Plant-Microbe Interactome: The Green Dialogue Within the Plant Holobiont

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 1462

Special Issue Editors


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Guest Editor
Department for Sustainability, Division Sustainable Agri-Food Systems, National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, 00123 Rome, Italy
Interests: food-associated bacteria; microbial ecology; soil microorganisms; plant-growth-promoting bacteria; bacterial-host interaction; plant-microbe interactions
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Guest Editor
Department for Sustainability, Division Biotechnologies, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, 00123 Rome, Italy
Interests: plant biotechnology; genomics; plant tissue culture; genetic engineering; plant breeding

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Guest Editor
Department for Sustainability, Division Sustainable Agri-Food Systems, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, 00123 Rome, Italy
Interests: applied microbiology; microbial biotechnology; microbiology microbial ecology

Special Issue Information

Dear Colleagues,

Beneficial bacteria associated with plants are important in promoting growth and preventing disease in plants. The application of plant growth-promoting rhizobacteria (PGPR) as biofertilizers or biocontrol agents has become an effective alternative to conventional fertilizers for increasing crop productivity at a low cost. The dynamic ecological systems comprising plants and their associated microbiomes, the so-called plant holobionts, harbor untapped potential for revolutionizing agriculture. Plant–microbe interactions depend upon host plant-secreted signals and the reactions of their associated bacteria. However, the molecular mechanisms of how beneficial bacteria respond to their associated plant-derived signals are not fully understood. The complex interactions that exist between the soil microbiome and plants have a significant impact on agricultural sustainability. Factors like soil characteristics, plant species, genetics, developmental stages, and agricultural practices shape soil/root/plant microbial communities. Developing multi-omics technologies—genomics, transcriptomics, proteomics, and metabolomics, along with plant pan-genomics and metagenomics, has completely changed our ability to analyze and comprehend the dynamics between plants and microbes.

We are pleased to invite you to submit your latest research to a Special Issue titled “Plant-Microbe Interactome: The Green Dialogue Within the Plant Holobiont”, which aims to explore cutting-edge research highlighting the mechanisms governing plant holobiont interactions, offering insights into sustainable agricultural practices and environmentally friendly approaches to optimizing plant–microbe relationships. The Special Issue will focus on plant microbiome interactions and their biotechnological potential to develop novel solutions for ecosystem health and sustainable agriculture. Understanding these complex interactions has great potential to advance sustainable methods and guarantee global food security when facing environmental and climate change. In this Special Issue, original research articles and reviews are welcome. Research areas may include (but need not be limited to) the following:

  • Plant–Microbe Interactions: Investigating the complex mechanisms governing the interactions between microorganisms and plants
  • Ecology: The impact of plant microbiome interactions and technologies on plant health and ecosystem resilience.
  • Biotechnology: Applications of techniques such as metagenomics, transcriptomics, and genetic engineering, including genome editing, to analyze and manipulate both plant genotypes and soil–plant microbiomes for crop yield and stress tolerance enhancement.
  • Sustainability: Strategies for developing resilient microbial inoculants and integrating the plant microbiome interactions into sustainable agriculture

We look forward to receiving your contributions.

Prof. Dr. Annamaria Bevivino
Dr. Alessia Fiore
Dr. Silvia Tabacchioni
Guest Editors

Manuscript Submission Information

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Keywords

  • soil microbiome
  • plant holobiont
  • one health
  • sustainable agriculture

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Published Papers (2 papers)

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Research

24 pages, 3301 KB  
Article
Integrative Genomics and Metabolomics Analyses Provide New Insights into the Molecular Basis of Plant Growth Promotion by Pantoea agglomerans
by Anna Grazia Ficca, Francesca Luziatelli, Renée Abou Jaoudé and Maurizio Ruzzi
Microorganisms 2025, 13(9), 2138; https://doi.org/10.3390/microorganisms13092138 - 12 Sep 2025
Viewed by 412
Abstract
Plant Growth-Promoting Rhizobacteria (PGPR) are emerging as a sustainable alternative in agriculture due to their environmentally friendly properties and their ability to enhance crop productivity. Among these, Pantoea agglomerans has gained attention for its versatility as both a biofertilizer and a biocontrol agent. [...] Read more.
Plant Growth-Promoting Rhizobacteria (PGPR) are emerging as a sustainable alternative in agriculture due to their environmentally friendly properties and their ability to enhance crop productivity. Among these, Pantoea agglomerans has gained attention for its versatility as both a biofertilizer and a biocontrol agent. In this study, we use comparative genomics to gain insight into the genetic diversity and functional specialization of members of this species. The pan-genome analysis of 20 representative P. agglomerans strains revealed that 32% of the genes constitute the core genome (2856 out of 8899), while the remaining 68% are classified as accessory or singleton genes, indicating a high level of genomic diversity within the species. Functional annotation showed that core genes are predominantly involved in central metabolic processes, whereas genes associated with specialized metabolic functions are found within the accessory and singleton categories. The comparative analysis demonstrated a mosaic distribution of genes related to nitrogen and sulfur metabolism, heavy metal resistance, defense mechanisms, and oligopeptide uptake, suggesting niche-specific adaptations and metabolic capabilities within this species. Exometabolome profiling of strains associated with different hosts, specifically plant (C1) or human (DSM3493T), demonstrated that omics-centered approaches can be utilized to select P. agglomerans strains tailored to specific agronomic requirements. Full article
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20 pages, 6718 KB  
Article
Genetic Diversification of Tomato and Agricultural Soil Management Shaped the Rhizospheric Microbiome of Tomato (Solanum lycopersicum)
by Máximo González, Juan Pablo Araya-Angel, Ashlie Muñoz, Adalid Alfaro-Flores, Massimiliano Cardinale and Alexandra Stoll
Microorganisms 2025, 13(7), 1550; https://doi.org/10.3390/microorganisms13071550 - 1 Jul 2025
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Abstract
The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to [...] Read more.
The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. Full article
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