Location: Wheat Health, Genetics, and Quality Research
2021 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 fifth report for this project which began in March of 2017. Wheat, barley, and biofuel crops are infected by soilborne pathogens that reduce yields 10 to 30% 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.
Under Sub-objective 1A, we continued to monitor for existing and emerging diseases in Washington State. This includes cereal cyst nematode (Heterodera avenae and H. filipjevi). In collaboration with a scientist at Oregon State Univerity, we used qPCR techniques to quantify Rhizoctonia and Fusarium species in under different tillage systems in northeast Oregon.
For Sub-objective 1B, we have transferred over 300 isolates to a collaborator at the University of Idaho and a student is characterizing races and avr genes. We have also been collaborating with researchers in Tunisia, Turkey, and Kazakhstan, who are conducting surveys of soilborne pathogens of wheat in their countries.
Under Sub-objective 1C, we continue to screen adapted varieties and germplasm for tolerance and resistance to cereal cyst nematode and Fusarium crown rot. In 2020, Washington State University breeders released the first Fusarium tolerant variety identified with our screening, a soft white winter wheat called Devote.
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, Long-Term Agriculture Research (LTAR) network, we have identified bacteria associated with soil health, yield and edaphic factors such as organic matter and pH. We have identified the effect of depth and time on bacterial communities. 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. We have also completed an analysis of the fungal community and showed that wheat yield is more highly correlated with fungal communities than bacterial communities in the bulk soil, suggesting a role for residue and carbon cycling. Finally, we are analyzing how landscape position and topography in the highly variable Cook LTAR shape bacterial communities.
Under Sub-objective 2B, in the 11th year of a field plot that has continued at Lind, Washington, we quantified the populations sizes of Streptomyces bacteria producing antifungal and antibacterial antibiotics over the growing season and as a function of irrigation. The presence of these bacteria was first predicted a year ago by a novel screening program suggesting that they are abundant in soil from Lind, Washington.
Also under Sub-objective 2B, we analyzed the dynamics of bacterial communities in the soil, rhizosphere, and endosphere of spring wheat as a function of drought or irrigation, both within three growing seasons and over a total of eight consecutive years, documenting trends towards stabilization of communities over time in relation to soil moisture.
In support of Sub-objective 2C, we conducted quantitative analyses of the osmolytes and compatible solutes present in root exudates of spring wheat cultivar Tara. These compounds contribute to the support of phenazine-producing bacteria under semi-arid field conditions such as those that occur over hundreds of hectares of wheat.
Under Sub-objective 3A, using RNA sequencing (transcriptomics) and proteomics approaches, we have identified wild oat seed genes and proteins induced during infection by a seed-decaying isolate of the soilborne fungal pathogen Fusarium avenaceum. Bioinformatic analyses indicated that wild oat seed harbored several hundred defense-related proteins. In contrast, Fusarium harbored modest numbers of defense and pathogenicity proteins when associated with semi-dry host seed, but 12- to 15-fold more proteins were found in the aqueous environment Since infection of wild oat, an unwanted weed pest, is desired, breeding programs could benefit by selection of crop genotypes or lines with naturally elevated expression of specific defense proteins, especially during early seedling growth. Real-time PCR assays were developed to monitor the pathogen population density in wild oat seed and soil samples, and to quantify the expression of defense genes in wheat seed, which are resistant to the pathogen.
For Sub-objective 3B, 48-hour and 72-hour root phenotyping assays were optimized to identify wheat genotypes with resistance to Rhizoctonia solani, a root rotting fungus on wheat. These rapid assays showed that very early differences in root growth rate and root biomass accumulation could distinguish strong resistance from strong susceptibility. Semi-automated phenomics approaches have been designed to monitor root growth rate and other traits that might be correlated to resistance.
Accomplishments
1. Fungal communities are better predictors of wheat yield than bacterial communities. Microbial communities (bacteria and fungi) play a major role in wheat health, nutrient uptake, residue decomposition and tolerance to abiotic stress. But, of the thousands of species in the soil, which ones play key roles? ARS scientists at Pullman, Washington, and the Cook Long Term Agroecosystems Research site sequenced both bacteria and fungi to determine the microbiome at numerous locations in the no-till (aspirational) reduced tillage (business as usual) paired farms, and correlated communities with soil factors such as soil pH and organic matter and yield. Fungi from the families Sordariaceae, Hydnodontaceae, Hypocreaceae, and Clavicipitaceae were positively correlated with yield, especially in the upper soil depth, while Glomeraceae and Phaeosphaeriaceae were negatively correlated. This may help growers determine soil health and how management practices may be adapted to favor beneficial microbiomes.
2. Previous crops of canola may shift the microbiome of the following wheat crop. Rotation crops often give a yield increase to the following wheat crop, due to breaking of diseases cycles, nitrogen (N) fixation and other benefits. However, a yield decrease in spring wheat after winter canola has been observed in intermediate and low precipitation areas, and water and nutrients were ruled out as factors. ARS scientists in Pullman, Washington, sampled the microbiome of spring wheat following winter canola, winter triticale, winter wheat, and spring barley. Spring wheat after canola had significantly less arbuscular mycorrhizal fungi and higher levels of a pathogen Waitea circinata. Canola is one of the few non-mycorrhizal plant families, and may deplete these beneficial, symbiotic fungi. This information is important for growers to consider in their cropping systems plans.
3. Phenazine-producing bacteria are enriched in plant microbiomes. Dryland wheat on the Columbia Plateau of the Pacific Northwest enrich for phenazine-1-carboxylic acid which reductively dissolves iron (Fe) and magnesium(Mn) oxyhydroxides in bacterial culture systems, but its impact upon Fe and Mn cycling in the rhizosphere is unknown. Here, ARS scientists in Pullman, Washington, in collaboration with a student at Washington State University, showed that concentrations of dithionite-extractable and poorly crystalline Fe were approximately 10% and 30-40% higher, respectively, in dryland and irrigated rhizospheres inoculated with the phenazine-producing bacteria than in rhizospheres inoculated with a phenazine deficient mutant. However, rhizosphere concentrations of Fe(II) and Mn did not differ significantly, indicating that phenazine-mediated redox transformations of Fe and Mn were transient or were masked by competing processes. Total Fe and Mn uptake into wheat biomass also did not differ significantly, but the phenazine-producing bacteria significantly altered iron translocation into shoots. X-ray absorption near edge spectroscopy revealed an abundance of Fe-bearing oxyhydroxides and phyllosilicates in all rhizospheres. These results are important because they show that phenazine producers enhanced the reactivity and mobility of Fe derived from soil minerals without producing parallel changes in plant Fe uptake. This is the first report that directly links significant alterations of Fe-bearing minerals in the rhizosphere to a single bacterial trait.
4. Rhizoctonia defense factors in wheat and Arabidopsis. Rhizoctonia root rot and damping off cause chronic crop yield losses in the Pacific Northwest and other parts of the world. Genetic resistance in wheat have been identified but molecular mechanisms of resistance need to be understood to select effective and durable resistance. Furthermore, root traits correlated to resistance will help identify resistant genotypes. In collaboration with university researchers, ARS scientists at Pullman, Washington, discovered that signaling through the damaged receptor P2K1/DORN, jasmonate and salicylate pathways were important for innate immunity to Rhizoctonia solani AG-8 and AG2-1 in the model plant Arabidopsis. In wheat, Rhizoctonia-resistant genotypes displayed a slower early root growth rate relative to susceptible genotypes. The findings suggested that there are multiple mechanisms for resistance in plants and led to the exploration of root phenomics for resistance screening.
Review Publications
Yin, C., Vargas, J.M., Schlatter, D.C., Hagerty, C., Hulbert, S., Paulitz, T.C. 2021. Wheat rhizosphere community selection reveals bacteria associated with reduced root disease. Microbiome. 9. Article 86. https://doi.org/10.1186/s40168-020-00997-5.
Gargouri, S., Balmas, V., Burgess, L., Paulitz, T., Laraba, I., Kim, H.-S., Proctor, R.H., Busman, M., Felker, F.C., Murray, T., O'Donnell, K. 2020. An endophyte of Macrochloa tenacissima (esparto or needle grass) from Tunisia is a novel species in the Fusarium redolens species complex. Mycologia. 112(4):792-807. https://doi.org/10.1080/00275514.2020.1767493.
Imren, M., Ozer, G., Paulitz, T.C., Morgounov, A., Dababat, A.A. 2021. Plant-parasitic nematode communities associated with wheat-growing areas in central, eastern, and south-eastern Kazakhstan. Plant Disease. https://doi.org/10.1094/PDIS-11-20-2424-SR.
Wang, M., Van Vleet, S., McGee, R.J., Paulitz, T.C., Porter, L.D., Schroeder, K., Vandemark, G.J., Chen, W. 2021. Chickpea seed rot and damping-off caused by metalaxyl-resistant Pythium ultimum and its management with ethaboxam. Plant Disease. 105(6):1728-1737. https://doi.org/10.1094/PDIS-08-20-1659-RE.
Wang, X., Schlatter, D.C., Glawe, D.A., Edwards, C.G., Weller, D.M., Paulitz, T.C., Abatzoglou, J.T., Okubara, P.A. 2021. Native yeast and non-yeast fungal communities of Cabernet Sauvignon berries from two Washington State vineyards, and persistence in spontaneous fermentation. International Journal of Food Microbiology. 350. Article 109225. https://doi.org/10.1016/j.ijfoodmicro.2021.109225.
Gargouri, S., Khemir, E., Souissi, A., Murray, T., Fakhfakh, M., Achour, I., Chekali, S., Mliki, M., Paulitz, T.C. 2020. Survey of take-all (Gaeumannomyces tritici) on cereals in Tunisia and impact of crop sequences. Crop Protection. 13. Article 10589. https://doi.org/10.1016/j.cropro.2020.105189.
Dar, D., Thomashow, L.S., Weller, D.M., Newman, D.K. 2020. Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes. eLife. https://doi.org/10.7554/eLife.59726.
Yang, M., Thomashow, L.S., Weller, D.M. 2021. Evaluation of the phytotoxicity of 2,4-Diacetylphloroglucinol and Pseudomonas brassicacearum Q8r1-96 on different wheat cultivars. Phytopathology. https://doi.org/10.1094/phyto-07-20-0315-R.
Yang, M., Xianguo, W., Dong, J., Zhao, W., Alam, T., Thomashow, L.S., Weller, D.M., Gao, X., Rustgi, S., Wen, S. 2020. Proteomics reveals the changes that contribute to Fusarium head blight resistance in wheat. Phytopathology. 111(2):386-397. https://doi.org/10.1094/PHYTO-05-20-0171-R.
Wang, X., Liu, Y., Li, Z., Gao, X., Dong, J., Zhang, J., Zhang, L., Thomashow, L.S., Weller, D.M., Yang, M. 2020. Genome-wide identification and expression profile analysis of the phospholipase C gene family in wheat (Triticum aestivum L.). Plants. 9(7). Article 885. https://doi.org/10.3390/plants9070885.
Hendry, S., Steinke, S., Wittstein, K., Adewunmi, Y., Sahukhal, G., Elasri, M., Thomashow, L.S., Weller, D.M., Mavrodi, O., Blankenfeldt, W., Mavrodi, D. 2021. Functional analysis of phenazine biosynthesis genes in Burkholderia spp.. Applied and Environmental Microbiology. 87. Article e02348-20. https://doi.org/10.1128/AEM.02348-20.
Yin, C., Schlatter, D.C., Kroese, D., Paulitz, T.C., Hagerty, C. 2021. Responses of soil fungal communities to lime application in wheat fields in the Pacific Northwest. Frontiers in Microbiology. 12. Article 576673. https://doi.org/10.3389/fmicb.2021.576763.
Schlatter, D.C., Kahl, K., Carlson, B.R., Huggins, D.R., Paulitz, T.C. 2020. Soil acidification modifies soil depth-microbiome relationships in a no-till wheat cropping system.. Soil Biology and Biochemistry. 149. Article 107939. https://doi.org/10.1016/j.soilbio.2020.107939.
Mavrodi, O.V., McWilliams, J.R., Peter, J.O., Berim, A., Hassan, K.A., Elbourne, L.D., LeTourneau, M., Gang, D.R., Paulsen, I.T., Weller, D.M., Thomashow, L.S., Flynt, A.S., Mavrodi, D.V. 2021. The effect of root exudates on the transcriptome of rhizosphere Pseudomonas spp.. Frontiers in Microbiology. 12. Article 651282. https://doi.org/10.3389/fmicb.2021.651282.
Nevada, S.S., Lupien, S.L., Watson, B., Okubara, P.A. 2021. Growth inhibition of Botrytis cinerea by native vineyard yeasts from Puget Sound, Washington State, USA. Journal of Biology and Nature. 13(1):42-53. https://www.ikprress.org/index.php/JOBAN/article/view/6534.
Bozoglu, T., Ozer, G., Imren, M., Paulitz, T.C., Dabaat, A.A. 2021. First report of crown rot caused by fusarium redolens on wheat in Kazakhstan. Plant Disease. https://doi.org/10.1094/PDIS-01-21-0015-PDN.
