Analysis of environmental variables and carbon input on soil microbiome, metabolome and disease control efficacy in strawberry attributable to anaerobic soil disinfestation

Authors: HEWAVITHARANA, SHASHIKA - California Polytechnic State University; KLARER, EMMI - Washington State University; MURAMOTO, JOJI - University Of California; SHENNAN, CAROL - University Of California; Mazzola, Mark

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2021
Publication Date: 7/31/2021
Citation: Hewavitharana, S.S., Klarer, E.R., Muramoto, J., Shennan, C., Mazzola, M. 2021. Analysis of environmental variables and carbon input on soil microbiome, metabolome and disease control efficacy in strawberry attributable to anaerobic soil disinfestation. Microorganisms. 9(8),Article 1638. https://doi.org/10.3390/microorganisms9081638.
DOI: https://doi.org/10.3390/microorganisms9081638

Interpretive Summary: Soil-borne disease management without chemical fumigants remains a major challenge for strawberry production in California, and modifications to existing regulations are likely to intensify this challenge by further limiting availability of fumigants on a large percentage of strawberry acreage. Anaerobic soil disinfestation (ASD) was developed in Japan and the Netherlands as an alternative to soil fumigation and involves the generation of an anaerobic environment through a combination of flooding and addition of a carbon source to the soil system. Studies were conducted to determine whether changes in ASD protocol could improve overall control of strawberry soil-borne diseases. In general, it was found that conducting ASD at higher soil temperature provided superior control of multiple lethal diseases including Fusarium wilt, Verticillium wilt and charcoal rot of strawberry. Extending the period under which soils remained anaerobic, from 3 weeks to 6 weeks, did not improve disease control. This latter finding is significant as the reduced treatment period allows for a more rapid return by the grower into using the soil system for strawberry production. Enhanced disease control at higher ASD incubation temperatures was associated with generation of specific fungitoxic volatile compounds, which were produced in greater quantities under the higher temperature conditions. The carbon resources used in the conduct of ASD also influenced treatment effectiveness, with superior control of Fusarium wilt obtained when grass residues were used as the carbon input than when ASD was conducted using rice bran.

Technical Abstract: Charcoal rot, Fusarium wilt, and Verticillium wilt, caused by Macrophomina phaseolina, Fusarium oxysporum f. sp. fragariae, and Verticillium dahliae, respectively, are major soil-borne diseases of strawberry that have caused significant crop losses in California. Anaerobic soil disinfestation (ASD) has been studied as an industry level option for replacing soil fumigants to manage these serious diseases. Studies were conducted to discern whether incubation temperature, duration or interaction among these variables influenced the disease control efficacy in response to ASD. A combination of growth chamber and greenhouse studies were conducted using strawberry field soils from California naturally infested with each of the targeted soil-borne pathogens. A confirmatory study was carried out using Washington field soil artificially infested with F. oxysporum f. sp. fragariae. Overall, ASD treatment and incubation temperature, but not duration of the incubation period, significantly influenced disease suppression. Fusarium wilt and charcoal rot suppression was superior when ASD was conducted at elevated temperatures in combination with a 3-week incubation period. In terms of plant growth, ASD implemented with grass residues was more effective than ASD utilizing rice bran when evaluated under medium (32/26 ºC) and high (40/34 ºC) temperature incubation conditions: although, pathogen suppression was not always directly linked to strawberry growth response. Findings indicate that ASD-mediated disease suppression may partly stem from the toxic volatile compounds generated in an incubation temperature-dependent manner which are then associated with soil physiochemical changes.