Soil Microbiome Dynamics: Catalysts of Ecosystem Services and Agricultural Resilience

Soil microbiome forms the biological core of terrestrial ecosystems, regulating processes essential for soil health, productivity, and environmental resilience. Microbial communities drive nutrient and organic matter cycling, carbon stabilization, and plant–soil interactions that underpin sustainable agriculture. Advances in molecular tools, imaging technologies, and ecological modeling have revealed the extraordinary diversity as well as structural and functional complexity of soil microbes, yet major knowledge gaps remain in how microbial communities assemble, adapt to disturbances, and respond to management practices. As agriculture faces increasing pressures from resource limitations and soil degradation, understanding microbiome dynamics has become critical for developing resilient and regenerative farming systems for sustainable agriculture. This Research Topic seeks to integrate emerging scientific insights to enhance soil health, crop performance, and agroecosystem sustainability.

The overarching goal of this Research Topic is to advance a mechanistic understanding of soil microbiome dynamics and translate that knowledge into pathways that improve soil health and agricultural resilience. Although soil microbes regulate key processes such as nutrient cycling, carbon storage, and plant stress tolerance, major challenges remain in predicting how microbial communities respond to environmental changes and management interventions, and emerging stressors. The complexity and spatial heterogeneity of soil environments make it difficult to link microbial composition to ecosystem function or to identify reliable biological indicators of soil health.

Recent advances in metagenomics, metabolomics, proteomics, micro- and nano-scale imaging, stable isotope tracing, and machine learning offer unprecedented opportunities to uncover microbial interactions and functional traits. Coupled with systems-level models and field-based experiments, these tools provide new ways to quantify microbial contributions to soil structure, greenhouse gas fluxes, pollution control and crop performance. This Research Topic aims to synthesize these advances, identify knowledge gaps, and promote integrative approaches that leverage microbiome science to guide sustainable and regenerative agricultural practices.

This Research Topic welcomes contributions that deepen our understanding of soil microbiome dynamics and their role in enhancing soil health, productivity, and agroecosystem resilience. We encourage submissions addressing themes such as microbial community assembly, plant–soil–microbe interactions, biogeochemical cycling, soil carbon stabilization, rhizosphere communities and microbial responses to conservation and regenerative management practices. Studies examining the influence of environmental stressors, soil physical structure, and landscape-scale variability on microbiome function are also welcome.

Authors may submit Original Research and Reviews, Methods papers, and/or Modeling Studies. Interdisciplinary work integrating molecular tools, advanced imaging, data-driven approaches, or ecosystem-scale experiments is strongly encouraged. Contributions that translate microbiome science into practical indicators, decision-support tools, or management strategies for sustainable agriculture are especially valued. This Research Topic aims to bring together diverse methodologies and perspectives to advance actionable, science-based insights for soil and agricultural 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
• Classification
• Data Report
• Editorial
• FAIR² Data
• 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
• Classification
• Data Report
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Soil microbiome, Soil health, Microbial ecology, Biogeochemical cycling, Plant–soil interactions, Plant-microbe interaction, Soil carbon dynamics, Agricultural resilience, Regenerative agriculture, Rhizosphere, Enzyme activities, Soil fertility

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.