Effect of fumigation, cover crops, and potato growth on shifts in soil microbial communities.

Fumigation as a broad-spectrum pesticide can affect both pathogenic and non-target microorganisms in the soil. As microbial communities are critical within the soil ecosystem, depletion of or changes in these communities can result in negative implications for soil health. Because cover crops are used to enhance soil health physically, chemically, and biologically, they might recover the soil health of the fumigated soil. However, little information is available on the interactive effect of these practices on soil health especially regarding the soil microbiome. This study was to investigate microbial community shifts as affected by fumigation and cover crops in different stages of potato field management practices. A year-long field test was conducted in Adkins sandy loam of Eastern Oregon following a split-plot design with fumigation as main plots and cover crops as subplots. Fumigation treatments included non-fumigated control, metam sodium, 1,3-dichloropropenene, and metam sodium+1,3-dichloropropenene. Soil samples were collected around the termination of cover crops and after potato harvesting for soil microbial analysis. 16S and ITS rRNA- gene sequencing analyses were employed to understand the prokaryote and eukaryote populations, respectively. Microbial community analysis indicated no significant interaction between the treatment conditions, with cover crops resulting in no significant shifts in the soil microbial community. Combination fumigation treatments (metam sodium+1,3-dichloropropenene) resulted in the largest community shifts for both prokaryotic and eukaryotic communities, with significant abundance changes in the bacterial phyla Acidobacteriota, Planctomycetota, and Verrucomicrobiota and the eukaryotic phyla Ascomycota and Basidiomycota compared with no fumigation control; and these changes did not repeat from cover crop planting, although subsequent years of study are needed to establish definitive trends in community shifts.