Environmental Microbiome最新文献

{"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":5.4,"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":"https://doi.org/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":5.4,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":"https://doi.org/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":5.4,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":"https://doi.org/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":5.4,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":5.4,"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":"https://doi.org/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":5.4,"publicationDate":"2026-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The composition and function succession of lignocellulose-degrading microbial consortia drives in situ decomposition of rice straw in paddy fields.","authors":"Binhan Zhao, Wenjun Dong, Yang Yu, Xin Zhao, Zhanjun Cai, Haoyue Zhang, Shaojie Li, Xianyun Sun","doi":"10.1186/s40793-026-00888-6","DOIUrl":"https://doi.org/10.1186/s40793-026-00888-6","url":null,"abstract":"<p><strong>Background: </strong>Straw incorporation into soil can increase soil organic matter content and improve soil structure. However, the in situ decomposition mechanisms of straw in field remain unclear.</p><p><strong>Results: </strong>The decomposition mechanisms of straw in paddy fields within the black soil region of Northeast China were investigated by analyzing the composition and functional succession of lignocellulose-degrading microbial consortia (LDMC). Straw decomposition predominantly occurred from May to September, coinciding with warmer temperatures. The alternating paddy-upland field patterns and temperature fluctuations significantly influenced soil microbial community diversity and function, thereby impacting straw decomposition. Through literature analysis, microbial isolation, and enzymatic activity assays, LDMC comprising 18 bacterial genera and 41 fungal genera were proposed. A comprehensive analysis of the dynamics of straw decomposition rates, microbial composition succession, enzymatic profiles, and the abundance of corresponding enzyme genes in soil revealed unique functional succession patterns of LDMC. During the paddy field phase (May-August), Pseudarthrobacter, Bacillus, Nocardioides, Tausonia, Mortierella, Pseudeurotium, etc. were the dominant microbial taxa driving straw decomposition. Tausonia, Mortierella and Pseudeurotium primarily contributed to cellulose degradation, while Bacillus and Nocardioides were involved in the breakdown of both cellulose and hemicellulose. In contrast, Pseudarthrobacter played a major role in lignin degradation. This phase was characterized by a high abundance of cellulase and hemicellulase genes, indicating that decomposition primarily targets these components. During the upland field phase in September, Bacillus, Bradyrhizobium, Mortierella, Mrakia, Pseudeurotium, etc. were the predominant decomposers. Mortierella and Mrakia contributed to the degradation of straw lignocellulose, while Bacillus and Pseudeurotium played a key role in the degradation of cellulose and hemicellulose. In contrast, Bradyrhizobium was predominantly involved in lignin degradation. This phase exhibited a higher abundance of ligninase genes, suggesting a shift towards lignin degradation as the dominant process.</p><p><strong>Conclusions: </strong>These findings provide novel insights into the ecological succession and functional roles of LDMC in rice straw decomposition. They offer a theoretical basis for identifying key lignocellulose-degrading microorganisms active at different phases, thereby laying a foundation for improving the efficiency of rice straw return to fields.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147634760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.","authors":"Pablo Bruna, Patricio Javier Barra, Matías García, Ivan Liachko, María de la Luz Mora, Bas E Dutilh, Michel Abanto","doi":"10.1186/s40793-026-00887-7","DOIUrl":"https://doi.org/10.1186/s40793-026-00887-7","url":null,"abstract":"<p><strong>Background: </strong>Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.</p><p><strong>Results: </strong>Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.</p><p><strong>Conclusions: </strong>This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147628797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.","authors":"Valentina Bočaj, Paula Pongrac, Matevž Likar","doi":"10.1186/s40793-026-00890-y","DOIUrl":"https://doi.org/10.1186/s40793-026-00890-y","url":null,"abstract":"<p><strong>Background: </strong>Noccaea praecox is a zinc (Zn), cadmium (Cd), and lead (Pb) hyperaccumulating plant native to the Italian peninsula and Western Balkans, where it occurs naturally in both metalliferous and non-metalliferous soils. In the present study, we investigated the effects of soil metal concentrations and the plant host on microbial functional traits, specifically the resistome (i.e., microbial functions associated with metal tolerance and resistance) in two soil compartments: the roots and rhizosphere of N. praecox. For this, we collected four plants from each metalliferous and non-metalliferous site and used a metagenomic sequencing approach to characterise microbial functions from paired root and rhizosphere samples, with three root samples per site obtained due to limited biomass, and four rhizosphere samples.</p><p><strong>Results: </strong>The compartment was the primary driver of the general microbial functional structure. By contrast, the soil metal concentrations and root compartment significantly shaped the microbial resistome. Functions associated with the cobalt-zinc-cadmium efflux system and copper-transporting P-type ATPase V were significantly enriched at the metalliferous compared to the non-metalliferous site, with log₂ fold change being 2.62 and 1.72, respectively. Transporters associated with manganese/iron and cobalt/nickel were shaped by the host, regardless of soil metal levels, consistent with host-mediated filtering of microbial functions. Notably, several Zn transporter-related microbial functions associated with the ZIP family were more abundant in the rhizosphere, potentially supporting the plant's high Zn demand.</p><p><strong>Conclusion: </strong>Overall, our results demonstrate that both environmental conditions and plant host play interactive roles in shaping the microbial functional potential, with the host sometimes exerting a stronger influence than soil metal content. The enrichment of Zn transporters (Zrt-/Irt-like proteins) in the rhizosphere of the Zn-hyperaccumulating N. praecox suggests a specific microbial adaptation that may facilitate Zn uptake. These findings provide new insight into the functional dynamics of plant-microbe interactions that support the N. praecox lifestyle.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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":"Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.","authors":"Valeria Castaldi, Wisnu Adi Wicaksono, Martina Chiara Criscuolo, Liberata Gualtieri, Emma Langella, Ilaria Di Lelio, Simona Maria Monti, Francesca De Filippis, Gabriele Berg, Rosa Rao","doi":"10.1186/s40793-026-00885-9","DOIUrl":"https://doi.org/10.1186/s40793-026-00885-9","url":null,"abstract":"<p><strong>Background: </strong>Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.</p><p><strong>Results: </strong>The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log₁₀ bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.</p><p><strong>Conclusion: </strong>Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147619178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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}