Environmental Microbiome最新文献

{"title":"Warming increases richness and shapes assemblages of eukaryotic parasitic plankton.","authors":"Amruta Rajarajan, Sławek Cerbin, Kingsly C Beng, Michael T Monaghan, Justyna Wolinska","doi":"10.1186/s40793-025-00724-3","DOIUrl":"10.1186/s40793-025-00724-3","url":null,"abstract":"<p><strong>Background: </strong>Anthropogenic activities have led to a global rise in water temperatures, prompting increased interest in how warming affects infectious disease ecology. While most studies have focused on individual host-parasite systems, there is a gap in understanding the impact of warming on multi-host, multi-parasite assemblages in natural ecosystems. To address this gap, we investigated freshwater eukaryotic parasite communities in ten natural lakes near Konin, Poland: five artificially heated and five non-heated \"control\" lakes. Since 1958, the heated lakes have experienced a mean annual temperature increase of 2 °C due to hot water discharge from two adjacent power plants. We collected seasonal environmental DNA (eDNA) samples from surface waters over a two-year period and applied targeted metabarcoding to compare the richness and distribution of eukaryotic parasites across lake types with a focus on protists and fungi.</p><p><strong>Results: </strong>Using literature searches and sequence metadata from GenBank, we identified putative parasites which included Alveolates, Stramenopiles, basal Fungi and Ichthyosporeans as well as their associated hosts. Heated lakes harboured distinct parasite assemblages with higher richness of chytrids and aphelids, suggesting thermal preferences among certain freshwater microeukaryotic parasites. Other groups exhibited clear seasonal trends with richness of oomycetes peaking in spring and summer, and that of Cryptomycota in winter and autumn. A general linear model revealed a marginally positive correlation between chytrid parasite richness and richness of their green algal, diatom, and dinoflagellate hosts. Post-hoc analyses indicated that heated lakes exhibited greater seasonal variation in chytrid parasite richness and a stronger correlation between host and parasite richness than control lakes.</p><p><strong>Conclusion: </strong>These findings demonstrate that warming can induce strong shifts in the richness and assemblages of freshwater microeukaryotic parasites. Using chytrids as a focal group, we additionally demonstrate that warming may amplify seasonal variation in parasite richness and strengthen host-parasite richness relationships.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"76"},"PeriodicalIF":6.2,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337115","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":"Contrasting stability of fungal and bacterial communities during long-term decomposition of fungal necromass in Arctic tundra.","authors":"Andrea Moravcová, Florian Barbi, Camelia Algora, Gabriele Tosadori, Petr Macek, Jana Albrechtová, Petr Baldrian, Petr Kohout","doi":"10.1186/s40793-025-00730-5","DOIUrl":"10.1186/s40793-025-00730-5","url":null,"abstract":"<p><p>Decomposition is a crucial process in terrestrial ecosystems, driving nutrient cycling and carbon storage dynamics. Considering the amount of fungal necromass produced in soils annually, its decomposition represents an important nutrient recycling process. Understanding the decomposition dynamics and associated microbial communities of fungal necromass is essential for elucidating ecosystem functioning, especially in environmentally sensitive regions such as the Arctic tundra, which remain under-explored. In a three-year field experiment conducted in the Svalbard archipelago, we investigated the decomposition of two types of fungal necromass with differing biochemical properties. We studied the decomposition rate, changes in chemical composition, and the succession of fungal and bacterial communities associated with the decaying fungal necromass. We discovered that up to 20% of fungal necromass remained even after three years of decomposition, indicating that the decomposition process was incomplete. Our results indicate the crucial role of Pseudogymnoascus in decomposing low-quality, highly melanized necromass with a high C:N ratio in Arctic soils, underscoring its importance in carbon cycling in the Arctic tundra. Notably, we observed dynamic changes in bacterial communities, with increasing richness over time and a shift from copiotrophic to oligotrophic species specializing in decomposing recalcitrant material. Our study indicates the strong potential that fungal necromass can play in carbon sequestration of arctic soils and reveals the distinct dynamics between rather stable fungal and rapidly changing bacterial communities associated with the decomposing fungal necromass in the Arctic tundra. These findings enhance our understanding of microbial succession during decomposition in extreme environments and highlight the potentially differing roles of fungi and bacteria in these processes.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"75"},"PeriodicalIF":6.2,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12180224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337114","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":"Comparative metagenomics indicates metabolic niche differentiation of benthic and planktonic Woeseiaceae.","authors":"Tomeu Viver, Katrin Knittel, Rudolf Amann, Luis H Orellana","doi":"10.1186/s40793-025-00732-3","DOIUrl":"10.1186/s40793-025-00732-3","url":null,"abstract":"<p><strong>Background: </strong>Benthic microbiomes exhibit remarkable temporal stability, contrasting with the dynamic, substrate-driven successions of bacterioplankton. Nonetheless, understanding their role in carbon cycling and interactions between these two microbial communities is limited due to the complexity of benthic microbiomes.</p><p><strong>Results: </strong>Here, we used a long-reads (LRs) metagenomic approach to examine benthic microbiomes and compared them to the microbiomes in the overlaying water column and on particles, sampled at the same site and time off the island Heligoland in the North Sea. Although the diversity is vast in marine sediments, we recovered high quality metagenome assembled genomes (MAGs). Based on taxonomy and metabolic annotation of predicted proteins, benthic microbiomes are distinctly different from pelagic microbiomes. When comparing the 270 MAGs from free living and particle attached microbes from the water column to 115 MAGs from sediments only 2 MAGs affiliated to Acidimicrobiia and Desulfocapsaceae were shared at species level. Although, we recovered MAGs with the same taxonomic annotation in pelagic and benthic microbiomes, their metabolic potentials were different. A prominent example was the family Woeseiaceae that was among the most abundant taxa in the sediments. In benthic Woeseiaceae MAGs, we found polysaccharide utilization loci (PULs), predicted to target laminarin, alginate, and α-glucan. In contrast, pelagic Woeseiaceae MAGs were only recovered in the particle attached but not in the free-living fraction, and lacked PULs. They encoded a significantly more sulfatases and peptidases genes. Additionally, while genes involved in iron acquisition, gene regulation, and iron storage were widespread in Woeseiaceae MAGs, genes linked to dissimilatory iron reduction were mostly restricted to benthic Woeseiaceae, suggesting niche-specific adaptations to sediment redox conditions. Both, benthic and pelagic particle-attached Woeseiaceae MAGs encoded pilus TadA genes, which are essential for adhesion, colonization, and biofilm formation.</p><p><strong>Conclusions: </strong>LR sequencing is currently the most valuable tool for analyzing highly diverse benthic microbiomes. The small overlap of MAGs from water column and sediments indicated a limited bentho-pelagic coupling. The data suggest that Woeseiaceae have habitat-specific metabolic specialization: while benthic Woeseiaceae possess the metabolic capabilities to utilize fresh organic compounds like laminarin derived from algae blooms, and to perform dissimilatory nitrate, nitrite and iron reduction for gain energy, particle attached Woeseiaceae from the water column may be specialized in degrading protein-rich and sulfated organic matter likely reflecting adaptation to the different types of organic matter and redox conditions in sediments vs. the water column.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"74"},"PeriodicalIF":6.2,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318432","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":"Salinization alters microbial methane cycling in freshwater sediments.","authors":"Lorena Selak, Dimitri V Meier, Maja Marinović, Andrea Čačković, Katarina Kajan, Petra Pjevac, Sandi Orlić","doi":"10.1186/s40793-025-00739-w","DOIUrl":"10.1186/s40793-025-00739-w","url":null,"abstract":"<p><p>Climate change-induced salinization poses a global threat to freshwater ecosystems and challenges microbial communities driving crucial biogeochemical processes, particularly methane cycling. This study examined the impact of salinization and the accompanying sulfate concentration increases on microbial community dynamics and methane cycling in coastal freshwater lake sediments. We show that sulfate enrichment in sediment profiles enables the proliferation of distinct sulfate-reducing bacteria (SRB) that reshape microbial niches by competing with methanogens and promoting sulfate-dependent anaerobic oxidation of methane (AOM). Freshwater SRB clusters, which compete with some methanogens for substrates but also degrade organic compounds into methanogenesis precursors, are replaced by the SEEP-SRB groups that form syntrophic relationships with ANME-1 in salinized sediments. As seawater intrudes and reshapes microbial communities, a methane pocket forms that escapes both aerobic and anaerobic oxidation. Underneath this methane pocket, SRB play a key role in enabling sulfate-dependent AOM, facilitating methane consumption at higher sediment depths. While all microorganisms demonstrated some physiological adaptability potential to elevated osmotic stress, SRB exhibited the highest resilience to increased salinity. These findings highlight how salinization-induced geochemical shifts, particularly sulfate enrichment, directly affect microbial community assembly and impact methane cycling in coastal freshwater ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"73"},"PeriodicalIF":6.2,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318433","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":"Symbiotic Symbiodiniaceae mediate coral-associated bacterial communities along a natural thermal gradient.","authors":"Qianxi Yang, Han Zhang, Jian-Wen Qiu, Dingyong Huang, Xijie Zhou, Xinqing Zheng","doi":"10.1186/s40793-025-00733-2","DOIUrl":"10.1186/s40793-025-00733-2","url":null,"abstract":"<p><p>The coral-associated microbiome plays a vital role in the holobiont, enabling coral adaptation to diverse environments by modulating its composition and mediating interactions among its constituents. However, the responses of coral microbiomes, particularly the interactions between Symbiodiniaceae and bacteria, to environmental changes remain unclear. To fill this knowledge gap, we examined Pocillopora acuta, an environmentally sensitive coral species, collected from three sites along the southeastern coast of Hainan which exhibit moderate environmental differences. We measured the physiological characteristics of Symbiodiniaceae and conducted amplicon sequencing to analyze the structure of Symbiodiniaceae and bacterial communities. Our results revealed that P. acuta in southeastern Hainan maintains stable symbiosis with Symbiodiniaceae sub-clades such as C1, C42.1, C3, D1, D4, and D6, as evidenced by ΔF/Fm' values ranging from 0.45 for P. acuta dominated by Durusdinium (PaD) to 0.6 for counterparts dominated by Cladocopium (PaC). However, the composition of Symbiodiniaceae varied among the three sites, primarily due to differences in the abundance of dominant sub-clades. These variations may reflect adaptations to distinct environmental conditions, which in turn significantly influence the associated bacterial communities. Notably, our results suggest that Symbiodiniaceae may exert a greater regulatory role on the coral-associated bacterial community than environmental differences. Specific bacteria, such as Endozoicomonas and Synechococcus_CC9902, exhibit strong correlations with particular Symbiodiniaceae genera or sub-clades, indicating that the dominant Symbiodiniaceae shape bacterial community dynamics. Despite the observed variations, we identified modular co-occurrence patterns in bacterial networks, with PaC exhibiting a more complex and stable structure. Overall, these results highlight the critical role of various Symbiodiniaceae genera in influencing bacterial community dynamics, emphasizing their importance in maintaining coral health and resilience in the face of changing environmental conditions.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"72"},"PeriodicalIF":6.2,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12172317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318434","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":"Composition and rhythmic variations in the microbiome of Southwestern Atlantic corals.","authors":"I G L Seiblitz, K C C Capel, R R Oliveira, C Zilberberg, C A M M Cordeiro, C L B Francini, A A Zanotti, A M Ciotti, M V Kitahara","doi":"10.1186/s40793-025-00725-2","DOIUrl":"10.1186/s40793-025-00725-2","url":null,"abstract":"<p><strong>Background: </strong>Diel and tidal rhythms can regulate the metabolism, physiology, behavior, and gene expression patterns of different organisms, with evidence of an integration on the circadian behavior of host species and their microbial community. Corals host a diverse and dynamic microbial community, with variable diversity and abundance across geographic and temporal scales. Within scleractinian corals, those that host endosymbiotic algae (i.e., zooxanthellate) display a diel variation in the oxygen levels, an oscillation in their internal environment that has the potential to influence its microbiome abundance and/or composition. Here we investigate in situ daily fluctuations on the microbial community of two zooxanthellate (Madracis decactis and Mussismilia hispida) and two azooxanthellate coral species (Tubastraea coccinea and T. tagusensis) along a 72-hour period.</p><p><strong>Results: </strong>Day and night alpha diversity values were similar for all species, with Ma. decactis hosting a significantly more diverse community. Similarly, there was no fluctuation in the microbiome composition at the Amplicon Sequence Variants (ASV) level between day and night within species, but all species were significantly different from each other. Interestingly, Mu. hispida, an endemic species to the Southwestern Atlantic, had a high proportion of unidentified microbial taxa at genus level, suggesting a species-specific microbiome community composed by unidentified taxa. Significant rhythmicity in the abundance of individual ASVs was observed for one ASV (genus Pseudoalteromonas) in T. tagusensis and one (genus Woeseia) in Ma. decactis, with 24 and 12-hour fluctuations, respectively. In addition, DESeq2 recovered 13 ASVs (four in Ma. decactis, two in Mu. hispida, six in T. coccinea, and one in T. tagusensis) with different abundances between day and night.</p><p><strong>Conclusions: </strong>Results show divergent microbial communities when comparing zooxanthellate and azooxanthellate species, with few significant changes within a 24-hour period. Future studies should focus on metabolic pathways to better understand how the microbiome community can adjust to environmental changes within the coral host in short time scales.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"71"},"PeriodicalIF":6.2,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295156","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":"Antarctic ice-free terrestrial microbial functional redundancy in core ecological functions and microhabitat-specific microbial taxa and adaptive strategy.","authors":"Mimi Zhang, Yao Xiao, Qianqian Song, Zhiyong Li","doi":"10.1186/s40793-025-00735-0","DOIUrl":"10.1186/s40793-025-00735-0","url":null,"abstract":"<p><strong>Background: </strong>Although ice-free terrestrial ecosystems in Antarctica cover only limited areas, they harbor diverse and metabolically active microbial communities. These ecosystems encompass distinct microhabitats such as mosses, lichens, and soils, each offering unique ecological niches. However, how different microbial taxa respond to microhabitat heterogeneity, ecological strategies such as functional redundancy and specialization contribute to adaptation in extreme environments remains underexplored. To address these questions, we employed high-throughput 16 S rRNA gene and ITS sequencing in combination with GeoChip-based functional gene profiling to assess the structure and functional potential of microbial communities across moss, lichen and soil microhabitats in Antarctic ice-free terrestrial ecosystem.</p><p><strong>Results: </strong>Microhabitat type has a greater influence on microbial community structure and function in the ice-free Antarctic terrestrial ecosystem than geographical location. Though all prokaryotic communities were dominated by Pseudomonadota, Nostoc and Endobacter were significantly enriched in the moss and lichen microhabitats, respectively. Meanwhile, all fungal communities were primarily dominated by Ascomycota and Basidiomycota, with Byssoloma and Usnea showing significant enrichment in the moss and lichen microhabitats, respectively. Despite these taxonomic differences, the three microhabitats show similar core ecological functions with widespread microbial functional redundancy. Nevertheless, clear microhabitat-specific functional specialization was suggested. For example, moss microhabitat was enriched in Pyoverdin_pvcC and Zeaxanthin_glucosyltransferase, sdhA, lichen microhabitat harbored higher levels of nhaA, nikC, vacuolar_iron_transport, mttB, glucoamylase, pel_Cdeg, pme_Cdeg, rgh, rgl, while soil microhabitat was enriched in 5f1_ppn and isopullulanase. Notably, genes involved in carotenoid biosynthesis were significantly more abundant in moss and lichen microhabitats than in soil microhabitat, indicating the adaptive capacity of symbiotic microorganisms to mitigate ultraviolet radiation and oxidative stress to protect their hosts.</p><p><strong>Conclusions: </strong>Microbial communities associated with distinct microhabitats (i.e. mosses, lichens, and soils) in Antarctic ice-free terrestrial ecosystem exhibit both functional redundancy in core ecological functions and microhabitat-specific specialization in key microbial taxa and adaptive strategy.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"70"},"PeriodicalIF":6.2,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295155","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":"Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations.","authors":"Ioannis D Kampouris, Theresa Kuhl-Nagel, Jan Helge Behr, Loreen Sommermann, Doreen Babin, Davide Francioli, Rita Zrenner, Susanne Kublik, Michael Schloter, Uwe Ludewig, Kornelia Smalla, Günter Neumann, Rita Grosch, Joerg Geistlinger","doi":"10.1186/s40793-025-00729-y","DOIUrl":"10.1186/s40793-025-00729-y","url":null,"abstract":"<p><strong>Background: </strong>Plant beneficial microorganisms as inoculants can improve crop performance, but factors affecting their impact on plant performance under field conditions remain unclear, thereby limiting their use in farming. Here, we investigated how farming practices (e.g., tillage and N-fertilization intensity) and growing seasons influenced the impact of a beneficial microorganism consortium (BMc: Trichoderma, Bacillus, and Pseudomonas strains) in maize and affected the rhizosphere competence of each BMc strain. In addition, we tested whether the consortium affects the resident rhizosphere microbiome and crop performance. In two growing seasons (2020 and 2021), we assessed how BMc inoculation affects maize growth, nutritional status, gene expression, and rhizosphere microbiome under different farming practices at the flowering stage.</p><p><strong>Results: </strong>Inoculated strains successfully colonized the maize rhizosphere independently of farming practice. BMc inoculation improved plant growth and iron uptake in 2020, regardless of farming practice. These effects co-occurred with lower precipitation levels in 2020 compared to 2021. BMc inoculation reduced the expression of several stress-related genes in maize in 2020 under drought. An increased iron uptake by the BMc-inoculated plants was observed in 2020 and was associated with the upregulation of the gene ZmNAS3, which is linked to iron uptake. Therefore, BMc inoculation mitigated the drought impact on maize. The microbial rhizosphere communities were altered by BMc inoculation in both years, but patterns of responder taxa differed between seasons. Metagenome analysis revealed that more genes (e.g., genes encoding biosurfactants and siderophores) were enriched in the rhizosphere of BMc-inoculated plants in 2020 than in 2021. Moreover, we identified bacterial and fungal taxa positively associated with maize iron uptake. The relative abundance of these iron uptake-associated bacterial and fungal taxa significantly increased due to BMc inoculation in 2020, while they showed overall higher relative abundances in 2021, independently of BMc inoculation. We mapped the sequences of these iron-associated taxa to publicly available genomes and verified the occurrence of various plant beneficial traits in several mapped genomes.</p><p><strong>Conclusions: </strong>Overall, we show that the growing season determined the effect of BMc inoculation on maize plants by shaping microbiome composition and function in the maize rhizosphere more than farming practice. These findings highlight the importance of the complex interplay between microbial inoculants and the resident rhizosphere microorganisms under abiotic stress conditions.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"69"},"PeriodicalIF":6.2,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12164104/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144286892","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":"Investigation on the aerobic methanotrophic community and the dominant taxon Methylomarinum in seagrass ecosystem.","authors":"Tongyin Liang, Junde Dong, Weiguo Zhou, Xiaofang Huang, Hongbin Liu, Yuhang Zhang, Qingsong Yang, Manzoor Ahmad, Luxiang Chen, Juan Ling","doi":"10.1186/s40793-025-00736-z","DOIUrl":"10.1186/s40793-025-00736-z","url":null,"abstract":"<p><strong>Background: </strong>Methanotrophs are a key biological methane sink, and aerobic methanotrophs critically reduce wetland methane emissions under global climate change. However, despite their ecological significance, investigations on aerobic methanotrophs within seagrass ecosystems remain scant. In this study, microcosmic culture experiments were used to assess aerobic methane oxidation (AMO) potential and its drivers across a vertical gradient of seagrass sediments. Moreover, the methanotrophic community structure was characterized by amplicon sequencing, and the dominant methanotroph's metagenome-assembled genome (MAG) and metabolic pathway was investigated.</p><p><strong>Results: </strong>Sediments of Halophila ovalis exhibited notable vertical differences in both physicochemical properties and methane oxidation rates. Furthermore, ammonium nitrogen (NH₄⁺-N) decreased with sediment depth, and was suggested by structural equation modeling (SEM) to significantly contribute to the vertical methane oxidation variability. Microbial community structure analysis revealed that type I methanotrophs were stimulated by methane addition and significantly impacted the oxidation of elevated methane, with Methylomarinum being the dominant taxon. Through metagenomic analysis, we assembled a phylogenetically novel methanotroph, Candidatus Methylomarinum sp. MAG81, which is distantly related to the extant Methylomarinum vadi IT-4. We conducted a comparative analysis of the two genomes and discovered that MAG81 not only possesses the capability for methane oxidation but also has the ability to participate in methanol oxidation via Xox-MDH. Furthermore, MAG81 also harbors nitrogen metabolism genes, particularly those involved in nitrogen fixation (nifHDK). This genetic characteristic suggests a potential role for MAG81 in facilitating the carbon and nitrogen cycles within seagrass ecosystems.</p><p><strong>Conclusions: </strong>In summary, our study revealed that the vertical variation of NH₄⁺-N significantly affected methane oxidation and that type I methanotrophs, especially the genus Methylomarinum played an important role in oxidizing methane in seagrass sediments, shedding new insights into the methane abatement in the seagrass ecosystem, which is essential for climate change mitigation.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"67"},"PeriodicalIF":6.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160114/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276265","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":"Interrow cover crops in a semi-arid vineyard increase plant beneficial functional potential of the soil microbiome, both in vine rows and interrows, a benefit that increases with cover crop duration.","authors":"Fernando Igne Rocha, Jean Carlos Rodriguez-Ramos, Margaret Fernando, Lauren Hale","doi":"10.1186/s40793-025-00726-1","DOIUrl":"10.1186/s40793-025-00726-1","url":null,"abstract":"<p><strong>Background: </strong>Cover crops are recognized for enhancing soil health and providing agroecosystem services, but are not widely adopted, particularly in water-limited regions. In Mediterranean vineyards, where water scarcity and soil degradation challenge productivity, interrow, cool-season cover cropping offers a promising strategy to improve microbial-mediated soil functions. However, the temporal and spatial effects of cover crops on vineyard soil microbiomes and soil health metrics remain poorly understood. This study evaluated the impacts of a California native (phacelia, Phacelia tanacetifolia) and introduced (rye, Secale cereale L.) plant species as interrow cover crops on soil properties in interrow and vine row soils across three years.</p><p><strong>Results: </strong>The study revealed distinct temporal and spatial dynamics in soil microbiomes elicited by the cover crop treatments. By the third year, phacelia exhibited the highest microbial biomass, fungal-to-bacterial ratios, and microbial network complexity. Interrow soils showed stronger responses to cover cropping, including enhanced microbial biomass and differentiation between treatments, while vine row soils demonstrated subtler but significant shifts in microbial metrics. Functional predictions indicated that cover crops reduced fungal pathogen prevalence and supported nutrient cycling processes. Deterministic processes driven by environmental selection became dominant under both treatments, promoting microbial resilience. Random Forest analysis identified NO₃^- as a key driver of microbial differentiation, with phacelia fostering communities reliant on labile organic inputs.</p><p><strong>Conclusions: </strong>This study highlights a crucial benefit of interrow cover crops in improving soil health and enhancing microbial-mediated ecosystem functions in adjacent vine row soils, even after cover crop termination. Long-term application of cover crops offers a sustainable approach to building resilient agroecosystems in water-scarce environments, with implications for sustainable viticulture practices.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"66"},"PeriodicalIF":6.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276264","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}