Hexanoic acid (Hx) is a naturally occurring fatty acid with antimicrobial properties and potential to induce plant defense responses. This study evaluated the in vitro effect of Hx on Xanthomonas vesicatoria and Xanthomonas euvesicatoria, focusing on bacterial growth and biofilm formation, key factors for pathogen survival and virulence. The obtained results indicate that Hx did not exert a direct lethal effect at low concentrations on bacterial cells, but higher doses (≥ 12 mM) displayed a bactericidal effect against both species, with X. euvesicatoria showing higher sensitivity than X. vesicatoria. Scanning electron microscopy (SEM) revealed cell wall damage and absence of biofilm at ≥ 10 mM Hx, consistent with the quorum sensing (QS) inhibition observed at this concentration. Moreover, exposure to 5 mM Hx triggered a significant increase in reactive oxygen species (ROS), indicating the inability of both bacteria to overcome the toxic environment generated by this compound. In addition, gene expression analysis demonstrated that Hx significantly impaired early biofilm establishment by downregulating motility- and virulence-related genes, particularly evident in X. euvesicatoria from lower concentrations. Although responses differed between the two species in survival strategies and sensitivities to Hx, both converged in a compromised biofilm formation and stress response capacity. Overall, this study provides mechanistic insights into Xanthomonas sensitivity to Hx and highlights biofilm disruption as a central mechanism underlying its antimicrobial activity under in vitro conditions.
己酸(Hx)是一种天然存在的脂肪酸,具有抗菌特性和诱导植物防御反应的潜力。本研究主要从病原菌生长和生物膜形成、病原菌存活和毒力的关键因素两方面评价了Hx对发白黄单胞菌和发紫黄单胞菌的体外作用。结果表明,低浓度的Hx对细菌细胞没有直接致死作用,但高剂量(≥12 mM)对两种细菌都有杀灭作用,其中鸡瘟x的敏感性高于鸡瘟x。扫描电镜(SEM)显示≥ 10 mM Hx时细胞壁损伤和生物膜缺失,与该浓度下观察到的群体感应(QS)抑制一致。此外,暴露于5 mM Hx引发活性氧(ROS)显著增加,表明这两种细菌无法克服该化合物产生的有毒环境。此外,基因表达分析表明,Hx通过下调运动性和毒力相关基因,显著损害了早期生物膜的形成,在低浓度的euvesicatoria中尤其明显。尽管这两个物种的生存策略和对Hx的敏感性不同,但它们的生物膜形成和应激反应能力都有所降低。总的来说,本研究提供了黄单胞菌对Hx敏感性的机制见解,并强调了生物膜破坏是其体外抗菌活性的核心机制。
{"title":"Hexanoic acid inhibits in vitro growth and biofilm formation in Xanthomonas vesicatoria and Xanthomonas euvesicatoria.","authors":"Lorena Sánchez-Giménez, Loredana Scalschi, Eugenio Llorens, Eva Falomir, Gemma Camañes, Begonya Vicedo","doi":"10.1016/j.micres.2026.128504","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128504","url":null,"abstract":"<p><p>Hexanoic acid (Hx) is a naturally occurring fatty acid with antimicrobial properties and potential to induce plant defense responses. This study evaluated the in vitro effect of Hx on Xanthomonas vesicatoria and Xanthomonas euvesicatoria, focusing on bacterial growth and biofilm formation, key factors for pathogen survival and virulence. The obtained results indicate that Hx did not exert a direct lethal effect at low concentrations on bacterial cells, but higher doses (≥ 12 mM) displayed a bactericidal effect against both species, with X. euvesicatoria showing higher sensitivity than X. vesicatoria. Scanning electron microscopy (SEM) revealed cell wall damage and absence of biofilm at ≥ 10 mM Hx, consistent with the quorum sensing (QS) inhibition observed at this concentration. Moreover, exposure to 5 mM Hx triggered a significant increase in reactive oxygen species (ROS), indicating the inability of both bacteria to overcome the toxic environment generated by this compound. In addition, gene expression analysis demonstrated that Hx significantly impaired early biofilm establishment by downregulating motility- and virulence-related genes, particularly evident in X. euvesicatoria from lower concentrations. Although responses differed between the two species in survival strategies and sensitivities to Hx, both converged in a compromised biofilm formation and stress response capacity. Overall, this study provides mechanistic insights into Xanthomonas sensitivity to Hx and highlights biofilm disruption as a central mechanism underlying its antimicrobial activity under in vitro conditions.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"308 ","pages":"128504"},"PeriodicalIF":6.9,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147494250","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}
Helicobacter pylori (H. pylori) infection is a major risk factor for gastric cancer (GC), but the molecular mechanisms driving H. pylori-induced gastric carcinogenesis remain incompletely understood. This study investigates the role of the AEG-1 3'-untranslated region (3'UTR) as a competitive endogenous RNA (ceRNA) in this process. A ceRNA network was constructed via whole-transcriptome sequencing of H. pylori-associated GC. Gain- and loss-of-function experiments were performed to assess the impact of the AEG-1 3'UTR on epithelial-mesenchymal transition (EMT) in infected GC cells. The regulatory mechanism was explored using bioinformatics, dual-luciferase reporter assays, and rescue experiments. In vivo effects were evaluated using AEG-1 knockout mouse models of H. pylori infection and nude mouse xenograft models. Results showed that AEG-1 and JAK2 were upregulated and miR-375-3p downregulated in H. pylori-infected GC cells and tissues. The AEG-1 3'UTR promoted proliferation, migration, invasion, and EMT by sponging miR-375-3p, thereby derepressing JAK2 and activating JAK2/STAT3 signaling. These oncogenic effects were reversed by JAK2 silencing or miR-375-3p overexpression. In AEG-1 knockout mice, H. pylori colonization and gastric inflammation were markedly reduced, accompanied by decreased expression of EMT and proliferation markers. Xenograft models further confirmed that the AEG-1/miR-375-3p/JAK2 axis drives GC growth and lung metastasis. These findings identify AEG-1 3'UTR as a ceRNA that regulates H. pylori-mediated EMT and carcinogenesis via the miR-375-3p/JAK2 axis, highlighting its potential as a therapeutic target.
{"title":"AEG-1 3'UTR functions as a ceRNA to facilitate Helicobacter pylori-induced gastric cancer EMT by regulating the miR-375-3p/JAK2 axis.","authors":"Jiale Chen, Xin Li, Furui Zhang, Xuebo Han, Meng He, Xuequan Wang, Jing Wu, Linhan Ni, Jing Liu, Juan Chen, Kunmei Liu, Le Guo","doi":"10.1016/j.micres.2026.128502","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128502","url":null,"abstract":"<p><p>Helicobacter pylori (H. pylori) infection is a major risk factor for gastric cancer (GC), but the molecular mechanisms driving H. pylori-induced gastric carcinogenesis remain incompletely understood. This study investigates the role of the AEG-1 3'-untranslated region (3'UTR) as a competitive endogenous RNA (ceRNA) in this process. A ceRNA network was constructed via whole-transcriptome sequencing of H. pylori-associated GC. Gain- and loss-of-function experiments were performed to assess the impact of the AEG-1 3'UTR on epithelial-mesenchymal transition (EMT) in infected GC cells. The regulatory mechanism was explored using bioinformatics, dual-luciferase reporter assays, and rescue experiments. In vivo effects were evaluated using AEG-1 knockout mouse models of H. pylori infection and nude mouse xenograft models. Results showed that AEG-1 and JAK2 were upregulated and miR-375-3p downregulated in H. pylori-infected GC cells and tissues. The AEG-1 3'UTR promoted proliferation, migration, invasion, and EMT by sponging miR-375-3p, thereby derepressing JAK2 and activating JAK2/STAT3 signaling. These oncogenic effects were reversed by JAK2 silencing or miR-375-3p overexpression. In AEG-1 knockout mice, H. pylori colonization and gastric inflammation were markedly reduced, accompanied by decreased expression of EMT and proliferation markers. Xenograft models further confirmed that the AEG-1/miR-375-3p/JAK2 axis drives GC growth and lung metastasis. These findings identify AEG-1 3'UTR as a ceRNA that regulates H. pylori-mediated EMT and carcinogenesis via the miR-375-3p/JAK2 axis, highlighting its potential as a therapeutic target.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"308 ","pages":"128502"},"PeriodicalIF":6.9,"publicationDate":"2026-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147486540","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}
The application of salt-tolerant plant growth-promoting rhizobacteria (PGPR) represents a promising strategy to alleviate salt stress in crops. However, the mechanisms by which volatile organic compounds (VOCs) from actinomycetes mitigate salinity stress remain unclear. In this study, exposure to VOCs from the halotolerant actinomycete Glutamicibacter halophytocola KLBMP 5180 significantly promotes the growth of tomato seedlings under salt stress, as evidenced by increased fresh weight, lateral root number, and chlorophyll content. Physiological analyses show that VOCs exposure reduces oxidative damage and enhances antioxidant enzyme activity. Furthermore, elevated levels of total phenolics and flavonoids are detected, along with decreased sodium ion accumulation and an improved Na⁺/K⁺ ratio. Transcriptome analysis reveales that VOCs treatment upregulates genes associated with pathways involved in phenylpropanoid biosynthesis, glutathione metabolism, MAPK signaling, plant hormone signal transduction, and plant-pathogen interactions under saline conditions. VOCs also increase levels of endogenous auxin, jasmonic acid (JA), and 1-aminocyclopropane-1-carboxylic acid (ACC), while activating genes related to their respective signaling pathways. The salt tolerance enhancement mediated by VOCs is compromised by ethylene and JA inhibitors, suggesting that KLBMP 5180-derived VOCs improve tomato salt tolerance by stimulating ethylene synthesis and signal transduction. Additional VOCs profiling identifies several key bioactive compounds, including 3-methyl-1-butanol, phenylethyl alcohol, 2-aminopropanediamide, and 2-undecanone. These findings demonstrate that VOCs from G. halophytocola KLBMP 5180 enhance tomato growth under salt stress and advance our understanding of the role of actinomycetes in pronoting plant growth and mitigating salinity stress.
{"title":"Volatile organic compounds from the salt-tolerant Glutamicibacter halophytocola KLBMP 5180 enhance salt stress tolerance in tomato seedlings by regulating antioxidant defense, ion homeostasis, and auxin, jasmonic acid/ethylene signaling pathways.","authors":"Jing Tao, Han-Xuan Huang, Yue-Ying Qin, Qing Wang, Su-Yun Kong, Yi-Fei Lu, Zhi-Yuan Wan, Ke Xing, Sheng Qin","doi":"10.1016/j.micres.2026.128501","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128501","url":null,"abstract":"<p><p>The application of salt-tolerant plant growth-promoting rhizobacteria (PGPR) represents a promising strategy to alleviate salt stress in crops. However, the mechanisms by which volatile organic compounds (VOCs) from actinomycetes mitigate salinity stress remain unclear. In this study, exposure to VOCs from the halotolerant actinomycete Glutamicibacter halophytocola KLBMP 5180 significantly promotes the growth of tomato seedlings under salt stress, as evidenced by increased fresh weight, lateral root number, and chlorophyll content. Physiological analyses show that VOCs exposure reduces oxidative damage and enhances antioxidant enzyme activity. Furthermore, elevated levels of total phenolics and flavonoids are detected, along with decreased sodium ion accumulation and an improved Na⁺/K⁺ ratio. Transcriptome analysis reveales that VOCs treatment upregulates genes associated with pathways involved in phenylpropanoid biosynthesis, glutathione metabolism, MAPK signaling, plant hormone signal transduction, and plant-pathogen interactions under saline conditions. VOCs also increase levels of endogenous auxin, jasmonic acid (JA), and 1-aminocyclopropane-1-carboxylic acid (ACC), while activating genes related to their respective signaling pathways. The salt tolerance enhancement mediated by VOCs is compromised by ethylene and JA inhibitors, suggesting that KLBMP 5180-derived VOCs improve tomato salt tolerance by stimulating ethylene synthesis and signal transduction. Additional VOCs profiling identifies several key bioactive compounds, including 3-methyl-1-butanol, phenylethyl alcohol, 2-aminopropanediamide, and 2-undecanone. These findings demonstrate that VOCs from G. halophytocola KLBMP 5180 enhance tomato growth under salt stress and advance our understanding of the role of actinomycetes in pronoting plant growth and mitigating salinity stress.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"308 ","pages":"128501"},"PeriodicalIF":6.9,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147474431","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 : 2026-03-10DOI: 10.1016/j.micres.2026.128493
Thomas Roach, Moritz Stegner, David Clara, Claudio G Ametrano, Stéphane Compant, Davide Gerna
Improper seed storage conditions, such as elevated temperature and moisture, accelerate ageing and compromise seed quality. However, the impacts of ageing on the seed microbiome and the resulting consequences for germination performance remain poorly understood. Here, we characterised how ageing soybean (Glycine max) seeds at 45 °C and 75% RH affects seed fungal communities, metabolism relevant to microbial growth, and sensitivity of germination to fungal challenge. Additionally, we assessed a role for endophytic bacteria in controlling pathogenic fungi. Amplicon sequencing revealed that ageing decreased fungal richness and reshaped community structure and composition of dominant taxa in seeds. Fusarium and Rhizopus isolates inhibited germination of non-aged seeds, whereas Sarocladium, Plectosphaerella, and Cladosporium impaired germination of aged seeds only. During imbibition, ageing increased seed metabolite leakage, including pinitol, glucose, and fructose, which promoted fungal growth in vitro. Among 39 endophytic bacteria previously isolated from soybean seeds, Bacillus toyonensis C55 and B. pumilus AM26 antagonised fungal growth, consistent with genomic regions associated with antifungal activity. Ageing oxidised the seed cellular redox state, and fungi tolerated oxidative growth conditions better than bacteria. In two cultivars, seed inoculation with B. toyonensis C55 increased germination, supporting a role in regulating fungal infections, whereas B. pumilus AM26 impaired germination. Notably, neither Bacillus strain affected germination of high-vigour non-aged seeds. Fluorescence in situ hybridisation microscopy revealed that both strains recolonised the seed endosphere following ageing. We conclude that oxidation during seed ageing contributes to increased sensitivity to fungal pathogens, which can be modulated by certain bacteria.
{"title":"Seed ageing increases the influence of native microorganisms on germination.","authors":"Thomas Roach, Moritz Stegner, David Clara, Claudio G Ametrano, Stéphane Compant, Davide Gerna","doi":"10.1016/j.micres.2026.128493","DOIUrl":"https://doi.org/10.1016/j.micres.2026.128493","url":null,"abstract":"<p><p>Improper seed storage conditions, such as elevated temperature and moisture, accelerate ageing and compromise seed quality. However, the impacts of ageing on the seed microbiome and the resulting consequences for germination performance remain poorly understood. Here, we characterised how ageing soybean (Glycine max) seeds at 45 °C and 75% RH affects seed fungal communities, metabolism relevant to microbial growth, and sensitivity of germination to fungal challenge. Additionally, we assessed a role for endophytic bacteria in controlling pathogenic fungi. Amplicon sequencing revealed that ageing decreased fungal richness and reshaped community structure and composition of dominant taxa in seeds. Fusarium and Rhizopus isolates inhibited germination of non-aged seeds, whereas Sarocladium, Plectosphaerella, and Cladosporium impaired germination of aged seeds only. During imbibition, ageing increased seed metabolite leakage, including pinitol, glucose, and fructose, which promoted fungal growth in vitro. Among 39 endophytic bacteria previously isolated from soybean seeds, Bacillus toyonensis C55 and B. pumilus AM26 antagonised fungal growth, consistent with genomic regions associated with antifungal activity. Ageing oxidised the seed cellular redox state, and fungi tolerated oxidative growth conditions better than bacteria. In two cultivars, seed inoculation with B. toyonensis C55 increased germination, supporting a role in regulating fungal infections, whereas B. pumilus AM26 impaired germination. Notably, neither Bacillus strain affected germination of high-vigour non-aged seeds. Fluorescence in situ hybridisation microscopy revealed that both strains recolonised the seed endosphere following ageing. We conclude that oxidation during seed ageing contributes to increased sensitivity to fungal pathogens, which can be modulated by certain bacteria.</p>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"308 ","pages":"128493"},"PeriodicalIF":6.9,"publicationDate":"2026-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147463671","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 : 2026-03-01Epub 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":"2026-03-01","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 : 2026-03-01Epub 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":"2026-03-01","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}
Pub Date : 2026-03-01Epub Date: 2025-11-19DOI: 10.1016/j.micres.2025.128399
Aida Nabila Rahim , Gwo Rong Wong , Kah Ooi Chua , Kausalyaa Kaliapan , Jennifer Ann Harikrishna , Siah Ying Tang , Bey Hing Goh , Purabi Mazumdar
Sclerotinia sclerotiorum is one of many fungal pathogens that threaten global crop production. Antagonistic rhizobacteria have emerged as promising eco-friendly alternatives to synthetic pesticides that can be deployed for effective and sustainable management of the fungal disease. From 60 rhizobacterial strains isolated in this study, eight were able to inhibit the in vitro growth of S. sclerotiorum. Among these, strain CS11 exhibited complete (100 %) inhibition and demonstrated multiple plant growth-promoting traits, including siderophore production, nitrogen assimilation, phosphate solubilisation, and lytic enzyme activity. Motility and root colonisation assays confirmed CS11 to have high motility and efficient rhizosphere establishment. Molecular identification using 16S rRNA sequencing and Multi-locus sequence analysis identified CS11 as Pseudomonas protegens. Whole-genome sequencing revealed gene clusters for key antifungal metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, hydrogen cyanide, and orfamides, widely associated with Pseudomonas spp. Although closely related to P. protegens CHA0, CS11 has additional coding sequences associated with protease production (thermostable alkaline protease), root colonisation (cyclic di-GMP phosphodiesterase), and rhizosphere fitness (quorum-sensing-related genes), highlighting its novelty and strong biocontrol potential. In greenhouse trials, treatment of S. sclerotiorum-infected tomato plants with CS11 led to complete suppression of disease progression and significantly enhanced plant height and chlorophyll content. Compared to untreated infected plants, CS11-treated plants had elevated GLU, Chi, PAL, and PPO activities, and RT-qPCR analysis demonstrated upregulation of salicylic acid (PR1, PR2, PR5) and jasmonic acid (PR3, PR4, PDF1.2, VSP2) pathway genes. Collectively, these findings establish P. protegens CS11 as a promising candidate for the development of biopesticides to control fungal pathogens and enhance plant defence.
{"title":"Genomic and functional analysis of Pseudomonas protegens CS11 reveals multifaceted biocontrol mechanisms against Sclerotinia sclerotiorum via antifungal metabolites, root colonisation and plant defence induction in tomato","authors":"Aida Nabila Rahim , Gwo Rong Wong , Kah Ooi Chua , Kausalyaa Kaliapan , Jennifer Ann Harikrishna , Siah Ying Tang , Bey Hing Goh , Purabi Mazumdar","doi":"10.1016/j.micres.2025.128399","DOIUrl":"10.1016/j.micres.2025.128399","url":null,"abstract":"<div><div><em>Sclerotinia sclerotiorum</em> is one of many fungal pathogens that threaten global crop production. Antagonistic rhizobacteria have emerged as promising eco-friendly alternatives to synthetic pesticides that can be deployed for effective and sustainable management of the fungal disease. From 60 rhizobacterial strains isolated in this study, eight were able to inhibit the <em>in vitro</em> growth of <em>S. sclerotiorum</em>. Among these, strain CS11 exhibited complete (100 %) inhibition and demonstrated multiple plant growth-promoting traits, including siderophore production, nitrogen assimilation, phosphate solubilisation, and lytic enzyme activity. Motility and root colonisation assays confirmed CS11 to have high motility and efficient rhizosphere establishment. Molecular identification using 16S rRNA sequencing and Multi-locus sequence analysis identified CS11 as <em>Pseudomonas protegens</em>. Whole-genome sequencing revealed gene clusters for key antifungal metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, hydrogen cyanide, and orfamides, widely associated with <em>Pseudomonas</em> spp. Although closely related to <em>P. protegens</em> CHA0, CS11 has additional coding sequences associated with protease production (thermostable alkaline protease), root colonisation (cyclic di-GMP phosphodiesterase), and rhizosphere fitness (quorum-sensing-related genes), highlighting its novelty and strong biocontrol potential. In greenhouse trials, treatment of <em>S. sclerotiorum</em>-infected tomato plants with CS11 led to complete suppression of disease progression and significantly enhanced plant height and chlorophyll content. Compared to untreated infected plants, CS11-treated plants had elevated GLU, Chi, PAL, and PPO activities, and RT-qPCR analysis demonstrated upregulation of salicylic acid (<em>PR1, PR2, PR5</em>) and jasmonic acid (<em>PR3, PR4, PDF1.2, VSP2</em>) pathway genes. Collectively, these findings establish <em>P. protegens</em> CS11 as a promising candidate for the development of biopesticides to control fungal pathogens and enhance plant defence.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128399"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145570972","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 : 2026-03-01Epub Date: 2025-09-14DOI: 10.1016/j.micres.2025.128342
Kaiyue Ding , Yuexue Huo , Kangzhe Fu , Yingting Chen , Lunyue Xia , Junhao Zhan , Jiahua Liu , Jiayu Liu , Yudi Liu , Mingyang Zhang , Xingchen Wu , HyokChol Choe , Danping Zhao , Junnan Ma , Chunmei Dai , Zhenlong Yu , Yulin Peng , Xiaochi Ma , Lin Zhang
Ovarian cancer (OC) is a highly lethal gynecologic malignancy characterized by limited availability of treatment options and frequent recurrence. The gut microbiota has emerged as a key regulator of tumor progression; however, the anticancer potential of individual probiotic species remains insufficiently characterized and warrants further investigation. Ferroptosis is a regulated iron-dependent cell death with therapeutic potential in cancer. In this study, we initially observed that the traditional herbal pair, Scutellaria barbata D. Don (SB) and Scleromitrion diffusum (Wild) R.J. Wang (SD) exerted antitumor effects in a mouse model of OC, which was accompanied by a marked increase in the abundance of Faecalibacterium prausnitzii (F.prausnitzii) — a beneficial commensal bacterium not previously associated with cancer or ferroptosis. This observation prompted us to explore the functional role of F.prausnitzii in OC and revealed that it significantly suppressed ovarian tumor growth both in vitro and in vivo. Mechanistically, F.prausnitzii treatment elevated Fe²⁺ levels, increased lipid peroxidation, and depleted glutathione (GSH), which are hallmarks of ferroptosis. Transcriptomic analysis of tumor tissues from F.prausnitzii-treated mice identified ferroptosis and metal ion homeostasis pathways as major regulatory networks. Furthermore, metabolomic profiling revealed the activation of phenylalanine metabolism and increased production of phenylacetylglutamine (PAGln), suggesting a microbiota-metabolite axis contributing to ferroptosis induction. Our findings reveal that F.prausnitzii represents a novel ferroptosis-inducing probiotic with potent antitumor activity in OC. This study reveals a previously unrecognized role for this gut commensal and provides a mechanistic basis for the development of microbiota-based, ferroptosis-targeted therapeutic strategies in oncology.
卵巢癌(OC)是一种高度致命的妇科恶性肿瘤,其特点是治疗选择有限,复发频繁。肠道微生物群已成为肿瘤进展的关键调节因子;然而,单个益生菌物种的抗癌潜力仍然不够充分,需要进一步研究。铁下垂是一种受调节的铁依赖性细胞死亡,具有治疗癌症的潜力。在这项研究中,我们最初观察到传统的草药对,黄芩(Scutellaria barbata D. Don, SB)和弥漫性白僵菌(scleroomitrion diffusum, Wild) R.J. Wang (SD)在OC小鼠模型中发挥抗肿瘤作用,同时伴随着Faecalibacterium prausnitzii (f.p prausnitzii)丰度的显著增加,Faecalibacterium prausnitzii是一种有益的共生细菌,以前与癌症或铁中毒无关。这一观察结果促使我们探索F.prausnitzii在卵巢癌中的功能作用,并发现其在体外和体内均能显著抑制卵巢肿瘤的生长。在机制上,F.prausnitzii处理升高了Fe 2 +水平,增加了脂质过氧化和谷胱甘肽(GSH)的消耗,这些都是铁死亡的标志。通过对prausnitzii治疗小鼠肿瘤组织的转录组学分析,发现铁凋亡和金属离子稳态通路是主要的调控网络。此外,代谢组学分析显示苯丙氨酸代谢的激活和苯乙酰谷氨酰胺(PAGln)的产生增加,表明微生物代谢轴有助于诱导铁下垂。我们的研究结果表明,F.prausnitzii是一种新的诱导铁中毒的益生菌,在OC中具有很强的抗肿瘤活性。这项研究揭示了这种肠道共生体以前未被认识到的作用,并为开发基于微生物群的肿瘤中以铁中毒为目标的治疗策略提供了机制基础。
{"title":"Faecalibacterium prausnitzii suppresses ovarian cancer by inducing ferroptosis via phenylalanine metabolism activation","authors":"Kaiyue Ding , Yuexue Huo , Kangzhe Fu , Yingting Chen , Lunyue Xia , Junhao Zhan , Jiahua Liu , Jiayu Liu , Yudi Liu , Mingyang Zhang , Xingchen Wu , HyokChol Choe , Danping Zhao , Junnan Ma , Chunmei Dai , Zhenlong Yu , Yulin Peng , Xiaochi Ma , Lin Zhang","doi":"10.1016/j.micres.2025.128342","DOIUrl":"10.1016/j.micres.2025.128342","url":null,"abstract":"<div><div>Ovarian cancer (OC) is a highly lethal gynecologic malignancy characterized by limited availability of treatment options and frequent recurrence. The gut microbiota has emerged as a key regulator of tumor progression; however, the anticancer potential of individual probiotic species remains insufficiently characterized and warrants further investigation. Ferroptosis is a regulated iron-dependent cell death with therapeutic potential in cancer. In this study, we initially observed that the traditional herbal pair, <em>Scutellaria barbata</em> D. Don (SB) and <em>Scleromitrion diffusum</em> (Wild) R.J. Wang (SD) exerted antitumor effects in a mouse model of OC, which was accompanied by a marked increase in the abundance of <em>Faecalibacterium prausnitzii</em> (<em>F.prausnitzii</em>) — a beneficial commensal bacterium not previously associated with cancer or ferroptosis. This observation prompted us to explore the functional role of <em>F.prausnitzii</em> in OC and revealed that it significantly suppressed ovarian tumor growth both <em>in vitro</em> and <em>in vivo</em>. Mechanistically, <em>F.prausnitzii</em> treatment elevated Fe²⁺ levels, increased lipid peroxidation, and depleted glutathione (GSH), which are hallmarks of ferroptosis. Transcriptomic analysis of tumor tissues from <em>F.prausnitzii</em>-treated mice identified ferroptosis and metal ion homeostasis pathways as major regulatory networks. Furthermore, metabolomic profiling revealed the activation of phenylalanine metabolism and increased production of phenylacetylglutamine (PAGln), suggesting a microbiota-metabolite axis contributing to ferroptosis induction. Our findings reveal that <em>F.prausnitzii</em> represents a novel ferroptosis-inducing probiotic with potent antitumor activity in OC. This study reveals a previously unrecognized role for this gut commensal and provides a mechanistic basis for the development of microbiota-based, ferroptosis-targeted therapeutic strategies in oncology.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"304 ","pages":"Article 128342"},"PeriodicalIF":6.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616568","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 : 2026-03-01Epub 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":"2026-03-01","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}
Pub Date : 2026-03-01Epub 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":"2026-03-01","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}