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Microorganisms
Special Issues
Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere
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Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 586

Special Issue Editor

Prof. Dr. Gustavo Santoyo

E-Mail Website
Guest Editor
Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo (UMSNH), Morelia, Mexico
Interests: PGPR; plant–microbe interactions; biocontrol; plant growth promotion
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

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. To exert their beneficial functions, the microbiome can influence different interaction zones with the plant, such as the rhizosphere, endosphere and phyllosphere. Each of these plant–microbiome interaction regions has its complexities of study, and new beneficial organisms are constantly being revealed, while molecules and compounds important for communication and protection against potential pathogens are being sought. Therefore, it is imperative to review the latest advances in plant microbiome-related research, where progress is exponential.

The 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
Guest Editor

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 100 words) can be sent to the Editorial Office for announcement on this website.

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

Published Papers (1 paper)

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Research

16 pages, 3953 KiB  
Article
Domestication and Genetic Improvement Alter the Symbiotic Microbiome Structure and Function of Tomato Leaf and Fruit Pericarp
by Fei Li, Hongjun Lyu, Henan Li, Kuanling Xi, Yin Yi and Yubin Zhang
Microorganisms 2024, 12(7), 1351; https://doi.org/10.3390/microorganisms12071351 - 2 Jul 2024
Viewed by 407
Abstract
Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit [...] Read more.
Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit are rare. In this study, we generated a comprehensive dataset including the metagenomic (leaf) and metatranscriptomic (fruit pericarp in the orange stage) data of hundreds of germplasms from three tomato clades: Solanum pimpinellifolium (PIM), cherry tomato (S. lycopersicum var. cerasiforme) (CER), and S. lycopersicum group (BIG). We investigated the effect of domestication and improvement processes on the structure of the symbiotic microbiome of tomato leaf and fruit pericarp, as well as its genetic basis. We were able to obtain the composition of the symbiotic microbiome of tomato leaf and fruit pericarp, based on which the tomato clade (PIM, CER, or BIG) was predicted with high accuracy through machine learning methods. In the processes of tomato domestication and improvement, changes were observed in the relative abundance of specific bacterial taxa, Bacillus for example, in the tomato leaf and fruit pericarp symbiotic microbiomes, as well as in the function of these symbiotic microbiomes. In addition, SNP loci that were significantly associated with microbial species that are characteristic of tomato leaf were identified. Our results show that domestication and genetic improvement processes alter the symbiotic microbiome structure and function of tomato leaf and fruit pericarp. We propose that leaf and fruit microbiomes are more suitable for revealing changes in symbiotic microbiomes during the domestication process and the underlying genetic basis for these changes due to the exclusion of the influence of environmental factors such as soil types on the microbiome structure. Full article
(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)
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