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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Research Project #432906

Research Project: Metabolic Network Approaches for Deciphering Microbial Functions in Amendment-Based Solutions for Soil-Borne Disease Suppression

Location: Physiology and Pathology of Tree Fruits Research

Project Number: 2094-21220-002-026-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Nov 1, 2017
End Date: Jul 31, 2021

Plant health relies on the interactions between the plant and its associated microbiome which is shaped by exudates secreted into the rhizosphere. Modifications in community structure may result in enhanced or diminished productivity due to its influence on the activity of soil-borne plant pathogens. In many perennial cropping systems, plant-induced modifications to the rhizosphere and soil microbiome commonly yield a community that not only diminishes productivity of the current orchard or plantation but also impedes successful establishment of a new planting of the same or related species on the site. The common management practice against the syndrome, termed replant disease, has been based on broad spectrum solutions, in particular the application of pre-plant soil fumigation. In apple orchards, sustainable solutions based on soil amendments have shown a more persistent and superior effect. However, to date, the efficacy of the approach may not be stable over the history of production and is not always repeatable across sites. Moreover, the applicability of sustainable approaches for other crop trees has not yet been tested. Understanding of the changes in microbial community function in response to plant establishment is the key to defining a generic approach for the development of sustainable solutions to such soil-borne disease syndromes. Metabolic network approaches provide a new frame-work for understanding how diversity changes, as detected in metagenomic surveys, are associated with functional changes in the corresponding community, and how external metabolic signals (such as those introduced by soil amendment treatments) control community shifts.

Here we suggest integrating microbiology, genomics and community-level metabolic-network analysis approaches for studying the role of microbial ecology in cause and control of soil-borne plant diseases. To this end, we will conduct comparative community analyses in soils from apple orchards expressing varying degrees of severity of soil-borne disease syndromes, following effective and ineffective soil amendment treatments. The comparative analyses will go beyond community structure and will aim at characterizing community functions that are associated with ‘healthy’ vs ‘sick’ community performances, leading to testable predictions for how to promote the assembly of disease suppressive communities. The overall aim is to garner an understanding of the processes shaping the causal microbiology of replant diseases and the mechanisms behind the function of successful treatments, with opportunity to take advantage of both the indigenous soil microbiome as well as host genotype to optimize the potential for disease control, using sustainable approaches.