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

健康的土壤提供各种生态系统服务，包括营养循环、支持植物生长、调节水的储存和质量以及气候和侵蚀控制。不健康的农业土壤可能会生产更少的优质粮食或纤维，这可能会导致经济损失。土壤中的活生物是调节生态系统服务的关键组成部分，可以通过各种方式进行研究，最主要的是通过DNA条形码(基因区域)的测序，该条形码可用于区分土壤细菌、真菌、原生动物、植物和土壤昆虫等大型分类群体中的不同生物(这一过程被称为“生物监测”)。关于土壤生物如何调节土壤健康，我们的知识存在一些空白，该项目旨在填补这些空白。知识差距包括：(1)我们缺乏农业土壤中土壤生物概况的基线测量，这是确定耕作做法，例如使用肠道种衣剂是否影响调节土壤健康的土壤生物所必需的；(2)我们缺乏用于农业土壤生物监测的植物杂草和害虫DNA条形码的良好数据库；以及(3)我们需要能够将不同类型土壤生物的多样性与对农业影响最大的特定土壤生态系统服务联系起来，例如氮和磷(肥料)营养循环。我们的目标是通过在Ridgetown(覆盖作物和残茬保留)、Elora(保护性耕作和轮作)和Woodslee(轮作)的长期田间试验来填补这些知识空白，在几年的每个生长季过程中采集样本。我们将使用各种既定的土壤健康指标和土壤质量测试(如土壤结构、容重、有机质含量、pH、盐度和其他)，以及分子生物学技术(包括生物监测)，旨在分析(I)土壤细菌和古生菌(Ii)后生动物(Iii)植物(包括杂草)和(Iv)土壤真菌。标准的形态和DNA条形码技术也将应用于土壤昆虫。我们将使用最先进的生物信息学和统计学方法分析收集到的关于土壤质量和土壤生物多样性的数据，以填补每个知识空白。

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.********