1a. Objectives (from AD-416):
The objectives of this cooperative research are: 1) to analyze the composition of wheat rhizosphere microbial communities in dryland and irrigated field soils; 2) to conduct metagenomic analysis of soil moisture-induced differences in the functional gene composition of microbial communities in the rhizosphere of field-grown wheat; and 3) to generate a high quality draft genome sequence of Pseudomonas fluorescens 2-79.
1b. Approach (from AD-416):
Global microbial community structure in the rhizosphere of wheat grown under irrigated and dryland conditions will be determined each year for two years at three time points during wheat maturation. Genes for 16S rDNA, phzF and cpn60 will be amplified by 454 Titanium pyrosequencing and the data will be deconvoluted and analyzed at Macquarie University. The results will provide information on the major phylogenetic microbial groups represented in each community, examine how each sample differs in terms of species diversity and composition, and reveal whether these differences can be correlated with soil moisture and wheat growth stage. In addition, metagenomic sequences will be determined for one sample each from the irrigated and dryland sites and analyzed to reveal soil moisture-induced differences in functional gene composition of microbial communities in the rhizosphere of field-grown wheat. Finally, DNA from the model biocontrol strain P. fluorescens 2-79 will be prepared in Pullman and sequenced at the Washington State University Genomics Core laboratory. The data will be assembled, ordered, oriented, verified, and subjected to automated annotation at Macquarie University.
3. Progress Report:
Root diseases, including take-all, Pythium, Rhizoctonia and common root rots, and Fusarium crown rot, cause $3.5 billion in losses annually to U.S. wheat and barley growers. For most of these diseases, there are no resistant varieties and chemical treatments are not available or are effective only during the seedling phase of the disease. Modern production practices of direct seeding, used to control soil erosion, exacerbates the incidence and severity of root diseases. This research focuses on fundamental microbe-plant interactions and microbial communities on the roots of wheat in order to develop effective biocontrol strategies that perform consistently against root diseases in sustainable cereal-based cropping systems. Specifically the research focuses on indigenous Pseudomonas bacteria that produce the antibiotic phenazine-1-carboxylate (PCA) on the roots of cereals grown in dryland agroecosystems, rhizosphere microbial communities that interact with PCA-producing bacteria and on Pseudomonas strain 2-79, a well-studied biocontrol agent that produces PCA and was isolated from wheat roots. The overall goal is to understand the factors leading to the enrichment of natural PCA-producing bacteria and their role in biocontrol and plant growth promotion in dryland wheat. To identify bacterial factors that contribute to the ability of PCA-producing bacteria to survive in dryland agroecosystems, researchers at Macquarie University, in collaboration with ARS scientists at Pullman, Washington, are assembling and analyzing the genomic DNA sequences of four different species of Pseudomonas, including strain 2-79, that produce PCA in soils of the Inland Pacific Northwest; and are conducting an analysis of 16S and phenazine gene sequences of microbial community DNA isolated from irrigated and non-irrigated plots located at the Washington State University's Dryland Research Station at Lind, Washington. This field study is in its third year. This research is providing wheat growers with new approaches to make use of the natural biocontrol provided by PCA-producing beneficial bacteria. This relates to Objective 2 of the parent project “Characterize microorganisms and mechanisms active in suppression of soilborne diseases”.