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The Molecular Basis of Plant–Microbe Interactions

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: 31 March 2025 | Viewed by 331

Special Issue Editors


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Guest Editor
Centro de Biotechnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo, 28223 Madrid, Spain
Interests: auxin biosynthesis; plant hormonal networks; auxin-jasmonate crosstalk; metabolomics; mass spectrometry
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Guest Editor
Multidisciplinary Agroindustry Research Laboratory, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Talca 3467987, Chile
Interests: controlled release; drug-delivery; hydrogels; molecular dynamics simulations; nanoencapsulation
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Instituto de Ciencias Biológicas (ICB), Universidad de Talca, Talca 3460787, Chile
Interests: plants and associated microorganisms; plant biotechnology; plant physiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants have evolved alongside a variety of microorganisms, including pathogens and beneficial microbes that support plant growth or stress tolerance. Given global climate change and its threats to food security, these beneficial microbes are vital resources for future agricultural strategies. Beneficial microorganisms interact with plant aerial organs (phyllosphere) and root systems (rhizosphere) as epiphytes or endophytes. They promote plant growth by mobilizing, transporting, and solubilizing nutrients, regulating plant physiology, and maintaining metabolism. Increasing evidence suggests comprehensive chemical communication between microbes and plants, with both producing metabolites and enzymes that influence plant immune and defense responses by regulating hormone levels and reprogramming biochemical and transcriptional pathways.

Over the past two decades, significant advancements have been made in elucidating the importance of beneficial microbes for sustainable agriculture and climate change mitigation. Soil microbiome engineering, utilizing individual microbial cultures or synthetic communities (SynComs), demonstrates potential for enhancing plant productivity under adverse conditions. However, further research is necessary for the broader applicability of this approach in agriculture.

The primary objective of this Special Issue is to provide a comprehensive overview of plant–microbe interactions and their molecular mechanisms, with a focus on the promotion of plant growth, biomass, photosynthesis, fruit development, fruit quality improvements, and the associated physiological processes, signaling pathways, and growth regulatory pathways involved. We cordially invite submissions, including original research articles and review papers, focused on this topic of significant importance to enhance human well-being.

Dr. Stephan Pollmann
Dr. Luis Morales-Quintana
Dr. Patricio Ramos
Guest Editors

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Keywords

  • plant immune and defense responses
  • microbe and microbiome function
  • microbial biodiversity
  • abiotic and biotic stress mitigation
  • gene regulatory mechanisms
  • plant hormones in plant–microbe interactions
  • molecular mechanisms of plant growth and microbe interactions
  • chemical communication in plant–microbe interactions
  • microbe effects on fruit quality
  • OMICs approaches (metagenomics, metatranscriptomics, epigenomics, transcriptomics, metabolomics)
  • bioinformatics

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Published Papers (1 paper)

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Research

26 pages, 17005 KiB  
Article
Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome
by Waqar Ahmed, Yan Wang, Wenxia Ji, Songsong Liu, Shun Zhou, Jidong Pan, Zhiguang Li, Fusheng Wang and Xinrong Wang
Int. J. Mol. Sci. 2025, 26(5), 1922; https://doi.org/10.3390/ijms26051922 (registering DOI) - 23 Feb 2025
Abstract
Endophytic Pseudomonas species from agricultural crops have been extensively studied for their plant-growth-promoting (PGP) potential, but little is known about their PGP potential when isolated from perennial trees. This study investigated the plant-growth-promoting (PGP) potential of an endophyte, Pseudomonas oryzihabitans GDW1, isolated from [...] Read more.
Endophytic Pseudomonas species from agricultural crops have been extensively studied for their plant-growth-promoting (PGP) potential, but little is known about their PGP potential when isolated from perennial trees. This study investigated the plant-growth-promoting (PGP) potential of an endophyte, Pseudomonas oryzihabitans GDW1, isolated from a healthy pine tree by taking tomato as a host plant. We employed multiomics approaches (transcriptome and bacteriome analyses) to elucidate the underlying PGP mechanisms of GDW1. The results of greenhouse experiments revealed that the application of GDW1 significantly improved tomato plant growth, increasing shoot length, root length, fresh weight, and biomass accumulation by up to 44%, 38%, 54%, and 59%, respectively, compared with control. Transcriptomic analysis revealed 1158 differentially expressed genes significantly enriched in the plant hormone signaling (auxin, gibberellin, and cytokinin) and stress response (plant–pathogen interaction, MAPK signaling pathway-plant, and phenylpropanoid biosynthesis) pathways. Protein–protein interaction network analysis revealed nine hub genes (MAPK10, ARF19-1, SlCKX1, GA2ox2, PAL5, SlWRKY37, GH3.6, XTH3, and NML1) related to stress tolerance, hormone control, and plant defense. Analysis of the tomato root bacteriome through 16S rRNA gene amplicon sequencing revealed that GDW1 inoculation dramatically altered the root bacterial community structure, enhancing the diversity and abundance of beneficial taxa (Proteobacteria and Bacteroidota). Co-occurrence network analysis showed a complex bacterial network in treated plants, suggesting increasingly intricate microbial relationships and improved nutrient absorption. Additionally, FAPROTAX and PICRUSt2 functional prediction analyses suggested the role of GDW1 in nitrogen cycling, organic matter degradation, plant growth promotion, and stress resistance. In conclusion, this study provides novel insights into the symbiotic relationship between P. oryzihabitans GDW1 and tomato plants, highlighting its potential as a biofertilizer for sustainable agriculture and a means of reducing the reliance on agrochemicals. Full article
(This article belongs to the Special Issue The Molecular Basis of Plant–Microbe Interactions)
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