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 Wheat Health, Genetics, and Quality Research: Pullman, WA
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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** 2023 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.

Under Sub-objective 1A, ARS researchers at the Cook Agronomy Farm in Pullman, Washington, for Long-Term Agroecosystems Research (LTAR), completed their sampling, and the data from a three-year temporal study is being analyzed. A large collection of bacterial isolates from the camelina rhizosphere have been tested (part of a 3000+ strain collection) for growth promotion of camelina under low nitrogen and organic nitrogen conditions. A manuscript is in preparation on the microbiome of camelina from 33 locations across eastern Washington. 

Under Sub-objective 1B, ARS researchers completed sampling rotation experiments in Ritzville, Washington, in canola, pea, triticale, barley, and wheat. DNA is being extracted and will be sent for amplicon sequencing. In the past, only bacteria and fungi were screened, but because canola is one of the few plant families that is non-mycorrhizal, it may affect AMF infection of the following rotation crops, so arbuscular mycorrhizal fungi (AMF) is also being analyzed.  

For Sub-objective 2A, axenic root exudates of wheat cultivars Tara, Finley, and Buchanan are currently being analyzed for metabolite composition by HPLC and mass spectrometry. The additional, more concentrated volumes of exudate needed to analyze their impact on the growth, production of DAPG and phytotoxicity of P. brassicacearum Q8r1-96 currently are being produced. 

The following progress has been achieved under Sub-objective 2B. Wheat and its associated microbiome are impacted by abiotic factors that shape their interactions over time, but long-term trends in microbial community dynamics are poorly characterized. ARS researchers in Pullman, Washington, determined seasonal and long-term bacterial population dynamics in monocropped dryland and irrigated wheat in central Washington State. Analyses revealed that some bacterial genera exhibit distinct seasonal periodicity whereas others maintain stable populations over time or decrease in abundance independent of irrigation. Taxa in the wheat endosphere declined in abundance regardless of irrigation, indicating that the maturing host, and not water, is the main driver of these populations. Our results provide insight into the effect of desiccation on bacterial communities to guide management of wheat crop performance under drought conditions. 

In support of Sub-objective 2C, ARS researchers isolated a large collection of Streptomyces isolates, including over 115 from the rhizosphere and 201 from the endosphere of wheat that were collected from irrigated and dryland plots at various stages of maturity in Lind, Washington, from 2021 through 2023. The isolates are being characterized phenotypically and phylogenetically by multilocus sequence analysis for identification and will be tested for their ability to suppress fungal root pathogens and to ameliorate drought stress in crops grown under a variety of soil moisture conditions. 

Under Sub-objective 3A, (wheat varieties and lines being grown in greenhouses and close to release are continuously being screened. ARS researchers are also testing prebreeding lines to find additional sources of resistance to Fusarium crown rot, including crosses between synthetic lines from the International Maize and Wheat Improvement Center (CIMMYT) in Ankara, Turkey, and Pacific Northwest varieties, double haploid lines between Cara (tolerant) and Xerpha (susceptible) and DNAM tauschii crosses (D-genome Nested Association) focusing on the D genome. The wheat D genome may contain unexplored sources of resistance.

Under Sub-objective 3B, ARS researchers set up field trials at Pendleton, Oregon, with our collaborator from Oregon State University and the pathogens in the root systems are being analyzed using real time PCR. **Accomplishments**
                                

1. Nematode communities can reveal soil health. Nematodes are the most numerous soil invertebrate and occupy all trophic levels in the food web, from fungal and bacterial feeders to herbivores to predators. ARS scientists in Pullman, Washington, and a Fulbright Scholar from Ibn Zohn University, Agadir, Morocco, sampled potato and wheat soils across eastern Washington and Oregon, including soils that have never been cropped. They morphologically identified over 30 genera and trophic levels based on mouth parts. Analysis showed that cropped soils are more disturbed and dominated by bacterial and fungal feeders, compared to native soils. These results show that nematode analysis may be used as another indication of soil health for growers, who want to know how their management systems are impacting their soils. 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 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. Bacteria isolated from the rhizosphere of camelina can promote growth. Camelina, a member of the Brassicaceae family, is a potential low-input bioenergy crop that can be grown in rotation with wheat in dryland areas. But nothing is known about the microbial communities on the roots, and how this may influence crop performance and nutrient uptake. ARS researchers at Pullman, Washington, and Washington State University and Montana State University scientists, funded by a grant from the Department of Energy, isolated a collection of over 3000 strains from the roots of camelina grown in 33 different locations in eastern Washington and Montana. They tested them for growth promotion in the lab and greenhouse, and have identified several promising strains, including isolates of Pseudomonas. In conjunction with microbiome analysis, researchers have identified key components of the camelina bacterial community that may play a role in increasing nutrient uptake, pathogen resistance and drought tolerance in this important biofuels crop. 4. Streptomyces are key members of the microbiome of wheat roots. Streptomyces are abundant in association with plants and are known for their ability to promote drought tolerance and produce antibiotics that inhibit a wide range of pathogens. To assess the role of these bacteria in the protection of cereal crops, ARS scientists in Pullman, Washington, made a large collection of Streptomyces isolates including over 115 from the rhizosphere and 201 from the endosphere of wheat collected from irrigated and dryland plots at various stages of maturity in Lind, Washington from 2021 through 2023. The isolates are being characterized phenotypically and phylogenetically by multilocus sequence analysis for their ability to suppress fungal root pathogens and to ameliorate drought stress in crops grown under a variety of soil moisture conditions. The results of these analyses are expected to provide new tools for growers to maintain crop productivity under conditions of increasing biotic and abiotic stress mediated by climate change. 5. Phenazines play a key role in the health and sustainability of dryland wheat. Wheat grown without irrigation in the low-precipitation zone of the Columbia Plateau of the Pacific Northwest (PNW) selects for phenazine-1-carboxylic acid (PCA)-producing Pseudomonas spp. that comprise one to 10 % of the culturable bacteria on wheat roots. ARS researchers in Pullman, Washington, and Washington State University scientists have analyzed the microbiome of dryland wheat and continue to show that PCA-producing Pseudomonas spp. suppress a wide range of soilborne fungal pathogens, including Gaeumannomyces, Fusarium, and Rhizoctonia. They produce biofilms, which help soil particles stick together, preventing erosion, enhancing the reactivity and mobility of iron (Fe) derived from soil minerals, thus increasing the quantities of bioavailable iron to the plants; and strongly induce resistance to foliar pathogens. These findings show that PCA producing pseudomonads are one of the most important groups of bacteria in soil microbiome contributing to the health and sustainability of dryland wheat. Growers can rely on these PCA producing pseudomonads to suppress these fungal diseases. **Review Publications**
                            *Cheng, W., Xue, H., Yang, X., Huang, D., Cai, M., Huang, F., Zheng, L., Peng, D., Thomashow, L.S., Weller, D.M., Yu, Z., Zhang, J. 2022. Multiple receptors contribute to the attractive response of Caenorhabditis elegans to pathogenic bacteria. Microbiology Spectrum. 11(1). Article e02319-22. https://doi.org/10.1128/spectrum.02319-22.*
                                *Yin, C., Hagerty, C., Paulitz, T.C. 2022. Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen. Frontiers in Microbiology. 13. Article 908981. https://doi.org/10.3389/fmicb.2022.908981.*
                                *Wen, T., Ding, Z., Thomashow, L.S., Hale, L.E., Yang, S., Xie, P., Liu, X., Wang, H., Shen, Q., Yuan, J. 2023. Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil. New Phytologist. 238(6):2634-2650. https://doi.org/10.1111/nph.18886.*
                                *Yin, C., Schlatter, D.C., Hagerty, C., Hulbert, S.H., Paulitz, T.C. 2023. Disease-induced assemblage of the rhizosphere fungal community in successive plantings of wheat. Phytobiomes Journal. 7 (1):100-112. https://doi.org/10.1094/PBIOMES-12-22-0101-R.*


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