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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Research Project #432145

Research Project: Biology, Ecology, and Genomics of Pathogenic and Beneficial Microorganisms of Wheat, Barley, and Biofuel Brassicas

Location: Wheat Health, Genetics, and Quality Research

2019 Annual Report


Objectives
The long-term objective of this project is to develop biologically based technologies 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: Define the pathogen diversity, host range, and geographical distribution of fungal and nematode root pathogens, especially those causing emerging diseases in cereal-based cropping systems in the Pacific Northwest. Subobjective 1A: Using conventional and molecular techniques, determine the biogeographical distribution and risk of emerging and chronic pathogens and diseases. Subobjective 1B: Examine the genetic and pathogenic diversity of emerging and chronic pathogens. Subobjective 1C: Develop and evaluate agronomic, genetic and cultural methods of root disease management. Objective 2: Determine the soil microorganisms, microbial communities, and molecular mechanisms that promote or reduce plant health in wheat, barley and canola in the Pacific Northwest. Subobjective 2A: Determine how cultural practices and chemical inputs affect the plant and soil microbiomes in wheat cropping systems. Subobjective 2B: Characterize the rhizosphere microbiome of wheat in take-all decline soils. Subobjective 2C: Evaluate the effect of the wheat cultivar on the robustness of biological control by Pseudomonas spp. and in take-all decline soils. Objective 3: Identify and characterize molecular mechanisms of host-microbe interactions, including the action of host genes governing disease resistance and biological control against soilborne pathogens of wheat, barley and canola. Subobjective 3A: Identify host responses to soilborne pathogens, biocontrol bacteria and bacterial metabolites. Subobjective 3B: Identify and characterize germplasm with resistance to soilborne pathogens.


Approach
Biological control of soilborne fungal pathogens such as Gaeumannomyces, Rhizoctonia, Pythium, Fusarium and plant-parasitic nematodes by naturally-occurring and recombinant 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 next-generation sequencing will be used to characterize the microbiomes of conducive and suppressive soils and the rhizosphere of small grain crops. 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 sequenced and 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.


Progress Report
This is the third report for this project which began in March of 2017. Wheat, barley and biofuel crops are infected by soilborne pathogens that reduce yields ten to thirty percent annually. Diseased crops cannot take full advantage of fertilizers and irrigation water, and unused nitrates move into surface and ground water and pollute the environment. The overarching goal of this project is to develop biologically-based technology for controlling root diseases of wheat, barley and biofuel brassica crops; to identify the diversity, host range, and geographical distribution of root pathogens, especially those causing emerging diseases; to determine the soil microbes, microbial communities, and molecular mechanisms that promote or reduce plant health, and to characterize the host microbe interactions involved in disease resistance and biocontrol of root diseases. Progress was made on all three objectives and their subobjectives. Under Sub-objective 1A, we continued to monitor for existing and emerging diseases in Washington. This includes cereal cyst nematode (Heterodera avenae and H. filipjevi). We published a paper on the distribution of these nematodes in eastern Washington from ten years of surveys. We continue to survey for black leg of canola (Leptosphaeria maculans), making collections, extracting and sequencing DNA, and making identifications. Under Sub-objective 1B, we have transferred over 300 isolates to a collaborator at University of Idaho to determine races and avr genes. Under Sub-objective 2A, we have determined the core rhizosphere microbiome of wheat across a range of precipitation zones and cropping systems. In collaboration with the Cook Farm LTAR (Long-Term Agriculture Research Network), we have identified bacteria associated with soil health, yield and edaphic factors such as organic matter and pH. This is the first work to decipher the microbial black box of soil health, by using next-generation sequencing to identify specific components of the bacterial community from over 120 sampling sites on the LTAR. Under Sub-objective 2B, we have continued the eighth year of a field plot at Lind, Washington, comparing the microbial communities in dryland vs irrigated plots, and quantifying the levels of DAPG (2,4-diacetylphloroglucinol) and phenazine. Under Sub-objective 2C, we identified amino acids and compatible solutes in exudates of the model grass Brachypodium distachyon and the wheat cultivar Buchanan, which supports increased production on roots of the antifungal metabolite 2,4-diacetylphloroglucinol. Under Sub-objective 3A, using an RNA sequencing (transcriptomics) approach, we have identified wheat root genes induced during infection by the nematodes Pratylenchus neglectus and P. thornii. Bioinformatic analysis indicated that genes encoding enzymes involved in oxidative stress metabolism and other defense-related processes were strongly induced in a species-specific manner.


Accomplishments
1. Distribution of cereal cyst nematode in eastern Washington. Cereal 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. However, little was known about where these nematodes occur. ARS scientists at Pullman, Washington, surveyed eastern Washington over a 10-year period and developed a molecular method to distinguish Heterodera avenae from H. filipjevi, two species difficult to distinguish morphologically. They found that H. avenae is widely distributed in the highest precipitation zone where crops are grown every year, but not as much in the dry wheat-fallow area. H. filipjevi is confined to southern Whitman County. This information is crucial for growers to know their risks, and knowledge of the species is critical for breeders to develop resistance, since different resistance genes are effective against different nematode species.

2. Specific groups of bacteria are associated with soil health. Despite the current interest in soil health and programs by the National Resources Conservation Service (NRCS), little is known about the specific microbial groups that play a role. ARS scientists at Pullman, Washington, used next-generation sequencing at a Long Term Agricultural Research (LTAR) site to compare bacterial communities to traditional soil health tests such as Haney and Solvita. They found significant positive correlations between grain yield and the bacterial family Caulobacteraceae and negative correlations with Micromonosporaceae. Oxalobacteraceae, Cytophagaceae, Comamonadaceae, Verrucomicrobiaceae and Pseudomonadaceae were positively correlated with the Haney and Solvita tests. Knowledge of specific community components are critical for developing management programs to improve soil health.

3. Phenazine producers mediate iron mineral transformation on roots. Dryland wheat on the Columbia Plateau of the Pacific Northwest selects for phenazine antibiotic-producing Pseudomonas spp. that suppress a wide range of soilborne plant pathogens. Scientists at ARS in Pullman, Washington, in collaboration with Washington State University, and Argonne National Labs, demonstrated that these phenazine producers also enhance the reactivity and mobility of Fe (iron) derived from soil minerals. In addition, they provide increased quantities of bioavailable iron to crop plants. These results provide evidence that biocontrol agents provide benefits to agroecosystems that extend beyond pathogen control.

6. Wheat root genes induced by Pratylenchus infection. In the Pacific Northwest, the root lesion nematodes Pratylenchus neglectus and P. thornei contribute up to 60 percent yield reductions in barley and wheat, with chronic losses of five percent, or $51 million. These nematodes also are problematic to cereals in other parts of the world. In collaboration with a Washington State University scientist, ARS scientists in Pullman, Washington, used an RNA sequencing (transcriptomics) approach to identify wheat root genes induced during infection by either species or by a combination of both species. Bioinformatic analysis indicated that genes encoding enzymes involved in oxidative stress metabolism and other defense-related processes were strongly induced in a species-specific manner. The data provide Pratylenchus-responsive promoters for driving expression of candidate wheat resistance genes, and a basis for comparing root defense responses to various types of soilborne pathogens.

8. Differential effect of biocontrol rhizobacteria on wheat. 2,4-Dicetylphloroglucinol (DAPG)-producing Pseudomonas rhizobacteria are responsible for the natural biocontrol of take-all disease of wheat, known as TAD, which occurs when these bacteria are enriched in the soil by wheat monoculture. DAPG has both broad-spectrum antibiotic and phytotoxic properties. ARS scientists at Pullman, Washington, in collaboration with scientists at Washington State University, explored how the wheat cultivar can affect the suppression of take-all by DAPG producers. They showed that these rhizobacteria can be both beneficial and deleterious to wheat depending on the genotype of the wheat. A test of over 50 wheat cultivars showed considerable differences among cultivars in their sensitivity to DAPG-producing rhizobacteria and DAPG and for some cultivars, DAPG can be quite phytotoxic and slow root growth, whereas other cultivars tolerated the antibiotic with no effect on growth. Thus, growers can enhance their yield in TAD soils enriched in DAPG producers by using varieties that are less sensitive to DAPG phytotoxicity.


Review Publications
Schlatter, D.C., Paul, N.C., Shah, D.H., Schillinger, W.F., Bary, A.L., Sharratt, B.S., Paulitz, T.C. 2019. Biosolids and tillage practices influence soil bacterial communities in dryland wheat. Microbial Ecology. 78(3):737-752. https://doi.org/10.1007/s00248-019-01339-1.
Hansen, J.C., Schillinger, W., Sullivan, T., Paulitz, T.C. 2018. Rhizosphere microbial communities of canola and wheat at six paired field sites. Applied Soil Ecology. 130:185-193. https://doi.org/10.1016/j.apsoil.2018.06.012.
Schroeder, K.L., Schlatter, D.C., Paulitz, T.C. 2018. Location-dependent impacts of liming and crop rotation on bacterial communities in acid soils of the Pacific Northwest. Applied Soil Ecology. 130:59-68. https://doi.org/10.1016/j.apsoil.2018.05.019.
Hansen, J.C., Schillinger, W., Sullivan, T., Paulitz, T.C. 2019. Soil microbial biomass and fungi reduced with canola introduced in long-term monoculture wheat rotations. Frontiers in Microbiology. 10:1488. https://doi.org/10.3389/fmicb.2019.01488.
Schlatter, D.C., Reardon, C.L., Maynard-Johnson, J.L., Brooks, E., Kahl, K.B., Norby, J., Huggins, D.R., Paulitz, T.C. 2019. Mining the drilosphere: bacterial communities and denitrifier abundance in a no-till wheat cropping system. Frontiers in Microbiology. 10:1339. https://doi.org/10.3389/fmicb.2019.01339.
Pollard, A.T., Okubara, P.A. 2018. Real-time PCR quantification of Fusarium avenaceum in soil and seeds. Journal of Microbial Methods. 157:21-30. https://doi.org/10.1016/j.mimet.2018.12.009.
Kim, D., Jeon, C., Shin, J., Weller, D.M., Thomashow, L.S., Kwak, Y. 2019. Function and distribution of a lantipeptide in strawberry Fusarium wilt disease suppressive soils. Molecular Plant-Microbe Interactions. 32(3):306-312. https://doi.org/10.1094/MPMI-05-18-0129-R.
Biessy, A., Novinscak, A., Blom, J., Leger, G., Thomashow, L.S., Cazorla, F.M., Josic, D., Filion, M. 2018. Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environmental Microbiology. 21(1):437-455. https://doi.org/10.1111/1462-2920.14476.
Shen, Z., Xue, C., Penton, C.R., Thomashow, L.S., Zhang, N., Wang, B., Ruan, Y., Li, R., Shen, Q. 2018. Suppression of banana Panama disease induced by soil microbiome reconstruction through an integrated agricultural strategy. Soil Biology and Biochemistry. 128:164-174. https://doi.org/10.1016/j.soilbio.2018.10.016.
Thomashow, L.S., Kwak, Y., Weller, D.M. 2019. Root-associated microbes in sustainable agriculture: models, metabolites and mechanisms. Pest Management Science. 75(9):2360-2367. https://doi.org/10.1002/ps.5406.
Dohnalkova, A.C., Tfaily, M.M., Smith, A.P., Chu, R.K., Crump, A.R., Brislawn, C.J., Varga, T., Shi, Z., Thomashow, L.S., Harsh, J.B., Keller, C.K. 2017. Molecular and microscopic insights into the formation of soil organic matter in a red pine rhizosphere. Soil Processes. 1(1):4. https://doi.org/10.3390/soils1010004.
Cai, M., Ma, S., Hu, R., Tomberlin, J.K., Thomashow, L.S., Zheng, L., Li, W., Yu, Z., Zhang, J. 2018. Rapidly mitigating antibiotic resistant risks in chicken manure by Hermetia illucens bioconversion with intestinal microflora. Environmental Microbiology. 20(11):4051-4062. https://doi.org/10.1111/1462-2920.14450.
Okubara, P.A., Peetz, A.B., Sharpe, R.M. 2019. Cereal root interactions with soilborne pathogens - from trait to gene and back. Agronomy. 9(4):188. https://doi.org/10.3390/agronomy9040188.
Knerr, A., Wheeler, D., Schlatter, D.C., Sharma-Poudyal, D., Du Toit, L.J., Paulitz, T.C. 2019. Arbuscular mycorrhizal fungal communities in organic and conventional onion crops in the Columbia Basin of the Pacific Northwest United States. Phytobiomes Journal. 2(4):194-207. https://doi.org/10.1094/PBIOMES-05-18-0022-R.
Thomashow, L.S., Letourneau, M., Kwak, Y., Weller, D.M. 2018. The soil-borne legacy in the age of the holobiont. Microbial Biotechnology. 12(1):51-54. https://doi.org/10.1111/1751-7915.13325.