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Developing genomics tools as indicators of soil health and sustainable productive agriculture

Principal Investigator

Kari Dunfield & Robert Hanner & Steven Newmaster

Research Institution

University of Guelph

Project Start

January 2018

Project End

February 2023


  • Determine a baseline measurement of soil biodiversity in agricultural soils;
  • Develop weed and pest databases for biomonitoring
  • Link measures of soil biodiversity to soil ecosystem services, including nutrient cycling of nitrogen and phosphorus.


  • The development of a weed biomonitoring technology tool may lead to the ability to rapidly assess the weed species present in the seedbank prior to the growing season and could become a key tool to manage herbicide resistance through Integrated Pest Management (IPM).
  • The greater understanding of soil health and soil biodiversity within the long-term research plots could be used to develop best management practices (BMPs) to maintain and improve soil health in production of grain crops, particularly in terms of intensive management practices, cover crop usage, biomass removal, seeding systems, tillage techniques, and crop rotation.
  • Improved understanding of a healthy soil microbiome in southern Ontario agricultural systems

Scientific Summary

Healthy soils provide a variety of ecosystem services, including nutrient cycling, supporting plant growth, regulating water storage and quality, and climate and erosion control. Agricultural soils which are not healthy may produce less high-quality food or fibre, and this may result in economic losses. The living organisms in soils are a key component in regulating ecosystem services, and can be studied in a variety of ways, most notably via a process known as ‘biomonitoring’ where sequencing of DNA barcodes (gene regions) can be used to distinguish different organisms, such as soil bacteria, fungi, protists, plants, and soil insects, to gain new insights into soil and plant communities. Soil health forms the basis of long-term agro-ecosystem sustainability but its characterization and quantification has been elusive. However, it is critical to integrate this genetic information with ecological and geochemical measurements so that linkages to agricultural productivity can be established. There are some gaps in our knowledge concerning how soil organisms regulate soil health, and this project aims to fill those gaps.

This project aims to test the ability to use genomics to predict soil health and agricultural sustainability of cropping systems. The research will be conducted on long-term field trials at Ridgetown (cover crops and residue retention), Elora (cover crops, conservation tillage and crop rotation) and Woodslee (crop rotation). Soil samples will be taken over the course of each growing season for several years. Samples will be tested using a variety of established soil health indicators, soil physical quality tests, and biomonitoring for soil and plant communities.   Information gathered through this project will address how soil health can directly impact agricultural productivity and if not properly managed may result in loss of farm income.

External Funding Partners

OMAFRA/University of Guelph funding partnership; Canada First Research Excellence Fund (CFREF); Natural Sciences and Engineering Research Council of Canada – Collaborative Research and Development (NSERC-CRD)