Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere, Second Edition

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

Deadline for manuscript submissions: 30 September 2026 | Viewed by 597

Special Issue Editors


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Guest Editor
Department of Biochemical and Environmental Engineering, Tecnológico Nacional de México en Celaya, Celaya 38010, Mexico
Interests: environmental microbiology; sustainable agriculture; bioinoculants; PGPR; agroecology; plant-soil-microorganism interactions
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Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere” (https://www.mdpi.com/journal/microorganisms/special_issues/MRH869875D).

The role played by microorganisms and their functions in plants is relevant in various research areas, from uncovering basic communication mechanisms to field applications aimed at increasing crop production. When exerting their beneficial functions, the microbiome can influence different interaction zones with the plant, such as the rhizosphere, endosphere and phyllosphere. The study of each of these plant–microbiome interaction regions is complex, with new beneficial organisms constantly being revealed while molecules and compounds important for communication and protection against potential pathogens are sought. Therefore, it is imperative to review the latest advances in plant microbiome-related research, the progress of which is exponential.

Specific topics include, but are not limited to, new developments in the following areas:

  • Role of the microbiome and its functions in promoting plant growth and production;
  • The microbiome and its mechanisms of action against plant pathogens;
  • Induction of the plant immune system by plant-associated microorganisms;
  • Microbial consortia and their synergistic benefits in plants;
  • Application of plant growth-promoting microorganisms (PGPM) as bioinoculants;
  • Genetic regulation of plant–microbe communication;
  • Omics tools in the study of plant microbiome;
  • Root exudates as a source of microbial nutrition;
  • Diversity and modulation by biotic and abiotic factors of the plant-associated microbiome.

Prof. Dr. Gustavo Santoyo
Dr. Ma. Del Carmen Orozco-Mosqueda
Guest Editors

Manuscript Submission Information

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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. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • PGPR
  • plant–microbe interactions
  • biocontrol
  • plant growth promotion

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Published Papers (1 paper)

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Research

14 pages, 1598 KB  
Article
Shared Microbial Blueprints Underlying Symbiotic Plasticity in Desert Plant Endophytes
by Walaa K. Mousa, Ruqaia AlShami and Rose Ghemrawi
Microorganisms 2026, 14(4), 836; https://doi.org/10.3390/microorganisms14040836 - 7 Apr 2026
Viewed by 270
Abstract
The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic [...] Read more.
The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments. Full article
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