ISME communications最新文献_第4页

Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence. 抗微生物药物耐药性作为143年时间序列土壤恢复的标志。

IF 6.4

ISME communications Pub Date : 2026-09-02 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag250

Tim Goodall, Briony Jones, Amy C Thorpe, Robert I Griffiths, Hyun S Gweon, Daniel S Read, Richard Pywell, Susheel Bhanu Busi

{"title":"Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence.","authors":"Tim Goodall, Briony Jones, Amy C Thorpe, Robert I Griffiths, Hyun S Gweon, Daniel S Read, Richard Pywell, Susheel Bhanu Busi","doi":"10.1093/ismeco/ycag250","DOIUrl":"10.1093/ismeco/ycag250","url":null,"abstract":"Restoring agriculturally degraded habitats to species-rich grasslands is a vital conservation objective. During restoration, how the soil resistome matures alongside microbial community composition and function remains unclear. Here, we tested two competing hypotheses: whether the soil resistome co-occurs through a microbial structural maturation, in which soil restoration is associated with higher-order biotic interactions, or whether antimicrobial resistance (AMR) is instead associated with the competitive pressures and high bacterial taxonomic richness found in disturbed, eutrophic arable land. Using a unique land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly following the cessation of agricultural activity. Our results demonstrate that AMR abundance increases significantly with restoration age, reaching a maximum in >143-year-old soils. The strongest predictor of this rise in AMR abundance was an increasing microbial eukaryotic signature rather than increasing microbial density, suggesting that resistome expansion is not associated with generalized spatial competition, but rather, co-occurs with structural maturation of the microbiome. We observed an order of magnitude increase in antibiotic biosynthetic potential, dominated by the emergence of streptomycin clusters. Microbial reorientation during soil maturation mirrors the expansion of a core resistome comprised of ancient, intrinsic mechanisms, such as Major Facilitator Superfamily (MFS) efflux pumps and RNA Polymerase-Binding Protein A (RbpA) target protection, in older soils. We demonstrate that endogenous AMR is a hallmark of healthy, restored soil ecosystems rather than a marker of anthropogenic soil degradation.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag250"},"PeriodicalIF":6.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13592167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Temperature modulates infection-associated metabolic responses in bloom-forming freshwater diatoms. 温度调节形成水华的淡水硅藻感染相关代谢反应。

IF 6.4

ISME communications Pub Date : 2026-08-26 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag240

Doris Ilicic, Marine Vallet, Fatemeh Salimi, Anthony T Buaya, Marco Thines, Hans-Peter Grossart

{"title":"Temperature modulates infection-associated metabolic responses in bloom-forming freshwater diatoms.","authors":"Doris Ilicic, Marine Vallet, Fatemeh Salimi, Anthony T Buaya, Marco Thines, Hans-Peter Grossart","doi":"10.1093/ismeco/ycag240","DOIUrl":"10.1093/ismeco/ycag240","url":null,"abstract":"Warmer waters are reshaping unseen interactions at the base of aquatic food webs, with potential consequences for microalgal bloom dynamics and carbon transfer to higher trophic levels. Two major groups of aquatic parasites-chytrids and oomycetes-infect the same algal host, and changes in temperature can alter the dynamics of these infections and determine their success. Using laboratory-controlled synthetic communities, we investigated the effect of temperature on chytrid and oomycete infection dynamics in the bloom-forming freshwater diatom Ulnaria ulna. Our findings reveal complex dynamics, with temperature shaping infection prevalence and host growth differently between the two infection systems. Notably, chytrid infection prevalence increased at lower temperatures, challenging the general applicability of the cold-water refuge theory in this host-parasite system, whereas oomycete infection dynamics showed a contrasting temperature response. Using UHPLC-HRMS analysis, we identified significant metabolic changes associated with parasite infection, while temperature further modulated these responses differently in chytrid- and oomycete-infected cultures. Chytrid infections were associated with metabolites potentially linked to stress- or defense-related responses, whereas oomycete infections exhibited metabolic signatures potentially associated with nutrient scavenging and manipulation of host metabolism. These different metabolic responses suggest that warming not only alters parasite success, but also modifies the biochemical composition of infected host-parasite systems, with possible implications for trophic transfer efficiency and carbon cycling. Together, these findings establish a conceptual framework linking temperature with infection-associated metabolic changes and provide first insights into how temperature affects parasitic infections of microalgae and their biochemical consequences for aquatic food webs.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag240"},"PeriodicalIF":6.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dispersal pathways and infection strategies within the Global Halophilic Virome. 全球嗜盐病毒群的传播途径和感染策略。

IF 6.4

ISME communications Pub Date : 2026-08-25 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag244

Borja Aldeguer-Riquelme, Cristina López, Eva Mayol, María Dolores Ramos-Barbero, Valentin Gangloff, Tomeu Viver, Ana S Ramírez, Souad Amiour, Aharon Oren, Stephanus N Venter, María E Llames, Bernardo González, Horia L Banciu, Catherine Lizama, Ramon Rossello-Mora, Fernando Santos, Josefa Antón

{"title":"Dispersal pathways and infection strategies within the Global Halophilic Virome.","authors":"Borja Aldeguer-Riquelme, Cristina López, Eva Mayol, María Dolores Ramos-Barbero, Valentin Gangloff, Tomeu Viver, Ana S Ramírez, Souad Amiour, Aharon Oren, Stephanus N Venter, María E Llames, Bernardo González, Horia L Banciu, Catherine Lizama, Ramon Rossello-Mora, Fernando Santos, Josefa Antón","doi":"10.1093/ismeco/ycag244","DOIUrl":"https://doi.org/10.1093/ismeco/ycag244","url":null,"abstract":"Microbial biogeography has recently attracted significant attention for its potential to provide novel ecological and evolutionary insights, with environmental connectivity emerging as a key factor in the global distribution of viruses and their hosts. Hypersaline systems, due to their geographical isolation and extreme conditions, are typically expected to exhibit low connectivity. However, reports of similar viral assemblages in geographically distant hypersaline environments suggest a higher level of connectivity than previously assumed, although the mechanisms underlying viral dispersal remain poorly understood. We hypothesized that seawater facilitates the dispersal of halophilic viruses (haloviruses). To test the hypothesis, we analyzed twenty hypersaline water samples from globally distributed sites across four continents and constructed \"The Global Halophilic Virome Dataset\" (GHV), containing 10 705 viral Operational Taxonomic Units (vOTUs). Additionally, we proposed a sample-adapted threshold to distinguish between \"abundant\" and \"rare\" members of the virosphere. Our findings indicate that coastal hypersaline systems harbor highly similar viral communities, whereas inland systems are dominated by endemic vOTUs, and that seawater may act as the primary carrier of halovirus dispersal. Infection strategies also varied across environments, with coastal salterns showing a lower potential for viral infection and a higher percentage of viruses with a potential integrative temperate lifestyle.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag244"},"PeriodicalIF":6.4,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oil composition determines microbial preference for carbon source between hydrocarbons and Necromass in water droplets within crude shale oil. 原油组成决定了微生物在原油页岩油水滴中的碳氢化合物和坏死物之间对碳源的偏好。

IF 6.4

ISME communications Pub Date : 2026-08-24 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag242

Qiao-Hui Wang, Yi-Fan Liu, Biao Wang, Qin Xiao, Lei Zhou, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu

{"title":"Oil composition determines microbial preference for carbon source between hydrocarbons and Necromass in water droplets within crude shale oil.","authors":"Qiao-Hui Wang, Yi-Fan Liu, Biao Wang, Qin Xiao, Lei Zhou, Shi-Zhong Yang, Ji-Dong Gu, Bo-Zhong Mu","doi":"10.1093/ismeco/ycag242","DOIUrl":"10.1093/ismeco/ycag242","url":null,"abstract":"Water droplets entrapped in crude oil have recently been recognized as unexpected but metabolically active microbial habitats in shale oil reservoirs. However, the key environmental drivers that shape the community composition and metabolic profiles of these droplet microorganisms remain poorly understood. Here, we investigated three shale oil samples from Jiangsu oilfield, all of which contained abundant water droplets (>105 droplets/ml oil) of ancient formation water origin. Integrated microscopy, metagenomics, and metabolomics revealed that the physicochemical properties of the enclosing oil, primarily API gravity and viscosity, are associated with droplet size and may influence the droplet microbiomes. These factors appear to jointly drive a fundamental metabolic dichotomy, where in light oil with low-salinity water, communities are enriched with hydrocarbon degraders together with molecular signatures of active petroleum hydrocarbon metabolism. In more viscous, light-to-medium oil with high-salinity water, however, communities shift towards necromass recycling and strong genetic adaptations to osmotic stress. Our findings demonstrate that microbial life in water droplets enclosed in shale oil is widely found in the shale oil reservoirs examined, and selected by carbon quality and environmental pressure. This study provides a mechanistic framework for understanding microbial ecology and biogeochemical processes in shale oil reservoirs and offers insights for microbial enhanced oil recovery in heavy oil reservoirs.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag242"},"PeriodicalIF":6.4,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573599/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148972285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The illusion of functional stability: functional redundancy does not equal functional insurance in a natural-engineered aquatic continuum. 功能稳定的错觉：在一个自然工程的水生连续体中，功能冗余并不等于功能保险。

IF 6.4

ISME communications Pub Date : 2026-08-24 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag229

Qiong Tang, Zhe Li, Lunhui Lu

{"title":"The illusion of functional stability: functional redundancy does not equal functional insurance in a natural-engineered aquatic continuum.","authors":"Qiong Tang, Zhe Li, Lunhui Lu","doi":"10.1093/ismeco/ycag229","DOIUrl":"https://doi.org/10.1093/ismeco/ycag229","url":null,"abstract":"Functional redundancy-the capacity of multiple species to perform similar ecological functions-is widely regarded as a buffer that stabilizes ecosystem processes. However, whether functional redundancy truly translates into functional insurance remains unverified in microbial communities. Here, by integrating metagenomics and metatranscriptomics from 52 samples across a natural-engineered aquatic continuum in the Yanjin River watershed, China, results show that functional redundancy and functional insurance are fundamentally decoupled. We constructed a dual-layer analytical framework linking genomic functional overlap (effect trait) with transcriptional response heterogeneity (response trait) and developed a functional insurance index (FII) that quantifies whether redundant species respond differently to environmental variation. Our results reveal a striking paradox: engineered systems harbor the highest genomic functional redundancy yet the lowest functional insurance, because their functionally redundant species respond synchronously to perturbations-creating an illusion of stability. In contrast, natural communities exhibit lower absolute redundancy but significantly higher insurance, driven by diversified transcriptional responses among functionally similar species. Critically, only FII-not redundancy, response diversity, or asynchrony alone-significantly predicted CO2 and CH4 concentrations and DOM compositional stability, closing the evidence chain from genotype through phenotype to ecosystem function. These findings challenge the prevailing assumption that functional redundancy ensures functional insurance and reveal that conventional redundancy-based assessments may systematically overestimate or underestimate the functional stability of aquatic ecosystems.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag229"},"PeriodicalIF":6.4,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Lineage-restricted genomic islands drive rhizosphere niche specialization in Pseudomonas capeferrum. 谱系限制的基因组岛驱动角孢假单胞菌根际生态位特化。

IF 6.4

ISME communications Pub Date : 2026-08-23 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag231

Miguel A López-Carrasco, Gabriela Purtschert-Montenegro, Marta Pinto-Carbo, Gerardo Cárcamo-Oyarce, Ratchara Kalawong, Leo Eberl

{"title":"Lineage-restricted genomic islands drive rhizosphere niche specialization in Pseudomonas capeferrum.","authors":"Miguel A López-Carrasco, Gabriela Purtschert-Montenegro, Marta Pinto-Carbo, Gerardo Cárcamo-Oyarce, Ratchara Kalawong, Leo Eberl","doi":"10.1093/ismeco/ycag231","DOIUrl":"https://doi.org/10.1093/ismeco/ycag231","url":null,"abstract":"In the rhizosphere, plant growth-promoting rhizobacteria play a pivotal role in plant health by efficiently colonizing roots and enhancing growth through diverse direct and indirect mechanisms. Many of these beneficial traits are associated with genomic islands (GEIs) acquired via horizontal gene transfer, yet their contribution to rhizosphere fitness remains poorly understood. Here, we report the whole-genome sequencing and comprehensive analysis of Pseudomonas putida strain IsoF, a highly efficient root colonizer originally isolated from the tomato rhizosphere that induces systemic resistance in plants. Phylogenomic analysis reclassified IsoF within the P. capeferrum group and revealed an extensive repertoire of GEIs encoding candidate functions to rhizosphere adaptation and plant growth promotion. Notably, IsoF harbours a unique combination of three GEIs absent in closely related strains. Phenotypic characterization and rhizosphere persistence assays using defined deletion mutants demonstrated that these islands significantly contribute to IsoF fitness and competitiveness in the rhizosphere. Together, our findings establish GEIs as key determinants of ecological success in beneficial rhizobacteria and position IsoF as a promising candidate for sustainable biocontrol applications.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag231"},"PeriodicalIF":6.4,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13600407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149042423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Calcidiscus leptoporus genome reveals vitamin-mediated holobiont interactions. 细鳞钙藻基因组揭示了维生素介导的全息离子相互作用。

IF 6.4

ISME communications Pub Date : 2026-08-23 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag222

Frederic Chaux, Tanja Vojvoda Zeljko, Borna Branimir Vuković, John A Burns, Titouan Le Perrun, Marta Žižek, Briget P Bannerman, Donald Tonye Bara Mason, Clotilde Garrido, Zhou Xu, Richard G Dorrell, Jelena Godrijan

{"title":"The Calcidiscus leptoporus genome reveals vitamin-mediated holobiont interactions.","authors":"Frederic Chaux, Tanja Vojvoda Zeljko, Borna Branimir Vuković, John A Burns, Titouan Le Perrun, Marta Žižek, Briget P Bannerman, Donald Tonye Bara Mason, Clotilde Garrido, Zhou Xu, Richard G Dorrell, Jelena Godrijan","doi":"10.1093/ismeco/ycag222","DOIUrl":"10.1093/ismeco/ycag222","url":null,"abstract":"Coccolithophores are major marine phytoplankton that contribute to ocean carbon cycling through both organic carbon fixation and calcium carbonate biomineralization, yet the functional basis of their interactions with phycosphere bacteria remains poorly resolved. Here, we present the nuclear genome of the haploid phase of the coccolithophore Calcidiscus leptoporus, a coccolithophore that calcifies in both life-cycle stages. We combined host genome analysis, genome-resolved characterization of associated bacteria, and a four-month vitamin-manipulation experiment to test how B-vitamin biosynthetic complementarity relates to host performance and phycosphere community assembly. Metabolic reconstructions indicate partitioned B-vitamin biosynthtic potential: the host encodes pathways for B2, B5, B6, and B9, including a rare fused B5 biosynthesis gene, but lacks complete pathways for B1, B3, B7, and B12. These missing functions were distributed among recurrent bacterial taxa, with no single bacterial MAG encoding the full set of host-missing vitamins. Across the experiment, bacterial community composition was structured primarily by the experimental phase, while vitamin treatments secondarily influenced which taxa became enriched at later stages. Consistent with genome-inferred auxotrophy, B-vitamin availability constrained long-term growth under the tested conditions, with B1 alone providing partial rescue and vitamin-replete treatments showing equal or stronger responses. Together, these data establish C. leptoporus as a genomic model for coccolithophore biology and holobiont interactions, while providing a testable framework linking vitamin economies to phycosphere assembly and host performance.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag222"},"PeriodicalIF":6.4,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13518057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148834890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unraveling the diversity, function, and virus-host interactions of archaeal proviruses. 揭示古细菌原病毒的多样性、功能和病毒与宿主的相互作用。

IF 6.4

ISME communications Pub Date : 2026-08-22 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag243

Yang Zhao, PengFei Liu, LinXing Chen, MeiLing Feng, Rong Wen, ZhiHao Zhang, XueFeng Zhang, HongFei Chi

{"title":"Unraveling the diversity, function, and virus-host interactions of archaeal proviruses.","authors":"Yang Zhao, PengFei Liu, LinXing Chen, MeiLing Feng, Rong Wen, ZhiHao Zhang, XueFeng Zhang, HongFei Chi","doi":"10.1093/ismeco/ycag243","DOIUrl":"10.1093/ismeco/ycag243","url":null,"abstract":"Archaea, the third domain of life, play critical roles in global biogeochemical cycles. However, archaeal proviruses integrated into host genomes remain largely unexplored. To bridge this gap, we conducted a large-scale mining of genomes spanning all presently known 21 archaeal phyla for their proviruses. We identified 770 archaeal proviruses across 12 archaeal phyla and 84 families, which clustered into 655 viral operational taxonomic units (vOTUs). Among these, 86.1% of the vOTUs were novel at the species level, and 69.3% could not be classified at the family level, substantially expanding the known diversity of archaeal viruses. Additionally, phylogenomic analysis supported the proposal of 16 putative novel viral families, further extending the current taxonomy landscape of archaeal viruses. Notably, 21.8% of the identified proviruses were predicted to adopt a lytic lifestyle, suggesting that these proviruses may retain the capacity to enter the lytic cycle under appropriate conditions. Host prediction indicated only 14 out of the 655 vOTUs might have potential across-lineage infection abilities. We detected 63 anti-defense genes encoded by 61 provirus genomes, such as anti-CRISPR and anti-RM, suggesting an ongoing evolutionary arms race between hosts and proviruses. However, only 10 auxiliary metabolic genes (AMGs) were identified, suggesting a limited impact of proviruses in the modulation of host metabolism through AMGs. This study establishes a systematic global genomic atlas of archaeal proviruses, advancing our understanding of their distribution and diversity while providing a foundation for future research into how proviruses regulate archaeal metabolism and ecosystem functioning.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag243"},"PeriodicalIF":6.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148972314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Boreal and subarctic freshwaters harbour a diversity of jumbophages. 北方和亚北极的淡水中栖息着各种各样的巨噬生物。

IF 6.4

ISME communications Pub Date : 2026-08-22 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag239

Meeri Niemi, Karyna Karneyeva, Lotta-Riina Sundberg, Hanna M Oksanen, Elina Laanto

{"title":"Boreal and subarctic freshwaters harbour a diversity of jumbophages.","authors":"Meeri Niemi, Karyna Karneyeva, Lotta-Riina Sundberg, Hanna M Oksanen, Elina Laanto","doi":"10.1093/ismeco/ycag239","DOIUrl":"10.1093/ismeco/ycag239","url":null,"abstract":"Bacteriophages (phages) are major drivers of microbial evolution and ecology, yet their diversity and functional roles remain poorly characterized in many natural environments, such as in freshwater systems. In boreal and subarctic freshwater habitats, where bacteria are typically slow-growing and nutrient-limited, phages are predicted to have a critical role in host regulation and horizontal gene exchange. However, only a few isolates have been obtained from such environments, leaving the genetic and functional diversity of these phages largely unexplored. Here, we present a collection of 40 bacteriophages isolated from boreal lakes and rivers using a set of diverse freshwater bacterial hosts. Despite using conventional isolation methods, eight of the isolates possess genomes larger than 200 kilobases and are classified as jumbophages. All jumbophages exhibited myovirus morphology and comparatively slow infection dynamics. These jumbophages include the first known representatives infecting members of Janthinobacterium and Herbaspirillum. Comparative genomic and phylogenetic analyses show that nearly all genomes are distinct from previously described phages, indicating substantial novelty. Diverse auxiliary metabolic and anti-defence systems were identified, including putative NAD+ salvage and acyl carrier protein modules, along with predicted Anti-Thoeris and Anti-CBASS elements. The Pseudomonas-infecting jumbophage Ahti encoded homologues of all 21 core genes that define the nucleus-forming family Chimalliviridae. Additionally, Ahti displayed compartmentalization of DNA during infection, establishing it as the first freshwater nucleus-forming phage. These findings expand our understanding of the ecological, genomic, and functional diversity of phages in boreal environments and highlight the role of freshwater ecosystems as significant reservoirs of novel viral lineages.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag239"},"PeriodicalIF":6.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148972303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Global in silico analysis reveals a core gut microbiota in fall armyworm (Spodoptera frugiperda) shaped by geography and diet. 全球硅分析揭示了秋粘虫（Spodoptera frugiperda）的核心肠道微生物群受地理和饮食的影响。

IF 6.4

ISME communications Pub Date : 2026-08-22 eCollection Date: 2026-01-01 DOI: 10.1093/ismeco/ycag233

Lakshay Anand, Kendall R Corbin

{"title":"Global in silico analysis reveals a core gut microbiota in fall armyworm (Spodoptera frugiperda) shaped by geography and diet.","authors":"Lakshay Anand, Kendall R Corbin","doi":"10.1093/ismeco/ycag233","DOIUrl":"10.1093/ismeco/ycag233","url":null,"abstract":"Fall armyworms (Spodoptera frugiperda) are an invasive agricultural pest whose adaptability and resilience are increasingly linked to their gut microbiota. In this study, we performed a global-scale in-silico meta-analysis of publicly available 16S rRNA datasets to identify a conserved core gut microbiota and assess how geography and diet shape microbial community structure and function. Using both prevalence-based and unsupervised clustering approaches, we defined a robust global core microbiota composed of 88 high-confidence ASVs, including genera such as Enterococcus, Pseudomonas, and Acinetobacter, which were consistently present regardless of geographical region or diet. These taxa are important in nutrient metabolism, detoxification, and stress tolerance, contributing to host fitness and ecological success. Geographic origin significantly influenced gut microbiota diversity and composition, with continent- and country-level differences supported by alpha/beta diversity metrics and supervised machine learning classification (AUC = 1.0). Diet also influenced microbial community structure, although its effect was weaker than that of geography, explaining 11.9% of the variation compared to 13.5%. Functional predictions using PICRUSt2 revealed region-specific enrichment of pathways related to xenobiotic degradation, amino acid metabolism, and vitamin biosynthesis, suggesting specific microbial taxa may contribute to host adaptation and resilience through these metabolic functions. This is the first global synthesis of the S. frugiperda gut microbiota that integrates geographic and dietary factors. The identification of a global-level conserved core microbiota provides a foundation for developing synthetic microbial communities and microbiome-informed pest management strategies aimed at enhancing control efficacy.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag233"},"PeriodicalIF":6.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13639100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0