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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Research Project #430475

Research Project: Managing Rhizosphere/Soil Microbiology via Apple Rootstock Chemistry

Location: Physiology and Pathology of Tree Fruits Research

Project Number: 2094-21220-002-08-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Apr 1, 2016
End Date: Sep 30, 2019

In the majority of crop production systems, including tree fruits, little is known regarding the mechanisms by which plant root systems attract or repel specific microorganisms. This interaction eventually determines composition of orchard soil and rhizosphere associated microbial communities that regulate numerous processes that determine overall soil health. Our preliminary research indicates that apple rootstocks may differ in root zone pH as well as in natural chemical compounds (metabolites) released into the rhizosphere. Previous research in other biological systems has demonstrated that pH can alter community composition of microbes as well as availability of soil nutrients. Additionally, certain chemical classes of compounds produced by roots can inhibit detrimental or recruit beneficial microbial communities. Our preliminary findings also indicate that different rootstock genotypes may attract different microbial communities from the same soil system. Outcomes from this research would include data for comparative metabolic phenotyping of popular apple rootstocks which has applications for rootstock breeding. Furthermore, potential delineation of natural chemical compounds that promote beneficial rhizosphere inhabiting microorganisms or inhibit various soil-borne pathogens will have application for soil treatment strategies. Finally, knowledge of rootstock effects on rhizosphere soil pH may forward tailoring rootstock selection to orchard soil type.

Soil, rhizosphere and endophytic microorganisms contribute directly and indirectly to crop performance through various processes including direct growth promotion, influence on nutrient availability and uptake, and limiting the activity of plant pathogenic organisms. Preliminary experiments have demonstrated that different apple rootstock genotypes differentially ‘recruit’ a disparate body of microorganisms from the same orchard soil system. If accurate, such a trait would have significant effects on the efficacy of a broad spectrum of orchard management issues including fertility management, pest/disease issues, soil health and overall scion development. The stability of rootstock genotype effect on the plant/soil microbiome will be assessed in studies conducted across three different orchard soils varying in texture (sandy loam, sandy, silt loam). Composition of the microbiome will be determined by through application of NextGen sequencing and subsequent bioinformatic analysis. Composition of root exudates across rootstock genotypes will be assessed by collection of exudates and characterization using liquid chromatography mass spectrometry analysis. Effect of rootstock specific exudates on beneficial and deleterious rhizosphere microbes will be assessed in vitro and in situ. Effect of rootstock genotype on soil pH will be determined and influence of pH on composition of the rhizosphere microbiome will be determined through NextGen sequence analysis.