Environmental Microbiome最新文献

{"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":6.2,"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}

{"title":"Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum.","authors":"Hildah Amutuhaire, Adi Faigenboim-Doron, Judith Kraut-Cohen, Jonathan Friedman, Eddie Cytryn","doi":"10.1186/s40793-025-00710-9","DOIUrl":"10.1186/s40793-025-00710-9","url":null,"abstract":"<p><strong>Background: </strong>Soilborne fungal phytopathogens pose a significant threat to global food security. While chemical control remains an effective method for managing these pathogens, increasing regulations due to health and environmental concerns, along with rising fungicide resistance, have restricted their use, underscoring the urgent need for sustainable alternatives. The use of compost to enhance soil fertility and suppress plant diseases is well documented. Several studies have underlined the role of microorganisms in disease suppression, but the mechanisms facilitating this disease suppression remain unclear. We evaluated the impact of compost amendment on the composition and functional capacity of the rhizosphere microbiome in cucumber plants (Cucumis sativus) inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum (FORC) under controlled greenhouse conditions using amplicon sequencing, shotgun metagenomic and culture-based techniques.</p><p><strong>Results: </strong>Compost amendment significantly reduced FORC-induced disease in cucumber relative to non-amended treatments. While FORC inoculation resulted in significant shifts in microbial (bacterial and fungal) community composition in the rhizosphere of non-amended plants, this phenomenon was substantially less pronounced in the rhizosphere of compost-amended plants. Specifically, compost amendment sustained the presence of Actinomycetota (Streptomyces, Actinomadura, Saccharomonospora, Pseudonocardia, Glycomyces, Thermobifida) and Bacillota (Planifilum, Novibacillus) in FORC inoculated plants, that diminished significantly in inoculated plants without compost. These taxa contained a myriad of non-ribosomal peptides and polyketides synthetases biosynthetic gene clusters (BGCs) with putative antimicrobial and iron-chelating functions. We successfully isolated two Streptomyces strains from FORC-suppressing compost amended rhizospheres that were almost identical to the Streptomyces bin2 (99% ortho ANI) metagenome assembled genome identified in the shotgun metagenome analysis. These strains produced extracellular metabolites that inhibited growth of FORC in-vitro and contained BGCs that encode for compounds with potential antimicrobial capacity.</p><p><strong>Conclusions: </strong>Based on results presented in this study, we demonstrate that compost alleviates FORC-induced dysbiosis of the rhizosphere microbiome, maintaining abundance of specific bacterial taxa. These bacterial groups may contribute to disease suppression through a myriad of mechanisms including iron chelation and production of fungal antagonizing secondary metabolites.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"52"},"PeriodicalIF":6.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144086895","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":"Spatial scale modulates stochastic and deterministic influence on biogeography of photosynthetic biofilms in Southeast Asian hot springs.","authors":"Christaline George, Chananwat Kortheerakul, Nitthiya Khunthong, Chitrabhanu Sharma, Danli Luo, Kok-Gan Chan, Maurycy Daroch, Kevin D Hyde, Patrick K H Lee, Kian Mau Goh, Rungaroon Waditee-Sirisattha, Stephen B Pointing","doi":"10.1186/s40793-025-00711-8","DOIUrl":"10.1186/s40793-025-00711-8","url":null,"abstract":"<p><p>Hot springs, with their well-characterized major abiotic variables and island-like habitats, are ideal systems for studying microbial biogeography. Photosynthetic biofilms are a major biological feature of hot springs but despite this large-scale studies are scarce, leaving critical questions about the drivers of spatial turnover unanswered. Here, we analysed 395 photosynthetic biofilms from neutral-alkaline hot springs (39-66 °C, pH 6.4-9.0) across a 2100 km latitudinal gradient in Southeast Asia. The Cyanobacteria-dominated communities were categorized into six biogeographic regions, each characterized by a distinct core microbiome and biotic interactions. We observed a significant decline in the explanatory power of major abiotic variables with increasing spatial scale, from 62.6% locally, 55% regionally, to 26.8% for the inter-regional meta-community. Statistical null models revealed that deterministic environmental filtering predominated at local and regional scales, whereas stochastic ecological drift was more influential at the inter-regional scale. These findings enhance our understanding of the differential contribution of ecological drivers and highlight the importance of spatial scale in shaping biogeographic distributions for microorganisms.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"50"},"PeriodicalIF":6.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12070648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144062788","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":"The unresolved struggle of 16S rRNA amplicon sequencing: a benchmarking analysis of clustering and denoising methods.","authors":"Mohamed Fares, Engy K Tharwat, Ilse Cleenwerck, Pieter Monsieurs, Rob Van Houdt, Peter Vandamme, Mohamed El-Hadidi, Mohamed Mysara","doi":"10.1186/s40793-025-00705-6","DOIUrl":"10.1186/s40793-025-00705-6","url":null,"abstract":"<p><strong>Background: </strong>Although 16S rRNA gene amplicon sequencing has become an indispensable method for microbiome studies, this analysis is not error-free, and remains prone to several biases and errors. Numerous algorithms have been developed to eliminate these errors and consolidate the output into distance-based Operational Taxonomic Units (OTUs) or denoising-based Amplicon Sequence Variants (ASVs). An objective comparison between them has been obscured by various experimental setups and parameters. In the present study, we conducted a comprehensive benchmarking analysis of the error rates, microbial composition, over-merging/over-splitting of reference sequences, and diversity analyses using the most complex mock community, comprising 227 bacterial strains and the Mockrobiota database. Using unified preprocessing steps, we were able to compare DADA2, Deblur, MED, UNOISE3, UPARSE, DGC (Distance-based Greedy Clustering), AN (Average Neighborhood), and Opticlust objectively.</p><p><strong>Results: </strong>ASV algorithms-led by DADA2- resulted in having a consistent output, yet suffered from over-splitting, while OTU algorithms-led by UPARSE-achieved clusters with lower errors, yet with more over-merging. Notably, UPARSE and DADA2 showed the closest resemblance to the intended microbial community, especially when considering measures for alpha and beta diversity.</p><p><strong>Conclusion: </strong>Our unbiased comparative evaluation examined the performance of eight algorithms dedicated to the analysis of 16S rRNA amplicon sequences with a wide range of mock datasets. Our analysis shed light on the pros and cons of each algorithm and the accuracy of the produced OTUs or ASVs. The utilization of the most complex mock community and the benchmarking comparison presented here offer a framework for the comparison between OTU/ASV algorithms and an objective method for the assessment of new tools and algorithms.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"51"},"PeriodicalIF":6.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12076876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143991544","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":"Jellyfish blooms through the microbial lens: temporal changes, cross-species and Jellyfish-water comparisons.","authors":"Noga Barak, Vera Brekhman, Dikla Aharonovich, Tamar Lotan, Daniel Sher","doi":"10.1186/s40793-025-00714-5","DOIUrl":"https://doi.org/10.1186/s40793-025-00714-5","url":null,"abstract":"<p><p>Jellyfish blooms have significant ecological and economic impacts, yet the microbial communities associated with these blooms remain poorly understood, despite their potential influence on host fitness and microbial communities in the surrounding water. In this study, we explored temporal and tissue-specific variations in the microbiota of Rhopilema nomadica, the dominant jellyfish species in the Eastern Mediterranean Sea, across winter and summer blooms. During late summer blooms, microbial richness declined, coinciding with an increase in Endozoicomonas and unclassified Rickettsiales, while Tenacibaculum predominantly characterized winter blooms. Tissue-specific analyses revealed bacterial groups that were more consistently associated with different jellyfish tissues (e.g., Bacteroides in the bell and Simkaniaceae in the gonads), suggesting different microbial niches within the host. Furthermore, some key bacteria associated with R. nomadica, including Endozoicomonas, unclassified Rickettsiales, and Bacteroides were detected in the surrounding bloom water but absent from remote seawater, suggesting potential localized transmission dynamics between jellyfish and their immediate marine environment. Finally, a comparative analysis with nine additional jellyfish species identified recurring microbial taxa, including Endozoicomonas, Mycoplasma, and Spiroplasma, though no universal core microbiota was observed. This study represents the first exploration of microbial dynamics within R. nomadica blooms and the most comprehensive analysis of jellyfish-associated microbiomes across bloom stages and tissues to date. Our findings reveal complex relationships between jellyfish species, bloom progression, their microbial communities, and the surrounding seawater.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"49"},"PeriodicalIF":6.2,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022999","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":"Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.","authors":"Adrien Vigneron, Lilian A Cloarec, Céline Brochier-Armanet, Jean Pierre Flandrois, Marc Troussellier, Cécile Bernard, Hélène Agogué, Philippe M Oger, Mylène Hugoni","doi":"10.1186/s40793-025-00699-1","DOIUrl":"https://doi.org/10.1186/s40793-025-00699-1","url":null,"abstract":"<p><strong>Background: </strong>Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.</p><p><strong>Results: </strong>Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.</p><p><strong>Conclusions: </strong>Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"48"},"PeriodicalIF":6.2,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053260","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 microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.","authors":"Josephine Herbert, Stanley Thompson, Angela H Beckett, Samuel C Robson","doi":"10.1186/s40793-025-00704-7","DOIUrl":"https://doi.org/10.1186/s40793-025-00704-7","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Introduction: &lt;/strong&gt;Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Aim and methods: &lt;/strong&gt;Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~ 97% accuracy) LSK109 chemistry, and newer more accurate (~ 99% accuracy) LSK112 Q20 + chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20 + nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive ","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"47"},"PeriodicalIF":6.2,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040652","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}