A Microbiome Analysis of Soil Samples from Three Abandoned Lead-Silver Mines in the Arizona Sonoran Desert

There are many abandoned mines throughout the Arizona Sonoran Desert region and their environmental impact is yet to be fully understood. It was hypothesized that mining would result in decreased microbiome diversity, although some bacteria may adapt to the mine waste conditions. Soil samples were collected from three different mines in the Sonoran Desert and matched control sites. Soil total DNA was extracted and analyzed via 16S rRNA sequencing and analysis. Elemental analysis of the soils by x-ray fluorescence showed very different concentrations of toxic elements between the mine soils and the control sites. The concentrations of Pb, As, and Cu were as high as 8.1%, 0.72%, and 0.33%, respectively, of the soil mass at the mine soils, and thus much different than the control soils. There was an overall decrease in soil microbiome diversity and species richness in mine samples. Overall, approximately 50% of assigned Operational Taxonomic Units (OTU) overlapped between mine and control soil samples. Additionally, a total of 12 OTUs were detected within all mine soil samples and none of the control soil samples, suggesting these bacteria do not naturally occur in undisturbed desert soils within this region and instead were able to adapt to the extreme conditions of the former mines. One of these 12 bacteria was found to be a previously undescribed species that appears to be closely related to the phylum Chloroflexi.