ISME Journal最新文献

Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut.

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-02-02 DOI: 10.1093/ismejo/wraf016

Chengfeng Yang, Benfeng Han, Junbo Tang, Jiawei Hu, Lifei Qiu, Wanzhi Cai, Xin Zhou, Xue Zhang

{"title":"Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut.","authors":"Chengfeng Yang, Benfeng Han, Junbo Tang, Jiawei Hu, Lifei Qiu, Wanzhi Cai, Xin Zhou, Xue Zhang","doi":"10.1093/ismejo/wraf016","DOIUrl":"https://doi.org/10.1093/ismejo/wraf016","url":null,"abstract":"The maintenance of bacterial diversity at both species- and strain-levels is crucial for the sustainability of honey bee gut microbiota and host health. Periodic or random fluctuation in diet typically alters the metabolic niches available to gut microbes, thereby continuously reshaping bacterial diversity and interspecific interactions. It remains unclear how closely related bacteria adapt to these fluctuations and maintain coexistence within the bee gut. Here, we demonstrate that the five predominant Gilliamella species associated with Apis cerana, a widely distributed Asiatic honey bee, have diverged in carbohydrate metabolism to adapt to distinct nutrient niches driven by dietary fluctuation. Specifically, the glycan-specialists gain improved growth on a pollen-rich diet, but are overall inferior in competition to non-glycan-specialist on either a simple sugar or sugar-pollen diet, when co-inoculated in the bee host and transmitted across generations. Strikingly, despite of their disadvantage in a high-sugar condition, the glycan-specialists are found prevalent in natural A. cerana guts. We further reveal that these bacteria have adopted a life history strategy characterized by high biomass yield on a low-concentration sugar diet, allowing them to thrive under poor nutritional conditions, such as when the bee hosts undergo periodical starvation. Transcriptome analyses indicate that the divergence in life history strategies is attributed to gene expression programming rather than genetic variation. This study highlights the importance of integrative metabolic strategies in carbohydrate utilization, which facilitate the coexistence of closely related Gilliamella species in a changing bee gut environment.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-30 DOI: 10.1093/ismejo/wraf019

Gi Yoon Shin, Jo Ann Asselin, Amy Smith, Brenna Aegerter, Teresa Coutinho, Mei Zhao, Bhabesh Dutta, Jennie Mazzone, Ram Neupane, Beth Gugino, Christy Hoepting, Manzeal Khanal, Subas Malla, Claudia Nischwitz, Jaspreet Sidhu, Antoinette Machado Burke, Jane Davey, Mark Uchanski, Michael L Derie, Lindsey J du Toit, Stephen Stresow-Cortez, Jean M Bonasera, Paul Stodghill, Brian Kvitko

{"title":"Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans.","authors":"Gi Yoon Shin, Jo Ann Asselin, Amy Smith, Brenna Aegerter, Teresa Coutinho, Mei Zhao, Bhabesh Dutta, Jennie Mazzone, Ram Neupane, Beth Gugino, Christy Hoepting, Manzeal Khanal, Subas Malla, Claudia Nischwitz, Jaspreet Sidhu, Antoinette Machado Burke, Jane Davey, Mark Uchanski, Michael L Derie, Lindsey J du Toit, Stephen Stresow-Cortez, Jean M Bonasera, Paul Stodghill, Brian Kvitko","doi":"10.1093/ismejo/wraf019","DOIUrl":"https://doi.org/10.1093/ismejo/wraf019","url":null,"abstract":"Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-24 DOI: 10.1093/ismejo/wraf012

Ya Liu, Yu Geng, Yiru Jiang, Peng Li, Yue-Zhong Li, Zheng Zhang

{"title":"Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.","authors":"Ya Liu, Yu Geng, Yiru Jiang, Peng Li, Yue-Zhong Li, Zheng Zhang","doi":"10.1093/ismejo/wraf012","DOIUrl":"https://doi.org/10.1093/ismejo/wraf012","url":null,"abstract":"One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Surfactin facilitates establishment of Bacillus subtilis in synthetic communities.

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-23 DOI: 10.1093/ismejo/wraf013

Carlos N Lozano-Andrade, Caja Dinesen, Mario Wibowo, Nil Arenos Bach, Viktor Hesselberg-Thomsen, Scott A Jarmusch, Mikael Lenz Strube, Ákos T Kovács

{"title":"Surfactin facilitates establishment of Bacillus subtilis in synthetic communities.","authors":"Carlos N Lozano-Andrade, Caja Dinesen, Mario Wibowo, Nil Arenos Bach, Viktor Hesselberg-Thomsen, Scott A Jarmusch, Mikael Lenz Strube, Ákos T Kovács","doi":"10.1093/ismejo/wraf013","DOIUrl":"https://doi.org/10.1093/ismejo/wraf013","url":null,"abstract":"Soil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied under in vitro conditions, revealing many roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communities in situ. Here, we specifically examine the influence of Bacillus subtilis-produced cyclic lipopeptides during the assembly of a bacterial synthetic community, and simultaneously, explore the impact of cyclic lipopeptides on B. subtilis establishment success in a synthetic community propagated in an artificial soil microcosm. We found that surfactin production facilitates B. subtilis establishment success within multiple synthetic communities. Although neither a wild type nor a cyclic lipopeptide non-producer mutant had a major impact on the synthetic community composition over time, both the B. subtilis and the synthetic community metabolomes were altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Long-term climate establishes functional legacies by altering microbial traits. 长期气候通过改变微生物特性来建立功能性遗产。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-13 DOI: 10.1093/ismejo/wraf005

Caitlin M Broderick, Gian Maria Niccolò Benucci, Luciana Ruggiero Bachega, Gabriel D Miller, Sarah E Evans, Christine V Hawkes

{"title":"Long-term climate establishes functional legacies by altering microbial traits.","authors":"Caitlin M Broderick, Gian Maria Niccolò Benucci, Luciana Ruggiero Bachega, Gabriel D Miller, Sarah E Evans, Christine V Hawkes","doi":"10.1093/ismejo/wraf005","DOIUrl":"https://doi.org/10.1093/ismejo/wraf005","url":null,"abstract":"Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series. 菌株系统群和环境限制塑造大肠杆菌动态和多样性超过20年的人类肠道时间序列。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wrae245

Bénédicte Condamine, Thibaut Morel-Journel, Florian Tesson, Guilhem Royer, Mélanie Magnan, Aude Bernheim, Erick Denamur, François Blanquart, Olivier Clermont

{"title":"Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series.","authors":"Bénédicte Condamine, Thibaut Morel-Journel, Florian Tesson, Guilhem Royer, Mélanie Magnan, Aude Bernheim, Erick Denamur, François Blanquart, Olivier Clermont","doi":"10.1093/ismejo/wrae245","DOIUrl":"10.1093/ismejo/wrae245","url":null,"abstract":"Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups, except C, were represented, with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty-five clones were identified based on their haplogroup and pairwise genomic single nucleotide polymorphism distance and classified in three phenotypes according to their abundance and residence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four over five dominant/resident clones belonged to B2 and closely related F phylogroups, whereas sub-dominant/transient clones belonged mainly to B1, A and D phylogroups. The long residence times of B2 clones seemed to be counterbalanced by lower colonization abilities. Clones with larger within-host frequency persisted for longer. By comparing ED strain genomes to a collection of commensal E. coli genomes from 359 French individuals, we identified ED-specific genomic properties including an enrichment in genes involved in a metabolic pathway (mhp cluster) and the presence of a very rare antiviral defense island. The E. coli colonization within the gut microbiota was shaped by both the intrinsic properties of the strain lineages, in particular longer residence of phylogroup B2, and the environmental constraints such as diet or phages.","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/PMC11728103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814841","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}

引用次数: 0

Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions. 群居细菌表现出发育阶段的转变，在新的区域建立分散的菌落。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wrae263

Amanda M Zdimal, Giacomo Di Dio, Wanxiang Liu, Tanya Aftab, Taryn Collins, Remy Colin, Abhishek Shrivastava

{"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":"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.","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}

引用次数: 0

Resurrection of a diatom after 7000 years from anoxic Baltic Sea sediment. 在缺氧的波罗的海沉积物中，硅藻在7000年后复活。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wrae252

Sarah Bolius, Alexandra Schmidt, Jérôme Kaiser, Helge W Arz, Olaf Dellwig, Ulf Karsten, Laura S Epp, Anke Kremp

{"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":"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.","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}

引用次数: 0

Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae. 从失落之城热液区分离的Pacmanvirus将转座子的概念扩展到迷你病毒科之外。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf002

Sébastien Santini, Audrey Lartigue, Jean-Marie Alempic, Yohann Couté, Lucid Belmudes, William J Brazelton, Susan Q Lang, Jean-Michel Claverie, Matthieu Legendre, Chantal Abergel

{"title":"Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae.","authors":"Sébastien Santini, Audrey Lartigue, Jean-Marie Alempic, Yohann Couté, Lucid Belmudes, William J Brazelton, Susan Q Lang, Jean-Michel Claverie, Matthieu Legendre, Chantal Abergel","doi":"10.1093/ismejo/wraf002","DOIUrl":"10.1093/ismejo/wraf002","url":null,"abstract":"The microbial sampling of submarine hydrothermal vents remains challenging, with even fewer studies focused on viruses. Here we report what is to our knowledge the first isolation of a eukaryotic virus from the Lost City hydrothermal field, by co-culture with the laboratory host Acanthamoeba castellanii. This virus, named pacmanvirus lostcity, is closely related to previously isolated pacmanviruses (strains A23 and S19), clustering in a divergent clade within the long-established family Asfarviridae. The icosahedral particles of this virus are 200 nm in diameter, with an electron-dense core surrounded by an inner membrane. The viral genome of 395 708 bp (33% G + C) has been predicted to encode 473 proteins. However, besides these standard properties, pacmanvirus lostcity was found to be associated with a new type of selfish genetic element, 7 kb in length, whose architecture and gene content are reminiscent of those of transpovirons, hitherto specific to the family Mimiviridae. As in previously described transpovirons, this selfishg genetic element propagates as an episome within its host virus particles and exhibits partial recombination with its genome. In addition, an unrelated episome with a length of 2 kb was also found to be associated with pacmanvirus lostcity. Together, the transpoviron and the 2-kb episome might participate in exchanges between pacmanviruses and other DNA virus families. It remains to be elucidated if the presence of these mobile genetic elements is restricted to pacmanviruses or was simply overlooked in other members of the Asfarviridae.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Spatial sensing as a strategy for public goods regulation by gut microbes. 空间感应是肠道微生物调节公共产品的一种策略。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-11-26 DOI: 10.1093/ismejo/wrae233

I Hashem, A Zhang, J Van Impe

引用次数: 0