ISME Journal最新文献

{"title":"Viralization as a microbial approach for enhancing coral reef restoration.","authors":"Jason Baer, Mark Little, Jenna Aquino, Anneke van der Geer, Andrés Sánchez-Quinto, Ashton Ballard, Catherine Lawrence, Jessica Carilli, Aaron Hartmann, Forest Rohwer","doi":"10.1093/ismejo/wraf110","DOIUrl":"10.1093/ismejo/wraf110","url":null,"abstract":"<p><p>Coral reef ecosystems rely on microorganisms to carry out biogeochemical processes essential to the survival of corals and the reef food web. However, widespread shifts from coral to algal dominance as a result of anthropogenic pressures have promoted microbial communities that compromise reef health through deoxygenation and disease. These degraded reefs become locked in a \"microbialized\" state characterized by high microbial biomass, low oxygen, and heightened pathogenic activity that stymie efforts to outplant corals onto the reef, a common approach applied to restore these ecosystems. Over 18 months, we compared viral and microbial dynamics alongside physical and chemical parameters (\"water quality\") between two coral outplanting sites and two midwater reef mesocosms called Coral Arks. Seafloor sites exhibited microbialization, whereas Arks maintained conditions with higher viral abundances and virus-to-microbe ratios, smaller and less abundant microorganisms, and consistently higher dissolved oxygen, water flow, and light availability. These conditions, which we term \"viralized\", supported enhanced coral growth and survival, greater benthic diversity, increased coral recruitment, reduced turf and macroalgae, and higher fish abundance compared to outplanting sites. Despite these benefits, analysis of microbial carbon metabolism genes revealed an underlying trend towards microbialization at both sites, reflecting larger-scale regional decline. These findings emphasize that microbial and physicochemical conditions are drivers of reef restoration outcomes; to be successful, restoration strategies must target the underlying environmental factors that support coral survival and resilience. We identify key microbial and physical variables-such as oxygen levels, flow, and viral activity-associated with viralized reef states, which should serve as focal points for developing new interventions and technologies aimed at creating conditions conducive to reef recovery.</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/PMC12198774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235795","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":"Culture-supported ecophysiology of the SAR116 clade demonstrates metabolic and spatial niche partitioning.","authors":"Jordan T Coelho, Lauren Teubner, Michael W Henson, V Celeste Lanclos, Conner Y Kojima, J Cameron Thrash","doi":"10.1093/ismejo/wraf124","DOIUrl":"10.1093/ismejo/wraf124","url":null,"abstract":"<p><p>Marine SAR116 bacterioplankton are ubiquitous in surface waters across global oceans and form their own order, Puniceispirillales, within the Alphaproteobacteria. To date no comparative physiology among diverse SAR116 isolates has been performed to capture the functional diversity within the clade, and further, diversity through the lens of metabolic potential and environmental preferences via clade-wide pangenomics continues to evolve with the addition of new genomes. Using high-throughput dilution-to-extinction cultivation, we isolated and genome sequenced five new and diverse SAR116 isolates from the northern Gulf of Mexico. Here we present a comparative physiological analysis of these SAR116 isolates, along with a pangenomic investigation of the SAR116 clade using a combination of metagenome-assembled genomes (MAGs, n = 258), single-amplified genomes (n = 84), previously existing (n = 2), and new isolate genomes (n = 5), totaling 349 SAR116 genomes. Phylogenomic investigation supported the division of SAR116 into three distinct subclades, each with additional structure totaling 15 monophyletic groups. Our SAR116 isolates belonged to three groups within subclade I representing distinct genera with different morphologies and varied phenotypic responses to salinity and temperature. Overall, SAR116 genomes encoded differences in vitamin and amino acid synthesis, trace metal transport, and osmolyte synthesis and transport. They also had genetic potential for diverse sulfur oxidation metabolisms, placing SAR116 at the confluence of the organic and inorganic sulfur pools. SAR116 subclades showed distinct patterns in habitat preferences across open ocean, coastal, and estuarine environments, and three of our isolates represented the most abundant coastal and estuarine subclade. This investigation provides the most comprehensive exploration of SAR116 to date anchored by new culture genomes and physiology.</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/PMC12262181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287004","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":"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":"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":"Climate warming enhances biodiversity and stability of grassland soil phosphorus-cycling microbial communities.","authors":"Zijian Wang, Il Han, Jangho Lee, Guangyu Li, Peisheng He, Mathew T Baldwin, Jenny Kao-Kniffin, Liyou Wu, Jizhong Zhou, April Z Gu","doi":"10.1093/ismejo/wraf118","DOIUrl":"10.1093/ismejo/wraf118","url":null,"abstract":"<p><p>Climate warming poses significant challenges to global phosphorus sustainability, an essential component of Earth biogeochemistry cycling and water-food-energy nexus. Despite the crucial role of polyphosphate-accumulating organism as key functional microbial agents in phosphorus cycling, the impacts of global climate warming on polyphosphate accumulating organism communities remain largely enigmatic. This study investigates the effects of climate warming on the taxonomic, network, and functional profiles of soil bacterial polyphosphate-accumulating organisms, leveraging fluorescence-activated cell sorting and single-cell Raman spectroscopy. Climate warming enhances both taxonomic and functional biodiversity of polyphosphate-accumulating organisms via biotic interactions and environmental filtering, with observed functionality-biodiversity relationships supporting the functional redundancy theory. Furthermore, polyphosphate-accumulating organism network complexity and stability rise under warming with strengthened positive relationships, supporting stress gradient hypothesis and the belief that complexity begets stability. Finally, polyphosphate-accumulating organisms are significantly correlated to key ecosystem functioning in carbon and phosphorus cycling under warming. Our study suggests that preserving polyphosphate-accumulating organism communities is crucial for maintaining soil ecosystem functioning and sustainable phosphorus management in a warming world and opens avenues for predicting the responses of other functional microbial groups to climate change, beneficially or maliciously.</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/PMC12366793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509221","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":"Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.","authors":"David W Armitage, Alexandro G Alonso-Sánchez, Samantha R Coy, Zhuli Cheng, Arno Hagenbeek, Karla P López-Martínez, Yong Heng Phua, Alden R Sears","doi":"10.1093/ismejo/wraf154","DOIUrl":"10.1093/ismejo/wraf154","url":null,"abstract":"<p><p>Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet, the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.</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/PMC12376041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735038","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":"Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment.","authors":"Sarah Bolius, Alexandra Schmidt, Jérôme Kaiser, Helge W Arz, Olaf Dellwig, Ulf Karsten, Laura S Epp, Anke Kremp","doi":"10.1093/ismejo/wrae252","DOIUrl":"10.1093/ismejo/wrae252","url":null,"abstract":"<p><p>Dormancy is a widespread key life history trait observed across the tree of life. Many plankton species form dormant cell stages that accumulate in aquatic sediments and, under anoxic conditions, form chronological records of past species and population dynamics under changing environmental conditions. Here we report on the germination of a microscopic alga, the abundant marine diatom Skeletonema marinoi Sarno et Zigone, that had remained dormant for up to 6871 ± 140 years in anoxic sediments of the Baltic Sea and resumed growth when exposed to oxygen and light. Resurrected diatom strains, representing cohorts from six different time points of the past 6871 ± 140 years, are genetically differentiated, and fundamental physiological functions such as growth and photosynthesis have remained stable through time despite distinct environmental dynamics. Showing that resurrection and full functional recovery, in comparison to 3 ± 2 years of dormancy, is possible after millennial resting, we emphasize the relevance of dormancy and living sediment archives. For the future, sediment archives, together with the resurrection approach, would offer a powerful tool to trace adaptive traits over millennia under distinct climatic conditions and elucidate the underlying mechanisms.</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/PMC11742256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142923862","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}