Environmental Microbiome最新文献

{"title":"Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.","authors":"Elizabeth R Denison, Helena L Pound, Eric R Gann, Naomi E Gilbert, David J Weston, Dale A Pelletier, Steven W Wilhelm","doi":"10.1186/s40793-025-00719-0","DOIUrl":"10.1186/s40793-025-00719-0","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"62"},"PeriodicalIF":6.2,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12142844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235586","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":"Mosses as extraordinary reservoir of microbial diversity: a comparative analysing of co-occurring 'plant-moss twins' in natural alpine ecosystem.","authors":"Dinesh Kumar Ramakrishnan, Birgit Wassermann, Christian Berg, Ahmed Abdelfattah, Gabriele Berg","doi":"10.1186/s40793-025-00728-z","DOIUrl":"10.1186/s40793-025-00728-z","url":null,"abstract":"<p><p>The decline in plant biodiversity is evident at global scale, but little is known about the loss of microbial diversity associated with diverse plant phyla and their influencing factors. This study investigates the microbial diversity associated with mosses and co-occurring vascular plants in the Alpine ecosystem, focusing on 52 plant \"twins\" growing on contrasting soil types (carbonate and silicate). Despite co-occurring in the same soil, mosses harbored significantly higher microbial richness and diversity than vascular plants. Across all samples, mosses supporting a total of 3,435 bacterial ASVs and 1,174 fungal ASVs. In contrast, vascular plants hosted a total of 1,760 bacterial ASVs and 911 fungal ASVs. Plant phyla strongly influenced microbial community composition, with vascular plants exhibiting a selective microbial assembly strategy, while mosses showed greater environmental influence. Soil type significantly influenced microbial composition in both plant types, with carbonate soils supporting greater bacterial richness, particularly in mosses. Linear discriminant analysis effect size (LEfSe) analysis highlighted consistent enrichments of Proteobacteria, i.e., Sphingomonadales, Rhizobiales, Burkholderiales and, Pseudomonadales, in vascular plants across soil types, whereas mosses displayed distinct microbial enrichment patterns between carbonate and silicate soils, suggesting a higher environmental connectedness. Our findings demonstrated that plant phyla are a major determinant of the phyllosphere microbiota, and that mosses represent a currently untapped source of microbial biodiversity. This study highlights the importance of considering both host traits and environmental factors for protecting microbial biodiversity and implementing them in global strategies for restoring biodiversity.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"61"},"PeriodicalIF":6.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227220","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":"Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.","authors":"Ahmad Nuruddin Khoiri, Nídia Raquel Costa, Carlos Alexandre Costa Crusciol, Cristiano Magalhães Pariz, Ciniro Costa, Juliano Carlos Calonego, André Michel de Castilhos, Daniel Martins de Souza, Paulo Roberto de Lima Meirelles, Igor Vilela Cru, Luiz Gustavo Moretti, João William Bossolani, Eiko Eurya Kuramae","doi":"10.1186/s40793-025-00727-0","DOIUrl":"10.1186/s40793-025-00727-0","url":null,"abstract":"<p><strong>Background: </strong>Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.</p><p><strong>Results: </strong>The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.</p><p><strong>Conclusions: </strong>These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"60"},"PeriodicalIF":6.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227221","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":"Metabarcoding insights into microbial drivers of flavor development and quality stability in traditional Chinese red pepper sauce: impacts of varietal selection and solar/shade fermentation.","authors":"Xuefeng Gong, Yi Xu, Sihao Hou, Hong Li, Xin Chen, Zhanfeng Song","doi":"10.1186/s40793-025-00717-2","DOIUrl":"10.1186/s40793-025-00717-2","url":null,"abstract":"<p><strong>Background: </strong>Red pepper sauce is a traditional Chinese condiment, which is rich in nutrients and popular worldwide. However, the changes in the microbial community of red pepper sauce during fermentation and the effects of such changes on quality stability have been under studied. In this study, we systematically analyzed the relationship between the microbial community composition of multiple red pepper sauces and the biochemical indexes. Moreover, we also explored the dynamics of changes in the microbial community composition using metabarcoding sequencing.</p><p><strong>Results: </strong>Our analysis revealed significant differences in amino acids (AA), lactate, pectin, reducing sugar, flavonoids, phenolics, pigments, and alcohol dehydrogenase (ADH) activity among the six red pepper sauces. Moreover, the relative abundance of bacteria and fungi showed significant differences among multiple red pepper sauces. Among these biochemical indexes, water content, pigment, and capsaicin showed a significant negative correlation with the abundance of multiple bacterial genera. ADH activity showed a significant positive correlation with the abundance of multiple bacterial genera. The content of AA, flavonoid, pectin, and gamma-aminobutyric acid (GABA) was significantly correlated with the relative abundance of multiple fungi such as Rhodotorula, Dipodascus, Leucosporidium, Hannaella, and Coniochaeta.</p><p><strong>Conclusions: </strong>These results provide a basis for revealing the biological basis of the quality stability and flavor characteristics of red pepper sauce, which are of great significance for further investigation of the fermentation mechanism and control of the product quality of red pepper sauce.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"59"},"PeriodicalIF":6.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188258","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":"Impact of fluoroquinolone and heavy metal pollution on antibiotic resistance maintenance in aquatic ecosystems.","authors":"Emilie Dehon, Stanislava Vrchovecká, Alban Mathieu, Sabine Favre-Bonté, Stanisław Wacławek, Arnaud Droit, Timothy M Vogel, Concepcion Sanchez-Cid","doi":"10.1186/s40793-025-00722-5","DOIUrl":"10.1186/s40793-025-00722-5","url":null,"abstract":"<p><strong>Background: </strong>Freshwater pollution with compounds used during anthropogenic activities could be a major driver of antibiotic resistance emergence and dissemination in environmental settings. Fluoroquinolones and heavy metals are two widely used aquatic pollutants that show a high stability in the environment and have well-known effects on antibiotic resistance selection. However, the impact of these compounds on antibiotic resistance maintenance in aquatic ecosystems remains unknown. In this study, we used a microcosm approach to determine the persistence of two fluoroquinolones (ciprofloxacin, ofloxacin) and two heavy metals (copper and zinc) in the Rhône river over 27 days. In addition, we established links between antibiotic and metal pollution, alone and in combination, and the composition of freshwater bacterial communities, the selection of specific members and the selection and maintenance of antibiotic and metal resistance genes (ARGs and MRGs) using a metagenomics approach.</p><p><strong>Results: </strong>Whereas ofloxacin was detected at higher levels in freshwater after 27 days, copper had the strongest influence on bacterial communities and antibiotic and metal resistance gene selection. In addition, heavy metal exposure selected for some ARG-harboring bacteria that contained MRGs. Our research shows a heavy metal-driven transient co-selection for fluoroquinolone resistance in an aquatic ecosystem that could be largely explained by the short-term selection of Pseudomonas subpopulations harboring both fluoroquinolone efflux pumps and copper resistance genes.</p><p><strong>Conclusion: </strong>This research highlights the complexity and compound-specificity of dose-response relationships in freshwater ecosystems and provides new insights into the medium-term community structure modifications induced by overall sub-inhibitory levels of antibiotic and heavy metal pollution that may lead to the selection and maintenance of antibiotic resistance in low-impacted ecosystems exposed to multiple pollutants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"58"},"PeriodicalIF":6.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162931","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":"Effect of applying oyster shell powder on soil properties and microbial diversity in the acidified soils of pomelo garden.","authors":"Yuanyuan Li, Qiong Zhang, Lixia Zhu, Jing Yang, Jingjing Wei, Yunhe Li, Xiaohuang Chen","doi":"10.1186/s40793-025-00721-6","DOIUrl":"10.1186/s40793-025-00721-6","url":null,"abstract":"<p><p>The application of oyster shell has recently been used to increase soil pH in Southern China. However, little is known about causal shifts in the rhizosphere microbial community of pomelo trees, especially in orchards that have experienced natural accumulation of heavy metals over many years due to continuous fertilization and soil acidification. This study evaluated the effects of oyster shell powder applied for 1 year (T1), 2 years (T2) and 3 years (T3), alongside a control group with no soil amendments (Control; CK), on soil acidification and microbial diversity. Our findings demonstrated that the application of oyster shell significantly increased soil pH and reduced the concentrations of heavy metals such as thallium (Tl), chromium (Cr), and manganese (Mn). Illumina sequencing-based community analysis revealed that oyster shell application significantly increased the alpha diversity indices of both bacterial and fungal communities and influenced their distribution in the soil. Notably, all oyster shell-treated groups (T1-T3) showed significantly higher relative abundances of beneficial microbes (e.g., Nitrolancea, Vicinamibacterales) and those involved in carbohydrate degradation and nitrogen fixation compared to the control. Conversely, the relative abundances of Acidibacter and Chujaibacter (associated with heavy metal degradation and soil-borne diseases), Trichoderma and Acremonium (plant-beneficial fungi), as well as functionally annotated groups linked to nitrogen assimilation and pathotrophic modes (predicted via FUNGuild analysis), decreased significantly. Our results suggest that the application of oyster shell powder amendments contributes to improved soil properties and microbial environments; however, the effects on soil nitrogen cycling and fungal function are complex, warranting further research.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"57"},"PeriodicalIF":6.2,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144094","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":"Rain-shelter cultivation promotes grapevine health by altering phyllosphere microecology in rainy areas.","authors":"Tao He, Romy Moukarzel, Mingxin Fu, Meng Yang, Ronghui Du, Jing Zhao, Jinyu Liu, Jiaqing Wu, Weiping Deng, Yifan Zhu, Min Yang, Shusheng Zhu, Fei Du","doi":"10.1186/s40793-025-00708-3","DOIUrl":"10.1186/s40793-025-00708-3","url":null,"abstract":"<p><p>Grapes are a globally significant fruit crop, but their cultivation is often challenged by leaf diseases, which limit industrial productivity. Rain-shelter cultivation has emerged as a sustainable agricultural strategy to mitigate these challenges. This study examines the effects of rain-shelter cultivation, compared to open-air cultivation, on the microclimate within the grape canopy and the microbial ecology of the grape phyllosphere. The research focused on two cultivation methods: rain-shelter and open-air cultivation. Key environmental factors such as temperature, relative humidity, and light intensity within the grape canopy were measured during the growing season. The study also explored how these conditions influence the biodiversity, stability, and functional roles of phyllosphere microbiota, particularly focusing on the community assembly processes of bacteria and oomycetes, and the efficacy of culturable microorganisms in combating grape leaf diseases. The results showed that rain-shelter cultivation signifcantly reduced leaf humidity, increased canopy temperature, and decreased light intensity, regardless of weather conditions. This approach led to a significant decrease in the incidence of grape downy mildew without affecting the overall Shannon diversity index of phyllosphere microbes. At the Class level, there was a reduction in Cystobasidiomycetes, Bacteroidia, Brocadiae, and Phycisphaerae, while Oligoflexia levels are significantly increased under rain-shelter conditions. Genus-level analysis revealed significant reductions in plant pathogens such as Erysiphe, Alternaria, and Cercospora. The study found that rain-shelter cultivation shifts fungal community assembly from stochastic to deterministic processes, while bacterial networks showed increased stability. Additionally, the beneficial microorganism Pseudomonas aeruginosa exhibited a preventive effect against grape leaf diseases, enhancing grape berry quality by increasing puncture resistance and leaf internode length. These findings provide understanding of the complex relationship between grape canopy microclimate, disease management, and microbial dynamics suggesting rain-shelter cultivation as a viable strategy for sustainable grape production, it offers insights into the research and development of future biological control agents.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"56"},"PeriodicalIF":5.4,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129030","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":"Plant microbiome responses to bioinoculants and volatiles.","authors":"Expedito Olimi, Martina Duller, Martina Stangl, Samuel Bickel, Angelika Battisti, Peter Kusstatscher, Wisnu Adi Wicaksono, Ahmed Abdelfattah, Tomislav Cernava, Gabriele Berg","doi":"10.1186/s40793-025-00715-4","DOIUrl":"10.1186/s40793-025-00715-4","url":null,"abstract":"<p><strong>Background: </strong>There is an increase in the adoption of biological solutions for plant production as a means of attaining sustainable agriculture. A detailed understanding of the influence of specific bioinoculants and their volatile metabolites on native soil and plant microbiomes can improve future microbiome management practices.</p><p><strong>Results: </strong>Here, we examined the effect of bacterial inoculants and volatile compounds as individual and combined treatments on apple plant and soil microbiome. The study used specially designed microcosms that facilitated the separation of the different plant compartments. A compartment- and soil-specific effect of treatments on the native soil and plant microbiome was observed. The live bacterial inoculants as compared to their volatiles had a stronger effect on the plant and soil microbiome, particularly the root microbial community. The combined effect of bacterial inoculants was higher compared to volatiles (R² = 5% vs. 3%). Treatment-specific effects were observed, like the influence of 2-butanone on the phyllosphere bacterial diversity, and an increase in fungal richness in Serratia-treated soils.</p><p><strong>Conclusions: </strong>Among the examined treatments, inoculation with bacteria compared to volatile metabolites induced more significant shifts within the plant and soil microbiome. This observation has implications regarding the merits of applying living microorganisms. The findings highlight the potential of microbiome management approaches for enhancing microbiota functions.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"55"},"PeriodicalIF":6.2,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144119978","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 microbial communities drive methane cycling in below- and above-ground compartments of tropical cloud forests growing on peat.","authors":"Fahad Ali Kazmi, Ülo Mander, Ramita Khanongnuch, Maarja Öpik, Reti Ranniku, Kaido Soosaar, Mohit Masta, Salla A M Tenhovirta, Kuno Kasak, Claudine Ah-Peng, Mikk Espenberg","doi":"10.1186/s40793-025-00718-1","DOIUrl":"10.1186/s40793-025-00718-1","url":null,"abstract":"<p><p>Cloud forests are unique yet understudied ecosystems regarding CH₄ exchange despite their significance in carbon storage. We investigated CH₄ fluxes in peat soil and tree stems of two tropical cloud forests on Réunion Island, one featuring Erica reunionensis and the second a mix of E. reunionensis and Alsophila glaucifolia. The study examined microbiomes across below-ground (soil) and above-ground (canopy soil, leaves, and stems) forest compartments. Metagenomics and qPCR analyses targeted key genes in methanogenesis and methanotrophy in soil and above-ground samples, alongside soil physicochemical measurements. CH₄ fluxes from peat soil and tree stems were measured using gas chromatography and portable trace gas analyzers. Peat soil in both forests acted as a CH₄ sink (- 23.8 ± 4.84 µg C m^- 2 h^- 1) and CO₂ source (55.5 ± 5.51 µg C m^- 2 h^- 1), with higher CH₄ uptake in sites dominated by endemic tree species E. reunionensis. In forest soils, a high abundance of n-DAMO 16 S rRNA gene (3.42 × 10⁷ ± 7 × 10⁶ copies/g dw) was associated with nitrate levels and higher rates of CH₄ uptake and CO₂ emissions. NC-10 bacteria (0.1-0.3%) were detected in only the Erica forest soil, verrucomicrobial methanotrophs (0.1-3.1%) only in the mixed forest soil, whereas alphaproteobacterial methanotrophs (0.1-3.3%) were present in all soils. Tree stems in both forests were weak sinks of CH₄ (-0.94 ± 0.4 µg C m^- 2 h^- 1). The canopy soil hosted verrucomicrobial methanotrophs (0.1-0.3%). The leaves in both forests exhibited metabolic potential for CH₄ production, e.g., exhibiting high mcrA copy numbers (3.5 × 10⁵ ± 2.3 × 10⁵ copies/g dw). However, no CH₄-cycling functional genes were detected in the stem core samples. Tropical cloud forest peat soils showed high anaerobic methanotrophy via the n-DAMO process, while aerobic methanotrophs were abundant in canopy soils. Leaves hosted methanotrophs but predominantly methanogens. These results highlight the significant differences between canopy and soil microbiomes in the CH₄ cycle, emphasizing the importance of above-ground microbiomes in forest CH₄ gas budgets.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"54"},"PeriodicalIF":6.2,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102960","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":"Metabarcoding with Illumina and Oxford Nanopore Technologies provides complementary insights into tree seed mycobiota.","authors":"Jana Mittelstrass, Renate Heinzelmann, René Eschen, Martin Hartmann, Quirin Kupper, Salome Schneider, Simone Prospero, Iva Franić","doi":"10.1186/s40793-025-00712-7","DOIUrl":"10.1186/s40793-025-00712-7","url":null,"abstract":"<p><strong>Background: </strong>Culturing of fungi is labor-intensive and reveals limited diversity, while high-throughput sequencing of barcodes (i.e., metabarcoding) enables a simultaneous detection of fungi from multiple environmental samples. Metabarcoding using short-read sequencers, such as Illumina platforms, provides high sequencing depths but results in many unidentified taxa. Long-read sequencing can improve species and genus assignments but might encompass lower sequencing depth and limit diversity coverage. In this study, fungi in seeds of eleven angiosperm and gymnosperm tree species were assessed using traditional culturing, Illumina short-read metabarcoding, and Oxford Nanopore Technologies long-read metabarcoding. We focused on seed-borne fungi as understanding their diversity and potential impacts on seedlings is crucial for securing plant health. We compared (1) the number and identity of fungal genera and species between metabarcoding approaches and traditional culturing and (2) fungal alpha- and beta-diversity between metabarcoding methods, considering different hosts and fungal lifestyles.</p><p><strong>Results: </strong>In both short- and long-read metabarcoding datasets, similar numbers of fungal reads and operational taxonomic units were assigned to comparable numbers of fungal genera and species. About one-third of the identified genera were plant pathogens, followed by saprotrophs and endophytes. Culturing overall revealed fewer fungal genera, while most of the fungal reads in short-read metabarcoding datasets stemmed from cultured taxa. Long-read metabarcoding revealed lower per-sample diversity than short-read metabarcoding and distinct fungal communities compared to those from the short-read datasets. Host-dependent patterns in alpha- and beta-diversity were observed across methods, with angiosperms harboring more fungal taxa than gymnosperms, and distinct community structuring across host tree groups and species, although the differences were stronger in short-read than long-read metabarcoding datasets.</p><p><strong>Conclusions: </strong>Illumina and Oxford Nanopore Technologies metabarcoding captured similar host-dependent diversity patterns despite observed differences in numbers and composition of fungi. Short-read metabarcoding might be optimal for fungal biodiversity studies due to higher sequencing depths and resultant breadth of diversity. As error rates are continuing to decrease, reference databases expand, and throughput improves, long-read metabarcoding is becoming a strong candidate for future diagnostic studies of fungi. Traditional culturing captures most of the fungi from short-read metabarcoding and remains valuable for obtaining isolates for further research.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"53"},"PeriodicalIF":6.2,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12090628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102961","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}