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ARS Home Pacific West Area Pullman, Washington WHGQ Research





- Paulitz, Timothy
- Weller, David
- Thomashow, Linda
- 2023
- 2022
- Publications
- Plant Diseases (303)
- Crop Protection & Quarantine (304)

Research Project: Ecology and Genomics of Soilborne Pathogens, Beneficial Microbes, and the Microbiome of Wheat, Barley, and Biofuel Brassicas **Location:
                            Wheat Health, Genetics, and Quality Research** 2022 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:   Determine the components of plant and soil microbiomes that promote the health of wheat, barley, and biofuel brassica crops and are responsible for disease suppressive soils. 
Sub-objective 1A:  Define components of the wheat microbiome correlated with soil health. Isolate, culture and identify specific bacterial and fungal taxa. Test in the greenhouse for ability to protect against biotic stress (soilborne pathogens) and abiotic stress. 
Sub-objective 1B:  Define the microbiome of rotational crops in cereals (canola, pea, camelina) and how they drive the microbiomes of the following wheat crop and influence yield and disease.

Objective 2:  Determine the molecular and biochemical mechanisms of host-microbe interactions, including plant-pathogen, plant-beneficial microbe, and host genetics.
Sub-objective 2A:  Determine the effect of the wheat cultivar on root exudate composition and the growth, production of DAPG and phytotoxicity of P. brassicacearum Q8r1-96.
Sub-objective 2B:  Characterize the rhizosphere microbiome of the wheat cultivars Tara, Finley, Louise and Buchanan in take-all decline soils.
Sub-objective 2C:  Identify Streptomyces strains associated with the soil, rhizosphere, and endosphere of dryland wheat, assess their effect on fungal root pathogens and wheat health under drought conditions, and identify antifungal metabolites they produce.

Objective 3:  Integrate disease management strategies to control root diseases of wheat, barley, and biofuel brassica crops.
Sub-objective 3A:  Screen wheat (germplasm and varieties) for resistance to cereal cyst nematode and Fusarium crown rot.
Sub-objective 3B:  Identify the microbial communities (fungal pathogens and bacteria components) involved in the greenbridge, role of weeds, dynamics and succession of populations in roots, and antagonists that displace pathogens from dying roots. **Approach**
                                

Objective 1:  
Hypothesis: By using correlations of communities with field traits, we can target our culturing and select isolates that can be tested for causation in the greenhouse. Hypothesis: The microbiome of the rotation crop will affect the microbiome of the next wheat crop and yield by stimulating growth and inhibiting pathogens.  

Approach: Sites at the Cook LTAR farm will be sampled for bacterial and fungal microbiomes and the taxa correlated with yield, biomass, organic matter, and pH. Organisms will be isolated and tested for ability to protect against pathogens, drought, and acidity. The microbiome of legume and oilseed crops grown in rotation with wheat will be characterized.

Contingencies: The culture collection may be skewed toward copiotrophs, but the use of low nutrient media will capture Streptomyces and oligotrophs. Several techniques will be used to ensure a wide sampling of the fungal community. 

Objective 2: 
Hypothesis: Differences in root exudates of cultivars drive the differential responses of wheat to P. brassicacearum, the bacteria responsible for take-all decline (TAD). Hypothesis: The microbiomes of wheat cultivars differ and contribute to their ability to support TAD. Hypothesis: Dryland wheat is colonized by Streptomyces that promotes growth under drought conditions and inhibits pathogens.

Approach:  Root exudates will be produced from cvs. Tara, Finley and Buchanan; their composition compared and their ability to support the growth and antibiotic production of  P. brassicacearum determined. The root microbiomes of Tara, Finley and Buchanan in TAD and conducive soils in the presence and absence of Gaeumannomyces tritici will be characterized. Streptomyces spp. will be isolated on semi-selective media and identified using DNA sequencing. Isolates will be tested for ability to protect wheat against diseases and drought stress. 

Contingencies: Wheat root exudates are easily produced, and their chemical composition can be determined. If fungi or bacteria of interest are not isolated, Q-PCR primers will  be used to detect and quantify specific taxa. 

Objective 3: 
Hypothesis: Genetic resistance to these two diseases exists  in exotic germplasm sources and adapted varieties. Certain weeds act as reservoirs for the greenbridge, and a succession of primarily fungi displace pathogens from the dying roots over time. 

Approach: Wheat germplasm will be screened for resistance to cereal cyst nematode (CCN) and Fusarium crown rot. Greenbridge reduction is a cultural control measure, but the microbiology of this phenomenon is not understood. We will identify the microbial communities  involved in the greenbridge, role of weeds, succession of microbes in roots, and antagonists that displace pathogens from dying roots.

Contingencies: Resistance genes may be difficult to identify.  Genes for resistance to CCN can be indentified, but phenotyping in the field is still needed. For Fusarium crown rot, germplasm from many sources is used to increase our chances of finding effective genes. Weather conditions may prevent plot establishment. but we can rely on other years’ trials for data. **Progress Report**
                                

This report documents progress for project 2090-22000-019-000D, Ecology and Genomics of Soilborne Pathogens, Beneficial Microbes, and the Microbiome of Wheat, Barley, and Biofuel Brassicas which was certified in May 2022 and continues research from project 2090-22000-017-000D Biology, Ecology, and Genomics of Pathogenic and Beneficial Microorganisms of Wheat, Barley, and Biofuel Brassicas.  Although the project has just started, we have made progress on some of the milestones.

Under Sub-objective 1A, we have completed sampling at the Cook Long Term Agriculture Research (LTAR) farm and all the amplicon sequencing and analysis. We have also completed a collection of over 3000 isolates from camelina and are testing a subset (Oxalobacteraceae) for growth response under low N conditions. Under Sub-objective 1B, we completed sampling three rotation studies at Ritzville, Washington, with canola, winter pea, winter triticale, spring barley, and continuous wheat rotations. This was done in November 2021 and May 2022. In support of Sub-objective 2A, a collection of exudates was completed and will be analyzed for metabolomics in 2022. Under Sub-objective 3A, we continue to screen lines for resistance to Heterodera filipjevi and H. avenae, as well as new populations for resistance to Fusarium crown rot, such as the D-genome Nested Association Mapping (DNAM) population derived from the D genome of wheat. In support of Sub-objective 3B, greenbridge trials have been set up in Pendleton, Oregon, and pathogen levels are being quanitified with qPCR. **Accomplishments**


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