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New Advances in Plant–Microbe Interaction
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New Advances in Plant–Microbe Interaction

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 October 2026 | Viewed by 5052

Special Issue Editors

Dr. Raja Ben-Laouane

E-Mail Website
Guest Editor
Laboratory of Environment and Health, Department of Biology, Faculty of Sciences & Techniques, Moulay Ismail University, Errachidia 52000, Morocco
Interests: biotic and abiotic stresses; plant stress response; biofertilizers/biostimulants; PGPR; rhizobia; compost; AMF; salinity; drought; biochar
Special Issues, Collections and Topics in MDPI journals
Dr. Mohamed Ait-El-Mokhtar

E-Mail Website
Guest Editor
Department of Biology, Hassan II University of Casablanca, Casablanca 20000, Morocco
Interests: plant tolerance; biotic and abiotic stresses; biostimu-lants/biofertilizers; salinity, drought; AMF; PGPR; organic amendments
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent advances in molecular biology have considerably improved our understanding of the interactions between plants and microbes. Studies on plant microbiota reveal that complex molecular signals regulate these interactions, promoting growth and resistance to abiotic and biotic stresses. In addition, mechanisms such as signalling by bacterial and fungal effectors, and the regulation of plant defence pathways via interfering RNA, are increasingly well understood. Omics approaches are making it possible to identify the key genes involved in these interactions. These advances pave the way for applications in sustainable agriculture, notably through the use of biofertilisers and biopesticides based on optimised symbioses. This special issue of IJMS will feature original research and review articles with the aim of providing an overview of advances in the molecular basis of interactions between plants and microbes. We particularly welcome research and review articles that contribute to (but are not limited to) the following topics:

  • Molecular recognition and signalling of the microbiota
  • Regulation of plant gene expression in response to microbes
  • Microbial modulation of plant immunity
  • Molecular mechanisms of plant-microbe communication 
  • Omics approaches to the study of plant-microbe interactions 
  • Molecular interaction plants-microbes for tolerance to a/biotic stresses
  • Molecular biotechnology for improving stress resistance

Dr. Raja Ben-Laouane
Dr. Mohamed Ait-El-Mokhtar
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomarkers
  • molecular biotechnology
  • cell signalling
  • microbiota signaling
  • genetic editing of microbes
  • plant-microbe stress response
  • plant-microbe stress mitigation
  • plant-microbe underlying mechanisms

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Published Papers (6 papers)

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Research

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30 pages, 8496 KB  
Article
Integrative Exploration of Paenibacillus sp. JSM-10 as a Potential Multi-Stress-Tolerant Microbial Inoculant for Sustainable Agriculture
by Zhasmin Zhaksybek, Adel Sattarova, Ainur Akimbekova, Aldan Shamukhan, Irina Rukavitsina, Sailau Abeldenov and Anuar Rysbekovich Zhumakayev
Int. J. Mol. Sci. 2026, 27(9), 4062; https://doi.org/10.3390/ijms27094062 - 30 Apr 2026
Viewed by 19
Abstract
Abiotic stress factors, including drought and salinity, severely limit crop productivity worldwide. Furthermore, the extensive use of herbicides, such as glyphosate, disrupts beneficial soil microbiota, further impairing crop growth. Plant growth-promoting bacteria (PGPB) represent a sustainable and efficient strategy to enhance crop yields, [...] Read more.
Abiotic stress factors, including drought and salinity, severely limit crop productivity worldwide. Furthermore, the extensive use of herbicides, such as glyphosate, disrupts beneficial soil microbiota, further impairing crop growth. Plant growth-promoting bacteria (PGPB) represent a sustainable and efficient strategy to enhance crop yields, particularly under unfavorable environmental and soil conditions. In this study, we characterized Paenibacillus sp. JSM-10, newly isolated from glyphosate-exposed agricultural soil, for its stress tolerance and plant growth-promoting potential, including its morphology examined using complementary microscopy techniques. The strain tolerated up to 0.5 g/L glyphosate, 15 g/L NaCl, and 100 g/L polyethylene glycol (PEG-6000) without significant growth inhibition (p > 0.05), demonstrating robust resilience to such multiple abiotic stresses. Beyond its tolerance, the strain exhibited several beneficial characteristics, including indole-3-acetic acid (IAA) synthesis, siderophore production, and inorganic phosphate solubilization. Furthermore, both living cells and culture filtrates of JSM-10 exhibited a positive trend toward enhancing buckwheat growth under normal and saline conditions, with effect sizes ranging from Hedges’ g = 0.56−0.92. In addition, JSM-10 exhibited antagonistic activity against a range of pathogenic microorganisms, including Nigrospora oryzae, Bipolaris sorokiniana, Alternaria spp., and Escherichia coli. Altogether, these characteristics highlight the Paenibacillus sp. JSM-10 strain and its culture filtrates as promising candidates for application in organic farming aimed at promoting plant growth and improving stress tolerance via plant–microbe interactions. Full article
(This article belongs to the Special Issue New Advances in Plant–Microbe Interaction)
16 pages, 4931 KB  
Article
Fluorescence Detection of Pyrene-Stained Bacillus amyloliquefaciens MHR24 in Tomato (Solanum lycopersicum L.) Stem Tissues
by Mónica Hernández-Rodríguez, Gleb Turlakov, Celín Lozano, Eduardo Arias, Alberto Flores-Olivas, Ivana Moggio and José Humberto Valenzuela-Soto
Int. J. Mol. Sci. 2026, 27(9), 4013; https://doi.org/10.3390/ijms27094013 - 30 Apr 2026
Viewed by 29
Abstract
The PGPR strain of Bacillus amyloliquefaciens MHR24 (MHR24) was recently reported as a strong biocontrol strain. In this study, MHR24 was used to investigate phyllosphere effects during inoculations of tomato leaves (Solanum lycopersicum L.). When MHR24 was inoculated on foliar tissue, it [...] Read more.
The PGPR strain of Bacillus amyloliquefaciens MHR24 (MHR24) was recently reported as a strong biocontrol strain. In this study, MHR24 was used to investigate phyllosphere effects during inoculations of tomato leaves (Solanum lycopersicum L.). When MHR24 was inoculated on foliar tissue, it caused apical chlorosis symptoms at 3–6 days after infiltration or submersion, which suggests that the bacterium may adopt a potentially pathogenic lifestyle in the phyllosphere. In order to detect the MHR24 interaction with the plant, it was stained with the commercial fluorophore 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt, selected from a pyrene series bearing diverse functional groups, based on several in vitro staining assays. Fluorescence used as a detection signal was observed by LSCM mainly in the vascular bundles, suggesting that rhizobacteria may preferentially colonize these tissue regions. Molecular docking, performed by analyzing the possible interactions between the outer membrane protein assembly factor BamB of the family protein B. amyloliquefaciens and the fluorophore, indicates that hydrogen bonds with serine 126 (SER126), serine 182 (SER182), isoleucine 180 (ILE180), and tryptophan 66 (TRP66), charges attraction and π-stacking with TRP66, and non-bonded attractions with leucine 224 (LEU224) can occur, which likely gives rise to a stable complex. These results are important in view of the application of MHR24 as part of a sustainable approach for increasing tomato crop production. Full article
(This article belongs to the Special Issue New Advances in Plant–Microbe Interaction)
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14 pages, 1640 KB  
Article
Growth-Promoting and Quality-Enhancing Effects of Insect-Derived Serratia marcescens BRC-CXG2 on Romaine Lettuce
by Xinran Hu, Yukun Zhu, Zhao Wu, Guoxi Ji, Zhitong Lin, Moyan Wang, Fen Li, Jiaping Xu, Kaiqi Wu, Wenyu Tian and Xiaohong Han
Int. J. Mol. Sci. 2026, 27(7), 3136; https://doi.org/10.3390/ijms27073136 - 30 Mar 2026
Viewed by 328
Abstract
To explore the application potential of insect-derived functional microorganisms in short-cycle leafy vegetable production, we evaluated the effects of Serratia marcescens BRC-CXG2, isolated from larvae of Monochamus alternatus, on romaine lettuce in a pot experiment. Plant growth traits, biomass accumulation, nutritional quality, [...] Read more.
To explore the application potential of insect-derived functional microorganisms in short-cycle leafy vegetable production, we evaluated the effects of Serratia marcescens BRC-CXG2, isolated from larvae of Monochamus alternatus, on romaine lettuce in a pot experiment. Plant growth traits, biomass accumulation, nutritional quality, endogenous hormones, and rhizosphere microbial communities were systematically evaluated. The results demonstrated that inoculation significantly promoted seedling development. Plant height and root length increased by 48.7% and 29.1%, respectively, while shoot and root dry weights were 1.78- and 1.85-fold higher than those of the control. Vitamin C and total sugar contents increased by 76.4% and 98%, respectively. The levels of gibberellins (GA3)-, indole-3-acetic acid (IAA)-, and abscisic acid (ABA)-immunoreactive equivalents increased by 1.5-, 1.29-, and 1.75-fold. High-throughput 16S rDNA gene and ITS amplicon sequencing further revealed that inoculation reshaped the composition of bacterial and fungal communities in the rhizosphere. Collectively, these findings demonstrate that insect-derived S. marcescens exhibits significant growth-promoting potential in short-cycle leafy vegetable systems, with effects associated with hormone regulation, enhanced total sugar accumulation, and shifts in rhizosphere microbial community structure. Full article
(This article belongs to the Special Issue New Advances in Plant–Microbe Interaction)
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16 pages, 2041 KB  
Article
Transcriptomic and Root Microbiome Responses of Lettuce to Beneficial Endophytic Bacteria in Hydroponic Systems
by Bimal Sajeewa Amaradasa, Robert L. Chretien, Scott Lowman and Chuansheng Mei
Int. J. Mol. Sci. 2026, 27(7), 3072; https://doi.org/10.3390/ijms27073072 - 27 Mar 2026
Viewed by 437
Abstract
Controlled environment agriculture (CEA) relies on hydroponic systems to achieve high yields, yet optimizing plant performance remains a challenge. Beneficial endophytic bacteria offer a sustainable solution by promoting growth and nutrient uptake. Here, we investigated the mechanistic basis of growth enhancement in lettuce [...] Read more.
Controlled environment agriculture (CEA) relies on hydroponic systems to achieve high yields, yet optimizing plant performance remains a challenge. Beneficial endophytic bacteria offer a sustainable solution by promoting growth and nutrient uptake. Here, we investigated the mechanistic basis of growth enhancement in lettuce (Lactuca sativa) inoculated with Pseudomonas psychrotolerans IALR632 in a nutrient film technique (NFT) system. Growth measurements showed significant increases in shoot and root biomass and leaf greenness. RNA-seq profiling at 4, 10, and 15 days after transplanting revealed dynamic transcriptional reprogramming, with 38, 796, and 7642 differentially expressed genes, respectively. MapMan and GO analyses indicated up-regulation of pathways related to cell wall remodeling, lipid metabolism, nitrogen assimilation, and stress adaptation, alongside modulation of ethylene signaling. Root bacterial microbiome through 16S metabarcoding sequencing demonstrated distinct community shifts, confirmed by analysis of similarity (ANOSIM) (R = 1, p = 0.028), with enrichment of genera linked to nutrient cycling and plant growth promotion. These findings provide integrated molecular and ecological evidence that IALR632 enhances lettuce growth by coordinating host gene expression and rhizobiome restructuring, offering a mechanistic framework for microbial inoculant strategies in hydroponic horticulture. Full article
(This article belongs to the Special Issue New Advances in Plant–Microbe Interaction)
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22 pages, 4413 KB  
Article
Integrated Transcriptomic and Metabolomic Analysis Reveals the Regulation Network of CEBiP in Rice Defense Against Magnaporthe oryzae
by Qi Zheng, Jiandong Bao, Lin Li, Zifang Shen, Jiaoyu Wang, Asen Daskalov, Xueming Zhu and Fucheng Lin
Int. J. Mol. Sci. 2025, 26(11), 5194; https://doi.org/10.3390/ijms26115194 - 28 May 2025
Cited by 3 | Viewed by 1399
Abstract
Rice blast disease is a major threat to rice yields. Sustainable control relies on resistant varieties, where plant immunity is triggered by pattern recognition receptors like receptor-like proteins (RLPs). The rice RLP chitin-elicitor binding protin (CEBiP) recognizes fungal chitin and confers blast resistance [...] Read more.
Rice blast disease is a major threat to rice yields. Sustainable control relies on resistant varieties, where plant immunity is triggered by pattern recognition receptors like receptor-like proteins (RLPs). The rice RLP chitin-elicitor binding protin (CEBiP) recognizes fungal chitin and confers blast resistance to pathogen Magnaporthe oryzae. However, understanding of the broader signaling and metabolomic pathways associated with CEBiP activation remains limited. Here, we performed an integrated transcriptomic and metabolomic analysis of the rice Zhonghua 11 genotype and CEBiP knockout plants. Both plants were infected with M. oryzae, and infected leaves were harvested at 24, 48, and 72 hpi for RNA sequencing and Liquid Chromatography-Tandem Mass Spectrometry analysis. Transcriptomics identified a total of 655 genes that were differentially regulated upon knockout of CEBiP; they were mainly related to diterpenoid/phenylpropanoid biosynthesis, nitrogen metabolism, the mitogen-activated protein kinasesignaling pathway, plant–pathogen interaction, and plant hormone signal transduction. The presence of a large number of pathogenesis-related protein 1 family genes indicates the key role of salicylic acid (SA) in CEBiP immunity. Metabolomics detected a total of 962 differentially accumulated metabolites and highlights the roles of caffeine and glutathione metabolism in CEBiP-mediated immunity. Since caffeine and glutathione metabolism can regulate SA signaling, we propose that SA signaling plays a central role in the CEBiP immune function. Full article
(This article belongs to the Special Issue New Advances in Plant–Microbe Interaction)
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Review

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33 pages, 1511 KB  
Review
Nodule–Microbiome Dynamics: Deciphering the Complexities of Nodule Symbiosis and the Root Microbiome
by Raja Ben-Laouane, Mohamed Ait-El-Mokhtar, Abdelilah Meddich and Marouane Baslam
Int. J. Mol. Sci. 2026, 27(3), 1487; https://doi.org/10.3390/ijms27031487 - 2 Feb 2026
Cited by 2 | Viewed by 916
Abstract
Microbiomes play a pivotal role in sustaining plant function and broader ecosystem processes. Leguminous plants host vast populations of intracellular bacteria within specialized root organs known as nodules. The intricate mutualism between legumes and rhizobia ensures a stable supply of biologically fixed nitrogen [...] Read more.
Microbiomes play a pivotal role in sustaining plant function and broader ecosystem processes. Leguminous plants host vast populations of intracellular bacteria within specialized root organs known as nodules. The intricate mutualism between legumes and rhizobia ensures a stable supply of biologically fixed nitrogen (N) essential for plant growth. While rhizobia remain the central actors in this symbiosis, recent discoveries reveal the presence of non-rhizobial endophytes within nodules, suggesting a complex interplay shaped by host selection and compatibility with rhizobial partners. Understanding the structure and dynamics of crop nodule-associated microbial communities is thus critical for optimizing host responses to rhizobia and for leveraging beneficial plant–microbe interactions. This review explores the dualistic nature—both facilitative and inhibitory—of the nodule microbiome in relation to nodulation. We examine the diversity of soil bacteria that stimulate nodulation and those that ultimately colonize nodule tissues, questioning whether these functional groups overlap. Furthermore, we discuss the molecular dialogs and counter-signaling mechanisms that regulate endophyte ingress into nodules, and evaluate how nodule endophytes contribute to plant performance and soil fertility. Full article
(This article belongs to the Special Issue New Advances in Plant–Microbe Interaction)
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