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

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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 sequencing of DNA barcodes (gene regions) that can be used to distinguish different organisms within large taxonomic groups such as soil bacteria, fungi, protists, plants, and soil insects (a process known as 'biomonitoring'). There are some gaps in our knowledge concerning how soil organisms regulate soil health, and this project aims to fill those gaps. Knowledge gaps include: (i) we lack a baseline measurement for the profile of soil organisms in agricultural soils, which is needed to establish whether farming practices such as the use of enteric seed coatings affect soil organisms that regulate soil health (ii) we lack good databases for plant weed and pest DNA barcodes for use in biomonitoring of agricultural soils, and (iii) we need to be able to link the diversity of different groups of soil organisms to specific soil ecosystem services of greatest impact on farming, such as nitrogen and phosphorus (fertilizer) nutrient cycling. We aim to fill these knowledge gaps using long-term field trials at Ridgetown (cover crops and residue retention), Elora (Conservation tillage and crop rotation) and Woodslee (crop rotation), taking samples over the course of each growing season for several years. We will use both a variety of established soil health indicators and soil quality tests (such as soil structure, bulk density, organic matter content, pH, salinity, and others), and molecular biology techniques (including biomonitoring) aimed at profiling (i) soil bacteria and archaea (ii) metazoan protists (iii) plants, including weeds, and (iv) soil fungi. Standard morphological as well as DNA barcoding techniques will also be applied to soil insects. We will analyze the collected data on soil quality and soil organism diversity using state-of-the art bioinformatic and statistical methods, in order to fill each knowledge gap.