Environmental Microbiome最新文献

{"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}

{"title":"Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection.","authors":"Hanareia Ehau-Taumaunu, Terrence H Bell, Javad Sadeghi, Kevin L Hockett","doi":"10.1186/s40793-025-00734-1","DOIUrl":"10.1186/s40793-025-00734-1","url":null,"abstract":"<p><strong>Background: </strong>Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities.</p><p><strong>Results: </strong>Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity.</p><p><strong>Conclusions: </strong>Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"77"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12211302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545549","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":"Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities.","authors":"Marie C Thomas, Gretel Waugh, Katarina Damjanovic, Inka Vanwonterghem, Nicole S Webster, Andrew P Negri, Heidi M Luter","doi":"10.1186/s40793-025-00741-2","DOIUrl":"10.1186/s40793-025-00741-2","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"81"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545545","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":"Multi-omics reveals the inhibition of asexual reproduction in the jellyfish Aurelia coerulea polyp by Bacillus pacificus.","authors":"Hao Sun, Xuerui Liu, Manzoor Ahmad, Xiangrui Guo, Zhen Yu, Ye Zhao, Pingping Shen, Yanying Zhang, Zhijun Dong","doi":"10.1186/s40793-025-00740-3","DOIUrl":"10.1186/s40793-025-00740-3","url":null,"abstract":"<p><strong>Background: </strong>Jellyfish blooms pose a serious threat to marine ecosystems and coastal socio-economic activities, requiring urgent development of control technologies to manage harmful jellyfish. Associated bacteria hold considerable importance in the growth and development of marine invertebrates. We isolated Bacillus pacificus SG15 from the seagrass rhizosphere and observed that this strain could inhibit the asexual reproduction of the jellyfish Aurelia coerulea polyp. However, the precise interaction processes underlying this inhibition remain unclear. Therefore, we aimed to elucidate these processes by performing a coculture experiment coupled with analyses utilizing high-throughput sequencing, transcriptomics, metabolomics, and fluorescence in situ hybridization.</p><p><strong>Results: </strong>Our findings indicate that the transcription of genes involved in the absorption of vitamins B5, B11, B12, C and biotin was inhibited with SG15 treatment despite relatively high concentrations of vitamins and their derivatives in the culture medium. SG15 treatment increased the levels of carbohydrate metabolism genes, including those involved in pyruvate metabolism, glycolysis/gluconeogenesis, pentose phosphate pathways, and citrate cycle metabolites. Furthermore, SG15 influenced both endodermal and ectodermal polyp cells.</p><p><strong>Conclusions: </strong>Collectively, our findings helped elucidate the interactions between associated bacteria and polyps and the process by which B. pacificus SG15 inhibits polyp asexual reproduction, providing novel insights into the role of bacteria in the development of marine invertebrates. This study could provide a theoretical framework and empirical evidence for the biological control of jellyfish blooms in the marine aquaculture area, which may help develop strategies aimed at mitigating the impacts of jellyfish blooms on marine ecosystems and coastal communities.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"78"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12210622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545548","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":"Biochar-based organic substrates enhance tomato growth by promoting specific microbial communities in rooftop farming.","authors":"Miguel de Celis, Laura L de Sosa, Giuseppe Picca, Noelia González-Polo, Cristina Gómez Ruano, Luciano Beneduce, Claudio Zaccone, Marco Panettieri","doi":"10.1186/s40793-025-00744-z","DOIUrl":"10.1186/s40793-025-00744-z","url":null,"abstract":"<p><strong>Background: </strong>Urban agriculture represents an opportunity to alleviate some of the issues related with the increased urbanization and global human population. Productive rooftops offer a promising solution that combines food production and recycling of organic waste, while providing green spaces without consuming urban soils. In addition, harnessing natural resources, including plant-associated microbiomes, is proposed as an effective approach to sustainably improve farm productivity and food quality. However, little attention has been given to the importance of selecting the appropriate organic substrate to enhance plant-microbe interactions and rooftop farming in urban areas. Here, we study the influence of different organic substrates on tomato, and its associated microbial community, in an open-air rooftop farming setup. Specifically, we evaluate combinations of peat with a high quantity (50% of volume) of compost derived from different feedstocks (seaweed biomass or coffee byproducts), and how biochar-blending alters these compositions.</p><p><strong>Results: </strong>We found that substrate properties were mainly defined by the compost feedstocks. Biochar blending had a minor influence on substrate composition, although it enhanced tomato yield. Overall, alternative substrates differed from peat mainly by showing higher phosphorus content, pH, and electric conductivity. Similarly, compost feedstock had a greater impact on microbial communities than biochar blending. Even though alternative substrates presented higher bacterial diversity than peat, the taxonomic composition was similar across alternative substrates, reflecting the functional redundancy of the bacterial communities. In addition, we identified specific microbes associated with each compost feedstock. The abundance of bacteria and fungi associated with composted seaweed biomass was positively associated with tomato yield. Among them, bacterial genera like Acidibacter, Altererythrobacter, Amaricoccus, Luteitalea, Microvirga, Pedomicrobium or Pseudorhodoplanes stood out presenting strong correlations with tomato yield.</p><p><strong>Conclusions: </strong>The studied substrates influenced tomato growth and yield directly via their chemical and physical properties and by influencing microbial community composition. Thus, our results reveal the importance of using the appropriate organic substrate for enhancing the effectiveness of rooftop agriculture while increasing microbial diversity in urban unexploited areas.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"82"},"PeriodicalIF":6.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12220821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144545544","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}