Microorganisms in Agriculture, 3rd Edition

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

Deadline for manuscript submissions: 31 October 2026 | Viewed by 442

Editor


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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 Issues, entitled “Microorganisms in Agriculture” and “Microorganisms in Agriculture, 2nd Edition”.

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: Plant disease suppression, mechanisms and efficacy of biocontrol agents' against phytopathogens, development of novel strategies for managing crop diseases while minimizing environmental impacts.
  • Microbial Bioremediation in Agricultural Settings: Potential of microorganisms to degrade chemical pesticides, detoxify metals in soil, and mitigate environmental contamination.
  • Microbial Diversity and Functional Genomics: Utilization of molecular techniques and omics approaches to characterize microbial communities, identify key functional genes, and decipher metabolic pathways relevant to agricultural ecosystems.
  • Microbial Role and Sustenance with Plants in the Rhizosphere.
  • Microbes in Agricultural Products: Contamination, sanitation, farm animal and zoonotic diseases, fermentation of agricultural products, and ensilage.
  • Composting of Agricultural Residues.
  • Antibiotic and Other Antimicrobial Residues in Agricultural Soils.

We look forward to your submissions.

Dr. Wen-Ching Chen
Guest Editor

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-anonymized 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

  • biofertilizer
  • biopesticide
  • functional microbes
  • plant diseases
  • rhizosphere
  • bioremediation
  • silage

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Published Papers (1 paper)

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Research

15 pages, 1498 KB  
Article
Bacterial Community Expansion and Nutrient Activation Underlie Yield Improvement Following Diazotrophic Inoculant Application in Paddy Soil
by Huai Shi and Guohong Liu
Microorganisms 2026, 14(7), 1495; https://doi.org/10.3390/microorganisms14071495 - 8 Jul 2026
Viewed by 247
Abstract
Reducing reliance on chemical nitrogen fertilizers while maintaining rice productivity is a key challenge in sustainable agriculture. In this study, a composite inoculant of three diazotrophic strains (Paenibacillus azotifigens, Paenibacillus azotofixans, and Phytobacter diazotrophicus) was applied by root drenching [...] Read more.
Reducing reliance on chemical nitrogen fertilizers while maintaining rice productivity is a key challenge in sustainable agriculture. In this study, a composite inoculant of three diazotrophic strains (Paenibacillus azotifigens, Paenibacillus azotofixans, and Phytobacter diazotrophicus) was applied by root drenching at the heading stage of field-grown rice. Soil physicochemical properties, rice yield, and soil bacterial and fungal communities were assessed at harvest using spike-in-based absolute quantification amplicon sequencing. Inoculation increased rice yield by 5.5% and significantly elevated soil nitrate nitrogen (NO3-N) (+343%), with a trend toward higher available phosphorus, while total nitrogen, phosphorus, and carbon remained unchanged. Bacterial absolute abundance was approximately 2.6-fold higher in inoculated plots, while fungal abundance declined, resulting in a substantially elevated bacteria-to-fungi ratio; community composition and diversity indices showed no significant changes. The inoculant strains were not detectably enriched at harvest, yet functional groups associated with nitrification, nitrogen fixation, and organic matter decomposition were consistently elevated and positively associated with reactive nutrient fractions. These results suggest that diazotrophic inoculants may promote yield through transient microbial community activation and nutrient form transformation rather than persistent colonization, and highlight the value of absolute quantification for detecting inoculation-induced shifts in microbial community size. Full article
(This article belongs to the Special Issue Microorganisms in Agriculture, 3rd Edition)
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