Environmental Microbiome最新文献

{"title":"Spatial scale modulates stochastic and deterministic influence on biogeography of photosynthetic biofilms in Southeast Asian hot springs.","authors":"Christaline George, Chananwat Kortheerakul, Nitthiya Khunthong, Chitrabhanu Sharma, Danli Luo, Kok-Gan Chan, Maurycy Daroch, Kevin D Hyde, Patrick K H Lee, Kian Mau Goh, Rungaroon Waditee-Sirisattha, Stephen B Pointing","doi":"10.1186/s40793-025-00711-8","DOIUrl":"https://doi.org/10.1186/s40793-025-00711-8","url":null,"abstract":"<p><p>Hot springs, with their well-characterized major abiotic variables and island-like habitats, are ideal systems for studying microbial biogeography. Photosynthetic biofilms are a major biological feature of hot springs but despite this large-scale studies are scarce, leaving critical questions about the drivers of spatial turnover unanswered. Here, we analysed 395 photosynthetic biofilms from neutral-alkaline hot springs (39-66 °C, pH 6.4-9.0) across a 2100 km latitudinal gradient in Southeast Asia. The Cyanobacteria-dominated communities were categorized into six biogeographic regions, each characterized by a distinct core microbiome and biotic interactions. We observed a significant decline in the explanatory power of major abiotic variables with increasing spatial scale, from 62.6% locally, 55% regionally, to 26.8% for the inter-regional meta-community. Statistical null models revealed that deterministic environmental filtering predominated at local and regional scales, whereas stochastic ecological drift was more influential at the inter-regional scale. These findings enhance our understanding of the differential contribution of ecological drivers and highlight the importance of spatial scale in shaping biogeographic distributions for microorganisms.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"50"},"PeriodicalIF":6.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144062788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The unresolved struggle of 16S rRNA amplicon sequencing: a benchmarking analysis of clustering and denoising methods.","authors":"Mohamed Fares, Engy K Tharwat, Ilse Cleenwerck, Pieter Monsieurs, Rob Van Houdt, Peter Vandamme, Mohamed El-Hadidi, Mohamed Mysara","doi":"10.1186/s40793-025-00705-6","DOIUrl":"https://doi.org/10.1186/s40793-025-00705-6","url":null,"abstract":"<p><strong>Background: </strong>Although 16S rRNA gene amplicon sequencing has become an indispensable method for microbiome studies, this analysis is not error-free, and remains prone to several biases and errors. Numerous algorithms have been developed to eliminate these errors and consolidate the output into distance-based Operational Taxonomic Units (OTUs) or denoising-based Amplicon Sequence Variants (ASVs). An objective comparison between them has been obscured by various experimental setups and parameters. In the present study, we conducted a comprehensive benchmarking analysis of the error rates, microbial composition, over-merging/over-splitting of reference sequences, and diversity analyses using the most complex mock community, comprising 227 bacterial strains and the Mockrobiota database. Using unified preprocessing steps, we were able to compare DADA2, Deblur, MED, UNOISE3, UPARSE, DGC (Distance-based Greedy Clustering), AN (Average Neighborhood), and Opticlust objectively.</p><p><strong>Results: </strong>ASV algorithms-led by DADA2- resulted in having a consistent output, yet suffered from over-splitting, while OTU algorithms-led by UPARSE-achieved clusters with lower errors, yet with more over-merging. Notably, UPARSE and DADA2 showed the closest resemblance to the intended microbial community, especially when considering measures for alpha and beta diversity.</p><p><strong>Conclusion: </strong>Our unbiased comparative evaluation examined the performance of eight algorithms dedicated to the analysis of 16S rRNA amplicon sequences with a wide range of mock datasets. Our analysis shed light on the pros and cons of each algorithm and the accuracy of the produced OTUs or ASVs. The utilization of the most complex mock community and the benchmarking comparison presented here offer a framework for the comparison between OTU/ASV algorithms and an objective method for the assessment of new tools and algorithms.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"51"},"PeriodicalIF":6.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143991544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Jellyfish blooms through the microbial lens: temporal changes, cross-species and Jellyfish-water comparisons.","authors":"Noga Barak, Vera Brekhman, Dikla Aharonovich, Tamar Lotan, Daniel Sher","doi":"10.1186/s40793-025-00714-5","DOIUrl":"https://doi.org/10.1186/s40793-025-00714-5","url":null,"abstract":"<p><p>Jellyfish blooms have significant ecological and economic impacts, yet the microbial communities associated with these blooms remain poorly understood, despite their potential influence on host fitness and microbial communities in the surrounding water. In this study, we explored temporal and tissue-specific variations in the microbiota of Rhopilema nomadica, the dominant jellyfish species in the Eastern Mediterranean Sea, across winter and summer blooms. During late summer blooms, microbial richness declined, coinciding with an increase in Endozoicomonas and unclassified Rickettsiales, while Tenacibaculum predominantly characterized winter blooms. Tissue-specific analyses revealed bacterial groups that were more consistently associated with different jellyfish tissues (e.g., Bacteroides in the bell and Simkaniaceae in the gonads), suggesting different microbial niches within the host. Furthermore, some key bacteria associated with R. nomadica, including Endozoicomonas, unclassified Rickettsiales, and Bacteroides were detected in the surrounding bloom water but absent from remote seawater, suggesting potential localized transmission dynamics between jellyfish and their immediate marine environment. Finally, a comparative analysis with nine additional jellyfish species identified recurring microbial taxa, including Endozoicomonas, Mycoplasma, and Spiroplasma, though no universal core microbiota was observed. This study represents the first exploration of microbial dynamics within R. nomadica blooms and the most comprehensive analysis of jellyfish-associated microbiomes across bloom stages and tissues to date. Our findings reveal complex relationships between jellyfish species, bloom progression, their microbial communities, and the surrounding seawater.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"49"},"PeriodicalIF":6.2,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.","authors":"Adrien Vigneron, Lilian A Cloarec, Céline Brochier-Armanet, Jean Pierre Flandrois, Marc Troussellier, Cécile Bernard, Hélène Agogué, Philippe M Oger, Mylène Hugoni","doi":"10.1186/s40793-025-00699-1","DOIUrl":"https://doi.org/10.1186/s40793-025-00699-1","url":null,"abstract":"<p><strong>Background: </strong>Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.</p><p><strong>Results: </strong>Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.</p><p><strong>Conclusions: </strong>Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"48"},"PeriodicalIF":6.2,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.","authors":"Josephine Herbert, Stanley Thompson, Angela H Beckett, Samuel C Robson","doi":"10.1186/s40793-025-00704-7","DOIUrl":"https://doi.org/10.1186/s40793-025-00704-7","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Introduction: &lt;/strong&gt;Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Aim and methods: &lt;/strong&gt;Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~ 97% accuracy) LSK109 chemistry, and newer more accurate (~ 99% accuracy) LSK112 Q20 + chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20 + nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive ","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"47"},"PeriodicalIF":6.2,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibiotic type and dose variably affect microbiomes of a disease-resistant Acropora cervicornis genotype.","authors":"Sunni Patton, Denise P Silva, Eddie Fuques, Grace Klinges, Erinn M Muller, Rebecca L Vega Thurber","doi":"10.1186/s40793-025-00709-2","DOIUrl":"https://doi.org/10.1186/s40793-025-00709-2","url":null,"abstract":"<p><strong>Background: </strong>As coral diseases become more prevalent and frequent, the need for new intervention strategies also increases to counteract the rapid spread of disease. Recent advances in coral disease mitigation have resulted in increased use of antibiotics on reefs, as their application may halt disease lesion progression. Although efficacious, consequences of deliberate microbiome manipulation resulting from antibiotic administration are less well-understood- especially in non-diseased corals that appear visually healthy. Therefore, to understand how apparently healthy corals are affected by antibiotics, we investigated how three individual antibiotics, and a mixture of the three, impact the microbiome structure and diversity of a disease-resistant Caribbean staghorn coral (Acropora cervicornis) genotype. Over a 96-hour, aquarium-based antibiotic exposure experiment, we collected and processed coral tissue and water samples for 16S rRNA gene analysis.</p><p><strong>Results: </strong>We found that antibiotic type and dose distinctively impact microbiome alpha diversity, beta diversity, and community composition. In experimental controls, microbiome composition was dominated by an unclassified bacterial taxon from the order Campylobacterales, while each antibiotic treatment significantly reduced the relative abundance of this taxon. Those taxa that persisted following antibiotic treatment largely differed by antibiotic type and dose, thereby indicating that antibiotic treatment may result in varying potential for opportunist establishment.</p><p><strong>Conclusion: </strong>Together, these data suggest that antibiotics induce microbiome dysbiosis- hallmarked by the loss of a dominant bacterium and the increase in taxa associated with coral stress responses. Understanding the off-target consequences of antibiotic administration is critical not only for informed, long-term coral restoration practices, but also for highlighting the importance of responsible antibiotic dissemination into natural environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"46"},"PeriodicalIF":6.2,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12049008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small-scale heterogeneity of soil properties in farmland affected fava beans growth through rhizosphere differential metabolites and microorganisms.","authors":"Linbin Wang, Yufeng Wu, Zhi-Bo Zhao, Tingsheng Jia","doi":"10.1186/s40793-025-00706-5","DOIUrl":"https://doi.org/10.1186/s40793-025-00706-5","url":null,"abstract":"<p><strong>Background: </strong>Soil heterogeneity has been acknowledged to influence plant growth, with the small-scale soil heterogeneity always being overlooked in practice. It remains unclear how rhizosphere soil biotics and abiotics respond to soil heterogeneity and how rhizosphere interactions influence crop growth.</p><p><strong>Results: </strong>In this study, we planted fava beans in a farmland around an e-waste dismantling site, and a distinct boundary (row spacing is 30 cm) was observed in the field during the flowering stage, which divided fava beans phenotypes into two distinct groups (Big vs Little) based on the differences in biomass and height. Soil total concentrations of As, B, Co, Cr, Cu, Pb, Sr, Zn, Ni, Cd and soil pH significantly differed in the rhizosphere of fava beans in the two adjacent rows, which were located on either side of the boundary, with a row-spacing of 30 cm. Random Forest analysis demonstrated that these differentiated soil properties (soil pH, total As, B, Cd, Co, Cr, Cu, Mo, Ni and Zn) substantially influenced fava beans growth (height and biomass). Metagenomic sequencing showed that microbial taxa were significantly enriched their abundance in rhizosphere soils between the two groups of fava beans, with eukaryotic taxa being more sensitively affected. A total of 20 metabolites including coniferyl alcohol, jasmonic acid, resveratrol, and L-aspartic acid, etc. were significantly correlated with fava beans growth. These metabolites were significantly enriched in 15 metabolic pathways (nucleotide metabolism, pyrimidine metabolism, purine metabolism, biosynthesis of plant secondary metabolites, lysine biosynthesis, etc.). Furthermore, 11 microbial genera involved in these metabolic pathways, and these genera were differentially enriched between the two groups and significantly correlated with fava beans growth.</p><p><strong>Conclusions: </strong>Overall, the integrated analysis of multi-omics revealed that soil properties heterogeneity at small-scale altered the rhizosphere differential microorganisms and metabolites, which functionally influenced fava beans growth and tolerance to environmental stress. Notably, even soil heterogeneity at such a small spatial scale can cause significant differences in plant growth, and the comprehensive explorations utilizing multi-omics techniques provide novel insights to the field management, which is crucial for the survival and sustainable development of humanity.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"45"},"PeriodicalIF":6.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12044778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144064916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A comparative study: impact of chemical and biological fungicides on soil bacterial communities.","authors":"Setu Bazie Tagele, Emma W Gachomo","doi":"10.1186/s40793-025-00713-6","DOIUrl":"https://doi.org/10.1186/s40793-025-00713-6","url":null,"abstract":"<p><p>Soil microbial communities play key roles in agroecosystems, particularly in processes like organic matter decomposition and nutrient cycling. However, human activities can negatively impact their community structure and, consequently, soil function. SoilGard and Ridomil are effective methods for controlling carrot cavity spots caused by Pythium spp., but their effects on bacterial taxonomic and metabolic function shifts are not well understood. This study aims to investigate the comparative impact of the chemical fungicide Ridomil and the biological fungicide SoilGard on the bacterial communities in soils cultivated with carrots. Our results showed that both SoilGard and Ridomil significantly impacted soil bacterial diversity, but their effects were distinct and time-dependent. Ridomil had an immediate negative effect on soil bacterial diversity two weeks after treatment, whereas SoilGard was initially less disruptive but showed delayed negative consequences 12 weeks after treatment, particularly when combined with Pythium inoculation. Ridomil treatment led to an increase in Proteobacteria, especially the Pseudomonas population, as confirmed by both MiSeq and qPCR data. In contrast, SoilGard depleted the Mycobacterium population at 12 weeks after treatment. Furthermore, the results of community-level physiological profiling using Biolog Ecoplates showed significant differences in substrate-level diversity between Ridomil and SoilGard-treated samples, indicating a shift in the metabolic activity of bacterial communities. Ridomil-treated samples showed the lowest metabolic activity of bacterial communities, based on the diversity and richness of carbon source utilization, compared to control. Overall, this research highlights the distinct and time-dependent effects of biological and chemical fungicides on soil bacterial communities when applied at recommended doses.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"44"},"PeriodicalIF":6.2,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Component specific responses of the microbiomes to common chemical stressors in the human food chain.","authors":"Wasimuddin, Aurea Chiaia-Hernandez, Céline Terrettaz, Lisa Thoenen, Veronica Caggìa, Pierre Mateo, Miquel Coll-Crespi, Matheus Notter, Mohana Mukherjee, Teresa Chavez-Capilla, Francesca Ronchi, Stephanie C Ganal-Vonarburg, Martin Grosjean, Moritz Bigalke, Sandra Spielvogel, Andrew Macpherson, Adrien Mestrot, Siegfried Hapfelmeier, Matthias Erb, Klaus Schlaeppi, Alban Ramette","doi":"10.1186/s40793-025-00700-x","DOIUrl":"https://doi.org/10.1186/s40793-025-00700-x","url":null,"abstract":"<p><p>Along a food chain, microbiomes occur in each component and often contribute to the functioning or the health of their host or environment. 'One Health' emphasizes the connectivity of each component's health. Chemical stress typically causes dysbiotic microbiomes, but it remains unclear whether chemical stressors consistently affect the microbiomes of food chain components. Here, we challenged food chain components, including water, sediments, soil, plants, and animals, with three chemical stresses consisting of arsenic (toxic trace element), benzoxazinoids (bioactive plant metabolites), and terbuthylazine (herbicide). We analysed 1064 microbiomes to assess their commonalities and differences in their stress responses. We found that chemical stressors overall decreased microbiome diversity in soil, but not in the other microbiomes. In response to stress, all food chain communities strongly shifted in their composition, generally becoming compositionally more similar to each other. In addition, we observed stochastic effects in host-associated communities (plant, animal). Dysbiotic microbiomes were characterized by different sets of bacteria, which responded specifically to the three chemical stressors. Microbial co-occurrence patterns significantly shifted with either decreased (water, sediment, plant, animal) or increased (soil) network sparsity and numbers of keystone taxa following stress treatments. These results suggest major re-distribution of specific taxa in the overall stress- and component-specific responses of microbiomes with the community stability of plant and animal microbiomes being the most affected by chemical stresses.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"43"},"PeriodicalIF":6.2,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12039292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling plasmid diversity and functionality in pristine groundwater.","authors":"Olga María Pérez-Carrascal, Akbar Adjie Pratama, Matthew B Sullivan, Kirsten Küsel","doi":"10.1186/s40793-025-00703-8","DOIUrl":"https://doi.org/10.1186/s40793-025-00703-8","url":null,"abstract":"<p><strong>Background: </strong>Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).</p><p><strong>Results: </strong>Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.</p><p><strong>Conclusions: </strong>Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"42"},"PeriodicalIF":6.2,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12023590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144046583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}