Environmental DNA as a tool for soil health monitoring and unveiling new ecological frontiers

Soil health is essential for sustainable agricultural practices, biodiversity conservation, and ecosystem functioning. Recent advancements in environmental DNA (eDNA) technology have revolutionized soil health monitoring by enabling sensitive, non-invasive assessments of soil biodiversity. With the widespread application of eDNA technology in soils, the demand for standardized methods has increased, which determines the comparability of eDNA datasets across studies. Here, we conducted a systematic literature review of 723 peer-reviewed papers on soil eDNA published between January 2001 to September 2023, and emphasized key methodologies, challenges, and emerging trends in the field. We observed a rapid increase in the use of eDNA for soil health, with more than 700 publications on soil eDNA methods since 2001, and an annual growth rate of over 20% since 2017. eDNA has been successfully applied to detect a wide range of taxa in soil, including bacteria, fungi, and metazoans, with bacteria being the most frequently studied group, accounting for 43% of total publications. Recent eDNA research has focused on species invasion, plant-microbial interactions, and fertilizer management, with indicator-based methods increasingly employed to assess soil health. As technology and methods advance, we identified the new frontiers in eDNA research, including its role in agricultural practices, soil biodiversity and agricultural land quality improvement. Overall, the integration of eDNA with emerging technologies such as GIS and remote sensing is expected to expand its applications in soil health monitoring, providing real-time, large-scale insights into soil ecosystem health and resilience.