The ISME Journal最新文献

{"title":"Spatio-temporal pattern formation of living organisms at the edge of chaos","authors":"Johannes Werner, Hartmut Arndt","doi":"10.1093/ismejo/wraf050","DOIUrl":"https://doi.org/10.1093/ismejo/wraf050","url":null,"abstract":"Understanding spatio-temporal dynamics is essential for predicting how populations fluctuate over time and space. Theoretical models have highlighted the ecological complexity of spatio-temporal dynamics, which can lead to the emergence of complex patterns, including nonlinear dynamics and chaotic behavior, important mechanisms for maintaining of biodiversity. However, these dynamics are difficult to observe experimentally due to a lack of temporal and spatial resolution. Here we show that even a single-species system exhibits complex spatio-temporal patterns without external forcing where order and chaos coexist (edge of chaos). Automated analyses of experimental dynamics of cells of a ciliate on a microfluidic chip environment with 50 interconnected patches documented pattern formation, including chaos-like dynamics, using several analytical methods. Different initial conditions caused changes in patterns, revealing the complexity and principal unpredictability of self-organized pattern formation. A model containing the stochastic fluctuations of the experiment verified the deterministic nature of patterns. The results show the intrinsic complexity of ecological systems, challenging predictions in nature conservation. Our results bridge the gap between theoretical models and experimental observations, offering new insights into the fundamental nature of living systems and their spatio-temporal organization.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143618427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecological and evolutionary responses of earthworm holobionts to environmental changes","authors":"Michael Opoku Adomako, Jing Wu, Fei-Hai Yu","doi":"10.1093/ismejo/wraf044","DOIUrl":"https://doi.org/10.1093/ismejo/wraf044","url":null,"abstract":"Global environmental change substantially affects soil detritivores, including earthworms, impacting host-microbiota interactions and altering key soil biogeochemical processes such as litter decomposition. As microbial communities are inherently capable of rapid evolution, responses of earthworms and associated microbiota (i.e., earthworm holobionts) to global environmental change may likely involve the interplay of ecological and evolutionary processes and feedbacks. Although species-level responses of earthworms to global environmental change are well-studied, the potential ecological and evolutionary responses of earthworm holobionts to environmental change remain unexplored. Here, we provide a conceptual framework to elaborate on the complex network of earthworm host−microbiota interactions that modify their traits in response to global environmental change, jointly shaping their ecology and evolution. Based on literature, we synthesize evidence of global environmental change impacts on earthworm host-microbiota and discuss evidence of their ecological and evolutionary responses to environmental change. Lastly, we highlight the agro- and eco-system level consequences of environmental change-mediated shift in earthworm host-microbiota functions. Soil legacies of environmental change have cascading detrimental impacts on the abundance, diversity, and functional dynamics of earthworm host-microbiota interactions in agriculture and ecosystems. The primary mechanisms driving such responses of earthworm hosts and associated microbial communities to environmental change include altered litter quality and host dietary preferences, competitive interactions and exclusion, habitat homogenization, and a shift in soil physicochemical and biological processes. Therefore, advancing knowledge of the intricate animal-microorganism interactions is crucial for belowground biodiversity management in a changing global environment.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"192 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143583057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate","authors":"Aditya Jeevannavar, Javier Florenza, Anna-Maria Divne, Manu Tamminen, Stefan Bertilsson","doi":"10.1093/ismejo/wraf046","DOIUrl":"https://doi.org/10.1093/ismejo/wraf046","url":null,"abstract":"Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143583058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic interdependence and rewiring in Radiolaria-microalgae Photosymbioses","authors":"Vera Nikitashina, Benjamin Bartels, Joost Samir Mansour, Charlotte LeKieffre, Johan Decelle, Christian Hertweck, Fabrice Not, Georg Pohnert","doi":"10.1093/ismejo/wraf047","DOIUrl":"https://doi.org/10.1093/ismejo/wraf047","url":null,"abstract":"Marine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments, they are among the most important primary producers. Systematic studies of radiolarian biology are limited because Radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian photosymbiosis we address here the metabolic contributions of the partners to the performance of the holobiont. Therefore, we describe the metabolic inventory of two highly abundant photosymbiotic Radiolaria – colony-forming Collodaria and single-celled Acantharia and compare their metabolomes to metabolomes of respective free-living algae. Most of the metabolites detected in the symbiosis are not present in the free-living algae, suggesting a significant transformation of symbionts' metabolites by the host. The metabolites identified in both the holobiont and the free-living algae encompass molecules of primary metabolism and a number of osmolytes, including dimethylsulfoniopropionate. Mass spectrometry imaging revealed the presence of dimethylsulfoniopropionate in both the symbionts and host cells, indicating that the algae provide osmolytic protection to the host. Furthermore, our findings suggest a possible dependence of Collodaria on symbiotic vitamin B3. Distinctive differences in phospholipid composition between free-living and symbiotic stages indicate that the algal cell membrane may undergo rearrangement in the symbiosis. Our results demonstrate a strong interdependence and rewiring of the algal metabolism underlying Radiolaria-microalgae photosymbioses.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"53 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143583064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant growth-promotion triggered by extracellular polymer is associated with facilitation of bacterial cross-feeding networks of the rhizosphere","authors":"Yian Gu, Wenhui Yan, Yu Chen, Sijie Liu, Liang Sun, Zhe Zhang, Peng Lei, Rui Wang, Sha Li, Samiran Banerjee, Ville-Petri Friman, Hong Xu","doi":"10.1093/ismejo/wraf040","DOIUrl":"https://doi.org/10.1093/ismejo/wraf040","url":null,"abstract":"Despite the critical role rhizosphere microbiomes play in plant growth, manipulating microbial communities for improved plant productivity remains challenging. One reason for this is the lack of knowledge on how complex substrates secreted in the microbiome ultimately shape the microbe-microbe and plant-microbe interaction in relation to plant growth. One such complex substrate is poly-γ-glutamic acid, which is a microbially derived extracellular polymer. While it has previously been linked with plant growth-promotion, the underlying mechanisms are not well understood. Here we show that this compound benefits plants by fostering cross-feeding networks between rhizosphere bacteria. We first experimentally demonstrate that poly-γ-glutamic acid application increases potassium bioavailability for tomato plants by driving a shift in the rhizosphere bacterial community composition. Specifically, application of poly-γ-glutamic acid increased the relative abundance of Pseudomonas nitroreducens L16 and Pseudomonas monteilii L20 bacteria which both promoted tomato potassium assimilation by secreting potassium-solubilizing pyruvic acid and potassium-chelating siderophores, respectively. Although either Pseudomonas strain could not metabolize poly-γ-glutamic acid directly, the application of poly-γ-glutamic acid promoted the growth of Bacillus species, which in turn produced metabolites that could promote the growth of both P. nitroreducens L16 and P. monteilii L20. Moreover, the P. monteilii L20 produced 3-hydroxycapric acid, which could promote the growth of P. nitroreducens L16, resulting in commensal cross-feeding interaction between plant growth-promoting bacteria. Together, these results show that poly-γ-glutamic acid plays a crucial role in driving plant growth-promotion via bacterial cross-feeding networks, highlighting the opportunity for using microbially derived, complex substrates as catalysts to increase agricultural productivity.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extracellular aminopeptidase regulates exopolysaccharide production of Pseudomonas aeruginosa via quorum sensing","authors":"Tianhu Zhao, Fanglin Lei, Zhenyu Zhang, Di Wang, Luyan Z Ma","doi":"10.1093/ismejo/wraf038","DOIUrl":"https://doi.org/10.1093/ismejo/wraf038","url":null,"abstract":"The biofilm matrix primarily consists of proteins, exopolysaccharides, and extracellular DNA. Pseudomonas aeruginosa aminopeptidase is one of the most abundant matrix proteins in P. aeruginosa biofilms and plays a crucial role in modulating biofilm development. In a previous study, we have revealed that the loss of aminopeptidase enhances the attachment ability of P. aeruginosa. However, the mechanism by which aminopeptidase affects attachment remains unclear. In the present study, we demonstrate that aminopeptidase is the primary protein associated with the matrix exopolysaccharide Psl. The loss of aminopeptidase leads to increased production of Psl, resulting in enhanced attachment of P. aeruginosa. Further investigation shows that aminopeptidase represses the transcription of the psl operon through the LasI/LasR quorum sensing system, rather than through other known psl regulators or the cyclic-di-GMP signaling molecule. Aminopeptidase inhibits the transcription of lasI via the short peptides cleaved from the proform of aminopeptidase during its activation, which results in reduced biosynthesis of the quorum sensing signaling molecule C12-HSL, further decreasing the production of Psl. In conclusion, our study reveals an interplay between two key matrix components via the quorum sensing signal, suggesting a mechanism by which bacteria control initial attachment and exopolysaccharide production in response to cell density.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"84 6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mice expressing the autism-associated neuroligin-3 R451C variant exhibit increased mucus density and altered distributions of intestinal microbiota","authors":"Madushani Herath, Joel C Bornstein, Elisa L Hill-Yardin, Ashley E Franks","doi":"10.1093/ismejo/wraf037","DOIUrl":"https://doi.org/10.1093/ismejo/wraf037","url":null,"abstract":"The intestinal mucus layer protects the host from invading pathogens and is essential for maintaining a healthy mucosal microbial community. Alterations in the mucus layer and composition of mucus-residing microbiota in people diagnosed with autism may contribute to dysbiosis and gastrointestinal dysfunction. Although microbial dysbiosis based on sequencing data is frequently reported in autism, spatial profiling of microbes adjacent to the mucosa is needed to identify changes in bacterial subtypes in close contact with host tissues. Here, we analysed the spatial distribution of the mucin-2 protein using immunofluorescence as well as total bacteria, Bacteroidetes, Firmicutes phyla and Akkermansia muciniphila using fluorescent in situ hybridization in mice expressing the autism-associated R451C variant in the Neuroligin-3 gene. We show that the Neuroligin-3 R451C variant increases mucus density adjacent to the distal ileal epithelium in mice. The relative density of total bacteria, Firmicutes and A. muciniphila was increased whereas the density of Bacteroidetes was decreased closer to the epithelium in Neuroligin-3R451C mice. In summary, the autism-associated R451C variant in the Neuroligin-3 gene increases mucus density adjacent to the epithelium and alters microbial spatial distribution in the mouse distal ileum.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome diversification of symbiotic fungi in beetle-fungus mutualistic symbioses","authors":"Yin-Tse Huang, Khaled Abdrabo El-Sayid Abdrabo, Guan Jie Phang, Yu-Hsuan Fan, Yu-Ting Wu, Jie-Hao Ou, Jiri Hulcr","doi":"10.1093/ismejo/wraf039","DOIUrl":"https://doi.org/10.1093/ismejo/wraf039","url":null,"abstract":"Ambrosia beetles and their fungal symbionts represent a widespread and diverse insect-fungus mutualism. This study investigates the genomic adaptations associated with the evolution of the ambrosia lifestyle across multiple fungal lineages. We performed comparative genomic analyses on 70 fungal genomes from four families (Irpicaceae, Ceratocystidaceae, Nectriaceae, and Ophiostomataceae), including 24 ambrosia and 34 non-ambrosia lineages. Our phylogenomic analyses reveal multiple independent colonization of insect vectors by the fungi, spanning from the mid-Cretaceous (114.6 Ma) to the early Quaternary (1.9 Ma). Contrary to expectations for obligate symbionts, ambrosia fungi showed no significant genome-wide modification in size, gene count, or secreted protein repertoire compared to their non-symbiotic relatives. Instead, we observed conservation of most assessed genomic features; where genome traits differ between free-living relatives and ambrosia fungi, the changes are lineage-specific, not convergent. Key findings include lineage-specific expansions in carbohydrate-active enzyme families (AA4 in Nectriaceae, CE4 in Ophiostomataceae, and GH3 in Ophiostomataceae and Ceratocystidaceae), suggesting potential enhancement or loss of lignin modification, hemicellulose deacetylation, and cellulose degradation in different ambrosia lineages. Repeat-Induced Point mutation analysis revealed family-specific patterns rather than lifestyle-associated differences. These results highlight the diverse genomic strategies employed by ambrosia fungi, demonstrating that symbiont evolution can proceed through refined, lineage-specific changes rather than genome-wide, or convergent alterations. Our genomic analyses do not reveal patterns typically associated with domestication in these ambrosia fungi, suggesting they may represent free-living fungi that co-opted wood boring beetles as vectors through subtle, lineage-specific adaptations.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"67 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes","authors":"Nathalie A Delherbe, Oscar Gomez, Alvaro M Plominsky, Aaron Oliver, Maximino Manzanera, Marina G Kalyuzhnaya","doi":"10.1093/ismejo/wraf026","DOIUrl":"https://doi.org/10.1093/ismejo/wraf026","url":null,"abstract":"Drylands cover one-third of the Earth’s surface and are one of the largest terrestrial sinks for methane. Understanding the structure–function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors—water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 to 12.73 μmol m2 h−1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"131 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143546384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiota contribute to regulation of the gut-testis axis in seasonal spermatogenesis","authors":"Zifang Wu, Long Li, Shaoxian Chen, Ye Gong, Yuyan Liu, Tianqi Jin, Yang Wang, Jie Tang, Qian Dong, Bangzhu Yang, Fangxia Yang, Wuzi Dong","doi":"10.1093/ismejo/wraf036","DOIUrl":"https://doi.org/10.1093/ismejo/wraf036","url":null,"abstract":"Seasonal breeding is an important adaptive strategy for animals. Recent studies have highlighted the potential role of the gut microbiota in reproductive health. However, the relationship between the gut microbiota and reproduction in seasonal breeders remains unclear. In this study, we selected a unique single food source animal, the flying squirrel (Trogopterus xanthipes), as a model organism for studying seasonal breeding. By integrating transcriptomic, metabolomic, and microbiome data, we comprehensively investigated the regulation of the gut-metabolism-testis axis in seasonal breeding. Here, we demonstrated a significant spermatogenic phenotype and highly active spermatogenic transcriptional characteristics in the testes of flying squirrels during the breeding season, which were associated with increased polyamine metabolism, primarily involving spermine and γ-amino butyric acid. Moreover, an enrichment of Ruminococcus was observed in the large intestine during the BS and may contribute to enhanced methionine biosynthesis in the gut. Similar changes in Ruminococcus abundance were also observed in several other seasonal breeders. These findings innovatively revealed that reshaping the gut microbiota regulates spermatogenesis in seasonal breeders through polyamine metabolism, highlighting the great potential of the gut-testis axis in livestock animal breeding and human health management.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"82 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}