Environmental Microbiome最新文献

{"title":"Soil organic matter composition affects ecosystem multifunctionality by mediating the composition of microbial communities in long-term restored meadows.","authors":"Wenyin Wang, Sisi Bi, Fei Li, A Allan Degen, Shanshan Li, Mei Huang, Binyu Luo, Tao Zhang, Shuai Qi, Tianyun Qi, Yanfu Bai, Peipei Liu, Zhanhuan Shang","doi":"10.1186/s40793-025-00678-6","DOIUrl":"10.1186/s40793-025-00678-6","url":null,"abstract":"<p><strong>Background: </strong>Soil organic matter composition and microbial communities are key factors affecting ecosystem multifunctionality (EMF) during ecosystem restoration. However, there is little information on their interacting mechanisms in degraded and restored meadows. To fill this knowledge gap, plant, root and soil samples from alpine swamp meadows, alpine Kobresia meadows, severely degraded alpine meadows, short-term restored meadows (< 5 years) and long-term restored meadows (6-14 years) were collected. We leveraged high-throughput sequencing, liquid chromatography and mass spectrometry to characterize soil microbial communities and soil organic matter composition, measured microbial carbon metabolism and determined EMF.</p><p><strong>Results: </strong>It emerged that the similarity of soil microorganisms in meadows decreased with increasing heterogeneity of soil properties. Dispersal limitation and ecological drift led to the homogenization of the bacterial community. Based on co-occurrence network analysis, an increase in microbial network complexity promoted EMF. Root total phosphorus and soil organic matter components were the key predictors of EMF, while organic acids and phenolic acids increased the stability of the microbial network in long-term restored meadows. Carbon metabolism did not increase in restored meadows, but the niche breadth of soil microorganisms and the utilization efficiency of small molecular carbon sources such as amino acids did increase.</p><p><strong>Conclusions: </strong>These findings emphasize the importance of soil organic matter composition in ecological restoration and that the composition should be considered in management strategies aimed at enhancing EMF.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"22"},"PeriodicalIF":6.2,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11807318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374881","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 and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula.","authors":"Swan L S Sow, Willem H van de Poll, Rachel Eveleth, Jeremy J Rich, Hugh W Ducklow, Patrick D Rozema, Catherine M Luria, Henk Bolhuis, Michael P Meredith, Linda A Amaral-Zettler, Julia C Engelmann","doi":"10.1186/s40793-025-00663-z","DOIUrl":"10.1186/s40793-025-00663-z","url":null,"abstract":"<p><strong>Background: </strong>The west Antarctic Peninsula (WAP) is a region of rapid environmental changes, with regional differences in climate warming along the north-south axis of the peninsula. Along the WAP, Palmer corresponds to a warmer region with lesser sea ice extent in the north compared to Rothera ~ 400 km to the south. Comprehensive and comparative, year-round assessments of the WAP microbial community dynamics in coastal surface waters at these two locations are imperative to understand the effects of regional climate warming variations on microbial community dynamics, but this is still lacking.</p><p><strong>Results: </strong>We report on the seasonal diversity, taxonomic overview, as well as predicted inter-and intra-domain causal effects (interactions) of the bacterial and microbial eukaryotic communities close to the Palmer station and at the Rothera time-series site between July 2013 and April 2014. Our 16S- and 18S-rRNA gene amplicon sequencing data showed that across all seasons, both bacteria and microbial eukaryotic communities were considerably different between the two sites which could be attributed to seawater temperature, and sea ice coverage in combination with sea ice type differences. Overall, in terms of biotic drivers, causal-effect modelling suggests that bacteria were stronger drivers of ecosystem dynamics at Palmer, while microbial eukaryotes played a stronger role at Rothera. The parasitic taxa Syndiniales persevered at both sites across the seasons, with Palmer and Rothera harbouring different key groups. Up to 62.3% of the negative causal effects were driven by Syndiniales at Rothera compared to only 13.5% at Palmer, suggesting that parasitism drives community dynamics at Rothera more strongly than at Palmer. Conversely, SAR11 Clade II, which was less abundant but persistent year-round at both sites, was the dominant driver at Palmer, evidenced by many (28.2% and 37.4% of positive and negative effects respectively) strong causal effects. Article note: Kindly check first page article notes are correct.</p><p><strong>Conclusions: </strong>Our research has shed light on the dynamics of microbial community composition and correlative interactions at two sampling locations that represent different climate regimes along the WAP.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"21"},"PeriodicalIF":6.2,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11807339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374920","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":"Phytochrome-mediated shade avoidance responses impact the structure and composition of the bacterial phyllosphere microbiome of Arabidopsis.","authors":"James A O'Rourke, Stacey A Vincent, Isabel E I Williams, Eleanor L Gascoyne, Paul F Devlin","doi":"10.1186/s40793-025-00679-5","DOIUrl":"10.1186/s40793-025-00679-5","url":null,"abstract":"<p><p>The shade avoidance response triggers a dramatic promotion of elongation growth, accompanied by a significant reprogramming of metabolic pathways as plants seek to prevent overtopping and adapt to vegetative shade. Here we demonstrate that simulated vegetative shade results in significant changes in the structure and composition of the phyllosphere bacterial microbiome. Our study uncovered significant shifts in the diversity, occurrence, abundance and activity of bacteria within the phyllosphere microbiome. A comparison of responses in both wild-type plants and phytochrome mutants, which inherently exhibit a shade-avoidance phenotype, revealed both indirect responses to host plant physiology and direct responses to light among the microbiota. Hierarchical clustering of response patterns further suggested that over a third of the taxa constituting the core phyllosphere microbiome in our assay show some degree of response to vegetative shade. Bacteria that increased in abundance on plants with a shade-avoidance phenotype corresponded to genera associated with beneficial traits such as enhanced disease resistance and growth promotion. Our findings suggests that plants manipulate their phyllosphere microbiome under shade conditions as a strategy to optimise fitness when competing for light. We discuss the implications of our findings in terms of furthering our understanding of plant-microbe signalling in the shaping of the phyllosphere microbiome and the possibility of manipulating the phyllosphere microbiome for plant health in an agricultural setting at high planting densities.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"20"},"PeriodicalIF":6.2,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800596/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366338","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":"Metabolic redundancy and specialisation of novel sulfide-oxidizing Sulfurimonas and Sulfurovum along the brine-seawater interface of the Kebrit Deep.","authors":"Rayyan Alamoudi, Alan Barozzi, Grégoire Michoud, Marc W Van Goethem, Charlene Odobel, Yue Chen, Ramona Marasco, Daniele Daffonchio","doi":"10.1186/s40793-025-00669-7","DOIUrl":"10.1186/s40793-025-00669-7","url":null,"abstract":"<p><strong>Background: </strong>Members of the Campylobacterota phylum are dominant key players in sulfidic environments, where they make up a stable portion of sulfide-oxidizing bacterial communities. Despite the significance of these bacteria in primary production being well recognised in several ecosystems, their genomic and metabolic traits in sulfidic deep hypersaline anoxic basins (DHABs) remain largely unexplored. This knowledge gap not only hampers our understanding of their adaptation and functional role in DHABs but also their ecological interactions with other microorganisms in these unique ecosystems.</p><p><strong>Results: </strong>Metabolic reconstructions from metagenome-assembled genomes (MAGs) of sulfide-oxidizing Campylobacterota were conducted at 10 cm spatial resolution within the halocline of the brine-seawater interface (BSI, salinity 91-155 PSU) of the 1466 m deep sulfidic Kebrit Deep in the Red Sea. Fifty-four Campylobacterota MAGs were assembled and dereplicated into three distinct groups, with the highest-quality genome retained as representative. These genomes represent novel sulfide-oxidizing species within the Sulfurimonas and Sulfurovum genera, which differ from those found in mildly saline deep-sea sulfidic pools. They are stratified along the BSI and utilise the reductive tricarboxylic acid cycle to fix carbon dioxide, acting as primary producers. Their energy generation processes include aerobic or anaerobic-nitrate-dependent sulfide oxidation, as well as hydrogen oxidation. In addition to the osmoprotectant pathways commonly observed in Campylobacterota, such as the synthesis and uptake of proline and glutamate, the two Kebrit Deep Sulfurovum species exhibit genomic signatures for ectoine synthesis, further aiding their adaptation to high salinity. This combination of metabolic redundancy and specialisation within the confined spatial boundaries (~1 m) of the BSI is pivotal in governing microbial interactions, including those with sulfate-reducers, heterotrophs, and other primary producers.</p><p><strong>Conclusions: </strong>These results show how the selective pressures mediated by the sulfidic and hypersaline conditions of Kebrit Deep have resulted in novel, adapted and metabolically redundant Sulfurimonas and Sulfurovum species that contribute to the energy coupling, nutrient turnover and metabolic continuity along the physico-chemical gradient of the BSI.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"19"},"PeriodicalIF":6.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143257076","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-microbe interactions influence plant performance via boosting beneficial root-endophytic bacteria.","authors":"Sai Guo, Rubin Pan, Yan Zhang, Quanwei Gu, Qirong Shen, Jian Yang, Luqi Huang, Zongzhuan Shen, Rong Li","doi":"10.1186/s40793-025-00680-y","DOIUrl":"10.1186/s40793-025-00680-y","url":null,"abstract":"<p><strong>Background: </strong>Salvia miltiorrhiza is a highly valuable medicinal plant and its cultivation is constrained by limited suitable land. Long-term continuous cropping practices alleviate limitations in planting area as well as causes the decline in plant yield and quality. Endophytic microorganisms colonize inside plant roots and are known to play important roles in improving the performance of model plants (such as Arabidopsis thaliana) and food crops (such as wheat, soybean, rice and maize). However, the understanding of how medicinal plants with different growth status (i.e., healthy and disease) shape the assembly of root-endophytic microorganisms and the functional importance of these microorganisms in improving plant performance remains largely unknown.</p><p><strong>Results: </strong>Here, we investigated the assembly of root-endophytic microorganisms in medicinal plants with different growth status and its links with plant performance improvement. We found that medicinal plants with different growth status had distinct root-endophytic bacterial communities. Healthy plant roots recruited some potentially beneficial bacteria partners, particularly Pseudomonas into the endosphere. We further investigated the functional importance of these potentially beneficial bacteria on plant performance in subsequent greenhouse and field experiments. We found that root-endophytic Pseudomonas effectively increased medicinal plant seedling growth, crop yield, and the content of effective medicinal components.</p><p><strong>Conclusions: </strong>Taken together, we demonstrate that healthy medicinal plants can form a distinct root-endophytic bacterial community, leading to an increase in plant growth-promoting endophytic bacteria (PGPEB) that contribute to the improvement of crop growth and quality. Our research provides valuable insights into the significant role of PGPEB in enhancing crop growth and improving medicinal plants quality for human health development in the future.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"18"},"PeriodicalIF":6.2,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A systematic scoping review reveals that geographic and taxonomic patterns influence the scientific and societal interest in urban soil microbial diversity.","authors":"Simon Masson, Matteo Chialva, Davide Bongiovanni, Martino Adamo, Irene Stefanini, Luisa Lanfranco","doi":"10.1186/s40793-025-00677-7","DOIUrl":"10.1186/s40793-025-00677-7","url":null,"abstract":"<p><p>Urban green areas provide multiple ecosystem services in cities, mitigating environmental risks and providing a healthier environment for humans. Even if urban ecology has become popular in the last decade, the soil environment with its microbiota, which sustains many other biodiversity layers, remains overlooked. Here, a comprehensive database of scientific papers published in the last 30 years investigating different aspects of soil microbial diversity was built and systematically reviewed. The aim was to identify the taxa, experimental methods and geographical areas that have been investigated, and to highlight gaps in knowledge and research prospects. Our results show that current knowledge on urban soil microbiota remains incomplete, mainly due to the lack of publications on functional aspects, and is biased, in terms of investigated taxa, with most studies focused on Prokaryotes, and geographic representativeness, with the interest focused on a few large cities in the Northern hemisphere. By coupling bibliometrics with statistical modelling we found that soil microbial traits such as biomass and respiration and omics techniques attract the interest of the scientific community while multi-taxa and time-course studies appeal more to the general public.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"17"},"PeriodicalIF":6.2,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190965","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":"Insights into quinoa endophytes: core bacterial communities reveal high stability to water stress and genotypic variation.","authors":"Isaac Maestro-Gaitán, Miguel Redondo-Nieto, Sara González-Bodí, Laura Rodríguez-Casillas, Javier Matías, Luis Bolaños, María Reguera","doi":"10.1186/s40793-025-00673-x","DOIUrl":"10.1186/s40793-025-00673-x","url":null,"abstract":"<p><strong>Background: </strong>Plant endophytes, comprising non-pathogenic bacteria, fungi, and archaea, inhabit various plant parts, including roots, stems, leaves, and seeds. These microorganisms play a crucial role in plant development by enhancing germination, growth, and stress resilience. Seed endophytes, in particular, represent the most adapted and conserved segment of plant microbiota, significantly influencing the initial stages of plant growth and microbial community establishment. This study investigates the impact of environmental and genotypic factors on the endophytic communities of Chenopodium quinoa Willd. (quinoa), a crop notable for its adaptability and nutritional value.</p><p><strong>Results: </strong>We aimed to characterize the core endophytic communities in quinoa seeds and roots from two distinct genotypes under well-watered (WW) and water-deficit (WD) conditions, utilizing various soil infusions as inoculants to explore potential changes in these endophytes. Our findings reveal distinct changes with quinoa seeds exhibiting a high degree of conservation in their endophytic microbiome, even between maternal and offspring seeds, with specific bacterial taxa showing only minor differences. Tissue specificity emerged as a key factor, with seeds maintaining a stable microbial community, while roots exhibited more pronounced shifts, highlighting the tissue-dependent patterns of microbial enrichment.</p><p><strong>Conclusions: </strong>The results highlight the stability and conservation of endophytic communities in quinoa seeds, even under varying water conditions and across different genotypes, emphasizing the role of tissue specificity in shaping microbial associations. These findings suggest that quinoa-associated endophytes, particularly those conserved in seeds, may play a crucial role in enhancing drought resilience. Understanding the dynamics of plant-microbe interactions in quinoa is vital for developing stress-resilient crop varieties, supporting sustainable agricultural practices, and ensuring food security in the face of climate change and environmental challenges.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"16"},"PeriodicalIF":6.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143123748","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":"Commercial bioinoculants improve colonization but do not alter the arbuscular mycorrhizal fungal community of greenhouse-grown grapevine roots.","authors":"Mariam P Berdeja, Nicole K Reynolds, Teresa Pawlowska, Justine E Vanden Heuvel","doi":"10.1186/s40793-025-00676-8","DOIUrl":"10.1186/s40793-025-00676-8","url":null,"abstract":"<p><strong>Background: </strong>Arbuscular mycorrhizal fungi (AMF) are beneficial root symbionts contributing to improved plant growth and development and resistance to abiotic and biotic stresses. Commercial bioinoculants containing AMF are widely considered as an alternative to agrochemicals in vineyards. However, their effects on grapevine plants grown in soil containing native communities of AMF are still poorly understood. In a greenhouse experiment, we evaluated the influence of five different bioinoculants on the composition of native AMF communities of young Cabernet Sauvignon vines grown in a non-sterile soil. Root colonization, leaf nitrogen concentration, plant biomass and root morphology were assessed, and AMF communities of inoculated and non-inoculated grapevine roots were profiled using high-throughput sequencing.</p><p><strong>Results: </strong>Contrary to our predictions, no differences in the microbiome of plants exposed to native AMF communities versus commercial AMF bioinoculants + native AMF communities were detected in roots. However, inoculation induced positive changes in root traits as well as increased AMF colonization, plant biomass, and leaf nitrogen. Most of these desirable functional traits were positively correlated with the relative abundance of operational taxonomic units identified as Glomus, Rhizophagus and Claroideoglomus genera.</p><p><strong>Conclusion: </strong>These results suggest synergistic interactions between commercial AMF bioinoculants and native AMF communities of roots to promote grapevine growth. Long-term studies with further genomics, metabolomics and physiological research are needed to provide a deeper understanding of the symbiotic interaction among grapevine roots, bioinoculants and natural AMF communities and their role to promote plant adaptation to current environmental concerns.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"15"},"PeriodicalIF":6.2,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143075990","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":"Peptide nucleic acid (PNA) clamps reduce amplification of host chloroplast and mitochondria rRNA gene sequences and increase detected diversity in 16S rRNA gene profiling analysis of oak-associated microbiota.","authors":"Usman Hussain, Jim Downie, Amy Ellison, Sandra Denman, James McDonald, Marine C Cambon","doi":"10.1186/s40793-025-00674-w","DOIUrl":"10.1186/s40793-025-00674-w","url":null,"abstract":"<p><strong>Background: </strong>Acquiring representative bacterial 16S rRNA gene community profiles in plant microbiome studies can be challenging due to the excessive co-amplification of host chloroplast and mitochondrial rRNA gene sequences that reduce counts of plant-associated bacterial sequences. Peptide Nucleic Acid (PNA) clamps prevent this by blocking PCR primer binding or binding within the amplified region of non-target DNA to stop the function of DNA polymerase. Here, we applied a universal chloroplast (p)PNA clamp and a newly designed mitochondria (m)PNA clamp to minimise host chloroplast and mitochondria amplification in 16S rRNA gene amplicon profiles of leaf, bark and root tissue of two oak species (Quercus robur and Q. petraea).</p><p><strong>Results: </strong>Adding PNA clamps to PCR led to an overall reduction of host chloroplast and mitochondrial 16S rRNA gene sequences of 79%, 46% and 99% in leaf, bark and root tissues, respectively. This resulted in an average increase in bacterial sequencing reads of 72%, 35%, and 17% in leaf, bark, and root tissue, respectively. Moreover, the bacterial diversity in the leaf and bark increased, with the number of ASVs rising by 105 in the leaf samples and 218 in the bark samples, respectively. In root tissues, where host oak chloroplast and mitochondria contamination were low, alpha and beta diversity did not change, suggesting the PNA clamps did not bias the bacterial community.</p><p><strong>Conclusion: </strong>In conclusion, this study shows that PNA clamps can effectively reduce host chloroplast and mitochondria PCR amplification and improve assessment of the detected bacterial diversity in Quercus petraea and Quercus robur bacterial 16S rRNA gene sequencing studies.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"14"},"PeriodicalIF":6.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061101","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":"Differential responses of root and leaf-associated microbiota to continuous monocultures.","authors":"Hao-Ran Li, Xiang-Yu Zhang, Kai-Ling He, Xin Xu, Xin-Wen Chen, Yaseen Ullah, Ting-Ting Zhang, Yan Chen, Chuan-Chao Dai, Wei Zhang","doi":"10.1186/s40793-025-00675-9","DOIUrl":"10.1186/s40793-025-00675-9","url":null,"abstract":"<p><p>Continuous monocultures alter the composition and function of root-associated microbiota, and thus compromise crop health and productivity. In comparison, little is known about how leaf-associated microbiota respond to continuous monocultures. Here, we profiled root and leaf-associated microbiota of peanut plants under monocropping and rotation conditions. Additionally, their protective effects against root pathogen Fusarium oxysporum and leaf pathogen Alternaria alstroemeriae were evaluated. We found that monocropping increased root and leaf disease severity. Meanwhile, the peanut growth and productivity were inhibited by monocropping. Microbiota analysis revealed that monocropping reduced rhizosphere microbial population and diversity, while increased leaf epiphytic microbial population and did not influence leaf epiphytic microbial diversity. Cropping conditions had a greater impact on the microbiota composition of leaf epiphytes than that of the rhizosphere. Moreover, in vitro and in vivo experiments, combined with correlation analyses showed that monocropping weakened the antagonistic activity of rhizosphere microbiota against F. oxysporum and root rot disease. This effect may be associated with the depletion of Bacillus sp. and Sphingomonas sp.. By contrast, leaf epiphytic microbiota under monocropping exhibited greater inhibition of A. alstroemeriae growth and leaf spot control. Together, our results demonstrated a differential response pattern of root and leaf-associated microbiota to continuous monocultures.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"13"},"PeriodicalIF":6.2,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053918","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}