The ISME Journal最新文献

{"title":"Arbuscular mycorrhizal hyphae facilitate rhizobia dispersal and nodulation in legumes","authors":"Jiadong He, Lin Zhang, Judith Van Dingenen, Sandrien Desmet, Sofie Goormachtig, Maryline Calonne-Salmon, Stéphane Declerck","doi":"10.1093/ismejo/wrae185","DOIUrl":"https://doi.org/10.1093/ismejo/wrae185","url":null,"abstract":"In soil ecosystems, rhizobia occupy the rhizosphere of legume roots to form nodules, a process triggered by microbial recognition of specific root-derived signals (i.e., flavonoids). However, soil conditions can limit bacterial motility, restricting signal perception to the area directly influenced by roots. Legumes, like most plants of agricultural interest, associate with arbuscular mycorrhizal fungi, whose hyphae develop extensively in the soil, potentially providing an effective dispersal network for rhizobia. We hypothesized that mycelial networks of arbuscular mycorrhizal fungi play a role in signal transmission and act as a highway, enabling rhizobia to migrate from distant soil to the roots of leguminous plants. Using in vitro and greenhouse microcosm systems, we demonstrated that Rhizophagus irregularis helps Shinorhizobium meliloti to migrate towards the legume Medicago truncatula, triggering nodulation, a mechanism absent without the arbuscular mycorrhizal fungus. Metabolomics analysis revealed eight flavonoids unique to the compartment containing extraradical hyphae of the arbuscular mycorrhizal fungus linked to M. truncatula roots, associated with S. meliloti growth and nod gene expression. Rhizobia plated on the extraradical hyphae connecting two plants (the legume M. truncatula and non-legume Solanum tuberosum) by a common mycelium network, showed preference for the legume, suggesting the chemoattraction by specific signals transported by the fungus connected to the legume. Simultaneously, S. meliloti stimulated the cytoplasmic/protoplasmic flow in the hyphae, likely increasing the release of nutrients and signals. Our results highlight the importance of extraradical hyphae (i.e. the mycorrhizal pathway) of arbuscular mycorrhizal fungi for the migration of rhizobia over long distances to the roots, leading to nodulation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Niche breadth specialisation impacts ecological and evolutionary adaptation following environmental change","authors":"Cécile Gubry-Rangin, Axel Aigle, Leonel Herrera-Alsina, Lesley T Lancaster, James I Prosser","doi":"10.1093/ismejo/wrae183","DOIUrl":"https://doi.org/10.1093/ismejo/wrae183","url":null,"abstract":"None declared.Conflicts of interestEcological theory predicts that organismal distribution and abundance depend on the ability to adapt to environmental change. It also predicts that eukaryotic specialists and generalists will dominate in extreme environments or following environmental change, respectively. This theory has attracted little attention in prokaryotes, especially in archaea, which drive major global biogeochemical cycles. We tested this concept in Thaumarchaeota using pH niche breadth as a specialisation factor. Responses of archaeal growth and activity to pH disturbance were determined empirically in manipulated, long-term, pH-maintained soil plots. The distribution of specialists and generalists was uneven over the pH range, with specialists being more limited to the extreme range. Nonetheless, adaptation of generalists to environmental change was greater than that of specialists, except for environmental changes leading to more extreme conditions. The balance of generalism and specialism over longer timescales was further investigated across evolutionary history. Specialists and generalists diversified at similar rates, reflecting balanced benefits of each strategy, but a higher transition rate from generalists to specialists than the reverse was demonstrated, suggesting that metabolic specialism is more easily gained than metabolic versatility. This study provides evidence for a crucial ecological concept in prokaryotes, significantly extending our understanding of archaeal adaptation to environmental change.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hidden syndinian and perkinsid infections in dinoflagellate hosts revealed by single-cell transcriptomics","authors":"Elizabeth C Cooney, Brian S Leander, Patrick J Keeling","doi":"10.1093/ismejo/wrae188","DOIUrl":"https://doi.org/10.1093/ismejo/wrae188","url":null,"abstract":"Free-living core dinoflagellates are commonly infected by members of two parasitic clades that are themselves closely related to dinoflagellates, the marine alveolates and perkinsids. These parasites are abundant and ecologically important, but most species have been difficult to observe directly or cultivate, so our knowledge of them is usually restricted to environmental 18S rRNA gene sequences, and genome-scale molecular data are not available for most species. Here, we report numerous syndinian parasites and one parasite that is sister to all known perkinsids from isolated single cells of diverse, free-living dinoflagellates. Of the 14 infected host cells collected, only five were noticeably infected via light microscopy at the time of collection. Single-cell transcriptome sequencing yielded relatively high transcriptomic coverage for parasites as well as their hosts. Host and parasite homologs were distinguished phylogenetically allowing us to infer a robust phylogenomic tree based on 198 genes. The tree showed one parasite belongs to an undescribed lineage that is sister to perkinsids, whereas the remainder are members of the syndinian clade. Close relatives of all these parasites have been observed in 18S rRNA gene surveys, but until now none had been linked to a specific host. These findings illustrate the efficacy of single-cell isolation and transcriptome sequencing as a strategy for gaining deeper insights into the evolutionary history and host relationships of hidden single-celled parasites.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity","authors":"Hugo Sentenac, Dirk S Schmeller, Solène Caubet, Adélaïde Carsin, Rémi Guillet, Jessica Ferriol, Joséphine Leflaive, Adeline Loyau","doi":"10.1093/ismejo/wrae189","DOIUrl":"https://doi.org/10.1093/ismejo/wrae189","url":null,"abstract":"Emerging infectious diseases threaten biodiversity and human health. Many emerging pathogens have aquatic life stages and all immersed substrates have biofilms on their surface, i.e., communities of microorganisms producing a gelatinous matrix. However, the outcome of the interactions between environmental biofilms and pathogens is poorly understood. Here we demonstrate that biofilms reduce the survival of the most impactful pathogen for vertebrate diversity, the invasive chytrid fungus Batrachochytrium dendrobatidis. Effects on its zoospores varied with biofilm composition in controlled settings and biofilm compositional variation also coincided with divergent impacts of chytridiomycosis on amphibian populations in nature. Our results suggest that biofilms form a biotic component of ecosystem resistance to Batrachochytrium dendrobatidis by reducing environmental transmission, and that they could be used to develop nature-based technologies to limit the impacts and spread of this invasive chytrid fungus. Our study warrants further research into the interactions between environmental biofilms and pathogenic and/or invasive micro-organisms.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pathogen non-planktonic phases within the urinary tract impact early infection and resistance evolution","authors":"Michael Raatz, Amanda de Azevedo-Lopes, Karolina Drabik, Arne Traulsen, Bartlomiej Waclaw","doi":"10.1093/ismejo/wrae191","DOIUrl":"https://doi.org/10.1093/ismejo/wrae191","url":null,"abstract":"Treatment of urinary tract infections and the prevention of their recurrence is a pressing global health problem. In a urinary infection, pathogenic bacteria not only reside in the bladder lumen but also attach to and invade the bladder tissue. Planktonic, attached, and intracellular bacteria face different selection pressures from physiological processes such as micturition, immune response, and antibiotic treatment. Here, we use a mathematical model of the initial phase of infection to unravel the effects of these different selective pressures on the ecological and evolutionary dynamics of urinary infections. We explicitly model planktonic bacteria in the bladder lumen, bacteria attached to the bladder wall, and bacteria that have invaded the epithelial cells of the bladder. We find that the presence of non-planktonic bacteria substantially increases the risk of infection establishment and affects evolutionary trajectories leading to resistance during antibiotic treatment. We also show that competitive inoculation with a fast-growing non-pathogenic strain can reduce the pathogen load and increase the efficacy of an antibiotic, but only if the antibiotic is used in moderation. Our study shows that including different compartments is essential to create more realistic models of urinary infections, which may help guide new treatment strategies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy","authors":"C Logan Pierpont, Jacob J Baroch, Matthew J Church, Scott R Miller","doi":"10.1093/ismejo/wrae184","DOIUrl":"https://doi.org/10.1093/ismejo/wrae184","url":null,"abstract":"Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142317576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global freshwater distribution of Telonemia protists.","authors":"Roudaina Boukheloua,Indranil Mukherjee,Hongjae Park,Karel Šimek,Vojtěch Kasalický,Maxon Ngochera,Hans-Peter Grossart,Antonio Picazo-Mozo,Antonio Camacho,Pedro J Cabello-Yeves,Francisco Rodriguez-Valera,Cristiana Callieri,Adrian-Stefan Andrei,Jakob Pernthaler,Thomas Posch,Albin Alfreider,Ruben Sommaruga,Martin W Hahn,Bettina Sonntag,Purificacion Lopez-Garcia,David Moreira,Ludwig Jardillier,Cécile Lepère,Corinne Biderre-Petit,Anna Bednarska,Mirosław Ślusarczyk,Viktor R Tóth,Horia L Banciu,Konstantinos Kormas,Sandi Orlic,Danijela Šantić,Gerard Muyzer,Daniel P R Herlemann,Helen Tammert,Stefan Bertilsson,Silke Langenheder,Thomas Zechmeister,Nico Salmaso,Nicola Storelli,Camilla Capelli,Fabio Lepori,Vojtěch Lanta,Helena Henriques Vieira,Fran Kostanjšek,Kateřina Kabeláčová,Maria-Cecilia Chiriac,Markus Haber,Tanja Shabarova,Clafy Fernandes,Pavel Rychtecký,Petr Znachor,Tiberiu Szőke-Nagy,Paul Layoun,Hon Lun Wong,Vinicius Silva Kavagutti,Paul-Adrian Bulzu,Michaela M Salcher,Kasia Piwosz,Rohit Ghai","doi":"10.1093/ismejo/wrae177","DOIUrl":"https://doi.org/10.1093/ismejo/wrae177","url":null,"abstract":"Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remains unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analysed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142275207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Drivers and consequences of microbial community coalescence","authors":"Xipeng Liu, Joana Falcão Salles","doi":"10.1093/ismejo/wrae179","DOIUrl":"https://doi.org/10.1093/ismejo/wrae179","url":null,"abstract":"Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Convergence of gut phage communities but not bacterial communities following wild mouse bacteriophage transplantation into captive house mice","authors":"Dagmar Čížková, Pavel Payne, Anna Bryjová, Ľudovít Ďureje, Jaroslav Piálek, Jakub Kreisinger","doi":"10.1093/ismejo/wrae178","DOIUrl":"https://doi.org/10.1093/ismejo/wrae178","url":null,"abstract":"Bacteriophages are abundant components of vertebrate gut microbial communities, impacting bacteriome dynamics, evolution, and directly interacting with the superhost. However, knowledge about gut phageomes and their interaction with bacteriomes in vertebrates under natural conditions is limited to humans and non-human primates. Widely used specific pathogen-free (SPF) mouse models of host-microbiota interactions have altered gut bacteriomes compared to wild mice, and data on phageomes from wild or other non-SPF mice are lacking. We demonstrate divergent gut phageomes and bacteriomes in wild and captive non-SPF mice, with wild mice phageomes exhibiting higher alpha-diversity and interindividual variability. In both groups, phageome and bacteriome structuring mirrored each other, correlating at the individual level. Re-analysis of previous data from phageomes of SPF mice revealed their enrichment in Suoliviridae crAss-like phages compared to our non-SPF mice. Disrupted bacteriomes in mouse models can be treated by transplanting healthy phageomes, but the effects of phageome transplants on healthy adult gut microbiota are still unknown. We show that experimental transplantation of phageomes from wild to captive mice did not cause major shifts in recipient phageomes. However, the convergence of recipient-to-donor phageomes confirmed that wild phages can integrate into recipient communities. The differences in the subset of integrated phages between the two recipient mouse strains illustrate the context-dependent effects of phage transplantation. The transplantation did not impact recipient gut bacteriomes. This resilience of healthy adult gut microbiomes to the intervention has implications for phage allotransplantation safety.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oxidation of sulfur, hydrogen, and iron by metabolically versatile Hydrogenovibrio from deep sea hydrothermal vents","authors":"Katja Laufer-Meiser, Malik Alawi, Stefanie Böhnke, Claus-Henning Solterbeck, Jana Schloesser, Axel Schippers, Philipp Dirksen, Thomas Brüser, Susann Henkel, Janina Fuss, Mirjam Perner","doi":"10.1093/ismejo/wrae173","DOIUrl":"https://doi.org/10.1093/ismejo/wrae173","url":null,"abstract":"Chemolithoautotrophic Hydrogenovibrio are ubiquitous and abundant at hydrothermal vents. They can oxidize sulfur, hydrogen or iron, but none are known to use all three energy sources. This ability though would be advantageous in vents hallmarked by highly dynamic environmental conditions. We isolated three Hydrogenovibrio strains from vents along the Indian Ridge, which grow on all three electron donors. We present transcriptomic data from strains grown on iron, hydrogen or thiosulfate with respective oxidation and autotrophic CO2 fixation rates, RubisCO activity, SEM, and EDX. Maximum estimates of one strain’s oxidation potential were 10, 24, and 952 mmol for iron, hydrogen and thiosulfate oxidation and 0.3, 1, and 84 mmol CO2 fixation, respectively, per vent per hour indicating their relevance for element cycling in-situ. Several genes were up- or downregulated depending on the inorganic electron donor provided. Although no known genes of iron-oxidation were detected, upregulated transcripts suggested iron-acquisition and so far unknown iron-oxidation-pathways.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}