Mehran Khan , Atul Kumar Srivastava , Mir Muhammad Nizamani , Muhammad Asif , Ali Kamran , Lingfeng Luo , Sanwei Yang , Songshu Chen , Zhiqiang Li , Xin Xie
{"title":"The battle within: Discovering new insights into phytopathogen interactions and effector dynamics","authors":"Mehran Khan , Atul Kumar Srivastava , Mir Muhammad Nizamani , Muhammad Asif , Ali Kamran , Lingfeng Luo , Sanwei Yang , Songshu Chen , Zhiqiang Li , Xin Xie","doi":"10.1016/j.micres.2025.128220","DOIUrl":"10.1016/j.micres.2025.128220","url":null,"abstract":"<div><div>Phytopathogen interactions are complicated and constantly evolving, driven by a never-ending war amongst the host’s immune defenses and the pathogen's virulence strategies. This comprehensive review examines the intricate mechanisms of effector-triggered immunity (ETI) and how pathogen effectors use host cellular progressions to promote infection. This review article investigates the modification of Phytopathogen effectors and plant resistance proteins, highlighting the role of meta-population dynamics and rapid adaptation. Additionally, it highlights the influence of environmental impact and climate change on host-pathogen interactions, describing their significant impact on disease dynamics and pathogen evolution. Effector proteins are crucial in sabotaging plant immunity, with bacterial, fungal, oomycete, and nematode effectors targeting common host protein networks and phytohormone pathways. Additionally, the review discusses advanced approaches for classifying effector targets, such as bioinformatics and single-cell transcriptomics, highlighting their importance in developing effective disease management strategies. Further insights are described into how effectors control phytohormone pathways, shedding light on how pathogens exploit host signaling. This review covers structural studies and protein modeling that have advanced effector prediction and our understanding of their functions and evolution, while providing an overview of phytopathogen interactions and future directions for effector research.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128220"},"PeriodicalIF":6.1,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090447","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}
Lijuan Ding , Lin Cui , Yuheng Wang , Beau Dronsella , Xu Liu , Huiying Luo , Huoqing Huang , Xiaoyun Su , Yingguo Bai , Jie Zhang , Tao Tu , Xing Qin , Yuan Wang , Yaru Wang , Bin Yao , Xianli Xue , Gang Guo , Xiaolu Wang
{"title":"Fructose metabolism in Entner-Doudoroff pathway-deficient Cupriavidus necator H16 depends on the Calvin shunt","authors":"Lijuan Ding , Lin Cui , Yuheng Wang , Beau Dronsella , Xu Liu , Huiying Luo , Huoqing Huang , Xiaoyun Su , Yingguo Bai , Jie Zhang , Tao Tu , Xing Qin , Yuan Wang , Yaru Wang , Bin Yao , Xianli Xue , Gang Guo , Xiaolu Wang","doi":"10.1016/j.micres.2025.128222","DOIUrl":"10.1016/j.micres.2025.128222","url":null,"abstract":"<div><div>As a facultative chemolithoautotrophic bacterium, <em>Cupriavidus necator</em> H16 uses the Entner-Doudoroff (ED) pathway for heterotrophic growth on carbohydrates such as fructose and the Calvin cycle for lithoautotrophic carbon dioxide fixation. In a previous study, we found that an ED pathway-deficient <em>C. necator</em> strain can survive on fructose, but the underlying metabolic pathway remained unclear. This study aimed to elucidate the metabolic mechanism of fructose metabolism in this ED pathway-deficient <em>C. necator</em> strain. First, the metabolic characteristics of fructose catabolism in the deficient strain were examined. Then, the roles of glycolysis/gluconeogenesis, the Calvin shunt, and the non-oxidative pentose phosphate pathway (non-OxPPP) in the metabolism of fructose were identified through comparative transcriptomic analysis combined with <sup>13</sup>C tracer experiments. Further growth experiments using knockout strains of key genes involved in these pathways confirmed that the non-OxPPP compensates for the blocked ED pathway to metabolize fructose and provide a precursor for the Calvin shunt, thereby driving subsequent carbon fluxes. Additionally, phosphoglycolate salvage pathways, particularly the malate cycle, are crucial for recycling glycolate-2-phosphate produced during RuBisCO-catalyzed oxidation. This study revealed a novel fructose metabolism mechanism in <em>C. necator</em> and highlighted its metabolic flexibility, thereby deepening our understanding of its carbon utilization strategies and providing a theoretical basis for further metabolic engineering research.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128222"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144107088","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}
Sk Soyal Parvez , Anupam Mondal , Kalpna Sharma , Andrei Stecca Steindorff , Igor V. Grigoriev , Utpal Bakshi , Avishek Banik
{"title":"Trichoderma sp. strain AM6 whole-genome guided untargeted metabolomics: Terpenoid backbone synthesis and modulation of VOCs in tea (Camellia sinensis L.)","authors":"Sk Soyal Parvez , Anupam Mondal , Kalpna Sharma , Andrei Stecca Steindorff , Igor V. Grigoriev , Utpal Bakshi , Avishek Banik","doi":"10.1016/j.micres.2025.128215","DOIUrl":"10.1016/j.micres.2025.128215","url":null,"abstract":"<div><div>Industrial cash crop tea is a cherished drink for its bioactive components like terpenoids and flavonoids shaping its flavor and health benefits. <em>Trichoderma</em> species are potent biocontrol agents and plant growth regulators, with unexplored potential in modulation of <em>C. sinensis</em> terpenoid biosynthesis. Genome sequencing of a tea root-associated <em>Trichoderma</em> sp. strain AM6 revealed a genome size of 39.91 Mbp, comprising 446 contigs organized into 406 scaffolds, with 98.8 % completeness. Single scaffold mitochondrial genome assembly of 34,430 bp in length with a GC content of 28.03 % encodes a total of 49 genes including 27 tRNA, 2 rRNA, and 20 protein-coding genes. Metabolic pathway analysis indicates exclusive reliance on the mevalonate pathway for terpenoid biosynthesis in <em>Trichoderma</em>, unlike <em>C. sinensis</em>, which utilizes both the mevalonate and non-mevalonate (MEP/DOXP) pathways. Untargeted LC-ESI-MS/MS analysis of <em>Trichoderma</em> identified 11,841 secondary metabolites, including 34 monoterpenoids, 72-diterpenoids, and 76-sesquiterpenoids, emphasizing its metabolic diversity. Comparative phylogenomic study positioned it as a phylogenetically distinct species with unique adaptive traits. Untargeted GC-MS shows high volatile abundance from microbial consortia (T5) followed by only <em>Trichoderma</em> treatment (T2) compared to control (T1). Terpenoid transcripts of <em>C. sinensis</em> from the plant-microbe consortium assembly sets illuminate upregulation of genes assigned to 3-hydroxy-3-methylglutaryl-Co-A reductase (HMGCR) and downregulation of genes assigned to 1-Deoxy-D-xylulose-5-phosphate (DXS), indicating metabolic shift towards more mevalonate pathway activity influenced by this novel <em>Trichoderma</em> strain itself and in combination with other tea root-associated microbes.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128215"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144115054","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}
Xuhang Wang , Wanqiu Lin , Linlin Ye , Xinru Chen , Jianluan Ren , Feng Xue , Jianjun Dai , Fang Tang
{"title":"Caspase-8 drove apoptosis of BMECs to promote neutrophil infiltration and DE205B clearance in meningitis","authors":"Xuhang Wang , Wanqiu Lin , Linlin Ye , Xinru Chen , Jianluan Ren , Feng Xue , Jianjun Dai , Fang Tang","doi":"10.1016/j.micres.2025.128223","DOIUrl":"10.1016/j.micres.2025.128223","url":null,"abstract":"<div><div>Avian pathogenic <em>Escherichia coli</em> (APEC), a significant virulence reservoir for human extraintestinal pathogenic <em>E. coli</em> (ExPEC), poses an escalating zoonotic risk through the food chain. Our previous study demonstrated that the poultry-derived strain DE205B shared high genetic similarity with the neonatal meningitis-associated <em>E. coli</em> (NMEC) strain RS218 and induced meningitis in a rat model. Here, we further demonstrated that DE205B crossed the blood-brain barrier (BBB) via a transcellular pathway without compromising barrier integrity. During this process, brain microvascular endothelial cells (BMECs) trigger limited RIPK1-independent apoptosis. Mechanistically, caspase-8 activation in BMECs drove the release of proinflammatory mediators, thereby promoting neutrophil recruitment into the cerebrospinal fluid (CSF). These neutrophils facilitated bacterial clearance through the formation of neutrophil extracellular traps (NETs). <em>In vivo</em> pharmacological inhibition of caspase-8 attenuated the ability of BMECs to recruit neutrophils, exacerbating meningitis progression. These findings suggested that limited apoptosis of BMECs contributed positively to APEC clearance in the brain. Collectively, this study systematically elucidated mechanisms underlying DE205B-mediated BBB invasion and host immune responses, providing insights into its cross-species pathogenic potential and zoonotic implications.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128223"},"PeriodicalIF":6.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144115548","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}
Yan Guo , Zhiying Liu , Jianfeng Wang , Xuming Deng , Liuqing He , Yong Zhang , Hongtao Liu , Jiazhang Qiu
{"title":"Equol neutralizes toxin B to combat Clostridioides difficile infection without disrupting the gut microbiota","authors":"Yan Guo , Zhiying Liu , Jianfeng Wang , Xuming Deng , Liuqing He , Yong Zhang , Hongtao Liu , Jiazhang Qiu","doi":"10.1016/j.micres.2025.128219","DOIUrl":"10.1016/j.micres.2025.128219","url":null,"abstract":"<div><div><em>Clostridioides difficile</em> (<em>C. difficile</em>) toxin B (TcdB) is essential for <em>C. difficile pathogenicity</em>. TcdB induces apoptosis in host cells by internalizing and utilizing its glycosyltransferase activity to modify members of the small GTPase protein family through glycosylation. The intestinal environment is critical for the colonization of <em>C. difficile</em>, and the use of broad-spectrum antibiotics disrupts the balance of the gut microbiota, leading to increased susceptibility of the host to <em>C. difficile</em>. At present, the mainstream clinical approach for treating <em>C. difficile</em> infection (CDI) involves antibiotic therapies such as vancomycin, which disrupt the gut microbiota and are associated with a considerable risk of infection recurrence. Therefore, there is an urgent clinical need to develop new strategies to combat CDI. Here, we have identified a natural compound, equol, which inhibits the TcdB-mediated glycosylation of Rac1 through direct interaction, thereby reducing TcdB-induced cell death. Equol functions as an inhibitor of indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO), effectively suppressing the conversion of tryptophan to kynurenine in the intestinal tract while preserving the integrity of the gut microbiota. Concurrently, equol exhibits robust antioxidant properties, which markedly reduced TcdB-mediated oxidative damage and subsequent cell death. These findings suggest that equol holds therapeutic potential for the treatment of CDI.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128219"},"PeriodicalIF":6.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143948176","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}
Juan Pablo Morán Torres, Jun Lyu, Xiaoyi Chen, Antonia M. Klaas, Peter Jan Vonk, Luis G. Lugones, Hans de Cock, Han A.B. Wösten
{"title":"Single and combinatorial gene inactivation in Aspergillus niger using selected as well as genome-wide gRNA library pools","authors":"Juan Pablo Morán Torres, Jun Lyu, Xiaoyi Chen, Antonia M. Klaas, Peter Jan Vonk, Luis G. Lugones, Hans de Cock, Han A.B. Wösten","doi":"10.1016/j.micres.2025.128204","DOIUrl":"10.1016/j.micres.2025.128204","url":null,"abstract":"<div><div><em>Aspergillus niger</em> is a saprotroph, a pathogen, an endophyte, a food spoiler and an important cell factory. Only a minor fraction of its genes has been experimentally characterized. We here set up a CRISPR/Cas9 mutagenesis screen for functional gene analysis using co-transformation of a pool of gene editing plasmids that are maintained under selection pressure and that each contain a gRNA. First, a pool of gRNA vectors was introduced in <em>A. niger</em> targeting five genes with easy selectable phenotypes. Transformants were obtained with all possible single, double, triple, quadruple and quintuple gene inactivation phenotypes. Their genotypes were confirmed using the gRNA sequences in the transforming vector as barcodes. Next, a gRNA library was introduced in <em>A. niger</em> targeting > 9600 genes. Gene <em>nsdC</em> was identified as a sporulation gene using co-transformation conditions that favored uptake of one or two gRNA construct(s) from the genome-wide vector pool. Together, CRISPR/Cas9 vectors with a (genome-wide) pool of gRNAs can be used for functional analysis of genes in <em>A. niger</em> with phenotypes that are the result of the inactivation of a single or multiple genes.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128204"},"PeriodicalIF":6.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cystathionine γ-lyase is an essential biocontrol-positive regulator of Trichoderma gamsii strain TC788","authors":"Hengxu Wang , Tianyou Zhao , Wenying Zhuang","doi":"10.1016/j.micres.2025.128218","DOIUrl":"10.1016/j.micres.2025.128218","url":null,"abstract":"<div><div>Some <em>Trichoderma</em> strains have been widely used in agriculture due to their biological control functions against plant pathogens. However, only a few intracellular biocontrol-related factors of them were explored. In this study, <em>T. gamsii</em> strain TC788 was discovered possessing comprehensive antagonistic capacity to the fungal phytopathogen <em>Rhizoctonia solani</em> causing damping-off disease of pepper, in which cystathionine γ-lyase is proved to be an essential biocontrol positive regulator as evidenced by combined analyses of transcriptome and proteome, proteins interaction network, and gene homologous recombination. Overexpression of cystathionine γ-lyase significantly up-regulated expression levels of six pathway proteins and enzyme activities of secreted proteins associated with biocontrol. It also increased contents of cysteine and hydrogen sulfide in enriched pathway of cysteine and methionine metabolism, and improved concentration of the main volatile organic compound, 6‑pentyl‑2H‑pyran‑2‑one, by 4.18 times. Pot experiments further confirmed that overexpressed strain of TC788 enhanced inhibiting ability against <em>R. solani</em>, promoted growth indicators, and induced systemic resistance of pepper seedlings compared with wild type strain. This work provides theoretical bases of biocontrol effects performed by strain TC788 against the phytopathogen, and explores preliminarily interaction between the strain and pepper plant.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128218"},"PeriodicalIF":6.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Unravelling the enzymatic wood decay repertoire of Cerrena zonata: A multi-omics approach","authors":"Niklas Broel , Franziska Daumüller , Arslan Ali , Jasmin Lemanschick , Katharina Maibach , Carolin Mewe , Boyke Bunk , Cathrin Spröer , Christiane Baschien , Holger Zorn , Hartmut Schlüter , Martin Rühl , Stefan Janssen , Martin Gand","doi":"10.1016/j.micres.2025.128214","DOIUrl":"10.1016/j.micres.2025.128214","url":null,"abstract":"<div><div>Lignocellulosic biomass (LCB), such as wheat straw, bagasse, or wood, is a cost-effective, sustainable carbon source but remains challenging to utilize due to the recalcitrance of lignin, which hinders efficient carbohydrate hydrolysis. Effective LCB degradation demands a wide range of enzymes, and commercial enzyme cocktails often require physical or chemical pretreatments. A fully enzymatic degradation could drastically improve the efficiency of these processes. Basidiomycota fungi naturally possess diverse enzymes suited for LCB breakdown. The white-rot fungus <em>Cerrena zonata</em>, a member of the phylum Basidiomycota, was analyzed for its Carbohydrate-Active Enzymes (CAZymes) using a multi-omics approach. Genomic and transcriptomic analyses of <em>C. zonata</em> identified 20,816 protein-encoding genes, including 487 CAZymes (2.3 %). Cultivating <em>C. zonata</em> with and without LCB addition revealed a total of 147 proteins, of which 36 were CAZymes (13 auxiliary activities (AA), 3 carbohydrate esterases, and 20 glycoside hydrolases). In accordance, laccase, manganese peroxidase (MnP) as well as versatile peroxidase (VP) activities were detected in the fungal culture supernatants. Furthermore, relevant enzymes were visualized via zymography. Consistent with these results, five putative peroxidases (AA2) and three putative laccases (AA1_1) were identified in all –omics dimensions. Further structure and sequence analysis of AA2 proteins supports that two proteins were classified as VPs and three as MnPs, based on their active and Mn<sup>2 +</sup> binding sites. In summary, <em>C. zonata</em> possesses a broad enzyme spectrum expressed under varied conditions, highlighting its potential for identifying efficient lignin-degrading enzymes for enzymatic pretreatment of food industry side streams and other LCBs.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128214"},"PeriodicalIF":6.1,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144068219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Organic amendments derived from Chinese herb residues enhance soil ecosystem multifunctionality by enriching key microorganisms","authors":"Peng Ren, Chuan You, Peijie Chen, Xinlan Mei, Tianjie Yang, Yangchun Xu, Xiaofang Wang, Qirong Shen, Zhong Wei","doi":"10.1016/j.micres.2025.128213","DOIUrl":"10.1016/j.micres.2025.128213","url":null,"abstract":"<div><div>Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, <em>Lysobacter</em> was enriched as a key genus. Further analysis revealed that <em>Lysobacter</em> drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.</div></div>","PeriodicalId":18564,"journal":{"name":"Microbiological research","volume":"298 ","pages":"Article 128213"},"PeriodicalIF":6.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143928273","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}