ISME communications最新文献

{"title":"Bacterial community adaptation after brackish and freshwater coalescence.","authors":"Xiu Jia, Torsten Schubert, Rick Beeloo, Aristeidis Litos, Swapnil Doijad, Pim G van Helvoort, Theodor Sperlea, Matthias Labrenz, Bas E Dutilh","doi":"10.1093/ismeco/ycag198","DOIUrl":"10.1093/ismeco/ycag198","url":null,"abstract":"<p><p>Microbial community coalescence, the merging of entire microbial communities, is common in estuaries, yet the ecological processes governing community assembly after coalescence remain unclear. To uncover these mechanisms, we conducted controlled microcosm experiments simulating coalescence between freshwater and brackish water bacterial communities across five mixing ratios and incubated them in either freshwater or brackish water. We tracked 40 mixed communities over six passages using Nanopore full-length 16S rRNA gene sequencing. Laboratory incubation reduced diversity and increased taxonomic overlap, but preserved habitat-associated compositional signatures. Coalescence outcomes were asymmetric and strongly shaped by the incubation water. In both environments, coalesced communities remained compositionally closer to the native than to the introduced community. However, the relative influence of environmental filtering differed between habitats. In freshwater, strong filtering drove communities to closely resemble the freshwater source, even when the freshwater inoculum was small. In brackish water, weaker filtering made coalescence outcomes more dependent on initial mixing ratios and propagule pressure. Neutral model analyses confirmed a greater contribution of stochastic processes in brackish water. Co-occurrence network analysis revealed predominantly positive associations within the same source community and fewer but negative associations across sources. These within-source associations may reinforce propagule pressure by facilitating the establishment of co-adapted species. Overall, our results demonstrate that environmental filtering primarily governs coalescence outcomes, modulated by source composition, stochasticity, and species co-adaptation, offering new insights into microbial assembly in dynamic estuarine systems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag198"},"PeriodicalIF":6.4,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13452456/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698529","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":"Contrasts in niche breadth and its drivers between soil microbes and plants in alpine grasslands.","authors":"Lei Chen, Ke Dong, Mengchen Zhao, Zhi Yu, Nan Li, Dorsaf Kerfahi, Yu Shi, Xin Jing, Litong Chen, Haiyan Chu, Jinsheng He, Sang-Seob Lee, Teng Yang, Jonathan M Adams","doi":"10.1093/ismeco/ycag193","DOIUrl":"10.1093/ismeco/ycag193","url":null,"abstract":"<p><p>Niche breadth reflects the extent to which taxa or communities can tolerate environmental variations, indicating their potential to respond to environmental changes. However, it remains unclear whether micro- and macro-organisms share similar patterns of niche breadth along the same environmental gradients, and which environmental filters regulates niche breadth across different trophic levels. In this study, 180 soil samples were collected from the northeastern and central Qinghai-Tibet Plateau. By integrating microbiome sequencing with plant community surveys, we quantified niche breadth for bacteria, fungi, and plants within a multidimensional environmental space defined by principal component analysis of environmental variables. We then compared niche breadth among the three groups and identified their primary environmental drivers. The results showed that fungal communities exhibited the broadest niche breadth overall, whereas plant communities displayed the greatest variability in mean niche breadth amongst sites. Elevation was a shared determinant of niche breadth in all groups, although with contrasting response patterns. Bacterial and fungal communities exhibited broader niche breadths at higher elevations, whereas plant communities reached their maximum niche breadths at mid-elevations, suggesting contrasting adaptive strategies. A combination of abiotic (geography and environment) and biotic (community diversity and composition) factors better explained the variation in niche breadth. In particular, compared with the niche breadth of fungal communities, that of bacterial and plant communities was more strongly regulated by biotic factors such as community composition. We further confirmed that abiotic factors influenced the niche breadth of the three biological groups, both directly and indirectly, by shaping their biotic attributes. From the perspective of niche breadth, this study revealed distinct environmental adaptation patterns and the underlying mechanisms of different biological groups in alpine grassland ecosystems. Better understanding of niche breadth patterns amongst different kingdoms of life may provide improved prediction of turnover and resilience of soil ecosystems under environmental change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag193"},"PeriodicalIF":6.4,"publicationDate":"2026-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13529343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148868262","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":"A <i>Wolbachia</i> coinfection in the common bed bug.","authors":"Hillary E Davis, Joseph Torres, Meaghan J Adler, Benjamin J Parker","doi":"10.1093/ismeco/ycag197","DOIUrl":"10.1093/ismeco/ycag197","url":null,"abstract":"<p><p>The common bed bug (<i>Cimex lectularius</i>) relies on an obligate mutualism with the <i>Wolbachia</i> strain <i>w</i>Cle to supplement B vitamins deficient in human blood. Using metatranscriptomic and metagenomic sequencing of hospital-collected bed bugs, we found that some individuals also harbor a second strain of <i>Wolbachia</i> (<i>w</i>Chem). Using publicly available data we showed that <i>w</i>Chem is distributed in bed bugs worldwide at intermediate frequencies and may have moved recently between <i>C. lectularius</i> and <i>Cimex hemipterus</i>, the tropical bed bug, which also feeds on human hosts. We found that <i>w</i>Chem encodes a highly expressed <i>cifA/B</i> operon in males and females, consistent with cytoplasmic incompatibility, a reproductive manipulation strategy used by <i>Wolbachia</i> to increase in frequency in host populations. Together, these results demonstrate that some bed bugs harbor a <i>Wolbachia</i> coinfection of a nutritional mutualist and a potentially manipulative facultative symbiont. This discovery identifies a previously hidden aspect of bed bug biology with significant implications for its evolution, spread, and potential control.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag197"},"PeriodicalIF":6.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455600/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708652","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":"Artificial sediments enable reproducible cultivation and recapitulate ecological interactions of cable bacteria.","authors":"Kartik Aiyer, Yuang Guo, Lea Emilie Plum-Jensen, Theresa Hagen Van, Marta Lidia Sudo, Robin Bonné, Marko Chavez, Mohamed Y El-Naggar, Lars Peter Nielsen, Ian P G Marshall, Andreas Schramm, Joshua T Atkinson","doi":"10.1093/ismeco/ycag199","DOIUrl":"https://doi.org/10.1093/ismeco/ycag199","url":null,"abstract":"","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag199"},"PeriodicalIF":6.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148763131","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":"Geminivirus diversity and community structure at the scale of agro-ecological systems in two localities of Burkina Faso.","authors":"Alassane Ouattara, Sélim Ben Chéhida, Murielle Hoareau, Sohini Claverie, Daniel Houa Otron, Edgar Valentin Traoré, Oumar Traoré, Nicolas Barro, Fidèle Tiendrébéogo, Darren P Martin, Jean-Michel Lett, Pierre Lefeuvre","doi":"10.1093/ismeco/ycag196","DOIUrl":"10.1093/ismeco/ycag196","url":null,"abstract":"<p><p>Circular replication-associated protein encoding single stranded (CRESS) deoxyribonucleic acid (DNA) viruses have emerged to become one of the largest and most devastating groups of crops-infecting viruses in tropical and subtropical regions of the world. In West Africa, renewed outbreaks of disease-like symptoms in the field have prompted surveys that revealed the circulation of multiple CRESS DNA virus species. Recognizing that plant viral diseases may be best understood at the ecosystem scale, we conducted a survey of plant-associated CRESS DNA virus communities in two localities of Burkina Faso (1068 plant samples). CRESS DNA viruses were detected in 41% and 13% of samples from cultivated and uncultivated plants, respectively. Virus community maps constructed from the 30 uncovered species of geminivirus and associated satellites revealed strong modularity. Whereas few co-infections involving viruses belonging to different host-virus modules were observed, evidence of recombination was nevertheless detected between viruses belonging to different modules. This suggests that co-infections between viruses in different modules does at least occasionally occur: possibly as a consequence of seasonal variations in virus-host community structures with the inter-cropping period in particular promoting such \"inter-module\" co-infections.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag196"},"PeriodicalIF":6.4,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13452460/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698509","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":"Fungi without borders: cross-ecosystem decomposition of riparian leaf litter.","authors":"Callie Ochs, Michaela Hayer, Raina Fitzpatrick, Shannon Trottier, Egbert Schwartz, Bruce Hungate, Jane Marks","doi":"10.1093/ismeco/ycag187","DOIUrl":"10.1093/ismeco/ycag187","url":null,"abstract":"<p><p>Fungi are key drivers of leaf litter decomposition in riparian zones, with communities made up of phyllosphere fungi (fungi present on leaves prior to senescence), and fungi that colonize from the environment. While phyllosphere fungi dominate early decomposition in both submerged and terrestrial litter, their contribution to fungal community structure and growth across these environments remains unclear. We used quantitative stable isotope probing to quantify taxon-specific growth rates of phyllosphere fungi and fungi colonizing from the environment, and to differentiate growing fungi from dormant or dead fungi. We quantified the growth rates of phyllosphere and colonizing fungi on two leaf types in aquatic and terrestrial environments over three time points. Growing fungal communities showed substantial overlap between aquatic and terrestrial environments, although this overlap decreased over time. Phyllosphere fungi were more likely to be shared between environments than colonizing fungi. Leaf type exerted a stronger influence on community composition than the environment. Phyllosphere fungi dominated relative abundance and growth during the study, and all fungi grew consistently faster on terrestrial litter. These findings demonstrate the central role of phyllosphere fungi in fungal communities across both aquatic and terrestrial ecosystems, as well as the importance of leaf species.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag187"},"PeriodicalIF":6.4,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13398703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148586179","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":"Thermal responses and Symbiodiniaceae shuffling in a Red Sea foraminifer holobiont.","authors":"Doron Pinko, Chen Kenigsberg, Sivan Levin, Dewi Langlet, Filip Husnik, Maria Holzmann, Uri Abdu, Sigal Abramovich","doi":"10.1093/ismeco/ycag195","DOIUrl":"10.1093/ismeco/ycag195","url":null,"abstract":"<p><p>Symbiont-bearing benthic foraminifera, like corals, rely on endosymbionts for growth and nutrition and experience bleaching under heat stress. <i>Sorites orbiculus</i>, found in tropical and subtropical waters, hosts a diverse range of endosymbionts belonging to Symbiodiniaceae. We examined the thermal tolerance of the Red Sea population, which is the source of an established, invasive population of <i>S. orbiculus</i> in the Eastern Mediterranean. The Red Sea population is expected to exhibit enhanced thermotolerance, potentially due to its greater variety of endosymbionts. We conducted temperature-manipulation experiments, measuring calcification rates and net photosynthesis, evaluating the thermotolerance of <i>S. orbiculus</i> and its endosymbionts. We also analyzed the diversity of Symbiodiniaceae by sequencing the internal transcribed spacer 2 (ITS2). Our results show that exposure to 35°C initially induced stress in the endosymbionts during the first week; however, net photosynthesis gradually recovered in subsequent weeks. In contrast, host calcification rates remained low at 35°C, though not completely inhibited. Amplicon sequencing revealed that by the end of the experiment, a single ITS2 type, belonging to Symbiodiniaceae <i>Clade F2</i> and initially present in field-collected specimens, became dominant in cultured individuals. Because this type became dominant across all temperature treatments, the observed shift likely reflects a response to laboratory conditions rather than direct thermal selection. Consequently, although the recovery at 35°C is consistent with acclimatory physiological responses, it does not provide direct evidence for symbiont-specific acclimation. Our findings suggest that holobiont physiological recovery and symbiont shuffling under laboratory conditions may contribute to the resilience of <i>S. orbiculus</i> in warming oceans.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag195"},"PeriodicalIF":6.4,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13452455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698265","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":"Unexpected novel clade III type nitrous oxide-reducing bacteria from incubated lake sediments.","authors":"Siyu Wang, Fei Shui, Yiwen Zhou, Xiao Wang, Yuli Zeng, Yinghao Shan, Jining Li, Liguo Zhang, Kang Song, Fengchang Wu","doi":"10.1093/ismeco/ycag194","DOIUrl":"https://doi.org/10.1093/ismeco/ycag194","url":null,"abstract":"<p><p>Nitrous oxide-reducing bacteria (N₂ORB) play a pivotal role in regulating N₂O emissions in aquatic ecosystems, with clade I and clade II <i>nosZ</i>-harboring microorganisms representing well-recognized contributors to microbial N₂O consumption. Beyond conventional N₂ORB, the recently identified clade III <i>nosZ</i> from soil may represent a previously overlooked potential N₂O sink, yet the distribution and characterization remain largely unexplored in aquatic ecosystems. Here we established microcosm systems using sediments from five lakes and subjected them to warming temperature gradients to investigate the diversity and genomic characteristics of N₂ORB. Hidden Markov model (HMM)-based analyses identified a total of 45 nonredundant <i>nosZ</i> sequences, including 12 affiliated with clade III <i>nosZ</i>. Clade III <i>nosZ</i> accounted for 10.2%-40.6% of total <i>nosZ</i> genes, indicating that clade III <i>nosZ</i>-harboring N₂ORB is widespread and non-negligible. Reconstruction of metagenome-assembled genomes (MAGs) identified four phylogenetically novel clade III <i>nosZ</i>-harboring N₂ORB, with these MAGs showing low average amino acid identity to their closest known reference genomes. These MAGs showed different denitrification gene inventories, with MAG33 lacking identifiable genes for upstream N₂O-producing steps, suggesting a potential non-denitrifying N₂O reducer. They also encoded oxygen-related stress-response genes, suggesting a potential ability to perform N₂O respiration in the presence of oxygen. Unlike canonical clade I/II <i>nosZ</i> clusters, clade III <i>nosZ</i>-harboring MAGs lacked typical accessory genes and instead exhibited distinct neighboring transporter- and cytochrome-related genes. Together, our results provide evidence for the occurrence of clade III <i>nosZ</i>-harboring N₂ORB in non-soil ecosystems and expand current understanding of their genomic traits.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag194"},"PeriodicalIF":6.4,"publicationDate":"2026-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13477213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148764276","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":"Spatial and depth structuring predominate over temporal variation in Mediterranean climate grassland soil viral communities.","authors":"Jane D Fudyma, Petar Penev, Katerina Estera-Molina, Jordan Hoff, Steven J Blazewicz, Jennifer Pett-Ridge, Joanne B Emerson","doi":"10.1093/ismeco/ycag189","DOIUrl":"10.1093/ismeco/ycag189","url":null,"abstract":"<p><p>Viruses have the potential to influence microbial community structure and elemental cycling in soils, but it remains unclear how these communities are distributed across space and time, which can shape how they respond to environmental change and impact ecosystem processes. Mediterranean climate ecosystems, with their pronounced seasonal moisture fluctuations, offer an ideal system to examine viral biogeography. While previous studies hint at spatial structuring and moisture controls on viral communities, temporal responses to seasonal moisture shifts have not been comprehensively investigated in situ. Here, we generated 59 viromes and leveraged 89 metagenomes from two Mediterranean climate annual grasslands to measure double-stranded DNA soil viral communities across horizontal space (sampling zone), depth, and key seasonal stages of the Mediterranean water year (e.g. plant productivity, dry down, and wetup). Sampling zone was the dominant driver of viral community composition in viromes, with time secondarily explaining variation in viral communities. In contrast, viral richness and DNA yields varied primarily across time. Spatial structuring also emerged in viruses recovered from metagenomes, with depth having the strongest effect, followed by sampling zone. Environmental variables and predicted host distributions partially explained these patterns, but substantial variation remained unaccounted for, suggesting that dispersal limitation, though not directly tested in this study, could potentially underlie these patterns. Overall, double-stranded DNA soil viral communities were primarily structured by spatial factors, with temporal and environmental influences acting secondarily, highlighting the importance of fine-scale spatial dynamics in understanding viral ecology. Future studies should explicitly examine the role of dispersal limitation and fine-scale host-environment interactions to fully resolve drivers of soil viral biogeography.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag189"},"PeriodicalIF":6.4,"publicationDate":"2026-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13494778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148802497","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: Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat.","authors":"","doi":"10.1093/ismeco/ycaf111","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf111","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycaf009.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycaf111"},"PeriodicalIF":6.4,"publicationDate":"2026-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13331343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148392627","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}