Environmental Microbiome最新文献

{"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}

{"title":"New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.","authors":"Duncan Sussfeld, Romain Lannes, Eduardo Corel, Guillaume Bernard, Pierre Martin, Eric Bapteste, Eric Pelletier, Philippe Lopez","doi":"10.1186/s40793-025-00697-3","DOIUrl":"10.1186/s40793-025-00697-3","url":null,"abstract":"<p><strong>Background: </strong>Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known Tree of Life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters.</p><p><strong>Results: </strong>Here, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40 million ORFs predicted in marine environments. We assessed the environmental diversity of 53 core gene families broadly distributed across the Tree of Life, with essential functions including translational, replication and trafficking processes. For nearly half of them, we identified clusters of remote environmental homologues that showed divergence from the known genetic diversity comparable to the divergence between Archaea and Bacteria, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential SMC (Structural Maintenance of Chromosomes) genes, divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases in Bacteria as well as viruses.</p><p><strong>Conclusions: </strong>These results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"65"},"PeriodicalIF":6.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276266","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":"Defining the cultured and uncultured bacterial fractions in Cannabis seeds.","authors":"Carolina Lobato, Ahmed Abdelfattah, Gabriele Berg, Tomislav Cernava","doi":"10.1186/s40793-025-00731-4","DOIUrl":"10.1186/s40793-025-00731-4","url":null,"abstract":"<p><strong>Background: </strong>Seeds provide a unique environment shaped by co-evolutionary processes, hosting diverse microbial communities. While microbiome studies have uncovered an extensive diversity of microorganisms, culture-based approaches remain crucial for understanding microbial potential and functional interactions. However, the factors influencing microbial culturability within seeds are not well understood.</p><p><strong>Results: </strong>In this study, we investigated the culturing patterns of bacteria inside Cannabis seeds, assessing their phylogenetic diversity, abundance, and putative interactions. Bacteria were cultured from 54 different Cannabis accessions using germinated seeds and a range of nutrient media including those supplemented with Cannabis extracts. The cultured fraction consisted of taxa from five prominent classes-Gammaproteobacteria, Bacilli, Actinobacteria, Alphaproteobacteria, and Bacteroidia-encompassing 36 genera. Despite representing only 6.3% of the total microbiota, these cultured bacteria accounted for 89.2% of the microbial population. Almost 60% of the amplicon sequence variants (ASVs) were phylogenetically distant from cultured taxa. Rare bacterial groups such as Acidobacteriae and Verrucomicrobiae, known for their plant growth-promoting traits, were exclusively found in the uncultured fraction. Network analyses revealed that uncultured taxa are centralized and more connected to hubs, suggesting that interspecies interactions strongly influence culturability.</p><p><strong>Conclusion: </strong>Our findings highlight the limitations of culture-based methods in capturing the full microbial diversity of Cannabis seeds and emphasize the importance of microbial interactions in determining culturability. The strong network connectivity of uncultured taxa suggests that interdependencies and competition within the seed microbiome may hinder the isolation of key bacterial groups. These insights provide a framework for refining cultivation strategies to recover ecologically significant microbes with potential agricultural applications.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"68"},"PeriodicalIF":6.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276254","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":"Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.","authors":"Monique E Smith, Vanessa N Kavamura, David Hughes, Rodrigo Mendes, George Lund, Ian Clark, Tim H Mauchline","doi":"10.1186/s40793-025-00723-4","DOIUrl":"10.1186/s40793-025-00723-4","url":null,"abstract":"<p><strong>Background: </strong>During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.</p><p><strong>Results: </strong>We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).</p><p><strong>Conclusions: </strong>Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"64"},"PeriodicalIF":6.2,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12145609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250396","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":"Severe drought impacts tree traits and associated soil microbial communities of clonal oaks.","authors":"Camilo Quiroga-González, Luis Daniel Prada-Salcedo, François Buscot, Mika Tarkka, Sylvie Herrmann, Marie-Lara Bouffaud, Kezia Goldmann","doi":"10.1186/s40793-025-00720-7","DOIUrl":"10.1186/s40793-025-00720-7","url":null,"abstract":"<p><strong>Background: </strong>Biotic and abiotic factors, including plant age, soil pH, soil organic matter concentration, and especially water availability, significantly influence soil microbial populations and plant characteristics. While many ecosystems are adapted to occasional droughts, climate change is increasing the frequency and severity of drought events, which negatively impacts plant productivity and survival. Long-lived, drought-sensitive tree species such as Quercus robur are particularly vulnerable to water shortages. Drought also alters soil microbial communities, reducing and reshaping microbial diversity, biomass, and activity, which can in turn disrupt key ecosystem functions. The objective of this study was to investigate the effects of natural drought conditions on soil physicochemical variables, plant traits and microbial communities of the oak clone DF159 in Central Germany. Our research focuses on two study sites, Bad Lauchstädt and Kreinitz, which differ in soil water retention capacity. Data collection spans two periods: before and after a severe drought in 2018. Oak traits and environmental data was collected from 2011 to 2023 covering two oak time series with trees planted annually between 2010 and 2019. Microbial communities were analyzed every second year between 2015 and 2021 around trees representing five different ages.</p><p><strong>Results: </strong>We found that plant traits, including apical growth, branch elongation and number of shoot flushes, were positively correlated with precipitation and relative humidity. Although the study sites differed in oak leaf number per shoot flush and number of shoot flushes, the 2018 drought negatively impacted all measured plant traits, regardless of sites. Soil bacterial richness and diversity declined at both study sites, independent of plant age, while fungal richness specifically increased in Bad Lauchstädt, which has a higher water-holding capacity, following the drought event. Bacterial community composition was more strongly affected by drought than fungal communities, whereas the latter was more responsive to plant age than bacterial communities.</p><p><strong>Conclusions: </strong>Given their strong functional links during drought, interactions among vegetation, microbial communities, and soil functioning may ultimately influence major ecosystem services. Bacterial communities were particularly sensitive to drought, while fungal communities exhibited greater resistance, suggesting their potential role in supporting plant survival under drought stress. These findings highlight the risk that prolonged drought may cause irreversible shifts in microbial communities, with significant implications for soil functions and plant-microbe interactions.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"63"},"PeriodicalIF":6.2,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250376","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}