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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Publications at this Location » Publication #361944

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

Location: Physiology and Pathology of Tree Fruits Research

Title: Impacts of anaerobic soil disinfestation carbon source on dynamics of the soil metabolome and microbiome

item KLARER, EMMI - Washington State University
item HEWAVITHARANA, SHASHIKA - Washington State University
item Rudell, David
item Mazzola, Mark

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: 4/6/2019
Publication Date: 10/25/2019
Citation: Klarer, E., Hewavitharana, S., Rudell Jr, D.R., Mazzola, M. 2019. Impacts of anaerobic soil disinfestation carbon source on dynamics of the soil metabolome and microbiome. Phytopathology. 109:S2.69.

Interpretive Summary:

Technical Abstract: Anaerobic soil disinfestation (ASD) is a pre-plant soil treatment which entails soil incorporation of a labile carbon source, saturation of soil pore spaces with water and subsequent tarping. ASD induces a shift in soil microbiome composition but the relationship between carbon input type and effects on subsequent trajectory of the microbiome and metabolome structure has not been assessed. With the appropriate carbon source, ASD has proven effective in control of specific soil-borne diseases in strawberry, such as Verticillium wilt caused by Verticillium dahliae. However, no such combination has consistently controlled Fusarium wilt in strawberry, caused by Fusarium oxysporum f. sp. fragariae (Fof). The impacts of ASD using different carbon amendments on the soil microbiome and metabolome were characterized over a time-course study conducted in pasteurized and native soils artificially infested with Fof. Carbon inputs tested were ground orchard grass 10 tons ha-1; rice bran 4.9 tons ha-1; ground wheat grass 10 tons ha-1 and compared to no amendment controls. Sampling was performed on days 0, 1, 3, 7, 15, and 21 during ASD and days 24, 28 and 31 post-ASD. DNA extracted from soil was used in quantification of Fof by RT-qPCR. To define potential mechanisms of disease suppression, the soil metabolome was characterized using LC-MS and GC-MS, the soil microbiome was described by amplicon sequencing, and resulting profiles were were analyzed relative to pathogen density.