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ARS Home » Pacific West Area » Corvallis, Oregon » Forage Seed and Cereal Research Unit » Research » Publications at this Location » Publication #419165
Research Project: Optimizing and Stabilizing Economic and Ecological Sustainability of Pacific Northwest Seed Cropping Systems Under Current and Future Climate Conditions

Location: Forage Seed and Cereal Research Unit

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

Author
item Deel, Heather
item Manter, Daniel
item Moore, Jennifer

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/4/2024
Publication Date: 12/2/2024
Citation: Deel, H.L., Manter, D.K., Moore, J.M. 2024. Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management. PLOS ONE. 19(12). Article e0314072. https://doi.org/10.1371/journal.pone.0314072.
DOI: https://doi.org/10.1371/journal.pone.0314072

Interpretive Summary: Soils are living systems containing a highly diverse community of soil microbes that provide the functions necessary to support plant productivity. In this study, we used a single cost-efficient molecular mass assay of bacterial enzymes to develop an index of soil health and function. A machine learning approach was first used to identify bacterial enzymes that were predictive of several soil physical and chemical processes across a national survey of agricultural systems from 52 different crops and 26 U.S. states. The top predictors were then combined into a single Molecular Index of Soil Health (MISH) that was related to conservation practice adoption and management strategies across this diverse dataset. This index can easily be applied to agricultural systems to identify the current functional status and health of the soil community and test new management strategies to influence soil function and health.

Technical Abstract: 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 without including molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can be helpful for guiding management practices. To explore the role of microbial function in soil health, 536 soil samples across 26 U.S. states representing 52 different crops and grazing lands were collected and analyzed for a suite of soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 for a prediction of metagenome functions. Functional data were used as predictors in an XGBoost model, 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, and several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This is a low-cost DNA-based approach to measuring soil health that is robust and generalizable across climates.