Metagenomic Analysis of Soil Microbial Communities under Regenerative and Conventional Agriculture

Abstract

Soil microbial communities are essential for maintaining ecosystem stability, nutrient cycling, agricultural productivity, and environmental sustainability. Metagenomic analysis has emerged as a powerful approach for investigating the diversity, structure, and functional potential of soil microorganisms under different agricultural systems. The present review evaluates the microbial dynamics associated with regenerative and conventional agriculture using advanced metagenomic tools including 16S rRNA sequencing and shotgun metagenomics. Findings from recent studies indicate that regenerative agricultural practices such as cover cropping, crop rotation, reduced tillage, and organic amendments significantly enhance microbial diversity, beneficial taxa abundance, nutrient cycling efficiency, and soil ecological resilience. In contrast, conventional agriculture characterized by intensive tillage and excessive chemical inputs is associated with reduced microbial diversity, increased pathogen prevalence, and enrichment of antimicrobial resistance genes. These microbial alterations have important implications for soil health, food safety, environmental quality, and public health within the One Health framework. The review highlights the importance of integrating metagenomic approaches into sustainable agricultural management and public health policy development.