Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics

PLoS One. 2015 Mar 25;10(3):e0069533. doi: 10.1371/journal.pone.0069533. eCollection 2015.

Abstract

Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Arctic Regions
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Drug Resistance, Bacterial / genetics*
  • Genes, Bacterial / drug effects*
  • Metagenomics
  • Soil
  • Soil Microbiology*

Substances

  • Anti-Bacterial Agents
  • Soil

Grant support

The authors would like to acknowledge support from the following funders: (GGP) Fonds de Recherche du Quebec – Nature et technologies (www.fqr.gouv.qc.ca) and the Natural Sciences and Engineering Research Council of Canada Banting fellowships program (www.nserc-crsng.gc.ca); (MMD) the James S. McDonnell Foundation (www.jsmf.org), the Alfred P. Sloan Foundation (www.sloan.org), and the Harvard Milton Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.