Environmental Microbiome最新文献

{"title":"Daily turnover of airborne bacterial communities in the sub-Antarctic.","authors":"Lucie A Malard, Peter Convey, David A Pearce","doi":"10.1186/s40793-025-00745-y","DOIUrl":"10.1186/s40793-025-00745-y","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"91"},"PeriodicalIF":6.2,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12273333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668788","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":"Crop rotation alleviates continuous cropping obstacles in Chrysanthemum morifolium production by regulating rhizosphere soil microbial communities and metabolites.","authors":"Qiaohuan Chen, Waseem Mushtaq, Xiao Wang, Zhiyuan Liao, Jinxin Li, Siqian Xiao, Yuhuan Miao, Dahui Liu","doi":"10.1186/s40793-025-00754-x","DOIUrl":"10.1186/s40793-025-00754-x","url":null,"abstract":"<p><strong>Background: </strong>Crop rotation is a well-established agricultural practice that enhances biodiversity in medicinal crop fields, thereby improving agroecosystem sustainability and efficiency. However, the impact of crop rotation involving Chrysanthemum morifolium on soil microbiomes and their correlation with key soil physicochemical factors remains insufficiently understood. This study investigates the effects of a rotation system (Prunella vulgaris-C. morifolium) on C. morifolium productivity and soil quality.</p><p><strong>Methods: </strong>In this study, we investigated two distinct planting models: the P. vulgaris-C. morifolium rotation system and the C. morifolium monoculture system. For each system, we comprehensively examined the agronomic traits, yield, and quality of C. morifolium. Additionally, we analyzed the soil physicochemical properties, soil enzyme activities, rhizospheric microbiome community structures, and rhizospheric metabolite levels to elucidate the underlying mechanisms and differences between the two planting models.</p><p><strong>Results: </strong>Our findings demonstrate that the rotation model significantly improves C. morifolium yield and quality compared to monoculture. The underlying mechanisms were further analyzed, revealing substantial enhancements in soil nutrient levels, including organic matter, ammonium nitrogen, available phosphorus, potassium, and iron. Similarly, the activity of key soil enzymes-acid phosphatase, sucrase, and β-glucosidase-was significantly increased in the rotation system. Additionally, the incidence of wilt disease was markedly reduced, likely due to a decline in Fusarium abundance. Redundancy analysis identified that soil nutrient enrichment and enzymatic activity enhancement in the rotation system were primarily influenced by Actinobacteria, Cyanobacteria, unclassified bacteria, and Basidiomycota. Furthermore, the presence of acidic metabolites in the rhizosphere notably affected microbial community composition.</p><p><strong>Conclusion: </strong>Crop rotation effectively modifies rhizospheric microbial communities and metabolite composition, increases soil fertility, enhances the abundance of beneficial microorganisms, and suppresses Fusarium, the pathogen responsible for wilt disease. These findings provide valuable insights into overcoming continuous cropping challenges and offer practical strategies for improving the yield and sustainability of medicinal plant cultivation.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"90"},"PeriodicalIF":6.2,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12273239/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660833","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":"Crop genotype modulates root rot resistance-associated microbial community composition and abundance of key taxa.","authors":"Valentin Gfeller, Michael Schneider, Natacha Bodenhausen, Matthew W Horton, Lukas Wille, Klaus H Oldach, Bruno Studer, Martin Hartmann, Monika M Messmer, Pierre Hohmann","doi":"10.1186/s40793-025-00755-w","DOIUrl":"10.1186/s40793-025-00755-w","url":null,"abstract":"<p><strong>Background: </strong>Plants are constantly challenged by pathogens, which can cause substantial yield losses. The aggressiveness of and damage by pathogens depends on the host-associated microbiome, which might be shaped by plant genetics to improve resistance. How different crop genotypes modulate their microbiota when challenged by a complex of pathogens is largely unknown. Here, we investigate if and how pea (Pisum sativum L.) genotypes shape their root microbiota upon challenge by soil-borne pathogens and how this relates to a genotype's resistance. Building on the phenotyping efforts of 252 pea genotypes grown in naturally infested soil, we characterized root fungi and bacteria by ITS region and 16 S rRNA gene amplicon sequencing, respectively.</p><p><strong>Results: </strong>Pea genotype markedly affected both fungal and bacterial community composition, and these genotype-specific microbiota were associated with root rot resistance. For example, genotype resistance was correlated (R² = 19%) with root fungal community composition. Further, several key microbes, showing a high relative abundance, heritability, connectedness with other microbes, and correlation with plant resistance, were identified.</p><p><strong>Conclusions: </strong>Our findings highlight the importance of crop genotype-specific root microbiota under root rot stress and the potential of the plant to shape its associated microbiota as a second line of defense.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"89"},"PeriodicalIF":6.2,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643864","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":"Reconsidering the ecological effect of seed endophytes in building plant microbial environments: lessons from a Chinese medicinal plant Panax notoginseng.","authors":"Yun Wen, Wei-Xi Yang, Yi-Qian Li, Chun-Xi Lu, Hong-Yan Hu, Li-Rong Guo, Shuang-Ye Huang, Xiao-Xia Pan, Shu-Sheng Zhu, Ming-Zhi Yang","doi":"10.1186/s40793-025-00753-y","DOIUrl":"10.1186/s40793-025-00753-y","url":null,"abstract":"<p><strong>Background: </strong>Seed endophytes (SEs) are of particular interest in the fields of plant science, microbiology and agronomy due to their unique spatial and functional relationship with the host plant. SEs formed originally in mother plants, represent the majority of vertically transmitted endophytes (VTEs) in plants, and the inheritance of SEs by plants is a strategy to cope with environmental challenges. However, despite the growing interest in seed endophytes (SEs), our understanding of the host effects of SEs and their transmission remains limited. Here, seeds of a Chinese medicinal plant, pseudoginseng (Pg), were germinated and cultivated separately in autoclaved and natural guest soils under aseptic conditions, and the vertically transferred SEs (sVTEs) in the progeny plant endophytic and rhizospheric soil microbiomes were examined using an amplicon-based approach.</p><p><strong>Results: </strong>We first categorized the detected Pg SE amplicon sequence variants (ASVs) into sVTEs and other SEs (nVTEs) based on the ASV overlap analyses, and an apparent taxa bias in sVTE was observed for both bacteria and fungi. Bacterial sVTEs are characteristically motile, biofilm forming and stress tolerant. The presence of soil-dwelling microbes did not prevent progeny plants from inheriting levels of sVTEs from seeds, but involved in shaping the composition of the acquired sVTEs. Most importantly, an aseptic cultivation experiment showed that the SEs alone were able to establish a high diversity of plant-associated microbiota (PAM) in progeny plants via vertical transmission; and sVTEs were acted as a core microbiota that dominated the assembly of the progeny PAM (with the relative abundances ranged from 21 to 79%) in both the natural and sterilized soil cultivation experiments. However, the impact of sVTEs on PAM assembly may be more significant than is currently recognized, given that proportions of SEs and sVTEs in plant seeds remain undetected due to technological limitations and small sample sizes.</p><p><strong>Conclusions: </strong>The work has advanced our knowledge of the nature of sVTEs and the ecological effects of SEs on host plants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"87"},"PeriodicalIF":6.2,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12261585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144638459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The chemosynthetic biofilm microbiome of deep-sea hydrothermal vents across space and time.","authors":"Ashley Grosche, Matteo Selci, Francesco Smedile, Donato Giovannelli, Sara Borin, Nadine Le Bris, Costantino Vetriani","doi":"10.1186/s40793-025-00738-x","DOIUrl":"10.1186/s40793-025-00738-x","url":null,"abstract":"<p><p>Microbial biofilms colonize mineral and biological substrates exposed to fluid circulation at deep-sea hydrothermal vents, providing a biologically active interface along redox boundaries. Since many biofilms at deep-sea vents are associated with invertebrates, microbial distribution and abundance are not only constrained by local fluid geochemistry, but also through host-microbe interactions. This study examined the spatial distribution and diversity of established microbial biofilm communities collected from three distinct biological regimes characteristic of the East Pacific Rise (9°50 N, 104°17 W) vent system, as well as newly established biofilms on experimental microbial colonization devices. Transcripts from 16S rRNA-based amplicon sequencing revealed that Campylobacterota of the Sulfurimonas and Sulfurovum genera dominated newly-formed biofilms across all biological regimes. Statistical analyses using environmental chemistry data from each sampling site suggest that community composition is significantly impacted by biofilm age, temperature and sulfide concentration ranges, and to a lesser extent, locality. Further, metatranscriptomic analyses were used to investigate changes in community gene expression between seafloor and subseafloor biofilms. Our findings revealed differences in the type and abundance of transcripts related to respiratory pathways, carbon fixation and reactive oxygen species (ROS) detoxification. Overall, this study provides a novel conceptual framework for evaluating biofilm structure and function at deep-sea vents by showing a transition from a niche-specific pioneer microbial community in newly-formed biofilms, to a complex population of increased diversity in established biofilms and by identifying key changes in gene expression in taxonomically similar biofilms during the transition from the shallow subseafloor to the seafloor.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"88"},"PeriodicalIF":6.2,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12261850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144638460","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":"Succinic acid reduces tomato bacterial wilt disease by recruiting Sphingomonas sp.","authors":"Ningqi Wang, Ling Ping, Xinlan Mei, Yaozhong Zhang, Yuling Zhang, Xinrun Yang, Yuting Guo, Yang Gao, Yangchun Xu, Qirong Shen, Tianjie Yang, Zhong Wei","doi":"10.1186/s40793-025-00742-1","DOIUrl":"10.1186/s40793-025-00742-1","url":null,"abstract":"<p><strong>Background: </strong>Root exudates are key mediators in maintaining plant health by mediating interactions with the rhizosphere microbiome. Plants release specific exudates to defend against pathogens, either directly by inhibiting pathogen growth or indirectly through alterations in the microbial community. However, the mechanisms by which root exudates influence the rhizosphere microbiome to enhance plant resistance remain poorly understood. In this study, we evaluated the effects of 23 root exudates on the growth of the pathogen Ralstonia solanacearum and tomato bacterial wilt.</p><p><strong>Results: </strong>Seventeen of the exudates reduced the disease index, with most having neutral or even promotive effects on R. solanacearum growth. Notably, succinic acid (SA) completely suppressed bacterial wilt without directly affecting the pathogen or tomato plants in the absence of the rhizosphere microbiome. We further explored the impact of SA on the rhizosphere bacterial community in both tomato rhizosphere and bulk soil. Only the bacterial community in the rhizosphere responded significantly to SA addition, with indicator species and network analyses identifying Sphingomonas sp. WX113 as the key taxa associated with this response. A subsequent greenhouse experiment showed that co-applying Sphingomonas sp. WX113 with SA achieved 100% biocontrol efficiency, outperforming either treatment alone. In vitro assays further demonstrated that SA enhanced the antagonistic activity of Sphingomonas sp. WX113 against R. solanacearum.</p><p><strong>Conclusions: </strong>Our findings emphasize the host-mediated role of root exudates, such as succinic acid, in selectively promoting beneficial Sphingomonas sp., thereby enhancing plant resistance to bacterial wilt. These results offer new perspectives on the combination of beneficial microbes and their matching compounds for soil-borne diseases management.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"85"},"PeriodicalIF":6.2,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12247338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144620925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The effect of developmental stages on microbiome assembly in the phyllosphere and rhizosphere of rice grown in urban area soil.","authors":"Qianze Peng, Shu'e Sun, Jiejia Ma, Silu Chen, Liming Gao, Xiaohua Du, Xian Liu, Feiying Zhu, Weiye Peng, Yong Liu, Pin Su, Tomislav Cernava, Deyong Zhang","doi":"10.1186/s40793-025-00748-9","DOIUrl":"10.1186/s40793-025-00748-9","url":null,"abstract":"<p><strong>Background: </strong>The plant microbiome can support plant health and fitness in the face of biotic and abiotic stress. Research has mostly focused on plant growth in natural and agricultural soils. However, as urban areas continue to expand and soils change in the Anthropocene, microbiome assembly during development of plants grown in urban area soil remains largely elusive. Here, we examined the effect of developmental stages on the phyllosphere and rhizosphere microbiomes of rice grown in soil from an urban area during the vegetative growth stages.</p><p><strong>Results: </strong>We found that the microbial alpha and beta diversity, networks, and functions of the phyllosphere and rhizosphere microbiomes significantly differed among rice seedling, tillering, and elongation stages. Notably, we observed that bacteria assigned to potential animal parasites or symbionts not only exhibited significantly higher relative abundances in the phyllosphere compared to the rhizosphere but are also influenced by the developmental stages. Plants grown in the urban area soil had a higher relative abundance of Bacteroidales and enriched bacteria assigned to potential animal parasites or symbionts in the phyllosphere in contrast to plants grown in field. Some of these bacteria were shown to significantly influence the assembly of the phyllosphere microbiome and to prevalently engage in negative interactions with other microbes.</p><p><strong>Conclusion: </strong>Our study provides new insights into developmental stage-resolved microbiome assembly of plants grown in urban areas. The insights could help in the development of strategies for promoting 'One Health' by highlighting the role of plants as alternative host for bacterial groups that are prevalently associated with animals.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"86"},"PeriodicalIF":6.2,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144620926","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":"Close encounters on a micro scale: microplastic sorption of polycyclic aromatic hydrocarbons and their potential effects on associated biofilm communities.","authors":"Jessica X Song, Brittan S Scales, Minh Nguyen, Emelie Westberg, Bartosz Witalis, Barbara Urban-Malinga, Sonja Oberbeckmann","doi":"10.1186/s40793-025-00747-w","DOIUrl":"10.1186/s40793-025-00747-w","url":null,"abstract":"<p><strong>Background: </strong>Within systems as dynamic as the aquatic environment, it is crucial to address the impacts of an ever-growing network of emerging pollutants at their intersection. With previous research having demonstrated the capacity of microplastics (MPs) to sorb persistent organic pollutants, we ask in our study how different plastic polymers that are found throughout aquatic systems interact with polycyclic aromatic hydrocarbons (PAHs) and how this intersection of pollutants might impact the bacterial communities that form on MP surfaces. We performed an in situ incubation experiment at different sites along the Baltic Sea coast and through a PAH and 16S amplicon analysis, we investigated the sorption patterns of different substrates and their potential impacts on associated biofilm communities.</p><p><strong>Results: </strong>PAH sorption patterns of polyethylene (PE), polystyrene (PS), and aquaria stone were found to be dictated predominantly by substrate type and secondly by incubation site. While PE showed a general positive trend of sorption, stone rather leached PAHs into the environment, whereas the PAH levels of PS remained relatively unchanged following incubation. These sorption patterns correlated significantly with the composition of biofilm communities observed on all three substrate types after a 6-week incubation period. Strong correlations between specific PAHs and bacterial taxa indicate a direct relationship between these factors. Elevated levels of specific 3- and 4-ring PAHs on PE and PS coincided with higher proportions of specific taxa reportedly capable of hydrocarbon utilisation as well as a reduced diversity among biofilm communities.</p><p><strong>Conclusion: </strong>The findings in our study highlight the importance of investigating contaminants such as MPs holistically, including any associated substances, to fully understand how they impact surrounding ecological systems as they traverse the different compartments of the aquatic ecosystem.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"84"},"PeriodicalIF":6.2,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239331/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144592610","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":"Parasitic plant Cistanche tubulosa shapes the bacterial community structure and functional composition of the salt-tolerant host Tamarix chinensis across different parasitic statuses.","authors":"Luyao Tang, Xiaoshan Liu, Shuhong Lin, Le Zhan, Yehua Chen, Yanan Han, Lei Wang, Jinchang Liang, Zhong Zhang","doi":"10.1186/s40793-025-00746-x","DOIUrl":"10.1186/s40793-025-00746-x","url":null,"abstract":"<p><strong>Background: </strong>Root-associated microbiomes are crucial for assisting host and parasitic plants cope with environmental stress. However, little research exists on bacterial community characteristics of parasites and hosts under different parasitic statuses. In this study, we used Cistanche tubulosa and Tamarix chinensis as parasitic and host plant models, respectively, and aimed to determine the assembly mechanisms and role in assisting plants in salt stress tolerance of root-associated bacterial communities.</p><p><strong>Results: </strong>The different parasitic statuses are closely related to the variations in bacterial communication and community assembly mechanisms between the host and parasitic plants. The percentages of potential microbiota sourced from the parasite to the host (44.83% and 83.50%) were greater than those from the host to the parasite (17.50% and 54.67%) in the re-parasitism and flowering stages, illustrating that parasites play a dominant role in shaping the host root microbiota. In addition, the host has a more complex and robust root microbiota co-occurrence network than the parasite does, whereas the KEGG results revealed that the predicted bacterial communities of the parasite-associated microbiota contain more genes in plant growth promotion, salt‒alkali stress resistance, and substance metabolism. Moreover, the salinity, NH₄⁺, and total potassium were significantly correlated with the bacterial community distributions of the two plants.</p><p><strong>Conclusion: </strong>Our results indicate that parasitic status significantly affects the distribution of root bacterial communities, bacterial transfer, and material metabolism of the two plants at different parasitic statuses, reflecting the adaptive mechanisms of plants and bacteria under parasitic relationships and providing ideas for the utilization of saline-alkaline land.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"83"},"PeriodicalIF":6.2,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12228383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565416","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":"Meloidogyne incognita parasitism is affected by Pseudomonas protegens CHA0 and its effects on tomato-associated microbiota.","authors":"Olivera Topalović, Enoch Narh Kudjordjie, Sanea Sheikh, Gnimavo Bonaventure Kenou, Frederik Bak, Flemming Ekelund, Mette Vestergård","doi":"10.1186/s40793-025-00743-0","DOIUrl":"10.1186/s40793-025-00743-0","url":null,"abstract":"<p><strong>Background: </strong>The multitrophic interactions in plant rhizosphere and endosphere can be beneficial or deleterious for the plant health. The parasitism by root-feeding nematodes is on the negative end of the interaction spectrum, and may be very difficult to control. Biological agents are a promising alternative to the environmentally harmful nematicides; however, their efficiency in natural soil often seems to be low due to their limited establishment and dispersal. Thus, understanding how the introduced biological agents interact with nematodes and the surrounding microbiota is necessary to improve sustainable management of root-feeding nematodes. Here, we conducted two experiments to study the effects of Pseudomonas protegens strain CHA0 (CHA0) on the performance of the root-knot nematode Meloidogyne incognita. In the first experiment, we compared M. incognita performance in natural and sterilized soil in the presence and absence of CHA0. In the second experiment, we studied the composition of microbes in the rhizosphere and endosphere of tomato plants grown in native soil in response to M. incognita and CHA0.</p><p><strong>Results: </strong>We found that nematode performance, especially nematode reproduction, was significantly increased in native soil amended with CHA0. In addition, we found the highest relative abundance of Pseudomonas in tomato endosphere in response to nematode co-inoculations with CHA0, which suggests that root wounding, caused by nematodes, increased the entrance of inoculated and/or native Pseudomonas spp. As many Pseudomonas spp. are plant growth promoting, this may explain that plant growth was highest in this treatment. Furthermore, the rhizosphere of nematode-inoculated plants was enriched with Flavobacterium, Hydrogenophaga and Variovorax, which are genera generally associated with nematode-suppressive soils. On the other hand, other known nematode-suppressive genera such as Bacillus, Lysobacter, Devosia and Rhizobium were depleted in plants where nematodes were co-inoculated with CHA0, which may explain the higher nematode performance when plants were co-inoculated with CHA0.</p><p><strong>Conclusions: </strong>Our findings show that the effect of P. protegens strain CHA0 on M. incognita parasitism is influenced by the multitrophic interactions in the rhizosphere and endosphere of tomato plants. We must understand these interactions thoroughly to optimize sustainable means to mitigate the root-knot nematodes.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"79"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545546","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}