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United States Department of Agriculture

Agricultural Research Service

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Research Project: Utilization of the Rhizosphere Microbiome and Host Genetics to Manage Soil-borne Diseases

Location: Physiology and Pathology of Tree Fruits Research

Project Number: 2094-21220-002-00-D
Project Type: In-House Appropriated

Start Date: Mar 17, 2017
End Date: Mar 16, 2022

Objective:
This project will investigate the effect of host genotype on composition and activity of the rhizosphere microbiome, in concert with host resistance attributes and organic soil amendment strategies, as a means to manage soil-borne diseases of fruit crops incited by diverse pathogen complexes. Objective 1: Define the metabolic and biological constituents functional in soil-borne disease suppression attained via organic input methodologies. [NP303, C3, PS3A] • Subobjective 1A: Determine the spectrum of metabolites produced during Anaerobic Soil Disinfestation (ASD) as affected by carbon input. • Subobjective 1B: Characterize shifts in soil/rhizosphere microbiome associated with ASD and correlate with suppression of apple and strawberry soil-borne pathogens. Objective 2: Assess plant genotype specificity for composition of the root microbiome and its relationship to disease susceptibility/tolerance. [NP303, C3, PS3A] • Subobjective 2A: Conduct microbial profiling (NextGen sequencing) to determine relative differences in composition of the microbiome recruited by tolerant and susceptible apple rootstocks. • Subobjective 2B: Determine the effect of apple rootstock genotype on efficacy of reduced rate Brassica seed meal amendments or ASD for control of replant disease. Objective 3: Determine the metabolic composition of exudates from disease tolerant and susceptible rootstocks and assess their effect on rhizosphere microbial recruitment. [NP303, C3, PS3B] • Subobjective 3A: Define differences in apple root exudate metabolite profiles produced by rootstock cultivars that differ in susceptibility to soil-borne plant pathogens. • Subobjective 3B: Test the impacts of apple root exudate metabolites, alone or in combination, on components/entirety of the soil microbiome. Objective 4: Define the functional roles of candidate genes conferring resistance to apple replant pathogens. [NP303, C3, PS3A] • Subobjective 4A: Evaluate apple root resistance phenotypes for genotypes in an apple rootstock cross population during their interactions with apple replant disease (ARD) pathogens. • Subobjective 4B: Analyze the function of selected apple candidate genes to infer their roles in activating defense responses and conferring ARD resistance. • Subobjective 4C: Examine the sequence features of genomic DNAs containing functionally analyzed apple genes.

Approach:
Obj 1: Anaerobic soil disinfestation (ASD) will be applied using different carbon inputs and soils sampled on a periodic basis. Metabolites extracted from soil will be analyzed using GC-MS and LC-MS methods. Concurrently, the effect of the ASD process on pathogen viability will be determined. Studies will be conducted in soils artificially infested with the target pathogens, and pathogen density will be determined using qPCR protocols. Community profiling using NextGen sequencing will be be used to associate specific microbial taxa with changes in the metabolome, and ultimately relationship to observed pathogen suppression. Operation Taxonomic Unit counts from soil microbial community analysis and relative metabolite amounts will be subjected to ANOVA-simultaneous component analysis. Network analysis can then indicate correlated metabolic and microbial activity unique to ASD treatment, potentially indicating metabolites produced in relation to activity of certain microbial taxa. Obj 2: A series of susceptible and tolerant apple rootstocks will be evaluated to asses the effect of genotype on the root microbiome and its influence on disease development. Root infestation by an introduced pathogen will be determined by qPCR and composition of the rhizosphere microbiome as well as the endophyte community will be determined by NextGen sequence analysis. Greenhouse and field trials will be performed to determine the influence of rootstock genotype on the efficacy of anaerobic soil disinfestation and Brassica seed meal amendments for the control of apple replant disease. Relative disease control efficacy of soil treatments will be assessed by monitoring components of the replant disease pathogen complex using qPCR methods. Obj 3: The interaction of the rhizosphere and orchard soil eventually determines composition of orchard soil and rhizosphere associated microbial communities that regulate numerous processes. Root exudates among genotypes will be evaluated for the presence of potentially antimicrobial exudates or symbiotic/mutualistic recruitment signaling molecules. Collected root exudates will be analyzed by LC-MS. Exudates will be assayed for capacity to inhibit the growth of soil-borne pathogens. Exudates will also be applied directly to orchard soils and their effect on pathogen population dynamics and composition of the soil microbiome will be assessed. Obj 4: Rootstock genotypes will be phenotypically analyzed for susceptibility to apple replant disease. A number of susceptible and potentially resistant genotypes will be utilized in studies to assess the function of selected apple candidate genes to infer their roles in activating defense reponses. Plants will be propagated through tissue culture and exposed individually to one of the target pathogens for a select period of time. Plants will be sampled and total RNA isolated to assess relative expression of the target genes. Based on gene expression pattern analysis, five to eight selected genes showing robust association with resistance phenotypes will be subject to in planta expression manipulation to further characterize the potential role of these genes in observed host resistance.

Last Modified: 05/25/2017
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