Bacterial evolution and adaptation to extreme industrial environments

The Cupriavidus metallidurans CH34 genome project: Bacterial evolution and adaptation to extreme environments through genomic rearrangements via mobile genetic elements

Cupriavidus metallidurans CH34 is a chemolithoautotrophic proteobacterium isolated and characterized for its capacity to tolerate a wide variety of heavy metal ions (including Zn, Cd, Co, Ni, Cu, Cr, Hg, Ag, As, Tl, Bi, Se, Te, and Pb). This type strain CH34 has been the subject of numerous taxonomic, ecological, biotechnological and genetic studies.

Its genome has been fully sequenced and consists of two megareplicons (3.9 Mb and 2.6 Mb in size) and two large plasmids (171 and 234 kb in size). To identify the key features of the CH34 genome and better understand the mechanisms involved in bacterial adaptation to extreme conditions a high-quality annotation effort was undertaken, using a remote system MaGe (from Génoscope, France) and a locally installed system GenDB (from Bielefeld University, Germany), installed on a SCK•CEN cluster of linux machines (177 CPUs). All genes and their products were structurally and functionaly defined. About 120 metal resistance and -response genes located on these plasmids cluster together on three large islands flanked by transposons that appear to be evolutionary inactivated to secure genetic stability. At least 10 additional Genomic Islands (GIs) in the size range of 20-105 kb were detected across the genome.

Based on the full genome sequence a whole-genome microarray chip covering all ~6,600 genes was constructed. These microarray chips are allow full genome comparative studies and are used to study the genetic responses of strain CH34 to a variety of stimuli including heavy metal toxicity, simulated microgravity and UV and gamma irradiation.

The elucidation of the microbial genetic adaptations to elevated metal concentrations and the potential of microbial activity on metal transformations is critical for efforts to predict the fate of metals, and particularly radionuclides, in the natural environment. Understanding these mechanisms is a key requirement for the design and implementation of bioremediation strategies and for gaining insights into synergistic interactions in high metal concentration environments.

Projects & Partners

Sebastien Monchy PreDoc project (SCK●CEN fellowship, ULB, 2002-2007), Pieter Monsieurs PostDoc project (SCK●CEN fellowship, 2008-2009)
In collaboration with : Dr. A. Lapidus from Joint Genome Institute (JGI) at Berkeley supported by the US Department of Energy (DoE) in USA, Dr. N. van der Lelie from BNL in USA, Prof. A. Toussaint from ULB in Belgium, Dr. C. Médigue from GénoScope in France, and Dr. A. Goesmann & Dr. B. Linke from CeBiTec in Germany.

Contact: Janssen Paul