Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management

Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates.