ISME communications最新文献

{"title":"Indole-3-acetic acid-mediated self-rescue in <i>Bacillus licheniformis</i> against <i>Saccharomyces cerevisiae</i> stress.","authors":"Lei Xu, Chen Ling, Yun Wang, Jiangnan Han, Shihao Liu, Shibo Ban, Qun Wu","doi":"10.1093/ismeco/ycag064","DOIUrl":"https://doi.org/10.1093/ismeco/ycag064","url":null,"abstract":"<p><p>Microorganisms have evolved complex metabolic adaptations to environmental stresses in intricate microbial communities. However, the adaptive strategies of bacteria against the competitive stress from fungi are still poorly understood. Here, we reported an adaptive strategy adopted by <i>Bacillus licheniformis</i> in response to <i>Saccharomyces cerevisiae</i> stress. The growth of <i>B. licheniformis</i> in the presence of <i>S. cerevisiae</i> was reduced at 24 h, followed by a complete recovery after 48 h, coupled with a full-process reduction in biofilm formation. Meantime, genes involved in carbohydrate metabolism were significantly upregulated, and those involved in biofilm formation were significantly downregulated in <i>B. licheniformis</i> at 24 h. When <i>B. licheniformis</i> was cultured in <i>S. cerevisiae</i> conditioned medium, differentially upregulated metabolites after 24 h of incubation were primarily enriched in tryptophan metabolism pathway, with significant accumulation of indole-3-acetic acid (IAA) and its precursors. Supplementation with IAA suppressed biofilm formation in a concentration-dependent manner and promoted biomass recovery at later fermentation stages, as well as upregulation of genes involved in carbohydrate metabolism and downregulation of genes involved in biofilm formation at 24 h. This study revealed that IAA acted as a bacterial signaling molecule via reducing biofilm formation to promote the growth recovery against the stress from fungi.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag064"},"PeriodicalIF":6.1,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13098187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791066","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: Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms.","authors":"","doi":"10.1093/ismeco/ycaf236","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf236","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycaf171.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycaf236"},"PeriodicalIF":6.1,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12998217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147488763","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":"Environmental quality affects the formation of generalist and specialist taxa in microbial communities.","authors":"Guo Yang, Feng Wen, Dianfu Wang, Didi Zhao, Qin Liu, Min Ren, Jinshui Zheng, Ruili Zhang, Zhanfeng Xia, Jing Zhang, Lili Zhang, Chuanxing Wan, Xiaoxia Luo","doi":"10.1093/ismeco/ycag057","DOIUrl":"https://doi.org/10.1093/ismeco/ycag057","url":null,"abstract":"<p><p>Microorganisms play a central role in global biogeochemical cycles, and generalists and specialists differ significantly in environmental adaptability, ecological functions, and community stability. However, current studies on generalists and specialists have mainly focused on habitat type or resource availability, while how habitat quality affects their geographic distribution and succession processes remains unclear. This study investigates how habitat quality influences the geographical distribution and community assembly of generalists and specialists. Using the Remote Sensing Ecological Index (RSEI), we assessed soil ecological quality in the Tarim River Basin and categorized the habitats into low-quality (extreme poor), moderate-quality (moderate poor), and high-quality (relatively good) zones. We analyzed the geographical patterns of generalists/specialists and their community assembly processes as habitat quality declined. Results indicated significant differences in microbial community composition (β-diversity, Bray-Curtis distance) between generalist and specialist groups across habitats. As RSEI decreased, the relative abundance of specialist microorganisms increased, while generalist microorganisms decreased. Microbial community assembly was shaped by both stochastic and deterministic processes, with stochastic processes accounting for >75%. Deterministic processes have a greater impact on specialists than generalists. This study provides insights into how environmental changes affect microbial ecosystems and their dynamics.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag057"},"PeriodicalIF":6.1,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13037473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147596642","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":"An enhanced domestication method for uncultured bacteria.","authors":"Andrew G Morrison, Raphaella Jackson, Paul S Freemont, Harry H Low","doi":"10.1093/ismeco/ycag062","DOIUrl":"https://doi.org/10.1093/ismeco/ycag062","url":null,"abstract":"<p><p>When environmental bacteria transition to laboratory conditions, a process termed domestication, the shift from the native habitat to a culture medium often reduces cell cultivability. Consequently, most bacteria remain uncultured using standard techniques, leaving the majority of their diversity unexplored. Here we introduce an enhanced domestication (EDEN) method for bacterial cultivation, which acclimatises environmental bacteria to culture media through a controlled and gradual exposure. To facilitate EDEN, we develop a 3D-printable microwell plate incorporating growth chambers integrated with a continuous-flow media reservoir. Using amplicon sequencing, we show that EDEN-acclimatised bacterial polycultures grow as distinct populations with significantly greater diversity and likely-uncultured taxa compared with standard cultivation methods. Similarly, EDEN-acclimatised bacterial monocultures show three-fold greater diversity and tenfold more likely-uncultured taxa. EDEN also doubled the cultivability of agarose-encapsulated microcolonies. Finally, we demonstrate the utility of EDEN by isolating a previously uncultured bacterium exhibiting broad-spectrum antimicrobial activity against drug-resistant pathogens.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag062"},"PeriodicalIF":6.1,"publicationDate":"2026-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13082232/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700925","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":"Deciphering microbial interactions using a label-free microbead sorting approach.","authors":"Sagarika B Govindaraju, Daan H de Groot, Rinke J van Tatenhove-Pel","doi":"10.1093/ismeco/ycag058","DOIUrl":"https://doi.org/10.1093/ismeco/ycag058","url":null,"abstract":"<p><p>Microorganisms form communities, and their interactions shape the function and stability of these communities. Understanding these interactions can aid in revealing ecosystem dynamics, enhancing community function, and informing the design of synthetic consortia for industrial applications. Deciphering microbial interactions is challenging due to the difficulty of culturing natural microorganisms and the exponential increase in experiments with expanding consortium size. One approach to improving culturing throughput is the use of microcompartments such as agarose microbeads. Microbead-based techniques enable the generation of large numbers of picolitre-sized compartments, facilitating high-throughput, parallel studies of microbial sub-communities. However, the existing microbead-based techniques for deciphering microbial interactions are dependent on single-culture isolates of consortium members and/or labelling of consortium members with fluorescent markers via genetic engineering. We developed a microbead-based, label-free method that eliminates the requirement of single-cell isolates to predict microbial interactions. Our method involves an isolation-independent manner of microbead inoculation with different sub-communities and microbead sorting to separate sub-communities based on growth. Using a probabilistic model, we predict interactions based on cell concentrations and relative abundances in the inoculum and after microbead sorting. We successfully predicted pairwise interactions in two three-member consortia. Additionally, we computationally showcased the validity of our approach for predicting pairwise interactions in larger consortia.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag058"},"PeriodicalIF":6.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13064671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147679231","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":"Revealing community dynamics in polymicrobial infections through a quantitative framework.","authors":"Aanuoluwa E Adekoya, Tyler E Boggs, Carolyn B Ibberson","doi":"10.1093/ismeco/ycag061","DOIUrl":"https://doi.org/10.1093/ismeco/ycag061","url":null,"abstract":"<p><p>Laboratory models provide tractable, reproducible systems that have long served as foundational tools in microbiology. However, the extent to which these models accurately mimic the biological environments they represent remains poorly understood. A quantitative framework was recently introduced to assess how well laboratory models capture microbial physiology in situ. However, applications of this framework have been limited to characterizing the physiology of a single species in human infections, leaving a gap in our understanding of overall microbial community physiology in polymicrobial contexts. Here, we extended this framework to evaluate the accuracy of laboratory model systems in capturing community-level functions in polymicrobial infection. As a proof of concept, we applied the extended framework to a polymicrobial model of human chronic wound (CW) infection. CWs harbor metabolically diverse bacterial species that engage in a range of microbe-microbe interactions, ultimately impacting community dynamics and disease progression. However, studies on the mechanistic drivers of chronic wound infection have relied on single species or pairwise approaches. Here, we demonstrate that our adapted framework can be used to develop accurate polymicrobial models. Further, we demonstrate that this extended framework can evaluate the occurrence of known microbe-microbe interactions. Building on our prior work in large-scale metagenomic and metatranscriptomic analysis, we propose a highly accurate 6-member synthetic bacterial community model i.e. representative of the taxonomic and functional complexity of human CW infections. This approach will support the development of ecologically relevant polymicrobial models and better treatment strategies.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag061"},"PeriodicalIF":6.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13064647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147679251","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":"Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.","authors":"Maria Elena Martino, Marialaura Gallo, Ilaria Nai, Andrea Quagliariello, Giulia Dalla Rovere, Massimiliano Babbucci, Giovanna Monticelli, Marco Graziano, Rafaella Franch, Mbarsid Racaku, Barbara Cardazzo, Massimo Milan, Luca Peruzza, Luca Bargelloni","doi":"10.1093/ismeco/ycag059","DOIUrl":"https://doi.org/10.1093/ismeco/ycag059","url":null,"abstract":"<p><p>In the context of rapidly accelerating global warming, the rising frequency of heatwaves is driving large-scale ecological shifts, profoundly affecting organismal physiology and ecosystem functioning. Thermal tolerance is a key determinant of species resilience. Evidence from diverse model systems indicates that this tolerance can be enhanced through thermal priming, a pre-adaptive process in which organisms are exposed to sublethal heat stress. Beyond intrinsic host factors, the adaptive potential of host-associated microbiomes is increasingly recognised as a critical role in shaping organismal thermal resilience. However, the extent to which microbiomes alone can enhance host thermal tolerance remains largely unknown. Here, we used the Manila clam (<i>Ruditapes philippinarum</i>), one of the most widely farmed bivalves, as a model system to test whether thermal pre-adaptation of the microbiome is sufficient to improve host thermal tolerance. Clams were thermally primed, their microbiota isolated, and subsequently transplanted into non-acclimated individuals, which were then exposed to simulated heatwave conditions. By integrating microbial community profiling, host physiological measurements, and transcriptomic analyses, we demonstrate that transplantation of a microbiome from animals previously exposed to heat stress is sufficient to enhance host resilience during subsequent heat stress. This effect arises from adaptive shifts in microbiome composition that promote energy conservation and survival through elevated antioxidant activity and a broad downregulation of host transcriptional pathways, placing the host in an energy-efficient, stress-mitigating state. Our findings provide novel insights into holobiont-level adaptive mechanisms to stress adaptation and hold practical potential for developing microbiome-based interventions to enhance thermal tolerance in aquaculture systems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag059"},"PeriodicalIF":6.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147693978","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":"Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.","authors":"Yao Xiao, Rui Zhao, Weishu Zhao, Pudi Wang, Xiang Xiao, Xiaotong Peng, Hongmei Jing","doi":"10.1093/ismeco/ycag011","DOIUrl":"10.1093/ismeco/ycag011","url":null,"abstract":"<p><p>Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. <i>Candidatus</i> Scalinduaceae, <i>Ca.</i> Anammoxibacteraceae, <i>Ca.</i> Subterrananammoxibiaceae, and <i>Ca.</i> Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with <i>Ca.</i> Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal <i>Ca.</i> Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived <i>Ca.</i> Subterrananammoxibiaceae and <i>Ca.</i> Bathyanammoxibiaceae, ABC-type Fe³⁺ transporter and sulfate transporter <i>Cys</i>Z could help trench-derived <i>Ca.</i> Anammoxibacteraceae genomes to uptake Fe³⁺ and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag011"},"PeriodicalIF":6.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12998229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147488705","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":"Improved characterisation of coral-associated fungal communities using host DNA depletion and a novel ITS primer.","authors":"Ming Sheng Ng, Min Yi Chin, Golam Rabbani, Lynn Drescher, Benjamin J Wainwright, Ying Chang","doi":"10.1093/ismeco/ycag060","DOIUrl":"https://doi.org/10.1093/ismeco/ycag060","url":null,"abstract":"<p><p>Fungi are increasingly recognised as integral components of the coral holobiont, with predicted roles in nitrogen cycling, nutrient acquisition and promoting stress tolerance. However, characterising coral-associated fungal communities using metabarcoding remains challenging due to extensive co-amplification of host DNA, often leading to low fungal read recovery and an underestimation of diversity. Here, we developed and validated a robust fungal metabarcoding protocol that consistently improved fungal reads across coral species for comprehensive diversity analyses. We addressed host co-amplification through two approaches: (i) host depletion with the Zymo HostZERO Microbial DNA kit and (ii) a newly designed forward primer, ITS3-CoralF, with mismatches to coral DNA to reduce their amplification when paired with the ITS4 reverse primer. We assessed the extraction kit and primer biases and performance across reef sediment samples, and the tissue and skeletal compartments of three species of corals, <i>Pocillopora acuta, Pachyseris speciosa</i>, and <i>Diploastrea heliopora</i>. The HostZERO kit consistently reduced non-target eukaryotic DNA across sample types, enhancing the detection of rare fungi despite shifts in community composition. In coral tissues, ITS3-CoralF achieved at least an 800-fold increase in fungal reads compared to universal primers, though with some bias against rare taxa. For skeletons, thorough removal of tissue prior to total DNA extraction was sufficient, though ITS3-CoralF further improved fungal recovery. Together, our results provide a validated pipeline for profiling fungi across coral hosts, allowing improved recovery of fungal diversity and a deeper understanding of the coral mycobiome.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag060"},"PeriodicalIF":6.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147693784","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":"Gas pipelines, highways for hydrogenotrophic spore-forming bacteria.","authors":"Magali Ranchou-Peyruse, Marion Guignard, Guilhem Caumette, Pierre Chiquet, Pierre Cézac, Anthony Ranchou-Peyruse","doi":"10.1093/ismeco/ycag006","DOIUrl":"10.1093/ismeco/ycag006","url":null,"abstract":"<p><p>A device capable of sampling natural gas under aseptic conditions and in complete safety has been deployed along the transmission grid for the first time. Microbial endospores, resilient enough to survive the extreme conditions of gas transmission and storage, have been detected and isolated throughout high-pressure pipelines and underground reservoirs. In four underground gas storage (UGS) facilities, three in deep aquifers and one in a depleted reservoir, endospores of the same hydrogenotrophic bacterial species from the family Peptococcaceae have been identified, sometimes separated by hundreds of kilometers, and at two different points in the pipeline network. Cultural and genomic analyses show these bacteria can perform acetogenesis, biofilm formation, and produce formate. Hidden within pipelines, these microbes survive long journeys and actively participate in biogeochemical cycles in UGS. Several recent studies on dihydrogen injection into deep aquifers have shown the ubiquity of bacteria similar to these, responsible for formate formation through modified acetogenesis. This formate can serve as a carbon source or inhibit sulfate reduction at high concentrations. Understanding their role offers critical insights into microbial life in the deep biosphere and the potential impacts of future dihydrogen injection into natural gas systems. Their ability to thrive in extreme environments makes these microbes key players in the evolving landscape of underground energy storage and transport.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag006"},"PeriodicalIF":6.1,"publicationDate":"2026-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12981674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147464325","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}