The data set contains results from a microbial survey project produced from a joint effort between the Genomes to Field (G2F) initiative and Indigo Ag. In this project Indigo performed microbial community analyses across 42 G2F and other locations across the Continental US, targeting the plant, soil, and rhizosphere in maize research plots. The objective of the survey was to develop a rich database of fungal and bacterial communities using DNA sequencing based assays across agronomically relevant locations of the US. This data may be used to understand the variation in microbial populations across locations and could provide important supporting data for scientist in different fields of research. Multiple soil and whole plant samples with attached rhizosphere were collected from G2F maize trials to support indigeneity data generation. Sample processing was completed with the primary goal of developing a reference sequences database of indigeneity data. Finally, a DNA sample repository was created to enable future work and public access.