2012 Annual Report
1a.Objectives (from AD-416):
The long-term objective of this program is to develop biologically based technology for controlling soilborne pathogens of wheat, barley and brassica crops, grown as part of cereal-based production systems. Three specific objectives will be addressed over the next five years.
Objective 1: Evaluate the pathogenic diversity, host range, and geographical distribution of fungal and nematode root pathogens, and the influence of cropping systems on soilborne diseases.
Objective 2: Characterize microorganisms and mechanisms active in suppression of soilborne diseases.
Objective 3: Identify and characterize molecular mechanisms of host-microbe interactions, including the action of host genes governing disease resistance and biological control.
1b.Approach (from AD-416):
Biological control of soilborne fungal pathogens such as Gaeumannomyces, Rhizoctonia, Pythium, Fusarium and nematodes by naturally-occurring and genetically-altered microorganisms will be developed and quantified in agricultural soils. Molecular approaches will be used to detect and quantify soilborne pathogens and their microbial antagonists, and to characterize microbial communities in bulk soil and the rhizosphere. Genetic determinants and molecular mechanisms responsible for root colonization and pathogen suppression will be characterized with emphasis on the genetics and regulation of phenazine and phloroglucinol biosynthesis in vitro and in situ. The genetic and physiological diversity of populations of root pathogens and their microbial antagonists, and influence of cropping systems on pathogens and antagonists will be determined. Genomes of pathogens and antagonists will be analyzed. New sources and mechanisms of host resistance will be identified. Practical disease control will be accomplished by maximizing the activity of natural biocontrol agents.
Most wheat, barley and biofuel crops are infected by soilborne fungal pathogens and parasitic nematodes that reduce yields 10-30% annually. Diseased crops cannot take full advantage of fertilizers and irrigation water, and unused nitrates move into surface and ground water. The goal of this project is to develop biologically-based technology for controlling root diseases of wheat, barley and biofuel brassica crops. Progress was made on all three objectives and their subobjectives, all of which fall under National Program 303 and encompass Component 1 Problem 1, Component 2 Problem C, or Component 3 Problem B. Under Objective 1.A, we made significant progress in the development of a molecular assay for detection of the lesion nematode in soil. This research aligns with Components 1 because it describes an assay that allows rapid detection and quantification of this nematode and an assessment of risk prior to planting. Under Objectives 1.A and C, we made significant progress in identifying the distribution of the lesion nematode in dryland wheat fields and showed that populations were positively correlated with spring precipitation and negatively correlated with summer temperature. This research aligns with Component 2 Problem C because it provides new fundamental information about the ecology and epidemiology of lesion nematode, helps growers with management decisions, and prevents the unnecessary waste of inputs such as fertilizer that will not solve the problem. Under Objective 2.A, we made significant progress in identifying large, unique, widespread and genetically diverse populations of phenazine-producing bacteria on the roots of dryland wheat and showed that these bacteria can suppress root-rotting pathogens that are a major constraint to wheat production. This research aligns with Component 3 Problem B because it identifies a naturally occurring group of bacteria on wheat roots that can suppress soilborne diseases. Under Objective 1.B, we made significant progress in identifying the geographic distribution of groups of pathogenic Rhizoctonia in wheat and barley fields and showed that some groups are cosmopolitan and other are more confined to certain agronomic zones. This research aligns with Component 2 Problem C because it shows how precipitation and management practices can impact the biogeography of important pathogens of cereal, grain legume and biofuel crops in the Pacific Northwest.
Novel bacterial groups associated with natural decline of Rhizoctonia bare patch.
Rhizoctonia bare patch, caused by R. solani AG-8, causes significant reductions of yield of wheat in summer fallow areas. Over the last 14 years at a study site near Ritzville, Washington, an increase and then disappearance of this disease was observed. ARS scientists in collaboration with scientists from Washington State University used pyrosequencing to identify bacterial communities from the roots of wheat associated with this natural suppression. Members of the Sphingobacteria (Chyrseobacterium) build up to high populations on diseased roots and reduced disease in greenhouse bioassays. Knowledge of these unique bacteria can provide a tool to understand how crop rotation and other cultural practices can be manipulated to enhance this natural suppression of disease under field conditions.
Molecular diagnostic assay for Pratylenchus neglectus. Root lesion nematodes of the genus Pratylenchus affect up to 60% of dryland wheat fields and account for an estimated $51 million annual loses of wheat in the Pacific Northwest. ARS scientists at Pullman, Washington, provided expertise in molecular assay development to collaborators at Oregon State University for the design of a rapid, sensitive and specific assay for Pratylenchus neglectus. The assay was used to quantify P. neglectus populations in at-risk field soils, and the results correlated strongly with populations estimated by conventional counting methods. Researchers now have a powerful new molecular tool to use in soil surveys, to assess the risk of nematode infection in a field and to help in the screening for Pratylenchus-resistant wheat.
Comparative genomics of the Magnaporthaceae. The take-all pathogen of wheat, Gaeumannomyces graminis var. tritici (Ggt), is genetically related to the rice blast pathogen, Magnaporthe oryzae, but these two pathogens have distinct modes and sites of infection of their hosts in nature. ARS scientists at Pullman, WA in collaboration with scientists in the U.S. and Canada have compared genome sequences of Ggt, M. oryzae and M. poae, a soilborne (root) pathogen that causes summer patch of turfgrass. Homologues of M. oryzae pathogenicity and housekeeping genes were found in Ggt and M. poae, and sequence identity, position and number of introns, and other gene features indicate that Ggt and M. poae are more related to each other than either is to M. oryzae. These unexpected findings have implications for the ecological and phylogenetic relationships among the Magnaporthaceae.
Comparative genomics of new strains of biocontrol Pseudomonas. Nine new strains of Pseudomonas were found to reduce the viability of plant-parastic nematodes and suppress symptoms caused by necrotophic soilborne fungal pathogens, but nothing is known about antimicrobial genes or factors produced by these strains. ARS scientists at Pullman, Washington, in collaboration with scientists at Oregon State University have analyzed genome sequence data from six new strains. Genome organization and preliminary gene annotation indicate that the new strains are related to known biocontrol Pseudomonas, but carry unique DNA. The data contribute to an understanding of genes that distinguish biocontrol strains from phytopathogenic or degradative strains of Pseudomonas, and provide leads to nematicidal and fungicidal factors.
Irrigation differentially impacts populations of indigenous antibiotic-producing bacteria on the roots of wheat. Many microorganisms have the capacity to produce natural antibiotics that can suppress soilborne plant pathogens, but little is known about the factors that influence populations of these bacteria in the environment. ARS scientists at Pullman, Washington, in collaboration with scientists from Washington State University determined the impact of irrigation on populations of beneficial bacteria producing phenazine and phloroglucinol antibiotics on the roots of wheat grown in the low precipitation zone (5.9 to 11.8 inches annually) of the Columbia Plateau of the Inland Pacific Northwest. Only phenazine-producing bacteria were detected on dryland winter wheat, whereas phloroglucinol producers predominated on the roots of irrigated wheat. These results show how crop management practices can influence natural populations of antibiotic-producing bacteria with the capacity to suppress soilborne diseases of cereals.
Diversity of phenazine antibiotic-producing bacterial populations in dryland wheat. Certain strains of beneficial bacteria that grow on the roots of plants produce natural phenazine antibiotics that protect crop plants against a wide variety of fungal pathogens. ARS scientists at Pullman, Washington, in collaboration with scientists from Washington State University identified large, unique, widespread and genetically diverse populations of phenazine producers on the roots of dryland wheat. They showed that these bacteria can suppress root-rotting pathogens that are a major constraint to wheat production in the Inland Pacific Northwest. These bacteria, with known mechanisms of biological activity, are a valuable resource for natural disease suppression under field conditions.
Geographic distribution of Rhizoctonia solani and R. oryzae. Rhizoctonia solani and R. oryzae are soilborne pathogens that can cause serious root rots of wheat, barley, canola and other crops in cereal-based production systems in the Pacific Northwest. ARS scientists at Pullman, Washington, in collaboration with scientists from Washington State University used classical and molecular techniques to identify the geographic distribution of pathogenic Rhizoctonia in fields located throughout the Inland Pacific Northwest. The most virulent Rhizoctonia isolates on wheat, barley and canola were cosmopolitan in their distribution, however, the isolates that caused the most serious damage on wheat and barley were most commonly found in the low-precipitation zone, which receives less than 12 inches of precipitation annually. This is the first study to plot the distribution of these pathogens in the Pacific Northwest and the results help to define the risk of these pathogens throughout the region.
Distribution of root lesion nematodes in eastern Washington is associated with precipitation. Root lesion nematodes (Pratylenchus spp.) attack the roots of wheat and barley and reduce yield, but little is known about their distribution in wheat growing areas of the Pacific Northwest. ARS scientists at Pullman, Washington, conducted a survey over hundreds of kilometers in dryland wheat production areas. Higher nematode populations were found in the annually cropped, high precipitation areas. Populations were positively correlated with spring precipitation and negatively correlated with summer temperature. Knowledge of the extent of infestation will help growers with management decisions, and prevent the unnecessary waste of inputs such as fertilizer that will not solve the problem. This information will be useful for growers to predict the risk of these pathogens, and for the deployment of future resistant or tolerant varieties.
Weller, D.M., Mavrodi, D., Van Pelt, J.A., Pieterse, C.M., Van Loon, L.C., Bakker, P.A. 2012. Induced systemic resistance (ISR) in Arabidopsis thaliana against Pseudomonas syringae pv. tomato by 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens. Phytopathology. 102(4): 403-412.
Weerakoon, D.M., Reardon, C.L., Paulitz, T.C., Izzo, A., Mazzola, M. 2012. Long-term suppression of Pythium abappressorium induced by Brassica juncea seed meal amendment is biologically mediated. Soil Biology and Biochemistry. 51:44-52.
Mavrodi, D.V., Mavrodi, O.V., Parejko, J.A., Bonsall, R.F., Kwak, Y., Paulitz, T.C., Thomashow, L.S., Weller, D.M. 2012. Accumulation of the Antibiotic Phenazine-1-Carboxylic Acid in the Rhizosphere of Dryland Cereals. Applied and Environmental Microbiology. 78:804-812.
Mavrodi, O.V., Mavrodi, D.V., Parejko, J.A., Thomashow, L.S., Weller, D.M. 2012. Irrigation differentially impacts populations of indigenous antibiotic-producing Pseudomonas spp. in the rhizosphere of wheat. Applied and Environmental Microbiology. 78:3214-3220.
Parejko, J.A., Mavrodi, D.V., Mavrodi, O.V., Weller, D.M., Thomashow, L.S. 2012. Population structure and diversity of phenazine-1-carboxylic acid producing fluorescent pseudomonas spp. from dryland cereal fields of central Washington State (U.S.). Microbial Ecology. 64:226-241.
Loper, J.E., Hassan, K.A., Mavrodi, D., Davis, E.W., Lim, C., Shaffer, B.T., Elbourne, L.H., Stockwell, V.O., Hartney, S.L., Breakwell, K., Henkels, M.D., Tetu, S.G., Rangel, L.I., Kidarsa, T.A., Wilson, N.L., Van Mortel, J., Song, C., Blumhagen, R., Radune, D., Hostetler, J.B., Brinkac, L.M., Durkin, A., Kluepfel, D.A., Wechter, W.P., Anderson, A.J., Kim, Y., Pierson Iii, L.S., Pierson, E.A., Lindow, S.E., Raaijmakers, J.M., Weller, D.M., Thomashow, L.S., Allen, A.E., Paulsen, I.I. 2012. Comparative genomics of plant-associated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genetics. 8(7):e1002784.
Lee, H., Ullrich, S.E., Burke, I.C., Yenish, J., Paulitz, T.C. 2012. Interactions between the root pathogen Rhizoctonia solani AG-8 and acetolacetate synthase-inhibiting herbicides in barley. Pest Management Science. 68(6):845-852.
Maketon, C., Fortuna, A., Okubara, P.A. 2012. Cultivar-Dependent Transcript Accumulation in Wheat Roots Colonized by Pseudomonas fluorescens Q8r1-96 Wild Type and Mutant Strains. Biological Control. 60(2):216-224.
Smiley, R.W., Yan, G., Okubara, P.A. 2012. Detection and Quantification of Pratylenchus thornei in DNA Extracted from Soil Using Real-Time PCR. Phytopathology. 102(1):14-22.
Kim, S.D., De La Fuente, L., Weller, D.M., Thomashow, L.S. 2012. Colonizing ability of Pseudomonas fluorescens 2112, among collections of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens spp. in pea rhizosphere.. Journal of Microbiology and Biotechnology. 22(6):763-770.
Mavrodi, D.V., Mavrodi, O.V., Parejko, J.A., Thomashow, L.S., Weller, D.M. 2012. The Role of 2,4-diacetylphloroglucinol- and phenazine-1-carboxylic acid-producing Pseudomonas spp. in Natural Protection of Wheat from Soilborne Pathogens. Book Chapter. 267-284.
Yang, M., Mavrodi, D.V., Mavrodi, O.V., Bonsall, R.F., Pareko, J.A., Paulitz, T.C., Thomashow, L.S., Hetong, Y., Weller, D.M., Guo, J. 2011. Biological control of take-all by phenazine-producing fluorescent Pseudomonas spp. from Chinese wheat fields. Phytopathology. 101(12):1481-1491.