Microbiome最新文献

{"title":"Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.","authors":"Zhanbiao Li, Wandi Luo, Huiting Xie, Cuiping Mo, Bixia Qin, Yige Zhao, Xiao Chen, Songbai Zhang, Yaling Zhao, Mengcen Wang, Yu Yang, Jianhe Cai, Baozhan Wang, Xu Liu, Yu Shi","doi":"10.1186/s40168-025-02188-6","DOIUrl":"https://doi.org/10.1186/s40168-025-02188-6","url":null,"abstract":"<p><strong>Background: </strong>Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.</p><p><strong>Results: </strong>By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15 days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.</p><p><strong>Conclusion: </strong>The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"214"},"PeriodicalIF":12.7,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.","authors":"Xiaodong Chen, Jingyi Xu, Lei Zhang, Bingxuan Xie, Jianrong Ren, Jinghui He, Tao Liu, Qingqing Liu, Yachen Dong, Xiaolong He, Junhu Yao, Shengru Wu","doi":"10.1186/s40168-025-02202-x","DOIUrl":"https://doi.org/10.1186/s40168-025-02202-x","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the β diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen ep","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"215"},"PeriodicalIF":12.7,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host miRNAs regulate Escherichia coli O157 mucosal colonization through host-mucosa-attached microbiota interactions in calves.","authors":"Zhe Pan, Yanhong Chen, Mi Zhou, Tim A McAllister, Tom N McNeilly, Le Luo Guan","doi":"10.1186/s40168-025-02184-w","DOIUrl":"https://doi.org/10.1186/s40168-025-02184-w","url":null,"abstract":"<p><strong>Introduction: </strong>Host responses to pathogen colonization are central to understanding host homeostasis dynamics. Here, we used Shiga toxin (Stx)-producing Escherichia coli (STEC) O157 as an example to illustrate how pathogen colonization alters host-microbiome interactions and stimulates host responses. The STEC O157 is a critical foodborne pathogen, and cattle are the major asymptotic carrier with rectal anal junction (RAJ) being the major colonization site, leading to the transmission of this organism through the production chain. Therefore, this study leverages the multi-omics to evaluate host mechanisms to STEC O157 and to illustrate how mucosa-attached microbiome together with host miRNAs respond to the colonization of STEC O157.</p><p><strong>Results: </strong>The calf model was orally challenged with E. coli O157 with and without Stx2a during the 30-day trial. Mucosa-attached microbiome analysis revealed that mucosal E. coli O157 colonization limited niche occupancy of mucosa-attached microbiota regardless of the presence or absence of Stx2a. The production of Stx2a did not induce proper local host mRNA responses but miRNA profiles were more responsive to this virulent factor during high fecal shedding. The shift of toll-like receptor (TLR) expressions together with Stx2a production possibly underlined varied miRNAome-mucosa-attached microbiota interactions. For instance, during the high fecal shedding, the increased expression of TLR2 promoted bta-miR-181b mediated host functionality, a response that was possibly blocked by Stx2a. Decreased fecal O157 shedding promoted activation of TLR4-stimulated host responses, which were coregulated by multiple miRNAs (i.e. bta-miR-146a and-184) and mucosa-attached microbes.</p><p><strong>Conclusion: </strong>Host mechanisms regulating STEC O157 colonization are complex interplay among mucosa-attached microbiota and host miRNAs where virulence factors could modulate such crosstalk and cause differential host responses, highlighting the importance of host-microbiome-pathogen virulence factor interactions for pathogen colonization process. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"213"},"PeriodicalIF":12.7,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"One Health, One Microbiome.","authors":"Abdifatah M Muhummed, Kayla C Lanker, Simon Yersin, Jakob Zinsstag, Pascale Vonaesch","doi":"10.1186/s40168-025-02231-6","DOIUrl":"https://doi.org/10.1186/s40168-025-02231-6","url":null,"abstract":"<p><p>One Health is a concept and framework for addressing the interconnected nature of humans, animals and their environments to improve the health and wellbeing of all three, along with added social and financial benefits. On a microscopic level, the microbiota is a clear biological connector with strains shared across domains (One Health Microbiome). In this review, we introduce the concept of One Health and the One Health Microbiome and discuss strain-sharing across and within domains. We also highlight its impact on the spread of antimicrobial resistance (AMR) genes as well as overall microbiome diversity and resilience to climate change. Finally, we discuss critical areas for further research and conceptual development, encouraging future research integrating One Health and microbiota-AMR concepts.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"216"},"PeriodicalIF":12.7,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving fecal transplantation precision for enhanced maturation of intestinal function in germ-free mice through microencapsulation and probiotic intervention.","authors":"Furong Ba, Wei Wang, Yilun Huang, Shuobo Zhang, Bo Qiu, Siyuan Xie, Lvwan Xu, Wang Gao, Xiaoqin Zhang, Zhenyu Wen, Qifan Wang, Hainv Gao, Guoping Sheng, Björn Berglund, Ping Li, Lanjuan Li, Mingfei Yao","doi":"10.1186/s40168-025-02204-9","DOIUrl":"https://doi.org/10.1186/s40168-025-02204-9","url":null,"abstract":"<p><strong>Background: </strong>Fecal microbiota transplantation (FMT) has emerged as a widely used treatment for various diseases. While previous efforts have focused on selecting \"super donors\", the precise modulation of donor microbiota to enhance FMT efficacy remains a critical challenge. This study aimed to develop strategies to modify donor microbiota to promote gastrointestinal development and maturation in germ-free mice. Probiotic Pediococcus pentosaceus Li05 (Li05) was used as gut microbiota modulator to establish a healthier donor fecal microbiota, and a microencapsulation method was applied to ensure high bacterial viability during gastrointestinal tract transition.</p><p><strong>Results: </strong>Probiotic intervention initially altered the stability of the gut microbiota but eventually fostered a more complex bacterial interaction network and established a new equilibrium within 14 days. Transplantation of encapsulated Li05-modulated fecal microbiota significantly promoted epithelial development, improved barrier function, and altered the colonic transcriptome profile. These effects were found to be more dependent on the abundance of some bacterial genera instead of their co-occurrence network, and the key functional bacterial genera associated with these benefits were believed to be Parabacteroides, Parasutterella, Lachnoclostridium, Muribaculum and Desulfovibrio. Notably, both encapsulation and probiotic modulation played critical roles in enhancing the functional efficacy of these key bacterial genera, and the community composed of key functional bacteria demonstrated an antagonistic relationship with other bacterial communities. Moreover, encapsulated Li05-modulated fecal microbiota induced dramatical changes in host lipid metabolism, especially the bile acids and their derives. Sporobiota gained the function of promoting epithelium development gene expression only after Li05-modulation since high abundance of Lachnoclostridium was introduced.</p><p><strong>Conclusion: </strong>These findings underscore the importance of encapsulation and donor microbiota modulation in FMT and provide valuable strategies for improving transplantation precision and outcomes.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"212"},"PeriodicalIF":12.7,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Megasphaera contributes to lactate-driven valerate production in the human gut.","authors":"Lucía Huertas-Díaz, Mensure Elvan Gezer, Angeliki Marietou, Jiri Hosek, Line Thams, Line Barner Dalgaard, Mette Hansen, Clarissa Schwab","doi":"10.1186/s40168-025-02207-6","DOIUrl":"10.1186/s40168-025-02207-6","url":null,"abstract":"<p><strong>Background: </strong>The human gut microbiota produces short-chain carboxylic acids (SCCA) through fermentation of undigested carbohydrates, and through chain elongation, a process that can be modulated through diet. Valerate is frequently recovered from human fecal samples, but little is known about dietary components, microbial contributors, and cross-feeding interactions that drive human intestinal valerate formation. We combined co-culture studies and in vitro human fecal microbiota batch fermentations (n = 20) with the analysis of a free-living cohort of obese and overweight women (n = 49) that monitored and modified (fermented) dairy consumption, to study the role of dairy-derived lactose and lactate in intestinal microbial formation of valerate.</p><p><strong>Results: </strong>While the valerate producer Megasphaera elsdenii was not able to use lactose in single culture, valerate was formed (6.2 ± 1.3 mM) in co-culture with the lactose-utilizing and lactate-producing food microbe Streptococcus thermophilus. In vitro, valerate was produced by fecal microbiota of most donors (15/20) in control medium. Lactose addition significantly (p < 0.05) increased valerate formation of fecal microbiota that harbored Megasphaera at levels ≥ 5 log cells/mL (n = 4), while valerate formation was lower when Megasphaera was less abundant or not detected (n = 15). The addition of M. elsdenii to batch fermentations increased valerate production in 80% of samples and correlation analysis showed a positive correlation (p < 0.001) between relative abundance of Megasphaera and valerate levels. In vivo, 30% of study participants harbored Megasphaera based on 16S rRNA gene amplicon sequencing and species-specific qPCR. Diet supplementation with drained yogurt (skyr) led to higher fecal microbial diversity (p < 0.05) and relative abundance of Streptococcaceae. Participants that harbored Megasphaera and consumed skyr daily had significantly (p < 0.05) higher fecal valerate levels at week 6 compared to controls. In addition, fecal levels of lactate were higher in the skyr compared to the control group at 12 weeks. Linear discriminant analysis suggested co-occurrence of Megasphaera with the lactate-producer Lactobacillus and competition with other lactate utilizers such as the Anaerobutyricum hallii group.</p><p><strong>Conclusion: </strong>This study brings forward new mechanistic understanding on the intestinal microbial formation of the SCCA valerate. Our findings identified Megasphaera as an infrequently occurring and low abundant keystone taxon contributing to lactose/lactate-driven valerate production in overweight/obese women. Our results highlight that the presence of Megasphaera affects the fermentative response to daily consumption of fermented dairy. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"210"},"PeriodicalIF":12.7,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12538753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145345957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms.","authors":"Júnia Schultz, Tahira Jamil, Pratyay Sengupta, Shobhan Karthick Muthamilselvi Sivabalan, Anamika Rawat, Niketan Patel, Srinivasan Krishnamurthy, Intikhab Alam, Nitin K Singh, Karthik Raman, Alexandre Soares Rosado, Kasthuri Venkateswaran","doi":"10.1186/s40168-025-02274-9","DOIUrl":"10.1186/s40168-025-02274-9","url":null,"abstract":"","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"211"},"PeriodicalIF":12.7,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12541926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145345979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Silica nanoparticles suppress fungal pathogenic allies to alleviate Astragalus root rot.","authors":"Jiamin Ai, Leilei Xu, Hao Ding, Zijing Dang, Liru Jian, Chun Chen, Gehong Wei, Zhefei Li","doi":"10.1186/s40168-025-02183-x","DOIUrl":"10.1186/s40168-025-02183-x","url":null,"abstract":"<p><strong>Background: </strong>Biological control mechanisms involve the inhibitory effect of antagonistic bacteria on pathogenic fungal growth. However, research on controlling crop diseases by inhibiting allies of pathogenic agents is relatively scarce.</p><p><strong>Results: </strong>In this study, the application of SiO₂ NPs resulted in an increase in the alpha diversity of the microbial communities in the rhizosphere of Astragalus, as well as an increase in the complexity of the co-occurrence network. SiO₂ NPs reduced the abundance of Pseudomonas and Microbacterium in the rhizosphere of Astragalus. Co-inoculated Fusarium with Pseudomonas aeruginosa and Microbacterium oxydans could exacerbate the root rot of disease in Astragalus. In addition, M. oxydans SCK-308 and P. aeruginosa XS-134-7 promoted the growth of Fusarium oxysporum and inhibited the growth of certain beneficial rhizosphere microorganisms, thereby facilitating the occurrence of the disease. Metabolomic analyses revealed that salicylic acid, indole-3-acetic acid, brassinosteroid, and palmitic acid were significantly enriched in the rhizosphere of Astragalus treated with SiO₂ NPs. Exogenous supplementation with these metabolites significantly inhibited the growth of P. aeruginosa and M. oxydans, thereby alleviating root rot in plants during coinfection with two bacteria and F. oxysporum. These results indicate that the metabolites enhance disease control efficacy through targeted inhibition of pathogen helpers. Additionally, SiO₂ NPs enhanced the enzymatic activities of ascorbate peroxidase, catalase, and peroxidase in Astragalus plants.</p><p><strong>Conclusions: </strong>Our findings suggest that SiO₂ NPs alter the composition of the rhizosphere microbial community and reduce the population of allies of F. oxysporum, activating salicylic acid-dependent systemic acquired resistance (SAR) in Astragalus and thereby decreasing the incidence of Fusarium root rot. These results suggest that SiO₂ NPs can serve as a sustainable agricultural practice. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"209"},"PeriodicalIF":12.7,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12539172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145345981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench.","authors":"Yongxin Lv, Lizhi Zhang, Yu Zhang","doi":"10.1186/s40168-025-02192-w","DOIUrl":"10.1186/s40168-025-02192-w","url":null,"abstract":"<p><strong>Background: </strong>The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000-10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches.</p><p><strong>Results: </strong>We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48 × (nxrA) and 1.28 × (aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis.</p><p><strong>Conclusion: </strong>Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth's deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"208"},"PeriodicalIF":12.7,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12532881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abundant and active acetogens enhance the carbon dioxide sink of Blue Carbon ecosystems.","authors":"Karen Rodriguez, Francesco Ricci, Gaofeng Ni, Naima Iram, Robin Palfreyman, Ricardo A Gonzalez-Garcia, James Heffernan, Chris Greening, Maria Fernanda Adame, Esteban Marcellin","doi":"10.1186/s40168-025-02209-4","DOIUrl":"10.1186/s40168-025-02209-4","url":null,"abstract":"<p><strong>Background: </strong>Blue Carbon ecosystems, which include all tidal wetlands, mitigate climate change by capturing and storing carbon dioxide (CO₂) from the atmosphere. Most carbon fixation in these systems is thought to be driven by plant and microbial photosynthesis, whereas chemosynthetic processes are assumed to play a minor role. However, these ecosystems often contain anoxic environments ideal for chemosynthetic microbes such as acetogens.</p><p><strong>Results: </strong>In this study, we show that acetogens are abundant and active mediators of carbon sequestration in tidal wetland soils. We combined metagenomic analysis of CO₂ fixation genes and reconstruction of microbial genomes with enrichment and analysis of gas-fermenting acetogens in bioreactors. Genome-resolved metagenomics revealed that diverse microbes can mediate carbon fixation, primarily through the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl pathway (WLP). These include various bacteria and archaea capable of reductive acetogenesis. Based on these findings, we established bacterial enrichment cultures from tidal wetland soils using hydrogen (H₂) and CO₂ as the sole energy and carbon sources. Bioreactor analysis revealed that these enrichments are dominated by clostridial acetogens that grow rapidly by converting CO₂ into acetate and other products.</p><p><strong>Conclusions: </strong>Collectively, these results reveal Blue Carbon ecosystems harbor microbial communities that can exclusively subsist by using CO₂ as their sole electron acceptor and carbon source. This provides evidence for a novel carbon sink pathway within these ecosystems beyond the well-known mechanisms of photosynthetic carbon fixation and soil sequestration. Additionally, the discovery and enrichment of these chemosynthetic communities provide opportunities for developing further mechanisms of CO₂ removal through industrial gas fermentation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"207"},"PeriodicalIF":12.7,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12529827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}