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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Research Project #432541

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

Location: Physiology and Pathology of Tree Fruits Research

2021 Annual Report

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. • Subobjective 1C: Characterize the effect of management practices on soil inoculum density of potential post-harvest pathogens and subsequent colonization of the phyllosphere and/or carposphere by these potential 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: Identify genetic sources of pathogen resistance and contribute to improved pest-resistant, size-controlling rootstocks to enhance orchard efficiency in pears. [NP303, C3, PS3A] Benefits will include availability of dwarfing, precocious, cold hardy, disease-resistant, and easily propagated rootstocks adapted to various U.S. production areas and enhanced genetic understanding of host-pathogen-environment interactions for sustainable and profitable pear orchard systems.

Objective 1: ASD will be applied using different carbon inputs and soils sampled on a periodic basis. Metabolites will be extracted from soil and analyzed using GCMS and LC-MS methods. Concurrently, the effect of the ASD process on pathogen viability will be determined. Effect of ASD on pathogen density will be determined using qPCR protocols. Profiling of the microbiome using NextGen sequencing will be conducted to associate specific microbial taxa with changes in the soil metabolome, and ultimately relationship to observed pathogen suppression. OTU taxonomic counts from soil microbial community analysis and relative metabolite amounts will be subjected to ANOVA-simultaneous component analysis. Network analysis will be used to correlate metabolic and microbial activity unique to ASD treatment, potentially indicating metabolites produced in relation to activity of certain microbial taxa. Objective 2: A series of susceptible and tolerant rootstocks will be evaluated to assess the effect of genotype on the root microbiome and its influence on disease development. Pathogen root infestation will be determined by qPCR and composition of the rhizosphere and endophytic microbiome will be determined by amplicon sequence analysis. Greenhouse and field trials will assess the influence of rootstock genotype on efficacy of ASD and Brassica seed meal amendments for the control of apple replant disease. Disease control efficacy of soil treatments will be assessed by monitoring the replant disease pathogen complex using qPCR methods. Objective 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. Objective 4: Rootstock genotypes will be phenotypically analyzed for susceptibility to apple replant disease. 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 responses. Tissue culture generated plants will be exposed individually to one of the target pathogens for a select period of time. Plant RNA will be isolated to assess relative expression of the target genes. Based on gene expression pattern analysis, 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. Objective 5: Using available plant resources, quantitative genetic and genomics will be used to identify the genetic underpinning of phenotypic traits of pear such as resistance to biotic and abiotic stresses, precocity, dwarfing and cold hardiness.

Progress Report
WIth regard to progress on Sub-objecives 1A and 1B, research on identification and manipulation of microbial and metabolic factors that influence the efficacy of anaerobic soil disinfestation (ASD) for the control of soil-borne diseases in apple and strawberry production systems was previously completed. For Sub-objective 2A, research on the examination of genotype effects on composition of the rhizosphere and endophytic microbiome recruited by different apple rootstocks and identification of important characteristics with potential to influence plant productivity continued. The effect of reduced rate Brassica seed meal (SM) amendments on apple rootstock physiology in M.26 vs. G.210 was explored/assessed via transcriptomic analysis. The temporal dynamics of gene expression indicated that the SM amendment altered the trajectory of the root transcriptome in a genotype-specific manner. Therefore, from a disease control perspective, the effect of this amendment in regard to treatment efficacy is likely to vary with rootstock genotype. This study also adds to our understanding of the multiple mechanisms by which SM soil amendment and the resulting microbiome affect apple rootstock physiology. For Sub-objective 2B, the monitoring of three orchard replant field trials established in 2017 to assess the efficacy of ASD and mustard seed meal (MSM) amendment for control of replant disease has been completed. There are no further updates for this sub-objective. Progress on Sub-objective 3A included research on the examination of differences in root exudate composition as affected by apple rootstock genotype, which has also been completed. For Objective 4, a new SY came on board in spring of 2020, and began planning and working towards this objective. With the goal of contributing to improved pest-resistant, size-controlling rootstocks to enhance orchard efficiency in pears, she began a collaboration with other scientists in Wenatchee, Washington, to improve genomic resources and identify dwarfing- and architecture-related gene families in pear. Further, connections with scientists in Wenatchee and Pullman, Washington, Hood River, Oregon, Davis, California, and Kearneysville, West Virginia, have been established, including experimental discussions, grant writing, and exchange of materials, to begin the development of projects and sharing of germplasm resources related to dwarfing, architecture, and fire-blight resistance in pears. In addition, steps were taken towards pear biotechnology capabilities: the new SY began establishing a tissue culture lab space, establishing key common pear rootstock accessions (OHxF 87 and 97), as well as common cultivars that have been used for genomics studies (Bartlett and Anjou). Collaborations and connections were established with ARS scientists in Riverside, California and Kearneysville, West Virginia, to explore rapid-cycle breeding history and options and obtain constructs for inducible flowering to be introduced into pears, with the goal of drastically shortening breeding cycles. Finally, work was conducted toward connecting and building the pear research community: a meeting of U.S. pear researchers in the fields of horticulture, genetics, and genomics was developed, planned, and executed, with the purpose of identifying common challenges and research topics between labs.

1. Evaluation of genetic basis of apple root disease resistance. ARS researchers in Wenatchee, Washington, identified components of the genetic basis for apple root disease resistance. Root health is crucial to the profitability of the apple industry as root disease can limit crop productivity. Root health among 65 types of apple rootstocks was assessed in response to pathogen infection. Rootstocks with contrasting disease resistance were shown to vary in disease-related gene expression. Stakeholders supported this research project as demonstrated by grant funding from Washington Tree Fruit Research Commission.

Review Publications
Somera, T.S., Freilich, S., Mazzola, M. 2021. Comprehensive analysis of the apple rhizobiome as influenced by different Brassica seed meals in the same soil/plant system. Applied Soil Ecology. 157. Article 103766.
Zhou, Z., Zhu, Y., Yi, T., Jia-Long, Y., Shuxun, B., Hengtao, Z., Ruiping, Z., Qiming, G., Zhenzhen, L., Zhenli, Y. 2021. MdPR4, a pathogenesis-related protein in apple, is involved in chitin recognition and resistance response to apple replant disease pathogens. Journal of Plant Physiology. 260.Article 153390.
Wang, L., Somera, T.S., Hargarten, H.L., Honaas, L.A., Mazzola, M. 2021. Comparative analysis of the apple root transcriptome as affected by rootstock genotype and Brassicaceae seed meal soil amendment: Implications for plant health. Microorganisms. 9(4). Article 763.
DuPont, T., Hewavitharana, S., Mazzola, M. 2021. Field scale application of Brassica seed meal and anaerobic soil disinfestation for the control of replant disease. Applied Soil Ecology. 166. Article 104076.
Waite, J.M., Dardick, C.D. 2021. The roles of the IGT/LAZY gene family in plant architecture: past, present, and future. Current Opinion in Plant Biology. 59:101983.