ISME communications最新文献

{"title":"Host habitat shapes the gut microbiomes of insular reptilian hosts in the Philippines.","authors":"Sierra N Smith, Jason B Fernandez, Cameron D Siler","doi":"10.1093/ismeco/ycaf141","DOIUrl":"10.1093/ismeco/ycaf141","url":null,"abstract":"<p><p>Islands have long served as ideal, replicative \"natural laboratories\" to help identify the mechanisms that shape the diversity and distribution of plant and animal communities, and a burgeoning body of literature has utilized island-like systems to better understand the processes that shape microbial community diversity. Despite this expanded application, few studies have explored patterns of microbial diversity spanning true islands, especially among communities of microorganisms that colonize vertebrate hosts (i.e. microbiomes). Here, we use 16S ribosomal ribonucleic acid microbial inventories to elucidate the roles that host evolutionary history, host habitat, host microhabitat, and geographic location play in the assemblage of gut microbiomes among reptilian hosts spanning multiple islands in the Philippines. Host habitat and microhabitat explained most of the variation in gut microbiome diversity observed among our focal hosts. Although we identified some significant differences in microbiome diversity across two of the host suborders (Lacertilia and Serpentes) and some host families, we did not find evidence of phylogenetic signal. We also conducted analyses of microbiome diversity across various geographic scales, and found that hosts inhabiting the same island, but different localities, did not possess significantly different gut microbiomes. However, the gut microbial diversity of hosts inhabiting distinct islands were significantly different across numerous measures of microbiome diversity. Results from this robust, comparative study contribute to our growing knowledge of the host-associated and geographic mechanisms that shape the vertebrate gut microbiome and represents one of the first studies to characterize variation in gut microbial communities among vertebrate hosts inhabiting multiple Philippine islands.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf141"},"PeriodicalIF":6.1,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139313","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":"Correction to: Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses.","authors":"","doi":"10.1093/ismeco/ycaf135","DOIUrl":"10.1093/ismeco/ycaf135","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycad017.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf135"},"PeriodicalIF":6.1,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12406690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002103","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":"Genomic recovery from rare terrestrial microbes enabled by DNA-based GC-fractionation.","authors":"Paul O Sheridan, Yiyu Meng, Dylan Bodington, David Coutts, Tom A Williams, Cécile Gubry-Rangin","doi":"10.1093/ismeco/ycaf152","DOIUrl":"10.1093/ismeco/ycaf152","url":null,"abstract":"<p><p>Genome reconstruction from metagenomic samples has dramatically increased our understanding of uncultivated lineages of life. However, untargeted metagenomic sequencing is biased towards the more abundant microbes, neglecting less abundant lineages playing important ecological roles, such as the ammonia-oxidising archaea. Here, we demonstrate that separating soil molecular DNA using a bisbenzimide-CsCl guanine-cytosine (GC)-content-based DNA fractionation approach separates microbial DNA along a GC-content gradient. The fractions from both extremes of the GC-content gradient possess different 16S rRNA gene composition than the original unfractionated DNA. The high diversity in the lower GC-content fractions (< 45%) contrasts with the higher DNA abundance in the higher GC-content fractions (50%-70%), highlighting the low GC fractions as an enriched source of rare microbe DNA. Metagenomic sequencing of specific low- and high-GC fractions enabled the reconstruction of 204 taxonomically diverse metagenome-assembled genomes from 31 microbial phyla, with at least 63 of these originating from rare (< 0.1% relative abundance) or very rare (< 0.01% relative abundance) microbial families. Therefore, this approach facilitates genomic assembly of rare taxa in resulting pseudo-communities. Ultimately, this technique enables a semi-targeted metagenomic approach to recover genomes from low-abundance microbes with GC-contents that differ significantly from the environmental microbial community of interest. As mounting evidence suggests that rare microbes drive critical ecosystem functions, this approach will facilitate a deeper understanding of their metabolic potential in the environment.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf152"},"PeriodicalIF":6.1,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12477608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145202197","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":"Fungal communities across a surface water permanence gradient in a non-perennial prairie stream network.","authors":"Charles T Bond, Brett A Nave, Andrielle L Kemajou Tchamba, Emily Stanley, Lydia H Zeglin, Colin R Jackson, Sam Zipper, Ken Aho, Amy J Burgin, Yaqi You, Rob Ramos, Kevin A Kuehn","doi":"10.1093/ismeco/ycaf151","DOIUrl":"10.1093/ismeco/ycaf151","url":null,"abstract":"<p><p>Over half of the world's streams are non-perennial, drying at some point in space and time, but most research on stream-inhabiting fungi comes from perennial (continuously flowing) streams. To improve our understanding of fungal communities in non-perennial streams, we used ITS rDNA metabarcoding to survey fungal communities in three natural substrates (rock surfaces, decaying leaves, and sediments) across a surface water permanence gradient (determined via in-stream sensors) in a non-perennial prairie stream system in Kansas, USA. Fungal community composition varied along a continuum from wooded downstream reaches to increasingly open canopies (with grassy riparian vegetation) further upstream. Independently of position along this continuum, fungal community composition varied with annual surface water permanence. Communities on rock surfaces were the most sensitive to water impermanence, where rock-inhabiting freshwater lichens (<i>Verrucariaceae</i>) were bioindicators of wetter (<i>Verrucaria humida</i>) or drier (<i>V. tallbackaensis</i>) conditions. Position along the stream continuum explained more variation in fungal community composition than surface water permanence, possibly because of increasing network connectivity downstream or distinct fungal assemblages associated with grassy versus woody plants. Known drying-tolerant decomposers were among the dominant taxa (e.g. <i>Alternaria</i> spp. and <i>Tetracladium marchalianum</i>). However, DNA-based studies of stream fungal communities remain challenging due to underrepresentation of aquatic hyphomycetes in reference databases and contributions of terrestrial fungi (some of which may be active in non-perennial streams) to measured diversity. As streamflow intermittency increases globally, this study provides unprecedented intra-watershed coverage of fungal communities and insights into how hydrology and riparian plants influence fungi across different benthic substrates.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf151"},"PeriodicalIF":6.1,"publicationDate":"2025-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145132910","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":"Long-term decline of marine viruses associated with warming and oligotrophication at a NW Mediterranean coastal site.","authors":"Xabier Lopez-Alforja, Elisabet L Sà, Maria V Quiroga, Massimo C Pernice, Clara Cardelús, Vanessa Balagué, Josep M Gasol, Felipe H Coutinho, Ramon Massana, Dolors Vaqué","doi":"10.1093/ismeco/ycaf150","DOIUrl":"10.1093/ismeco/ycaf150","url":null,"abstract":"<p><p>Viruses play key roles in controlling microbial abundance and community composition, nutrient cycling, and productivity in marine systems. Rising ocean temperatures, alongside increasing oligotrophy, are expected to alter the availability of inorganic nutrients and oxygen-key environmental factors that shape microbial community structure and virus-host interactions. While many studies have investigated viral abundances and community structure across spatial gradients, less is known about their long-term temporal variations, which is particularly relevant in the current context of global change. To address this gap, we analyzed two decades of surface water data from the Blanes Bay Microbial Observatory, located at the North-Western Mediterranean, to describe how biotic and abiotic variables influence temporal dynamics of viral abundances and community composition. Statistical tools for time series, including GAMMs, anomaly analysis, and neural networks, allowed us to demonstrate that viral abundance follows strong seasonality and a clear decrease starting midway (ca. 2011) through the sampled period (2005-2022). Fingerprint analysis evidenced that viral community composition was significantly influenced by seasonality and some environmental and biotic factors, with strong differences in viral communities between summer and winter months. Our analyses revealed that over the last 18 years, the abundance of most microbial groups, including viruses and their potential hosts, has declined, coinciding with an increase in seawater temperature and transparency, as well as a notable decrease in nutrient concentrations and phytoplankton biomass. We identified the ongoing shift toward more oligotrophic conditions as a potential driver of the observed decline in viral abundance, particularly in the last decade.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf150"},"PeriodicalIF":6.1,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145132875","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":"Vitamin B₁₂ release through bacteriophage-mediated cell lysis of the marine bacterium <i>Sulfitobacter</i> sp. M39.","authors":"Sabiha Sultana, Stefan Bruns, Armando Pacheco-Valenciana, Maliheh Mehrshad, Heinz Wilkes, Meinhard Simon, Sarahi Garcia, Gerrit Wienhausen","doi":"10.1093/ismeco/ycaf136","DOIUrl":"10.1093/ismeco/ycaf136","url":null,"abstract":"<p><p>Vitamin B₁₂ (B₁₂) is an essential cofactor for vital metabolic processes in both prokaryotes and eukaryotes. <i>De novo</i> B₁₂ biosynthesis is exclusively carried out by a modicum of prokaryotes, although being required by most organisms. Recently, it has been demonstrated that not all B₁₂-prototrophic bacteria voluntarily share this vital cofactor and, therefore, are termed B₁₂-retainers. Consequently, low biosynthesis potential and limited voluntary release lead to a large discrepancy between availability and demand for B₁₂ in the ocean, indicating that release of B₁₂ may be an important control. Hence, in this study, we examined a specific release process, cell lysis after phage infection. We isolated bacteriophages specific for the B₁₂-prototrophic, yet B₁₂-retainer bacterium <i>Sulfitobacter</i> sp. M39. The addition of the bacteriophages to a <i>Sulfitobacter</i> sp. M39 mono-culture led to a significant increase in virus-like particles, reduced bacterial growth, and quantifiable extracellular dissolved B₁₂. When introducing bacteriophages to a co-culture comprising the host bacterium and the B₁₂-auxotrophic diatom <i>Thalassiosira pseudonana</i>, we observed rapid response in the form of microalgal growth. Our results indicate that B₁₂ is released as a result of bacteriophage-mediated cell lysis of <i>Sulfitobacter</i> sp. M39, enabling the growth of <i>T. pseudonana</i> in co-culture and possibly other microbes in nature. Therefore, we propose that bacteriophage-mediated cell lysis is a key mechanism for the release of essential metabolites, including vitamins, and given the estimated bacteriophage infection rates in the ocean, it plays a crucial role in the B-vitamin cycle in the marine environment.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf136"},"PeriodicalIF":6.1,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139338","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":"Prophages in marine <i>Citromicrobium</i>: diversity, activity, and interaction with the host.","authors":"Ruijie Ma, Bu Xu, Xiaowei Chen, Qiang Sun, Yingying Li, Qiang Zheng, Nianzhi Jiao, Rui Zhang","doi":"10.1093/ismeco/ycaf148","DOIUrl":"10.1093/ismeco/ycaf148","url":null,"abstract":"<p><p>Lysogeny was frequently detected in marine ecosystems, while how temperate phage genomes (prophages) impact marine microbial population or individual dynamics remained poorly understood. Using marine <i>Citromicrobium</i> strain collection as a model system, we revealed that 58% (22/38) were lysogens harboring 31 prophages that can be grouped into five novel genera (φA-φE). Prophage-encoded genes constituted 9% of host accessory genome, significantly expanding the microdiversity among citromicrobial clonal strains. Metagenomic abundance correlations indirectly supported the \"Piggyback-the-Winner\" dynamics for φA/φE, evidenced by their sublinear growth pattern with increasing host abundance. Most prophages were capable of spontaneous induction and exhibited high lytic activity when triggered by mitomycin C. Importantly, host-range profiling revealed these prophages deployed a dual \"Kill-the-Relatives\" and \"Colonize-the-Relatives\" strategy, and meanwhile, they protected parental host strains through superinfection immunity and enhanced phage resistance with greater prophage carriage. Sequencing data showed the dominance of Mu-like phages over non-Mu-like partners upon induced from the double lysogens. Our analysis further hinted at a unique Mu-type within-host competitive strategy: selectively targeting genes of co-resident prophages and host hypothetical genes, while avoiding self-damage and host metabolic genes potentially essential for phage lytic growth or progeny release. Collectively, this work establishes prophages as key architects of bacterial adaptation and provides new perspectives for prophage-driven evolution in marine bacterial hosts.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf148"},"PeriodicalIF":6.1,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486242/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214573","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":"Endogenous glycoside hydrolases reveal foraminiferal capacity to degrade terrestrial and marine polysaccharides.","authors":"Manabu W L Tanimura, Yukiko Nagai, Kazumi Matsuoka, Takashi Toyofuku","doi":"10.1093/ismeco/ycaf149","DOIUrl":"10.1093/ismeco/ycaf149","url":null,"abstract":"<p><p>Foraminifera, a major component of sediment biomass, play a critical role in sedimentary food webs. In this study, we identified and characterized endogenous glycoside hydrolases (GHs) in <i>Cymbaloporetta bradyi</i>, demonstrating their capacity to degrade both terrestrial and marine polysaccharides. Through transcriptomic and <i>in silico</i> analyses, prokaryotic, and eukaryotic contamination was minimized, ensuring the identified GHs were of foraminiferal origin. Our results revealed that cellulases, xylanases, chitinases, and mannanases are the most highly expressed GHs, even under nutrient-rich conditions. Pectinases, fucosidases, and laminarinases are also verified being possessed by <i>C. bradyi</i>. The presence of signal peptides in cellulases and cellulosome-related genes suggests an extracellular cellulose-degrading system in <i>C. bradyi</i>. These findings indicate that <i>C. bradyi</i> can metabolize polysaccharides from terrestrial plants and marine algae, reflecting adaptability to diverse sedimentary environments. As foraminifera are consumed by various deposit feeders and predators, the ability to degrade complex polysaccharides observed in <i>C. bradyi</i> may help explain their success in sedimentary environments. Although further studies on other foraminiferal species are necessary, having this metabolic capacity could make foraminifera important contributors to sedimentary food webs and the carbon cycle.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf149"},"PeriodicalIF":6.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145132837","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":"Diversity and ecological potentials of viruses inhabiting in the Kermadec and Diamantina trench sediments.","authors":"Pudi Wang, Xiaotong Peng, Hongmei Jing","doi":"10.1093/ismeco/ycaf147","DOIUrl":"10.1093/ismeco/ycaf147","url":null,"abstract":"<p><p>Viruses are the most abundant biological entities in marine ecosystems, playing an important role in biogeochemical cycling and the regulation of microbial dynamics. However, their assembly driving force, genomic evolution, and potential ecological functions in the hadal trench remain largely unknown. Here, 32 359 viral operational taxonomic units were derived from metagenomes of 40 sediment samples in the Kermadec and Diamantina trenches. High novelty and habitat-specific endemism of viruses based on the protein-sharing network analysis were demonstrated. Their auxiliary metabolic genes were involved in the biogeochemical cycles and compensatory metabolic process of the host inferring from the virus-host linkage prediction. Distinct viral community assembly in the two trenches and among different sampling depths was mainly driven by the stochastic processes, especially dispersal limitation. This was further proved by the low genomic mutation rates at deeper depths with potentially high hydrostatic pressures. These niche-dependent distribution patterns and genomic features together reflected the survival and adaptative strategy of viruses. This study provided new insights into the high diversity, ecological potentials, evolution, and adaptive mechanism of viruses in the deep biosphere.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf147"},"PeriodicalIF":6.1,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145115231","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":"FISH-FACS proteomics: enhanced label-free quantitative proteome analysis from low cell numbers of uncultured environmental microorganisms.","authors":"Vaikhari Kale, Ga Yan Grace Ho, Sandra Maaß, Anke Trautwein-Schult, Daniel Bartosik, Thomas Schweder, Bernhard M Fuchs, Dörte Becher","doi":"10.1093/ismeco/ycaf145","DOIUrl":"10.1093/ismeco/ycaf145","url":null,"abstract":"<p><p>Metaproteomics is an essential approach to analyze the <i>in situ</i> metabolic activity of microbes across various environments. In such highly diverse environmental samples, the functionality of specific microorganisms of importance often remains underexplored due to the protein inference problem arising from sequence similarities between organisms. One approach to overcome this challenge is the enrichment of uncultured target organisms. However, this often results in samples with low protein content. In this study, we have developed a workflow that combines fluorescence <i>in situ</i> hybridization (FISH) and fluorescence-activated cell sorting (FACS) with mass spectrometry-based proteomics to analyze proteins from uncultured bacteria directly from environmental samples. We demonstrate that 1 × 10⁵ bacterial cells are sufficient for reliable qualitative protein identifications, while 5 × 10⁵ to 1 × 10⁶ cells allow for both reproducible protein identification and quantification after FISH and FACS. In addition, the use of a clade-specific database enhances data analysis by improving peptide mapping, especially when compared to metaproteomics results.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf145"},"PeriodicalIF":6.1,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145132887","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}