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Microorganisms
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Microbiome-Driven Agriculture: Transforming Sustainability and Resilience Through Functional Microbial Insights...
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Microbiome-Driven Agriculture: Transforming Sustainability and Resilience Through Functional Microbial Insights and Metagenomics

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 9571

Special Issue Editor

Dr. Nazrul Islam

E-Mail Website
Guest Editor
Agriculture and Agri-Food Canada (AAFC), Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5, Canada
Interests: soil and crop microbiomes; sustainable agriculture; metagenomics; microbial inoculants; biofertilizers; biopesticides; nutrient cycling; disease suppression; plant growth promotion; climate change resilience; biodiversity; environmental impact; food security; farming practices
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The growing acknowledgment of soil and crop microbiomes, including bacteria, fungi, protists, and viruses, as essential elements of sustainable agriculture has spurred a revolution in agricultural practices. These microbiomes are vital in nutrient cycling, disease suppression, and plant growth promotion. As climate change imposes new challenges on agricultural systems, harnessing the potential of microbial communities becomes increasingly critical. The focus on microbiome-driven agriculture is driven by the need to enhance productivity and resilience while reducing the environmental impact of chemical-dependent traditional farming practices.

This Special Issue aims to explore how integrating functional microbial insights and metagenomics can transform agriculture. By leveraging the genetic and functional diversity within soil and crop microbiomes, researchers aim to develop targeted biofertilizers and biopesticides that reduce dependence on synthetic chemicals. This approach fosters sustainable farming systems more adaptable to environmental stressors, such as drought and disease, and helps maintain soil health and biodiversity.

The research featured in this issue demonstrates the potential of metagenomic approaches to uncover the intricate roles of microbial communities. Studies have shown that tailored microbial inoculants can improve nutrient availability and pest control. This research underscores the importance of customizing microbial solutions to specific crop, soil, and climatic conditions, optimizing their effectiveness and contributing to improved crop performance and resilience.

The primary objective of this Special Issue is to bridge the gap between microbiome science and practical agricultural applications. The issue aims to inspire innovative microbial strategies for sustainable agriculture that address modern farming challenges by presenting a collection of research articles, reviews, and case studies.

Microbiome-driven agriculture offers a promising path to achieving productive, resilient, and environmentally friendly agricultural systems. By fostering a deeper understanding of microbiome dynamics, this Special Issue seeks to inspire the development of transformative agricultural practices that promote biodiversity, reduce environmental impact, and support food security in the face of climate change.

Dr. Nazrul Islam
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

  • microbiome
  • agriculture
  • metagenomics

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Published Papers (5 papers)

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Research

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21 pages, 4731 KiB  
Article
Modulating the Plant Microbiome: Effects of Seed Inoculation with Endophytic Bacteria on Microbial Diversity and Growth Enhancement in Pea Plants
by Shervin Hadian, Donald L. Smith and Skaidrė Supronienė
Microorganisms 2025, 13(3), 570; https://doi.org/10.3390/microorganisms13030570 - 3 Mar 2025
Viewed by 917
Abstract
Understanding plant microbe interactions is crucial for achieving sustainable agriculture. This study investigated the effects of inoculating pea plants (Pisum sativum) with two endophytic Bacillus strains, AR11 and AR32, isolated from Artemisia species and characterized by phosphate solubilization, nitrogen fixation, and [...] Read more.
Understanding plant microbe interactions is crucial for achieving sustainable agriculture. This study investigated the effects of inoculating pea plants (Pisum sativum) with two endophytic Bacillus strains, AR11 and AR32, isolated from Artemisia species and characterized by phosphate solubilization, nitrogen fixation, and pathogen antagonism. Utilizing cutting-edge methods such as rarefaction curves, rank abundance modeling, and metagenomic analysis, this research provides a detailed understanding of how these bacterial strains influence plant associated microbiomes. AR11 significantly enhanced microbial diversity, while AR32 showed a moderate effect. Beta diversity analyses revealed distinct shifts in microbial community composition, with AR11-treated samples enriched with beneficial taxa such as Paenibacillus, Flavobacterium, and Methylotenera, known for their roles in nutrient cycling, pathogen suppression, and plant health promotion. This innovative methodological framework surpasses traditional approaches by offering a comprehensive view of ecological and functional microbiome shifts. The study highlights the potential of nonhost bacteria as biostimulants and their role in developing microbiome engineering strategies to enhance plant resilience. These findings contribute to sustainable agriculture by demonstrating how microbial inoculants can be employed to enhance crop productivity and environmental resilience in diverse agricultural systems. Full article
(This article belongs to the Special Issue Microbiome-Driven Agriculture: Transforming Sustainability and Resilience Through Functional Microbial Insights and Metagenomics)
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22 pages, 6678 KiB  
Article
Enhancing Bacillus thuringiensis Performance: Fertilizer-Driven Improvements in Biofilm Formation, UV Protection, and Pest Control Efficacy
by Fan Zhao, Yufei Mao, Jiahong Yang, Sheng Yang, Xiong Guan, Zixuan Wang and Tianpei Huang
Microorganisms 2025, 13(3), 499; https://doi.org/10.3390/microorganisms13030499 - 24 Feb 2025
Viewed by 729
Abstract
This study investigated the effects of fertilizers on the biofilm formation, ultraviolet (UV) resistance, and insecticidal activity of Bacillus thuringiensis (Bt). Bacillus thuringiensis, a widely used microbial pesticide, has a minimal environmental impact and is highly effective against specific pests but is [...] Read more.
This study investigated the effects of fertilizers on the biofilm formation, ultraviolet (UV) resistance, and insecticidal activity of Bacillus thuringiensis (Bt). Bacillus thuringiensis, a widely used microbial pesticide, has a minimal environmental impact and is highly effective against specific pests but is susceptible to environmental factors in field applications. Bacterial biofilms provide protection for Bt, enhancing its survival and functionality in the environment. However, the mechanisms by which fertilizers regulate the characteristics of microbial pesticides and enhance biofilm formation are not well understood. This study evaluated the effects of six fertilizers on the bacterial biofilm formation, the UV resistance, and the insecticidal activities of Bt wettable powders. The results demonstrated that fertilizers significantly enhanced the performance of three Bt preparations (Lv’an, Kang’xin, and Lu’kang). A compound fertilizer with 8.346 g/L of KCl, 2.751 g/L of ZnSO4·7H2O, and 25.681 μL/mL of humic acid was identified by response surface optimization, achieving the maximum BBF formation with OD595 value of 2.738. Furthermore, KH2PO4, HA, and ZnSO4·7H2O notably improved the survivability of Bt preparations under prolonged UV exposure, with the compound fertilizer providing the greatest protection. What’s more, fertilizers reduced the LC50 values of all Bt preparations, with the compound fertilizer decreasing the LC50 of the Lv’an Bt wettable powder to 0.139 g/L, a 3.12-fold increase in efficacy. This study demonstrated that fertilizers significantly enhance the UV resistance and insecticidal activity of Bt wettable powders by promoting bacterial biofilm formation. Herein, this study provides new strategies and theoretical support for Bt applications in modern sustainable agriculture. Full article
(This article belongs to the Special Issue Microbiome-Driven Agriculture: Transforming Sustainability and Resilience Through Functional Microbial Insights and Metagenomics)
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15 pages, 5486 KiB  
Article
Genome-Wide Identification and Analysis of Glycosyltransferases in Colletotrichum graminicola
by Yafei Wang, Honglian Li, Jiaxin Chang, Yu Zhang, Jinyao Li, Shaofeng Jia and Yan Shi
Microorganisms 2024, 12(12), 2551; https://doi.org/10.3390/microorganisms12122551 - 11 Dec 2024
Cited by 1 | Viewed by 894
Abstract
Corn leaf blight and stem rot caused by Colletotrichum graminicola are significant diseases that severely affect corn crops. Glycosyltransferases (GTs) catalyze the transfer of sugar residues to diverse receptor molecules, participating in numerous biological processes and facilitating functions ranging from structural support to [...] Read more.
Corn leaf blight and stem rot caused by Colletotrichum graminicola are significant diseases that severely affect corn crops. Glycosyltransferases (GTs) catalyze the transfer of sugar residues to diverse receptor molecules, participating in numerous biological processes and facilitating functions ranging from structural support to signal transduction. This study identified 101 GT genes through functional annotation of the C. graminicola TZ–3 genome. Subsequent analyses revealed differences among the C. graminicola GT (CgGT) genes. Investigation into subcellular localization indicated diverse locations of CgGTs within subcellular structures, while the presence of multiple domains in CgGTs suggests their involvement in diverse fungal biological processes through versatile functions. The promoter regions of CgGT genes are enriched with diverse cis-acting regulatory elements linked to responses to biotic and abiotic stresses, suggesting a key involvement of CgGT genes in the organism’s multi-faceted stress responses. Expression pattern analysis reveals that most CgGT genes were differentially expressed during the interaction between C. graminicola and corn. Integrating gene ontology functional analysis revealed that CgGTs play important roles in the interaction between C. graminicola and corn. Our research contributes to understanding the functions of CgGT genes and investigating their involvement in fungal pathogenesis. At the same time, our research has laid a solid foundation for the development of sustainable agriculture and the utilization of GT genes to develop stress-resistant and high-yield crop varieties. Full article
(This article belongs to the Special Issue Microbiome-Driven Agriculture: Transforming Sustainability and Resilience Through Functional Microbial Insights and Metagenomics)
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Review

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40 pages, 3022 KiB  
Review
Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience
by Israt Jahan Misu, Md. Omar Kayess, Md. Nurealam Siddiqui, Dipali Rani Gupta, M. Nazrul Islam and Tofazzal Islam
Microorganisms 2025, 13(2), 233; https://doi.org/10.3390/microorganisms13020233 - 22 Jan 2025
Cited by 2 | Viewed by 3973
Abstract
The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, [...] Read more.
The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts. Full article
(This article belongs to the Special Issue Microbiome-Driven Agriculture: Transforming Sustainability and Resilience Through Functional Microbial Insights and Metagenomics)
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34 pages, 3130 KiB  
Review
White Mold: A Global Threat to Crops and Key Strategies for Its Sustainable Management
by Md. Motaher Hossain, Farjana Sultana, Md. Tanbir Rubayet, Sabia Khan, Mahabuba Mostafa, Nusrat Jahan Mishu, Md. Abdullah Al Sabbir, Nabela Akter, Ahmad Kabir and Mohammad Golam Mostofa
Microorganisms 2025, 13(1), 4; https://doi.org/10.3390/microorganisms13010004 - 24 Dec 2024
Cited by 2 | Viewed by 2219
Abstract
White mold, caused by the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, is a significant biotic stress impacting horticultural and field crops worldwide. This disease causes plants to wilt and ultimately die, resulting in considerable yield losses. This monocyclic disease progresses through a [...] Read more.
White mold, caused by the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, is a significant biotic stress impacting horticultural and field crops worldwide. This disease causes plants to wilt and ultimately die, resulting in considerable yield losses. This monocyclic disease progresses through a single infection cycle involving basal infections from myceliogenically germinated sclerotia or aerial infections initiated by ascospores from carpogenically germinated sclerotia. The pathogen has a homothallic mating system with a weak population structure. Relatively cool temperatures and extended wetness are typical conditions for spreading the disease. Each stage of infection triggers a cascade of molecular and physiological events that underpin defense responses against S. sclerotiorum. Molecular markers can help rapid diagnosis of this disease in plants. Effective management strategies encompass altering the crop microclimate, applying fungicides, reducing inoculum sources, and developing resistant plant varieties. Integrated approaches combining those strategies often yield the best results. This review discusses the latest insights into the biology, epidemiology, infection mechanisms, and early detection of white mold. This review also aims to provide comprehensive guidelines for sustainable management of this destructive disease while reducing the use of excessive pesticides in crop fields. Full article
(This article belongs to the Special Issue Microbiome-Driven Agriculture: Transforming Sustainability and Resilience Through Functional Microbial Insights and Metagenomics)
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