Environmental Microbiome最新文献

{"title":"Microbial community succession along the entrance to distant zone in karst cave ecosystem: community assembly and distance decay patterns in weathered rock and sediment habitats.","authors":"Jiaming Du, Liyuan Ma, Xinping Huang, Xiaolu Lu, Hongmei Wang","doi":"10.1186/s40793-026-00900-z","DOIUrl":"10.1186/s40793-026-00900-z","url":null,"abstract":"<p><strong>Background: </strong>Microbial communities in karst caves represent highly specialized and distinct assemblages shaped by the unique physicochemical properties of cave environments. Although recent research has advanced our understanding of community composition, the underlying assembly mechanisms and spatial structuring processes, including distance decay relationships, remain insufficiently resolved. The aim of this research was to elucidate the community assembly mechanisms and distance decay patterns of microbial communities in weathered rock and sediment habitats.</p><p><strong>Results: </strong>We analyzed 16S rRNA gene sequencing data from 333 weathered rock and sediment samples collected across karst caves in the southwestern region of China, India, Italy, and Mexico. Distinct microbial communities were observed between weathered rock and sediment habitats, with sediment communities showing higher alpha diversity and more pronounced compositional shifts with increasing distance from the entrance. Both weathered rock and sediment communities showed distance-decay relationships, suggesting that geographic distance contributes to microbial community differentiation in caves. Moreover, stochastic processes, particularly dispersal limitation, play a dominant role in the assembly of microbial communities in both weathered rock and sediment. However, the influence of ecological drift is more prominent at local scales but declines at larger spatial scales. Sediment habitat and photic zone have higher connectivity, meaning the stable subgroups were formed to enhance ecological adaptability.</p><p><strong>Conclusion: </strong>This study revealed that microbial communities in karst caves are strongly shaped by habitat type, the distance from the cave entrance, and spatial scale. The observed distance-decay patterns indicate that geographic distance contributes to microbial community differentiation in caves, but its influence is weaker than that of local environmental and habitat-specific controls. Stochastic processes dominate community assembly, with dispersal limitation as the key mechanism. The findings provide new insights into the ecological mechanisms underlying microbial distribution in extreme subsurface environments and highlight the importance of integrating large-scale datasets for understanding microbial biogeography in karst systems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13244834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple origins of the apple seed microbiome: disentangling sexual and asexual transmission pathways.","authors":"Maria Faticov, Ayco J M Tack, Doris Köberl, Gabriele Berg, Ahmed Abdelfattah","doi":"10.1186/s40793-026-00901-y","DOIUrl":"10.1186/s40793-026-00901-y","url":null,"abstract":"<p><strong>Background: </strong>The seed microbiome plays a key role in the assembly of the plant microbiome, which has major impacts on plant health. Nonetheless, little is known about the origin of the seed microbiome. We investigated the relative contributions of two potential transmission routes: sexual inheritance (via reproductive organs) and asexual inheritance (via the plant vascular system). To do that, we sampled flower ovaries and pollen sacs, fruiting spurs both before bloom and at seed maturity stages and mature seeds from five field-grown apple trees (Malus domestica BORKH. cv 'Gala Galaxy Selecta').</p><p><strong>Results: </strong>We showed that bacterial alpha diversity differed among tissues: spurs sampled before bloom had significantly higher richness and Shannon diversity than all other compartments, whereas ovary, pollen, spurs at seed maturity, and seeds did not differ in either richness or Shannon diversity. In addition, bacterial community composition differed significantly across all tissue types (ovary, pollen, spurs before bloom, spurs at seed maturity, and seeds). Source tracking revealed that both sexual (30.3%) and asexual (23.8%) pathways contributed to seed microbiome assembly, with spurs at seed maturity being the dominant source. Notably, a large proportion (45.9%) of the seed microbiome originated from unknown sources.</p><p><strong>Conclusions: </strong>Overall, such insights into seed microbiome origin offer new opportunities to enhance seed health and crop productivity through microbiome-assisted breeding.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.","authors":"Martial Leroy, Valentine Cyriaque, Thomas Rattei, Isabelle Laurion, Jérôme Comte","doi":"10.1186/s40793-026-00892-w","DOIUrl":"10.1186/s40793-026-00892-w","url":null,"abstract":"<p><p>Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13227707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147718614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the colonization process of microeukaryotic communities on artificial micro-ecological islands.","authors":"Siyu Gu, Chuanqi Jiang, Peng Zhang, Shuai Luo, Yingchun Gong, Weisong Feng, Jie Xiong, Jing Zhang, Kai Chen, Kang Ning, Wei Miao","doi":"10.1186/s40793-026-00897-5","DOIUrl":"10.1186/s40793-026-00897-5","url":null,"abstract":"<p><strong>Background: </strong>Micro-ecological islands provide unique habitats for microbes and play a crucial role in the functioning of aquatic ecosystems. Microbes settle on these micro-ecological islands, forming distinct microbial communities. Previous studies have provided some understanding of the colonization processes and regulatory mechanisms of protozoa in microbial communities. However, these islands are also subject to colonization by a variety of microbes beyond protozoa, and comprehensive cross-kingdom studies and their potential mechanisms remain largely unexplored.</p><p><strong>Results: </strong>Using polyurethane foam units (PFU) to simulate micro-ecological islands, we studied the colonization dynamics of microbes in two distinct aquatic ecosystems, the Yangtze River and East Lake. Over 10-day colonization survey was conducted, we applied eDNA-PFU technology combined with metagenomic sequencing to comprehensively identify species present in the microbial communities, including bacteria, fungi, flagellates, protozoa, and metazoa. We found that microeukaryotes, rather than prokaryotes, were the primary colonizers in these two aquatic ecosystems. Our study reveals a colonization process of microeukaryotes in PFUs, profoundly influenced by their motility modes. Additionally, we propose a hypothetical food web framework within micro-ecological islands that maintains community stability, representing the most fundamental biological interactions.</p><p><strong>Conclusions: </strong>Overall, this study enriches our understanding of micro-ecological islands and provides deeper insights into the colonization processes and regulatory mechanisms of microbial communities. It highlights the practical significance of micro-ecological islands in biological resource management, environmental protection, and biodiversity conservation.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13202779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence for cable bacteria inhabiting deep in anoxic sediment reveals a novel ecological niche.","authors":"Alexis Fonseca, Martijn Hermans, Francisco J A Nascimento, Christian Stranne, Alf Norkko, Bo G Gustafsson, Christoph Humborg","doi":"10.1186/s40793-026-00895-7","DOIUrl":"10.1186/s40793-026-00895-7","url":null,"abstract":"<p><strong>Background: </strong>Cable bacteria are filamentous sulphide-oxidisers capable of cm-scale electron transport. They are generally considered restricted to the upper few oxic-suboxic cm of marine sediments, where they couple sulphide oxidation to oxygen or nitrate reduction. Despite their influence on redox gradients, trace metal mobility, and nutrient cycling, their presence and activity in deeper anoxic sediment layers remain unknown. The presence and activity of marine cable bacteria (Candidatus Electrothrix) were investigated at four stations in Sweden and Finland, including deep vertical profiles of anoxic sediment layers, to assess their presence and activity under different environmental contexts.</p><p><strong>Results: </strong>Using metatranscriptomic data for rRNA-based community profiling and gene expression combined with porewater geochemistry, evidence of abundant and active cable bacteria was found, peaking below 20 cm depth in deep anoxic sediment layers of Koljö Fjord on the Swedish West Coast. This zone coincided with elevated gene expressions related to sulphide oxidation (including sqr) and nitrate reduction (napA), as well as an abundant presence of sulphide and a sharp nitrate peak. Phylogenetic analyses revealed a diverse assemblage of Ca. Electrothrix includes several potential novel taxa. The co-occurrence of cable bacteria activity, sulphide availability, and a nitrate peak at depth suggests that these organisms may be supported by local nitrate production under anoxic conditions.</p><p><strong>Conclusions: </strong>Our findings challenge the prevailing view that cable bacteria are restricted to shallow sediment horizons and demonstrate their activity and diversity in deep, anoxic layers. This expands the known ecological niche of cable bacteria and suggests that locally produced nitrate under anoxic conditions may facilitate their activity at depth. This discovery advances our understanding of ecology in anoxic marine environments, providing new insights into marine cable bacteria, sediment biogeochemistry, and analogues of early Earth microbial ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13081432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147693066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.","authors":"Stella Brachmann, Kasey N Kiesewetter, Craig Liddicoat, Kiri J Wallace, Martin F Breed, Nico Eisenhauer, Andrew D Barnes","doi":"10.1186/s40793-026-00896-6","DOIUrl":"10.1186/s40793-026-00896-6","url":null,"abstract":"<p><strong>Background: </strong>Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.</p><p><strong>Methods: </strong>To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63 years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.</p><p><strong>Results: </strong>Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.</p><p><strong>Conclusions: </strong>Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13192061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147693094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of silage bacterial clusters and analysis of their microecological characteristics.","authors":"Mao Li, Shuo Wu, Xuejuan Zi","doi":"10.1186/s40793-026-00891-x","DOIUrl":"10.1186/s40793-026-00891-x","url":null,"abstract":"<p><strong>Background: </strong>Enterotypes refer to the different bacterial clusters in the gut microecosystem, which are closely related to host physiology, digestion, disease, and other phenotypes. However, whether there are clear clusters in the silage microecosystem, and the fermentation quality and characteristics of unique cluster silage remain unknown. To determine whether distinct bacterial clusters exist in the silage microecosystem and to characterize their fermentation properties, we analyzed the bacterial community composition and fermentation quality of 156 silage samples, and further explored their underlying microbial ecological features.</p><p><strong>Results: </strong>We confirmed three distinct clusters in the silage microbiome, which were named according to their dominant bacterial taxa: the E-cluster (characterized by a higher abundance of unclassified Enterobacteriaceae (UG)), the P-cluster (enriched with Pseudomonas and Janthinobacterium), and the L-cluster (dominated by Lactobacillus). These microbial clusters were closely associated with fermentation quality: the L-cluster exhibited superior silage quality compared to the E- and P-clusters. Meanwhile, the microbial functional profiles differed significantly among the three clusters of silage. Numerous pathways were significantly enriched in the P-cluster, such as the Biosynthesis of other secondary metabolites, etc. Moreover, bacterial co-occurrence networks of three clusters silage displayed cooperative interactions mainly, P-cluster silage network was more complex and tighter, E-cluster silage has more functional microbial units and more stable. Furthermore, the assembly of microbial communities in the three silage clusters was dominated by stochastic processes. Specifically, the E-cluster and L-cluster were governed by ecological drift, while dispersal limitation was more influential in the P-cluster.</p><p><strong>Conclusions: </strong>Overall, we found in our study that the silage microbiome can be divided into three clusters, and different clusters have significant differences in fermentation quality, microbial diversity and compositions, functional profiles, microbial network characteristics and community assembly mechanisms. These results could broaden our comprehension of the silage microbial ecology processes and also provide a scientific basis on which to develop a method to precisely regulate silage quality.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13185350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147693041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distinct taxonomic signatures in the rhizobiome of two native plants from the polyextreme Salar de Huasco ecosystem.","authors":"Juan Castro-Severyn, Coral Pardo-Esté, João Saraiva, Jonathan Fortt, Ramona Mörchen, Virginia H Albarracin, Claudia P Saavedra, Roland Bol, Eduardo Castro-Nallar, Ulisses Nunes da Rocha, Francisco Remonsellez","doi":"10.1186/s40793-026-00894-8","DOIUrl":"10.1186/s40793-026-00894-8","url":null,"abstract":"<p><strong>Background: </strong>Global food security faces mounting pressure from population growth, climate change, and deteriorating soil conditions. Rhizospheric microbial communities (rhizobiomes) play a key role in plant physiology, enhancing growth and tolerance to abiotic stress. To explore their potential contribution to plant resilience in extreme environments, we characterized the rhizobiomes of Deyeuxia curvula and Werneria incisa across the Salar de Huasco (SH) in the Chilean Altiplano (~ 3800 masl), a polyextreme ecosystem characterized by high UV radiation, salinity gradients, water scarcity, and high metal concentrations. Our objectives were to identify microbial taxa associated with plant adaptation and to infer functional traits linked to survival under these conditions.</p><p><strong>Results: </strong>We generated 16S rRNA amplicon sequencing data from 200 rhizosphere samples. Both host plant identity and geographic location significantly shaped microbial community composition, with site explaining a larger proportion of variance than plant identity alone. Actinomycetota dominated both rhizobiomes, with genera such as Modestobacter and Blastococcus (known for UV resistance, desiccation tolerance, and genomic plasticity) contributing to species-specific profiles. At the genus level, Ilumatobacter, Nesterenkonia, Tropicimonas, and Nitriliruptor were enriched in D. curvula, whereas Pseudarthrobacter, Kocuria, Crossiella, and Blastococcus were more abundant in W. incisa. Network analysis revealed greater complexity and functional redundancy in D. curvula, while W. incisa harbored a more generalist network. Functional predictions indicated that chemoheterotrophy dominates both rhizobiomes, while denitrification, methylotrophy, and ureolysis were enriched in W. incisa, and osmotic stress-tolerance functions such as glycine betaine cycling were enriched in D. curvula.</p><p><strong>Conclusion: </strong>The two plants follow contrasting ecological strategies: D. curvula relies on a specialization and resilience strategy supported by a diverse, stress-adapted rhizobiome, while W. incisa employs a nutritional versatility strategy through a generalist, metabolically flexible community. These findings highlight the value of high-altitude Andean rhizobiomes as reservoirs of great biodiversity with relevant functions for future biotechnological applications particularly for agriculture under arid and saline conditions. This underscores the importance of extending conservation policies to native microbial communities in protected areas such as the Salar de Huasco.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13235159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147677856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpretable multi-omics machine learning reveals drought-driven shifts in plant-microbe interactions.","authors":"Hayato Yoshioka, Pavla Debeljak, Soizic Prado, Yushiro Fuji, Yasunori Ichihashi, Hiroyoshi Iwata","doi":"10.1186/s40793-026-00883-x","DOIUrl":"10.1186/s40793-026-00883-x","url":null,"abstract":"<p><strong>Background: </strong>Plant-microbe interactions in the rhizosphere are central to plant growth, nutrient acquisition, and stress resilience. Although multi-omics approaches enable comprehensive profiling of different biological layers, integrating these data to understand the mechanisms underlying plant-microbe symbiosis, particularly under drought stress, remains a challenge.</p><p><strong>Results: </strong>Genomic, metabolomic, and microbiome data from 198 soybean accessions grown under both control and drought conditions were integrated to identify environment-specific predictive features of the plant phenotypes. We compared best linear unbiased prediction (BLUP), genome-wide association study (GWAS), and a nonlinear machine learning model to evaluate their ability to detect informative features. The machine learning models provided flexible variable selection and outperformed linear models in capturing nonlinear dependencies. Model interpretation using SHapley Additive exPlanations (SHAP) indicated that the isoflavone derivative, daidzin, and the drought-tolerant Candidatus Nitrosocosmicus, were major contributors to phenotypic variation, specifically under drought stress. SHAP-based interaction networks indicated cross-omics links, including connections between daidzin, gamma-aminobutyric acid (GABA), and Paenibacillus.</p><p><strong>Conclusion: </strong>The proposed interpretable machine learning approach for plant phenotype prediction identified multi-omics biomarkers and interactions, providing insights into plant adaptation to drought stress through environment-dependent rhizosphere networks and symbiotic associations.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101135/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147654670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.","authors":"Panji Cahya Mawarda, Arjen Speksnijder, Daan Krijger, Juliette Berkhout, Angela Hoogenboom, Deniz Antonie Duijker, Ahmad Nuruddin Khoiri, Ken Kraaijeveld, Michael Stech, Floyd Wittink","doi":"10.1186/s40793-026-00886-8","DOIUrl":"10.1186/s40793-026-00886-8","url":null,"abstract":"<p><strong>Background: </strong>Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.</p><p><strong>Results: </strong>Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.</p><p><strong>Conclusions: </strong>Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13169696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147647162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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}