2012 Annual Report 1a.Objectives (from AD-416): The objectives of this cooperative research are to:. 1)genotypically and phenotypically characterize plant pathogens that cause diseases of crops grown in cereal-based cropping systems,. 2)to genotypically and phenotypically characterize microbial biocontrol agents that suppress plant pathogens in these cropping systems, and. 3)to determine the molecular genetic and biochemical basis of plant-microbe interactions and plant defense. 1b.Approach (from AD-416): Plant pathogens and their biocontrol agents will be characterized through a combination of molecular fingerprinting techniques and methods of classical plant pathology and microbiology. The population structures of pathogens and biocontrol agents will be determined by statistical analysis of DNA banding patterns generated by techniques such as rep-PCR and RAPDs, RFLPs, and AFLPs, and by sequence analysis of 16S rDNA and key genes. Results of genotypic and phenotypic analyses will be compared. Plant-microbe interactions will be characterized using a combination of laboratory, greenhouse and field studies, and molecular biology and bioanalytical tools. Biologically active metabolites produced by pathogens and antagonists will be characterized using techniques such as high performance liquid chromatography (HPLC) and mass spectrometry. 3.Progress Report: This research relates directly to Objectives 1a, b and c and 2a, b and c because it identifies the ecology of soilborne pathogens in cereal-based cropping systems and biologically based methods of control. Root diseases, including take-all, Pythium, Rhizoctonia and common root rots, and Fusarium crown rot, cause billions in losses annually to U.S. wheat and barley producers. There are no resistant varieties for most of these diseases and chemical pesticides are not available or they protect only during the seedling phase of the disease. Modern farming practices of direct seeding and intensive cereal production increase the severity of root diseases. Researchers at Washington State University, in collaboration with ARS scientists at Pullman, Washington, used a combination of molecular fingerprinting techniques, conventional and real-time Polymerase Chain Reaction(PCR) and methods of classical plant pathology and mycology to characterize the genetic diversity in populations of root pathogens including Pythium, Gaeumannomyces, Pratylenchus, Hederodera, Fusarium and Rhizoctonia that attack crops grown in cereal-based production systems. Methods to isolate fungal and nematode DNA from soil were developed and commercialized, allowing detection and quantification of pathogens in soil by using real-time PCR. The biogeography of pathogenic Rhizoctonia groups and species was determined in Inland Pacific Northwest fields; some groups were shown to be cosmopolitan and others were more limited in distribution. Rhizoctonia responsible for root rot and bare patch of wheat and barley was cosmopolitan, yet its populations were greatest in the low-precipitation zone. Population of this pathogen declined as precipitation increased, yet the take-all pathogen is more abundant in areas of high precipitation and in irrigated fields. Knowledge of pathogen population structure, virulence and distribution insures that research to develop resistant wheat, barley, and canola germplasm utilizes pathogen isolates typical of field populations. This work provides to growers rapid molecular assays and information for determining the risk from soilborne pathogens present in their fields. The antibiotic phenazine-1-carboxylic acid (PCA) was isolated from roots of wheat and barley grown in fields throughout the low precipitation zone of the Columbia Plateau. Populations of PCA-producing root—associated bacteria were greatest in the low-precipation zone and decreased with increasing precipitation and under irrigation. Current studies indicate a role for PCA in suppression of Rhizoctonia or mobilization of minerals. PCA was detected on roots of wheat throughout the growing season. PCA producing bacteria suppressed Rhizoctonia root rot of wheat when applied as a seed treatment. Collectively, these findings will hasten the development of biocontrol technology, a sustainable approach to control root diseases in cereal-based production systems.