Page Banner

United States Department of Agriculture

Agricultural Research Service



2009 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 Brassicas, grown as part of cereal-based production systems. Five specific objectives will be addressed over the next five years. Objective 1: Evaluate the genotypic diversity between species and within pathogen populations of root pathogens in direct-seeded cereal-based cropping systems. Objective 2: Identify and characterize microorganisms and mechanisms active in the suppression of soilborne pathogens by rhizobacteria. Objective 3: Identify the determinants responsible for differential rhizosphere competence among genotypes of DAPG-producing Pseudomonas fluorescens strains. Objective 4: Identify and characterize the molecular mechanisms of host-microbe interactions, including the action of host genes governing disease resistance and biological control. Objective 5: Identify and develop biocontrol technology for suppression of root pathogens in cereal-based cropping systems.

1b. Approach (from AD-416)
Biological control of root pathogens Gaeumannomyces, Pythium, Rhizoctonia, and Fusarium by naturally occurring and genetically engineered microorganisms will be developed and quantified in different soils. The 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. Structural loci for these anti-fungal metabolites will be used to engineer improved biocontrol agents. The genetic and physiological diversity of populations of the root pathogens, and influence of cropping system on pathogen populations and diversity will be determined. New sources & mechanisms of resistance will be identified. Practical root diseases control will be accomplished by both maximizing the activity of natural biocontrol agents. Formerly 5348-22000-012-00D.

3. Progress Report
Most wheat and barley is infected by root diseases including take-all, Rhizoctonia and Pythium root rots, common root rot, and Fusarium foot rot caused by soilborne fungi, which 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 pathogens of crops, especially wheat and barley, grown as part of cereal-based production systems in the Pacific Northwest. Brassica crops, such as canola, are grown as rotation crops in dryland areas, but have the potential to significantly expand in acreage because of increased demand for biodiesel, edible oils, and seedmeal. Brassicas are attacked by many of the same fungi that infect cereals. Project objectives include: 1) evaluate the genotypic diversity between species and within populations of root pathogens in direct-seeded cereal-based cropping systems; 2) identify and characterize microorganisms and mechanisms active in the suppression of root pathogens by rhizobacteria; 3) identify the determinants responsible for differential rhizosphere competence among genotypes of 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas fluorescens strains; 4) identify and characterize the molecular mechanisms of host-microbe interactions, including the action of host genes governing disease resistance and biological control; and 5) identify and develop biocontrol technology for suppression of root pathogens in cereal-based cropping systems. This project encompasses all components of NP 303. Characterization of bacterial communities in the soil by cultureless techniques such as pyrosequencing aligns with Components 4 because it identifies new components of communities that can play a role in soil health and suppression of root diseases. Demonstration that certain grassy weeds are better hosts of Rhizoctonia species and that the sprayout of the weeds 2-3 weeks before planting reduces the spread of Rhizoctonia to cereal crops aligns with Components 4 because it provides growers with a powerful tool for managing this root disease. Development of a rapid method of evaluating wheat crosses with resistance to Fusarium crown rot aligns with Component 2 because it speeds the deployment of resistance found in Australian and Middle Eastern lines into wheat varieties adapted to the Pacific Northwest. Demonstration that perennial wheats have tolerance/resistance to root pathogens aligns with Component 3 because it identifies novel sources of genetic resistance that can be used in wheat improvement programs. Development of a molecular diagnostic assay for the pathogen causing Fusarium wilt of spinach aligns with Component 1 because it identifies whether a field harbors a problematic level of the pathogen before sowing spinach. Identification of biocontrol bacteria that can inhibit up to three types of parasitic nematodes aligns with Component 4 because it demonstrates novel approaches for controlling these important soilborne pathogens.

4. Accomplishments
1. Soil microbial communities are influenced by cropping practices. Soil microbes play an important role in soil health, nutrient cycling and disease suppression. A pinch of soil contains thousands of species, but only a few can be cultured out and identified. Using a new technique called pyrosequencing, ARS scientists at Pullman, WA in collaboration with researchers at Washington State University, studied over 20,000 DNA sequences from a rotation/tillage experiment, and identified 300 bacteria groups. One predominant group, only described since 2003, was affected by cropping practices. These results show that there are large components of the bacterial communities that have not been studied, and may play a role in improving soil health and suppression of root diseases.

2. Grassy weeds serve as disease reservoirs for the Rhizoctonia root rot pathogen in wheat and barley. Rhizoctonia species cause root rots of wheat and other cereal crops. These pathogens can also attack grassy weeds in the field. ARS scientists at Pullman, WA in collaboration with researchers at Washington State University found that some weeds are better hosts than others. By spraying out these weeds with herbicides at least 2-3 weeks before planting, the bridging of the pathogen from the weeds to the crop can be reduced. This offers growers a powerful tool for managing this disease.

3. Resistance to Fusarium crown rot of wheat can be evaluated in the greenhouse. Fusarium crown rot is an important disease in dryland low-rainfall production areas of the Pacific Northwest, causing an average 9.5% yield loss. Genetic resistance has been found in Australian and Middle Eastern lines. But to move these genes into locally adapted varieties, a fast method of evaluating the crosses was needed. ARS scientists at Pullman, WA tested and optimized inoculation and rating techniques that can evaluate plants in 3 weeks. This technique will be useful for identifying DNA markers for resistance genes, to speed up the breeding process even more (from the present 7-9 years to get a variety in the field.

4. New sources of resistance found for Rhizoctonia and Pythium root rot. All commercial varieties of wheat are susceptible to the soilborne pathogens that cause root rot, and genetic resistance to these diseases is lacking. ARS scientists at Pullman, WA in collaboration with researchers at Washington State University tested three types of perennial wheat for tolerance to root diseases. All types of plants exhibited lower disease severity ratings and sustained less root damage compared to non-perennial wheats when infected with one or more pathogens. Perennial wheats offer a sustainable alternative to combating Rhizoctonia and Pythium root rot, and are novel sources of genetic resistance that should eventually prove valuable to wheat improvement programs.

5. Diagnostic assay developed for the Fusarium wilt pathogen. The pathogen causing Fusarium wilt of spinach is exceptionally persistent in soils of spinach seed production regions, and Pacific Northwest growers need to know whether their fields harbor problematic levels of the pathogen before they plant. ARS scientists at Pullman, WA in collaboration with researchers at Washington State University developed a rapid and sensitive diagnostic assay for monitoring pathogen levels in soil and seed samples. The pathogen was detected in a majority of soils known to cause Fusarium wilt of spinach. The assay provided estimates of pathogen levels in problematic soils, and is being used to evaluate disease management strategies.

6. Crop-parasitic nematodes inhibited by biocontrol bacteria. Plant-parasitic nematodes attack about 170 crops and cause annual yield losses of $7 to 9 billion in the U.S. ARS scientists at Pullman, WA in collaboration with researchers at Washington State University tested novel strains of biocontrol bacteria (pseudomonads) for ability to inhibit four types of plant-parasitic nematodes. Certain strains of biocontrol bacteria inhibited the growth of three types of nematodes in laboratory or greenhouse assays. The work led to the identification of biocontrol strains that show promise for commercialization.

7. Nematicidal biocontrol bacteria colonize roots of wheat and soybean differently. Plant-parasitic nematodes are among the most devastating pests to agriculture in the U.S. and worldwide, and their control by beneficial (biocontrol) bacteria will provide growers with an additional, sustainable management tool. ARS scientists at Pullman, WA tested novel nematicidal biocontrol bacteria for their ability to colonize the roots of two nematode hosts, wheat and soybean. The bacteria colonized wheat roots more extensively than soybean roots, although specific bacteria could colonize soybean roots well. The findings have implications for use against mobile versus sedentary types of nematodes on wheat and soybean.

8. Phenazine producing biocontrol pseudomonads are abundant in dryland wheat. Rhizoctonia root rot is the most important disease of no-till wheat and barley in the Northwest. A survey of dryland fields in Washington conducted by ARS scientists in Pullman, WA revealed high populations of phenazine-producing Pseudomonas bacteria on cereals grown within an area of about three million acres. Presence of the pseudomonads correlated with high levels of the antibiotic phenazine-1-carboxylic acid on roots of wheat. These bacteria and the phenazine are thought to be involved in natural Rhizoctonia suppression and mobilization of minerals, and thus contribute to the sustainability of this cropping system.

9. The take-all pathogen does not develop tolerance to 2,4-diacetylphloroglucinol. Take-all is the most important root disease of wheat worldwide. When wheat is grown in monoculture a natural suppression of the disease develops because of the build up of beneficial bacteria that produce the biocontrol antibiotic 2,4-diacetylphloroglucinol on the roots. ARS scientists in Pullman, WA compared the isolates of the pathogen from monoculture fields, where the antibiotic-producing bacteria are abundant, to isolates of non-monoculture, where they are not, showed no difference in sensitivity to the antibiotic. 2,4-diacetylphloroglucinol was shown to act on multiple basic cellular processes, which would limit the possibility of the development of resistance. This research indicates that the natural suppression of take-all is highly sustainable.

10. New resistance found to the cereal cyst nematode. The cereal cyst nematode possess a threat to cereal production in at least seven western states. ARS scientists in Pullman, WA collaboratored with Oregon State University, Pendelton, OR to demonstrate that the Cre1 resistance gene, available in exotic wheat accessions, prevented reproduction of cyst nematode populations from fields in Oregon. A Cre1 donor parent was crossed with six Pacific Northwest wheat varieties and the crosses were evaluated and found to carry the resistance. The researchers also showed that the Cre1 gene was equally effective against cyst nematode populations from fields in Idaho and Washington, confirming that the Cre1 resistance gene is a valuable resource for the Pacific Northwest wheat industry.

5. Significant Activities that Support Special Target Populations
ARS scientists at Pullman, WA lead a science outreach and engagement program, with participation by USDA, NRCS, Washington State University Cooperative Extension, WSU Plant Pathology Department, and Bellevue College, to The Confederated Tribes of the Colville Reservation and the region surrounding Omak, WA. This is one of the most remote, poorest and underserved regions in Washington State. The program entitled “Pumping-Up the Math and Science Pipeline: Grade School to College” has five components: i) development of energy independence on the Colville Reservation through the production of biofuels; ii) hands-on science education in reservation schools by ARS research scientists, WSU faculty and BC instructors; iii) development of and participation in on-reservation summer science camps; iv) supporting Native American, Hispanic, African American and rural high school summer science interns in ARS laboratories, and v) mentoring WSU undergraduates participating in the College Assistance Migrant Program (CAMP). Examples of these activities include: 1) field tests of spring and winter canola varieties and biodiesel production on Colville Reservation land; 2) monthly visits to Nespelem Elementary School and Pascal Sherman Indian School on the Colville Reservation to present science modules, October 2008 to May, 2009; 3) sponsorship of and participation in the Third Annual Skwant Life Science Camp for 5th-8th graders at the Pascal Sherman Indian School (Skwant is translated as ‘Waterfalls’), June 15-19, 2009, (total of 44 campers); and 4) molecular biology training for 6 summer high school interns and one Native American grade school teacher (July 2009) in ARS labs at Pullman. The award-winning Pipeline Program is promoting economic development on the Colville Reservation, enhancing science awareness among Native American, Hispanic and rural youth, and training the next generation of STEM professionals. Native American reservations and rural communities throughout the Pacific Northwest have requested expansion of this ARS program to their communities.

Review Publications
Yan, G., Smiley, R., Okubara, P.A., Skantar, A.M., Easley, S.A., Sheedy, J.G., Thompson, A.L. 2008. Detection and Discrimination of Pratylenchus neglectus and P. thornei in DNA Extracts from Soil. Plant Disease. 92(11):1480-1487.

Okubara, P.A., Steber, C.M., Demacon, V.L., Walter, N., Paulitz, T.C., Kidwell, K.K. EMS-treated hexaploid wheat genotype Scarlet has enhanced tolerance to the soilborne necrotrophic pathogens Rhizoctonia solani AG-8 and R. oryzae. 2009. Theor. Appl. Genet. 119(February): 293-303. Theoretical and Applied Genetics.

Smiley, R.W., Backhouse, D., Lucas, P., Paulitz, T.C. 2009. Chapter 6.Diseases Which Challenge Global Wheat Production- Root, Crown, and Culm Rots.p. 125-153 Wheat: Science and Trade, B.F. Carver, ed. Blackwell Publishing, Ames, IA.

Mavrodi, D.V., Loper, J.E., Paulsen, I.T., Thomashow, L.S. 2009. Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5. BMC Microbiology. 9:8.

Kwak, Y., Bakker, P.A., Glandorf, D., Topham, J., Paulitz, T.C., Weller, D.M. 2009. Diversity, virulence and 2,4-diacetylphloroglucinol sensitivity of Gaeumannomyces graminis var. tritici isolates from Washington State. Phytopathology Vol. 99, No. 5, p. 472-479.

Baley, G.J., Campbell, K., Yenish, J., Kidwell, K.K., Paulitz, T.C. 2009. Influence of Glyphosate, Crop Volunteer and Root Pathogens on Glyphosate-Resistant Wheat under Controlled Environment Conditions. Pest Management Science Vol 65, No. 3, p.288-299.

Peter, R.R., Dessaux, Y., Thomashow, L.S., Weller, D.M. 2009. Rhizosphere engineering and management for sustainable agriculture. Plant and Soil Journal, 321 (1-2): 363-383.

Last Modified: 2/23/2016
Footer Content Back to Top of Page