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Microorganisms
Special Issues
Advances in Plant–Soil–Microbe Interactions
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Advances in Plant–Soil–Microbe Interactions

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 2268

Special Issue Editors

Dr. Zelaya Molina Lily Xochilt

E-Mail Website
Guest Editor
Centro Nacional de Recursos Genéticos, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Boulevard de la Biodiversidad 400, Tepatitlán de Morelos 47600, Mexico
Interests: agricultural microbiology; microbial ecology; plant growth promoters; biocontrol
Prof. Dr. Sergio de los Santos Villalobos

E-Mail Website
Guest Editor
Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, Obregón 85000, Mexico
Interests: microbial ecology of plant-growth-promoting microorganisms and biological control agents in agro-systems; genetic and functional diversity of microbial communities associated with soil, rhizosphere, and crops; crop–microorganisms interactions at physiological, metabolic, and molecular levels; agricultural soil conservation using isotopic techniques
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue will explore advances in plant–soil–microbe interactions, highlighting their critical role in terrestrial ecosystems and agriculture. It delves into the rhizosphere microbiome's influence on nutrient cycling and disease suppression, and features research on beneficial symbioses, their contribution to sustainable agriculture, and how these interactions adapt to environmental stressors. Articles studying biotechnology and microbial inoculants with which to enhance plant productivity in a changing climate are also welcome. Ultimately, this Special Issue will focus on fostering more resilient agroecosystems.

Dr. Zelaya Molina Lily Xochilt
Prof. Dr. Sergio de los Santos Villalobos
Guest Editors

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

  • plant–soil–microbe interactions
  • rhizosphere microbiome
  • sustainable agriculture
  • environmental stressors
  • microbial inoculants

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Published Papers (3 papers)

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Research

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21 pages, 1667 KB  
Article
Rhizosphere-Associated Bacteria of Saltgrass [Distichlis spicata (L.) Greene] Show Enhanced Ability to Tolerate Saline Environments and Stimulate Plant Growth
by Ángel Mena-García, Alejandro Alarcón, Fernando C. Gómez-Merino, María G. Peralta-Sánchez and Libia I. Trejo-Téllez
Microorganisms 2025, 13(9), 2046; https://doi.org/10.3390/microorganisms13092046 - 2 Sep 2025
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Abstract
The use of plant growth-promoting bacteria (PGPB) tolerant to abiotic stress factors can enhance plant performance when applied under both optimal and stress conditions in crops. In this study, bacterial strains associated with the rhizosphere of the halophyte Distichlis spicata were isolated and [...] Read more.
The use of plant growth-promoting bacteria (PGPB) tolerant to abiotic stress factors can enhance plant performance when applied under both optimal and stress conditions in crops. In this study, bacterial strains associated with the rhizosphere of the halophyte Distichlis spicata were isolated and characterized for their ability to produce siderophores, solubilize phosphate, synthesize indole-3-acetic acid (IAA) and exopolysaccharides (EPS), and tolerate salinity. IAA production and antioxidant capacity were further assessed under saline stress. As expected, salinity negatively impacted bacterial growth, IAA biosynthesis, and antioxidant activity—even in strains from a salt-tolerant plant. Nevertheless, all strains except RD2 maintained growth and IAA production in LB broth supplemented with up to 1 M NaCl. Five halotolerant strains (RD2, RD4, RD17, RD26, and RD27) were selected for greenhouse inoculation assays in tomato (Solanum lycopersicum) seedlings. Inoculation with RD26 significantly enhanced seedling performance, promoting tomato growth, increasing leaf area by 22%, stem diameter by 17%, shoot dry biomass by 30%, and root biomass by 27% as compared to the uninoculated control. RD27 and RD4 also improved shoot biomass by 25 and 23%, respectively. Based on 16S rRNA gene sequencing, RD26 was identified as Pseudomonas sp. and RD27 as Zhihengliuella halotolerans. These findings demonstrate that salt stress impairs plant growth-promoting traits in rhizospheric bacteria, yet selected strains such as RD26 and RD27 can significantly promote plant growth. Their use as bioinoculants represents a promising strategy for improving crop performance in saline environments. Full article
(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)
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18 pages, 330 KB  
Article
Bacterial Isolates from Avocado Orchards with Different Agronomic Management Systems with Potential for Promoting Plant Growth in Tomate and Phytopathogen Control
by Adilene Velázquez-Medina, Evangelina Esmeralda Quiñones-Aguilar, Ernestina Gutiérrez-Vázquez, Nuria Gómez-Dorantes, Gabriel Rincón-Enríquez and Luis López-Pérez
Microorganisms 2025, 13(9), 1974; https://doi.org/10.3390/microorganisms13091974 - 23 Aug 2025
Viewed by 668
Abstract
The bacterial diversity of soils cultivated with avocado (Persea americana M.) is influenced by different factors, perhaps the most decisive being the type of agronomic management used by farmers. In conventional agronomic management (CM), high doses of agrochemicals are applied, in contrast [...] Read more.
The bacterial diversity of soils cultivated with avocado (Persea americana M.) is influenced by different factors, perhaps the most decisive being the type of agronomic management used by farmers. In conventional agronomic management (CM), high doses of agrochemicals are applied, in contrast to organic agronomic management (OM), where organic fertilizers are used. This alters the diversity and abundance of soil microorganism populations, which in turn affects crop health. This study aimed to isolate and morphologically characterize rhizospheric bacteria from avocado trees under different agronomic management systems (CM and OM). For the bacterial isolates, their ability to promote plant growth in vitro was determined through biochemical tests for phosphorus and calcium solubilization and nitrogen fixation. In addition, their in vivo effect on tomato (S. lycopersicum) growth was evaluated, and their antagonistic capacity against Fusarium sp. was assessed. The results showed differences in the quantity, diversity, and morphologies of bacterial isolates depending on the type of agronomic management. A higher Shannon diversity index was found in OM (2.44) compared to CM (1.75). A total of 35 bacterial isolates were obtained from both management types. A greater number of isolates from OM soils exhibited in vitro PGP activity; notably, eight isolates from OM plots showed phosphate-solubilizing activity, compared to only one from CM plots. Furthermore, although all isolates demonstrated nitrogen fixing capacity, those from OM orchards produced significantly higher nitrate levels than the control (Azospirillum vinelandii). On the other hand, inoculation of tomato plants with bacterial isolates from OM soils increased plant height, root length, and total fresh and dry biomass compared to isolates from CM soils. Likewise, OM isolates exhibited greater antagonistic activity against Fusarium sp. These findings demonstrate the impact of agronomic management on soil bacterial populations and its effect on plant growth and protection against pathogens. Full article
(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

Review

Jump to: Research

15 pages, 771 KB  
Review
Trichoderma: Dual Roles in Biocontrol and Plant Growth Promotion
by Xiaoyan Chen, Yuntong Lu, Xing Liu, Yunying Gu and Fei Li
Microorganisms 2025, 13(8), 1840; https://doi.org/10.3390/microorganisms13081840 - 7 Aug 2025
Viewed by 1010
Abstract
The genus Trichoderma plays a pivotal role in sustainable agriculture through its multifaceted contributions to plant health and productivity. This review explores Trichoderma’s biological functions, including its roles as a biocontrol agent, plant growth promoter, and stress resilience enhancer. By producing various [...] Read more.
The genus Trichoderma plays a pivotal role in sustainable agriculture through its multifaceted contributions to plant health and productivity. This review explores Trichoderma’s biological functions, including its roles as a biocontrol agent, plant growth promoter, and stress resilience enhancer. By producing various enzymes, secondary metabolites, and volatile organic compounds, Trichoderma effectively suppresses plant pathogens, promotes root development, and primes plant immune responses. This review details the evolutionary adaptations of Trichoderma, which has transitioned from saprotrophism to mycoparasitism and established beneficial symbiotic relationships with plants. It also highlights the ecological versatility of Trichoderma in colonizing plant roots and improving soil health, while emphasizing its role in mitigating both biotic and abiotic stressors. With increasing recognition as a biostimulant and biocontrol agent, Trichoderma has become a key player in reducing chemical inputs and advancing eco-friendly farming practices. This review addresses challenges such as strain selection, formulation stability, and regulatory hurdles and concludes by advocating for continued research to optimize Trichoderma’s applications in addressing climate change, enhancing food security, and promoting a sustainable agricultural future. Full article
(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)
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