Microbial communities in the rhizosphere of plants play a critical role in terrestrial nutrient cycling. The composition and abundance of bacteria and fungi has been attributed to a plant host effect and to microbial host preference, as well as to the chemical and physical properties of soils. The goal of this study was to better understand how the influence of plant host and soil properties affect the distribution of bacterial and fungal communities across a variety of native (Eastern North America) and non-native (East Asian) plant taxa planted in a single artificial setting. Soil samples from the Morris Arboretum of the University of Pennsylvania (Philadelphia, PA USA) were selected from one native and non-native species from each of the following genera—Acer, Quercus, and Pinus. To characterize a profile of microbial species associated with each tree, DNA was extracted directly from soil samples in preparation for Ilumina amplicon sequencing of loci targeting fungi (ITS & LSU rDNA) and bacteria (V4, 16S, SSU). A low concentration of high molecular weight genomic DNA was extracted, suggesting that soil amendments, pesticide application, and slightly elevated pH may be inhibiting microbial growth, and/or that seasonal fluctuations may considerably affect microbial abundance at the Arboretum. Future work should aim to purify extracted DNA of any contaminant prior to sequencing. Suggestions for more efficient soil maintenance are described in order to promote soil microbes that facilitate nutrient uptake by their plant hosts.