Location: Wheat Health, Genetics, and Quality Research
2018 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 second report for this new 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 sub-objectives, all of which fall under NP 303 and encompass Component 1 Problem 1A, Component 2 Problem 2C or Component 3 Problem 3A or B.
Sub-objective 1A: Monitoring for existing and emerging diseases in Washington continued. This includes cereal cyst nematode (Heterodera avenae and Heterodera filipjevi) and black leg of canola (Leptosphaeria maculans) and involves making collections, extracting and sequencing DNA, and making identifications. We have also developed a collection of Leptosphaeria biglobosa, thought to be a closely related but mildly virulent pathogen. Future experiments will test this assumption. We have also started to make collections of Fusarium graminearum, the cause of head blight. This is becoming an increasing problem in irrigated wheat, especially in rotation with corn.
Sub-objective 1B: Heterodera filipjevi was tested on a set of differentials acquired from colleagues in Turkey, to determine the pathotypes or races of this nematode in the Pacific Northwest. This is important, so we know which resistance genes to deploy.
Sub-objective 2A: It was determined that glyphosate (Roundup), the most widely used herbicide in the Pacific Northwest and the world, has very minor and subtle effects on bacterial and fungal communities in the soil. This is an important finding, the first research to use next-generation sequencing to answer this concern that growers have posed. The effects of biosolid (sewage sludge) applications on fungal and bacterial communities, both in the soil and dust were examined. Dryland wheat growers in the Columbia Basin are using sludge (which originates in the Seattle area) as a source of nitrogen. We can identify the signature of bacteria from human gut in the soil and dust, but pathogenic bacteria were not detected. However, biosolids provide a source of nutrients for bacteria and fungi originating from the soil that colonize the biosolids, resulting in a shift in populations.
Sub-objective 2C: Isolation and analysis of Tara root exudate is complete. New methods have been devised for sterilization of seed from Buchanan. Exudate from Buchanan has been collected and analysis will be completed in the coming weeks. Cultivars have been selected for field screening of winter wheat cultivars in take-all decline soil.
Sub-objective 3B: A recently developed greenhouse method to continue to identify wheat lines with resistance to the cereal cyst nematodes, both Heterodera avenae and H. filipjevi, is being used. We are also developing DNA markers to identify the source of resistance in these lines.
Accomplishments
1. Glyphosate (Roundup) has subtle and minor effects on soil microbes. The herbicide glyphosate is the most widely used herbicide in the U.S. and is a key tool in the direct-seed no-till system which reduces soil erosion and fossil fuel inputs. But growers in the Pacific Northwest have been concerned about non-target effects on soil microbes such as bacteria and fungi, which perform beneficial functions. ARS scientists in Pullman, Washington, using next-generation sequencing, compared microbial communities in treatments with and without glyphosate, that were taken from fields with a long history and no history of use. They showed that location and cropping system had much larger effects on fungal and bacterial communities. The effects of glyphosate were very minor, and in fact more communities were increased with glyphosate use, because of the habitat provided by dying roots. This is valuable information for farmers who are concerned about glyphosate and want to continue to use this important tool as previously there was little scientific literature to reference.
2. Black leg is becoming more widespread. Black leg of canola is the most serious disease of crucifers worldwide. Until a few years ago, the Pacific Northwest was considered free of this disease; however, it was discovered in the Willamette Valley of Oregon in 2014 and in the Camus Prairie of Idaho in the Spring of 2015. ARS scientists in Pullman, Washington, in collaboration with state and county colleagues, launched surveys, grower talks, extension publications and other information to warn growers in Washington about this seed-borne disease. In 2017, we identified several new outbreaks in Washington, accurately identified another disease that could be mistaken for black leg (Alternaria black spot), and identified another species, Leptosphaeria biglobosa. However, these outbreaks have been contained as the industry was proactively mobilized. The data needed by the Washington State Department of Agriculture to enact phytosanitary regulation was provided, which slowed the spread of the disease and saved Washington growers millions of dollars.
3. Resistance to cereal cyst nematode found in adapted wheat lines. 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. There are presently no chemical controls or resistant varieties to control this pathogen. ARS scientists in Pullman, Washington, developed a greenhouse method to screen advanced and early generation lines. They identified several resistant varieties of club, soft white winter and soft durum wheats from ARS breeding programs, including ARS Crescent, Selbu, Cara, and Pritchett. These can be immediately used by growers to manage this disease. In addition, discovery of this resistance will aid breeders to more quickly develop further varieties, without having to breed out undesirable characteristics present in poorly adapted germplasm.
4. Biosolids can shift bacterial communities in soil. Biosolids are processed sewage sludge that are being applied to dryland wheat fields as a source of nitrogen. However, it is unclear what impact these sludge materials may have on soil microbial communities, and whether bacteria from the human gut can persist in these biosolids. ARS scientists in Pullman, Washington, used next-generation sequencing of soil and dust samples from field-applied biosolids. They found biosolids applied to the soil significantly shifted the bacterial communities both in the soil and dust, even when applied a few years before. Some of the groups are gut inhabitants, but most came from soil bacteria that colonized the biosolids. This information is important for assessing the safety of biosolids, especially in dust that can blow off the fields and be transported for hundreds of miles.
5. Fungal communities change with soil depth. Fungi play important roles in residue breakdown, nutrient cycling and root attacks of cereal crops. In the Palouse region of eastern Washington, the loess soils are very deep (10 feet or more) and wheat roots can grow down to these layers to extract water. But little is known about the fungal communities at these depths. ARS scientists in Pullman, Washington, sampled soils down to 5 feet and used next-generation sequencing to examine fungal communities. Fungi in the top layers are involved in residue breakdown, but in the lower layers the fungi are root colonizers, pathogens, or symbionts, and communities are less diverse. This work leads to a greater understanding of how fungi may play important functions for no-till wheat growers, especially in determining soil and plant health.
6. Root phenotyping for disease resistance. Resistance in wheat and barley to soilborne root rot pathogens has been elusive, and screening for disease resistance has been slow and time-consuming. ARS researchers in Pullman, Washington, have extended a screen for early root growth in 17 resistant and 17 susceptible wheat plants to plant responses to pathogens in the laboratory and greenhouse. Resistance to root rot is also observed in both laboratory and greenhouse seedling assays. These assays will provide a more rapid means of identifying candidate resistant plants and will shorten the current screening interval up to five-fold.
7. Diagnostic assay for a soilborne pathogen of oat and wild oat. Wild oat is among the most yield-limiting weeds in cereal production systems of the Pacific Northwest and other parts of the U.S. ARS scientists in Pullman, Washington, and scientists at Washington State University developed a rapid and sensitive molecular assay to quantify the oat microbe in seed tissues and in soil. The assay has enhanced understanding of the preferential decay of wild oat but not wheat seed by the oat pathogen. This has implications for weed seed control in wheat and barley production systems.
8. Dryland wheat selects for beneficial microbiomes. 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. ARS scientists in Pullman, Washington, and scientists at Washington State University showed that phenazine-producing populations and antibiotic accumulation were greatest early in the spring and then declined as the soil dried and the wheat matured. These results provide insight into why biocontrol efficacy differs over the growing season, facilitating the development of more reliable and efficacious biologically-based disease management strategies.
9. Phenazine producers enhance biofilm production 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 Pullman, Washington State University, and the Department of Energy's Pacific Northwest National Laboratories demonstrated that the phenazine producers promote biofilm production on roots. This enhances water retention, likely influencing crop nutrition and soil health in dryland wheat fields. These results provide evidence that biocontrol agents provide benefits to crops that extend beyond pathogen control.
10. Molecular communication in the wheat rhizosphere. Plant roots secrete exudates that sustain and mediate communication with their rhizosphere microbiome. But the biochemical basis of these processes in cereals is poorly understood. ARS scientists in Pullman, Washington, with collaborators at Southern Mississippi University, identified amino acids and compatible solutes in exudates of the wheat cultivar Tara, which supports superior populations of the suppressive bacterium Pseudomonas brassicacearum. These compounds, and the technology developed to recover and analyze the exudates, are important because they can help to explain the persistence of populations of disease-suppressive rhizobacteria on the roots of wheat suppressive of take-all throughout the Pacific Northwest.
Review Publications
James, M.S., Pollard, A.T., Okubara, P.A., Fuerst, E.P. 2018. Defense enzyme responses in dormant wild oat and wheat caryopses challenged with a seed decay pathogen. Frontiers in Plant Science. 8:2259.
Okubara, P.A., Kumar, N., Hohenarter, L., Graham, D., Kandel, S., Doty, S.L., Micknass, U., Kogel, K.H., Imani, J. 2017. Inhibition of plant-interacting microbes by Vegelys®, an allium-based antimicrobial formulation. Journal of Biology and Nature. 8:40-51.
Mavrodi, D., Mavrodi, O., Elbourne, L., Tetu, S., Bonsall, R., Parejko, J., Yang, M., Paulsen, I., Weller, D.M., Thomashow, L.S. 2018. Long-term irrigation affects the dynamics and activity of the wheat rhizosphere microbiome. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2018.00345.
Paulitz, T.C., Schlatter, D.C., Kinkel, L., Thomashow, L.S., Weller, D.M. 2017. Disease suppressive soils: New insights from the soil microbiome. Phytopathology. 107(11):1284-1297. https://doi.org/10.1094/PHYTO-03-17-0111-RVW.
Schillinger, W., Paulitz, T.C. 2018. Canola versus wheat rotation effects on subsequent wheat yield. Field Crops Research. 223:26-32.
Schlatter, D.C., Burke, I., Paulitz, T.C. 2018. Succession of fungal and oomycete communities in glyphosate-killed wheat roots. Phytopathology. 108:582-594.
Mahoney, A.K., Babiker, E.M., See, D.R., Paulitz, T.C., Okubara, P.A., Hulbert, S.H. 2017. Analysis and mapping of Rhizoctonia root rot resistance traits from the synthetic wheat (Triticum aestivum L.) line SYN-172. Molecular Breeding. https://doi 10.1007/s11032-017-0730-9.
Schlatter, D.C., Yin, C., Hulbert, S., Burke, I., Paulitz, T.C. 2017. Subtle impacts of repeated glyphosate use on wheat-associated bacteria are small and depend on glyphosate use history. Applied and Environmental Microbiology. https://doi.10.1128/AEM.01354-17.
Sharma-Poudyal, D., Schlatter, D.C., Yin, C., Hulbert, S., Paulitz, T.C. 2017. Long-term no-Till: A major driver of fungal communities in dryland wheat cropping systems. PLoS One. https://doi.org/10.1371/journal.pone.0184611.
Mahoney, A., Babiker, E.M., Okubara, P.A., See, D.R., Paulitz, T.C., Hulbert, S.H. 2017. Analysis and mapping of Rhizoctonia root rot resistance traits from the synthetic wheat (Triticum aestivum L.) line SYN-172. Molecular Breeding. 37:130. https://doi.org/10.1007/s11032-017-0730-9.
Schlatter, D.C., Schillinger, W.F., Bary, A.I., Sharratt, B.S., Paulitz, T.C. 2017. Biosolids and conservation tillage: Impacts on soil fungal communities in dryland wheat-fallow cropping systems. Soil Biology and Biochemistry. 115:556-567.
Schlatter, D.C., Yin, C., Hulbert, S., Burke, I., Paulitz, T.C. 2017. Location, root proximity, and glyphosate-use history modulate the effects of glyphosate on fungal community networks of wheat. Microbial Ecology. https://doi.org/10.1007/s00248-017-1113-9.
Schlatter, D.C., Schillinger, W.F., Bary, A.I., Sharratt, B.S., Paulitz, T.C. 2018. Dust-associated microbiomes from dryland wheat fields differ with tillage practice and biosolids application. Atmospheric Environment. 185:29-40.
Schlatter, D.C., Kahl, K., Carlson, B.R., Huggins, D.R., Paulitz, T.C. 2018. Fungal community composition and diversity vary with soil depths and landscape position in a no-till wheat cropping system. FEMS Microbiology Ecology. 94:1-15. https://doi.org/10.1093/femsec/fiy098.
Wang, X., Glawe, D.A., Kramer, E., Weller, D.M., Okubara, P.A. 2018. Biological control of Botrytis cinerea: interactions with native vineyard yeasts from Washington State. Phytopathology. https://apsjournals-apsnet-org.nal.idm.oclc.org/doi/pdf/10.1094/PHYTO-09-17-0306-R.
Cho, G., Kim, J., Park, C., Nislow, C., Kwak, Y., Weller, D.M. 2018. Caryolan-1-ol, an antifungal volatile produced by Streptomyces spp., inhibits the endomembrane system of fungi. The Open Biology Journal. 7:170075.
Zhai, Y., Shao, Z., Cai, M., Zheng, L., Li, G., Huang, D., Cheng, W., Thomashow, L.S., Weller, D.M., Yu, Z., Zhang, J. 2018. Multiple modes of nematode control by volatiles of Pseudomonas putida 1A00316 from Antarctic soil against Meloidogyne incognita. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2018.00253.
Cheng, W., Cheng, J., Nie, Q., Huang, D., Yu, C., Zheng, L., Cai, M., Yu, Z., Zhang, J., Thomashow, L.S., Weller, D.M. 2017. Volatile organic compounds from Paenibacillus polymyxa KM2501-1 control Meloidogyne incognita by multiple strategies. Scientific Reports. 7:16213.
Coates, R., Bowen, B.P., Oberortner, E., Thomashow, L.S., Hadjithomas, M., Zhao, Z., Ke, J., Silva, L., Louie, K., Wang, G., Robinson, D., Tarver, A., Hamilton, M., Lubbe, A., Feltcher, M., Dangl, J., Pati, A., Weller, D.M., Northen, T.R., Cheng, J., Mouncey, N.J., Deutsch, S., Yoshikuni, Y. 2018. An integrated workflow for phenazine biosynthetic gene cluster discovery and characterization. Journal of Industrial Microbiology and Biotechnology. 45(7):567-577. https://doi.org/10.1007/s10295-018-2025-5.
