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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Publications at this Location » Publication #403434
Research Project: Uncovering Rootstock Disease Resistance Mechanisms in Deciduous Tree Fruit Crops and Development of Genetics-Informed Breeding Tools for Resistant Germplasm

Location: Physiology and Pathology of Tree Fruits Research

Title: Engineering disease-suppressive soil microbiomes using network-based analysis of metagenomics data [abstract]

Author
item Somera, Tracey
item BERIHU, MARIA - Agricultural Research Organization - Volcani Center
item MALIK, ASSAF - University Of Haifa
item MEDINA, SHLOMIT - University Of Torino
item PIOMBO, EDOARDO - Swedish University
item TAL, OFIR - Agricultural Research Organization - Volcani Center
item COHEN, MATAN - Agricultural Research Organization - Volcani Center
item GINATT, ALON - Agricultural Research Organization - Volcani Center
item OFEK-LALZAR, MAYA - University Of Haifa
item DORON-FAIGENBOIM, ADI - Agricultural Research Organization - Volcani Center
item MAZZOLA, MARK - Stellenbosch University
item FREILICH, SHIRI - Agricultural Research Organization - Volcani Center

Submitted to: APS Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/15/2023
Publication Date: 8/15/2023
Citation: Somera, T.S., Berihu, M., Malik, A., Medina, S., Piombo, E., Tal, O., Cohen, M., Ginatt, A., Ofek-Lalzar, M., Doron-Faigenboim, A., Mazzola, M., Freilich, S. 2023. Engineering disease-suppressive soil microbiomes using network-based analysis of metagenomics data [abstract]. APS Annual Meeting. Paper No. 524.

Interpretive Summary:

Technical Abstract: Sustainable agricultural practices seeking to harness the potential of the native soil microbiome commonly rely on the application of complex organic mixtures in which the resources/metabolites stimulating beneficial microbial groups are not well characterized. Outcomes of such indirect approaches are unpredictable in terms of achieving a plant-beneficial environment. In this study, shotgun metagenomic analysis of ‘sick’ (apple plants grown in diseased soil) vs. ‘healthy/recovered’ rhizobiomes (apple plants grown in diseased soil amended with Brassica seed meal formulations) was conducted. Network analysis of metagenomics data was then used to explore amendment-derived transformations in the rhizosphere microbiome of apple leading to the suppression of soil-borne pathogens. Simulations of community-level metabolic interactions examined functional contributions of bacterial groups and linked them with specific metabolites induced by the seed meal amendments. Metabolites predicted to either stimulate (e.g. dopamine) or suppress (e.g. vitamin B12) specific bacterial groups were tested for their effect on rhizobiome composition. The metabolite enrichment experiment with dopamine corroborated its role as a modulator of specific plant-beneficial taxa. This research provides a computational framework for enabling the development of informed, amendment-based solutions for engineering native soil microbiomes in agroecosystems.