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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Research Project #432886

Research Project: Managing Soil and Rhizosphere Microbiology for Soil-borne Disease Control in Tree Fruits

Location: Physiology and Pathology of Tree Fruits Research

Project Number: 2094-21220-002-25-A
Project Type: Cooperative Agreement

Start Date: Aug 1, 2017
End Date: Apr 30, 2019

Poor growth when establishing new fruit tree orchards on ground previously planted to the same crop is caused by a diverse soil-borne pathogen complex and is termed replant disease. The disease can cost growers more than $70,000 to $150,000 an acre in reduced returns over the first four years of orchard production. Management of replant disease has historically relied on pre-plant application of broad spectrum soil fumigants. Increasing public concern over toxicity to humans and aquatic organisms as well as impacts on the ozone layer has led to a new set of US Environmental Protection Agency regulations to reduce the risk of soil fumigants and new regional restrictions prohibiting certain fumigant chemistries. Practical, effective alternatives will be critical in the long term if increased regulation removes soil fumigant chemistries as tools for orchardists. Such alternatives are also required now for the expanding organic tree fruit industry which currently lacks any replant disease control strategy. Mustard seed meal (MSM) soil amendment and anaerobic soil disinfestation (ASD) have demonstrated effective control of replant disease in small scale field studies. For both methods, disease control is attained through the activity of chemical and microbiologically-controlled mechanisms. The functionality of mechanisms controlled by soil and rhizosphere-inhabiting microorganisms is likely to be modulated by rootstock genotype as previous studies have demonstrated differential capacity of apple rootstocks to recruit beneficial microorganisms to the rhizosphere. Although mustard seed meal soil amendment and anaerobic soil disinfestation approaches have been successful in research trials, it is critical to demonstrate efficacy and practicality on a large scale in orchards in order to catalyze adoption. This project builds on many years of past efforts to move MSM amendment protocols and ASD onto the farm where we hope to provide growers with more effective mitigation of replant disease. If successful, 47,000 acres at risk to apple replant disease every year could be more productive with less potential environmental risk. Specific objectives are to: 1.) Characterize the effect of apple rootstock genotype on composition of the rhizosphere and orchard soil microbiome and its relationship with replant disease tolerance/susceptibility. 2.) Establish large scale field trials in commercial orchard settings to test the efficacy of mustard seed meal amendment and anaerobic soil disinfestation as alternatives to soil fumigation for the control of apple replant disease. 3.) Assess the effect of rootstock genotype on efficacy of MSM and ASD in control of replant disease.

Sequential planting of rootstock liners in greenhouse trials will be conducted and assessment of the effect of rootstock genotype on composition of the microbiome will be determined. Carbon sources to be used in anaerobic soil disinfestation and rates of soil amendment used in ASD and mustard seed meal treatments are based upon our previous controlled environment and small scale field trials. Triticale will be grown on site and incorporated into soils to be treated with ASD at a rate of 6 t per acre. MSM treatment will use a Brassica juncea/Sinapis alba formulation and applied at the rate of 3 t per acre. The site will be planted to Honeycrisp grafted onto G.41 rootstock. It is evident that soil-borne disease suppression in response to ASD and MSM amendment involves the activity of the resident soil microbiome and disease control efficacy of ASD and MSM has been associated with shifts in soil microbial community structure. Therefore, field studies will be established employing both ASD and MSM treatments and will be planted to a spectrum of apple rootstock genotypes either as rootstock liners or grafted trees bearing cv. Honeycrisp as the scion. Treatment efficacy will be assessed based upon increase in tree cross-sectional area, yield and suppression of target pathogens. Colonization of tree roots by individual pathogens and lesion nematode will be conducted using real-time quantitative PCR methods. For large scale grower-based field trial, soil and rhizosphere microbial community analyses will be conducted on samples collected periodically over a three year post-treatment period using Terminal Restriction Fragment Length Polymorphism analyses of bacterial 16S rRNA genes and the fungal rDNA internal transcribed spacer region.