Climate change resilience of Prairie oilseed crops and their below-ground microbiota under drought stress in controlled and field environments

Project Summary

Overview

Climate change is presenting challenges to established agronomic practices and can stretch the adaptive capacity of currently available crop cultivars due to extreme weather events such as early and intense heat and drought conditions. Adapting to such challenges within a suitable time frame will require the application of modern tools of plant breeding and genomics for plant improvement, along with the exploitation of existing breeding lines that possess inherent traits conferring resilience to such stresses. While breeding and genomic analysis remain critical tools for crop adaptation to changing conditions, it is also important to consider the contribution of the microbial species that associate with the root systems of crop plants to their resiliency.

Plants excrete compounds (exudates) from their roots that attract and enhance the growth of particular microorganisms. Thus plants modify the environment of the rhizosphere, which alters the composition of the rhizosphere microbiome. This can have detrimental or beneficial effects on the plant; these effects can include beneficial interactions that provide some level of adaptive capacity according to plant growth conditions. The microbial component of the agricultural ecosystem therefore represents a resource of genes and metabolic capabilities that must be examined alongside plant genomes to present a complete picture of the plant when grown under conditions of water stress.

The current project aims to complement a federally-funded project that will examine the adaptive capacity of existing breeding lines of canola (among other oilseed species) to conditions of drought stress. It will examine the soil, rhizosphere, and root microorganisms that are recruited by canola plants under stress conditions. In addition to relating the recruitment of microbial species to the performance of the examined lines, the project will result in the isolation by culture of microbes (or groups of microbes) that could help plants adapt to the changing conditions currently being experienced on the Canadian Prairies.

Purpose

To maximize the potential for adapting oilseed crops such as Brassica napus to such conditions, a multi-disciplinary approach must be employed that exploits the strengths of modern DNA sequencing technologies and integrates genomic analysis with studies of the microbial species that associate with the root systems of the plants. It is also critical to leverage existing efforts and research materials to provide translatable results in a relatively short time frame.

Oilseed crops including Brassica napus are the subject of a major climate change-related study funded by the federal government (Genomics Research and Development Initiative – GRDI), which will examine genomic and phenotypic aspects of drought stress in these crops.

This research will leverage these efforts, and will specifically examine the root-associated microbiota of canola under drought conditions, with a view to identifying microorganisms that are associated with, and potentially confer, enhanced drought tolerance to canola. It is anticipate that the two combined projects will result not only in the identification of B. napus lines with improved tolerance to agronomic challenges such as drought, but also in the identification and isolation of microbial species that are recruited from the soil by the plant under water-limited conditions. This may also result in improved crop cultivars as well as microbial inoculants that can enhance the performance of the most drought-tolerant lines identified in the GRDI study.

Objectives

The objectives of this project are:

1. Determination of microbial taxa associated with canola plants using natural soils under water stress.
   • Compositions of root and rhizosphere microbial communities for each line under normal and water-limited conditions will be determined using 16S/ITS amplification. This will be complemented by chaperonin-60 (cpn60) analysis as necessary to provide complete, high-resolution taxonomic profiles of the samples.
2. Determine the relationship between microbial taxa identified and phenotypic traits.
   • Relationships between microbial community structures and phenotypic traits will be determined, providing critical data on the microbial taxa recruited by crop plants for resilience to and recovery after drought stress. Strain level taxonomic data will guide culture efforts for mechanistic studies and identification and isolation of microbial inoculants.
3. Refine established methods for analysis of plant root exudates.
   • Methods for sample collection and processing will be expanded and refined to more accurately identify changes in root exudate profiles in response to drought conditions.