Pub Date : 2025-12-06DOI: 10.1016/j.micres.2025.128415
Xinya Pan , Somayah S. Elsayed , Gilles P. van Wezel , Jos M. Raaijmakers , Víctor J. Carrión
Endophytic microorganisms colonize internal plant tissues and enhance host resistance to pathogens. We previously showed that endophytic Flavobacterium sp. 98 (Fl98) protects sugar beet against the fungal root pathogen Rhizoctonia solani via biosynthetic gene cluster 298 (BGC298). However, the molecular mechanisms underlying this protection remained poorly understood. Here, comparative metabolomic analyses revealed that knockout of BGC298 led to reduced production of the antifungal compound 5,6-dimethylbenzimidazole (DMB) in Fl98. We hypothesized that BGC298 is involved in regulating DMB biosynthesis and therefore contributes to Fl98’s disease suppression as a novel protective mechanism. Subsequent site-directed mutagenesis of the DMB-synthase gene bluB abolished DMB production by Fl98, and both ΔBGC298 and ΔbluB mutants were compromised in protecting sugar beet seedlings in greenhouse bioassays. Bioinformatic analyses further indicated that bluB is widespread across Flavobacterium, while BGC298 is limited to a small subset of plant-associated strains. Together, our findings highlight the pivotal role of BGC298 and DMB biosynthesis in plant protection by endophytic Flavobacterium sp. 98.
{"title":"Disentangling the molecular mechanisms of disease suppression by endophytic Flavobacterium sp. 98","authors":"Xinya Pan , Somayah S. Elsayed , Gilles P. van Wezel , Jos M. Raaijmakers , Víctor J. Carrión","doi":"10.1016/j.micres.2025.128415","DOIUrl":"10.1016/j.micres.2025.128415","url":null,"abstract":"<div><div>Endophytic microorganisms colonize internal plant tissues and enhance host resistance to pathogens. We previously showed that endophytic <em>Flavobacterium</em> sp. 98 (Fl98) protects sugar beet against the fungal root pathogen <em>Rhizoctonia solani</em> via biosynthetic gene cluster 298 (BGC298)<em>.</em> However, the molecular mechanisms underlying this protection remained poorly understood. Here, comparative metabolomic analyses revealed that knockout of BGC298 led to reduced production of the antifungal compound 5,6-dimethylbenzimidazole (DMB) in Fl98. We hypothesized that BGC298 is involved in regulating DMB biosynthesis and therefore contributes to Fl98’s disease suppression as a novel protective mechanism. Subsequent site-directed mutagenesis of the DMB-synthase gene <em>bluB</em> abolished DMB production by Fl98, and both ΔBGC298 and Δ<em>bluB</em> mutants were compromised in protecting sugar beet seedlings in greenhouse bioassays. Bioinformatic analyses further indicated that <em>bluB</em> is widespread across <em>Flavobacterium</em>, while BGC298 is limited to a small subset of plant-associated strains. Together, our findings highlight the pivotal role of BGC298 and DMB biosynthesis in plant protection by endophytic <em>Flavobacterium</em> sp. 98.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128415"},"PeriodicalIF":6.9,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145733988","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}
Bacterial infections pose a significant threat to host cells by inducing DNA damage, potentially leading to chromosomal instability, cell cycle arrest, apoptosis, or even cancer. Pseudomonas aeruginosa (P. aeruginosa) infection-induced DNA double-strand breaks (DSBs) activates DNA damage response (DDR) to facilitate repair. However, the mechanisms linking P. aeruginosa infection and host DNA repair remain unclear. Here, we demonstrate that DSBs-induced by P. aeruginosa in lung epithelial cells promote Tip60 activation and stabilization, which help counteract DNA damage. However, diminished Tip60 activation and reduced protein levels during the post-infection recovery phase exacerbate DNA damage. Mechanistically, elevated Tip60 levels during infection are associated with suppressed K33- and K48-linked ubiquitination, whereas the decline of Tip60 during recovery coincides with enhanced K33- and K48-linked ubiquitination. These specific ubiquitination modifications promote proteasomal degradation of Tip60, thereby reducing its stability. Supporting this, we observed that wild-type Tip60 undergoes markedly less K33- and K48-linked ubiquitination than its histone acetyltransferase (HAT) activity-deficient mutant. Notably, we identify the E3 ubiquitin ligase TRIM37 as a positive regulator of Tip60 stability, largely independent of its E3 ligase activity. Silencing TRIM37 enhances K33- and K48-linked ubiquitination and accelerates Tip60 degradation, thereby exacerbating DNA damage during both infection and recovery. TRIM37 binds to the C-terminal MYST domain of Tip60, with this interaction strengthened during infection but weakened upon recovery. This dynamic regulation arises because TRIM37 preferentially associates with the activated form of Tip60. Collectively, our findings identify the TRIM37-Tip60 axis as a critical regulator of host DDR in response to P. aeruginosa infection, offering new insights into infection-associated DDR and therapeutic strategies.
{"title":"Dynamic regulation of K33- and K48-linked ubiquitination of Tip60 by TRIM37 orchestrates host DNA damage response during Pseudomonas aeruginosa infection and recovery","authors":"Hua Yu , Xingmin Wang , Junzhi Xiong, Xiaomei He, Caifeng Ma, Qilin Wang, Rongrong Chen, Yuanyuan Li, Qian Dai, Qian Min, Jianyun Zhou, Kebin Zhang","doi":"10.1016/j.micres.2025.128414","DOIUrl":"10.1016/j.micres.2025.128414","url":null,"abstract":"<div><div>Bacterial infections pose a significant threat to host cells by inducing DNA damage, potentially leading to chromosomal instability, cell cycle arrest, apoptosis, or even cancer. <em>Pseudomonas aeruginosa</em> (<em>P. aeruginosa</em>) infection-induced DNA double-strand breaks (DSBs) activates DNA damage response (DDR) to facilitate repair. However, the mechanisms linking <em>P. aeruginosa</em> infection and host DNA repair remain unclear. Here, we demonstrate that DSBs-induced by <em>P. aeruginosa</em> in lung epithelial cells promote Tip60 activation and stabilization, which help counteract DNA damage. However, diminished Tip60 activation and reduced protein levels during the post-infection recovery phase exacerbate DNA damage. Mechanistically, elevated Tip60 levels during infection are associated with suppressed K33- and K48-linked ubiquitination, whereas the decline of Tip60 during recovery coincides with enhanced K33- and K48-linked ubiquitination. These specific ubiquitination modifications promote proteasomal degradation of Tip60, thereby reducing its stability. Supporting this, we observed that wild-type Tip60 undergoes markedly less K33- and K48-linked ubiquitination than its histone acetyltransferase (HAT) activity-deficient mutant. Notably, we identify the E3 ubiquitin ligase TRIM37 as a positive regulator of Tip60 stability, largely independent of its E3 ligase activity. Silencing TRIM37 enhances K33- and K48-linked ubiquitination and accelerates Tip60 degradation, thereby exacerbating DNA damage during both infection and recovery. TRIM37 binds to the C-terminal MYST domain of Tip60, with this interaction strengthened during infection but weakened upon recovery. This dynamic regulation arises because TRIM37 preferentially associates with the activated form of Tip60. Collectively, our findings identify the TRIM37-Tip60 axis as a critical regulator of host DDR in response to <em>P. aeruginosa</em> infection, offering new insights into infection-associated DDR and therapeutic strategies.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"305 ","pages":"Article 128414"},"PeriodicalIF":6.9,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145828015","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}
Pub Date : 2025-12-05DOI: 10.1016/j.micres.2025.128413
Yanan Zhou , Xue-Xian Zhang , Dandan Wang , Mengguang Zhao , Li Sun , Weiwei Huang , Zhihong Xie
Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant–microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development—all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles in planta. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.
{"title":"Microbial acetyl-CoA synthesis as an emerging metabolic and regulatory hub in plant-microbe interactions","authors":"Yanan Zhou , Xue-Xian Zhang , Dandan Wang , Mengguang Zhao , Li Sun , Weiwei Huang , Zhihong Xie","doi":"10.1016/j.micres.2025.128413","DOIUrl":"10.1016/j.micres.2025.128413","url":null,"abstract":"<div><div>Acetyl-CoA synthetase (ACS) is a well-characterized enzyme that catalyzes the ATP-dependent ligation of acetate and coenzyme A to produce acetyl-CoA, a central metabolite coordinating energy metabolism, carbon flux distribution, and post-translational protein modification. Recently, ACS has emerged as a metabolic nexus with broad implications for plant–microbe interactions in agriculture. Beyond its canonical role in primary metabolism, ACS governs diverse physiological processes in beneficial plant-associated microorganisms, including rhizosphere colonization, stress adaptation, secondary metabolite biosynthesis, and morphological development—all of which enhance plant growth and resilience. In contrast, in phytopathogens, ACS is closely related to the expression of virulence factors. Thus, ACS exerts a dual influence, shaping both mutualistic and antagonistic microbial lifestyles <em>in planta</em>. This review synthesizes recent advances in the structural and catalytic diversity of ACS, delineates its ecological and functional roles in agriculturally relevant microorganisms, and explores the environmental and host-derived signals that regulates its expression and activity. Particular attention is given to the interplay between ACS-mediated carbon metabolism and protein acetylation, which together modulate microbial physiology and plant-associated behaviors. ACS is thereby positioned as a strategic metabolic hub, providing a framework for future research at the interface of microbial metabolism, environmental adaptation, and plant health.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128413"},"PeriodicalIF":6.9,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145714781","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}
Crop domestication has long been known to reshape rhizosphere microbial communities, yet research has focused disproprotionately on bacteria and fungal responses to crop domestication while neglecting protist communities. Protists, as key microbial predators regulating bacterial populations and thereby their functionalities, remain understudied in this context. Here, we investigate the influence of soybean domestication on both bacterial and protist communities, with a focus on the reorganization of ecological strategies, specifically generalists and specialists, within these microbiomes. We analyzed 270 rhizosphere samples from 27 domesticated and 63 wild soybean varieties. Domestication significantly altered community compositions of bacterial communities, with wild soybeans harboring higher proprotions of Pseudomonadota (71.4 %) and Bacillota (4.8 %), while domesticated soybeans exhibited an enrichment of Bacteroidota (11.0 %). Protist communities also diverged: wild soybeans were dominated by Cercozoa (58.2 %) and Gyrista (23.5 %), while domesticated plants had more Ciliophora (7.1 %) and Evosea (5.7 %). Domesticated soybeans hosted fewer generalist and specialist bacteria but more generalist protists, suggesting divergent microbial responses to domestication. Correlation analyses revealed that bacterial and protist generalists exhibited strong positive correlations with each other. At the same time, bacterial and protist specialists also showed positive correlations in wild soybeans-patterns that were largely absent in their domesticated counterparts. Functionally, wild soybeans supported more ureolytic and methylotrophic bacteria, while domesticated soybeans favored nitrate-respiration taxa. Notably, predatory protists in wild soybeans were significantly correlated with bacteria involved in carbon and nitrogen cycling, a key ecological relationship lost with domestication. These findings suggest that domestication exerts different selection pressures on bacteria and protists, disrupting potential relationships between bacterial and protist functional groups.
{"title":"Soybean domestication alters rhizosphere microbial assembly and disrupts the potential bacteria-protist relationships.","authors":"Shaoguan Zhao, Chen Liu, Ying Yuan, Qingyun Zhao, Zhiyang Zhang, Xiangyu Ren, Yang Yue, Shuo Sun, Shiqi Sun, Qi Zhang, Guangnan Xing, Ming Wang, Wu Xiong, Qirong Shen","doi":"10.1016/j.micres.2025.128295","DOIUrl":"10.1016/j.micres.2025.128295","url":null,"abstract":"<p><p>Crop domestication has long been known to reshape rhizosphere microbial communities, yet research has focused disproprotionately on bacteria and fungal responses to crop domestication while neglecting protist communities. Protists, as key microbial predators regulating bacterial populations and thereby their functionalities, remain understudied in this context. Here, we investigate the influence of soybean domestication on both bacterial and protist communities, with a focus on the reorganization of ecological strategies, specifically generalists and specialists, within these microbiomes. We analyzed 270 rhizosphere samples from 27 domesticated and 63 wild soybean varieties. Domestication significantly altered community compositions of bacterial communities, with wild soybeans harboring higher proprotions of Pseudomonadota (71.4 %) and Bacillota (4.8 %), while domesticated soybeans exhibited an enrichment of Bacteroidota (11.0 %). Protist communities also diverged: wild soybeans were dominated by Cercozoa (58.2 %) and Gyrista (23.5 %), while domesticated plants had more Ciliophora (7.1 %) and Evosea (5.7 %). Domesticated soybeans hosted fewer generalist and specialist bacteria but more generalist protists, suggesting divergent microbial responses to domestication. Correlation analyses revealed that bacterial and protist generalists exhibited strong positive correlations with each other. At the same time, bacterial and protist specialists also showed positive correlations in wild soybeans-patterns that were largely absent in their domesticated counterparts. Functionally, wild soybeans supported more ureolytic and methylotrophic bacteria, while domesticated soybeans favored nitrate-respiration taxa. Notably, predatory protists in wild soybeans were significantly correlated with bacteria involved in carbon and nitrogen cycling, a key ecological relationship lost with domestication. These findings suggest that domestication exerts different selection pressures on bacteria and protists, disrupting potential relationships between bacterial and protist functional groups.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"301 ","pages":"128295"},"PeriodicalIF":6.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812125","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}
Plant growth-promoting rhizobacteria (PGPR) can stimulate crop growth and performance through multiple mechanisms, making them promising bioinoculants for sustainable agriculture. Among known PGPR species, Pseudomonas fluorescens has attracted considerable attention because of its superior growth-promoting mechanisms and broad adaptability. Although P. fluorescens P34 has excellent colonization and growth-promoting abilities, the molecular and ecological mechanisms underlying its growth-promoting effects remain poorly understood. Here, we conducted a 25-day pot experiment utilizing an integrated approach combining transcriptomics and microbial amplicon sequencing to investigate how P. fluorescens P34 influences wheat gene expression profiles and the response of the indigenous rhizosphere microbial community to P34 colonization. P34 application increased the seedling fresh weight, seedling dry weight, root fresh weight, root dry weight, phosphorus content, nitrogen content in wheat leaves and available phosphorus content in rhizosphere soil by 39.61 %, 29.67 %, 84.07 %, 64.71 %, 43.05 %, 17.79 % and 14.45 %, respectively, while it increased the length, projected area and number of forks of the wheat root system by 17.35 %, 35.87 % and 23.57 %, respectively. RNA sequencing revealed 3166 differentially expressed genes that were predominantly involved in nitrogen and phosphorus transport, carbohydrate metabolism, phytohormone biosynthesis and transport, and plantmicrobe signaling recognition. Moreover, microbial community dynamic modulation demonstrated that strain P34 induced shifts in the indigenous rhizosphere microbiome by enriching beneficial microorganisms (e.g., Massilia and Pseudomonas) while reducing potential pathogens. These findings revealed the molecular and ecological mechanisms underlying PGPR-mediated plant growth promotion, providing new insights for optimizing PGPR applications in sustainable agriculture and demonstrating its potential to reduce chemical fertilizer dependency while enhancing soil health in agroecosystems.
{"title":"Pseudomonas fluorescens P34 colonization impacts expression changes in wheat roots, reshapes rhizosphere microbial communities and promotes wheat plant growth.","authors":"Wenfeng Ai, Yanping Qiu, Jiajia Hua, Zixuan Chen, Wei Cheng, Yiping Chen, Shengxian Zhang, Yuanyuan Xue, Sha Li, Run Hong, Ruijie Dong, Yuanyuan Cao","doi":"10.1016/j.micres.2025.128306","DOIUrl":"10.1016/j.micres.2025.128306","url":null,"abstract":"<p><p>Plant growth-promoting rhizobacteria (PGPR) can stimulate crop growth and performance through multiple mechanisms, making them promising bioinoculants for sustainable agriculture. Among known PGPR species, Pseudomonas fluorescens has attracted considerable attention because of its superior growth-promoting mechanisms and broad adaptability. Although P. fluorescens P34 has excellent colonization and growth-promoting abilities, the molecular and ecological mechanisms underlying its growth-promoting effects remain poorly understood. Here, we conducted a 25-day pot experiment utilizing an integrated approach combining transcriptomics and microbial amplicon sequencing to investigate how P. fluorescens P34 influences wheat gene expression profiles and the response of the indigenous rhizosphere microbial community to P34 colonization. P34 application increased the seedling fresh weight, seedling dry weight, root fresh weight, root dry weight, phosphorus content, nitrogen content in wheat leaves and available phosphorus content in rhizosphere soil by 39.61 %, 29.67 %, 84.07 %, 64.71 %, 43.05 %, 17.79 % and 14.45 %, respectively, while it increased the length, projected area and number of forks of the wheat root system by 17.35 %, 35.87 % and 23.57 %, respectively. RNA sequencing revealed 3166 differentially expressed genes that were predominantly involved in nitrogen and phosphorus transport, carbohydrate metabolism, phytohormone biosynthesis and transport, and plantmicrobe signaling recognition. Moreover, microbial community dynamic modulation demonstrated that strain P34 induced shifts in the indigenous rhizosphere microbiome by enriching beneficial microorganisms (e.g., Massilia and Pseudomonas) while reducing potential pathogens. These findings revealed the molecular and ecological mechanisms underlying PGPR-mediated plant growth promotion, providing new insights for optimizing PGPR applications in sustainable agriculture and demonstrating its potential to reduce chemical fertilizer dependency while enhancing soil health in agroecosystems.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"301 ","pages":"128306"},"PeriodicalIF":6.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812124","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}
Pub Date : 2025-11-29DOI: 10.1016/j.micres.2025.128411
Shuai Li , Xin-Ran Wang , Jia-Rui Han , Wen-Hui Lian , Mukhtiar Ali , Yong-Hong Liu , Jun Liu , Jie Huang , Huan-Huan He , Rajivgandhi Govindan , Osama Abdalla Abdelshafy Mohamad , Bao-Zhu Fang , Lei Dong , Wen-Jun Li
Desert ecosystems cover nearly one-third of Earth’s land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.
{"title":"Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria","authors":"Shuai Li , Xin-Ran Wang , Jia-Rui Han , Wen-Hui Lian , Mukhtiar Ali , Yong-Hong Liu , Jun Liu , Jie Huang , Huan-Huan He , Rajivgandhi Govindan , Osama Abdalla Abdelshafy Mohamad , Bao-Zhu Fang , Lei Dong , Wen-Jun Li","doi":"10.1016/j.micres.2025.128411","DOIUrl":"10.1016/j.micres.2025.128411","url":null,"abstract":"<div><div>Desert ecosystems cover nearly one-third of Earth’s land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with <em>Actinomycetota</em>, <em>Pseudomonadota</em>, and <em>Bacillota</em> dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128411"},"PeriodicalIF":6.9,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145661404","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}
Global agriculture is increasingly constrained by soil degradation, with salinization and alkalization reducing crop productivity, soil function, and long-term ecosystem stability. Among salt-affected soils, soda saline-alkali soils represent a particularly challenging subtype, characterized by excessive accumulation of soluble salts, elevated pH, and high sodium content, all of which exacerbate soil structural decline. Haloalkaliphilic bacteria, adapted to high salinity and alkalinity, offer a sustainable bioremediation strategy. This review presents a conceptual framework elucidating the mechanisms by which haloalkaliphilic bacteria mitigate soda saline-alkali stress through osmoprotectant synthesis, ion homeostasis regulation, pH neutralization, extracellular polymeric substance (EPS) formation, and extremozyme activity, thereby enhancing nutrient mobilization and organic-matter turnover. These microbial processes facilitate contaminant degradation and stimulate plant growth by improving nutrient availability and promoting phytohormone production. The resulting plant-microbe synergy translates microbial activity into enhanced soil function by reducing bulk salinity and pH, improving structure and water retention, and promoting overall soil fertility. This review further identifies critical challenges to translating mechanistic insights into field practice, including ecological variability, inoculant efficacy and resilience, regulatory frameworks, scalable inoculant manufacturing, a paucity of multi-season field trials, and socioeconomic constraints. Prospects include integrative multi-omics to link gene expression with ecosystem outcomes; systematic exploration of extremozymes; incorporation of nutrient-rich biomass for consortium support; AI-guided consortia design and predictive modeling for site-specific optimization, and long-term monitoring. These strategies enhance our understanding of tolerance to high salinity and alkalinity, paving the way for innovative microbial interventions to restore soda saline-alkali soils and support more resilient, sustainable agricultural systems.
{"title":"Microbial strategies for soda saline-alkali soil remediation: The role of haloalkaliphilic bacteria","authors":"Bonaventure Chidi Ezenwanne , Charles Obinwanne Okoye , Huifang Jiang , Lu Gao , Xunfeng Chen , Yanfang Wu , Jianxiong Jiang","doi":"10.1016/j.micres.2025.128410","DOIUrl":"10.1016/j.micres.2025.128410","url":null,"abstract":"<div><div>Global agriculture is increasingly constrained by soil degradation, with salinization and alkalization reducing crop productivity, soil function, and long-term ecosystem stability. Among salt-affected soils, soda saline-alkali soils represent a particularly challenging subtype, characterized by excessive accumulation of soluble salts, elevated pH, and high sodium content, all of which exacerbate soil structural decline. Haloalkaliphilic bacteria, adapted to high salinity and alkalinity, offer a sustainable bioremediation strategy. This review presents a conceptual framework elucidating the mechanisms by which haloalkaliphilic bacteria mitigate soda saline-alkali stress through osmoprotectant synthesis, ion homeostasis regulation, pH neutralization, extracellular polymeric substance (EPS) formation, and extremozyme activity, thereby enhancing nutrient mobilization and organic-matter turnover. These microbial processes facilitate contaminant degradation and stimulate plant growth by improving nutrient availability and promoting phytohormone production. The resulting plant-microbe synergy translates microbial activity into enhanced soil function by reducing bulk salinity and pH, improving structure and water retention, and promoting overall soil fertility. This review further identifies critical challenges to translating mechanistic insights into field practice, including ecological variability, inoculant efficacy and resilience, regulatory frameworks, scalable inoculant manufacturing, a paucity of multi-season field trials, and socioeconomic constraints. Prospects include integrative multi-omics to link gene expression with ecosystem outcomes; systematic exploration of extremozymes; incorporation of nutrient-rich biomass for consortium support; AI-guided consortia design and predictive modeling for site-specific optimization, and long-term monitoring. These strategies enhance our understanding of tolerance to high salinity and alkalinity, paving the way for innovative microbial interventions to restore soda saline-alkali soils and support more resilient, sustainable agricultural systems.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128410"},"PeriodicalIF":6.9,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145668962","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}
Pub Date : 2025-11-28DOI: 10.1016/j.micres.2025.128401
Banyon H. Carnell , Jay Jayaraman , Jose Benjamin P. Dar Juan , Matthew D. Templeton , Iain D. Hay
The Pseudomonas syringae complex is an important group within the Gammaproteobacteria and comprises several pathovars of agricultural significance. Genome mining of the P. syringae species complex has uncovered high-molecular-weight phage tail complexes termed tailocins. Tailocins exert specific bactericidal action against both closely and more distantly related bacteria and significantly shape the ecology of the microbiome. Tailocin targeting specificity is currently understood to be dependent on tail-fibers (TFs) binding to specific molecular epitopes, including lipopolysaccharide (LPS) as a bacterial cell surface receptor for tailocin TF-targeting domains. Recent work in P. syringae has strongly correlated variation at the common polysaccharide antigen of LPS with tailocin sensitivity. Here we provide biochemical evidence for LPS as the major receptor for P. syringae tailocins; examine the mechanisms and genetic basis of tailocin TF targeting; and predict strains that can provide protective colonization of plants. We then use the understanding of these mechanisms that determine the tailocin targeting spectrum and genetic knockouts and complementation to modify the bacterial canker pathogen of kiwifruit plants to predict LPS-mediated tailocin targeting by naturally occurring host microbiota, and then demonstrate the efficacy of these applied microbiome-derived tailocin-carrying commensal strains as biocontrol agents.
{"title":"Understanding the dynamics of Pseudomonas syringae tailocin targeting allows for predictive protective microbial inoculation of Actinidia chinensis","authors":"Banyon H. Carnell , Jay Jayaraman , Jose Benjamin P. Dar Juan , Matthew D. Templeton , Iain D. Hay","doi":"10.1016/j.micres.2025.128401","DOIUrl":"10.1016/j.micres.2025.128401","url":null,"abstract":"<div><div>The <em>Pseudomonas syringae</em> complex is an important group within the Gammaproteobacteria and comprises several pathovars of agricultural significance. Genome mining of the <em>P. syringae</em> species complex has uncovered high-molecular-weight phage tail complexes termed tailocins. Tailocins exert specific bactericidal action against both closely and more distantly related bacteria and significantly shape the ecology of the microbiome. Tailocin targeting specificity is currently understood to be dependent on tail-fibers (TFs) binding to specific molecular epitopes, including lipopolysaccharide (LPS) as a bacterial cell surface receptor for tailocin TF-targeting domains. Recent work in <em>P. syringae</em> has strongly correlated variation at the common polysaccharide antigen of LPS with tailocin sensitivity. Here we provide biochemical evidence for LPS as the major receptor for <em>P. syringae</em> tailocins; examine the mechanisms and genetic basis of tailocin TF targeting; and predict strains that can provide protective colonization of plants. We then use the understanding of these mechanisms that determine the tailocin targeting spectrum and genetic knockouts and complementation to modify the bacterial canker pathogen of kiwifruit plants to predict LPS-mediated tailocin targeting by naturally occurring host microbiota, and then demonstrate the efficacy of these applied microbiome-derived tailocin-carrying commensal strains as biocontrol agents.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128401"},"PeriodicalIF":6.9,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145682410","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}
Pub Date : 2025-11-25DOI: 10.1016/j.micres.2025.128402
Zhibo Yuan , Yibo Zan , Xu Li , Bin Lu , Yanjie Chao , Xinwu Xiong , Yanpo Yao , Di Wu , Ben Niu , Dong Pei
Mycotoxin contamination of nuts, frequently attributed to inappropriate storage, causes substantial economic losses and health concerns globally. Biological control using beneficial microorganisms has emerged as an environment friendly method for efficient mitigation of Aspergillus flavus pollution and consequent mycotoxin elimination in foodstuffs. Nevertheless, the exact mechanisms by which these biocontrol microbes protect nuts from this toxigenic fungus remain largely unknown. Using a fungal infection assay, we observed a remarkable inhibitory effect of Enterobacter ludwigii AA4 against the growth of A. flavus colonizing walnut kernels and aflatoxin B1 production. Mutant E. ludwigii AA4 strains, generated by genetically modifying five biofilm-related genes, notably fadR (which encodes a transcriptional regulator), exhibited significantly impaired biofilm development and reduced efficacy in suppressing A. flavus. These results indicated that biofilm establishment is indispensable for the inhibitory effect of E. ludwigii AA4 against A. flavus. We further investigated the kernel colonization of fadR knockout mutant, which exhibited the most pronounced reduction in biofilm formation, via colony counting and laser scanning confocal microscopy. We found that fadR contributed to the suppression of A. flavus by influencing bacterial biofilm production and kernel settlement. Gene expression analysis and site-directed mutagenesis revealed that fadR modulated biofilm development by negatively regulating the transcription of rcsA, an auxiliary protein gene within the Rcs phosphorelay system, potentially by influencing acetyl phosphate-mediated RcsB phosphorylation. These findings highlight the potential of AA4 in the biological control of A. flavus contamination in walnut kernels.
{"title":"Regulatory effect of fadR on the inhibition of Aspergillus flavus infection of walnut kernels by Enterobacter ludwigii AA4","authors":"Zhibo Yuan , Yibo Zan , Xu Li , Bin Lu , Yanjie Chao , Xinwu Xiong , Yanpo Yao , Di Wu , Ben Niu , Dong Pei","doi":"10.1016/j.micres.2025.128402","DOIUrl":"10.1016/j.micres.2025.128402","url":null,"abstract":"<div><div>Mycotoxin contamination of nuts, frequently attributed to inappropriate storage, causes substantial economic losses and health concerns globally. Biological control using beneficial microorganisms has emerged as an environment friendly method for efficient mitigation of <em>Aspergillus flavus</em> pollution and consequent mycotoxin elimination in foodstuffs. Nevertheless, the exact mechanisms by which these biocontrol microbes protect nuts from this toxigenic fungus remain largely unknown. Using a fungal infection assay, we observed a remarkable inhibitory effect of <em>Enterobacter ludwigii</em> AA4 against the growth of <em>A</em>. <em>flavus</em> colonizing walnut kernels and aflatoxin B<sub>1</sub> production. Mutant <em>E. ludwigii</em> AA4 strains, generated by genetically modifying five biofilm-related genes, notably <em>fadR</em> (which encodes a transcriptional regulator), exhibited significantly impaired biofilm development and reduced efficacy in suppressing <em>A</em>. <em>flavus</em>. These results indicated that biofilm establishment is indispensable for the inhibitory effect of <em>E. ludwigii</em> AA4 against <em>A. flavus</em>. We further investigated the kernel colonization of <em>fadR</em> knockout mutant, which exhibited the most pronounced reduction in biofilm formation, via colony counting and laser scanning confocal microscopy. We found that <em>fadR</em> contributed to the suppression of <em>A. flavus</em> by influencing bacterial biofilm production and kernel settlement. Gene expression analysis and site-directed mutagenesis revealed that <em>fadR</em> modulated biofilm development by negatively regulating the transcription of <em>rcsA</em>, an auxiliary protein gene within the Rcs phosphorelay system, potentially by influencing acetyl phosphate-mediated RcsB phosphorylation. These findings highlight the potential of AA4 in the biological control of <em>A. flavus</em> contamination in walnut kernels.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128402"},"PeriodicalIF":6.9,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145654911","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}
Pub Date : 2025-11-21DOI: 10.1016/j.micres.2025.128400
Peigen Li , Yujie Shi , Yujie Zhao , Xiaotong Lu , Jingtao Duan , Qingsong Yang , Yangchun Xu , Xiaogang Li , Caixia Dong , Zhonghua Wang , Qirong Shen
Growth of container-grown Pyrus calleryana is often containered in heavy clay soils. Trichoderma-based bio-organic fertilizer (BOF) can improve seedling performance, yet how BOF mobilizes microbiome-hormone interactions under such conditions remains unclear. Here, we conducted a pot experiment with three treatments— water control (CK), 10 % (v/v) BOF and 20 % (v/v) BOF—under controlled conditions to assess plant growth, root hormone profiles, and rhizosphere communities. With 20 % BOF, seedling height, root length and root biomass increased (up to +131 %, +160 % and +165 %), bacterial diversity rose, and Firmicutes/Actinobacteria were enriched with an 8.3-fold increase of Bacillus. The ferment filtrates supported growth of the isolated Bacillus. Across treatments, Bacillus abundance correlated positively with indole-3-acetic acid (IAA) and isopentenyladenine (IP) and negatively with abscisic acid (ABA) (P < 0.05). Consistently, co-inoculation of Trichoderma and Bacillus increased IAA/IP and reduced ABA (P < 0.05), yielding stronger growth responses than single inoculations. These findings outline a BOF-mediated path in which Trichoderma-guided microbiome restructuring, together with a Trichoderma-responsive Bacillus, rebalances IAA/IP/ABA and promotes pear rootstock growth.
{"title":"Trichoderma bio-organic fertilizer modulates the rhizosphere microbiome and Bacillus-assisted plant hormone regulation to promote pear rootstock growth","authors":"Peigen Li , Yujie Shi , Yujie Zhao , Xiaotong Lu , Jingtao Duan , Qingsong Yang , Yangchun Xu , Xiaogang Li , Caixia Dong , Zhonghua Wang , Qirong Shen","doi":"10.1016/j.micres.2025.128400","DOIUrl":"10.1016/j.micres.2025.128400","url":null,"abstract":"<div><div>Growth of container-grown <em>Pyrus calleryana</em> is often containered in heavy clay soils. <em>Trichoderma</em>-based bio-organic fertilizer (BOF) can improve seedling performance, yet how BOF mobilizes microbiome-hormone interactions under such conditions remains unclear. Here, we conducted a pot experiment with three treatments— water control (CK), 10 % (v/v) BOF and 20 % (v/v) BOF—under controlled conditions to assess plant growth, root hormone profiles, and rhizosphere communities. With 20 % BOF, seedling height, root length and root biomass increased (up to +131 %, +160 % and +165 %), bacterial diversity rose, and Firmicutes/Actinobacteria were enriched with an 8.3-fold increase of <em>Bacillus</em>. The ferment filtrates supported growth of the isolated <em>Bacillus</em>. Across treatments, <em>Bacillus</em> abundance correlated positively with indole-3-acetic acid (IAA) and isopentenyladenine (IP) and negatively with abscisic acid (ABA) (P < 0.05). Consistently, co-inoculation of <em>Trichoderma</em> and Bacillus increased IAA/IP and reduced ABA (P < 0.05), yielding stronger growth responses than single inoculations. These findings outline a BOF-mediated path in which <em>Trichoderma</em>-guided microbiome restructuring, together with a <em>Trichoderma</em>-responsive Bacillus, rebalances IAA/IP/ABA and promotes pear rootstock growth.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128400"},"PeriodicalIF":6.9,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616569","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号