Journal Article

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Cartee, John C., Beasley, James C., Thomas, Jesse C., Kieran, Troy J., Rhodes, Olin E., Oladeinde, Adelumola, Bayona‐Vásquez, Natalia J., Finger, John W., Glenn, Travis C., McArthur, J Vuan, Seaman, John C.

2020

Overview

Summary Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co‐selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim’s Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co‐occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment. We present a comprehensive analysis of the soil microbiome in several areas affected by legacies of heavy‐metal and radionuclide contamination. We explore how these contaminants affect bacterial community composition and diversity, and the enrichment of antibiotic, biocide, and metal‐resistance genes. We find that these contaminants can not only have a profound impact on soil microbiome composition, but it can also affect how it functions.

• Publisher: John Wiley & Sons, Inc,Wiley,John Wiley and Sons Inc
• Subject: Anti-Bacterial Agents - pharmacology / Antibiotic resistance / Antibiotics / Antimicrobial agents / Antimicrobial resistance / Arsenic / Bacteria / Bacteria - genetics / BASIC BIOLOGICAL SCIENCES / Basins / Biocides / Biotechnology & Applied Microbiology / Contaminants / Contamination / Disinfectants / Drug resistance / Gene sequencing / Genes / Genes, Bacterial / Heavy metals / Humans / Metagenomics / Metals, Heavy - toxicity / Microbiology / Nickel / Radioisotopes / Relative abundance / Rivers / RNA, Ribosomal, 16S - genetics / rRNA 16S / Savannahs / Soil / Soil contamination / Soil Microbiology / Soil microorganisms / Soil pollution / Soil structure / Soils / Vancomycin / Water pollution