A High-Throughput Molecular Toolkit for Soil Health Evaluation

Soil health stems from a complex network of interconnected biological, chemical, and physical processes. Yet, biological diagnostics remain largely limited to indirect proxies with low functional resolution, obscuring the mechanistic role of microbial communities in regulating biogeochemical cycles. To bridge this gap, we developed a scalable molecular framework that quantifies functional genes and proteins of high ecological relevance. This approach elevates microbial indicators to the same analytical depth as conventional physicochemical metrics, enabling an integrated assessment grounded in ecosystem function.We designed a high-throughput panel targeting markers for key ecosystem services, including carbon, nitrogen, and phosphorus cycling, stress tolerance, and microbial interactions. A central innovation is its operational scalability: automated pipelines and standardized protocols ensure high reproducibility and lower per-sample costs, facilitating landscape-scale applications.This framework is currently deployed across diverse land-use systems, including 500,000 hectares of ecological restoration, regenerative agriculture, and integrated crop-livestock-forestry (ICLF) systems. Our results show that functional markers reveal critical shifts in nutrient cycling and energy flow, often preceding detectable changes in vegetation structure or bulk soil properties. By translating microbial traits into practical diagnostics, this framework provides a robust early-warning system for monitoring and managing soil biogeochemical functions in support of sustainable land use.