Soil microorganisms have a variety of beneficial and deleterious effects on plants, impacting such processes as plant growth, soil nutrient cycling, crop yield, disease resistance and tolerance to an array of biotic and abiotic stressors. The disruption of soil microbial community structures, particularly when beneficial soil biota are altered, has been shown to reduce crop yield and leave plants susceptible to disease. Long-term disruption of microbial communities may occur with repeated fumigation, being the application of gaseous pesticides, in agricultural soils. For this reason, we characterized bacterial, fungal, oomycete and nematode populations in paired fumigated and nonfumigated potato fields located in Idaho, Oregon, Washington and Minnesota. Samples were taken at three distinct timepoints: one before a fall fumigation event and two others at important stages in potato production, row closure and vine death. Soil biota populations were assessed by targeting the 16S, 18S and ITS1 gene regions. FunGuild, a database capable of guild and trophic assignment of fungal lineages, was used to sort fungal OTUs in different trophic modes. Fungal analyses indicated an increase in relative abundances of saprotrophic fungal populations and a decrease in pathotrophic fungal populations, both during row closure. Principally, the fungal genera of Humicola and Mortierella were responsible for the increase of saprotrophs while Alternaria decreased the most for pathotrophs. Other fungi occupying multiple trophic modes, such as Fusarium, also decreased during row closure. We found that fumigation treatments, in combination with various pesticide and fertilizer applications, alter both alpha- and beta- bacterial soil diversity although certain treatments, i.e. chloropicrin, may alter bacterial populations more than other treatment types such as metam-sodium. Nematode populations were likewise distinct at each location with soils from Boardman, OR, Minidoka, ID and Pine Point, MN with these having higher levels of nematodes associated with better soil health, i.e. Dorylaimidae. Conversely, nematodes associated with plant pathogenesis were found in higher relative abundances at Minidoka, ID and Quincy, WA. In this study, we characterize the populations of bacteria, fungi, oomycetes and nematodes with an emphasis on fungal taxa. We found that relative abundances of fungal trophic modes vary temporally. Additionally, we catalogue several other high abundance taxa with seasonal differential abundances whose functional capacity in potatoes remain uncharacterized.