ISME communications最新文献

{"title":"Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes.","authors":"Lijuan Li, Songcan Chen, Ximei Xue, Jieyin Chen, Jian Tian, Lijuan Huo, Tuo Zhang, Xibai Zeng, Shiming Su","doi":"10.1093/ismeco/ycae106","DOIUrl":"10.1093/ismeco/ycae106","url":null,"abstract":"<p><p>Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe-arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher <i>acr3</i> (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher <i>aoxA</i> (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11370035/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues.","authors":"Maryam Mahmoudi, Juliana Almario, Katrina Lutap, Kay Nieselt, Eric Kemen","doi":"10.1093/ismeco/ycae103","DOIUrl":"10.1093/ismeco/ycae103","url":null,"abstract":"<p><p>Leaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here, we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and nonfungal eukaryotic communities colonizing the surface and endosphere of six wild <i>Arabidopsis thaliana</i> populations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Among environmental factors, radiation- and humidity-related factors are the most important drivers of diversity patterns in the leaf, with stronger effects on epiphytic communities. Using linear models, we identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that environmental factors could impact interactions within microbial communities, we analyzed the seasonal patterns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at both micro (leaf compartment) and macro (site) scales. These findings could have practical implications for predicting and developing field-adapted microbes in the face of global change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11333920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses.","authors":"Louis Berrios, Andressa M Venturini, Tillson Bertie Ansell, Esther Tok, William Johnson, Claire E Willing, Kabir G Peay","doi":"10.1093/ismeco/ycae104","DOIUrl":"10.1093/ismeco/ycae104","url":null,"abstract":"<p><p>Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Bacteroidia</i> and <i>Clostridia</i> are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish <i>Kyphosus sydneyanus</i>.","authors":"Cesar T Facimoto, Kendall D Clements, W Lindsey White, Kim M Handley","doi":"10.1093/ismeco/ycae102","DOIUrl":"10.1093/ismeco/ycae102","url":null,"abstract":"<p><p>The gut microbiota of the marine herbivorous fish <i>Kyphosus sydneyanus</i> are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by <i>Bacteroidia</i> and <i>Clostridia</i>. Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer <i>Gammaproteobacteria</i> and <i>Verrucomicrobiae</i>. Results indicate that <i>Bacteroidia</i> utilize substrates in both brown and red algae, whereas other taxa, namely, <i>Clostridia</i>, <i>Bacilli</i>, and <i>Verrucomicrobiae</i>, utilize mainly brown algae. <i>Bacteroidia</i> had the highest CAZyme gene densities overall, and <i>Alistipes</i> were especially enriched in CAZyme gene clusters (<i>n</i> = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the <i>K. sydneyanus</i> gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that <i>Bacteroidia</i> encompass specialized macroalgae degraders.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11333855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"c-di-GMP and AHL signals-triggered chemical communication under electrical signaling disruption restores <i>Geobacter sulfurreducens</i> biofilm formation.","authors":"Qian Zhu, Yanyan Zheng, Xingwang Zhou, Dunjia Wang, Mengjiao Yuan, Dingkang Qian, Sha Liang, Wenbo Yu, Jiakuan Yang, Huijie Hou, Jingping Hu","doi":"10.1093/ismeco/ycae096","DOIUrl":"10.1093/ismeco/ycae096","url":null,"abstract":"<p><p>Electrogenic biofilms, which have attracted considerable attention in simultaneous wastewater treatment and energy recovery in bioelectrochemical systems, are regulated by chemical communication and potassium channel-mediated electrical signaling. However, how these two communication pathways interact with each other has not been thoroughly investigated. This study first explored the roles of chemical communication, including intracellular bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) and extracellular N-acyl-homoserine lactone (AHL)-mediated quorum sensing, in electrogenic biofilm formation through an integrated analysis of transcriptomics and metabolomics. Electrical signaling disruption inhibited the formation and electroactivity of <i>Geobacter sulfurreducens</i> biofilm, which was mainly ascribed to the reduction in biofilm viability and extracellular protein/polysaccharide ratio. The upregulation of expression levels of genes encoding c-di-GMP and AHL synthesis by transcriptomic analysis, and the increased secretion of N-butanoyl-L-homoserine lactone by metabolomic analysis confirmed the enhancement of chemical communication under electrical signaling disruption, thus indicating a compensatory mechanism among different signaling pathways. Furthermore, protein-protein interaction network showed the convergence of different signaling pathways, with c-di-GMP-related genes acting as central bridges. This study highlights the interaction of different signaling pathways, especially the resilience of c-di-GMP signaling to adverse external stresses, thereby laying the foundation for facilitating electrogenic biofilm formation under adverse conditions in practical applications.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11283642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141790218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite <i>Coptotermes formosanus</i>.","authors":"Masayuki Kaneko, Tatsuki Omori, Katsura Igai, Takako Mabuchi, Miho Sakai-Tazawa, Arisa Nishihara, Kumiko Kihara, Tsuyoshi Yoshimura, Moriya Ohkuma, Yuichi Hongoh","doi":"10.1093/ismeco/ycae097","DOIUrl":"10.1093/ismeco/ycae097","url":null,"abstract":"<p><p>Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts' fermentative metabolism by consuming excess H₂. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the <i>Cononympha</i> protists in the hindgut of the termite <i>Coptotermes formosanus</i>. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here \"<i>Candidatus</i> Methanobrevibacter cononymphae\", is associated with both <i>Cononympha leidyi</i> and <i>Cononympha koidzumii</i> and that its infection rate in <i>Cononympha</i> cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both <i>Cononympha</i> species and also on the gut wall. Thus, \"<i>Ca.</i> Methanobrevibacter cononymphae\" is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a <i>Cononympha</i> cell. The genome of \"<i>Ca</i>. Methanobrevibacter cononymphae\" showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene <i>fdhA</i>, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Arctic Seawater and Coastal Soil Microbiome Co-occurrence and Composition Structure and Their Potential Hydrocarbon Biodegradation","authors":"Nastasia J. Freyria, Esteban Góngora, Charles W Greer, L. Whyte","doi":"10.1093/ismeco/ycae100","DOIUrl":"https://doi.org/10.1093/ismeco/ycae100","url":null,"abstract":"\u0000 The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal community possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbon under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141640467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Air monitoring by nanopore sequencing.","authors":"Tim Reska, Sofya Pozdniakova, Sílvia Borràs, Albert Perlas, Ela Sauerborn, Lídia Cañas, Michael Schloter, Xavier Rodó, Yuanyuan Wang, Barbro Winkler, Jörg-Peter Schnitzler, Lara Urban","doi":"10.1093/ismeco/ycae099","DOIUrl":"10.1093/ismeco/ycae099","url":null,"abstract":"<p><p>While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome's composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city's boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287864/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recovering sedimentary ancient DNA of harmful dinoflagellates accumulated over the last 9000 years off Eastern Tasmania, Australia.","authors":"Linda Armbrecht, Christopher J S Bolch, Bradley Paine, Alan Cooper, Andrew McMinn, Craig Woodward, Gustaaf Hallegraeff","doi":"10.1093/ismeco/ycae098","DOIUrl":"10.1093/ismeco/ycae098","url":null,"abstract":"<p><p>Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (<i>sed</i>aDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array (\"HABbaits1\") to target three harmful dinoflagellate genera, <i>Alexandrium</i>, <i>Gymnodinium</i>, and <i>Noctiluca</i>. Bioinformatic and DNA damage analyses verified the authenticity of the <i>sed</i>aDNA sequences. Our results show that dinoflagellates of <i>Alexandrium</i> genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of <i>Gymnodinium catenatum</i> that were present offshore up to ~7600 years ago. We also recovered <i>sed</i>aDNA of the fragile, soft-bodied <i>Noctiluca scintillans</i> with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of <i>sed</i>aDNA sequence validation (in particular for <i>G. catenatum</i>, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"scMicrobe PTA: near complete genomes from single bacterial cells.","authors":"Robert M Bowers, Veronica Gonzalez-Pena, Kartika Wardhani, Danielle Goudeau, Matthew James Blow, Daniel Udwary, David Klein, Albert C Vill, Ilana L Brito, Tanja Woyke, Rex R Malmstrom, Charles Gawad","doi":"10.1093/ismeco/ycae085","DOIUrl":"10.1093/ismeco/ycae085","url":null,"abstract":"<p><p>Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11253033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}