Abstract

Agricultural soils are significant sources of greenhouse gases (GHGs), with soil microbiomes playing crucial roles in regulating the production and consumption of carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O). This comprehensive study investigated the relationship between soil microbial community structure, diversity, and GHG emissions across 150 agricultural sites representing diverse management practices, soil types, and climatic conditions. We employed high-throughput sequencing of 16S rRNA and functional genes, coupled with automated GHG flux measurements over two growing seasons. Results revealed that microbial diversity indices were negatively correlated with N₂O emissions (r = -0.68, p< 0.001) but positively associated with CH₄ oxidation potential (r = 0.54, p< 0.01). Key functional guilds, including ammonia-oxidizing bacteria (AOB), methanotrophs, and denitrifiers, showed distinct responses to soil management practices. Conservation tillage and cover cropping significantly enhanced microbial diversity and reduced net GHG emissions by 23% and 31%, respectively, compared to conventional practices. Structural equation modeling identified soil pH, organic carbon content, and microbial Shannon diversity as primary drivers of GHG fluxes. These findings provide critical insights for developing microbiome-based strategies to mitigate agricultural GHG emissions while maintaining soil health and productivity.