ISME communications最新文献

{"title":"High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules.","authors":"Hugo Sallet, Marion Calvo, Matteo Titus, Nicolas Jacquemin, Karin Lederballe Meibom, Rizlan Bernier-Latmani","doi":"10.1093/ismeco/ycaf117","DOIUrl":"10.1093/ismeco/ycaf117","url":null,"abstract":"<p><p>Over the past two decades, metagenomics has greatly expanded our understanding of microbial phylogenetic and metabolic diversity. However, most microbial taxa remain uncultured, hindering research and biotechnological applications. Isolating environmental anaerobes using traditional methods is particularly cumbersome and low throughput. Here, we present a novel, high-throughput approach for the cultivation and isolation of anaerobes, which involves trapping and growing single microbes within selectively permeable hydrogel capsules followed by fluorescence-activated cell sorting to distribute compartmentalized isolates into liquid medium for further growth. We show that diverse anaerobes can grow within capsules and that slower-growing ones (e.g. methanogens) can be enriched with this platform. We also applied this approach to isolate anaerobes from soil, including strains of the sulfate-reducing bacteria <i>Desulfovibrio desulfuricans</i> and <i>Nitratidesulfovibrio vulgaris</i>. Overall, this work introduces a robust, high-throughput alternative to traditional techniques for isolating environmental anaerobes and expands the emerging set of microfluidics-based tools for the cultivation of novel taxa.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf117"},"PeriodicalIF":6.1,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12319321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144786131","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":"Expanding the use of circulating microbiome in fish: contrast between the gut and blood microbiome of <i>Sebastes fasciatus</i>.","authors":"Fanny Fronton, Arthur Gandin, David Deslauriers, Daniel Small, Dominique Robert, Yves St-Pierre","doi":"10.1093/ismeco/ycaf116","DOIUrl":"10.1093/ismeco/ycaf116","url":null,"abstract":"<p><p>The study of microbiomes in fish populations offers vital insights for ecological and fisheries management, particularly in responses to environmental changes. Although traditional studies have concentrated on the gut microbiome, the emerging concept of a circulating blood microbiome suggests it may act as an early indicator of dysbiosis and various health conditions by reflecting transient bacterial DNA presence. In this study, we examined the gut and blood microbiomes of <i>Sebastes fasciatus</i> (Storer, 1854), a species of redfish of significant economic and ecological importance in the Gulf of St. Lawrence, to obtain critical information for health monitoring, pathogen detection, and ecological management in fisheries. Our results revealed that the gut and blood microbiomes of <i>S. fasciatus</i> have distinct bacterial DNA signatures, with significant differences in microbial diversity. Notably, although both microbiomes exhibited similar dominant genera, specific amplicon sequence variants varied significantly. Through a controlled experimental design, we found that the dietary impacts on microbiome composition were statistically significant yet minimal, suggesting that environmental factors play a more substantial role in shaping microbial communities. Finally, we report the presence of potential pathogens and opportunistic bacteria found exclusively in the blood microbiome. Our results highlight the blood microbiome's value as a sensitive health and environmental stress indicator, essential for sustainable fish population management. Integrating microbiome indicators can improve fisheries management and ecosystem sustainability, offering a model applicable to various marine species and environments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf116"},"PeriodicalIF":6.1,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12342392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839256","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":"Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community.","authors":"Veera Partanen, Svjetlana Dekić Rozman, Antti Karkman, Johanna Muurinen, Teppo Hiltunen, Marko Virta","doi":"10.1093/ismeco/ycaf113","DOIUrl":"10.1093/ismeco/ycaf113","url":null,"abstract":"<p><p>One of the most important knowledge gaps in the antimicrobial resistance crisis is the lack of understanding regarding how genes spread from their environmental origins to bacteria pathogenic to humans. In this study our aim was to create a system that allows the conduction of experiments in laboratory settings that mimic the complexity of natural communities with multiple resistance genes and mobile genetic elements circulating at the same time. Here we report a new sequence-based barcode system that allows simultaneous tracking of the spread of antimicrobial resistance genes from multiple genetic origins. We tested this concept with an experiment in which we added an antimicrobial resistance gene to different genetic environments in alive and dead donors and let the gene spread naturally in an artificial microbial community under different environmental conditions to provide examples of factors that can be investigated. We used emulsion, paired-isolation, and concatenation polymerase chain reaction to detect the new gene carriers and metagenomic analysis to see changes in the genetic environment. We observed the genes moving and were able to recognise the barcode from the gene sequences, thus validating the idea of barcode use. We also saw that temperature and gene origin had effects on the number of new host species. Our results confirmed that our system worked and can be further developed for more complicated experiments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf113"},"PeriodicalIF":6.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12343072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839218","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":"Water mass mixing controls methane cycling and emission in highly hydrodynamic regions of the open ocean.","authors":"Xiao-Jun Li, Jinyan Wang, Hao-Nan Wang, Shuang Li, Zhen Zhou, Zhao-Hui Chen, Jiarui Liu, Gui-Ling Zhang, Hong-Hai Zhang, Gui-Peng Yang, Jonathan D Todd, Guang-Chao Zhuang","doi":"10.1093/ismeco/ycaf114","DOIUrl":"10.1093/ismeco/ycaf114","url":null,"abstract":"<p><p>Ocean circulations and water mass exchange can exert significant influences on seawater biogeochemistry, microbial communities, and carbon cycling in marine systems. However, the detailed mechanisms of the impacts of physical processes in the open ocean on the cycle of greenhouse gases, particularly methane, remain poorly understood. In this study, we integrated high-resolution underway observations, experimental incubations, radioisotope labelling, and molecular analysis to constrain the controls of methanogenic pathways, methanotrophic activity, and emission fluxes in the highly hydrodynamic Kuroshio and Oyashio Extension (KOE) region of the Northwest Pacific. The mixing of high-temperature, nutrient-rich Kuroshio waters with methane-rich Oyashio currents significantly affected not only methane abundance, but also methane production pathways and oxidation rates. Water mass mixing caused changes in the dominance of phytoplankton communities to <i>Bacillariophyta</i>, with less production of the methane precursor dimethylsulphoniopropionate, thus reducing dimethylsulphoniopropionate-dependent methanogenesis. The alteration of nutrient levels due to mixing of Kuroshio and Oyashio at KOE is also likely to affect microbial utilization of dissolved organic phosphorus, thus influencing methane production from the C-P cleavage of methylphosphonate. Furthermore, the abundances of methanotrophs, such as <i>Methylocystis</i> and <i>Methylosinus</i>, were much higher at the KOE sites than those observed at the Oyashio Extension, which contributed to elevated methane oxidation rates in the mixing region. Microbial oxidation as a biological sink of methane accounted for ~43.7% ± 28.8% of the total methane loss, which reduced methane emissions to the atmosphere. These data highlight the physical controls on biogeochemical methane cycling, indicating that intensive mixing of water masses may regulate methane emissions from the open oceans.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf114"},"PeriodicalIF":6.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12342928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839220","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":"Validating digital polymerase chain reaction for 16S rRNA gene amplification from low biomass environmental samples.","authors":"Veronika V Koziaeva, Katja Engel, Josh D Neufeld","doi":"10.1093/ismeco/ycaf115","DOIUrl":"10.1093/ismeco/ycaf115","url":null,"abstract":"<p><p>Digital polymerase chain reaction (dPCR) is a DNA quantification technology that offers absolute quantification of DNA templates. In this study, we optimized and validated a chip-based dPCR EvaGreen assay with commonly used 16S rRNA gene primer pairs and compared its performance to quantitative real-time PCR (qPCR). We compared measurements of low amounts of template DNA using a newly designed synthetic DNA standard to assess precision, accuracy, and sensitivity. Optimization approaches were tested to minimize partitions with intermediate fluorescence levels between true positive and true negative partitions (so-called \"rain\") for dPCR. Both dPCR and qPCR demonstrated similar quantification performance, with variability in accuracy increasing for samples containing fewer than 30 copies μl^-1 template concentrations. Both tested 16S rRNA gene primer sets amplified non-target template contaminants within both qPCR and dPCR mixtures, which could not be eliminated by ultraviolet light or DNAse treatment and negatively affected the apparent sensitivity of both PCR assays. Digital PCR was less susceptible to common PCR inhibitors, such as ethanol and humic acids, but was more susceptible to tannic acid inhibition than qPCR. These findings demonstrate the suitability of dPCR for 16S rRNA gene quantification of low biomass environmental samples.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf115"},"PeriodicalIF":6.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12342375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839219","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":"Roles of physical disturbance and biome properties in shaping microbial communities within Indian Ocean eddies.","authors":"Melissa L Brock, Alyse A Larkin, Adam C Martiny","doi":"10.1093/ismeco/ycaf110","DOIUrl":"10.1093/ismeco/ycaf110","url":null,"abstract":"<p><p>Oceanic eddies create localized upwelling and downwelling systems and are thought to alter microbial communities through environmental selection and dispersal. Though how these eddy-driven mechanisms contribute to microbial outcomes within a broader environmental context is unknown. We proposed that (1) eddies are a large disturbance that exert a significant influence on bacterial community and functional diversity as well as taxonomic and functional composition and (2) that the combined processes of environmental selection and dispersal determine bacterial outcomes within eddies. To address these hypotheses, we integrated bacterial genomics and environmental conditions from 26 eddies across the Indian Ocean. We observed that the biome had a strong, primary influence in shaping all aspects of bacterial communities with eddies playing a weak, secondary role. Additionally, there was minimal evidence of an effect of environmental selection or dispersal in shaping bacterial community diversity. Our observations highlight the variability in bacterial responses within and between eddy types and emphasize the importance of understanding eddy characteristics and broader biome attributes in interpreting bacterial responses.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf110"},"PeriodicalIF":6.1,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144746303","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":"Ecological pattern of microalgal communities and associated risks in coastal ecosystems.","authors":"Li Zhang, Anqi Xiong, Changchao Li, Xintong Liu, Xiaohua Zhang, Shihao Gong, Meng Yan, Xian Qin, Yang Liu, Zhangxi Hu, James Kar-Hei Fang, Huanfeng Duan, Hongbin Liu, Leo L Chan, Ling N Jin","doi":"10.1093/ismeco/ycaf109","DOIUrl":"10.1093/ismeco/ycaf109","url":null,"abstract":"<p><p>Eukaryotic harmful and toxic microalgae, along with their derived toxins, pose significant threats to seafood safety, human health, and marine ecosystems. Here, we developed a novel full-length 18S rRNA database for harmful and toxic microalgae and combined metabarcoding with toxin analyses to investigate the ecological patterns of phytoplankton communities and the underlying mechanism of associated toxic microalgae risks. We identified 79 harmful and toxic species in Hong Kong's coastal waters, with dinoflagellates and diatoms representing the majority of toxic and harmful taxa, respectively. Distinct seasonal succession patterns were observed in phytoplankton communities, driven by different ecological assembly processes. Deterministic processes dominated during the dry season, correlating with elevated toxic microalgae abundance and temperature stress. Seasonal shifts in temperature played a pivotal role in shaping toxic algal communities. The dominance of dinoflagellates, particularly <i>Alexandrium</i> spp., <i>Dinophysis</i> spp., <i>Prorocentrum</i> spp., and <i>Karenia</i> spp., during the dry season was consistent with elevated toxin concentrations. These toxin profiles highlight the heightened risk in a warming climate, where the prevalence and impacts of toxigenic algae are expected to intensify.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf109"},"PeriodicalIF":6.1,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12404660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994483","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":"Expanding ISME Communications to taxonomy and nomenclature.","authors":"Maria Chuvochina, Marike Palmer, Stephanus N Venter","doi":"10.1093/ismeco/ycaf106","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf106","url":null,"abstract":"","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf106"},"PeriodicalIF":5.1,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676748","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 spatial organization: insights from synthetic and engineered communities.","authors":"Estelle Pignon, Yolanda Schaerli","doi":"10.1093/ismeco/ycaf107","DOIUrl":"10.1093/ismeco/ycaf107","url":null,"abstract":"<p><p>Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between community members, initial growth condition or environmental factors. Understanding the mechanisms that drive these spatial patterns is essential for uncovering fundamental principles of microbial ecology and for developing applications. Using genetic engineering and synthetic microbial communities allows us to decipher how specific parameters influence spatial organization. In this review, we highlight recent studies that leverage synthetic microbial communities to deepen our understanding of microbial spatial ecology. We begin by exploring how initial conditions, such as cell density and relative species abundance, influence spatial organization. We then focus on studies that examine the role of individual microbial traits, such as cell shape and motility. Next, we discuss the impact of contact-dependent and long-range interactions, including metabolite exchange and toxin release. Furthermore, we highlight the influence of environmental factors on spatial dynamics. Finally, we address the current limitations of synthetic approaches and propose future directions to bridge the gap between engineered and natural systems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf107"},"PeriodicalIF":6.1,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12354948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144877142","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":"How do host age and nutrition affect density regulation of obligate versus facultative bacterial symbionts? Insights from the tsetse fly.","authors":"Mathilda Whittle, Antoine M G Barreaux, Lee R Haines, Michael B Bonsall, Sinead English, Fleur Ponton","doi":"10.1093/ismeco/ycaf108","DOIUrl":"10.1093/ismeco/ycaf108","url":null,"abstract":"<p><p>Host-symbiont relationships can vary tremendously in the extent to which hosts depend on and control their symbionts. Obligate symbionts that provide micronutrients to their host are often compartmentalised to specialised host organs and depend on their hosts for survival, whereas facultative symbionts retain the ability to survive outside of their hosts. Few studies compare the extent to which a host controls and adjusts the density of obligate and facultative symbionts directly. We used tsetse as a model for teasing apart the relationships between a host (<i>Glossina morsitans morsitans</i>) and obligate (<i>Wigglesworthia glossinidia</i>) and facultative (<i>Sodalis glossinidius</i>) symbionts. We hypothesised that tsetse actively regulate the density of <i>Wigglesworthia</i> according to the host's requirements, depending on their current nutritional state and developmental age. In contrast, we postulated that <i>Sodalis</i> retains some independence from host control and that the growth of this symbiont is dependent on the conditions of the immediate environment, such as nutrient availability. Using qPCR, we examined how symbiont densities change across host age and the hunger cycle. Additionally, we investigated how host nutrition influences symbiont density, by comparing tsetse that were fed nutrient-poor or vitamin enriched diets. We found that the density of <i>Wigglesworthia</i> was not influenced by the nutritional status of the host but reflected long-term host nutritional needs. In contrast, the density of facultative <i>Sodalis</i> depended on the nutrient availability. We propose that tsetse tightly regulate <i>Wigglesworthia</i> but exert only partial control over <i>Sodalis</i> growth due to the relatively recent transition of this symbiont to host-associated living.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf108"},"PeriodicalIF":6.1,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12309370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755286","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}