ISME Journal最新文献

{"title":"Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions.","authors":"Amanda M Zdimal, Giacomo Di Dio, Wanxiang Liu, Tanya Aftab, Taryn Collins, Remy Colin, Abhishek Shrivastava","doi":"10.1093/ismejo/wrae263","DOIUrl":"10.1093/ismejo/wrae263","url":null,"abstract":"<p><p>The collective surface motility and swarming behavior of microbes play a crucial role in the formation of polymicrobial communities, shaping ecosystems as diverse as animal and human microbiota, plant rhizospheres, and various aquatic environments. In the human oral microbiota, T9SS-driven gliding bacteria transport non-motile microbes and bacteriophages as cargo, thereby influencing the spatial organization and structural complexity of these polymicrobial communities. However, the physical rules governing the dispersal of T9SS-driven bacterial swarms are barely understood. Here, we collected time-lapse images, under anaerobic conditions, of developing swarms of a T9SS-driven microbe common to the human oral microbiota. Tracking of swarms revealed that small peripheral flares emerging from a colony develop structures that resemble fireworks displaying a chrysanthemum effect and flower-like patterns that convert to wave-like patterns and which further evolve into scattered microcolonies. Particle-image velocimetry showed density-dependent phase transitions and initial vorticity within these emerging patterns. Numerical simulations demonstrate that these patterns arise due to changes in swarm speed and alignment strength. Our data reveal a strategy used by an anaerobic swarming bacterium to control swarm behavior, resulting in scattered microcolonies distant from the mother colony, thus reducing competition for resources among colony members. This might ensure species survival even if conditions change drastically in one location of the human oral cavity.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacillus subtilis ensures high spore quality in competition with Salmonella Typhimurium via the SigB-dependent pathway.","authors":"Eli Podnar, Kristina Dendinovic, Tjaša Danevčič, Bram Lories, Eva Kovačec, Hans Steenackers, Ines Mandic-Mulec","doi":"10.1093/ismejo/wraf052","DOIUrl":"10.1093/ismejo/wraf052","url":null,"abstract":"<p><p>The interactions between beneficial bacteria and pathogens are understudied. Here we investigate the interactions between the probiotic strain Bacillus subtilis PS-216 and the pathogen Salmonella Typhimurium SL1344. We show here that the sporulation of B. subtilis is impaired when it competes with S. Typhimurium in a nutrient-depleted medium. The sporulation impairment in B. subtilis is mediated by the sigma factor B (SigB)-dependent general stress response, as the ΔsigB mutant remains blind to manipulative cues from S. Typhimurium. Furthermore, we show that decreased sporulation frequency in B. subtilis depends on cell-cell contact between the two species involving the S. Typhimurium Type VI Secretion System, whereas B. subtilis uses the SigB-dependent response to trade spore quantity for higher spore quality.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11994997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lysis of Escherichia coli by colicin Ib contributes to bacterial cross-feeding by releasing active β-galactosidase.","authors":"Nicole A Lerminiaux, Jaycee M Kaufman, Laura J Schnell, Sean D Workman, Danae M Suchan, Carsten Kröger, Brian P Ingalls, Andrew D S Cameron","doi":"10.1093/ismejo/wraf032","DOIUrl":"10.1093/ismejo/wraf032","url":null,"abstract":"<p><p>The diffusible toxin ColIb produced by Salmonella enterica serovar Typhimurium SL1344 is a potent inhibitor of Escherichia coli growth. To identify and parameterize metabolic cross-feeding in states of competition, we established defined communities in which E. coli was the only species able to access a sole carbon source, lactose. Although ColIb was predicted to undermine cross-feeding by killing the lactose-converting E. coli, S. enterica populations thrived in co-culture. We discovered that ColIb caused the release of active β-galactosidase from E. coli cells, which induced galactose uptake by S. enterica. Although iron limitation stimulates ColIb production and makes E. coli more sensitive to the toxin, ColIb killing in iron-limited conditions did not enhance iron acquisition or siderophore scavenging by S. enterica. Also unexpected was the rapid rate at which resistance to ColIb evolved in E. coli through spontaneous mutation of the ColIb receptor gene cirA or horizontal acquisition of the S. enterica colicin immunity gene imm. Mathematical modelling effectively predicted the growth kinetics of E. coli and S. enterica populations, revealing a tractable system in which ColIb can shrink a competitor population while simultaneously amplifying the metabolic contributions of the suppressed population.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environment-mediated interactions cause an externalized and collective memory in bacteria.","authors":"Shubham Gajrani, Xiaozhou Ye, Christoph Ratzke","doi":"10.1093/ismejo/wraf173","DOIUrl":"10.1093/ismejo/wraf173","url":null,"abstract":"<p><p>Bacteria usually live in complex communities interacting with many other microbial species. These interactions determine who can persist in a community and how the overall community forms and functions. Bacteria often exert interactions by chemically changing the environment, like taking up nutrients or producing toxins. These environmental changes can persist over time. We show here that such lasting environmental changes can cause a \"memory effect\" where current growth conditions alter interaction outcomes in the future. This memory is only stored in the environment and not inside bacterial cells. Only the collective effort of many bacteria can build up this memory, making it an emergent property of bacterial populations. This externalized and collective memory can also impact the assembly of more complex communities and lead to different final compositions depending on the system's past. Overall, we show that to understand interaction outcomes fully, we have to consider not only the interacting species and abiotic conditions but also the system's history.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456175/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144838471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Artificial symbiont replacement in a vertically transmitted plant symbiosis reveals a role for microbe-microbe interactions in enforcing specificity.","authors":"Léa Ninzatti, Thibault G Sana, Tessa Acar, Sandra Moreau, Marie-Françoise Jardinaud, Guillaume Marti, Olivier Coen, Aurelien L Carlier","doi":"10.1093/ismejo/wraf177","DOIUrl":"10.1093/ismejo/wraf177","url":null,"abstract":"<p><p>Some plants engage in permanent, vertically transmitted symbioses with bacteria. Often, these bacteria are hosted extracellularly within structures on the leaves, where they produce specialized bioactive metabolites that benefit their host. These associations are highly specific, with one plant species associating with a single bacterial species, but little is known about how these symbioses originate and how specificity is maintained. In this study, we show that the symbiotic association between a wild yam and a bacterium can be manipulated experimentally and that bacteria-free plants are open to colonization by environmental bacteria. Through metabolic profiling, we show that the endophytic niche is rich in organic acids and intermediates of the tricarboxylic acid cycle cycle. Environmental bacteria capable of utilizing these acids, such as the soil bacterium Pseudomonas putida, readily colonize aposymbiotic plants. However, successful colonization is contingent upon the absence of the vertically transmitted symbiont or the impairment of its type VI secretion system. Unexpectedly for a vertically transmitted symbiosis, these findings suggest that microbe-microbe interactions, including antagonism, may play a crucial role in maintaining the specificity of an association. However, low transmission rates of synthetic symbionts provide evidence that transmission barriers or bottlenecks may still occur, further enforcing partner fidelity. Together, these results highlight the complexity of mechanisms underlying mutualistic associations, and provide insights into the evolution of bacterial leaf symbiosis.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Downy mildew disease-suppressive soils transmit a protective core microbiome to the phyllosphere.","authors":"Jelle Spooren, Yadong Shao, Tilda Tarrant, Hannah Ploemacher, Run Qi, Syb Hopkoper, Umut G Yüce, Hangyu Dong, Pim Goossens, Saskia C M van Wees, Corné M J Pieterse, Roeland L Berendsen","doi":"10.1093/ismejo/wrag016","DOIUrl":"10.1093/ismejo/wrag016","url":null,"abstract":"<p><p>Plants can respond to pathogen attack by assembling disease-suppressive microbiomes. In Arabidopsis thaliana, infection by the obligate foliar downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) consistently led to the formation of a soil microbial community, referred to as \"soilborne legacy\" (SBL), that enhanced resistance in subsequent plant populations grown in the same soil. Previous work identified an enrichment of specific \"Hpa-associated microbiota\" (HAM) in the phyllospheres of infected plants, which suppressed pathogen proliferation. Here, we demonstrate how the assembly of protective HAM in the phyllosphere contributes to a disease-suppressive SBL. We identified a community of 25 core-HAM that consistently dominated the phyllospheres of 14 sets of distinct Hpa-infected plant populations across six independent experiments. Using HAM-free, gnotobiotic Hpa spores, the infection-driven assembly of a core-HAM representative was recapitulated, showing de novo and progressive enrichment under sustained disease pressure. Despite being transmitted via soil as SBL, HAM are phyllosphere specialists with infected leaves as their primary niche. Disease-induced HAM assembly is initiated in the phyllosphere rather than the rhizosphere, and once transmitted, they particularly accumulate on aboveground tissues. Leaf wash-offs from plant populations that inherited SBL were shown to effectively suppress downy mildew disease when applied to leaves of plants grown in unconditioned soil. These findings reveal that downy mildew disease-suppressive soils transmit a protective core microbiome to the phyllosphere, highlighting a crucial link between belowground and aboveground plant-driven microbiome assembly processes. Paradoxically, the phyllosphere thus emerges as a key assembly hub for disease-suppressive soil microbiomes.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12927876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to 29 articles due to inaccurate manuscript submission dates.","authors":"","doi":"10.1093/ismejo/wraf008","DOIUrl":"10.1093/ismejo/wraf008","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"19 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temperature influences outcomes of an environmentally acquired symbiosis.","authors":"Patrick T Stillson, Kaisy Martinez, Johnathan Adamson, Arshya Tehrani, Alison Ravenscraft","doi":"10.1093/ismejo/wraf056","DOIUrl":"10.1093/ismejo/wraf056","url":null,"abstract":"<p><p>Microbial symbioses are essential for many animals, but their outcomes are often context dependent. For example, rising temperatures can disrupt symbioses by eliminating thermally sensitive symbionts. The temperature tolerance of a symbiont may therefore limit the temperature range of its host, but switching to a more thermally tolerant partner could expand this range. Eastern leaf footed bugs (Leptoglossus phyllopus) depend on symbiotic Caballeronia bacteria which they must acquire from the environment early in development. Could this result in intergenerational partner switching that improves host outcomes under changing conditions? As a first step towards answering this question, we tested the hypothesis that host outcomes in this symbiosis vary among symbiont strains in a temperature-dependent manner. Nymphs were provided with one of six Caballeronia strains with varying thermal optima and reared at temperatures from 24-40°C. We observed temperature- and strain-dependent tradeoffs in host outcomes, with different strains conferring improved host weight, development time, and survival at cooler versus warmer temperatures. Differences in host outcomes were most pronounced at high temperatures, with some strains imposing severe costs. However, Caballeronia's in vitro thermal optima did not predict in vivo outcomes. Regardless, strain- and temperature- dependent outcomes suggest that environmental symbiont acquisition could mitigate the effects of thermal stress on host populations. It is often assumed that vertical transmission of a beneficial symbiont from parent to offspring is the optimal strategy, but our results suggest that environmental acquisition could offer unique benefits under changing conditions.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11995993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment.","authors":"Melody R Lindsay, Timothy D'Angelo, Elizabeth Goodell, Jacob H Munson-McGee, Melissa Herring, Michael Budner, Julia M Brown, Gregory S Gavelis, Corianna Mascena, Laura C Lubelczyk, Nicole J Poulton, Ramunas Stepanauskas, Beth N Orcutt, David Emerson","doi":"10.1093/ismejo/wraf042","DOIUrl":"10.1093/ismejo/wraf042","url":null,"abstract":"<p><p>The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption-impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01-4.7 fmol SO42- cell-1 h-1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23-40 nmol h-1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean.","authors":"Changfei He, Michael Gonsior, Jihua Liu, Nianzhi Jiao, Feng Chen","doi":"10.1093/ismejo/wraf049","DOIUrl":"10.1093/ismejo/wraf049","url":null,"abstract":"<p><p>SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled genomes from different oceans, with 18% of these SAR202 genomes characterized by small genome sizes (<2 Mbp), low GC content (<40%), and high gene density. The 70 genome-streamlined SAR202 bacteria constitute more than an average of 90% of SAR202 in the euphotic zone and exhibit streamlined metabolic features compared to the dark ocean SAR202. Genome-streamlined SAR202 is distributed in many major SAR202 lineages (i.e. I, II, III, and VI). Phylogenomic analysis shows that the genome-streamlined SAR202 clades diverged from the non-genome-streamlined SAR202 lineages and evolved independently within the same clades. Certain genes are enriched in genome-streamlined SAR202, such as proteorhodopsin genes and the coding genes of major facilitator superfamily transporters, nucleoside transporters, and deoxyribodipyrimidine photo-lyase, indicating their adaptation to sunlit oligotrophic water. A detailed comparison between genome-streamlined SAR202 and non-genome-streamlined SAR202 was made to illustrate their distinct niche distribution and metabolic buildup. In addition, the metatranscriptomic analysis supports that genome-streamlined SAR202 bacteria are active in the upper ocean. This study represents a systematic study of streamlined SAR202 bacteria that occupy the euphotic ocean and provides a comprehensive view of the ecological roles of SAR202 bacteria in the ocean.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11994032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}