ISME Journal最新文献

{"title":"Multimodular flavobacterial enzymes specialised in coordinated decomposition of cellulose and alginate in brown algal cell walls.","authors":"Fei Xu, Xiao-Hui Sun, Xiao-Dong Zhang, Xiao-Fei Wang, Yan Wang, Hai-Yan Cao, Peng Wang, Jian-Xun Li, Xi-Ying Zhang, Qi-Long Qin, Xiu-Lan Chen, Yu-Zhong Zhang, Yin Chen, Yu-Qiang Zhang","doi":"10.1093/ismejo/wrag112","DOIUrl":"https://doi.org/10.1093/ismejo/wrag112","url":null,"abstract":"<p><p>Brown algal cell walls are complex matrices composed primarily of alginate, cellulose, and fucoidan. Their depolymerization is important in marine carbon cycling. Although numerous algal polysaccharide-degrading enzymes have been characterized, most studies focus on breaking down single, purified polysaccharides, leaving the degradation mechanisms of native cell walls containing mixed polysaccharides poorly understood. Here we report the integrated modular enzymes involved in brown algal cell wall polysaccharides (BACWPs) degradation. Using the marine flavobacterium Aquimarina sp. 2-A2 as a model, we isolated a bifunctional enzyme, CelAly, which integrates a glycoside hydrolase family 5 cellulase domain and a polysaccharide lyase family 31 alginate lyase domain within a single polypeptide, enabling the degradation of cellulose and alginate in brown algal cell walls. In vivo relevance of CelAly was confirmed by upregulation of its gene during growth on algal biomass. CelAly also contains three distinctive substrate-binding modules (B1, B2, UKD) that support its multimodular functionality; among these, UKD is notable for its dual substrate-binding capability. CelAly's modular architecture and interdomain flexibility may facilitate coordinated degradation of BACWPs. Bioinformatic analyses and biochemical validation revealed three additional types of such modular enzymes from marine microbes. CelAly and related modular enzymes are strongly associated with marine environments and exhibit conserved modular strategy for substrate recognition and catabolism. Thus, these enzyme architectures represent a previously unrecognized strategy specialised for BACWPs decomposition. This study elucidates the unique structural and functional adaptations of the integrated multimodular enzymes and highlights their ecological prevalence among marine bacteria, providing insights into natural biomass decomposition.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857541","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}

{"title":"Short-term antagonism between bacteriophages and macrophages decreases with bacteria-phage coevolution.","authors":"Meaghan Castledine, Zuzanna Szczutkowska, Andrew Matthews, Sarah K Walsh, Rai Lewis, Suzanne Kay, Janet A Willment, Gordon D Brown, Angus Buckling","doi":"10.1093/ismejo/wrag116","DOIUrl":"https://doi.org/10.1093/ismejo/wrag116","url":null,"abstract":"<p><p>Phage therapy, the use of viruses that infect bacteria (bacteriophages), is a promising complement to antibiotics during the antimicrobial resistance crisis, but treatment success is very variable. A key variable which likely influences treatment outcomes is how different immune components interact with bacteriophage, with studies finding neutrophils work synergistically while macrophages work antagonistically with bacteriophage. However, many of these studies characterise interactions and outcomes over short timescales, not considering the potential for the evolution of resistance to bacteriophages which can itself greatly affect treatment outcomes. Here, we measure how macrophages and bacteriophages affect densities and resistance evolution of the pathogen Pseudomonas aeruginosa in vitro. Consistent with previous studies, we find macrophages interact antagonistically with bacteriophages in the short term. However, this antagonism was lost following bacterial population recovery associated with rapidly evolved resistance to bacteriophages. Macrophages resulted in greater net levels of resistance and hindered increases in bacteriophage infectivity, but this did not lead to differences in bacteria-phage population dynamics. This work emphasises the importance of characterising the effect of the immune system on phage therapy outcomes over both shorter- and longer- timescales.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857597","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}

{"title":"Rapid Adaptive Evolution of Oxylipin-Based Chemical Defence Against Algicidal Bacteria in a Bloom-Forming Diatom.","authors":"Muhaiminatul Azizah, Janine F M Otto, Nico Ueberschaar, Markus Werner, Oliver Werz, Georg Pohnert","doi":"10.1093/ismejo/wrag111","DOIUrl":"https://doi.org/10.1093/ismejo/wrag111","url":null,"abstract":"<p><p>Phytoplankton, the photosynthetic microalgae driving nearly half of Earth's primary production, are the foundation of marine food webs and central to climate regulation. Skeletonema marinoi is a globally distributed and often dominant diatom species in marine phytoplankton communities. It inhabits a dynamic and frequently hostile microbial environment in which interactions with bacteria can negatively affect its survival. S. marinoi is susceptible to the algicidal bacterium Kordia algicida that can lyse the algal cells and even terminate entire blooms. The extent to which resistance against such a lysis can evolve in diatoms exposed to biotic stress by algicidal bacteria remains unknown. Using adaptive laboratory evolution, we investigated how S. marinoi adapts to toxins produced by K. algicida. S. marinoi evolved resistance already after eleven growth cycles under sub-lethal exposure to algicides. This was accompanied by changes in DNA methylation. Untargeted comparative metabolomics of the original and the evolved population revealed the up-regulation of the oxylipins 5-hydroxyeicosapentaenoic acid (5-(R)-HEPE), prostaglandin E2 (PGE2), and 17-hydroxydocosahexaenoic acid (17-HDHA). These oxylipins significantly inhibited the growth of K. algicida, indicating their role in chemical defense. The metabolic plasticity of diatoms and the rapid evolution observed after exposure to bacteria open new perspectives on our understanding of diatom bloom dynamics in nature.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857602","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}

{"title":"Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug resistance plasmids.","authors":"Daniel Cazares, Eliza Rayner, Adrian Cazares, Wendy Figueroa, David Goulding, Samuel T E Greenrod, Adam J Mulkern, Michelle Y Y Yin, Tao He, Nick Thomson, Michael A Brockhurst, R Craig MacLean","doi":"10.1093/ismejo/wrag113","DOIUrl":"https://doi.org/10.1093/ismejo/wrag113","url":null,"abstract":"<p><p>Phage therapy offers a promising alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill targeted pathogens and prevent the further spread of antibiotic resistance genes encoded by plasmids. However, the evolutionary trajectories of multidrug-resistance (MDR) plasmids under the selective pressure of PDPs remain poorly understood, particularly in eco-evolutionary contexts that remain permissive to plasmid conjugation. We experimentally evolved populations of Escherichia coli carrying the MDR plasmid RP4 in the presence of the plasmid-dependent phage PRD1 under conditions where the benefits of conjugation were either strong or weak. When opportunities for conjugation were rare, PRD1 only transiently suppressed the conjugative plasmid population due to the rapid evolution of phage-resistant plasmids lacking conjugative ability. Increasing ecological opportunities for conjugation enhanced plasmid suppression and delayed the evolution of phage-resistant plasmids. PRD1 resistance was associated with plasmid loss and reduced conjugative ability, although this trade-off was complex because resistance mutations had heterogeneous effects on pilus production and conjugation. Mutations and IS-mediated inactivation in conjugation genes generated a spectrum of resistance phenotypes, from partial resistance (trbB, trbL) to complete resistance (virB4/trbE). Bioinformatic analysis of publicly available IncP plasmids revealed frequent truncations of the VirB4/TrbE protein, suggesting that plasmid-dependent phages may represent an important selective pressure shaping plasmid evolution in natural populations. Our results demonstrate an evolutionary trade-off between conjugative ability and phage resistance that cannot be easily circumvented by plasmids. Targeting multidrug-resistance plasmids with PDPs is likely to drive loss of conjugation, limiting the transfer of antibiotic resistance genes in microbial communities.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857566","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}

{"title":"Contrasting salinity regimes reshape microbe-DOM coupling and reduce recalcitrant dissolved organic carbon preservation in a salt lake.","authors":"Xiding Wang, Yang Liu, Xinyue Yang, Ruikai Zhang, Xudong Liu, Fangru Nan, Qi Liu, Junping Lv, Jia Feng, Shulian Xie","doi":"10.1093/ismejo/wrag107","DOIUrl":"https://doi.org/10.1093/ismejo/wrag107","url":null,"abstract":"<p><p>Salt lakes account for nearly half of the world's inland water area and play an irreplaceable role as \"carbon conversion and stabilization factories,\" making substantial contributions to the global carbon cycle. Central to this function is the transformation of dissolved organic carbon (DOC) and its accumulation into recalcitrant dissolved organic carbon (RDOC), which together underpin internal carbon processing in these systems. However, the pathways through which DOC is converted to RDOC in salt lakes, and how these pathways are shaped by salinity and microbial communities, remain poorly resolved. Here, using Yuncheng Salt Lake as a within-lake system, we combined field-based in situ characterization with long-term incubation experiments to examine how contrasting salinity regimes were associated with microbial and dissolved organic matter (DOM) variation. Higher salinity was associated with reduced bacterial and dissolved organic matter diversity, stronger deterministic bacterial assembly, and a restructured bacteria-DOM association network. Under the standardized nutrient-replete incubation conditions used here, samples from the higher-salinity regime exhibited higher biodegradable DOC, lower RDOC preservation, and greater overall DOC loss over the 100-day experimental timescale. Salinity-related differences in microbial community composition, metabolomic profiles, and dissolved organic matter characteristics were closely associated with variation in RDOC dynamics, suggesting that these carbon-processing differences were accompanied by coordinated microbial and metabolic reorganization. Together, these results provide process-relevant, condition-specific evidence that contrasting salinity regimes within Yuncheng Salt Lake were associated with differences in microbe-DOM coupling and in DOC/RDOC outcomes.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845436","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}

{"title":"Tissue-Specific Experimental Evolution Reveals Adaptive Trade-Offs in the Plant Vascular Pathogen Clavibacter michiganensis.","authors":"Raj Kumar Verma, Veronica Roman-Reyna, Nathan Benmoche, Evanson Ngugi, Eduard Belausov, Noa Sela, Maya Bar, Jonathan M Jacobs, Doron Teper","doi":"10.1093/ismejo/wrag110","DOIUrl":"https://doi.org/10.1093/ismejo/wrag110","url":null,"abstract":"<p><p>The plant pathogenic bacterium Clavibacter michiganensis (Cm) is a systemic vascular pathogen that colonizes both xylem vessels and the intracellular apoplast during different stages of infection. To identify traits and loci associated with adaptation to these distinct host microenvironments, we conducted tissue-specific experimental evolution. Twenty independent Cm lineages were repeatedly passaged in either tomato stems or leaves to promote adaptation to vascular or apoplastic lifestyles, respectively. After fifteen passages, adapted clones were characterized for virulence and virulence-related traits. These characterizations demonstrated clear differential associations of virulence-associated traits with the adapted tissue. The majority of vascular-adapted clones displayed enhanced surface attachment, reduced cellulase activity, reduced exopolysaccharide (EPS) production, and attenuated virulence on tomato compared to the parent clone. In contrast, apoplast-adapted clones displayed reduced biofilm formation and enhanced EPS production and retained their virulence on tomato. Whole-genome sequencing of all adapted clones revealed candidate loci linked to tissue adaptation. Six of ten vascular-adapted clones carried two independent mutations in CMM_1284, a putative HipB/XRE-type transcriptional regulator. A CMM_1284 marker exchange mutant displayed phenotypes similar to vascular-adapted clones, suggesting a role for this regulator in vascular colonization. Together, these findings highlight the role of phenotypic plasticity in tissue adaptation of plant pathogens, showing that tissue-specific adaptation involves modulation of surface attachment, EPS production, and cell wall-degrading enzymes and suggest a trade-off between vascular persistence, supported by strong surface attachment, and systemic virulence, which depends on bacterial dispersal and migration.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845390","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}

{"title":"Trait-based signatures associated with persistence and thermal benefit in a genomically decayed coral probiotic.","authors":"Mei Xie, Congjuan Xu, Nan Xiang, Tianhua Liao, Xing Liu, Zhiqi Liu, Xiaoyuan Feng, Qian He, Zizhen Liang, Weiqi Wang, Yifan Dai, Lili Yan, Claudia Pogoreutz, Lena Barra, Shannon Wing Ngor Au, Liwen Jiang, Christian R Voolstra, Haiwei Luo","doi":"10.1093/ismejo/wrag106","DOIUrl":"https://doi.org/10.1093/ismejo/wrag106","url":null,"abstract":"<p><p>A key bottleneck in microbiome engineering is ensuring long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of population MC10, identified by such signatures, showed persistent coral colonization in a companion study. Whether this persistence translates into measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both controls. To understand the mechanistic basis, we characterized the functional profile of MC10-B4 using integrated multi-omics. The MC10 genome is enriched in host-interaction genes, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, confirmed phenotypically by iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated \"motile-to-sessile\" proteomic reprogramming, downregulating flagellar motor components whereas upregulating flagellin and biofilm regulators. This response was distinct from sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4's functional profile, particularly its oxidative stress sensitivity, contrasts with traits favored in conventional probiotic screens. Our results provide mechanistic insight into traits associated with long-term host association and thermal benefit, validating an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities for rational probiotic design.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845372","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}

{"title":"Stable association of a chlamydial symbiont with the freshwater predator Hydra suggests broad host potential.","authors":"Angelika Schwarzhans, Justine Boutry, Jácint Tökölyi, Norbert Cyran, Martin Kunert, Matthias Horn, Astrid Collingro","doi":"10.1093/ismejo/wrag104","DOIUrl":"https://doi.org/10.1093/ismejo/wrag104","url":null,"abstract":"<p><p>Symbiotic associations between microorganisms often involve eukaryotes partnering with microbes for nutrient exchange, protection, and resource acquisition. Bacterial lineages like the Chlamydiota have evolved entirely symbiotic lifestyles, exploiting their eukaryotic hosts for energy, diverse metabolites, and shelter. The study of environmental chlamydiae - outside the well-studied vertebrate host range - has revealed diverging interactions on the mutualism-parasitism spectrum. This highlights their potentially important roles in host-microbe interactions underscoring the relevance of obtaining isolates from diverse environments and hosts. Here, we describe an isolate of a chlamydial symbiont of the freshwater cnidarian Hydra. The symbiont could be isolated and stably maintained in insect cell lines and represents a member of the recently described family-level lineage Chlamydiae Clade III for which we propose the name Endochlamydiaceae. Fluorescence and electron microscopy reveal the symbiont morphology and its endodermal location. Comparative genomics shows the isolate, named Endochlamydia hydrae, encodes a conserved set of genes involved in host invasion, communication, and pathogenicity. Instead of displaying unique genomic adaptations to its animal host, E. hydrae shows signs consistent with ongoing genome reorganisation and streamlining, suggesting a more recent host shift. Screening for closely related 16S rRNA gene sequences in public environmental microbiomes also indicates a broader host range. Moreover, exploration of environmental Hydra oligactis populations revealed they might serve as host for a wider spectrum of chlamydial species. This study highlights the evolutionary success of chlamydiae and their genomic toolkit to infect a wide range of hosts and their ecological significance by interacting with diverse organisms.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147787909","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}

{"title":"Temperature-dependent photostasis and nitrogen limitation in streamlined-genome red algae Cyanidiophyceae from natural habitats.","authors":"Dai Tsujino, Takayuki Fujiwara, Shota Yamashita, Kei Tamashiro, Jin Izumi, Fumi Yagisawa, Beifeng Zhou, Shunsuke Hirooka, Yuki Sunada, Kintake Sonoike, Shin-Ya Miyagishima","doi":"10.1093/ismejo/wrag105","DOIUrl":"https://doi.org/10.1093/ismejo/wrag105","url":null,"abstract":"<p><p>Photosynthetic microorganisms must continuously balance light energy absorption with metabolic demand to maintain photostasis under fluctuating environments. Cyanidiophyceae, unicellular red algae from acidic hot springs with highly streamlined genomes (9-18 Mb), nevertheless thrive across a wide temperature range (20-56°C), posing the question of how such minimalist eukaryotic cells sustain photostasis in nature. Here, we combined field observations of natural mats in sulfuric hot springs in Japan with laboratory experiments under habitat-mimicking conditions. Spring-water chemistry remained nearly constant year-round, characterized by low nitrogen availability (<30 μM), whereas temperature varied spatially and seasonally. Growth increased with temperature (up to 47°C) and nearly ceased at 20-25°C, yet photosynthetic pigment levels and apparatus components remained largely unchanged, indicating sustained light absorption even under conditions of minimal growth. At low temperatures, photosystem efficiency and regulated energy dissipation decreased, whereas non-regulated dissipation and reactive oxygen species (ROS) increased, indicating excess excitation energy was mainly dissipated through non-regulated pathways. Proteomic and transcriptomic analyses showed accumulation of ROS scavengers and chromosome maintenance/repair proteins at low temperature, suggesting that excess reducing power/ATP, even after partial energy dissipation, was redirected toward stress mitigation rather than growth. At higher temperatures, nitrogen-deficiency responses emerged, reflecting nitrogen limitation relative to elevated demand for rapid growth. Together, these results reveal a temperature-dependent trade-off in Cyanidiophyceae in natural habitats: oxidative stress at low temperature versus nitrogen limitation at high temperature. Overall, our findings highlight a simple yet robust photostasis strategy and provide environmental and omics resources for studies of this model lineage.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147787888","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}

{"title":"Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.","authors":"Alejandro De Santiago, Shelby Barnes, Tiago José Pereira, Mirayana Marcellino-Barros, Lekeah Durden, Min Khant Han, J Cameron Thrash, Holly M Bik","doi":"10.1093/ismejo/wrag091","DOIUrl":"10.1093/ismejo/wrag091","url":null,"abstract":"<p><p>Despite growing insights into the composition of marine invertebrate microbiomes, our understanding of their ecological and evolutionary patterns remains poor, owing to limited sampling depth and low-resolution datasets. Previous studies have provided conflicting results that both confirm and deny the existence of phylosymbiosis between marine invertebrates and marine bacteria. Here, we investigated potential animal-microbe symbioses in Pseudoalteromonas, a bacterial genus consistently identified as a core microbiome taxon in diverse invertebrates. Using a pangenomic analysis of 236 free-living and invertebrate-associated bacterial strains (including two new nematode-associated isolates generated in this study), we confirm that Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (e.g., Nematoda, Mollusca, and Cnidaria). Patterns of symbiosis were consistent irrespective of geography (including in Antarctica), with FISH images from nematodes indicating that bacterial symbionts form biofilms in the mouth and esophagus and are sometimes present in female nematode ovaries exhibiting stunted development. The evolutionary history of Pseudoalteromonas is marked by substantial host-switching and lifestyle transitions, and host-associated genomes suggest that these bacteria are facultative symbionts involved in nutritional symbioses. In marine environments, we hypothesize that horizontally acquired symbionts may have co-evolved with invertebrates, using host mucus as a physical niche and food source, while providing their animal hosts with Vitamin B, amino acids, and bioavailable carbon compounds in return.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147724557","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}