Evaluating soil microbes as an indicator of soil health

Soil health describes the functional characteristics of soil that have agricultural and ecological value. These soil characteristics include the potential to store carbon, retain moisture, suppress disease, prevent erosion, and mitigate greenhouse gas and other off-site pollution, in addition to sustaining crop yields in the long-term. Soil health is determined by routine testing, which would benefit from the use of microbiome analysis. Crop and soil researchers can better support agriculture with a nationwide dataset linking soil microbiome composition to soil health.

The purpose of the study was to test the predictive value of the soil microbiome for properties of soil health and identify differences in the ecological function of populations indicative of poor versus good health. Researchers collected soil health and microbiome data for 950 soil samples from agricultural sites across 40 of the contiguous states with the help of a network of trained professionals. From the samples, bacterial communities were profiled, DNA was collected, and machine learning approaches were used to determine the predictive ability of the soil microbiome. We then tested whether bacterial groups identified in these studies were predictive of or associated with soil health. We identified trends in several major bacterial populations associated with properties of soil health and in ecological traits relevant to carbon cycling. The value of leveraging publicly available data to interpret trends in microbiome data led researchers to build a database of 45 studies focused on agricultural soils and management practices, termed the ecoDB. Work to build the ecoDB is ongoing and seeks to develop a set of taxa with known ecological-attributes that are predictive of soil health.