Molecular Plant-microbe Interactions最新文献

{"title":"Modern Genomics Reshapes Soybean Cyst Nematode Research: Integrating Host Resistance, Nematode Virulence, and Functional Discovery.","authors":"Esmaeil Miraeiz, Lucas Borges Dos Santos, Matthew E Hudson","doi":"10.1094/MPMI-10-25-0150-FI","DOIUrl":"10.1094/MPMI-10-25-0150-FI","url":null,"abstract":"<p><p>The soybean cyst nematode (SCN), <i>Heterodera glycines</i>, remains the most damaging pathogen of soybean worldwide. Genomic advances over the past two decades have transformed our understanding of both the nematode and its host. On the soybean side, genome sequencing, pangenome development, and multi-omics studies have clarified how classical resistance loci such as <i>Rhg1</i> and <i>Rhg4</i> function while also revealing a broader and more complex landscape of resistance mechanisms. On the nematode side, effector discovery, high-quality genome assemblies, and evolutionary analyses have shed light on how SCN adapts to resistant cultivars and remodels host cellular processes. Despite these advances, overreliance on a single resistance source, PI 88788, continues to accelerate virulence shifts in SCN populations. This underscores the urgent need for diversified resistance, improved monitoring of nematode adaptation, and deeper mechanistic insight into the interaction. In this review, we integrate current knowledge of soybean-SCN interactions across genomics, transcriptomics, proteomics, cell biology, and microbiome research. We highlight how integrative functional genomics is reshaping the discovery of resistance genes, clarifying nematode virulence strategies, and guiding the development of more durable management approaches. Finally, we outline emerging directions, including pangenomics, dual host-pathogen analyses, and predictive breeding, that are expected to advance innovation in SCN control. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"205-220"},"PeriodicalIF":3.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Trichoderma virens</i> DM5 Against <i>Agroathelia rolfsii</i> in Tomato: A Gateway to Understanding Its Biocontrol-Biostimulant Trade-Off.","authors":"Naveen Arakkal Thaiparambil, Chien-Hua Chen, Hung-Chia Chang, Ramkumar Katturajan, Lourena Arone Maxwell","doi":"10.1094/MPMI-07-25-0075-FI","DOIUrl":"10.1094/MPMI-07-25-0075-FI","url":null,"abstract":"<p><p><i>Agroathelia rolfsii</i> causes stem rot in multiple crops, survives as sclerotia in the absence of host plants, and remains a difficult-to-manage pathogen globally. Although <i>Trichoderma</i> species offer a sustainable biocontrol solution, their dual roles as antagonists and plant biostimulants present a complex trade-off under stress conditions that remains underexplored. This study analyzed the pathogen suppression and plant growth promotion induced by <i>Trichoderma virens</i> DM5 in the context of tomato protection against <i>A</i>. <i>rolfsii</i>. Using a combination of phenotypic assays and transcriptomic analyses, we observed that <i>T</i>. <i>virens</i> DM5 suppressed <i>A. rolfsii</i> via both mycoparasitism and antibiosis, producing antifungal compounds that inhibited pathogen growth. Simultaneously, it enhanced host vigor by increasing seed germination by 54.5% and plant survival rates by 70% under pathogen pressure. Molecular analyses revealed that plants treated with <i>T</i>. <i>virens</i> DM5 exhibited rapid early activation of defense-associated pathways, including MAPK signaling, MYB transcription factors, and amino sugar metabolism within 24 h post inoculation, followed by attenuation of prolonged defense responses. These responses reduced the need for prolonged immune activation, suggesting an energy-saving strategy, allowing the plant to allocate resources toward development and survival. These findings highlight the multifaceted role of <i>T</i>. <i>virens</i> DM5 in sustaining tomato growth and disease suppression under <i>A</i>. <i>rolfsii</i>-conducive conditions. By combining direct antagonism with strategic modulation of plant defense, <i>T</i>. <i>virens</i> facilitates an optimized biocontrol-biostimulant trade-off. Understanding this interplay is critical for enhancing the efficacy of <i>Trichoderma</i>-based applications in climate-smart, sustainable agriculture. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"233-243"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145378009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Novel Genetic Resources for Broad-Based Soybean Cyst Nematode Resistance Independent of Conventional Loci.","authors":"Sushil Satish Chhapekar, Vikas Devkar, Aamir W Khan, Heng Ye, Sonam Singh, Naoufal Lakhssassi, Tri D Vuong, Khalid Meksem, Henry T Nguyen, Gunvant B Patil","doi":"10.1094/MPMI-06-25-0069-FI","DOIUrl":"10.1094/MPMI-06-25-0069-FI","url":null,"abstract":"<p><p>Soybean cyst nematode (SCN, <i>Heterodera glycines</i> Ichinohe) is the most economically damaging soilborne pathogen affecting soybean, causing significant yield losses in the United States and worldwide. Current commercial cultivars rely heavily on a limited genetic resistance base, primarily from PI 88788 and Peking, which has led to the emergence of virulent SCN populations that threaten the durability of this resistance. To address this challenge, we performed a comprehensive allelic analysis of key resistance loci (<i>rhg1</i>, <i>Rhg4</i>, <i>qSCN10</i> (<i>O</i>), and <i>qSCN18</i> (<i>G</i>)) using whole-genome resequencing data from 1,110 diverse soybean accessions. Our study identified novel nonsynonymous single-nucleotide polymorphisms in 27 accessions, including PI 602492 (<i>Glycine max</i>) and two <i>Glycine soja</i> accessions (PI 522226, PI 522228), that display strong to moderate resistance across multiple SCN HG types (<i>Heterodera glycines</i>) or SCN races. Additionally, we identified two <i>G</i>. <i>soja</i> accessions, PI 507380B and PI 507752, that exhibited strong resistance to HG type 2.5.7 (race 5). Notably, accessions with genotypes similar to these five showed variable resistance phenotypes, suggesting the presence of additional, yet unidentified, genes contributing to broad-based SCN resistance. Among these, PI 602492 stands out as a valuable new resistance source with strong activity against multiple HG types (races), making it an excellent candidate for gene discovery and breeding efforts to enhance resistance independently of conventional germplasm. These findings provide important, underutilized genetic resources that can expand the resistance base and drive the development of more durable SCN-resistant soybean cultivars. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"227-232"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145125300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Partners in Crime: Elucidating the Molecular Underpinnings of Nematode-Pathogen Disease Complexes.","authors":"Alison Blundell, Bardo Castro, Veronica I Casey, Valerie M Williamson, Shahid Siddique","doi":"10.1094/MPMI-10-25-0154-FI","DOIUrl":"10.1094/MPMI-10-25-0154-FI","url":null,"abstract":"<p><p>Plant-parasitic nematodes (PPNs) are a serious threat to global food security, with estimated annual losses exceeding $173 billion. Beyond their direct damage, interactions between PPNs and other phytopathogens can lead to synergistic relationships, referred to as disease complexes, which result in more severe symptoms than either pathogen alone. Disease complexes have been documented across diverse PPN species with distinct lifestyles, including migratory ectoparasites, migratory endoparasites, and sedentary endoparasites, and have been shown to involve partners spanning viruses, bacteria, oomycetes, and fungi. In this review, we discuss specific aspects of PPN life cycles that may facilitate disease complex formation. Nematode-induced wounding may provide entry points or release exudate signals that promote secondary pathogen infection. Nutrient-rich feeding sites established by endoparasitic nematodes may support proliferation of secondary parasites. Furthermore, certain PPN families can vector pathogens such as viruses directly into the plant via their stylet or by carrying bacteria on the cuticle surface. Finally, PPNs can suppress or evade host immune responses, thereby increasing plant susceptibility to other microbial pathogens. Elucidating the molecular mechanisms underlying these interactions will improve our understanding of disease complexes associated with PPN infection and may inform the development of novel management strategies to mitigate their impact on agricultural systems. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 \"No Rights Reserved\" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"184-191"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145708762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and Transcriptomic Insights into the Evolution and Parasitic Strategy of the Woody-Plant Nematode <i>Pratylenchus vulnus</i>.","authors":"Dadong Dai, Yali Zhang, Romnick Latina, Xuyun Yang, Valerie M Williamson, Simon C Groen, Syed Shamsullah, Charles A Leslie, Bardo Castro, Shahid Siddique","doi":"10.1094/MPMI-10-25-0133-FI","DOIUrl":"10.1094/MPMI-10-25-0133-FI","url":null,"abstract":"<p><p>The root-lesion nematode <i>Pratylenchus vulnus</i> parasitizes a wide range of hosts, including woody perennials such as walnut (<i>Juglans regia</i>) and grapevine (<i>Vitis vinifera</i>), significantly damaging roots and reducing yields. Here, we present a high-quality, chromosome-level genome assembly of <i>P</i>. <i>vulnus</i> (61.7 Mb across six chromosomes). Comparative genomic analysis revealed high collinearity in protein-coding genes between <i>P</i>. <i>vulnus</i> and the root-knot nematode included in this analysis, <i>Meloidogyne graminicola</i>, indicating a close evolutionary relationship between these genera of plant parasites. Large chromosomal regions in <i>P. vulnus</i> lack synteny with other nematode genomes, have comparatively low GC content (<30%), and are enriched in genes with unique or lineage-specific functions. Transcriptome analysis highlighted dynamic, stage-specific expression of genes involved in parasitism, development, and metabolism. Additionally, we identified an extensive repertoire of putative effector genes and characterized lineage-specific expansions of cell wall-degrading enzyme families. Overall, these findings provide insight into the genome organization, chromosome evolution, and parasitism-related gene repertoire in a woody plant-parasitizing nematode. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"265-277"},"PeriodicalIF":3.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13263060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145959868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Stress Response Kinase Cascade Is Conserved in Arabidopsis and Modulated by a Parasite Effector.","authors":"Parijat S Juvale, Gennady Pogorelko, Gaoyuan Song, Rick Masonbrink, Tom R Maier, Tarek Hewezi, Justin W Walley, Thomas J Baum","doi":"10.1094/MPMI-11-25-0159-FI","DOIUrl":"10.1094/MPMI-11-25-0159-FI","url":null,"abstract":"<p><p>We report that a novel <i>Arabidopsis thaliana</i> kinase cascade shows telltale similarities to the kinase cascades of oxidative stress response kinases (OSRKs) from humans and animals. A previously uncharacterized <i>A</i>. <i>thaliana</i> OSRK-like serine/threonine protein kinase (AtOSRK1) physically interacts with the kinase \"With No Lysine\" Kinase 5 (WNK5) and the plasma membrane-bound SNARE protein AtSYP132. The physical interaction between AtOSRK1 and AtWNK5 is governed by conserved domains also found in animal proteins; however, in all plants assayed, one of the interaction domains is found in the opposite kinase when compared with human/animal counterparts. We show that AtOSRK1 and AtWNK5 are members of a kinase cascade in which AtWNK5 phosphorylates and activates AtOSRK1, and both kinases then phosphorylate syntaxin AtSYP132. Homologous human/animal proteins have been shown to function in a strikingly similar fashion in stress responses and are involved in known inherited hypertensive disease states. We show that a novel effector protein (Hs28B03) of the plant-parasitic cyst nematode <i>Heterodera schachtii</i> specifically targets AtOSRK1 and interferes with the <i>A</i>. <i>thaliana</i> kinase cascade, resulting in a suppression of the phosphorylation of AtSYP132. <i>A</i>. <i>thaliana</i> lines constitutively expressing the <i>Hs28B03</i> coding sequence showed elevated susceptibility to the cyst nematode while also exhibiting a larger size, suggesting suppressed defense in favor of vegetative growth. These findings document a functional <i>A</i>. <i>thaliana</i> protein kinase cascade that is structurally and functionally conserved in plants and humans/animals. Furthermore, the manipulation of this kinase cascade by a parasite effector revealed a novel mechanism of parasitism influencing growth-defense tradeoffs. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"292-307"},"PeriodicalIF":3.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147434423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Symbiotic and Pathogenic Interactions in the Rhizosphere.","authors":"Tarek Hewezi, Hari B Krishnan, Kevin Garcia, Mina Ohtsu","doi":"10.1094/MPMI-04-26-0033-FI","DOIUrl":"10.1094/MPMI-04-26-0033-FI","url":null,"abstract":"<p><p>The rhizosphere is one of the most dynamic biological environments on Earth. Within this narrow zone surrounding plant roots, plants interact constantly with diverse communities of microorganisms including bacteria, fungi, oomycetes, and nematodes. These interactions range from mutually beneficial associations that enhance nutrient acquisition and stress tolerance to detrimental relationships that compromise plant health and agricultural productivity. Understanding the molecular and ecological processes governing these interactions is therefore central to plant biology and sustainable agriculture. This Focus Issue of <i>Molecular Plant-Microbe Interactions</i> brings together 14 research and review articles that explore the complex system of relationships that shape plant health in the rhizosphere. The studies span beneficial associations such as plant growth-promoting rhizobacteria and symbiotic microbes, as well as pathogenic interactions involving bacteria, fungi, oomycetes, and plant-parasitic nematodes. Collectively, these contributions highlight emerging concepts in microbial recognition, immune regulation, microbial community assembly, and effector-mediated host manipulation. By integrating perspectives from molecular genetics, functional genomics, microbiology, and ecology, this special issue highlights recent advances in our understanding of rhizosphere interactions and illustrates how these findings may inform new strategies for improving crop resilience and sustainable agricultural production. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":"39 2","pages":"154-157"},"PeriodicalIF":3.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Not All Allies Are Welcome: Partner Discrimination in Legume-Rhizobium Symbiosis.","authors":"Csaba Gellért, Niloofar Ebrahimkhalili, Shristi Siwakoti, Hongyan Zhu, Attila Kereszt","doi":"10.1094/MPMI-08-25-0108-FI","DOIUrl":"10.1094/MPMI-08-25-0108-FI","url":null,"abstract":"<p><p>The nitrogen-fixing symbiosis between leguminous plants and soil bacteria, collectively termed rhizobia, is a major contributor of fixed nitrogen to the biosphere. The ability of legumes to secure nitrogen from the atmosphere underlies their ecological success and has made them important crops in both traditional and modern sustainable agriculture. Many genes directing the establishment and functioning of this beneficial interaction have been identified under laboratory conditions using a limited number of bacterial strains and plant species in pairwise combinations. Under natural and field conditions, however, plants encounter numerous potential partners, as soil microbiomes contain diverse bacteria equipped with the necessary toolkit for symbiosis. Consequently, legumes must possess mechanisms to select for or against specific partners. This review highlights how legumes employ elements of their immune system for the negative selection of rhizobia via processes resembling the gene-for-gene model of effector-triggered immunity in plant-pathogen interactions. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"192-204"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145708775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Controlled Activation of NLR-Mediated Immunity in Roots Using a Copper-Inducible Expression System.","authors":"Hiroshi Yoshida, Kodai Honda, Saki Matsuoka, Hiroaki Adachi, Mina Ohtsu","doi":"10.1094/MPMI-11-25-0160-FI","DOIUrl":"10.1094/MPMI-11-25-0160-FI","url":null,"abstract":"<p><p>Plant nucleotide-binding leucine-rich repeat receptors (NLRs) function in both shoots and roots as key components of plant immunity, yet their biological roles in roots remain poorly understood. Here, we established a copper-inducible gene expression system for tomato (<i>Solanum lycopersicum</i>) hairy roots that enables precise, on-demand activation of immune signaling in the root tissue. The system integrates the copper-binding transcription factor CUP2, the CUP2-dependent chimeric <i>CBS4-miniDFR</i> promoter (CBS, copper-binding site; DFR, dihydroflavonol-4-reductase) driving the target gene, and a fluorescent marker for root identification, together within a single transferred DNA construct. This all-in-one vector system provided easy isolation of transgenic root cells and clear on-off control of immune activation with minimal basal expression. Using this platform, we induced autoactive NLR variants NRC4^DV-EGFP and Gpa2^NB-EGFP, which triggered reactive oxygen species accumulation and hypersensitive cell death in roots. Confocal imaging further revealed distinct subcellular dynamics of active and inactive NLRs in root cells upon induction, consistent with those in leaf cells. This system provides a robust and versatile tool for investigating root immune signaling and NLR dynamics under controlled conditions. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"221-226"},"PeriodicalIF":3.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147321805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Analysis of Rice Response to Rhizobacteria Highlights Transcriptional Signatures to Detrimental and Beneficial Interactions.","authors":"Ludivine Guigard, Eoghan King, Aurore Comte, Nicolas Busset, Anne-Alicia Gonzalez, Lionel Moulin, Pierre Czernic","doi":"10.1094/MPMI-09-25-0129-FI","DOIUrl":"10.1094/MPMI-09-25-0129-FI","url":null,"abstract":"<p><p>The microbiota of plants is composed of a large diversity of microbes, engaging with their host via various types of interactions, from beneficial to detrimental. Consequently, how plants perceive mutualistic from pathogenic microbes and which molecular pathways drive the outcome of the interaction (partnership or defense) are critical questions for the understanding of plant-microbe interactions. In this study, we evaluated the rice transcriptional response to a diversity of bacteria spanning from root pathogens to plant growth-promoting rhizobacteria (PGPRs) in hydroponic conditions. A transcriptomic analysis of rice leaf and root tissues was performed to identify common and specific transcriptional signatures during interaction with non-plant-isolated (<i>Escherichia coli</i> and <i>Stenotrophomonas maltophilia</i>), plant-isolated (<i>Pseudomonas defensor</i> and <i>Bradyrhizobium</i> sp. ORS278), or rice-isolated bacteria (<i>Azospirillum</i> sp. B510 and <i>Burkholderia plantarii</i>). Among all tested groups, the pools of differentially expressed genes (DEGs) modulated by all bacteria or by the PGPRs represented only a fraction of the total DEGs, highlighting the specificity of response to each bacterium. However, plant-isolated bacteria induced a stronger response than non-plant-isolated bacteria. The rice response to PGPRs, pertaining to growth induction and stress mitigation, allowed us to identify putative marker genes of beneficial interaction. Ten genes (such as <i>OsPR1b</i> and <i>rNBS41</i>, related to defense response) were oppositely regulated: repressed upon pathogenic and induced upon PGPR interactions. These genes could be pivotal to triggering mutualism or immunity signals. These transcriptomic clues to bacterial mitigation of rice health were confirmed in a greenhouse experiment, in which PGPRs demonstrated strong biocontrol potential against a foliar phytopathogen. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.</p>","PeriodicalId":19009,"journal":{"name":"Molecular Plant-microbe Interactions","volume":" ","pages":"308-322"},"PeriodicalIF":3.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147609512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}