Soil Health Studies Based on DNA Extraction: A Review

Soil health refers to the capacity of soil to support essential ecological functions and agricultural productivity, and it is profoundly influenced by its microbial communities. This review Synthesizes advancements in DNA extraction methods, from traditional phenol-chloroform techniques to commercial kits. (MoBio PowerSoil®) and automated systems (BioSprint 96) and their critical role in enabling robust characterization of soil microbiomes. We demonstrate that the choice of extraction protocol introduces significant biases in microbial diversity assessments, particularly affecting the recovery of fungal, archaeal, and bacterial taxa, while humic acids and methodological inconsistencies hinder cross-study comparability. Downstream analytical techniques, including amplicon sequencing (targeting 16S rRNA/ITS), shotgun metagenomics, and qPCR, reveal crucial linkages between microbial communities and soil functions such as nutrient cycling, carbon sequestration, and disease suppression. However, the efficacy of these methods depends fundamentally on initial DNA quality. Persistent challenges include the lack of standardized protocols, technical artifacts from inhibitors (humic substances), and the disconnect between molecular data and traditional soil health indices. Future progress hinges on multi-omics integration, portable field technologies, and interdisciplinary frameworks to bridge molecular insights with sustainable land management. Optimizing DNA extraction thus emerges as the cornerstone of accurate soil health evaluation and global ecosystem stewardship.