Environmental Science and Pollution Research

, Volume 25, Issue 2, pp 1470–1483 | Cite as

Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters

  • Florence Arsène-Ploetze
  • Olfa Chiboub
  • Didier Lièvremont
  • Julien Farasin
  • Kelle C. Freel
  • Stephanie Fouteau
  • Valérie Barbe
Research Article


Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.


Acid mine drainage (AMD) Comparative genomics Extrusion pumps Genome evolution Horizontal gene transfer 



We thank Abdelmalek ALIOUA for performing the Sanger sequencing experiments and Fabienne Battaglia-Brunet for providing the Tm. delicata DSM16361 strain.

Author contributions

O. C., D. L., J. F., K. C. F., S. F., and F. A.-P. performed research; O. C., K. C. F., V.B., and F.A.-P. wrote the paper.

Funding information

This work was supported by the Université de Strasbourg (unistra), the Centre National de la Recherche Scientifique (CNRS) and the Region Alsace to J. F. This study was financed by the THIOFILM (ANR-12-ADAP-0013) projects. O. C., J. F., and K. C. F. were supported by the Agence Nationale de la Recherche, ANR THIOFILM (ANR-12-ADAP-0013).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11356_2017_535_MOESM1_ESM.xlsx (22 kb)
ESM 1 (XLSX 21 kb)


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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de StrasbourgStrasbourgFrance
  2. 2.Institut de Biologie Moléculaire des Plantes, CNRS, Université de StrasbourgStrasbourgFrance
  3. 3.Institut de Chimie de Strasbourg, UMR7177 CNRS-Université de StrasbourgStrasbourgFrance
  4. 4.Laboratoire de Biologie Moléculaire pour l’Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/GenoscopeEvryFrance

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