Location: New England Plant, Soil and Water Research Laboratory
Project Number: 8030-21600-001-003-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2023
End Date: Aug 31, 2024
Objective:
1) Understand the microbial dynamics for accelerated biodegradation of the fumigant methyl isothiocyanate (MITC) in fumigated soil;
2) Examine soil amendments for the suppression of MITC degradation.
Approach:
1. Understand the microbial dynamics for accelerated biodegradation of MITC in fumigated soil.
a) Field trial. Replicated field plots either Vapam (metam sodium)-treated (45 gal/A) or non-treated will be planted to potato (var. ‘Russet Burbank'). The soil will be sampled using a soil probe and composite 20 cores in each plot, which will be conducted prior to fumigation, at planting, and immediately after harvesting for DNA extraction and bacterial isolation. Verticillium wilt and black scurf during the growing season and post-harvest and potato yield will be measured after harvesting.
b.) Microbial community. The soil DNAs obtained above will be analyzed using an Illumina sequencing platform based on the V3–V4 region of the 16S rDNA gene for bacteria and ITS region for fungi. Microbial communities will be analyzed using the QIIME 2 platform by classifying reads to taxa counts, and the Phyloseq procedure to visualize community differences between samples. Individual sequences of operational taxonomic units (OTUs) will be determined at various levels of the taxonomic hierarchy. Microbial diversity and abundance will be determined at phylum, family, and genus levels. Detected microorganisms will be grouped by function. Microorganisms targeting MITC-degrading bacteria will be isolated using dilution plating on a modified MITC-amended agar plate followed by incubation . Colonies will be purified and identified through a polymerase chain reaction (PCR) and DNA sequence analysis. PCR primers will be designed based on the amplified sequences and will be used for the identification of these MITC-degrading microorganisms in the soil.
2. Examining soil amendments on the suppression of MITC degradation
Field trials will be established at the Aroostook Farm in Maine for two years. The grain-seed-based inoculum of V. dahliae and R. solani will be broadcast and mixed in the soil followed by fumigation with Vapam at 45 gal/A in the fall. The trials will follow a randomized complete block design with 8 treatments and 4 replicates. Treatments are 1-2) non-treated; 3-5) cover crops such as winter rye, mustard, and winter pea, respectively will be planted 2 weeks after soil fumigation; 6-8) organic amendments such as cattle manure, biochar, and lobster shell meals will be applied in the following spring. Prior to fumigation, the isolated MITC-degrading organisms will be applied to the plots of treatments 2 to 8. Before manure application, the field will be planted with winter rye as a cover crop to reduce soil erosion. In the next spring, potato ‘Russet Burbank’ will be planted, and its growth, yield, and quality will be monitored throughout the crop season. Verticillium wilt and black scurf will be evaluated, and yield will be measured after harvest. The soil will be sampled at planting, one month, and two months after planting, at the middle of the bulking stage, and at harvest, and soil DNA will be extracted. MITC-degrading microorganisms, V. dahliae and R. solani will be quantified using a quantitative PCR.
