Manipulation of the orchard soil microbiome: Implications for soil-borne disease suppression and apple production

Authors: Mazzola, Mark; Somera, Tracey; Van Horn, Christopher; LEISSO, RACHEL - Montana State University; FREILICH, S - Newe Ya'Ar Research Center

Submitted to: Symposium Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 8/3/2019
Publication Date: 9/9/2019
Citation: Mazzola, M., Somera, T.S., Van Horn, C.R., Leisso, R., Freilich, S. 2019. Manipulation of the orchard soil microbiome: Implications for soil-borne disease suppression and apple production. Symposium Proceedings. p. 16.

Interpretive Summary:

Technical Abstract: Interventions targeted to manipulation of the soil/rhizosphere microbiome is a tool commonly employed to suppress activity of soil-borne pathogens. Such strategies often utilize an undirected approach, such as soil fumigation, or directed approaches that take advantage of host and non-host resistance (crop rotation) to a specific pathogen. The biologically multifaceted phenomenon termed apple replant disease is resistant to extended suppression, with soil fumigation generally providing a temporally limited (<1-year) period of disease control. This research program has sought to direct assembly of the soil/rhizosphere microbiome in a manner that provides initial soil-borne disease control while also limiting subsequent pathogen re-infestation of the orchard soil system. We have employed various strategies to attain this goal including pre-plant application of defined soil amendments and exploitation of rootstock genotypes to amplify or recruit specific microbial consortia to the rhizosphere. Sustained suppression of multiple soil-borne pathogens in response to Brassicaceae seed meal amendment was found to rely upon transformation of the indigenous soil microbiome. The dominant microbial elements contributing to disease suppression differed with the target pathogen with multiple functional modes of action inferred. Apple rootstock genotype also influenced composition of the rhizosphere microbiome and was associated with differences in the root exudate metabolome. Field trials demonstrated persistent (multi-year) changes to the rhizosphere microbiome and associated suppression of soil-borne pathogens in response to seed meal treatments. Non-target benefit, including suppressed inoculum potential of post-harvest pathogens, may also be realized. Our findings suggest that plant rhizosphere and amendment-based engineering of the soil microbiome may yield more resilient and productive orchard systems than that attained in response to pre-plant soil fumigation.