Environmental Microbiome最新文献

{"title":"Microbial composition on microplastics mediated by stream impairment.","authors":"Anne L Gilewski, Saurav Shrestha, Sharon N Kahara, Nikolas M Stasulli","doi":"10.1186/s40793-025-00685-7","DOIUrl":"10.1186/s40793-025-00685-7","url":null,"abstract":"<p><strong>Background: </strong>Studies into biofilm interactions with microplastic polymers in marine environments are widespread in the literature. Increasing evidence suggests that lotic microplastics are a significant contributor and may accumulate harmful or pathogenic organisms, thereby contributing to the degradation of marine ecosystems where they meet riverine systems. Suboptimal water quality of these riverine systems may influence these biomes. This project compared the microbial diversity of biofilms that developed on microplastics to natural stone substrates in an impaired and unimpaired section of the Quinnipiac River Watershed. In this project, the influence of impairment was studied based on microbial diversity via 16S rRNA gene sequencing while monitoring total colony and fecal coliform colony counts using standard water sampling methods.</p><p><strong>Results: </strong>Total coliform colony counts were greater in the impaired Quinnipiac River site than in the unimpaired Honeypot Brook tributary and on the microplastic substrate than the stone substrate. Sequenced features to the class level were dominated by Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, comprising 75% of the community biome. Simpson's Diversity indices indicated that within the two substrates, there was little variation between the communities. However, it was noted that microplastic alpha diversity trended slightly lower than the stone. Further analysis of common aquatic enteropathogens showed that the genus Citrobacter was significantly more abundant on the microplastics at both locations.</p><p><strong>Conclusions: </strong>Our results indicate impaired waterbodies with a microplastic burden may retain greater fecal coliform bacterial loads than unimpaired waterbodies. Increased microplastic loads in compromised lotic systems may have an additive impact. Water quality remediation and careful monitoring are recommended to reduce this effect. Comparing this study with environmental community analysis could provide valuable insight into preferential surface attachment of bacteria onto microplastic.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"32"},"PeriodicalIF":6.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651467","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 transcriptome patterns highlight increased pedogenesis-related activity in arid soils under simulated humid conditions.","authors":"Victoria Rodríguez, Alexander Bartholomäus, Susanne Liebner, Romulo Oses, Thomas Scholten, Dirk Wagner","doi":"10.1186/s40793-025-00689-3","DOIUrl":"10.1186/s40793-025-00689-3","url":null,"abstract":"<p><strong>Background: </strong>In arid and semiarid environments, microbial activity is restricted by low water availability and high evapotranspiration rates, and soil development is limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis by microbial processes. Our study aims to broaden our understanding of soil development under a climate change scenario toward humid conditions and to identify the microorganisms that help transform initial soils from arid and semiarid sites. We characterized pedogenetic microbial processes and how their gene expression differs between soils from arid and semiarid sites under a sixteen-week climate simulation experiment using metagenomic and metatranscriptomic approaches.</p><p><strong>Results: </strong>We found that an intense functional response is triggered under humid climate conditions in the arid site compared to the semiarid site, which showed greater resilience. The arid site undergoes higher transcription of genes involved in soil aggregate formation, phosphorus metabolism, and weathering, potentially adapting the development of arid sites to climate change. Additionally, a transcriptional reconfiguration linked to soil carbon and nitrogen dynamics suggests that soil microorganisms use available organic resources alongside autotrophy in response to increased moisture. Pseudomonadota and Actinomycetota dominated the overall transcriptional profile and specific functions associated with the early stages of soil development in both sites.</p><p><strong>Conclusions: </strong>Our findings highlight the rapid activation of pathways related to pedogenesis under humid conditions in arid sites, potentially driven by their metabolic requirements and environmental stressors, influencing soil development dynamics under global climate change.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"31"},"PeriodicalIF":6.2,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651481","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":"Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.","authors":"Morgane Duret, Adrian Wallner, Ludovic Besaury, Aziz Aziz","doi":"10.1186/s40793-025-00690-w","DOIUrl":"10.1186/s40793-025-00690-w","url":null,"abstract":"<p><strong>Background: </strong>Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.</p><p><strong>Results: </strong>Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.</p><p><strong>Conclusions: </strong>This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"30"},"PeriodicalIF":6.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634741","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":"Ironing out the conflicts: iron supplementation reduces negatives bacterial interactions in the rhizosphere of an Atacama-endemic perennial grass.","authors":"Constanza Aguado-Norese, Jonathan E Maldonado, Christian Hodar, Gabriel Galvez, Daniel E Palma, Verónica Cambiazo, Mauricio Gonzalez","doi":"10.1186/s40793-024-00661-7","DOIUrl":"10.1186/s40793-024-00661-7","url":null,"abstract":"<p><strong>Background: </strong>In plants, root exudates selectively influence the growth of bacteria that colonize the rhizosphere. Bacterial communities associated with root systems are involved in macro and micronutrients cycling and organic matter transformation. In particular, iron is an essential micronutrient required for the proper functioning of iron-containing enzymes in processes such as photosynthesis, respiration, biomolecule synthesis, redox homeostasis, and cell growth in plants. However, the impact of changes of iron availability on the structure and set of ecological interactions taking place in the rhizosphere remains poorly understood. In this study, field experiments were conducted to compare the effects of iron supplementation (0.1 and 0.5 mM of FeSO₄) on the assembly of the bacterial community of rhizosphere soil and bulk soil in a perennial grass present in the Andes steppe of Atacama Desert.</p><p><strong>Results: </strong>The results indicated that the difference in beta diversity between bulk soil and rhizosphere soil detected before supplementation did not persist after iron supplementation, in addition, co-occurrence networks showed a significant reduction in negative interactions among soil bacteria, mainly in rare taxa (< 0.1% relative abundance).</p><p><strong>Conclusions: </strong>These observations suggest that iron availability contributes to the differentiation between bulk soil and rhizosphere bacterial communities, a process that is linked to significant changes in the relative abundance of more abundant species (> 0.1% relative abundance) and with a decrease in the negative interactions in both compartments after metal exposure. The differential effect of iron on the competition/cooperation ratio between bulk soils and the rhizosphere microbiome supports the hypothesis that the host limits the degree of cooperation that can be achieved by the bacterial community associated with an organ dedicated to nutrient absorption.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"29"},"PeriodicalIF":6.2,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606694","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":"Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.","authors":"Absar Talat, Yasir Bashir, Nadeem Khalil, Connor L Brown, Dinesh Gupta, Asad Ullah Khan","doi":"10.1186/s40793-024-00658-2","DOIUrl":"10.1186/s40793-024-00658-2","url":null,"abstract":"<p><strong>Background: </strong>Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.</p><p><strong>Results: </strong>The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, bla_OXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (bla_NDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.</p><p><strong>Conclusions: </strong>Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"27"},"PeriodicalIF":6.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11884044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574438","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":"Alternative stable states of microbiome structure and soil ecosystem functions.","authors":"Hiroaki Fujita, Shigenobu Yoshida, Kenta Suzuki, Hirokazu Toju","doi":"10.1186/s40793-025-00688-4","DOIUrl":"10.1186/s40793-025-00688-4","url":null,"abstract":"<p><strong>Background: </strong>Theory predicts that biological communities can have multiple stable states in terms of their species/taxonomic compositions. The presence of such alternative stable states has been examined in classic ecological studies on the communities of macro-organisms (e.g., distinction between forest and savanna vegetation types). Nonetheless, it remains an essential challenge to extend the target of the discussion on multistability from macro-organismal systems to highly species-rich microbial systems. Identifying alternative stable states of taxonomically diverse microbial communities is a crucial step for predicting and controlling microbiome processes in light of classic ecological studies on community stability.</p><p><strong>Results: </strong>By targeting soil microbiomes, we inferred the stability landscapes of community structure based on a mathematical framework of statistical physics. We compiled a dataset involving 11 archaeal, 332 bacterial, and 240 fungal families detected from > 1,500 agroecosystem soil samples and applied the energy landscape analysis to estimate the stability/instability of observed taxonomic compositions. The statistical analysis suggested that both prokaryotic and fungal community structure could be classified into several stable states. We also found that the inferred alternative stable states differed greatly in their associations with crop disease prevalence in agroecosystems. We further inferred \"tipping points\", through which transitions between alternative stable states could occur.</p><p><strong>Conclusion: </strong>Our results suggest that the structure of complex soil microbiomes can be categorized into alternative stable states, which potentially differ in ecosystem-level functioning. Such insights into the relationship between structure, stability, and functions of ecological communities will provide a basis for ecosystem restoration and the sustainable management of agroecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"28"},"PeriodicalIF":6.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11887376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574435","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":"Effects of drainage and long-term tillage on greenhouse gas fluxes in a natural wetland: insights from microbial mechanisms.","authors":"Fengqin Liu, Jiale Yang, Wenyan Shen, Jiale Fu, Jia Meng, Yupeng Zhang, Jianzheng Li, Zhiliang Yuan","doi":"10.1186/s40793-025-00682-w","DOIUrl":"10.1186/s40793-025-00682-w","url":null,"abstract":"<p><strong>Background: </strong>The conversion of natural wetlands to agricultural land through drainage contributes to 62% of the global wetland loss. Such conversion significantly alters greenhouse gas (GHG) fluxes, yet the underlying mechanisms of GHG fluxes resulting from drainage and long-term tillage practices remain highly uncertain. In this study, we measured GHG fluxes of a natural reed wetland (referred to as \"Wetland\") and a drained wetland that used as farmland (referred to as \"Dryland\").</p><p><strong>Results: </strong>The results demonstrated that annual cumulative N₂O and CO₂ fluxes in Dryland were 282.77% and 53.79% higher than those in Wetland, respectively. However, CH₄ annual cumulative fluxes decreased from 12,669.45 ± 564.69 kg·ha^- 1 to 8,238.40 ± 207.72 kg·ha^- 1 in Dryland compared to Wetland. The global warming potential (GWP) showed no significant difference between Dryland and Wetland, with comparable average rates of 427.50 ± 48.83 and 422.21 ± 73.59 mg·CO₂-eq·m^- 2·h^- 1, respectively. Metagenomic analysis showed a decrease in the abundance of acetoclastic methanogens and their functional genes responsible for CH₄ production. Functional genes related to CH₄ oxidation (pmoA) and gene related to N₂O reduction (nosZ) exhibited a substantial sensitivity to variations in TOC concentration (p < 0.05). Candidatus Methylomirabilis, belonging to the NC10 phylum, was identified as the dominant methanotroph and accounted for 49.26% of the methanotrophs. Its relative abundance was significantly higher in Dryland than in Wetland, as the nitrogenous fertilizer applied in Dryland acted as an electron acceptor, with the nearby Wetland produced CH₄ serving as an electron donor. This suggests that Dryland may act as a CH₄ sink, despite the significant enhancement in CO₂ and N₂O fluxes.</p><p><strong>Conclusions: </strong>In conclusion, this study provides insights into the influence of drainage and long-term tillage on GHG fluxes in wetlands and their contribution to global warming.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"26"},"PeriodicalIF":6.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143558379","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":"Microbial landscape of Indian homes: the microbial diversity, pathogens and antimicrobial resistome in urban residential spaces.","authors":"Saraswati Awasthi, Vikas M Hiremath, Sonam Nain, Shweta Malik, Vanita Srinivasan, Pooja Rose, Ashutosh Choudhury, Ritika Grover, Rakesh Sharma","doi":"10.1186/s40793-025-00684-8","DOIUrl":"10.1186/s40793-025-00684-8","url":null,"abstract":"<p><strong>Background: </strong>Urban dwellings serve as complex and diverse microbial community niches. Interactions and impact of house microbiome on the health of the inhabitants need to be clearly defined. Therefore, it is critical to understand the diversity of the house microbiota, the presence and abundance of potential pathogens, and antimicrobial resistance.</p><p><strong>Results: </strong>Shotgun metagenomics was used to analyze the samples collected from 9 locations in 10 houses in New Delhi, India. The microbiota includes more than 1409 bacterial, 5 fungal, and 474 viral species en masse. The most prevalent bacterial species were Moraxella osloensis, Paracoccus marcusii, Microbacterium aurum, Qipengyuania sp YIMB01966, and Paracoccus sphaerophysae, which were detected in at least 80 samples. The location was the primary factor influencing the microbiome diversity in the Indian houses. The overall diversity of different houses did not differ significantly from each other. The surface type influenced the microbial community, but the microbial diversity on the cemented and tiled floors did not vary significantly. A substantial fraction of the bacterial species were potentially pathogenic or opportunistic pathogens, including the ESKAPE pathogens. Escherichia coli was relatively more abundant in bedroom, foyer, and drawing room locations. Analysis of the house microbiome antimicrobial resistome revealed 669 subtypes representing 22 categories of antimicrobial resistance genes, with multidrug resistance genes being the most abundant, followed by aminoglycoside genes.</p><p><strong>Conclusions: </strong>This study provides the first insight into the microbiomes of houses in New Delhi, showing that these houses have diverse microbiomes and that the location within the house significantly influences the microbiota. The presence of potential pathogens and a repertoire of antimicrobial resistance genes reflect possible health risks, as these could lead to infectious disease transmission. This study builds a framework for understanding the microbial diversity of houses in terms of geographical location, environment, building design, cleaning habits, and impact on the health of occupants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"25"},"PeriodicalIF":6.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143504468","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":"A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential.","authors":"Pierre Foucault, Sébastien Halary, Charlotte Duval, Midoli Goto, Benjamin Marie, Sahima Hamlaoui, Ludwig Jardillier, Dominique Lamy, Emilie Lance, Emmanuelle Raimbault, Fayçal Allouti, Marc Troussellier, Cécile Bernard, Julie Leloup, Sébastien Duperron","doi":"10.1186/s40793-025-00681-x","DOIUrl":"10.1186/s40793-025-00681-x","url":null,"abstract":"<p><p>With more than 12 million inhabitants, the Greater Paris offers a \"natural laboratory\" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"24"},"PeriodicalIF":6.2,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442441","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":"Spatiotemporal dynamics reveal high turnover and contrasting assembly processes in fungal communities across contiguous habitats of tropical forests.","authors":"Chieh-Ping Lin, Yu-Fei Lin, Yu-Ching Liu, Mei-Yeh Jade Lu, Huei-Mien Ke, Isheng Jason Tsai","doi":"10.1186/s40793-025-00683-9","DOIUrl":"10.1186/s40793-025-00683-9","url":null,"abstract":"<p><strong>Background: </strong>The variation in fungal community composition within a single habitat space has been extensively studied in forest ecosystems. However, the spatial and temporal distribution of fungi across contiguous habitats, particularly at a local scale and in tropical regions, remains underexplored. In this study, we examined the fungal community composition across multiple habitats proximal to each other over two seasons in seven Fagaceae species in Taiwanese broadleaf forests. We tested how local spatial scale and habitat influence community assembly.</p><p><strong>Results: </strong>Using a metabarcoding approach, we sequenced ITS2 regions from 864 samples collected from four distinct habitats-leaves, twigs, litter, and soil. We identified 11,600 fungal amplicon sequence variants (ASVs), with community composition differing significantly between habitats proximal to each other. Generalized dissimilarity modeling (GDM) revealed that spatial distance, interacting with precipitation, was the strongest predictor of fungal turnover, particularly in the phyllosphere. Normalized Stochasticity Ratio (NST) analyses further highlighted contrasting assembly processes, with deterministic influences dominating in the phyllosphere habitat, while stochasticity prevailed in soil and litter. Random forest analysis accurately classified habitats based on ASVs' relative abundances, with strong predictors were mostly habitat-specific ASVs prevalent in soil. Misclassified samples were due to secondary contact of fungi between adjacent habitats. Co-occurrence network analysis revealed more complex and deterministic networks in leaf and twig habitats, while soil was driven by stochastic processes and contained most habitat-specific ASVs. A Cladosporium sp. emerged as a keystone species, maintaining network stability across forests.</p><p><strong>Conclusion: </strong>This study reveals how local spatial variation and habitat shape distinct fungal communities in tropical forests, with deterministic processes dominating in some habitats and stochasticity playing a key role in others. We show extremely high turnover in fungal community are present over very short distances and that local fungal taxa are strong habitat predictors. These findings highlight the importance of studying coexisting habitats to gain a deeper understanding of fungal biogeography and ecosystem function.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"23"},"PeriodicalIF":6.2,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11830174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426378","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}