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United States Department of Agriculture

Agricultural Research Service

Research Project: Biology and Biological Control of Root Diseases of Wheat, Barley and Biofuel Brassicas

Location: Wheat Health, Genetics, and Quality Research

2013 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.

3. Progress Report:
Wheat, barley and biofuel crops are infected by soilborne pathogens 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 NP 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 cereal cyst nematode. This research aligns with Component 1 because it describes an assay that allows quantification of the nematode and an assessment of risk prior to planting. Under Objectives 1.A and C, we made significant progress in identifying the distribution of Fusarium crown rot in dryland wheat. We described the distribution of Fusarium pseudograminearum, F. culmorum and crown rot disease throughout the dryland Pacific Northwest (PNW)and modeled the relationship of these distributions with climatic factors. F. pseudograminearum was more widespread in hotter, drier areas and F. culmorum was more dominant in cooler, wetter areas at higher elevation. This research aligns with Component 2 Problem C because it provides new information about the ecology and epidemiology of Fusarium crown rot, helps growers with management decisions, and prevents the waste of inputs like fertilizer that will not solve the problem. Under Objective 2.A, we made significant progress in identifying large and genetically diverse populations of phenazine-producing bacteria on the roots of dryland wheat, demonstrated that they belong to four Pseudomonas species, and showed that they suppress soilborne pathogens by producing a phenazine antibiotic. This research aligns with Component 3 Problem B because it identifies a group of bacteria that can suppress soilborne diseases. Under Objectives 1.B, we made significant progress in identifying the geographic distribution of groups of pathogenic Rhizoctonia and Pythium in wheat and barley fields and showed that some groups are widespread, while others are more confined to certain agronomic zones. This research was expanded to pea and onion, crops grown with irrigation in rotation with wheat. The role of wheat in the etiology of Rhizoctonia on pea and onion is being elucidated. This research aligns with Component 2 Problem Statement 2C because it shows how management practices can impact the biogeography of pathogens of cereal, grain legume and biofuel crops. Under Objective 1.C, we solved an acute problem of low-pH soils and aluminum toxicity occurring on over 50,000 acres, such that wheat can’t be grown. With breeders, we identified aluminum tolerant cultivars adapted to the PNW. With soil scientists, we developed strategies to reverse the decline in soil pH. This research aligns with Component 3, Problem Statements 3A and 3B, since it uses both plant genetics and cultural practices to solve this abiotic problem.

4. Accomplishments
1. Distribution of Fusarium crown rot of wheat in the Pacific Northwest is associated with climatic factors. Fusarium culmorum and F. pseudograminearum cause Fusarium crown rot, which can reduce yield from 9-35%, but little is known about their distribution in wheat growing areas of the Pacific Northwest. ARS scientists at Pullman, Washington, conducted a two-year survey over hundreds of kilometers in dryland wheat production areas. Using regional climate data, logistic models and factor analysis, they showed that F. culmorum is associated with cooler areas with higher precipitation, whereas F. pseudograminearum is more predominate in drier, hotter areas. This information will be useful for growers to predict the risk of these pathogens, and for the deployment of future resistant or tolerant varieties. In addition, this information will be useful for predicting distributions under future climate change scenarios.

2. Crop genetics is a solution for acid soils and aluminum toxicity. Since 2007, ARS scientists at Pullman, Washington, have shown that low pH (of about 4) and aluminum toxicity affects over 50,000 acres of wheat in Spokane County, Washington and Latah County, Idaho, resulting in up to 90% yield losses. Grower’s only options have been to grow triticale or heavily lime the soil, which is not economical. ARS scientists, in collaboration with scientists at Washington State University, tested adapted wheat varieties, and identified several with tolerance to Al and significantly improved yields. This information was transmitted via grower talks and extension bulletins. Proper selection of tolerant varieties will allow growers to continue to produce wheat in these affected areas.

3. 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 at Pullman, Washington, in collaboration with scientists at Washington State University, used pyrosequencing to identify bacterial communities from the roots of wheat associated with this natural suppression. Members of the Sphingobacteria (Chyrseobacterium) and Oxalobacteriaceae build up to high populations on diseased roots and reduced disease in greenhouse bioassays. Similar community shifts were found in samples from Australian suppressive soils. 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.

4. Molecular diagnostic assay for the cereal cyst nematode. Cyst nematodes are among several types of plant-parasitic nematodes that reduce yields in Pacific Northwest dryland wheat fields, accounting for about $51 million in annual losses. ARS scientists at Pullman, Washington in collaboration with scientists at Oregon State University developed molecular diagnostic assays to distinguish two types of cyst nematode, Heterodera avenae and H. filipjevi, in field soils from Washington, Idaho and Oregon. This research provides the means to accurately identify the nematodes so that the appropriate wheat cultivars and management practices can be selected. Commercial diagnostic laboratories, other scientists, extension agencies and action agencies engaged in nematode research and control will use this information.

5. Comparative genomics of the mitochondria of Magnaporthaceae members. 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 sites and modes of host infection. ARS scientists at Pullman, Washington, have compared the mitochondrial genome sequences of Ggt, M. oryzae and M. poae, a root pathogen that causes summer patch of turfgrass. All three mitochondrial genomes encoded a core set of proteins, tRNAs, and small and large ribosomal RNA subunits, but many of the root pathogen mitochondrial genes harbored endonuclease-class introns I, supporting nuclear genome comparisons showing that the two root pathogens are more closely related to each other compared to the foliar rice blast pathogen. Fungal phylogeneticists, evolutionary biologists and ecologists are using the findings to correlate genome content and structure to pathogen infection processes and mitochondrial genome evolution.

6. Improving the robustness of the natural biological control of take-all disease. Take-all, caused by Gaeumannomyces graminis var. tritici, is the most important root disease of wheat worldwide and there is no genetic resistance to the disease. A natural biocontrol of take-all called take-all decline (TAD) occurs during wheat monoculture due to the buildup of beneficial Pseudomonas bacteria on the roots, but the length of time before disease suppression occurs and its intensity differ among fields and years. ARS scientists at Pullman, Washington, grew different wheat cultivars in soil from a TAD field and demonstrated that the amount of take-all that developed on the roots of the cultivars differed significantly. This research shows that wheat cultivars, although equally susceptible to take-all, vary in ability to take advantage of this natural biocontrol. These results will provide to growers the information need to make the best use of natural disease suppression that requires no off-farm inputs. They also show that breeders should consider supportiveness of beneficial bacteria as a trait to select for when developing new wheat varieties.

7. Agroclimatic zone and soil silt content differentially impact species of indigenous phenazine-producing beneficial 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, identified phenazine-producing beneficial bacteria and determined the impact of agroclimatic zone and abiotic soil factors on populations of these beneficial bacteria 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. Five distinct species of phenazine producers were identified, two of which were provisionally considered to be new. Agroclimactic zone and soil silt content affected the species diversity across the region. These results show how soil edaphic factors can influence natural populations of antibiotic-producing bacteria with the capacity to suppress soilborne diseases of cereals and improve plant growth.

Review Publications
Agostini, A., Johnson, D.A., Hulbert, S., Demoz, B., Fernando, W., Paulitz, T.C. 2013. First report of blackleg caused by Leptosphaeria maculans on canola in Idaho. Plant Disease. 97(6):842.

Babiker, E.M., Hulbert, S.H., Paulitz, T.C. 2012. Hyaloperonospora camelinae on Camelina sativa (L.) in Washington State: Detection, seed transmission, and chemical control. Plant Disease. 96(8):1670-1674.

Babiker, E.M., Hulbert, S.H., Schroeder, K., Paulitz, T.C. 2013. Evaluation of Brassica species for resistance to Rhizoctonia solani and binucleate Rhizoctonia (Ceratobasidum spp.) under controlled environment conditions. European Journal of Plant Pathology. Volume 136, Issue 4, pp. 763-772.

Mavrodi, D.V., Parejko, J.A., Mavrodi, O.V., Kwak, Y., Weller, D.M., Blankenfeldt, W., Thomashow, L.S. 2013. Recent insights into the diversity, frequency and ecological roles of phenazines in fluorescent Pseudomonas spp. Environmental Microbiology. 15(3):675-686.

Smiley, R., Marshall, J.M., Gourlie, J.A., Paulitz, T.C., Kandel, S.L., Pumphrey, M.O., Garland Campbell, K.A., Yan, G., Anderson, M.D., Flowers, M.D., Jackson, C.A. 2013. Spring wheat tolerance and resistance to Heterodera avenae in the Pacific Northwest. Plant Disease. 97(5):590-600.

Sharma-Poudyal, D., Paulitz, T.C., Porter, L., Eggers, J., Hamm, P.B., Du Toit, L. 2013. Efficacy of fungicides to manage onion stunting caused by Rhizoctonia spp. in the Columbia Basin of Oregon and Washington, 2011-2012 Plant Disease Management Reports. No. 7:V047.

Schroeder, K., Martin, F.N., De Cock, A., Levesque, C.A., Spies, C., Okubara, P.A., Paulitz, T.C. 2013. Molecular detection and quantification of Pythium species: Evolving taxonomy, new tools and challenges. Plant Disease. 97(1):4-20.

Kwak, Y., Bonsall, R.F., Okubara, P.A., Paulitz, T.C., Thomashow, L.S., Weller, D.M. 2012. Factors impacting the activity of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens against take-all of wheat. Soil Biology and Biochemistry. 54:48-56.

Parejko, J.A., Mavrodi, D.M., Mavrodi, O.V., Weller, D.M., Thomashow, L.S. 2013. Taxonomy and distribution of phenazine-1-carboxylic acid-producing Pseudomonas spp. in the dryland agroecosystem of the Inland Pacific Northwest. Applied and Environmental Microbiology. 79(12):3887-3891.

Xu, N., Ahuja, E., Janning, P., Mavrodi, D.V., Thomashow, L.S., Blankenfeldt, W. 2013. Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis. Acta Crystallographica, Section D: Biological Crystallography. D69, 1403-1413.

Okubara, P.A., Harrison, L.A., Gatch, E.W., Schroeder, K.L., Vandemark, G.J., Du Toit, L.J. 2013. Development and evaluation of a TaqMan Real-Time PCR assay for Fusarium oxysporum f. sp. spinaciae. Plant Disease. 97(7):927-937.

Sharma-Poudyal, D., Paulitz, T.C., Porter, L., Eggers, J., Hamm, P.B., Du Toit, L. 2013. Effect of timing of glyphosate application to a winter wheat cover crop on stunting of spring-sown onions caused by Rhizoctonia spp. in the Columbia Basin of Washington, 2012. Plant Disease Management Reports. No. 7:V046.

Sharma-Poudyal, D., Paulitz, T.C., Porter, L., Eggers, J., Hamm, P.B., Du Toit, L. 2013. Yield responses of three onion cultivars to stunting caused by Rhizoctonia spp. in the Columbia Basin of Oregon and Washington, 2012 Plant Disease Management Reports. No. 7:V048.

Last Modified: 04/26/2017
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