Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/23/2016
Publication Date: 5/25/2016
Citation: Smiley, R.W., Machado, S., Rhinhart, K., Reardon, C.L., Wuest, S.B. 2016. Rapid quantification of soilborne pathogen communities in wheat-based long-term field experiments. Plant Disease. 100(8):1692-1708. doi: 10.1094/PDIS-09-15-1020-RE.

Interpretive Summary: Traditional methods of monitoring soil pathogens is difficult. Quantitative PCR methods have been developed to rapidly identify and quantify many of these pathogens using DNA extracted from soil. Rainfed experiments operated up to 84 years in eastern Oregon are among the oldest agronomic trials in North America. Diseases in these trials had been monitored but pathogens have not been quantified. Inoculum of fungal and nematode pathogens was evaluated using DNA extracts over a 2-year period on eight trials. The crop type influenced the amount of pathogen and in some cases which pathogen dominated in number. This DNA-based survey provided guidance for research on dynamics of root-infecting pathogens of rainfed field crops in semiarid eastern Oregon, and identified two fungal pathogens not previously known to occur at the experimental location.

Technical Abstract: Traditional isolation and quantification of inoculum density is difficult for most soilborne pathogens. Quantitative PCR methods have been developed to rapidly identify and quantify many of these pathogens using a single DNA extract from soil. Rainfed experiments operated continuously for up to 84 years in eastern Oregon are among the oldest agronomic trials in North America. Diseases in these trials had been monitored but quantification of inoculum density had not been attempted. Inoculum of fungal and nematode pathogens was evaluated using DNA extracts over a 2-year period on eight trials. Crop had a large effect on the pathogens or on pathogen species dominance. In plots were spring cereals were grown, Fusarium culmorum and Pratylenchus thornei were more dominant than F. pseudograminearum and P. neglectus. However, the opposite occurred where winter wheat was the principle crop. Bipolaris sorokiniana was only detected where spring cereals were grown, and Phoma pinodella was only found where pulse crops were either grown or where pea residue was applied to soil. Drechslera tritici-repentis was detected in wheat and in perennial pasture. Helgardia spp. occurred in winter wheat-fallow rotations but not in annual winter wheat. Inoculum of Gaeumannomyces graminis var. tritici was greater in cultivated than in non-cultivated soils and the opposite generally occurred for Rhizoctonia solani AG-8. Pythium spp. densities were high in most experiments but were strongly influenced by treatments. This DNA-based survey provided guidance for research on dynamics of root-infecting pathogens of rainfed field crops in semiarid eastern Oregon, and identified two pathogens (D. tritici-repentis and Phoma pinodella) not previously known to occur at the experimental location.