Location: Wheat Health, Genetics, and Quality Research
Project Number: 2090-22000-019-026-I
Project Type: Interagency Reimbursable Agreement
Start Date: Jan 1, 2026
End Date: Jul 31, 2026
Objective:
Rhizosphere microbial communities (rhizobiome) positively influence plant fitness and offer much potential for improving crop resilience to drought and diseases. However, our understanding of the mechanisms through which water-stressed plants recruit rhizobacteria and the subsequent feedbacks of the rhizobiome to plant growth and fitness remains limited. We will address these gaps by focusing on the dryland agroecosystem of the Inland Pacific Northwest. The overarching goal is to understand how water stress and crop monoculture shape the interactions between plants, microbial communities, and soilborne pathogens. We hypothesize that the dryland rhizobiome differs in metagenomic content from microbial communities of plants from well-watered soils and that the microbial adaptation to dryland conditions is mediated by changes in rhizodeposition. Our objectives are 1) to identify metagenome features associated with crop production under dryland conditions; 2) to characterize how root exudates mediate rhizosphere plant-microbe interactions under water stress; 3) to characterize the capacity of the dryland microbiome to control soilborne diseases and alleviate plant water stress.
Approach:
The project will use "omics" technologies and microbiome manipulation to determine molecular mechanisms and signal exchange involved in microbiome assembly and interactions under stress and disease.
The first Objective will characterize rhizosphere metagenome features associated with dryland conditions and determine whether different dryland crops share these features. Our approach will be to sequence rhizosphere metagenomes from
neighboring irrigated and dryland Inland Pacific Northwest fields to characterize the effect of water stress on the microbial gene content. Specifically, we will focus on the neighboring dryland and irrigated wheat plots at Lind, WA, and dryland and irrigated plots with alfalfa at Ritzville, WA. The conclusion of Objective 1 will enable us to identify pathways strongly associated with the adaptation of rhizosphere microbial communities to crop monoculture and changes in soil moisture.
The second Objective will determine how the enrichment of dryland metagenome features reflect changes in the exudation patterns observed in water-stressed plants. Our approach will be to compare root exudates of well-watered and water-stressed plants and correlate changes in the exudation patterns with shifts in the rhizosphere metagenome and metatranscriptome. The metabolome profiling will focus on exometabolites that can serve as C and N sources for rhizobacteria, in quaternary amines, amino acids, and carbohydrates that act as osmoprotectants, and in metabolites that perturb plant growth-promotion pathways.
These experiments will help to integrate the results of the microbiome studies, metagenome analysis, and metatranscriptome profiling, and to identify key metabolites and pathways that drive mutualistic interactions between plants and rhizobacteria under conditions of drought stress.
Finally, the third Objective will characterize the microbiomes of wheat and alfalfa that are subjected to abiotic stress (drought) and biotic stress (soilborne root pathogen). The approach will be to perform a greenhouse experiment that will expose plants to both stressors and assess the capacity of the dryland-adapted rhizobiome to reduce or delay symptoms of drought stress and/or disease. This approach will enable us to characterize the bacterial and fungal microbiome of wheat and alfalfa under controlled conditions, with the only two variables being drought stress and diseases. At the conclusion of these experiments, we expect to identify microbial taxa contributing to the alleviation of drought and disease stress.
Collectively, the project will identify functional pathways and metabolites involved in disease control, drought tolerance, and host-microbiome interactions.