In temperate forests, understory herbaceous plants are often affected by the abundance of white tailed deer, both directly through herbivory and indirectly through soil compaction. Soil chemistry, particularly soil pH, also has a large effect on the soil microbial communities that influence plant growth and survival. The objective of this study was to study the interactive effects of deer herbivory and soil chemistry on plant mutualists in forest soil using Jack-in-the-Pulpit plants. Jack-in-the-Pulpit are common understory herbs in temperate forests that deer will eat but are not preferred. In Bole Woods at the Holden Arboretum, 760 Jack-in-the-Pulpit plants were planted into 19 plots (both deer exclosures and un-fenced controls), each containing 4 subplots, 3 where soil chemistry had been altered and a control. Soil samples were collected from each subplot to be used for DNA analysis. Using PCR-terminal restriction fragment length polymorphism, we determined community structure of the fungal and bacterial communities. Our results showed that across communities of general fungal, AM fungi and bacteria, there were taxonomic differences present with soil chemistry alteration. Subplots that were amended with limestone and calcium had similar communities compared to subplots that were amended with triple superphosphate or the control. These differences reflected changes in soil pH that we had seen previously.