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Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site


Morris, James; Goswami, Anuradha; Adkins-Jablonsky, Sarah (2023), Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site, Dryad, Dataset,


The data in this archive are the results of a study on the impact of heavy metals (HMs) on the soil microbiota of an urban Superfund site in Alabama. HMs are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease.


Full methods are contained in our publication "Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site" in Microbiology Spectrum. Briefly, we collected soils from replicate locations in two zip codes in North Birmingham, Alabama. One zip code contains the heavy-metal-polluted 35th Avenue Superfund Site, and the second is demographically comparable but outside of the Superfund borders. Using a mixture of culture-based and next generation sequencing approaches, we characterized the microbial communities and their levels of heavy metal and antibiotic resistance in both zip codes to test the hypothesis that chronic anthropogenic metal contamination selects for antimicrobial resistance in environmental bacterial populations.

Usage notes

All of our analyses can be run using R, mothur, and QIIME, all of which are open-source.


National Science Foundation, Award: OCE-1851085

National Institute of Environmental Health Sciences, Award: NIH P42-ES027723