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Microorganisms
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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: 28 February 2025 | Viewed by 6969

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

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Published Papers (4 papers)

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Research

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28 pages, 8013 KiB  
Article
A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields
by Fangming Zhu, Takehiro Kamiya, Toru Fujiwara, Masayoshi Hashimoto, Siyu Gong, Jindong Wu, Hiromi Nakanishi and Masaru Fujimoto
Microorganisms 2025, 13(1), 41; https://doi.org/10.3390/microorganisms13010041 - 29 Dec 2024
Viewed by 819
Abstract
The assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In this study, [...] Read more.
The assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In this study, we performed amplicon sequencing targeting fungal ITS and the bacterial 16S rRNA gene to characterize and compare bacterial and fungal community dynamics of the rice root endosphere and soil in organic and conventional paddy fields. Our analysis revealed that root microbial diversity and composition was significantly influenced by agricultural practices and rice developmental stages (p < 0.05). The root microbiome in the organic paddy field showed greater temporal variability, with typical methane-oxidizing bacteria accumulating during the tillering stage and the amount of symbiotic nitrogen-fixing bacteria increasing dramatically at the early ripening stage. Redundancy analysis identified ammonium nitrogen, iron, and soil organic matter as key drivers of microbial composition. Furthermore, correlation analysis between developmental stage-enriched bacterial biomarkers in rice roots and leaf mineral nutrients showed that highly mobile macronutrient concentrations positively correlated with early-stage biomarkers and negatively correlated with later-stage biomarkers in both paddy fields. Notably, later-stage biomarkers in the conventional paddy field tended to show stronger correlations with low-mobility nutrients. These findings suggest potential strategies for optimizing microbiome management to enhance productivity and sustainability. Full article
(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)
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18 pages, 3215 KiB  
Article
Inoculation with Azospirillum brasilense as a Strategy to Reduce Nitrogen Fertilization in Cultivating Purple Maize (Zea mays L.) in the Inter-Andean Valleys of Peru
by Tatiana Condori, Susan Alarcón, Lucero Huasasquiche, Cayo García-Blásquez, César Padilla-Castro, José Velásquez and Richard Solórzano
Microorganisms 2024, 12(10), 2107; https://doi.org/10.3390/microorganisms12102107 - 21 Oct 2024
Cited by 2 | Viewed by 1163
Abstract
Purple maize has gained global significance due to its numerous nutraceutical benefits. However, sustaining its production typically requires high doses of nitrogen fertilizers, which, when applied in excess, can contaminate vital resources such as soil and water. Inoculation with nitrogen-fixing microorganisms, such as [...] Read more.
Purple maize has gained global significance due to its numerous nutraceutical benefits. However, sustaining its production typically requires high doses of nitrogen fertilizers, which, when applied in excess, can contaminate vital resources such as soil and water. Inoculation with nitrogen-fixing microorganisms, such as those from the Azospirillum genus, has emerged as an alternative to partially or fully replace nitrogen fertilizers. This study aimed to evaluate the inoculation effect with A. brasilense and varying nitrogen fertilization levels on the yield and quality of purple maize. The experiment was carried out using a randomized complete block design (RCBD) with a 2 × 5 factorial arrangement and five replications. Treatments comprised two inoculation levels (control without inoculation and inoculation with A. brasilense) under five nitrogen doses (0, 30, 60, 90, and 120 kg∙ha−1, applied as urea). Inoculation with A. brasilense resulted in a 10.5% increase in plant height, a 16.7% increase in root length, a 21.3% increase in aboveground fresh biomass, a 30.1% increase in root fresh biomass, and a 27.7% increase in leaf nitrogen concentration compared to the non-inoculated control. Regarding yield, the inoculated plants surpassed the control in both purple maize yield (kg∙ha−1) and cob weight by 21.8% and 11.6%, respectively. Across all fertilization levels and parameters assessed, the inoculated treatments outperformed the control. Furthermore, for parameters, namely plant height, leaf nitrogen content, and cob dimensions (length, diameter, and weight), the A. brasilense inoculation treatment with 90 kg N∙ha−1 was statistically equivalent or superior to the non-inoculated control with 120 kg N∙ha−1. These results indicate that inoculation with A. brasilense positively impacted purple maize at all nitrogen levels tested and improved nitrogen use efficiency, enabling a reduction of 30 kg N∙ha−1 without compromising performance in key parameters. Full article
(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)
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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 1146
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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Review

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19 pages, 839 KiB  
Review
Microbial Contributions to Heavy Metal Phytoremediation in Agricultural Soils: A Review
by Zobia Khatoon, Ma. del Carmen Orozco-Mosqueda and Gustavo Santoyo
Microorganisms 2024, 12(10), 1945; https://doi.org/10.3390/microorganisms12101945 - 25 Sep 2024
Viewed by 3149
Abstract
Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with [...] Read more.
Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with heavy metals such As, Pb, Cd, Hg, and Cr, plants can sequester, degrade, or stabilize contaminants more efficiently. Remarkably, some plant species are known for their hyper-accumulative traits in synergy with their microbial partners and can successfully mitigate heavy metal pollutants. This sustainable biotechnology based on plant–microbe associations not only aids in environmental cleanup but also enhances biodiversity, improves soil structure, and promotes plant growth and health, making it a promising solution for addressing agro-pollution challenges worldwide. The current review article emphasizes the potential of synergistic plant–microbe interactions in developing practical and sustainable solutions for heavy metal remediation in agricultural systems, which are essential for food security. Full article
(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)
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