Environmental Microbiome最新文献

{"title":"A cooperative cobalamide biosynthesis guild in the endosphere of the edible aquatic plant Wolffia globosa Mankai.","authors":"Rhishika Dutta, Olabiyi Obayomi, Avital Freidjung Yosef, Lusine Ghazaryan, Vered Chalifa-Caspi, Miri Lapidot, Osnat Gillor","doi":"10.1186/s40793-026-00917-4","DOIUrl":"10.1186/s40793-026-00917-4","url":null,"abstract":"<p><strong>Background: </strong>Cobalamin (vitamin B₁₂) is synthesized only by certain bacteria and archaea and is rarely found in plant-derived foods because plants neither synthesize nor require this cofactor. The edible duckweed Wolffia globosa Mankai is unusual in containing bioavailable cobalamin, suggesting a microbial origin. However, how cobalamin biosynthetic capacity is organized within angiosperm-associated microbiomes remains largely unresolved. Here, we investigated bacterial community structure and cobamide biosynthetic potential across the cultivation medium, plant surface, and internal tissues of Mankai to determine how cobalamin production is maintained in this aquatic plant microbiome.</p><p><strong>Results: </strong>Bacterial communities differed significantly among compartments, with the endosphere forming a low-diversity, host-filtered microbiome enriched in specialized taxa. Genome-resolved metagenomics showed that only a minority of endophytic bacteria encoded near-complete cobamide biosynthesis pathways consistent with de novo synthesis. In contrast, many co-occurring taxa lacked multiple biosynthetic steps but were enriched in genes associated with cobamide precursor salvage and remodeling. Network analysis identified putative producer taxa as highly connected hubs linked to salvager populations, consistent with metabolite cross-feeding. Comparative genomic analysis demonstrated reduced cobamide biosynthetic gene complements in endophytic genomes relative to closely related free-living strains, supporting adaptive pathway reduction in the host-associated niche.</p><p><strong>Conclusions: </strong>Cobalamin production in the Mankai endosphere appears to arise from a metabolically interdependent bacterial consortium rather than from single autonomous producers. These findings identify cooperative micronutrient biosynthesis as an organizing principle in plant-associated microbiomes and position Mankai as a tractable model for studying cobamide-mediated microbial cooperation in aquatic crops. Understanding these interactions may support microbiome-informed strategies to stabilize micronutrient production and functional resilience in controlled aquatic plant cultivation systems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13508461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148266843","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":"Unveiling the mycobiome of healthy and Esca diseased grapevines: fungal community dynamics across different microhabitats, seasons, years, and cultivars.","authors":"Adrienn Geiger, Carla Mota Leal, Zoltán Karácsony, Richárd Golen, Luca Annamária Lepres, Anna Molnár, Kálmán Zoltán Váczy, József Geml","doi":"10.1186/s40793-026-00911-w","DOIUrl":"10.1186/s40793-026-00911-w","url":null,"abstract":"<p><strong>Background: </strong>Grapevines host diverse microbial communities, including fungal pathogens associated with grapevine trunk diseases (GTDs), which pose a major challenge in viticulture. Despite extensive research, the ecological drivers shaping fungal community composition across different grapevine microhabitats remain insufficiently understood. Using ITS2 metabarcoding, we characterized fungal communities in bark, wood, and soil from Esca symptomatic and asymptomatic vines, and evaluated the effects of season, year, cultivar, microhabitat, and plant health on key functional groups.</p><p><strong>Results: </strong>Seasonal variation had limited effects on fungal richness, whereas interannual differences had a strong impact on functional group diversity. Microhabitat played a key role: plant pathogens, particularly GTD-associated taxa, were most prominent in bark and wood; mycoparasites were dominant in bark; generalist saprotrophs prevailed in soil and bark; and GTD-related wood saprotrophs were most abundant in bark. Soil harbored the highest overall fungal diversity. Plant health status significantly affected only GTD pathogens, which showed higher abundance and diversity in symptomatic vines. Cultivar influenced only the richness of GTD-related wood saprotrophs.</p><p><strong>Conclusions: </strong>Year (vintage) emerged as a major driver of fungal community composition across plant tissues and soil, driving the most pronounced shifts in the mycobiome. Abiotic factors (year and season) were most strongly associated with soil fungal communities, whereas biotic factors (cultivar and plant health) exerted a greater influence on fungi associated with grapevine tissues. These findings underscore the central role of microhabitat and temporal variation in structuring the grapevine mycobiome.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13487917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148240388","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":"Protaetia brevitarsis larvae frass affects substrate microecological systems via two suggestive pathways to enhance cherry tomato growth.","authors":"Kui Wang, Qi Peng, Lili Geng, Fang Zhang, Ruoyun Liu, Xingyu Liu, Jie Zhang, Changlong Shu","doi":"10.1186/s40793-026-00915-6","DOIUrl":"10.1186/s40793-026-00915-6","url":null,"abstract":"<p><strong>Background: </strong>The identification and development of high-quality humus sources to enhance the productivity and performance of substrate-based vegetable cultivation systems remains a significant challenge in sustainable agriculture. Protaetia brevitarsis larvae (PBL) exhibit exceptional efficiency in decomposing decaying crop straw and produce nutrient-rich frass with high humic acid content and a complex microbial community. However, its impacts on substrate microecological systems and the underlying functional mechanisms remain unclear, limiting its rational application in substrate cultivation. This study aimed to investigate the effects of PBL frass on substrate microecology and elucidate the associated mechanisms using cherry tomato (Lycopersicon esculentum Mill. var. cerasiforme Alef) pot experiments.</p><p><strong>Results: </strong>Incorporation of 2% or 4% (w/w) PBL frass into cherry tomato cultivation substrates significantly promoted plant growth, characterized by reduced plant height (indicating more robust, dwarf-type growth) and increased aboveground (stem) and belowground (root) biomass. Furthermore, PBL frass application enhanced substrate microbial diversity through two distinct, complementary pathways: (ⅰ) Frass-derived microbes, which possess specific colonization capabilities, directly augmented microbial communities in both the rhizoplane and bulk substrate; and (ⅱ) Organic compounds in PBL frass may have activated a broad range of microbes, enriching the rhizosphere microbiome. This enhanced microbial diversity was associated with an increased abundance of plant-beneficial taxa, which likely contributed to growth promotion and substrate health maintenance.</p><p><strong>Conclusions: </strong>This study uncovers the multifaceted contributions of PBL frass to substrate microbial ecology and reveals its two suggestive regulatory pathways. These results provide a theoretical basis for the sustainable utilization of PBL frass and advance the development of eco-friendly amendments for modern vegetable production.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13474501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148206569","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":"Potato foliar infection with Phytophthora infestans drives strong, cultivar-specific shifts in rhizosphere communities.","authors":"Vivien Pichon, Mout De Vrieze, Fares Bellameche, Rares Cristea, Floriane L'Haridon, Laurent Falquet, Laure Weisskopf","doi":"10.1186/s40793-026-00910-x","DOIUrl":"10.1186/s40793-026-00910-x","url":null,"abstract":"<p><strong>Background: </strong>Potato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress (\"cry-for-help\" mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating plant microbiota members to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight.</p><p><strong>Results: </strong>Controlled foliar infection triggered substantial, cultivar-specific shifts in rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were involved in the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly upon infection than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates through sequence alignment. Their inhibition potential against P. infestans sporangia and zoospores was assessed through biological assays. These revealed the biocontrol potential of genera otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one.</p><p><strong>Conclusion: </strong>Taken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains that are able to inhibit pathogen development and possibly contribute to its higher resistance against P. infestans.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13474836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148200752","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 microecological mechanism of Cordyceps chanhua promoting soil nitrogen cycling.","authors":"Gongping Hu, Youcui Yang, Tao Wang, Jiaojiao Qu, Zhongshun Xu, Yanling Ren, Yeming Zhou, Gangxiang Fei, Yanfeng Han, Jian Zhang, Chunbo Dong, Tengxia He, Ye Deng, Xiao Zou","doi":"10.1186/s40793-025-00838-8","DOIUrl":"10.1186/s40793-025-00838-8","url":null,"abstract":"<p><strong>Background: </strong>The nitrogen cycle is crucial to the function of the Earth's biosphere. Entomogenous fungi have been proven to promote nitrogen metabolism and cycling in host insects, and transfer nitrogen from insects to soil. However, little is known about the microecological mechanism of entomogenous fungus participating in nitrogen cycling and the microecological impact of exonitrogen from entomogenous fungus on soil.</p><p><strong>Results: </strong>Here, we report that the entomogenous fungus Cordyceps chanhua secretes nitrate nitrogen and organic nitrogen from its mycelia into the soil environment and absorbs ammonium nitrogen, nitrite nitrogen and hydroxylamine nitrogen from the soil environment into the C. chanhua. Along with the nitrogen exchange process, the bacterial communities related to nitrogen metabolism in the sclerotium of C. chanhua emerge in the soil environment, promoting the soil organic nitrogen cycling process. Redundancy analysis demonstrated that the endogenous/symbiotic bacterial communities within C. chanhua have the greatest impact on ammonium nitrogen and organic nitrogen at the genus level. During the growth process of C. chanhua, the diversity of the bacterial community in its microenvironment significantly decreased. Consistent with this, this study also verified that the exonitrogen of C. chanhua can reduce the diversity of bacterial communities in the soil environment and enrich the bacterial group of Sporosarcina spp., which has a positive promoting effect on nitrogen metabolism. Furthermore, we isolated three highly active nitrogen-transforming dominant strains from the sclerotia of C. chanhua, which further indicates that the nitrogen transport of C. chanhua is closely related to the bacterial community in its mycelia.</p><p><strong>Conclusions: </strong>The results of this study demonstrate that the associated/endophytic bacteria of C. chanhua facilitates the participation of C. chanhua in soil nitrogen cycling in its microenvironment.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148158590","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":"Exploring the role of ergothioneine and mycorrhizal fungi in shaping the wheat soil microbiome.","authors":"Sri Sai Nandini Ravi, Alexandra Pipinos, Nick Insley, Charanpreet Kaur, Jinjun Kan, Wade Heller, Andrew H Smith, Gladis Zinati, John Richie, Harsh Bais","doi":"10.1186/s40793-026-00913-8","DOIUrl":"10.1186/s40793-026-00913-8","url":null,"abstract":"<p><strong>Background: </strong>The association between plants and soil microbes is critical for both soil and plant health. Introducing beneficial microbial inoculants, such as arbuscular mycorrhizal fungi (AMF), can enhance the uptake of nutrients and compounds in plants including ergothioneine (ERGO), a well-known antioxidant and anti-inflammatory compound that humans must obtain through diet. However, little is known about how ERGO and inoculated AMF influence ERGO uptake in plants or affect soil microbiome composition, including bacteria, archaea, and fungi. This study investigates the interaction between soil-applied ERGO and AMF inoculation in plant-microbe symbioses to assess (1) whether these treatments increase ERGO content in the staple crop wheat (Triticum aestivum), and (2) how they alter soil microbiome structure.</p><p><strong>Results: </strong>Combined treatment with ERGO and AMF significantly increased wheat (Triticum aestivum) biomass and ERGO accumulation in roots and shoots. This co-treatment also led to higher bacterial diversity in rhizosphere. PERMANOVA analysis confirmed that both AMF and AMF/ERGO treatments significantly influenced microbiome composition, particularly bacterial communities. Indicator species analysis showed enrichment of Thioalkalivibrio, Chlorobi bacterium, Planctomycetes (Planctomycete A-2) and Candida subhashi, Paecilomyces zollerniae under ERGO and AMF/ERGO treatments.</p><p><strong>Conclusions: </strong>Overall, the data show that plants can readily take up ERGO from the soil, with or without AMF, and that both ERGO and AMF amendments reshape soil microbiome communities. These findings highlight the broader role of ERGO and AMF in connecting soil microbiome to plant and human nutrition, a link that warrants further investigation.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148145258","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":"Aeonium decorum as a microbial recruitment platform for atmospheric polycyclic aromatic hydrocarbons mitigation in urban gardens.","authors":"Felix Velando, Lázaro Molina, Irene Hurtado, Pieter van Dillewijn, Ana Segura","doi":"10.1186/s40793-026-00914-7","DOIUrl":"10.1186/s40793-026-00914-7","url":null,"abstract":"<p><strong>Background: </strong>In the context of the Sustainable Architecture, green roofs, green walls, green belts or urban farms are becoming popular infrastructures in cities and have been proposed as promising elements to ameliorate air pollution. Atmospheric contaminants are deposited not only on the foliar surface of plants, but also in soils. Plants may interact with pollutants, but their associated microbiomes (epiphytic, endophytic and rhizospheric) may harbor contaminant-degrading bacteria which could play an important role in pollutant mitigation. Therefore, we explored the effects of atmospheric contaminants, using naphthalene as a model compound, on some of the living elements of urban gardens (plants and microbiomes).</p><p><strong>Results: </strong>Exposure to gaseous naphthalene had weak effects on Aeonium decorum and Trifolium repens plants (measured as efficiency of photosystem II), and on soil bacterial diversity. Although the presence of naphthalene is not the major driver of soil bacterial community structure, metagenomic and qPCR analysis revealed an increase in polycyclic aromatic hydrocarbon (PAH)-ring hydroxylating dioxygenases in Aeonium planted soils, suggesting a positive effect of this plant species for the selection of potential contaminant-degrading microbes. We have also observed an increment in Pseudomonas (known for their capacity to degrade contaminants) and Solimonas in response to naphthalene. Validation of tools designed to evaluate the exposure of plants to atmospheric contaminants was performed creating urban gardens planted with A. decorum plants and exposed to environmental conditions.</p><p><strong>Conclusions: </strong>Our results suggest that Pseudomonas and Solimonas could be used as markers for biodegradation. A. decorum is proposed as a good candidate for amelioration of atmospheric contaminants and gardens constructed with these plants carried PAH degrading bacteria on leaf surfaces indicating that they have the capacity to respond to the presence of contaminants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148139503","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":"Distinct filtering processes shape bacterial and fungal communities and their co-occurrence patterns across garlic-associated compartments.","authors":"Tianshu Wang, Bangyan Niu, Shibo Xia, Dali Song, Yi Yang, Hailei Wei, Miao Gao, Wei Zhou","doi":"10.1186/s40793-026-00870-2","DOIUrl":"10.1186/s40793-026-00870-2","url":null,"abstract":"<p><strong>Background: </strong>Garlic (Allium sativum L.) is an important economic crop that is often subjected to continuous monoculture practices. Although the garlic rhizosphere is known to harbor growth‑promoting and disease‑suppressive potential, comprehensive investigations of microbial communities and interactions across the rhizosphere, roots, and leaves remain limited. In this study, bacterial and fungal communities in the rhizosphere soil, roots, and leaves of garlic plants grown under long-term monoculture in four major production regions of China were examined using amplicon sequencing, aiming to characterize the garlic‑associated microbiome and explore the potential pathogen‑antagonistic taxa under continuous monoculture.</p><p><strong>Results: </strong>Microbial communities and their predicted functions were more strongly influenced by the compartment niche than by the production area, with distinct bacterial and fungal community patterns in each compartment niche. Source-tracking analysis revealed distinct colonization routes for bacterial and fungal communities in the garlic leaf endosphere. Bacterial communities in leaves appeared to be predominantly derived from the root endosphere, while fungal communities in leaves showed a potential direct derivation from the rhizosphere soil rather than roots. Potential pathogenic fungi were more abundant in rhizosphere soil and leaves than in roots. In the bacterial co-occurrence network, two modules abundant in roots and characterized by Pseudomonas and Flavobacterium were negatively associated with pathogen relative abundance. In the cross-kingdom network, keystone taxa included potential pathogenic ASVs from Verticillium and Fusarium, and they were negatively associated with bacterial taxa such as Lysinimonas and Microbacterium.</p><p><strong>Conclusions: </strong>These findings provide insights into the distinct colonization patterns of bacterial and fungal communities in garlic and their co-occurrence networks under long-term monoculture. The identification of bacterial taxa with antagonistic potential offers candidates for developing biocontrol agents to improve soil-borne disease management in garlic production.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13440225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148057738","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":"Using feeding regime as a microbial selective pressure to optimise biogas production and digestate sanitisation from slurry-based anaerobic digestion.","authors":"S Nolan, A Trego, N Waters, C Thorn, O Fenton, K G Richards, V O'Flaherty, U Z Ijaz, F Abram","doi":"10.1186/s40793-026-00902-x","DOIUrl":"10.1186/s40793-026-00902-x","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;The urgent need to adopt sustainable agricultural practices has positioned anaerobic digestion (AD) as a pivotal technology. Indeed, slurry-based AD can mitigate agricultural pollution by capturing greenhouse gas from stored slurry and converting it into biomethane, a valuable source of renewable energy, while generating digestate that can be used as fertiliser. For such a strategy to be effectively and widely deployed however, AD must be optimised. To this end, efforts have typically focused solely on biogas yields, yet improvements in pathogen load reduction may potentially negate the need for a costly pasteurisation step. Hence, optimisation of AD for sanitisation as well as improved biogas output is desirable. To address this, we set up triplicate 10-L CSTR bioreactors, which were fed with a combination of slurry and fats, oils and grease for 216 days. An organic loading rate (OLR) of 2 g VS L&lt;sup&gt;-1&lt;/sup&gt; d&lt;sup&gt;-1&lt;/sup&gt; was used throughout the trial, with a retention time of 21 days. For the first 98 days, bioreactors were fed each weekday (Monday to Friday), with 3 × feedstock on Fridays to maintain the OLR over the weekend. On Day 99 and for the remainder of the trial, the feeding regime was changed to every three days, still maintaining the 2 g VS L&lt;sup&gt;-1&lt;/sup&gt; d&lt;sup&gt;-1&lt;/sup&gt; OLR. The change in feeding regime was prompted by a noticeable increase in E. coli removal on Mondays, indicating that feeding regime could potentially function as a controllable ecological selection pressure.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;After an initial period of adaptation to the new operating conditions (from day 99-150), the change in feeding regime resulted in improved E. coli removal, achieving consistently the required reduction in numbers to satisfy EU sanitisation standards (&lt; 1000 CFU g&lt;sup&gt;-1&lt;/sup&gt;). Additionally, methane production increased significantly in all bioreactors with an average of 58% higher methane yield per gram VS fed when compared to the previous 5-day feeding regime. Interestingly, process optimisation led to a more tailored microbial community as revealed by metagenomics. Specifically, we observed selection for improved carbon oxidation, syntrophic acetate oxidation and methanogenesis, as well as overall reduced microbial richness and decreased functional diversity. This could potentially lead to a reduced ecosystem stability however the emergence of Methanosarcina prevalence, known for its robustness, together with the detection of the two main methanogenic pathways-acetoclastic and hydrogenotrophic-after process optimisation might confer some resistance against future perturbations. The impact of microbial shifts on ecosystem stability needs to be further assessed experimentally.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;Taken together, we demonstrate that feeding regime can function as a microbial selection pressure in anaerobic digestion. The switch from a 5-day to a 3-day feeding regime led to shifts i","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13404572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007150","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":"Bacillus inoculation drives fine-scale taxonomic shifts in the bacterial communities of saline-alkaline wheat rhizosphere soil.","authors":"Huicheng Zhao, Linqi Zhang, Mengshuai Liu, Xinhui Fu, Meiyu Liu, Peng Guo, Wenliang Yang","doi":"10.1186/s40793-026-00882-y","DOIUrl":"10.1186/s40793-026-00882-y","url":null,"abstract":"<p><strong>Background: </strong>Soil salinization severely restricts wheat production in the coastal regions of northern China, and inoculation with plant growth-promoting rhizobacteria (PGPR) is a promising strategy for alleviating salt stress. However, the response mechanisms of indigenous bacterial communities to PGPR remain unclear, partly because of the limitations of short-read sequencing in terms of taxonomic resolution. This study combined pot and field experiments with PacBio third-generation sequencing (TGS) to investigate bacterial community dynamics in rhizosphere and bulk soils after Bacillus inoculation.</p><p><strong>Results: </strong>The dominant phyla across treatments were Proteobacteria, Acidobacteria, and Bacteroidetes, with Proteobacteria being enriched in rhizosphere soils. Bacillus inoculation altered the bacterial community structure, increasing diversity and reducing intergroup dissimilarity, particularly in the pot experiments. Key ASVs responsive to inoculation were identified by intergroup difference analysis, including the enrichment of Pseudomonas spp. (ASV4007) in the inoculated treatments, which exhibited syntrophic interactions with Bacillus. Inoculation increased the abundance of functional genes, which were annotated using PICRUSt2, involved in phosphorus and nitrogen cycling and improved bacterial co-occurrence network resilience reflected by the natural connectivity.</p><p><strong>Conclusions: </strong>This study demonstrated that Bacillus inoculation reshaped indigenous bacterial communities to mitigate salt stress, and TGS served as a powerful tool for identifying key functional taxa and supports the development of microbe-based saline soil remediation strategies.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13455373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147989313","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}