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Microorganisms
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Microorganisms in Agriculture, 2nd Edition
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Microorganisms in Agriculture, 2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 611

Special Issue Editor

Dr. Wen-Ching Chen

E-Mail Website
Guest Editor
International Bachelor Program in Agribusiness, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 40227, Taiwan
Interests: soil remediation; soil microbiology; pesticide; environmental toxicology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, titled “Microorganisms in Agriculture”.

This Special Issue aims to explore the pivotal role of microorganisms in enhancing agricultural productivity, sustainability, and resilience. Microorganisms, including bacteria, fungi, viruses, archaea, and protozoa, play diverse and crucial roles in agricultural ecosystems, influencing soil health, plant growth, nutrient cycling, disease suppression, and overall ecosystem functioning.

In this Special Issue, original research articles, reviews, and perspectives are welcome. Research areas may include various aspects of microbial involvement in agriculture, including, but not limited to, the following:

  • Crop–Microbe Interactions: Research focusing on the symbiotic and pathogenic interactions between crops and microorganisms, including beneficial associations such as mycorrhizal symbiosis, nitrogen-fixing bacteria, and biocontrol agents against plant pathogens.
  • Microbial Biostimulants and Biofertilizers: Exploration of microbial-based products and formulations designed to enhance crop growth, nutrient uptake, stress tolerance, and overall crop productivity in sustainable agricultural practices.
  • Microbial Control of Crop Diseases: Investigations into the mechanisms underlying microbial biocontrol agents' efficacy against phytopathogens and the development of novel strategies for managing crop diseases while minimizing environmental impacts.
  • Microbial Bioremediation: Studies assessing the potential of microorganisms to degrade pollutants, detoxify soil, and mitigate environmental contamination in agricultural settings.
  • Microbial Diversity and Functional Genomics: Utilization of advanced molecular techniques and omics approaches to characterize microbial communities, identify key functional genes, and decipher metabolic pathways relevant to agricultural ecosystems.

We look forward to your submissions.

Dr. Wen-Ching Chen
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

  • bio-fertilizer
  • bio-pesticide
  • functional microbes
  • microbial ecology
  • plant growth-promoting microorganisms
  • bio-remediation

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Related Special Issue

Published Papers (2 papers)

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Research

16 pages, 3661 KiB  
Article
Effect of Rare, Locally Isolated Entomopathogenic Fungi on the Survival of Bactrocera oleae Pupae in Laboratory Soil Conditions
by Spiridon Mantzoukas, Alexandros Margaritis, Chrysanthi Zarmakoupi, Vasileios Papantzikos, Thomais Sourouni, Vasiliki Georgopoulou, Panagiotis A. Eliopoulos, Ioannis Lagogiannis and George Patakioutas
Microorganisms 2025, 13(4), 811; https://doi.org/10.3390/microorganisms13040811 - 2 Apr 2025
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Abstract
Greece’s olive oil production is significantly affected by the olive fruit fly Bactrocera oleae (Diptera: Tephritidae), and its presence is perceived when it is too late to act for damage recovery. In this work, some unexplored entomopathogenic fungi (EPFs) were studied for their [...] Read more.
Greece’s olive oil production is significantly affected by the olive fruit fly Bactrocera oleae (Diptera: Tephritidae), and its presence is perceived when it is too late to act for damage recovery. In this work, some unexplored entomopathogenic fungi (EPFs) were studied for their efficacy on olive fruit fly pupae in soil samples. Olive grove soil samples were collected to evaluate the effect of EPFs in their natural environment. The parameters that were analyzed to evaluate the performance of EPFs on B. oleae included the adult survival time, pupa hatch time, and the presence of mycelium on B. oleae pupae and dead adults. The efficacy of some EPFs was highlighted by the mycelium present on dead B. oleae adults after treating pupae with fungal isolates on the soil substrate. The results showed that for the soil substrate, external fungal growth was observed in dead adults with A. contaminans, A. keveii, A. flavus P. lilacinum, and T. annesophieae (100%). Remarkably, the lowest male proportion for soil and non-soil substrates was for A. flavus (0.41–0.42) for the first time, for A. keveii (0.36), and for P. citreosulfuratum (0.41) on the soil-only substrate in contrast to the control treatment (0.5 for both substrates). Given the high infestation caused by the olive fruit flies in Greece, the results of the study emphasize to use of incorporating certain EPF-based biopesticides into integrated pest management (IPM) programs. Full article
(This article belongs to the Special Issue Microorganisms in Agriculture, 2nd Edition)
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17 pages, 2253 KiB  
Article
Unveiling the Thermotolerance and Growth-Promoting Attributes of Endophytic Bacteria Derived from Oryza sativa: Implications for Sustainable Agriculture
by Wonder Nathi Dlamini, Wei-An Lai, Wen-Ching Chen and Fo-Ting Shen
Microorganisms 2025, 13(4), 766; https://doi.org/10.3390/microorganisms13040766 - 27 Mar 2025
Viewed by 264
Abstract
High temperatures pose significant challenges to rice plants’ growth and their associated endophytic bacteria. Understanding how these bacteria respond to heat stress is vital. We assessed the potential of five endophytic bacterial strains derived from Oryza sativa—Bacillus tequilensis LB3, B. coagulans [...] Read more.
High temperatures pose significant challenges to rice plants’ growth and their associated endophytic bacteria. Understanding how these bacteria respond to heat stress is vital. We assessed the potential of five endophytic bacterial strains derived from Oryza sativa—Bacillus tequilensis LB3, B. coagulans LB6, B. paralicheniformis AS9, B. pumilus LB16, and B. paranthracis i40C—to mitigate heat stress effects on rice plants. These strains demonstrated robust abilities in producing indole-3-acetic acid (IAA) and siderophores, nitrogen fixation, and solubilization of phosphate and potassium. Under high-temperature conditions, they significantly enhanced rice plant growth, with increases in plant length of up to 78% at 40 °C. Notably, LB6 showed the highest biomass increase (195%). The strains also improved chlorophyll SPAD values, an indicator of reduced heat stress effects and improved plant health. Phytohormone profiling and biochemical analyses revealed significant increases in abscisic acid (ABA) levels, reduced lipid peroxidation (MDA), and elevated osmoprotectant proline accumulation under heat stress. Inoculated plants exhibited up to 539 ng g−1 of ABA (vs. 62 ng g−1 in uninoculated controls), a 68% reduction in MDA (indicating less oxidative damage), and enhanced proline synthesis, collectively suggesting improved stress adaptation. These changes were linked to bacterial IAA production and nutrient modulation, which alleviated heat-induced physiological decline. These findings underscore the potential of these endophytes as biofertilizers to improve rice resilience under heat stress. Among the strains, LB6 exhibited superior performance, offering the greatest promise for heat-stress mitigation in rice production. This study advances our understanding of phytohormonal, heat stress signaling, and chemical processes underlying bacterial-mediated thermotolerance, providing a foundation for sustainable agricultural strategies. Future research can explore morphological and biochemical analyses, stress-responsive gene expression (e.g., HSPs, DREBs, and APX) linked to thermotolerance, and the combined effects of selected strains with fertilizers in high-temperature rice cultivation. Full article
(This article belongs to the Special Issue Microorganisms in Agriculture, 2nd Edition)
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