ISME communications最新文献

{"title":"Correction: Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.","authors":"","doi":"10.1093/ismeco/ycag274","DOIUrl":"https://doi.org/10.1093/ismeco/ycag274","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycag081.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag274"},"PeriodicalIF":6.4,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149198195","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":"Substrate complexity and species number jointly shift the balance between competition and facilitation in a chitin-degrading bacterial consortium.","authors":"Moritz Mohrlok, Lauren Alteio, Julia Berger, Ksenia Guseva, Erika Salas, Monika Schmoll, Dave Sirbu, Christina Kaiser","doi":"10.1093/ismeco/ycag272","DOIUrl":"https://doi.org/10.1093/ismeco/ycag272","url":null,"abstract":"<p><p>Biopolymer-degrading microbial communities exhibit complex interactions like division of labor, sharing of public goods, and resource-competition, resulting in intricate social dynamics between their diverse members that shape the functions they perform. How these interactions shift with substrate complexity as species number increases remains largely unresolved, especially as substrate type can fluctuate. Here, we investigated how these factors modulate microbial interactions and community functioning in a synthetic three-species chitin-degrading soil bacterial consortium. All mono-, duo-, and tri-cultures were grown under well-mixed conditions on a labile substrate (N-acetylglucosamine, NAG), a complex polymer (chitin), or a combination of both. We quantified respiration, final biomass, and community structure, chitinase activities, degradation products and cross-feeding responses, and integrated these data with consumer-resource modeling. Substrate complexity altered interaction patterns. On NAG, we frequently observed competitive exclusion; while on chitin less competitive species were still detectable at the end. This suggests a shift from competition toward facilitation. The tri-culture showed significant final biomass increases on NAG, likely related to cross-feeding effects and enhanced polymer degradation and respiration on chitin, indicating multi-species facilitation. Model-experiment discrepancies indicate that competition for primary resources and decomposition product-sharing alone cannot explain the observed community dynamics, suggesting additional metabolic and behavioral interactions. While it remains to be tested whether our findings translate beyond the well-mixed conditions studied here, they show how the balance between positive and negative interactions in this consortium shifts with substrate complexity and species number, shaping community structure and functioning.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag272"},"PeriodicalIF":6.4,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149198216","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":"To cohabit or inoculate? Testing the limits of microbiota transplantation in Manila clams.","authors":"Giovanna Monticelli, Chiara Mascitelli, Giulia Dalla Rovere, Ilaria Bernardini, Nicole Macrì, Maria Elena Martino, Barbara Cardazzo, Maura Benedetti, Alessandro Nardi, Luca Peruzza, Luca Bargelloni, Tomaso Patarnello, Massimo Milan","doi":"10.1093/ismeco/ycag271","DOIUrl":"https://doi.org/10.1093/ismeco/ycag271","url":null,"abstract":"<p><p>Microbiota transplantation has emerged as a powerful tool to investigate host-microbe interactions across a wide range of organisms, yet its applicability and ecological limits in marine bivalves remain poorly understood. Here, we experimentally test whether microbiota associated with chronic environmental contamination can be transferred and persist in adult Manila clams (<i>Ruditapes philippinarum</i>). We compared two water-mediated approaches: (i) inoculation of a donor tissue homogenate into the water and (ii) cohabitation with live donor clams through shared seawater flow. Donors originated from a chronically contaminated site (Porto Marghera, Italy) while recipients were naïve clams (France), never previously exposed. Each approach was performed with and without antibiotic pretreatment to evaluate whether transient microbiota disruption could enhance donor signal acquisition. Using RNA-based 16S rRNA profiling, we tracked both overall community similarity to the donor prokaryotic community and the presence of donor-exclusive amplicon sequence variants (ASVs) through a Transfer Index. Although similarity-based metrics suggested modest convergence, donor-exclusive ASVs were detected at low levels and did not persist, indicating weak establishment rather than stable colonization. Antibiotic pretreatment did not significantly reduce prokaryotic diversity or total bacterial load, nor did it improve transfer efficiency or promote convergence toward the donor prokaryotic community. Finally, predicted functional profiles further revealed that pathways associated with xenobiotic metabolism in donor clams were not transmitted under short-term experimental conditions. Together, our results demonstrate that prokaryotic community transplantation in adult bivalves is experimentally achievable but results in limited and transient donor community establishment, providing new insight into the host- and environment-driven ecological constraints governing this process.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag271"},"PeriodicalIF":6.4,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13653611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149169296","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":"Salinity and diatom host community jointly shape chytrid parasite diversity along a natural salinity gradient.","authors":"Jonna Kangas, Simon Bilik, Lumi Haraguchi, Kaisa Kraft, Maliheh Mehrshad, Conny Sjöqvist, Silke Van den Wyngaert","doi":"10.1093/ismeco/ycag269","DOIUrl":"https://doi.org/10.1093/ismeco/ycag269","url":null,"abstract":"<p><p>Parasitic fungi of the phylum Chytridiomycota are known parasites of phytoplankton, yet little is known about drivers of their diversity and host interaction dynamics in marine and brackish habitats. This study investigates the diversity and distribution patterns of phytoplankton-chytrid associations during a phytoplankton spring bloom along a natural salinity gradient of the Baltic Sea at a bi-weekly temporal resolution. Direct linking of chytrids to their host species using single-cell picking and sequencing (SCPS), combined with community composition analyses using amplicon sequencing and quantitative imaging flow cytometry, enabled a high-resolution profiling of spatiotemporal patterns of host-chytrid interactions and infection dynamics along the salinity gradient. This showed an increase in the relative abundance of parasitic chytrids coupled with the increase in phytoplankton biomass towards the end of the spring bloom. Moreover, SCPS revealed 5 novel chytrid-phytoplankton associations and aligning their sequences with spatiotemporal amplicon sequencing data showed a greater diversity and relative abundance of parasitic chytrids below a salinity of 8. Above this threshold, chytrid diversity and abundance declined considerably, coinciding with host community turnover and a shift towards marine non-fungal parasites. These results indicate that salinity structures chytrid communities primarily through its effects on host composition and parasite competition rather than through direct physiological limitation alone. Our findings leverage a combination of methods to provide novel insights at single-cell resolution on drivers of parasitic chytrids associated with phytoplankton blooms. Covering a spatial salinity gradient and temporal dynamics, our data highlights the role of phytoplankton blooms in shaping fungal communities.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag269"},"PeriodicalIF":6.4,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13653609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171670","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":"Urban effluents override drying legacy in stream biofilm bacterial communities.","authors":"Javier Ortiz-Rivero, Paula Siñeriz, Sergi Sabater, Anna Freixa","doi":"10.1093/ismeco/ycag270","DOIUrl":"https://doi.org/10.1093/ismeco/ycag270","url":null,"abstract":"<p><p>Bacterial communities in stream biofilms play a fundamental role in the ecological functioning of fluvial ecosystems, contributing to nutrient cycling, organic matter decomposition, and primary production, while also serving as indicators of ecosystem health. In Mediterranean streams, these communities are increasingly exposed to multiple sequential stressors of varying intensity, such as drying and chemical pollution, yet their combined effects remain poorly understood. Here, we conducted a field experiment in four streams by colonizing artificial substrates, which were subsequently subjected to contrasting drying regimes (intermittent vs. continuous) and later translocated to reaches receiving urban effluents. Bacterial communities were characterized using high-throughput sequencing of the 16S rRNA gene. Both stressors significantly modified community diversity and composition, with consistent responses across streams. Continuous drying acted as a strong environmental filter, reducing diversity and favoring stress-tolerant taxa such as Bacilli and Actinobacteria while decreasing the relative abundance of Cyanobacteria. In contrast, effluent exposure promoted community homogenization and recolonization by effluent-derived taxa, largely dominated by Cyanobacteria and Gammaproteobacteria. Across both intermittent and continuous regimes, sequential exposure to drying followed by urban effluents further shaped bacterial communities. However, legacy effects of drying were generally weak and largely overridden by effluent inputs. Although some early-colonizing, stress-tolerant taxa persisted, community reorganization was mainly driven by effluent-derived colonization and local environmental conditions. Overall, these results show that the sequence and intensity of disturbances, together with initial community composition, regulate microbial resilience and community reorganization, with clear implications for the functioning of river ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag270"},"PeriodicalIF":6.4,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13653610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149171386","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":"Bacteriophages in Antarctic subglacial lakes reveal novel biodiversity and biogeochemical potential.","authors":"David M Robinson, Wei Li, Mya Breitbart, Cristina Takacs-Vesbach, John C Priscu","doi":"10.1093/ismeco/ycag252","DOIUrl":"10.1093/ismeco/ycag252","url":null,"abstract":"<p><p>Of the more than 600 subglacial lakes identified in Antarctica thus far, Whillans Subglacial Lake and Mercer Subglacial Lake are the only lakes to have been directly and cleanly sampled. Although hydrologically isolated from direct marine contact for approximately 6.3 ± 1.0 ka, both lakes periodically discharge into the Ross Ice Shelf marine cavity. We present the first direct characterization of bacteriophages in Antarctic subglacial lakes, combining microscopy, metagenomics, and gene-sharing network analyses with bacteriophages found in the Ross Ice shelf marine cavity. The data reveal that bacteriophages are less abundant than their microbial hosts, with virus to prokaryote ratios below those of typical oligotrophic environments. Eight hundred sixty-one double-stranded DNA viral contigs were recovered forming 66 distinct viral clusters; only 18.4% could be identified at ≥85% sequence similarity in the IMG/VR database, showing high genetic novelty. The data showed 114 putative auxiliary metabolic genes involved in nutrient cycling and DNA methylation, and we predicted hosts spanning 13 prokaryotic classes. Several genetic clusters were shared with Antarctic subglacial lakes and Ross Ice Shelf cavity, indicating ecological connectivity that may extend the influence of subglacial phages to carbon and nutrient cycling in downstream Antarctic coastal ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag252"},"PeriodicalIF":6.4,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13615525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066114","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":"Genome-resolved metagenomics reveals rare taxa and functional traits in two contrasting agricultural fields.","authors":"Ioanna Chatzigiannidou, Tanvi Taparia, Pi Lærke Johansen, Lelde Berzina, Joseph Nesme, Morten Petersen, Søren J Sørensen, Susanne Brix, Karsten Kristiansen","doi":"10.1093/ismeco/ycag268","DOIUrl":"https://doi.org/10.1093/ismeco/ycag268","url":null,"abstract":"<p><p>Agricultural soils harbor highly diverse and functionally rich microbial communities, yet much of their genomic potential remains unexplored. Here, we present a genome-resolved metagenomic analysis of 455 soil samples collected at different depths and seasonal stages across two Danish agricultural fields representing sandy and clay soil types. Ultra-deep shotgun sequencing enabled the recovery of 58 831 medium to high-quality prokaryotic metagenome-assembled genomes (MAGs), which were dereplicated into 56 340 strain-level MAGs and 9090 species-level genome bins (SGBs) spanning 49 prokaryotic phyla. The majority of the SGBs represented previously uncharacterized species. Functional annotation revealed extensive biosynthetic and metabolic potential, including 46 913 biosynthetic gene clusters and prevalent genes linked to nitrogen cycling. Notably, 378 MAGs harbored the nitrous oxide reductase gene <i>nosZ</i>. Soil type and depth strongly influenced microbial diversity and functional traits. These findings provide a resource for linking microbial traits to soil function of potential value for better sustainable agricultural practice.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag268"},"PeriodicalIF":6.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13653607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149172152","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":"Associations among soil microbial and plant richness across global terrestrial biomes.","authors":"Samuel Bickel, Ahmed Abdelfattah, Ayco J M Tack, Wisnu Adi Wicaksono, Gabriele Berg","doi":"10.1093/ismeco/ycag266","DOIUrl":"https://doi.org/10.1093/ismeco/ycag266","url":null,"abstract":"<p><p>Soil microbiomes play a crucial role in terrestrial ecosystems by influencing plant diversity and ecosystem functions, yet global patterns linking soil microbial and plant species richness remain unclear. Here we employed machine learning models integrating environmental variables to map global richness patterns of plants, bacteria, and fungi across terrestrial biomes and examined their associations. We found distinct biogeographical distributions and high diversity regions: plant richness peaked in tropical forests, soil bacterial richness was highest toward arid and transitional zones, and soil fungal richness was prominent in tundra and boreal forests. Notably, plant richness correlated positively with microbial richness and strongly with fungal endophyte richness, supporting the concept that diversity fosters further diversity. These findings reveal complex cross-kingdom interactions shaping terrestrial biodiversity and underscore the importance of integrated conservation strategies that consider multiple organismal groups and their environmental drivers.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag266"},"PeriodicalIF":6.4,"publicationDate":"2026-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637820/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119346","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: Behavioural phase transitions in the migratory locust, <i>Locusta migratoria</i>, are related to changes in the gut bacterial composition.","authors":"","doi":"10.1093/ismeco/ycag235","DOIUrl":"https://doi.org/10.1093/ismeco/ycag235","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycag009.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag235"},"PeriodicalIF":6.4,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13583360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992861","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: <i>Penicillium hordei</i> acidification precipitates <i>Bacillus subtilis</i> lipopeptides to evade inhibition.","authors":"","doi":"10.1093/ismeco/ycag234","DOIUrl":"https://doi.org/10.1093/ismeco/ycag234","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycaf172.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag234"},"PeriodicalIF":6.4,"publicationDate":"2026-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13583359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992791","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}