Microbial drivers of soil health: Integrating physical, chemical and biological properties for food security under climate change

Highlights

  • •
    Climate stressors restructure soil microhabitats, reassembling microbial guilds that regulate C–N–P cycling and resilience.
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    Cross-domain feedbacks link pore architecture and soil chemistry to microbiome functions and emergent soil health outcomes.
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    Rhizosphere mechanisms (exudates, siderophores, ACC deaminase, ISR, AMF/N-fixing symbioses) provide actionable leverage points under stress.
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    Integrative indicators connect physical, chemical, and biological metrics to soil multifunctionality for monitoring under climate extremes.
  • •
    Emerging tools (meta-omics, 3D imaging, spectroscopy, isotopic tracing, in situ sensors) enable mechanistic diagnosis and decision support.

ABSTRACT

Climate change is intensifying heat, drought/flooding extremes, salinity, and CO2-driven shifts that disrupt soil structure, chemistry, and biological activity, with cascading consequences for crop productivity and food security. This review synthesizes evidence that soil health results from the interconnected interactions among physical structure (aggregation, porosity, bulk density, and pore connectivity), chemical constraints (pH, salinity, nutrient availability, cation exchange capacity, and redox heterogeneity), and biological activity (microbial biomass, diversity, and functional pathways). A central conclusion is that climate impacts are frequently mediated through pore-scale microhabitats (oxygen and moisture gradients, redox microsites, and substrate accessibility), which reorganize microbial functional guilds and regulate C-N-P transformations, organic matter turnover, and aggregation dynamics. We highlight mechanistic pathways by which microbiomes actively shape soil resilience, including EPS/biofilm-mediated aggregate stabilization, extracellular enzyme systems that control depolymerization and nutrient acquisition, and metabolite-driven nutrient mobilization (e.g., organic acids and siderophores), alongside nitrogen and phosphorus cycling processes that are highly sensitive to aeration and moisture regimes. Evidence across agroecosystems indicates that effective climate-smart soil management is most robust when “habitat-first” practices (reduced disturbance, continuous plant inputs, organic amendments) are combined with context-dependent microbiome steering (diversified rotations/cover crops and targeted inoculants). Overall, integrating cross-domain indicators with mechanistic understanding offers actionable pathways to strengthen soil multifunctionality, stabilize yields under climate variability, and support sustainable food systems.

Read full article for free (open access):
https://www.sciencedirect.com/science/article/pii/S2666517426000921



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