Plant and Soil Microbiomes Determining Plant Health in Agricultural Regimes

Soil microbiomes are critical determinants of plant health in agricultural systems, directly influencing nutrient uptake, stress tolerance, disease suppression, and crop productivity. As modern agriculture contends with increasing environmental pressures and the need for sustainable intensification, understanding the microbiological drivers of plant performance has become essential. Across different farming regimes—from conventional high-input systems to organic and regenerative practices—the composition and function of soil microbial communities can differ markedly.
Beneficial microbes, including plant-growth-promoting rhizobacteria (PGPR), mycorrhizal fungi, and biocontrol agents, interact with soil management practices and abiotic factors to shape plant resilience to both biotic and abiotic stresses. These interactions are especially important in determining how crops respond to fertilization, irrigation, tillage, and pesticide use. Moreover, microbial indicators such as community structure, functional gene diversity, and biogeochemical cycling potential are emerging as reliable predictors of soil health and long-term agricultural sustainability. Leveraging microbial insights in agricultural regimes holds great promise for improving soil fertility, reducing input dependency, and enhancing crop yields.

This Research Topic, Plant and Soil Microbiomes Determining Plant Health in Agricultural Regimes, aims to explore the vital role of soil microbial communities in supporting plant health across a range of agricultural regimes and environmental conditions. From conventional high-input systems to organic and regenerative practices, the composition and function of microbiomes are key to optimizing nutrient dynamics, enhancing crop resilience, and promoting sustainable productivity.
By deepening our understanding of plant-soil-microbe interactions, this topic seeks to uncover how management practices influence microbial communities and how these, in turn, shape plant responses to biotic and abiotic stresses. We invite contributions that offer novel insights into leveraging soil microbiomes for improved soil fertility, reduced chemical inputs, climate resilience, and long-term sustainability in farming systems.
Researchers from microbiology, plant science, agronomy, and environmental science are encouraged to submit original research, reviews, and perspectives that advance our collective understanding of microbiome-driven solutions in agriculture. We look forward to your contributions and to advancing the dialogue on how soil microbiology is reshaping the future of plant health and sustainable agriculture.

This Research Topic will bring together cutting-edge research on how soil microbial communities drive plant health across diverse agricultural regimes. From intensively managed farmlands to regenerative systems and marginal soils, we seek contributions that enhance our understanding of the complex, dynamic interactions among plants, soils, and microbiomes in cultivated ecosystems.
We welcome submissions on a broad range of topics, including:
• The role of soil and plant microbiomes in enhancing crop health and resilience under varied agricultural practices and environmental conditions
• Microbial mechanisms contributing to nutrient cycling, soil fertility, and natural suppression of plant diseases
• Impacts of land-use changes, farming systems, and climate variability on soil microbial composition and function
• Innovations in microbiome engineering, biocontrol applications, and microbial inoculants aimed at improving agricultural sustainability
• Integration of multi-omics technologies to decode soil-plant-microbiome interactions in managed cropping systems

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• Methods
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Microbiomes, Next Generation Sequencing, Environmental Stresses, Phytohormone, Soil Characteristics, Plant Health, Competition, Pathogen invasion

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.