Environmental microbiology最新文献

{"title":"Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases","authors":"Kati Mäkelä,&nbsp;Elina Laanto,&nbsp;Lotta-Riina Sundberg","doi":"10.1111/1462-2920.16670","DOIUrl":"10.1111/1462-2920.16670","url":null,"abstract":"<p>The influence of environmental factors on the interactions between phages and bacteria, particularly single-stranded DNA (ssDNA) phages, has been largely unexplored. In this study, we used <i>Finnlakevirus</i> FLiP, the first known ssDNA phage species with a lipid membrane, as our model phage. We examined the infectivity of FLiP with three <i>Flavobacterium</i> host strains, B330, B167 and B114. We discovered that FLiP infection is contingent on the host strain and conditions such as temperature and bacterial growth phase. FLiP can infect its hosts across a wide temperature range, but optimal phage replication varies with each host. We uncovered some unique aspects of phage infectivity: FLiP has limited infectivity in liquid-suspended cells, but it improves when cells are surface-attached. Moreover, FLiP infects stationary phase B167 and B114 cells more rapidly and efficiently than exponentially growing cells, a pattern not observed with the B330 host. We also present the first experimental evidence of endolysin function in ssDNA phages. The activity of FLiP's lytic enzymes was found to be condition-dependent. Our findings underscore the importance of studying phage ecology in contexts that are relevant to the environment, as both the host and the surrounding conditions can significantly alter the outcome of phage–host interactions.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16670","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141476238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to “Xenobiotic estradiol-17ß alters gut microbiota of hatchling American alligators (Alligator mississippiensis)”","authors":"","doi":"10.1111/1462-2920.16667","DOIUrl":"10.1111/1462-2920.16667","url":null,"abstract":"<p>\u0000 <span>Murphy, K.M.</span>, <span>Watkins, M.M.</span>, <span>Finger, J.W.</span>, <span>Kelley, M.D.</span>, <span>Elsey, R.M.</span>, <span>Warner, D.A.</span>, <span>Mendonça, M.T.</span> (<span>2022</span>) <span>Xenobiotic estradiol-17ß alters gut microbiota of hatchling American alligators (<i>Alligator mississippiensis</i>)</span>. <i>Environmental Microbiology</i>, <span>24</span>(<span>12</span>), <span>6336</span>–<span>6347</span>. https://doi.org/10.1111/1462-2920.16222\u0000 </p><p>In Figure 2B, we report no statistical significance between treatment groups (<i>P</i> &gt; 0.05) using a non-metric multidimensional scaling plot (NMDS) followed by an analysis of similarity (ANOSIM). We later state “Bray–Curtis NMDS showed different patterns of clustering of samples across treatment groups (Figure 2B). However, bacterial community structure did not differ between groups (R = 0.026, p = 0.28), suggesting that microbiomes of each treatment group were similar.”</p><p>In the following discussion, we expand on this by stating “One of the most interesting results from our study shows that exposure to a relatively low concentration of E2 increases microbiota absolute abundances but does not influence microbiota diversity. This dose-dependent effect suggests that varying concentrations of E2 may influence microbial community composition, in terms of alpha and beta diversity, in different ways.”</p><p>Upon revisiting these analyses, we discovered that the metadata file used to generate the NMDS plot was out of order; meaning, the samples displayed in the published beta diversity plot are not correctly associated to treatment groups. When this file is in the correct order, we found a different pattern in that the experimental groups do significantly differ from the control group.</p><p>We would like to issue a correction to Figure 2B and to correct our statement in the results section to read “Bray–Curtis NMDS showed different patterns of clustering of samples across treatment groups (Figure 2B). Indeed, bacterial community structure differs between groups (R = 0.208, p = 0.002), suggesting that microbiomes of each treatment group were distinct from one another.” We would also like to correct the statement in the discussion section to read “One of the most interesting results from our study shows that exposure to rising concentrations of E2 increases microbiota abundances but decreases alpha diversity. Additionally, community composition was distinct between treatment groups. This dose-dependent effect suggests that varying concentrations of E2 may influence microbial community composition in different ways.”</p><p>We apologize for this error and even though this result becomes statistically significant after our re-analysis, it has minimal effect on the scientific conclusions of our work.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16667","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141448922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances","authors":"Charlène Lawruk-Desjardins,&nbsp;Veronika Storck,&nbsp;Dominic E. Ponton,&nbsp;Marc Amyot,&nbsp;David A. Walsh","doi":"10.1111/1462-2920.16669","DOIUrl":"10.1111/1462-2920.16669","url":null,"abstract":"<p>Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of <i>hgcAB</i> from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16669","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141445010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems","authors":"Jonathan Parra,&nbsp;Scott A. Jarmusch,&nbsp;Katherine R. Duncan","doi":"10.1111/1462-2920.16635","DOIUrl":"10.1111/1462-2920.16635","url":null,"abstract":"<p>Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus <i>Pseudonocardia</i> and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free-living <i>Pseudonocardia</i> remains understudied. This study applies a multi-omics approach to investigate the chemical ecology of free-living actinomycetes from the genus <i>Pseudonocardia</i>. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry-based metabolomic profiles of nine <i>Pseudonocardia</i> species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix-assisted laser desorption/ionisation-mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free-living <i>Pseudonocardia</i>. Moreover, two features at <i>m</i>/<i>z</i> 441.15 and <i>m</i>/<i>z</i> 332.20 were identified as metabolites related to these interspecies interactions.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16635","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pinpointing the microbiota of tardigrades: What is really there?","authors":"Bartłomiej Surmacz,&nbsp;Daniel Stec,&nbsp;Monika Prus-Frankowska,&nbsp;Mateusz Buczek,&nbsp;Łukasz Michalczyk,&nbsp;Piotr Łukasik","doi":"10.1111/1462-2920.16659","DOIUrl":"10.1111/1462-2920.16659","url":null,"abstract":"<p>Microbiota are considered significant in the biology of tardigrades, yet their diversity and distribution remain largely unexplored. This is partly due to the methodological challenges associated with studying the microbiota of small organisms that inhabit microbe-rich environments. In our study, we characterized the microbiota of 31 species of cultured tardigrades using 16S rRNA amplicon sequencing. We employed various sample preparation strategies and multiple types of controls and estimated the number of microbes in samples using synthetic DNA spike-ins. We also reanalysed data from previous tardigrade microbiome studies. Our findings suggest that the microbial communities of cultured tardigrades are predominantly composed of bacterial genotypes originating from food, medium, or reagents. Despite numerous experiments, we found it challenging to identify strains that were enriched in certain tardigrades, which would have indicated likely symbiotic associations. Putative tardigrade-associated microbes rarely constituted more than 20% of the datasets, although some matched symbionts identified in other studies. We also uncovered serious contamination issues in previous tardigrade microbiome studies, casting doubt on some of their conclusions. We concluded that tardigrades are not universally dependent on specialized microbes. Our work underscores the need for rigorous safeguards in studies of the microbiota of microscopic organisms and serves as a cautionary tale for studies involving samples with low microbiome abundance.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch","authors":"Brittan S. Scales,&nbsp;Christiane Hassenrück,&nbsp;Lynn Moldaenke,&nbsp;Julia Hassa,&nbsp;Christian Rückert-Reed,&nbsp;Christoph Rummel,&nbsp;Corinna Völkner,&nbsp;Robby Rynek,&nbsp;Tobias Busche,&nbsp;Jörn Kalinowski,&nbsp;Annika Jahnke,&nbsp;Mechthild Schmitt-Jansen,&nbsp;Katrin Wendt-Potthoff,&nbsp;Sonja Oberbeckmann","doi":"10.1111/1462-2920.16639","DOIUrl":"10.1111/1462-2920.16639","url":null,"abstract":"<p>The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet-exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the <i>Rhodobacteraceae</i> family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta-carotene and beta-cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria-produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16639","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From ubiquity to specificity: The diverse functions of bacterial thioredoxin systems","authors":"Cyril Anjou,&nbsp;Aurélie Lotoux,&nbsp;Claire Morvan,&nbsp;Isabelle Martin-Verstraete","doi":"10.1111/1462-2920.16668","DOIUrl":"10.1111/1462-2920.16668","url":null,"abstract":"<p>The thioredoxin (Trx) system, found universally, is responsible for the regeneration of reversibly oxidized protein thiols in living cells. This system is made up of a Trx and a Trx reductase, and it plays a central role in maintaining thiol-based redox homeostasis by reducing oxidized protein thiols, such as disulfide bonds in proteins. Some Trxs also possess a chaperone function that is independent of thiol-disulfide exchange, in addition to their thiol-disulfide reductase activity. These two activities of the Trx system are involved in numerous physiological processes in bacteria. This review describes the diverse physiological roles of the Trx system that have emerged throughout bacterial evolution. The Trx system is essential for responding to oxidative and nitrosative stress. Beyond this primary function, the Trx system also participates in redox regulation and signal transduction, and in controlling metabolism, motility, biofilm formation, and virulence. This range of functions has evolved alongside the diversity of bacterial lifestyles and their specific constraints. This evolution can be characterized by the multiplication of the systems and by the specialization of cofactors or targets to adapt to the constraints of atypical lifestyles, such as photosynthesis, insect endosymbiosis, or spore-forming bacteria.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16668","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative proteomics reveals the Sox system's role in sulphur and arsenic metabolism of phototroph Halorhodospira halophila","authors":"Giulia D'Ermo,&nbsp;Stéphane Audebert,&nbsp;Luc Camoin,&nbsp;Britta Planer-Friedrich,&nbsp;Corinne Casiot-Marouani,&nbsp;Sophie Delpoux,&nbsp;Régine Lebrun,&nbsp;Marianne Guiral,&nbsp;Barbara Schoepp-Cothenet","doi":"10.1111/1462-2920.16655","DOIUrl":"10.1111/1462-2920.16655","url":null,"abstract":"<p>The metabolic process of purple sulphur bacteria's anoxygenic photosynthesis has been primarily studied in <i>Allochromatium vinosum</i>, a member of the <i>Chromatiaceae</i> family. However, the metabolic processes of purple sulphur bacteria from the <i>Ectothiorhodospiraceae</i> and <i>Halorhodospiraceae</i> families remain unexplored. We have analysed the proteome of <i>Halorhodospira halophila</i>, a member of the <i>Halorhodospiraceae</i> family, which was cultivated with various sulphur compounds. This analysis allowed us to reconstruct the first comprehensive sulphur-oxidative photosynthetic network for this family. Some members of the <i>Ectothiorhodospiraceae</i> family have been shown to use arsenite as a photosynthetic electron donor. Therefore, we analysed the proteome response of <i>Halorhodospira halophila</i> when grown under arsenite and sulphide conditions. Our analyses using ion chromatography-inductively coupled plasma mass spectrometry showed that thioarsenates are chemically formed under these conditions. However, they are more extensively generated and converted in the presence of bacteria, suggesting a biological process. Our quantitative proteomics revealed that the SoxAXYZB system, typically dedicated to thiosulphate oxidation, is overproduced under these growth conditions. Additionally, two electron carriers, cytochrome <i>c</i>₅₅₁/<i>c</i>₅ and HiPIP III, are also overproduced. Electron paramagnetic resonance spectroscopy suggested that these transporters participate in the reduction of the photosynthetic Reaction Centre. These results support the idea of a chemically and biologically formed thioarsenate being oxidized by the Sox system, with cytochrome <i>c</i>₅₅₁/<i>c</i>₅ and HiPIP III directing electrons towards the Reaction Centre.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16655","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141426561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation","authors":"Marie Le Geay,&nbsp;Kyle Mayers,&nbsp;Martin Küttim,&nbsp;Béatrice Lauga,&nbsp;Vincent E. J. Jassey","doi":"10.1111/1462-2920.16666","DOIUrl":"10.1111/1462-2920.16666","url":null,"abstract":"<p>Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16666","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141418414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes","authors":"Manan Shah,&nbsp;Till L. V. Bornemann,&nbsp;Julia K. Nuy,&nbsp;Martin W. Hahn,&nbsp;Alexander J. Probst,&nbsp;Daniela Beisser,&nbsp;Jens Boenigk","doi":"10.1111/1462-2920.16634","DOIUrl":"10.1111/1462-2920.16634","url":null,"abstract":"<p>Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows for proliferation. Genome streamlining is associated with genomic properties such as %GC content, genes encoding sigma factors, percent coding regions, gene redundancy, and functional shifts in processes like cell motility and ATP binding cassette transporters, among others. The current study aims to unveil the impact of nutrition on the genome size, %GC content, and functional properties of pelagic freshwater bacteria. We do this at finer taxonomic resolutions for many metagenomically characterized communities. Our study confirms the interplay of trophic level and genomic properties. It also highlights that different nutrient types, particularly phosphorus and nitrogen, impact these properties differently. We observed a covariation of functional traits with genome size. Larger genomes exhibit enriched pathways for motility, environmental interaction, and regulatory genes. ABC transporter genes reflect the availability of nutrients in the environment, with small genomes presumably relying more on metabolites from other organisms. We also discuss the distinct strategies different phyla adopt to adapt to oligotrophic environments. The findings contribute to our understanding of genomic adaptations within complex microbial communities.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16634","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}