm load by 0.2 to 0.4 log10 Geq/mL, which increased with additional treatment cycles. Although the bacterial load of the treated biofilms recovered to the same level as the control biofilms within 24 h, the CLSM detected structural alterations. Compositional alterations were also detected by SEM, corroborating the v-qPCR findings that showed ≈≤10% incidence of pathogenic species compared to nontreated biofilms that encompassed ≈45% and 13% pathogenic species in dysbiotic and symbiotic biofilms, respectively. Spray cryotherapy showed promising results in a novel conceptual approach to the control of oral biofilms. Acting selectively by targeting oral pathobionts and retaining commensals, spray cryotherapy could modify the ecology of in vitro oral biofilms to become more symbiotic and prevent the evolution of dysbiosis without the use of antiseptics/antimicrobials.},
}

@article {pmid37275175,
year = {2023},
author = {Timmusk, S and Pall, T and Raz, S and Fetsiukh, A and Nevo, E},
title = {The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1141862},
doi = {10.3389/fmicb.2023.1141862},
pmid = {37275175},
issn = {1664-302X},
abstract = {Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.},
}

@article {pmid37272971,
year = {2023},
author = {Zhang, Y and Wang, M and Cheng, W and Huang, C and Ren, J and Zhai, H and Niu, L},
title = {Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37272971},
issn = {1432-184X},
abstract = {Urban landscape lakes are closely related to human activity, but there are limited studies on their bacterial community characteristics and risks to human health. In this study, four different types of urban landscape lakes in Xi'an were selected, and the bacterial community structures in different seasons were analyzed by Illumina Nova high-throughput sequencing technology. Seasonal variations in bacterial communities were analyzed by linear discriminant analysis, STAMP difference analysis, and nonmetric multidimensional scaling. Redundancy analysis was used to investigate the influencing factors. Furthermore, the metabolic functions of bacterial communities were predicted by Tax4Fun. There were clear seasonal differences in the α-diversity of bacteria, with bacterial diversity being higher in winter than in summer in the four urban landscape lakes, and the diversity of different water sources was different; the distributions of Proteobacteria, Actinobacteria, Chloroflexi, and Verrucomicrobia had significant seasonal differences; and the dominant bacteria at the genus level had obvious temporal and spatial differences. Furthermore, a variety of environmental factors had an impact on bacterial communities, and temperature, DO, and nitrogen were the primary factors affecting the seasonal variation in bacteria. There are also significant seasonal differences in the metabolic functions of bacterial communities. These results are helpful for understanding the current status of bacteria in the aquatic environments of such urban landscape lakes.},
}

@article {pmid37272815,
year = {2023},
author = {Tang, K and Tao, L and Wang, Y and Wang, Q and Fu, C and Chen, B and Zhang, Z and Fu, Y},
title = {Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0074723},
doi = {10.1128/aem.00747-23},
pmid = {37272815},
issn = {1098-5336},
abstract = {Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.},
}

@article {pmid37272792,
year = {2023},
author = {Wu, X and Gushgari-Doyle, S and Lui, LM and Hendrickson, AJ and Liu, Y and Jagadamma, S and Nielsen, TN and Justice, NB and Simmons, T and Hess, NJ and Joyner, DC and Hazen, TC and Arkin, AP and Chakraborty, R},
title = {Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0050023},
doi = {10.1128/aem.00500-23},
pmid = {37272792},
issn = {1098-5336},
abstract = {Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.},
}

@article {pmid37272710,
year = {2023},
author = {Miller, SE and Colman, AS and Waldbauer, JR},
title = {Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0123822},
doi = {10.1128/msystems.01238-22},
pmid = {37272710},
issn = {2379-5077},
abstract = {Microbial activity in Arctic soils controls the cycling of significant stores of organic carbon and nutrients. We studied in situ processes in Alaskan soils using original metaproteomic methods in order to relate important heterotrophic functions to microbial taxa and to understand the microbial response to Arctic greening. Major bacterial groups show strong metabolic specialization in organic topsoils. α-/β-/γ-Proteobacteria specialized in the acquisition of small, soluble compounds, whereas Acidobacteria, Actinobacteria, and other detritosphere groups specialized in the degradation of plant-derived polymers. α-/β-/γ-Proteobacteria dominated the expression of transporters for common root exudates and limiting nitrogenous compounds, supporting an ecological model of dependence upon plants for carbon and competition with plants for nitrogen. Detritosphere groups specialized in distinct substrates, with Acidobacteria producing the most enzymes for hemicellulose depolymerization. Acidobacteria was the most active group across the three plant ecotypes sampled-the largely nonvascular, lower biomass intertussock and the largely vascular, higher biomass tussock and shrub. Functional partitioning among bacterial groups was stable between plant ecotypes, but certain functions associated with α-/β-/γ-Proteobacteria were more strongly expressed in higher biomass ecotypes. We show that refined metaproteomic approaches can elucidate soil microbial ecology as well as biogeochemical trajectories of major carbon stocks.IMPORTANCEThe Arctic is warming twice as fast as the rest of the planet, and Arctic soils currently store twice as much carbon as the entire atmosphere-two facts that make understanding how Arctic soil microbial communities are responding to climate change particularly urgent. Greening of vegetation cover across the Arctic landscape is one of the most prominent climate-driven shifts in Arctic terrestrial ecology, with potentially profound effects on biogeochemical cycling by the soil microbiome. Here we use metaproteomics to document microbial metabolic functions that drive soil carbon and nutrient cycling processes in an Arctic tundra landscape. We identify functional roles among bacterial taxonomic groups that are largely stable across vegetation types, with certain functions strongly expressed by rhizosphere groups reflecting a community metabolic response to greening.},
}

@article {pmid37270320,
year = {2023},
author = {M Venturini, A and B Gontijo, J and A Mandro, J and Berenguer, E and Peay, KG and M Tsai, S and Bohannan, BJM},
title = {Soil microbes under threat in the Amazon Rainforest.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2023.04.014},
pmid = {37270320},
issn = {1872-8383},
abstract = {Soil microorganisms are sensitive indicators of land-use and climate change in the Amazon, revealing shifts in important processes such as greenhouse gas (GHG) production, but they have been overlooked in conservation and management initiatives. Integrating soil biodiversity with other disciplines while expanding sampling efforts and targeted microbial groups is crucially needed.},
}

@article {pmid37268771,
year = {2023},
author = {Listmann, L and Peters, C and Rahlff, J and Esser, SP and Schaum, CE},
title = {Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37268771},
issn = {1432-184X},
abstract = {Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.},
}

@article {pmid37268258,
year = {2023},
author = {Yu, Y and Fu, D and Zhou, H and Su, J and Chen, S and Lv, G},
title = {Potential application of Atractylodes macrocephala Koidz. as a natural drug for bone mass regulation: A review.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {116718},
doi = {10.1016/j.jep.2023.116718},
pmid = {37268258},
issn = {1872-7573},
abstract = {The root of Atractylodes macrocephala Koidz. (AM) has been used for thousands of years in China, and it's extracts contain various constituents, such as volatile oils, polysaccharides, and lactones, with a myriad of pharmacological effects, including improves the healthy state of the gastrointestinal system and regulating immunity, hormone secretion, anti-inflammatory, antibacterial, antioxidation, anti-aging, and antitumor properties. Recently, researchers have focused on the effect of AM in regulating bone mass; therefore, its potential mechanism of action in regulating bone mass needs to be elucidated.

AIM OF REVIEW: This study reviewed the known and possible mechanisms of bone mass regulation by AM.

MATERIALS AND METHODS: Cochrane, Medline via PubMed, Embase, CENTRAL, CINAHL, Web of Science, Chinese biomedical literature database, Chinese Science and Technology Periodical Database, and Wanfang Database were used to search AM root extracts-related studies. The retrieval date was from the establishment of the database to January 1, 2023.

RESULTS: By summarizing 119 natural active substances that have been isolated from AM root to date, we explored its possible targets and pathways (such as Hedgehog, Wnt/β-catenin, and BMP/Smads pathways etc.) for bone growth and presented our position on possible future research/perspectives in the regulation of bone mass using this plant.

CONCLUSIONS: AM root extracts (incuding aqueous, ethanol etc.) promotes osteogenesis and inhibits osteoclastogenesis. These functions promote the absorption of nutrients, regulate gastrointestinal motility and intestinal microbial ecology, regulate endocrine function, strengthen bone immunity, and exert anti-inflammatory and antioxidant effects.},
}

@article {pmid37266990,
year = {2023},
author = {Nikolaidis, M and Hesketh, A and Frangou, N and Mossialos, D and Van de Peer, Y and Oliver, SG and Amoutzias, GD},
title = {A panoramic view of the genomic landscape of the genus Streptomyces.},
journal = {Microbial genomics},
volume = {9},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001028},
pmid = {37266990},
issn = {2057-5858},
abstract = {We delineate the evolutionary plasticity of the ecologically and biotechnologically important genus Streptomyces, by analysing the genomes of 213 species. Streptomycetes genomes demonstrate high levels of internal homology, whereas the genome of their last common ancestor was already complex. Importantly, we identify the species-specific fingerprint proteins that characterize each species. Even among closely related species, we observed high interspecies variability of chromosomal protein-coding genes, species-level core genes, accessory genes and fingerprints. Notably, secondary metabolite biosynthetic gene clusters (smBGCs), carbohydrate-active enzymes (CAZymes) and protein-coding genes bearing the rare TTA codon demonstrate high intraspecies and interspecies variability, which emphasizes the need for strain-specific genomic mining. Highly conserved genes, such as those specifying genus-level core proteins, tend to occur in the central region of the chromosome, whereas those encoding proteins with evolutionarily volatile species-level fingerprints, smBGCs, CAZymes and TTA-codon-bearing genes are often found towards the ends of the linear chromosome. Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at the species and strain level. Finally, we observed a moderate, but statistically significant, correlation between the total number of CAZymes and three categories of smBGCs (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria.},
}

@article {pmid37264467,
year = {2023},
author = {Wainwright, BJ and Millar, T and Bowen, L and Semon, L and Hickman, KJE and Lee, JN and Yeo, ZY and Zahn, G},
title = {The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {47},
pmid = {37264467},
issn = {2524-6372},
abstract = {BACKGROUND: Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival.

CONCLUSION: The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.},
}

@article {pmid37264141,
year = {2023},
author = {Zehnle, H and Laso-Pérez, R and Lipp, J and Riedel, D and Benito Merino, D and Teske, A and Wegener, G},
title = {Candidatus Alkanophaga archaea from Guaymas Basin hydrothermal vent sediment oxidize petroleum alkanes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {37264141},
issn = {2058-5276},
abstract = {Methanogenic and methanotrophic archaea produce and consume the greenhouse gas methane, respectively, using the reversible enzyme methyl-coenzyme M reductase (Mcr). Recently, Mcr variants that can activate multicarbon alkanes have been recovered from archaeal enrichment cultures. These enzymes, called alkyl-coenzyme M reductase (Acrs), are widespread in the environment but remain poorly understood. Here we produced anoxic cultures degrading mid-chain petroleum n-alkanes between pentane (C5) and tetradecane (C14) at 70 °C using oil-rich Guaymas Basin sediments. In these cultures, archaea of the genus Candidatus Alkanophaga activate the alkanes with Acrs and completely oxidize the alkyl groups to CO2. Ca. Alkanophaga form a deep-branching sister clade to the methanotrophs ANME-1 and are closely related to the short-chain alkane oxidizers Ca. Syntrophoarchaeum. Incapable of sulfate reduction, Ca. Alkanophaga shuttle electrons released from alkane oxidation to the sulfate-reducing Ca. Thermodesulfobacterium syntrophicum. These syntrophic consortia are potential key players in petroleum degradation in heated oil reservoirs.},
}

@article {pmid37263428,
year = {2023},
author = {Van Peteghem, L and Matassa, S and Rabaey, K and Sakarika, M},
title = {Microbial protein from recovered nitrogen: Nutritional quality, safety, and feasibility assessment.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {164525},
doi = {10.1016/j.scitotenv.2023.164525},
pmid = {37263428},
issn = {1879-1026},
abstract = {In contrast to traditional agriculture, microbial protein (MP) production is highly efficient in nitrogen (N) usage and can be employed to valorize a variety of recovered resources, thereby increasing the overall sustainability of food production. The present study aimed to establish the potential of seven recovered N sources originating from different waste streams for MP production using ethanol and acetate as growth substrates. The evaluation was based on specific growth rate, biomass yield, nutritional quality (i.e. macromolecular composition, amino acid (AA) and lipid profile) and food safety (i.e. concentration of heavy metals, polyaromatic hydrocarbons (PAH), pesticides and antibiotics) of the MP. The majority of the recovered N sources did not affect the kinetics and had a minor impact on the biomass yield, compared to their commercial equivalents. The nutritional content of the biomass was similar to soy flour and did not show major variations in AA and lipid profile for the different recovered N sources. Considering the heavy metal content, an average-weighing adult should not consume >53-213 g of the microbial biomass produced on recovered N per day due to its high copper content. A substantial amount of PAH were also found in the biomass. A daily consumption of 20 g/person/day would impose 2.0-2.8 times higher dietary exposure than the mean PAH exposure through nutrition in the EU, indicating a potential concern for human health. On the other hand, the biomass was free of antibiotics, and the traces of pesticides found did not raise any major concern for food applications. Based on the results of this work, no evidence was found to restrict the application of microbial biomass produced on recovered nitrogen as food.},
}

@article {pmid37260833,
year = {2023},
author = {Myers, KS and Ingle, AT and Walters, KA and Fortney, NW and Scarborough, MJ and Donohue, TJ and Noguera, DR},
title = {Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {11},
number = {},
pages = {1197175},
pmid = {37260833},
issn = {2296-4185},
abstract = {The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.},
}

@article {pmid37260392,
year = {2023},
author = {Putman, LI and Schaerer, LG and Wu, R and Kulas, DG and Zolghadr, A and Ong, RG and Shonnard, DR and Techtmann, SM},
title = {Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0036223},
doi = {10.1128/spectrum.00362-23},
pmid = {37260392},
issn = {2165-0497},
abstract = {Over half of the world's plastic waste is landfilled, where it is estimated to take hundreds of years to degrade. Given the continued use and disposal of plastic products, it is vital that we develop fast and effective ways to utilize plastic waste. Here, we explore the potential of tandem chemical and biological processing to process various plastics quickly and effectively. Four samples of compost or sediment were used to set up enrichment cultures grown on mixtures of compounds, including disodium terephthalate and terephthalic acid (monomers of polyethylene terephthalate), compounds derived from the chemical deconstruction of polycarbonate, and pyrolysis oil derived from high-density polyethylene plastics. Established enrichment communities were also grown on individual substrates to investigate the substrate preferences of different taxa. Biomass harvested from the cultures was characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. These data reveal low-diversity microbial communities structured by differences in culture inoculum, culture substrate source plastic type, and time. Microbial populations from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteriae were significantly enriched when grown on substrates derived from high-density polyethylene and polycarbonate. The metagenomic data contain abundant aromatic and aliphatic hydrocarbon degradation genes relevant to the biodegradation of deconstructed plastic substrates used here. We show that microbial populations from diverse environments are capable of growth on substrates derived from the chemical deconstruction or pyrolysis of multiple plastic types and that paired chemical and biological processing of plastics should be further developed for industrial applications to manage plastic waste. IMPORTANCE The durability and impermeable nature of plastics have made them a popular material for numerous applications, but these same qualities make plastics difficult to dispose of, resulting in massive amounts of accumulated plastic waste in landfills and the natural environment. Since plastic use and disposal are projected to increase in the future, novel methods to effectively break down and dispose of current and future plastic waste are desperately needed. We show that the products of chemical deconstruction or pyrolysis of plastic can successfully sustain the growth of low-diversity microbial communities. These communities were enriched from multiple environmental sources and are capable of degrading complex xenobiotic carbon compounds. This study demonstrates that tandem chemical and biological processing can be used to degrade multiple types of plastics over a relatively short period of time and may be a future avenue for the mitigation of rapidly accumulating plastic waste.},
}

@article {pmid37259890,
year = {2023},
author = {Geisen, S and Lara, E and Mitchell, E},
title = {Contemporary issues, current best practice and ways forward in soil protist ecology.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13819},
pmid = {37259890},
issn = {1755-0998},
abstract = {Soil protists are increasingly studied due to a release from previous methodological constraints and the acknowledgement of their immense diversity and functional importance in ecosystems. However, these studies often lack sufficient depth in knowledge, which is visible in the form of falsely used terms and false- or over-interpreted data with conclusions that cannot be drawn from the data obtained. As we welcome that also non-experts include protists in their still mostly bacterial and/or fungal-focused studies, our aim here is to help avoid some common errors. We provide suggestions for current terms to use when working on soil protists, like protist instead of protozoa, predator instead of grazer, microorganisms rather than microflora and other terms to be used to describe the prey spectrum of protists. We then highlight some dos and don'ts in soil protist ecology including challenges related to interpreting 18S rRNA gene amplicon sequencing data. We caution against the use of standard bioinformatic settings optimized for bacteria and the uncritical reliance on incomplete and partly erroneous reference databases. We also show why causal inferences cannot be drawn from sequence-based correlation analyses or any sampling/monitoring, study in the field without thorough experimental confirmation and sound understanding of the biology of taxa. Together, we envision this work to help non-experts to more easily include protists in their soil ecology analyses and obtain more reliable interpretations from their protist data and other biodiversity data that, in the end, will contribute to a better understanding of soil ecology.},
}

@article {pmid37258870,
year = {2023},
author = {Yung, PYM and Tan, SM},
title = {Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {303-315},
pmid = {37258870},
issn = {1940-6029},
abstract = {Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.},
}

@article {pmid37257612,
year = {2023},
author = {Cheng, X and Zeng, Z and Liu, X and Li, L and Wang, H and Zhao, R and Bodelier, PLE and Wang, W and Wang, Y and Tuovinen, OH},
title = {Methanotrophs dominate methanogens and act as a methane sink in a subterranean karst cave.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {164562},
doi = {10.1016/j.scitotenv.2023.164562},
pmid = {37257612},
issn = {1879-1026},
abstract = {Karst caves are potential sinks of atmospheric methane due to microbial consumption. However, knowledge gaps on methanogens (methane producing microorganisms) and their interaction with methane-oxidizing bacteria (MOB) hinder our further understanding about methane dynamics in karst caves. Here we reported methanogen community composition and their interaction with MOBs in the Heshang Cave to comprehensively understand methane cycling in subsurface biosphere. MOBs in karst cave were dominated by high-affinity MOB, upland soil cluster (USC), with USCγ pmoA gene abundance within the range of 1.34 × 10[4] to 1.8 × 10[7] copies·g[-1] DW. In contrast, methanogens were dominated by Methanoregula and cluster ZC-I. The mcrA numbers were 7.21 × 10[3] to 8.31 × 10[4] copies·g[-1] DW, 1-3 orders of magnitude lower than those of MOB. The inter-domain network analysis indicated that MOBs and methanogens cooperated more in the interior of the cave. Despite of the higher number of methanogenic nodes in the network, MOB dominated the keystone taxa, suggesting a leading functional role of MOB. MOB in caves showed a comparable with or higher potential methane oxidizing rate (PMOR, 0.63 ng CH4·g[-1] DW·h[-1] in sediment versus 11.02 ng CH4·g[-1] DW·h[-1] in weathered rock) than those in soils, whereas methane produced by methanogens was undetected. Collectively, high absolute abundances of MOB, high PMORs, the dominance of methanotrophic keystone taxa in the inter-domain network confirmed the superiority of MOB over methanogens in the oligotrophic karst cave, mounting new evidence on caves as important methane sink in terms of the interaction between methanogens and MOBs.},
}

@article {pmid37257501,
year = {2023},
author = {Osorio-Doblado, AM and Feldmann, KP and Lourenco, JM and Stewart, RL and Smith, WB and Tedeschi, LO and Fluharty, FL and Callaway, TR},
title = {Forages and Pastures Symposium: Forage biodegradation: Advances in ruminal microbial ecology.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skad178},
pmid = {37257501},
issn = {1525-3163},
abstract = {The rumen microbial ecosystem provides ruminants a selective advantage, the ability to utilize forages, allowing them to flourish worldwide in various environments. For many years, our understanding of the ruminal microbial ecosystem was limited to understanding the microbes (usually only laboratory-amenable bacteria) grown in pure culture, meaning that much of our understanding of ruminal function remained a "black box." However, the ruminal degradation of plant cell walls is performed by a consortium of bacteria, archaea, protozoa, and fungi that produces a wide variety of carbohydrate active enzymes (CAZymes) that are responsible for the catabolism of cellulose, hemicellulose, and pectin. The past 15 years have seen the development and implementation of numerous next-generation sequencing (NGS) approaches (e.g., pyrosequencing, Illumina, and shotgun sequencing), which have contributed significantly to a greater level of insight regarding the microbial ecology of ruminants fed a variety of forages. There has also been an increase in the utilization of liquid chromatography (LC) and mass spectrometry (MS) that revolutionized transcriptomic approaches, and further improvements in the measurement of fermentation intermediates and end products have advanced with metabolomics. These advanced NGS techniques along with other analytic approaches, such as metaproteomics, have been utilized to elucidate the specific role of microbial CAZymes in forage degradation. Other methods have provided new insights into dynamic changes in the ruminal microbial population fed different diets and how these changes impact the assortment of products presented to the host animal. As more omics-based data has accumulated on forage-fed ruminants, the sequence of events that occur during fiber colonization by the microbial consortium has become more apparent, with fungal populations and fibrolytic bacterial populations working in conjunction, as well as expanding understanding of the individual microbial contributions to degradation of plant cell walls and polysaccharide components. In the future, the ability to predict microbial population and enzymatic activity and end products will be able to support the development of dynamic predictive models of rumen forage degradation and fermentation. Consequently, it is imperative to understand the rumen's microbial population better to improve fiber degradation in ruminants and, thus, stimulate more sustainable production systems.},
}

@article {pmid37257378,
year = {2023},
author = {Sun, W and Jing, Z},
title = {Migration of rare and abundant species, assembly mechanisms, and ecological networks of microbiomes in drinking water treatment plants: Effects of different treatment processes.},
journal = {Journal of hazardous materials},
volume = {457},
number = {},
pages = {131726},
doi = {10.1016/j.jhazmat.2023.131726},
pmid = {37257378},
issn = {1873-3336},
abstract = {Microorganisms play an important role in the degradation of pollutants. However, they also cause problems in drinking water distribution systems, such as pipe corrosion and biofilm growth. The microbial assembly mechanisms and molecular ecological networks associated with different drinking water treatment processes have not yet been clearly analyzed. Therefore, this study investigated the microbiomes of three processes (coal filtration-activated carbon, ozone-activated carbon and UV, and ozone-activated carbon) during different seasons. The results showed that the microbial composition and diversity among the different processes and during different seasons. Water treatment processes had deterministic effects on the microbial assembly process and significantly changed the composition of rare and abundant species, altering the size and modules of molecular ecology networks. Rare species considered as keystone species play important roles in microbial ecology and microbial community construction. Ozone-activated carbon and UV/chlorination decreased the bacterial concentration, increased the deterministic process of microbial assembly, and significantly reduced the size of the network, which is of great significance to microbial control in drinking water. This research broadens our perspectives on the microbial assembly associated with drinking water treatment processes and contributes to ensuring the safe supply of drinking water.},
}

@article {pmid37253619,
year = {2023},
author = {Takahashi, N and Terauchi, Y and Tanaka, T and Yoshimi, A and Yabu, H and Abe, K},
title = {Involvement of ionic interactions in self-assembly and resultant rodlet formation of class I hydrophobin RolA from Aspergillus oryzae.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbad066},
pmid = {37253619},
issn = {1347-6947},
abstract = {Hydrophobins are small amphiphilic proteins that are conserved in filamentous fungi. They localized on the conidial surface to make it hydrophobic, which contributes to conidial dispersal in air, and help fungi to infect plants and mammals and to degrade polymers. Hydrophobins self-assemble and undergo structural transition from the amorphous state to the rodlet (rod-like multimeric structure) state. However, it remains unclear whether the amorphous or rodlet state is biologically functional and what external factors regulate state transition. In this study, we analyzed the self-assembly of hydrophobin RolA of Aspergillus oryzae in detail and identified factors regulating this process. Using atomic force microscopy, we observed RolA rodlet formation over time, and determined "rodlet elongation rate" and "rodlet formation frequency." Changes in these kinetic parameters in response to pH and salt concentration suggest that RolA rodlet formation is regulated by the strength of ionic interactions between RolA molecules.},
}

@article {pmid37249591,
year = {2023},
author = {Wu-Chuang, A and Hartmann, D and Maitre, A and Mateos-Hernández, L and Frantová, H and Urbanová, V and Obregon, D and Cabezas-Cruz, A and Perner, J},
title = {Variation of bacterial community assembly over developmental stages and midgut of Dermanyssus gallinae.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37249591},
issn = {1432-184X},
abstract = {Bacterial microbiota play an important role in the fitness of arthropods, but the bacterial microflora in the parasitic mite Dermanyssus gallinae is only partially explored; there are gaps in our understanding of the microbiota localization and in our knowledge of microbial community assembly. In this work, we have visualized, quantified the abundance, and determined the diversity of bacterial occupancy, not only across developmental stages of D. gallinae, but also in the midgut of micro-dissected female D. gallinae mites. We explored community assembly and the presence of keystone taxa, as well as predicted metabolic functions in the microbiome of the mite. The diversity of the microbiota and the complexity of co-occurrence networks decreased with the progression of the life cycle. However, several bacterial taxa were present in all samples examined, indicating a core symbiotic consortium of bacteria. The relatively higher bacterial abundance in adult females, specifically in their midguts, implicates a function linked to the biology of D. gallinae mites. If such an association proves to be important, the bacterial microflora qualifies itself as an acaricidal or vaccine target against this troublesome pest.},
}

@article {pmid37247701,
year = {2023},
author = {Garrido-Benavent, I and de Los Ríos, A and Núñez-Zapata, J and Ortiz-Álvarez, R and Schultz, M and Pérez-Ortega, S},
title = {Ocean crossers: a tale of disjunctions and speciation in the dwarf-fruticose Lichina (lichenized Ascomycota).},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {107829},
doi = {10.1016/j.ympev.2023.107829},
pmid = {37247701},
issn = {1095-9513},
abstract = {Lichens thrive in rocky coastal areas in temperate and cold regions of both hemispheres. Species of the genus Lichina, which form characteristic black fruiting thalli associated with cyanobacteria, often create distinguishable bands in the intertidal and supralittoral zones. The present study uses a comprehensive specimen dataset and four gene loci to (1) delineate and discuss species boundaries in this genus, (2) assess evolutionary relationships among species, and (3) infer the most likely causes of their current geographic distribution in the Northern and Southern hemispheres. A dated phylogeny describes the time frame in which extant disjunctions of species and populations were established. The results showed that the genus is integrated by four species, with Lichina pygmaea, L. confinis and the newly described L. canariensis from rocky seashores in the Canary Islands, occurring in the Northern Hemisphere, whereas L. intermedia is restricted to the Southern Hemisphere. Lichina intermedia hosted a much higher intraspecific genetic diversity than the other species, with subclades interpreted as species-level lineages by the different species delimitation approaches. However, a conservative taxonomic approach was adopted. This species showed a striking disjunct distribution between Australasia and southern South America. The timing for the observed interspecific and intraspecific divergences and population disjunctions postdated continental plate movements, suggesting that long-distance dispersal across body waters in the two hemispheres played a major role in shaping the current species distributions. Such ocean crossings were, as in L. canariensis, followed by speciation. New substitution rates for the nrITS of the genus Lichina were inferred using a tree spanning the major Ascomycota lineages calibrated using fossils. In conclusion, this work lays the foundation for a better understanding of the evolution through time and space of maritime lichens.},
}

@article {pmid37247028,
year = {2023},
author = {Gao, K and Li, W and Gan, E and Li, J and Jiang, L and Liu, Y},
title = {Impacts of 10 Years of Elevated CO2 and Warming on Soil Fungal Diversity and Network Complexity in a Chinese Paddy Field.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37247028},
issn = {1432-184X},
abstract = {Climatic change conditions (elevated CO2 and warming) have been known to threaten agricultural sustainability and grain yield. Soil fungi play an important role in maintaining agroecosystem functions. However, little is known about the responses of fungal community in paddy field to elevated CO2 and warming. Herein, using internal transcribed spacer (ITS) gene amplicon sequencing and co-occurrence network methods, the responses of soil fungal community to factorial combinations of elevated CO2 (550 ppm), and canopy warming (+2 °C) were explored in an open-air field experiment for 10 years. Elevated CO2 significantly increased the operational taxonomic unit (OTU) richness and Shannon diversity of fungal communities in both rice rhizosphere and bulk soils, whereas the relative abundances of Ascomycota and Basidiomycota were significantly decreased and increased under elevated CO2, respectively. Co-occurrence network analysis showed that elevated CO2, warming, and their combination increased the network complexity and negative correlation of the fungal community in rhizosphere and bulk soils, suggesting that these factors enhanced the competition of microbial species. Warming resulted in a more complex network structure by altering topological roles and increasing the numbers of key fungal nodes. Principal coordinate analysis indicated that rice growth stages rather than elevated CO2 and warming altered soil fungal communities. Specifically, the changes in diversity and network complexity were greater at the heading and ripening stages than at the tillering stage. Furthermore, elevated CO2 and warming significantly increased the relative abundances of pathotrophic fungi and reduced those of symbiotrophic fungi in both rhizosphere and bulk soils. Overall, the results indicate that long-term CO2 exposure and warming enhance the complexity and stability of soil fungal community, potentially threatening crop health and soil functions through adverse effects on fungal community functions.},
}

@article {pmid37242886,
year = {2023},
author = {Mattelin, V and Verfaille, L and Kundu, K and De Wildeman, S and Boon, N},
title = {A New Colorimetric Test for Accurate Determination of Plastic Biodegradation.},
journal = {Polymers},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/polym15102311},
pmid = {37242886},
issn = {2073-4360},
abstract = {As plastic waste is accumulating in both controlled waste management settings and natural settings, much research is devoted to search for solutions, also in the field of biodegradation. However, determining the biodegradability of plastics in natural environments remains a big challenge due to the often very low biodegradation rates. Many standardised test methods for biodegradation in natural environments exist. These are often based on mineralisation rates in controlled conditions and are thus indirect measurements of biodegradation. It is of interest for both researchers and companies to have tests that are more rapid, easier, and more reliable to screen different ecosystems and/or niches for their plastic biodegradation potential. In this study, the goal is to validate a colorimetric test, based on carbon nanodots, to screen biodegradation of different types of plastics in natural environments. After introducing carbon nanodots into the matrix of the target plastic, a fluorescent signal is released upon plastic biodegradation. The in-house-made carbon nanodots were first confirmed regarding their biocompatibility and chemical and photostability. Subsequently, the effectivity of the developed method was evaluated positively by an enzymatic degradation test with polycaprolactone with Candida antarctica lipase B. Finally, validation experiments were performed with enriched microorganisms and real environmental samples (freshwater and seawater), of which the results were compared with parallel, frequently used biodegradation measures such as O2 and CO2, dissolved organic carbon, growth and pH, to assess the reliability of the test. Our results indicate that this colorimetric test is a good alternative to other methods, but a combination of different methods gives the most information. In conclusion, this colorimetric test is a good fit to screen, in high throughput, the depolymerisation of plastics in natural environments and under different conditions in the lab.},
}

@article {pmid37236880,
year = {2023},
author = {Malard, LA and Guisan, A},
title = {Into the microbial niche.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2023.04.015},
pmid = {37236880},
issn = {1872-8383},
abstract = {The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.},
}

@article {pmid37236039,
year = {2023},
author = {Anderson, AG and Bedford, MR and Parsons, CM},
title = {Effects of adaptation diet and exogenous enzymes on true metabolizable energy and cecal microbial ecology, short-chain fatty acid profile, and enzyme activity in roosters fed barley and rye diets.},
journal = {Poultry science},
volume = {102},
number = {7},
pages = {102768},
doi = {10.1016/j.psj.2023.102768},
pmid = {37236039},
issn = {1525-3171},
abstract = {Three experiments evaluated effects of adaptation diet and exogenous β-glucanase and xylanase on TMEn of barley and rye. Single Comb White Leghorn roosters were fed adaptation diets based on corn/soybean meal (SBM), barley/SBM with and without β-glucanase, or rye/corn/SBM with and without xylanase for 4 wk. In Experiments 1 and 2, after the adaptation period, TMEn was determined using a 48 h precision-fed rooster assay for 100% barley or 100% rye diets with or without β-glucanase or xylanase, respectively. Experiment 3 consisted only of feeding adaptation diets for 4 wk. Cecal samples were collected at the end of experiments for microbial ecology, short-chain fatty acid (SCFA) profiles, and enzyme activity analyses. In Experiments 1 and 2, β-glucanase increased (P < 0.05) TMEn of barley, and there was no significant effect of adaptation diet on TMEn values. Total cecal Eubacteria and Ruminococcaceae were decreased (P < 0.05) and Escherichia coli were increased (P < 0.05) at the end of the TMEn assay compared with the end of the adaptation period (with no TMEn assay). There was a large decrease (P < 0.05) for most cecal SCFA at the end of the TMEn assay compared with the end of the adaptation period. Both cecal β-glucanase and xylanase activity were increased for birds fed adaptation diets containing the respective enzyme. In Experiment 3, there were no consistent effects of adaptation diet on cecal microbial profiles or SCFA but cecal β-glucanase activity was increased (P < 0.05) by exogenous β-glucanase for barley and cecal xylanase activity was increased (P < 0.05) by exogenous xylanase for rye. Overall, the results indicated that TMEn of barley was increased by exogenous β-glucanase, adaptation diet did not significantly influence the TMEn response to the dietary enzymes, and cecal fermentation (based on cecal SCFA) was greatly reduced by the TMEn assay. Cecal β-glucanase and xylanase activity, however, were often increased by feeding high barley and high rye diets containing exogenous enzymes.},
}

@article {pmid37235689,
year = {2023},
author = {Esteves, SM and Jadoul, A and Iacono, F and Schloesser, M and Bosman, B and Carnol, M and Druet, T and Cardol, P and Hanikenne, M},
title = {Natural variation of nutrient homeostasis among laboratory and field strains in Chlamydomonas reinhardtii.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erad194},
pmid = {37235689},
issn = {1460-2431},
abstract = {Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macro-nutrients have a wide range of functions in photosynthetic organisms and mineral nutrition plays thus a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, twenty-four Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared to autotrophy and 9 deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, -S) and micronutrients (-Cu, -Fe, -Mn, -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.},
}

@article {pmid37235378,
year = {2023},
author = {Gomes, TC and Conrado, R and Oliveira, RC and Selari, PJRG and Melo, IS and Araújo, WL and Maria, DA and De Souza, AO},
title = {Effect of Monocerin, a Fungal Secondary Metabolite, on Endothelial Cells.},
journal = {Toxins},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/toxins15050344},
pmid = {37235378},
issn = {2072-6651},
abstract = {This study reports the isolation and identification of the endophytic fungus Exserohilum rostratum through molecular and morphological analysis using optical and transmission electron microscopy (TEM), as well as the procurement of its secondary metabolite monocerin, an isocoumarin derivative. Considering the previously observed biological activities of monocerin, this study was performed on human umbilical vein endothelial cells (HUVECs) that are widely used as an in vitro model for several different purposes. Important parameters, such as cell viability, senescence-associated β-galactosidase, cellular proliferation by using 5(6)-carboxyfluorescein diacetate N-succinimidyl ester (CFSE), apoptosis analysis with annexin, cellular morphology through scanning electron microscopy (SEM), and laser confocal analysis were evaluated after exposing the cells to monocerin. After 24 h of exposure to monocerin at 1.25 mM, there was more than 80% of cell viability and a low percentage of cells in the early and late apoptosis and necrosis. Monocerin increased cell proliferation and did not induce cell senescence. Morphological analysis showed cellular integrity. The study demonstrates aspects of the mechanism of action of monocerin on endothelial cell proliferation, suggesting the possibility of its pharmaceutical application, such as in regenerative medicine.},
}

@article {pmid37234538,
year = {2023},
author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB},
title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1203870},
doi = {10.3389/fmicb.2023.1203870},
pmid = {37234538},
issn = {1664-302X},
}

@article {pmid37233803,
year = {2023},
author = {Leonhardt, F and Keller, A and Arranz Aveces, C and Ernst, R},
title = {From Alien Species to Alien Communities: Host- and Habitat-Associated Microbiomes in an Alien Amphibian.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37233803},
issn = {1432-184X},
abstract = {Alien species can host diverse microbial communities. These associated microbiomes may be important in the invasion process and their analysis requires a holistic community-based approach. We analysed the skin and gut microbiome of Eleutherodactylus johnstonei from native range populations in St Lucia and exotic range populations in Guadeloupe, Colombia, and European greenhouses along with their respective environmental microbial reservoir through a 16S metabarcoding approach. We show that amphibian-associated and environmental microbial communities can be considered as meta-communities that interact in the assembly process. High proportions of bacteria can disperse between frogs and environment, while respective abundances are rather determined by niche effects driven by the microbial community source and spatial environmental properties. Environmental transmissions appeared to have higher relevance for skin than for gut microbiome composition and variation. We encourage further experimental studies to assess the implications of turnover in amphibian-associated microbial communities and potentially invasive microbiota in the context of invasion success and impacts. Within this novel framework of "nested invasions," (meta-)community ecology thinking can complement and widen the traditional perspective on biological invasions.},
}

@article {pmid37230675,
year = {2022},
author = {Haskell-Ramsay, CF and Dodd, FL and Smith, D and Cuthbertson, L and Nelson, A and Lodge, JK and Jackson, PA},
title = {Mixed Tree Nuts, Cognition, and Gut Microbiota: A 4-Week, Placebo-Controlled, Randomized Crossover Trial in Healthy Nonelderly Adults.},
journal = {The Journal of nutrition},
volume = {152},
number = {12},
pages = {2778-2788},
doi = {10.1093/jn/nxac228},
pmid = {37230675},
issn = {1541-6100},
abstract = {BACKGROUND: Beneficial effects of nut supplementation on cognitive function have previously been demonstrated in young and older adults. Alterations to gut microbiota have also been shown following tree nut consumption. However, no data exists on the effects of nuts on cognition and intestinal microbial communities assessed within the same study.

OBJECTIVES: The study aimed to examine the effects of daily consumption of tree nuts for 4 wk on cognitive function (primary outcome), mood, metabolomics, and gut microbial species (secondary outcomes) in healthy, nonelderly adults.

METHODS: This randomized, placebo-controlled, double-blind, counterbalanced crossover study assessed the effects of 4 wk of supplementation with 30 g/d mixed tree nuts versus placebo on cognition and mood in 79 healthy adults aged 18-49 y. Metabolic responses, gut bacterial community structure, and the potential for these to impact cognition were explored using a multi-omic approach. Bacterial community analysis was conducted in Quantitative Insights Into Microbial Ecology 2 (QIIME2).

RESULTS: Mixed model analysis indicated that nut consumption led to significant improvements to accuracy (placebo M = 92.2% compared with NUTS M = 94.5%; P = 0.019) and speed of response (placebo M = 788 ms compared with NUTS M = 757 ms; P = 0.004) on a picture recognition task. No significant changes to bacterial community α or β diversity were observed when comparing nut consumption to the placebo arm. However, an unclassified Lachnospiraceae amplicon sequence variant (ASV) was significantly enriched in participants when supplemented with nuts (P = 0.015). No correlations were observed between the changes to picture recognition and the changes to the unclassified Lachnospiraceae ASV. There were no significant changes to the urinary metabolome.

CONCLUSIONS: These findings indicate a positive effect of nut on cognition following only 4 wk of consumption in a healthy nonelderly sample, as well as upregulation of a microbial taxa associated with gut health. The effects appear to be independent of one another, but further exploration is required in those experiencing cognitive decline and/or gut dysbiosis.},
}

@article {pmid37230351,
year = {2023},
author = {Bossolani, JW and Leite, MFA and Momesso, L and Ten Berge, H and Bloem, J and Kuramae, EE},
title = {Nitrogen input on organic amendments alters the pattern of soil-microbe-plant co-dependence.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {164347},
doi = {10.1016/j.scitotenv.2023.164347},
pmid = {37230351},
issn = {1879-1026},
abstract = {The challenges of nitrogen (N) management in agricultural fields include minimizing N losses while maximizing profitability and soil health. Crop residues can alter N and carbon (C) cycle processes in the soil and modulate the responses of the subsequent crop and soil- microbe-plant interactions. Here, we aim to understand how organic amendments with low and high C/N ratio, combined or not with mineral N may change soil bacterial community and their activity on the soil. Organic amendments with different C/N ratios were combined or not with N fertilization as follows: i) unamended soil (control), ii) grass clover silage (GC; low C/N ratio), and iii) wheat straw (WS; high C/N ratio). The organic amendments modulated the bacterial community assemblage and increased microbial activity. WS amendment had the strongest effects on hot water extractable carbon, microbial biomass N and soil respiration, which were linked with changes in bacterial community composition compared with GC-amended and unamended soil. By contrast, N transformation processes in the soil were more pronounced in GC-amended and unamended soil than in WS-amended soil. These responses were stronger in the presence of mineral N input. WS amendment induced greater N immobilization in the soil, even with mineral N input, impairing crop development. Interestingly, N input in unamended soil altered the co-dependence between the soil and the bacterial community to favor a new co-dependence among the soil, plant and microbial activity. In GC-amended soil, N fertilization shifted the dependence of the crop plant from the bacterial community to soil characteristics. Finally, the combined N input with WS amendment (organic carbon input) placed microbial activity at the center of the interrelationships between the bacterial community, plant, and soil. This emphasizes the crucial importance of microorganisms in the functioning of agroecosystems. To achieve higher yields in crops managed with various organic amendments, it is essential to incorporate mineral N management practices. This becomes particularly crucial when the soil amendments have a high C/N ratio.},
}

@article {pmid37229861,
year = {2023},
author = {Zou, J and Cai, L and Lin, J and Wang, R and Li, J and Jia, M},
title = {Anaerobic fermentation of aerobic granular sludge: Insight into the effect of granule size and sludge structure on hydrolysis and acidification.},
journal = {Journal of environmental management},
volume = {343},
number = {},
pages = {118202},
doi = {10.1016/j.jenvman.2023.118202},
pmid = {37229861},
issn = {1095-8630},
abstract = {Aerobic granular sludge (AGS) has different physicochemical properties and microbial communities compared to conventional activated sludge (CAS), which may result in different behaviors during anaerobic fermentation and require further investigation. This study investigated the effect of granule size and sludge structure on the hydrolysis and acidification of AGS. Experimental results show that AGS exhibited significantly higher soluble chemical oxygen demand (SCOD) dissolution and total volatile fatty acids (TVFA) production (330.6-430.3 mg/gVSS and 231.0-312.5 mgCOD/gVSS) compared to conventional activated sludge (CAS) (167.0 mg/gVSS and 133.3 mgCOD/gVSS). This is because AGS (90.6-96.9 mg/gVSS) had higher extracellular polymeric substances (EPS) content than CAS (81.2 mg/gVSS). EPS can not only serve as substrates but also release the trapped hydrolases. Moreover, the relative abundances of hydrolytic/acidogenic bacteria and genes were higher in AGS (0.46%-3.60% and 3.01 × 10[-3]%-4.04 × 10[-3]%) than in CAS (0.30% and 1.23 × 10[-3]%). The optimal granule size for AGS fermentation was found to be 500-1600 μm. The crushing of granule structure promoted the dissolution of small amounts of EPS and the release of some trapped hydrolases, thereby potentially enhancing the enzyme-substrate contacts and bacteria-substrate interactions. Therefore, the highest SCOD dissolution (510.6 mg/gVSS) and TVFA production (352.1 mgCOD/gVSS) from crushed 500-1600 μm AGS were observed. Overall, the findings of this study provide valuable insights into the recovery of organic carbon from AGS via anaerobic fermentation.},
}

@article {pmid37227467,
year = {2023},
author = {S Camargo, T and A Nickele, M and Reis Filho, W and do R C Penteado, S and C de Queiroz, E and G Auer, C},
title = {Correction to: Fungal Community Associated with the Leaf-Cutting Ant Acromyrmex crassispinus (Hymenoptera: Formicidae) Colonies: A Search for Potential Biocontrol Agents.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-023-02247-1},
pmid = {37227467},
issn = {1432-184X},
}

@article {pmid37225998,
year = {2023},
author = {Tao, F and Huang, Y and Hungate, BA and Manzoni, S and Frey, SD and Schmidt, MWI and Reichstein, M and Carvalhais, N and Ciais, P and Jiang, L and Lehmann, J and Wang, YP and Houlton, BZ and Ahrens, B and Mishra, U and Hugelius, G and Hocking, TD and Lu, X and Shi, Z and Viatkin, K and Vargas, R and Yigini, Y and Omuto, C and Malik, AA and Peralta, G and Cuevas-Corona, R and Di Paolo, LE and Luotto, I and Liao, C and Liang, YS and Saynes, VS and Huang, X and Luo, Y},
title = {Microbial carbon use efficiency promotes global soil carbon storage.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {37225998},
issn = {1476-4687},
abstract = {Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.},
}

@article {pmid37225918,
year = {2023},
author = {Elston, KM and Phillips, LE and Leonard, SP and Young, E and Holley, JC and Ahsanullah, T and McReynolds, B and Moran, NA and Barrick, JE},
title = {The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {49},
pmid = {37225918},
issn = {2730-6151},
abstract = {Toolkits of plasmids and genetic parts streamline the process of assembling DNA constructs and engineering microbes. Many of these kits were designed with specific industrial or laboratory microbes in mind. For researchers interested in non-model microbial systems, it is often unclear which tools and techniques will function in newly isolated strains. To address this challenge, we designed the Pathfinder toolkit for quickly determining the compatibility of a bacterium with different plasmid components. Pathfinder plasmids combine three different broad-host-range origins of replication with multiple antibiotic resistance cassettes and reporters, so that sets of parts can be rapidly screened through multiplex conjugation. We first tested these plasmids in Escherichia coli, a strain of Sodalis praecaptivus that colonizes insects, and a Rosenbergiella isolate from leafhoppers. Then, we used the Pathfinder plasmids to engineer previously unstudied bacteria from the family Orbaceae that were isolated from several fly species. Engineered Orbaceae strains were able to colonize Drosophila melanogaster and could be visualized in fly guts. Orbaceae are common and abundant in the guts of wild-caught flies but have not been included in laboratory studies of how the Drosophila microbiome affects fly health. Thus, this work provides foundational genetic tools for studying microbial ecology and host-associated microbes, including bacteria that are a key constituent of the gut microbiome of a model insect species.},
}

@article {pmid37225767,
year = {2023},
author = {Przybylska, MS and Violle, C and Vile, D and Scheepens, JF and Lacombe, B and Le Roux, X and Perrier, L and Sales-Mabily, L and Laumond, M and Vinyeta, M and Moulin, P and Beurier, G and Rouan, L and Cornet, D and Vasseur, F},
title = {AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {314},
pmid = {37225767},
issn = {2052-4463},
abstract = {Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.},
}

@article {pmid37223788,
year = {2023},
author = {Venbrux, M and Crauwels, S and Rediers, H},
title = {Current and emerging trends in techniques for plant pathogen detection.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1120968},
pmid = {37223788},
issn = {1664-462X},
abstract = {Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.},
}

@article {pmid37222807,
year = {2023},
author = {Broman, E and Abdelgadir, M and Bonaglia, S and Forsberg, SC and Wikström, J and Gunnarsson, JS and Nascimento, FJA and Sjöling, S},
title = {Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37222807},
issn = {1432-184X},
abstract = {Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.},
}

@article {pmid37222806,
year = {2023},
author = {Korpita, TM and Muths, EL and Watry, MK and McKenzie, VJ},
title = {Captivity, Reintroductions, and the Rewilding of Amphibian-associated Bacterial Communities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37222806},
issn = {1432-184X},
abstract = {Many studies have noted differences in microbes associated with animals reared in captivity compared to their wild counterparts, but few studies have examined how microbes change when animals are reintroduced to the wild after captive rearing. As captive assurance populations and reintroduction programs increase, a better understanding of how microbial symbionts respond during animal translocations is critical. We examined changes in microbes associated with boreal toads (Anaxyrus boreas), a threatened amphibian, after reintroduction to the wild following captive rearing. Previous studies demonstrate that developmental life stage is an important factor in amphibian microbiomes. We collected 16S marker-gene sequencing datasets to investigate: (i) comparisons of the skin, mouth, and fecal bacteria of boreal toads across four developmental life stages in captivity and the wild, (ii) tadpole skin bacteria before and after reintroduction to the wild, and (iii) adult skin bacteria during reintroduction to the wild. We demonstrated that differences occur across skin, fecal, and mouth bacterial communities in captive versus wild boreal toads, and that the degree of difference depends on developmental stage. Skin bacterial communities from captive tadpoles were more similar to their wild counterparts than captive post-metamorphic individuals were to their wild counterparts. When captive-reared tadpoles were introduced to a wild site, their skin bacteria changed rapidly to resemble wild tadpoles. Similarly, the skin bacterial communities of reintroduced adult boreal toads also shifted to resemble those of wild toads. Our results indicate that a clear microbial signature of captivity in amphibians does not persist after release into natural habitat.},
}

@article {pmid37222805,
year = {2023},
author = {Rodríguez, MF and Gomez, AP and Parra-Giraldo, CM and Ceballos-Garzon, A},
title = {Proteomics and Genetic Approaches Elucidate the Circulation of Low Variability Staphylococcus aureus Strains on Colombian Dairy Farms.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37222805},
issn = {1432-184X},
abstract = {Staphylococcus aureus is one of the most prevalent pathogens causing bovine mastitis in the world, in part because of its ease of adaptation to various hosts and the environment. This study aimed to determine the prevalence of S. aureus in Colombian dairy farms and its relationship with the causal network of subclinical mastitis. From thirteen dairy farms enrolled, 1288 quarter milk samples (QMS) and 330 teat samples were taken from cows with positive (70.1%) and negative California Mastitis Test (CMT). In addition, 126 samples from the milking parlor environment and 40 from workers (nasal) were collected. On each dairy farm, a survey was conducted, and the milking process was monitored on the day of sampling. S. aureus was identified in 176 samples, i.e., 138 QMS, 20 from teats, 8 from the milking parlor environment, and 10 from workers' nasal swabs. Isolates identified as S. aureus underwent proteomics (clustering of mass spectrum) and molecular (tuf, coa, spa Ig, clfA, and eno genes) analysis. Regarding proteomics results, isolates were distributed into three clusters, each with members from all sources and all farms. Concerning molecular analysis, the virulence-related genes clfA and eno were identified in 41.3% and 37.8% of S. aureus isolates, respectively. We provide evidence on the circulation of S. aureus strains with limited variability among animals, humans, and the environment. The parameters with the lowest compliance in the farms which may be implicated in the transmission of S. aureus are the lack of handwashing and abnormal milk handling.},
}

@article {pmid37222804,
year = {2023},
author = {Liu, B and Wang, Y and Zhang, H and Zhou, Y and Zhang, C and Yang, N and Wang, W},
title = {The Variations of Microbial Diversity and Community Structure Along Different Stream Orders in Wuyi Mountains.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37222804},
issn = {1432-184X},
abstract = {The surface water is an important habitat for freshwater microorganisms, but there is a lack of understanding of the pattern of microbial diversity and structure in stream continuums of small subtropical forest watersheds. Therefore, this study aimed to understand the variations in microbial diversity and community structure along stream orders (1-5) in the small subtropical forest catchments of the Wuyi Mountains. Using GIS software, 20 streams were chosen and classified into 5 orders. Illumina sequencing was used to analyze the dynamics of microbial communities, along with stream orders and hydro-chemical properties of stream water were also determined. Our results indicated that the bacterial and fungal richness (ACE index) was higher in low-order (1 and 2 orders) streams than in high-order (3, 4, and 5 orders) streams, with the highest value in the order 2 streams (P < 0.05). The water temperature and dissolved oxygen were positively correlated with fungal richness (P < 0.05). The bacterial rare taxa had a significant correlation with the abundance taxa (P < 0.05). The relative abundances of Bacteroidetes, Actinobacteria, and Chytridiomycota microbial phyla were significantly different among different order streams (P < 0.05). Using the neutral community model, we found that the fungal community structure was significantly shaped by hydro-chemical properties, while the bacterial community structure was largely regulated by stochastic processes. Our findings suggest that variations in microbial community structure in subtropical headwaters are largely shaped by the water temperature and dissolved oxygen.},
}

@article {pmid37222803,
year = {2023},
author = {Malesevic, M and Stanisavljevic, N and Matijasevic, D and Curcic, J and Tasic, V and Tasic, S and Kojic, M},
title = {Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37222803},
issn = {1432-184X},
abstract = {The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.},
}

@article {pmid37221307,
year = {2023},
author = {Djotan, AKG and Matsushita, N and Fukuda, K},
title = {Correction to: Paired root-soil samples and metabarcoding reveal taxon-based colonization strategies in arbuscular mycorrhizal fungi communities in Japanese cedar and cypress stands.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-023-02246-2},
pmid = {37221307},
issn = {1432-184X},
}

@article {pmid37221014,
year = {2023},
author = {Carr, EC and Barton, Q and Grambo, S and Sullivan, M and Renfro, CM and Kuo, A and Pangilinan, J and Lipzen, A and Keymanesh, K and Savage, E and Barry, K and Grigoriev, IV and Riekhof, WR and Harris, SD},
title = {Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkad110},
pmid = {37221014},
issn = {2160-1836},
abstract = {Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primarily yeast form. These fungi grow in xeric, nutrient deplete environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community is not well understood. We have isolated two novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e., E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin that can potentially provide UV resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.},
}

@article {pmid37216901,
year = {2023},
author = {Cao, Y and Almeida-Silva, F and Zhang, WP and Ding, YM and Bai, D and Bai, WN and Zhang, BW and Van de Peer, Y and Zhang, DY},
title = {Genomic Insights into Adaptation to Karst Limestone and Incipient Speciation in East Asian Platycarya spp. (Juglandaceae).},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad121},
pmid = {37216901},
issn = {1537-1719},
abstract = {When challenged by similar environmental conditions, phylogenetically distant taxa often independently evolve similar traits (convergent evolution). Meanwhile, adaptation to extreme habitats might lead to divergence between taxa that are otherwise closely related. These processes have long existed in the conceptual sphere, yet molecular evidence, especially for woody perennials, is scarce. The karst endemic Platycarya longipes, and its only congeneric species, P. strobilacea, which is widely distributed in the mountains in East Asia, provide an ideal model for examining the molecular basis of both convergent evolution and speciation. Using chromosome-level genome assemblies of both species, and whole genome resequencing data from 207 individuals spanning their entire distribution range, we demonstrate that P. longipes and P. strobilacea form two species-specific clades, which diverged around 2.09 million years ago. We find an excess of genomic regions exhibiting extreme interspecific differentiation, potentially due to long-term selection in P. longipes, likely contributing to the incipient speciation of the genus Platycarya. Interestingly, our results unveil underlying karst adaptation in both copies of the calcium influx channel gene TPC1 in P. longipes. TPC1 has previously been identified as a selective target in certain karst-endemic herbs, indicating a convergent adaptation to high calcium stress among karst-endemic species. Our study reveals the genic convergence of TPC1 among karst endemics, and the driving forces underneath the incipient speciation of the two Platycarya lineages.},
}

@article {pmid37213502,
year = {2023},
author = {Díaz, M and Monfort-Lanzas, P and Quiroz-Moreno, C and Rivadeneira, E and Castillejo, P and Arnau, V and Díaz, W and Agathos, SN and Sangari, FJ and Jarrín-V, P and Molina, CA},
title = {The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1154815},
pmid = {37213502},
issn = {1664-302X},
abstract = {A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.},
}

@article {pmid37212664,
year = {2023},
author = {Wu, SY and Ou, CC and Lee, ML and Hsin, IL and Kang, YT and Jan, MS and Ko, JL},
title = {Polysaccharide of Ganoderma lucidum Ameliorates Cachectic Myopathy Induced by the Combination Cisplatin plus Docetaxel in Mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0313022},
doi = {10.1128/spectrum.03130-22},
pmid = {37212664},
issn = {2165-0497},
abstract = {Cachexia is a lethal muscle-wasting syndrome associated with cancer and chemotherapy use. Mounting evidence suggests a correlation between cachexia and intestinal microbiota, but there is presently no effective treatment for cachexia. Whether the Ganoderma lucidum polysaccharide Liz-H exerts protective effects on cachexia and gut microbiota dysbiosis induced by the combination cisplatin plus docetaxel (cisplatin + docetaxel) was investigated. C57BL/6J mice were intraperitoneally injected with cisplatin + docetaxel, with or without oral administration of Liz-H. Body weight, food consumption, complete blood count, blood biochemistry, and muscle atrophy were measured. Next-generation sequencing was also performed to investigate changes to gut microbial ecology. Liz-H administration alleviated the cisplatin + docetaxel-induced weight loss, muscle atrophy, and neutropenia. Furthermore, upregulation of muscle protein degradation-related genes (MuRF-1 and Atrogin-1) and decline of myogenic factors (MyoD and myogenin) after treatment of cisplatin and docetaxel were prevented by Liz-H. Cisplatin and docetaxel treatment resulted in reducing comparative abundances of Ruminococcaceae and Bacteroides, but Liz-H treatment restored these to normal levels. This study indicates that Liz-H is a good chemoprotective reagent for cisplatin + docetaxel-induced cachexia. IMPORTANCE Cachexia is a multifactorial syndrome driven by metabolic dysregulation, anorexia, systemic inflammation, and insulin resistance. Approximately 80% of patients with advanced cancer have cachexia, and cachexia is the cause of death in 30% of cancer patients. Nutritional supplementation has not been shown to reverse cachexia progression. Thus, developing strategies to prevent and/or reverse cachexia is urgent. Polysaccharide is a major biologically active compound in the fungus Ganoderma lucidum. This study is the first to report that G. lucidum polysaccharides could alleviate chemotherapy-induced cachexia via reducing expression of genes that are known to drive muscle wasting, such as MuRF-1 and Atrogin-1. These results suggest that Liz-H is an effective treatment for cisplatin + docetaxel-induced cachexia.},
}

@article {pmid37211607,
year = {2023},
author = {Liu, Y and Wang, H and Qian, X and Gu, J and Chen, W and Shen, X and Tao, S and Jiao, S and Wei, G},
title = {Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {109},
pmid = {37211607},
issn = {2049-2618},
abstract = {BACKGROUND: Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.

RESULTS: Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.

CONCLUSIONS: Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.},
}

@article {pmid37211183,
year = {2023},
author = {Yokoyama, D and Kikuchia, J},
title = {Inferring microbial community assembly in an urban river basin through geo-multi-omics and phylogenetic bin-based null-model analysis of surface water.},
journal = {Environmental research},
volume = {},
number = {},
pages = {116202},
doi = {10.1016/j.envres.2023.116202},
pmid = {37211183},
issn = {1096-0953},
abstract = {Understanding the community assembly process is a central issue in microbial ecology. In this study, we analyzed the community assembly of particle-associated (PA) and free-living (FL) surface water microbiomes in 54 sites from the headstream to the river mouth of an urban river in Japan, the river basin of which has the highest human population density in the country. Analyses were conducted from two perspectives: (1) analysis of deterministic processes considering only environmental factors using a geo-multi-omics dataset and (2) analysis of deterministic and stochastic processes to estimate the contributions of heterogeneous selection (HeS), homogeneous selection (HoS), dispersal limitation (DL), homogenizing dispersal (HD), and drift (DR) as community assembly processes using a phylogenetic bin-based null model. The variation in microbiomes was successfully explained from a deterministic perspective by environmental factors, such as organic matter-related, nitrogen metabolism, and salinity-related parameters, using multivariate statistical analysis, network analysis, and habitat prediction. In addition, we demonstrated the dominance of stochastic processes (DL, HD, and DR) over deterministic processes (HeS and HoS) in community assembly from both deterministic and stochastic perspectives. Our analysis revealed that as the distance between two sites increased, the effect of HoS sharply decreased while the effect of HeS increased, particularly between upstream and estuary sites, indicating that the salinity gradient could potentially enhance the contribution of HeS to community assembly. Our study highlights the importance of both stochastic and deterministic processes in community assembly of PA and FL surface water microbiomes in urban riverine ecosystems.},
}

@article {pmid37209180,
year = {2023},
author = {Kostešić, E and Mitrović, M and Kajan, K and Marković, T and Hausmann, B and Orlić, S and Pjevac, P},
title = {Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37209180},
issn = {1432-184X},
abstract = {Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.},
}

@article {pmid37207751,
year = {2023},
author = {Jin, Z and Shen, M and Wang, L and Wang, C and Gao, M and Yu, G and Chang, Z and Zhang, X},
title = {Antibacterial and immunoregulatory activity of an antimicrobial peptide hepcidin in loach (Misgurnus anguillicaudatus).},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {124833},
doi = {10.1016/j.ijbiomac.2023.124833},
pmid = {37207751},
issn = {1879-0003},
abstract = {Antimicrobial peptides (AMPs) are members of humoral immunity and particpate in resisting microbial invasion. In this study, an AMP gene hepcidin was obtained from the oriental loach Misgurnus anguillicaudatus and named Ma-Hep. This Ma-Hep encodes a peptide of 90 amino acids, with a predicted active peptide segment (Ma-sHep) of 25 amino acids at C terminus. Stimulation by a bacterial pathogen Aeromonas hydrophila resulted in significant up-regulation of Ma-Hep transcripts in loach midgut, head kidney, and gill. Ma-Hep and Ma-sHep proteins were expressed in Pichia pastoris and their antibacterial activity was examined. Results showed that Ma-sHep possessed stronger antibacterial activity against various Gram-positive and Gram-negative bacteria, compared to Ma-Hep. Scanning electron microscopy showed that Ma-sHep might kill bacteria by destroying bacterial cell membranes. Moreover, we found that Ma-sHep had an inhibitory effect on blood cell apoptosis induced by A. hydrophila and facilitated the bacterial phagocytosis and clearance in loach. Histopathological analysis indicated Ma-sHep could protect liver and gut of loach from bacterial infection. Ma-sHep has high thermal stability and PH stability, which is conducive to further feed addition. Feed supplemented with Ma-sHep expressing yeast improved the intestinal flora of loach by increasing the dominant bacteria and decreasing the harmful bacteria. Feed supplemented with Ma-sHep expressing yeast also regulated the expression of inflammatory related factors in various tissues of loach and reduced the mortality of loach upon bacterial infection. These findings show that the antibacterial peptide Ma-sHep is involved in the antibacterial defense of loach and can be used as a candidate for new antimicrobial agents in aquaculture.},
}

@article {pmid37206339,
year = {2023},
author = {Rasmussen, KL and Stamps, BW and Vanzin, GF and Ulrich, SM and Spear, JR},
title = {Spatial and temporal dynamics at an actively silicifying hydrothermal system.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1172798},
doi = {10.3389/fmicb.2023.1172798},
pmid = {37206339},
issn = {1664-302X},
abstract = {Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.},
}

@article {pmid37206314,
year = {2023},
author = {Van de Walle, A and Kim, M and Alam, MK and Wang, X and Wu, D and Dash, SR and Rabaey, K and Kim, J},
title = {Greywater reuse as a key enabler for improving urban wastewater management.},
journal = {Environmental science and ecotechnology},
volume = {16},
number = {},
pages = {100277},
doi = {10.1016/j.ese.2023.100277},
pmid = {37206314},
issn = {2666-4984},
abstract = {Sustainable water management is essential to guaranteeing access to safe water and addressing the challenges posed by climate change, urbanization, and population growth. In a typical household, greywater, which includes everything but toilet waste, constitutes 50-80% of daily wastewater generation and is characterized by low organic strength and high volume. This can be an issue for large urban wastewater treatment plants designed for high-strength operations. Segregation of greywater at the source for decentralized wastewater treatment is therefore necessary for its proper management using separate treatment strategies. Greywater reuse may thus lead to increased resilience and adaptability of local water systems, reduction in transport costs, and achievement of fit-for-purpose reuse. After covering greywater characteristics, we present an overview of existing and upcoming technologies for greywater treatment. Biological treatment technologies, such as nature-based technologies, biofilm technologies, and membrane bioreactors (MBR), conjugate with physicochemical treatment methods, such as membrane filtration, sorption and ion exchange technologies, and ultraviolet (UV) disinfection, may be able to produce treated water within the allowable parameters for reuse. We also provide a novel way to tackle challenges like the demographic variance of greywater quality, lack of a legal framework for greywater management, monitoring and control systems, and the consumer perspective on greywater reuse. Finally, benefits, such as the potential water and energy savings and sustainable future of greywater reuse in an urban context, are discussed.},
}

@article {pmid37204848,
year = {2023},
author = {Rattray, JB and Kramer, PJ and Gurney, J and Thomas, S and Brown, SP},
title = {The dynamic response of quorum sensing to density is robust to signal supplementation and individual signal synthase knockouts.},
journal = {Microbiology (Reading, England)},
volume = {169},
number = {5},
pages = {},
doi = {10.1099/mic.0.001321},
pmid = {37204848},
issn = {1465-2080},
abstract = {Quorum sensing (QS) is a widespread mechanism of environment sensing and behavioural coordination in bacteria. At its core, QS is based on the production, sensing and response to small signalling molecules. Previous work with Pseudomonas aeruginosa shows that QS can be used to achieve quantitative resolution and deliver a dosed response to the bacteria's density environment, implying a sophisticated mechanism of control. To shed light on how the mechanistic signal components contribute to graded responses to density, we assess the impact of genetic (AHL signal synthase deletion) and/or signal supplementation (exogenous AHL addition) perturbations on lasB reaction-norms to changes in density. Our approach condenses data from 2000 timeseries (over 74 000 individual observations) into a comprehensive view of QS-controlled gene expression across variation in genetic, environmental and signal determinants of lasB expression. We first confirm that deleting either (∆lasI, ∆rhlI) or both (∆lasIrhlI) AHL signal synthase gene attenuates QS response to density. In the ∆rhlI background we show persistent yet attenuated density-dependent lasB expression due to native 3-oxo-C12-HSL signalling. We then test if density-independent quantities of AHL signal (3-oxo-C12-HSL, C4-HSL) added to the WT either flatten or increase responsiveness to density and find that the WT response is robust to all tested concentrations of signal, alone or in combination. We then move to progressively supplementing the genetic knockouts and find that cognate signal supplementation of a single AHL signal (∆lasI +3-oxo-C12-HSL, ∆rhlI +C4HSL) is sufficient to restore the ability to respond in a density-dependent manner to increasing density. We also find that dual signal supplementation of the double AHL synthase knockout restores the ability to produce a graded response to increasing density, despite adding a density-independent amount of signal. Only the addition of high concentrations of both AHLs and PQS can force maximal lasB expression and ablate responsiveness to density. Our results show that density-dependent control of lasB expression is robust to multiple combinations of QS gene deletion and density-independent signal supplementation. Our work develops a modular approach to query the robustness and mechanistic bases of the central environmental sensing phenotype of quorum sensing.},
}

@article {pmid37201636,
year = {2023},
author = {He, Y and Xu, M and Lu, S and Zou, W and Wang, Y and Fakhar-E-Alam Kulyar, M and Iqbal, M and Li, K},
title = {Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106159},
doi = {10.1016/j.micpath.2023.106159},
pmid = {37201636},
issn = {1096-1208},
abstract = {Gastrointestinal (GI) disease is a common digestive tract disease effects health of millions of human globally each year, thus the role of intestinal microflora had been emphasized. Seaweed polysaccharides featured a wide range of pharmacological activities, such as antioxidant activity and pharmacological action, but whether they can alleviate the dysbiosis of gut microbial ecology caused by lipopolysaccharide (LPS) exposure has not been well conducted. In this study, we investigated the effects of different concentration of seaweed polysaccharides on LPS-induced intestinal disorder by using microscope and 16S rRNA high-throughput sequencing. Histopathological results indicated that the intestinal structure in the LPS-induced group was damaged. Furthermore, LPS exposure not only reduced the intestinal microbial diversity in mice but also induced momentous transformation in its composition, including a significantly increased in some pathogenic bacteria (Helicobacter, Citrobacter and Mucispirillum) and decreased in several beneficial bacteria (Firmicutes, Lactobacillus, Akkermansia and Parabacteroides). Nonetheless, seaweed polysaccharide administration could recover the gut microbial dysbiosis and the loss of gut microbial diversity induced by LPS exposure. In summary, seaweed polysaccharides were effective against LPS-induced intestinal damage in mice via the modulation of intestinal microecology.},
}

@article {pmid37200211,
year = {2023},
author = {Pascual, J and Lepleux, C and Methner, A and Spröer, C and Bunk, B and Overmann, J},
title = {Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {5},
pages = {},
doi = {10.1099/ijsem.0.005895},
pmid = {37200211},
issn = {1466-5034},
abstract = {A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2[T], was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2[T] was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2[T] was closely related to Arcobacter lekithochrous LFT 1.7[T] and Arcobacter caeni RW17-10[T](95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2[T] was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2[T] represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2[T] as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2[T] (DSM 29169[T]=KCTC 52423[T]).},
}

@article {pmid37196970,
year = {2023},
author = {Farrell, ML and Chueiri, A and O'Connor, L and Duane, S and Maguire, M and Miliotis, G and Cormican, M and Hooban, B and Leonard, A and Gaze, WH and Devane, G and Tuohy, A and Burke, LP and Morris, D},
title = {Assessing the impact of recreational water use on carriage of antimicrobial resistant organisms.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {164201},
doi = {10.1016/j.scitotenv.2023.164201},
pmid = {37196970},
issn = {1879-1026},
abstract = {Understanding the role of exposure to natural recreational waters in the acquisition and transmission of antimicrobial resistance (AMR) is an area of increasing interest. A point prevalence study was carried out in the island of Ireland to determine the prevalence of colonisation with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and carbapenem-resistant Enterobacterales (CRE) in recreational water users (WU) and matched controls. A total of 411 adult participants (199 WU, 212 controls) submitted at least one faecal sample between September 2020 - October 2021. In total, 80 Enterobacterales were isolated from 73 participants. ESBL-PE were detected in 29 (7.1 %) participants (7 WU, 22 controls), and CRE were detected in nine (2.2 %) participants (4 WU, 5 controls). No carbapenemase-producing Enterobacterales (CPE) were detected. WU were significantly less likely to harbour ESBL-PE than controls (risk ratio = 0.34, 95 % CI 0.148 to 0.776, χ[2] 7.37, p = 0.007). This study demonstrates the occurrence of ESBL-PE and CRE in healthy participants in Ireland. Recreational exposure to bathing water in Ireland was associated with a decreased prevalence of colonisation with ESBL-PE and CRE.},
}

@article {pmid37196741,
year = {2023},
author = {Lin, B and Tan, B and Zhang, Q and Li, M and Peng, H and Su, J and He, J and Zhang, Y and Liu, X and Wu, N},
title = {Unraveling the nexus of Cr (Ⅵ), Aniline, and Microbial Ecology on aniline-degrading biosystem: Removal efficiency, sludge type, microbial ecology.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {129185},
doi = {10.1016/j.biortech.2023.129185},
pmid = {37196741},
issn = {1873-2976},
abstract = {In order to explore the stress principle of Cr (Ⅵ) on aniline biodegradation system, a control group and experimental groups with the concentration of Cr (Ⅵ) at 2, 5, 8 mg/L were set up. The results demonstrated that Cr (Ⅵ) had minimal effects on the degradation efficiency of aniline but significantly inhibited nitrogen removal function. When Cr (Ⅵ) concentration was below 5 mg/L, the nitrification performance recovered spontaneously, while denitrification performance was severely impaired. Furthermore, the secretion of extracellular polymeric substances (EPS) and its fluorescence substance concentration were strongly inhibited with increasing Cr (Ⅵ) concentration. High-throughput sequencing revealed that the experimental groups were enriched with Leucobacter and Cr (Ⅵ)-reducing bacteria, but the abundance of nitrifiers and denitrifiers was significantly decreased compared to the control group. Overall, the effects of Cr (Ⅵ) stress at different concentrations on nitrogen removal performance were more significant than those on aniline degradation.},
}

@article {pmid37196568,
year = {2023},
author = {Xu, Y and Teng, Y and Wang, X and Ren, W and Zhao, L and Luo, Y and Christie, P and Greening, C},
title = {Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil.},
journal = {Environment international},
volume = {176},
number = {},
pages = {107962},
doi = {10.1016/j.envint.2023.107962},
pmid = {37196568},
issn = {1873-6750},
abstract = {Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of [13]C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.},
}

@article {pmid37193669,
year = {2023},
author = {Delbaere, K and Roegiers, I and Bron, A and Durif, C and Van de Wiele, T and Blanquet-Diot, S and Marinelli, L},
title = {The small intestine: dining table of host-microbiota meetings.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuad022},
pmid = {37193669},
issn = {1574-6976},
abstract = {Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host's nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo and in vitro models developed to simulate the small intestinal environment, some applied for (diet-)host-bacteria interaction studies. Lastly, we highlight recent technological, medical and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.},
}

@article {pmid37191674,
year = {2023},
author = {Zhao, J and Fan, D and Guo, W and Wu, J and Zhang, X and Zhuang, X and Kong, W},
title = {Precipitation Drives Soil Protist Diversity and Community Structure in Dry Grasslands.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37191674},
issn = {1432-184X},
abstract = {Protists are essential components of soil microbial communities, mediating nutrient cycling and ecosystem functions in terrestrial ecosystems. However, their distribution patterns and driving factors, particularly, the relative importance of climate, plant and soil factors, remain largely unknown. This limits our understanding of soil protist roles in ecosystem functions and their responses to climate change. This is particularly a concern in dryland ecosystems where soil microbiomes are more important for ecosystem functions because plant diversity and growth are heavily constrained by environmental stresses. Here, we explored protist diversity and their driving factors in grassland soils on the Tibetan Plateau, which is a typical dryland region with yearly low temperatures. Soil protist diversity significantly decreased along the gradient of meadow, steppe, and desert. Soil protist diversity positively correlated with precipitation, plant biomass and soil nutrients, but these correlations were changed by grazing. Structural equation and random forest models demonstrated that precipitation dominated soil protist diversity directly and indirectly by influencing plant and soil factors. Soil protist community structure gradually shifted along meadow, steppe and desert, and was driven more by precipitation than by plant and soil factors. Soil protist community compositions were dominated by Cercozoa, Ciliophora and Chlorophyta. In particular, Ciliophora increased but Chlorophyta decreased in relative abundance along the gradient of meadow, steppe and desert. These results demonstrate that precipitation plays more important roles in driving soil protist diversity and community structure than plant and soil factors, suggesting that future precipitation change profoundly alters soil protist community and functions in dry grasslands.},
}

@article {pmid37190986,
year = {2023},
author = {Yang, Y and Suyamud, B and Liang, S and Liang, X and Wan, W and Zhang, W},
title = {Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16400},
pmid = {37190986},
issn = {1462-2920},
abstract = {The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.},
}

@article {pmid37188915,
year = {2023},
author = {Moeller, FU and Herbold, CW and Schintlmeister, A and Mooshammer, M and Motti, C and Glasl, B and Kitzinger, K and Behnam, F and Watzka, M and Schweder, T and Albertsen, M and Richter, A and Webster, NS and Wagner, M},
title = {Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37188915},
issn = {1751-7370},
abstract = {Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, 'Candidatus Taurinisymbion ianthellae', residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. 'Candidatus Taurinisymbion ianthellae' incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, 'Candidatus Nitrosospongia ianthellae'. Metaproteogenomic analyses also suggest that 'Candidatus Taurinisymbion ianthellae' imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.},
}

@article {pmid37188366,
year = {2023},
author = {Harder, CB and Hesling, E and Botnen, SS and Lorberau, KE and Dima, B and von Bonsdorff-Salminen, T and Niskanen, T and Jarvis, SG and Ouimette, A and Hester, A and Hobbie, EA and Taylor, AFS and Kauserud, H},
title = {Mycena species can be opportunist-generalist plant root invaders.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16398},
pmid = {37188366},
issn = {1462-2920},
abstract = {Traditional strict separation of fungi into ecological niches as mutualist, parasite or saprotroph is increasingly called into question. Sequences of assumed saprotrophs have been amplified from plant root interiors, and several saprotrophic genera can invade and interact with host plants in laboratory growth experiments. However, it is uncertain if root invasion by saprotrophic fungi is a widespread phenomenon and if laboratory interactions mirror field conditions. Here, we focused on the widespread and speciose saprotrophic genus Mycena and performed (1) a systematic survey of their occurrences (in ITS1/ITS2 datasets) in mycorrhizal roots of 10 plant species, and (2) an analysis of natural abundances of [13] C/[15] N stable isotope signatures of Mycena basidiocarps from five field locations to examine their trophic status. We found that Mycena was the only saprotrophic genus consistently found in 9 out of 10 plant host roots, with no indication that the host roots were senescent or otherwise vulnerable. Furthermore, Mycena basidiocarps displayed isotopic signatures consistent with published [13] C/[15] N profiles of both saprotrophic and mutualistic lifestyles, supporting earlier laboratory-based studies. We argue that Mycena are widespread latent invaders of healthy plant roots and that Mycena species may form a spectrum of interactions besides saprotrophy also in the field.},
}

@article {pmid37187536,
year = {2023},
author = {Liao, Q and Ye, Y and Li, Z and Chen, H and Zhuo, L},
title = {Prediction of miRNA-disease associations in microbes based on graph convolutional networks and autoencoders.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1170559},
doi = {10.3389/fmicb.2023.1170559},
pmid = {37187536},
issn = {1664-302X},
abstract = {MicroRNAs (miRNAs) are short RNA molecular fragments that regulate gene expression by targeting and inhibiting the expression of specific RNAs. Due to the fact that microRNAs affect many diseases in microbial ecology, it is necessary to predict microRNAs' association with diseases at the microbial level. To this end, we propose a novel model, termed as GCNA-MDA, where dual-autoencoder and graph convolutional network (GCN) are integrated to predict miRNA-disease association. The proposed method leverages autoencoders to extract robust representations of miRNAs and diseases and meantime exploits GCN to capture the topological information of miRNA-disease networks. To alleviate the impact of insufficient information for the original data, the association similarity and feature similarity data are combined to calculate a more complete initial basic vector of nodes. The experimental results on the benchmark datasets demonstrate that compared with the existing representative methods, the proposed method has achieved the superior performance and its precision reaches up to 0.8982. These results demonstrate that the proposed method can serve as a tool for exploring miRNA-disease associations in microbial environments.},
}

@article {pmid37186228,
year = {2023},
author = {Woksepp, H and Camara, F and Bonnedahl, J},
title = {High prevalence of blaCTX-M-15 type extended-spectrum beta-lactamases in Gambian hooded vultures (Necrosyrtes monachus): A threatened species with substantial human interaction.},
journal = {MicrobiologyOpen},
volume = {12},
number = {2},
pages = {e1349},
doi = {10.1002/mbo3.1349},
pmid = {37186228},
issn = {2045-8827},
abstract = {One hundred fecal samples from hooded vultures in the Gambia (Banjul area) were investigated for the presence of bacteria with extended-spectrum cephalosporin- (ESBL/AmpC), carbapenemases, and colistin resistance. No Enterobacteriales carrying carbapenemases or resistance against colistin were detected. Fifty-four ESBL-producing Escherichia coli and five ESBL-producing Klebsiella pneumoniae isolates were identified in 52 of the samples, of which 52 E. coli and 4 K. pneumoniae yielded passed sequencing results. Fifty of the E. coli had ESBL phenotype and genotype harboring blaCTX-M genes, of which 88.5% (n = 46) were the blaCTX-M-15 gene, commonly found on the African continent. Furthermore, the genetic context around blaCTX-M-15 was similar between isolates, being colocalized with ISKpn19. In contrast, cgMLST analysis of the E. coli harboring ESBL genes revealed a genetic distribution over a large fraction of the currently known existing E. coli populations in the Gambia. Hooded vultures in the Gambia thus have a high ESBL E. coli-prevalence (>50%) with low diversity regarding key resistance genes. Furthermore, given the urban presence and frequent interactions between hooded vultures and humans, data from this study implies hooded vultures as potential vectors contributing to the further dissemination of antibiotic-resistance genes.},
}

@article {pmid37185621,
year = {2023},
author = {Li, J and Liu, T and McIlroy, SJ and Tyson, GW and Guo, J},
title = {Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {39},
pmid = {37185621},
issn = {2730-6151},
abstract = {The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m[3]/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.},
}

@article {pmid37184385,
year = {2023},
author = {Sänger, PA and Knüpfer, M and Kegel, M and Spanier, B and Liebler-Tenorio, EM and Fuchs, TM},
title = {Regulation and Functionality of a Holin/Endolysin Pair Involved in Killing of Galleria mellonella and Caenorhabditis elegans by Yersinia enterocolitica.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0003623},
doi = {10.1128/aem.00036-23},
pmid = {37184385},
issn = {1098-5336},
abstract = {The insecticidal toxin complex (Tc) proteins are produced by several insect-associated bacteria, including Yersinia enterocolitica strain W22703, which oscillates between two distinct pathogenicity phases in invertebrates and humans. The mechanism by which this high-molecular-weight toxin is released into the extracellular surrounding, however, has not been deciphered. In this study, we investigated the regulation and functionality of a phage-related holin/endolysin (HE) cassette located within the insecticidal pathogenicity island Tc-PAIYe of W22703. Using the Galleria mellonella infection model and luciferase reporter fusions, we revealed that quorum sensing contributes to the insecticidal activity of W22703 upon influencing the transcription of tcaR2, which encodes an activator of the tc and HE genes. In contrast, a lack of the Yersinia modulator, YmoA, stimulated HE gene transcription, and mutant W22703 ΔymoA exhibited a stronger toxicity toward insect larvae than did W22703. A luciferase reporter fusion demonstrated transcriptional activation of the HE cassette in vivo, and a significantly larger extracellular amount of subunit TcaA was found in W22703 ΔymoA relative to its ΔHE mutant. Using competitive growth assays, we demonstrated that at least in vitro, the TcaA release upon HE activity is not mediated by cell lysis of a significant part of the population. Oral infection of Caenorhabditis elegans with a HE deletion mutant attenuated the nematocidal activity of the wild type, similar to the case with a mutant lacking a Tc subunit. We conclude that the dual holin/endolysin cassette of yersiniae is a novel example of a phage-related function adapted for the release of a bacterial toxin. IMPORTANCE Members of the genus Yersinia cause gastroenteritis in humans but also exhibit toxicity toward invertebrates. A virulence factor required for this environmental life cycle stage is the multisubunit toxin complex (Tc), which is distinct from the insecticidal toxin of Bacillus thuringiensis and has the potential to be used in pest control. The mechanism by which this high-molecular-weight Tc is secreted from bacterial cells has not been uncovered. Here, we show that a highly conserved phage-related holin/endolysin pair, which is encoded by the genes holY and elyY located between the Tc subunit genes, is essential for the insecticidal activity of Y. enterocolitica and that its activation increases the amount of Tc subunits in the supernatant. Thus, the dual holY-elyY cassette of Y. enterocolitica constitutes a new example for a type 10 secretion system to release bacterial toxins.},
}

@article {pmid37182790,
year = {2023},
author = {Refisch, A and Sen, ZD and Klassert, TE and Busch, A and Besteher, B and Danyeli, LV and Helbing, D and Schulze-Späte, U and Stallmach, A and Bauer, M and Panagiotou, G and Jacobsen, ID and Slevogt, H and Opel, N and Walter, M},
title = {Microbiome and immuno-metabolic dysregulation in patients with major depressive disorder with atypical clinical presentation.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {109568},
doi = {10.1016/j.neuropharm.2023.109568},
pmid = {37182790},
issn = {1873-7064},
abstract = {Depression is highly prevalent (6% 1-year prevalence) and is the second leading cause of disability worldwide. Available treatment options for depression are far from optimal, with response rates only around 50%. This is most likely related to a heterogeneous clinical presentation of major depression disorder (MDD), suggesting different manifestations of underlying pathophysiological mechanisms. Poorer treatment outcomes to first-line antidepressants were reported in MDD patients endorsing an "atypical" symptom profile that is characterized by preserved reactivity in mood, increased appetite, hypersomnia, a heavy sensation in the limbs, and interpersonal rejection sensitivity. In recent years, evidence has emerged that immunometabolic biological dysregulation is an important underlying pathophysiological mechanism in depression, which maps more consistently to atypical features. In the last few years human microbial residents have emerged as a key influencing variable associated with immunometabolic dysregulations in depression. The microbiome plays a critical role in the training and development of key components of the host's innate and adaptive immune systems, while the immune system orchestrates the maintenance of key features of the host-microbe symbiosis. Moreover, by being a metabolically active ecosystem commensal microbes may have a huge impact on signaling pathways, involved in underlying mechanisms leading to atypical depressive symptoms. In this review, we discuss the interplay between the microbiome and immunometabolic imbalance in the context of atypical depressive symptoms. Although research in this field is in its infancy, targeting biological determinants in more homogeneous clinical presentations of MDD may offer new avenues for the development of novel therapeutic strategies for treatment-resistant depression.},
}

@article {pmid37180236,
year = {2023},
author = {Huang, W and Li, S and Li, S and Laanbroek, HJ and Zhang, Q},
title = {Pro- and eukaryotic keystone taxa as potential bio-indicators for the water quality of subtropical Lake Dongqian.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1151768},
doi = {10.3389/fmicb.2023.1151768},
pmid = {37180236},
issn = {1664-302X},
abstract = {The microbial community plays an important role in the biogeochemical cycles in water aquatic ecosystems, and it is regulated by environmental variables. However, the relationships between microbial keystone taxa and water variables, which play a pivotal role in aquatic ecosystems, has not been clarified in detail. We analyzed the seasonal variation in microbial communities and co-occurrence network in the representative areas taking Lake Dongqian as an example. Both pro- and eukaryotic community compositions were more affected by seasons than by sites, and the prokaryotes were more strongly impacted by seasons than the eukaryotes. Total nitrogen, pH, temperature, chemical oxygen demand, dissolved oxygen and chlorophyll a significantly affected the prokaryotic community, while the eukaryotic community was significantly influenced by total nitrogen, ammonia, pH, temperature and dissolved oxygen. The eukaryotic network was more complex than that of prokaryotes, whereas the number of eukaryotic keystone taxa was less than that of prokaryotes. The prokaryotic keystone taxa belonged mainly to Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacteroidetes. It is noteworthy that some of the keystone taxa involved in nitrogen cycling are significantly related to total nitrogen, ammonia, temperature and chlorophyll a, including Polaromonas, Albidiferax, SM1A02 and Leptolyngbya so on. And the eukaryotic keystone taxa were found in Ascomycota, Choanoflagellida and Heterophryidae. The mutualistic pattern between pro- and eukaryotes was more evident than the competitive pattern. Therefore, it suggests that keystone taxa could be as bio-indicators of aquatic ecosystems.},
}

@article {pmid37178239,
year = {2023},
author = {Nandni, and Rani, S and Chopra, G and Wati, L},
title = {Deciphering the Potential of Sulphur-Oxidizing Bacteria for Sulphate Production Correlating with pH Change.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37178239},
issn = {1432-184X},
abstract = {Sulphur, available in the form of sulphate, is one of the essential nutrients that is required by plants. Bacteria capable of oxidizing reduced forms of sulphur to sulphate play an important role in sulphur nutrition for plants. The present study was conducted to isolate, screen, and characterize sulphur-oxidizing bacteria from different soil samples collected from mustard rhizosphere and fly ash mixed soil. A total of 33 sulphur-oxidizing bacterial isolates (HMSOB1-33) were retrieved from soil and further screened for sulphur-oxidizing ability. Maximum solubilization index (3.76), pH reduction (3.93), and sulphate production (173.61 µg/ml) were observed for the isolate HMSOB2 which on the basis of 16S rDNA sequencing was identified as Pantoea dispersa with sequence similarity 98.22%. Four other selected bacterial isolates were identified as Bacillus megaterium, Bacillus tropicus, Bacillus velezensis, and Bacillus cereus. Sulphate solubilization index (SSI) correlated positively (r = 0.91) with sulphate production; however, pH showed negative correlation (r = - 0.82) with SSI as well as sulphate production after 120 h of incubation. These promising bacterial isolates could be further explored as bioinoculant after assessing plant growth traits.},
}

@article {pmid37177981,
year = {2023},
author = {Bier, RL and Mosher, JJ and Kaplan, LA and Kan, J},
title = {Spatial scale impacts microbial community composition and distribution within and across stream ecosystems in North and Central America.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16396},
pmid = {37177981},
issn = {1462-2920},
abstract = {A mechanistic understanding of factors that structure spatiotemporal community composition is a major challenge in microbial ecology. Our study of microbial communities in the headwaters of three freshwater stream networks showed significant community changes at the small spatial scale of benthic habitats when compared to changes at mid- and large-spatial scales associated with stream order and catchment. Catchment (which included temperate and tropical catchments) had the strongest influence on community composition followed by habitat type (epipsammon or epilithon) and stream orders. Alpha diversity of benthic microbiomes resulted from interactions between catchment, habitat, and canopy. Epilithon contained relatively more Cyanobacteria and algae while Acidobacteria and Actinobacteria proportions were higher in epipsammic habitats. Turnover from replacement created ~60%-95% of beta diversity differences among habitats, stream orders, and catchments. Turnover within a habitat type generally decreased downstream indicating longitudinal linkages in stream networks while between habitat turnover also shaped benthic microbial community assembly. Our study suggests that factors influencing microbial community composition shift in dominance across spatial scales, with habitat dominating locally and catchment dominating globally.},
}

@article {pmid37173204,
year = {2023},
author = {Pan, X and Raaijmakers, JM and Carrión, VJ},
title = {Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2023.03.018},
pmid = {37173204},
issn = {1878-4380},
abstract = {Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.},
}

@article {pmid37173060,
year = {2023},
author = {Krebs, NF and Belfort, MB and Meier, PP and Mennella, JA and O'Connor, DL and Taylor, SN and Raiten, DJ},
title = {Infant factors that impact the ecology of human milk secretion and composition-a report from "Breastmilk Ecology: Genesis of Infant Nutrition (BEGIN)" Working Group 3.},
journal = {The American journal of clinical nutrition},
volume = {117 Suppl 1},
number = {},
pages = {S43-S60},
doi = {10.1016/j.ajcnut.2023.01.021},
pmid = {37173060},
issn = {1938-3207},
abstract = {Infants drive many lactation processes and contribute to the changing composition of human milk through multiple mechanisms. This review addresses the major topics of milk removal; chemosensory ecology for the parent-infant dyad; the infant's inputs into the composition of the human milk microbiome; and the impact of disruptions in gestation on the ecology of fetal and infant phenotypes, milk composition, and lactation. Milk removal, which is essential for adequate infant intake and continued milk synthesis through multiple hormonal and autocrine/paracrine mechanisms, should be effective, efficient, and comfortable for both the lactating parent and the infant. All 3 components should be included in the evaluation of milk removal. Breastmilk "bridges" flavor experiences in utero with postweaning foods, and the flavors become familiar and preferred. Infants can detect flavor changes in human milk resulting from parental lifestyle choices, including recreational drug use, and early experiences with the sensory properties of these recreational drugs impact subsequent behavioral responses. Interactions between the infant's own developing microbiome, that of the milk, and the multiple environmental factors that are drivers-both modifiable and nonmodifiable-in the microbial ecology of human milk are explored. Disruptions in gestation, especially preterm birth and fetal growth restriction or excess, impact the milk composition and lactation processes such as the timing of secretory activation, adequacy of milk volume and milk removal, and duration of lactation. Research gaps are identified in each of these areas. To assure a sustained and robust breastfeeding ecology, these myriad infant inputs must be systematically considered.},
}

@article {pmid37169795,
year = {2023},
author = {Conners, R and León-Quezada, RI and McLaren, M and Bennett, NJ and Daum, B and Rakonjac, J and Gold, VAM},
title = {Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {2724},
pmid = {37169795},
issn = {2041-1723},
abstract = {Phages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.},
}

@article {pmid37166501,
year = {2023},
author = {Weber, M and Göpfert, B and von Wezyk, S and Savin-Hoffmeyer, M and Lipski, A},
title = {Correlation between Bacterial Cell Density and Abundance of Antibiotic Resistance on Milking Machine Surfaces Assessed by Cultivation and Direct qPCR Methods.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37166501},
issn = {1432-184X},
abstract = {The relative abundance of antibiotic-resistant bacteria and antibiotic-resistance genes was surveyed for different parts of a milking machine. A cultivation approach based on swab samples showed a highly diverse microbiota, harboring resistances against cloxacillin, ampicillin, penicillin, and tetracycline. This approach demonstrated a substantial cloxacillin resistance of numerous taxa within milking machine microbiota coming along with regular use of cloxacillin for dry-off therapy of dairy cows. For the less abundant tetracycline-resistant bacteria we found a positive correlation between microbial cell density and relative abundance of tetracycline-resistant microorganisms (R[2] = 0.73). This indicated an accelerated dispersion of resistant cells for sampling locations with high cell density. However, the direct quantification of the tetM gene from the swap samples by qPCR showed the reverse relation to bacterial density if normalized against the abundance of 16S rRNA genes (R[2] = 0.88). The abundance of 16S rRNA genes was analyzed by qPCR combined with a propidium monoazide treatment, which eliminates 16S rRNA gene signals in negative controls.},
}

@article {pmid37166500,
year = {2023},
author = {Zeng, Z and Yang, Z and Yang, A and Li, Y and Zhang, H},
title = {Genetic Evidence for Colletotrichum gloeosporioides Transmission Between the Invasive Plant Ageratina adenophora and Co-occurring Neighbor Plants.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37166500},
issn = {1432-184X},
abstract = {To understand the disease-mediated invasion of exotic plants and the potential risk of disease transmission in local ecosystems, it is necessary to characterize population genetic structure and spatio-temporal dynamics of fungal community associated with both invasive and co-occurring plants. In this study, multiple genes were used to characterize the genetic diversity of 165 strains of Colletotrichum gloeosporioides species complex (CGSC) isolated from healthy leaves and symptomatic leaves of invasive plant Ageratina adenophora, as well as symptomatic leaves of its neighbor plants from eleven geographic sites in China. The data showed that these CGSC strains had a high genetic diversity in each geographic site (all Hd > 0.67 and Pi > 0.01). Haplotype diversity and nucleotide diversity varied greatly in individual gene locus: gs had the highest haplotype diversity (Hd = 0.8972), gapdh had the highest nucleotide diversity (Pi = 0.0705), and ITS had the lowest nucleotide diversity (Pi = 0.0074). Haplotypes were not clustered by geographic site, invasive age, or isolation source. AMOVA revealed that the genetic variation was mainly from within-populations, regardless of geographic or isolation origin. Both AMOVA and neutrality tests indicated these CGSC strains occurred gene exchange among geographic populations but did not experience population expansion along with A. adenophora invasion progress. Our data indicated that A. adenophora primarily accumulated these CGSC fungi in the introduced range, suggesting a high frequency of CGSC transmission between A. adenophora and co-occurring neighbor plants. This study is valuable for understanding the disease-mediated plant invasion and the potential risk of disease transmission driven by exotic plants in local ecosystems.},
}

@article {pmid37163314,
year = {2023},
author = {Cai, P and Zhang, W and Duan, X and Gong, S and Qiu, Z and Zhu 朱, M墨},
title = {First Report of Powdery Mildew Caused by Golovinomyces bolayi on Veronica persica in Central China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-04-23-0641-PDN},
pmid = {37163314},
issn = {0191-2917},
abstract = {Veronica persica, Persian speedwell, is a flowering plant belonging to the family Plantaginaceae. Due to its showy flowers, this plant is widely planted in many home gardens, city parks and universities in China. From April to June 2021, signs and symptoms of powdery mildew were found on leaves of V. persica growing on the campus of Henan Normal University, Henan Province, China. Signs initially appeared as thin white colonies and subsequently white powdery masses were abundant on the adaxial and abaxial surfaces of leaves and covered up to 99 % of the leaf area. The infected leaves showed chlorotic, deformed or senescence features. About 150 V. persica plants were monitored and more than 90 % of the plants showed these signs and symptoms. Conidiophores (n = 20) were 108 to 220 × 10 to 13 μm and composed of foot cells, followed by short cells and conidia. Conidia were hyaline, doliiform-subcylindrical shaped, 21 to 37 × 15 to 22 μm, and showed distinct fibrosin bodies. Conidial germ tubes were produced at the perihilar position. No chasmothecia were observed. The observed morphological characteristics were consistent with those of previously documented Golovinomyces bolayi (Braun and Cook 2012). To further confirm the powdery mildew fungus, structures of the pathogen were harvested and total genomic DNA was isolated using the method previously described by Zhu et al. (2019, 2021). Using the primers ITS1/ITS4, the internal transcribed spacer (ITS) region of rDNA was amplified (White et al. 1990) and the amplicon was sequenced. The resulting sequence was deposited into GenBank under Accession No. MZ343575 and was 100 % identical (592/592 bp) to G. bolayi on Kalanchoe blossfeldiana (LC417096) (Braun et al. 2019). The additional phylogenetic analysis clearly illustrated that the identified fungus and G. bolayi were clustered in the same branch (Zhu et al. 2022a; Zhu et al. 2022b). To test pathogenicity, healthy V. persica plants were collected from the campus of Henan Normal University and leaf surfaces of three plants were inoculated by dusting fungal conidia from mildew-infested leaves using pressurized air. Three plants without inoculation served as a control. The spore-treated and non-treated plants were separately placed in two growth chambers (temperature, 18℃; humidity, 60%; light/dark, 16h/8h). Seven- to eight-days post-inoculation, pathogen signs were noticeable on inoculated plants, whereas control plants remained healthy. Similar results were obtained by conducting the pathogenicity assays twice. Therefore, based on the analysis, G. bolayi was identified and confirmed as the causal agent of the powdery mildew. This pathogen has been reported on V. persica in Iran (Golmohammadi et al. 2019). However, to our best knowledge, there is no report concerning the powdery mildew caused by G. bolayi on V. persica in China. Recently, G. bolayi was segregated from species clades of G. orontii complex (Braun et al. 2019). Our record of the molecular characterization of G. bolayi will support the further phylogeny and taxonomy analysis of the G. orontii complex. The sudden outbreak of powdery mildew caused by G. bolayi on V. persica may detract from plant health and ornamental value. The identification and confirmation of this disease expands the understanding of this causal agent and will offer support for future powdery mildew control.},
}

@article {pmid37162342,
year = {2023},
author = {Cruz-Paredes, C and Tájmel, D and Rousk, J},
title = {Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0209022},
doi = {10.1128/aem.02090-22},
pmid = {37162342},
issn = {1098-5336},
abstract = {Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (Tmin) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.},
}

@article {pmid37161621,
year = {2023},
author = {Talukdar, D and Bandopadhyay, P and Ray, Y and Paul, SR and Sarif, J and D'Rozario, R and Lahiri, A and Das, S and Bhowmick, D and Chatterjee, S and Das, B and Ganguly, D},
title = {Association of gut microbial dysbiosis with disease severity, response to therapy and disease outcomes in Indian patients with COVID-19.},
journal = {Gut pathogens},
volume = {15},
number = {1},
pages = {22},
pmid = {37161621},
issn = {1757-4749},
abstract = {BACKGROUND: Severe coronavirus disease 2019 (COVID-19) is associated with systemic hyper-inflammation. An adaptive interaction between gut microbiota and host immune systems is important for intestinal homeostasis and systemic immune regulation. The association of gut microbial composition and functions with COVID-19 disease severity is sparse, especially in India. We analysed faecal microbial diversity and abundances in a cohort of Indian COVID-19 patients to identify key signatures in the gut microbial ecology in patients with severe COVID-19 disease as well as in response to different therapies. The composition of the gut microbiome was characterized using 16Sr RNA gene sequences of genomic DNA extracted from faecal samples of 52 COVID-19 patients. Metabolic pathways across the groups were predicted using PICRUSt2. All statistical analyses were done using Vegan in the R environment. Plasma cytokine abundance at recruitment was measured in a multiplex assay.

RESULTS: The gut microbiome composition of mild and severe patients was found to be significantly different. Immunomodulatory commensals, viz. Lachnospiraceae family members and Bifidobacteria producing butyrate and short-chain fatty acids (SCFAs), were under represented in patients with severe COVID-19, with an increased abundance of opportunistic pathogens like Eggerthella. The higher abundance of Lachnoclostridium in severe disease was reduced in response to convalescent plasma therapy. Specific microbial genera showed distinctive trends in enriched metabolic pathways, strong correlations with blood plasma cytokine levels, and associative link to disease outcomes.

CONCLUSION: Our study indicates that, along with SARS-CoV-2, a dysbiotic gut microbial community may also play an important role in COVID-19 severity through modulation of host immune responses.},
}

@article {pmid37158858,
year = {2023},
author = {Bi, S and Lai, H and Guo, D and Yi, H and Li, H and Liu, X and Chen, Q and Chen, J and Zhang, Z and Wei, X and Li, G and Xin, G},
title = {The characteristics of the intestinal bacterial community from Oreochromis mossambicus and its interaction with microbiota from artificial fishery habitats.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {16},
pmid = {37158858},
issn = {2730-7182},
abstract = {BACKGROUND: Artificial habitats can allow many fish to flock together and interact and have been widely used to restore and protect fishery resources. The piece of research intends to elucidate the relationship of microbial communities between tilapia (Oreochromis mossambicus) intestines and artificial fishery habitats (water and sediments). Hence, 16 S rDNA sequencing technology was used to study the bacterial communities from intestines, water, and sediments.

RESULTS: The results showed that the tilapia intestines had the lowest richness of Operational Taxonomic Units (OTUs) and the lowest diversity of the bacterial community compared to water and sediments. The intestine, water, and sediment microbial communities shared many OTUs. Overall, 663 shared OTUs were identified from the tilapia intestines (76.20%), the surrounding water (71.14%), and sediment (56.86%) in artificial habitats. However, there were unique OTUs that were detected in different sample types. There were 81, 77 and 112 unique OTUs observed in tilapia intestines, the surrounding water and sediment, respectively. Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Fusobacteria, and Bacteroidetes were the most common and dominant bacterial phyla between the tilapia intestines and habitats. In the two groups, the microbial communities were similar in the taxonomic composition but different in the abundance of bacterial phyla. Interestingly, Firmicutes increased, while Fusobacteria decreased in artificial habitats. These findings indicated that the artificial habitats had fewer effects on the water environment and indicated that the mode of artificial habitats could have an effect on the enriched bacteria in the tilapia intestines.

CONCLUSIONS: This study analysed the bacterial communities of artificial habitats from the intestines, water, and sediments, which can explain the relationship between the tilapia intestines and habitats and strengthen the value of ecological services provided by artificial habitats.},
}

@article {pmid37156959,
year = {2023},
author = {Banaszkiewicz, S and Tabiś, A and Wałecki, B and Łyżwińska, K and Bystroń, J and Bania, J},
title = {spa Types and Staphylococcal Enterotoxin Production of Staphylococcus aureus Isolated from Wild Boar.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37156959},
issn = {1432-184X},
abstract = {Little is known about the structure of S. aureus population and the enterotoxin gene content in wild boar. In 1025 nasal swabs from wild boars, 121 S. aureus isolates were identified. Staphylococcal enterotoxin (SE) genes were identified in 18 isolates (14.9%). The seb gene was found in 2 S. aureus isolates, sec in 2 isolates, the see and seh genes were found in 4 and 11 isolates, respectively. The production of SEs was evaluated in bacteria grown in microbial broth. Concentration of SEB reached 2.70 µg/ml after 24 h and 4.46 µg/ml at 48 h. SEC was produced at 952.6 ng/ml after 24 h and 7.2 µg/ml at 48 h. SEE reached 124.1 ng/ml after 24 h and 191.6 ng/ml at 48 h of culture. SEH production reached 4.36 µg/ml at 24 h and 5.42 µg/ml at 48 h of culture. Thirty-nine spa types were identified among S. aureus isolates. The most prevalent spa types were t091 and t1181, followed by t4735 and t742, t3380 and t127. Twelve new spa types, i.e., t20572‒t20583 were identified. The wild boar S. aureus population was shown to contain previously identified animal/human-associated spa types and spa types not identified in humans or animals. We also indicate that wildlife animals can be a significant reservoir of see-positive S. aureus.},
}

@article {pmid37155494,
year = {2023},
author = {Gomez-Alvarez, V and Siponen, S and Kauppinen, A and Hokajärvi, AM and Tiwari, A and Sarekoski, A and Miettinen, IT and Torvinen, E and Pitkänen, T},
title = {A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.},
journal = {Water research},
volume = {229},
number = {},
pages = {119495},
doi = {10.1016/j.watres.2022.119495},
pmid = {37155494},
issn = {1879-2448},
abstract = {The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.},
}

@article {pmid37154919,
year = {2023},
author = {Pan, Q and Shikano, I and Liu, TX and Felton, GW},
title = {Helicoverpa zea-Associated Gut Bacteria as Drivers in Shaping Plant Anti-herbivore Defense in Tomato.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {37154919},
issn = {1432-184X},
abstract = {Insect-associated bacteria can mediate the intersection of insect and plant immunity. In this study, we aimed to evaluate the effects of single isolates or communities of gut-associated bacteria of Helicoverpa zea larvae on herbivore-induced defenses in tomato. We first identified bacterial isolates from the regurgitant of field-collected H. zea larvae by using a culture-dependent method and 16S rRNA gene sequencing. We identified 11 isolates belonging to the families Enterobacteriaceae, Streptococcaceae, Yersiniaceae, Erwiniaceae, and unclassified Enterobacterales. Seven different bacterial isolates, namely Enterobacteriaceae-1, Lactococcus sp., Klebsiella sp. 1, Klebsiella sp. 3, Enterobacterales, Enterobacteriaceae-2, and Pantoea sp., were selected based on their phylogenetic relationships to test their impacts on insect-induced plant defenses. We found that the laboratory population of H. zea larvae inoculated with individual isolates did not induce plant anti-herbivore defenses, whereas larvae inoculated with a bacterial community (combination of the 7 bacterial isolates) triggered increased polyphenol oxidase (PPO) activity in tomato, leading to retarded larval development. Additionally, field-collected H. zea larvae with an unaltered bacterial community in their gut stimulated higher plant defenses than the larvae with a reduced gut microbial community. In summary, our findings highlight the importance of the gut microbial community in mediating interactions between herbivores and their host plants.},
}

@article {pmid37150906,
year = {2023},
author = {Rasmussen, TS and Mentzel, CMJ and Danielsen, MR and Jakobsen, RR and Zachariassen, LSF and Castro Mejia, JL and Brunse, A and Hansen, LH and Hansen, CHF and Hansen, AK and Nielsen, DS},
title = {Fecal virome transfer improves proliferation of commensal gut Akkermansia muciniphila and unexpectedly enhances the fertility rate in laboratory mice.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2208504},
doi = {10.1080/19490976.2023.2208504},
pmid = {37150906},
issn = {1949-0984},
abstract = {Probiotics are intended to improve gastrointestinal health when consumed. However, the probiotics marketed today only colonize the densely populated gut to a limited extent. Bacteriophages comprise the majority of viruses in the human gut virome and there are strong indications that they play important roles in shaping the gut microbiome. Here, we investigate the use of fecal virome transplantation (FVT, sterile filtrated feces) as a mean to alter the gut microbiome composition to lead the way for persistent colonization of two types of probiotics: Lacticaseibacillus rhamnosus GG (LGG) representing a well-established probiotic and Akkermansia muciniphila (AKM) representing a putative next-generation probiotic. Male and female C57BL/6NTac mice were cohoused in pairs from 4 weeks of age and received the following treatment by oral gavage at week 5 and 6: AKM+FVT, LGG+FVT, probiotic sham (Pro-sham)+FVT, LGG+Saline, AKM+Saline, and control (Pro-sham+Saline). The FVT donor material originated from mice with high relative abundance of A. muciniphila. All animals were terminated at age 9 weeks. The FVT treatment did not increase the relative abundance of the administered LGG or AKM in the recipient mice. Instead FVT significantly (p < 0.05) increased the abundance of naturally occurring A. muciniphila compared to the control. This highlights the potential of propagating the existing commensal "probiotics" that have already permanently colonized the gut. Being co-housed male and female, a fraction of the female mice became pregnant. Unexpectedly, the FVT treated mice were found to have a significantly (p < 0.05) higher fertility rate independent of probiotic administration. These preliminary observations urge for follow-up studies investigating interactions between the gut microbiome and fertility.},
}

@article {pmid37150044,
year = {2023},
author = {Hu, D and Li, S and Liu, X and Liu, H and Liu, G},
title = {Kinetic model derivation for design, building and operation of solid waste treatment unit based on system dynamics and computer simulation.},
journal = {Waste management (New York, N.Y.)},
volume = {166},
number = {},
pages = {58-69},
doi = {10.1016/j.wasman.2023.04.037},
pmid = {37150044},
issn = {1879-2456},
abstract = {Solid waste disposal is significantly important to maintaining normal operation of both natural and artificial ecosystems. In this study, a kinetic model of solid waste treatment unit (SWTU) was upfront developed based on microbial ecology, system dynamics, cybernetics and digital simulation, which accurately described the relationships and interactions between solid waste decomposition (SWD) processes and biotic/abiotic factors. Then a specific SWTU prototype was designed and built from this kinetic model. A 370-day experiment demonstrated that SWTU maintained normal operation with robust stability and desired dynamic behaviors, and effectively disposed the solid waste. Therefore, this kinetic model was highly valid due to its high structural and behavioral similarity with the prototype. This research could lay a strong theoretical foundation for further closed-loop control as well as optimization of SWTU, and provide scientific guidance to environmental management as well as sustainable development.},
}

@article {pmid37149807,
year = {2023},
author = {Pjevac, P and Bartosik, T and Schneider, S and Eckl-Dorna, J},
title = {Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2023.04.001},
pmid = {37149807},
issn = {1097-6825},
}

@article {pmid37149500,
year = {2023},
author = {Kharshandi, F and Kayang, H},
title = {Antagonistic potential of rhizobacterial isolates against fungal pathogens causing rhizome rot in turmeric.},
journal = {Archives of microbiology},
volume = {205},
number = {6},
pages = {221},
pmid = {37149500},
issn = {1432-072X},
abstract = {The study aims to select potent bacterial antagonists to be used as biocontrol agents against rhizome rot disease in turmeric (Curcuma longa L.). A total of 48 bacterial isolates were isolated from the rhizosphere of turmeric. These isolates were screened for their in vitro antagonism against Fusarium solani FS-01 and Pythium aphanidermatum (ITCC 7908). Production of volatile organic compounds and chitinase activity were also performed. Among the tested isolates, two bacterial isolates (IJ2 and IJ10) showed the highest inhibitory activity against these fungal pathogens. GC/MS analysis of the crude extract produced by Pseudomonas sp. IJ2 and B. subtilis IJ10 was found to contain many bioactive compounds with antifungal and antimicrobial activities. The rhizome treatment with these isolates exhibited the lowest percent disease severity with high biocontrol efficacy against the tested pathogens. These isolates with promising antagonistic potential, therefore, can be used as biocontrol agents against rhizome rot in turmeric.},
}

@article {pmid37149269,
year = {2023},
author = {Li, Y and Kuramae, EE and Nasir, F and Wang, E and Zhang, Z and Li, J and Yao, Z and Tian, L and Sun, Y and Luo, S and Guo, L and Ren, G and Tian, C},
title = {Addition of cellulose degrading bacterial agents promoting keystone fungal-mediated cellulose degradation during aerobic composting: Construction the complex co-degradation system.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {129132},
doi = {10.1016/j.biortech.2023.129132},
pmid = {37149269},
issn = {1873-2976},
abstract = {To excavate a complex co-degradation system for decomposing cellulose more efficiently, cellulose-degrading bacteria, including Bacillus subtilis WF-8, Bacillus licheniformis WF-11, Bacillus Cereus WS-1 and Streptomyces Nogalater WF-10 were added during maize straw and cattle manure aerobic composting. Bacillus and Streptomyces successfully colonized, which improve cellulose degrading ability. Continuous colonization of cellulose-degrading bacteria can promote the fungi to produce more precursors for humus and promote the negative correlation with Ascomycota. In the current study, the addition of cellulose-degrading bacteria has resulted in the rapid development of Mycothermus and Remersonia in the phylum Ascomycota as keystone fungal genera which constitute the foundation of the co-degradation system. Network analysis reveals the complex co-degradation system of efficient cellulose bacteria and mature fungi to treat cellulose in the process of straw aerobic composting mainly related to the influence of total carbon (TC) /total nitrogen (TN) and humic acid (HA)/fulvic acid (FA). This research offers a complex co-degradation system more efficiently to decompose cellulose aiming to maintain the long-term sustainability of agriculture.},
}