SREL Reprint #3420

Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA

Ashish Pathak1, Ashvini Chauhan1, Paul Stothard2, Stefan Green3, Mark Maienschein-Cline3, Rajneesh Jaswal1, and John Seaman4

1Environmental Biotechnology and Genomics Laboratory, School of the Environment,
1515 S.Martin Luther King Jr. Blvd., Suite 305B, FSH Science Research Center,
Florida A&MUniversity, Tallahassee, FL 32307, USA
2Department of Agricultural, Food and Nutritional Science, University of Alberta,
Edmonton, AB T6G2P5, Canada
3DNA Services Facility, University of Illinois at Chicago, Chicago, IL 60612, USA
4Savannah River Ecology Laboratory, University of Georgia, Aiken, SC 29802, USA

Abstract: Savannah River Site (SRS), an approximately 800-km2 former nuclear weapons production facility located near Aiken, SC remains co-contaminated by heavy metals and radionuclides. To gain a better understanding on microbially-mediated bioremediation mechanisms, several bacterial strains resistant to high concentrations of Uranium (U) and Nickel (Ni) were isolated from the Steeds Pond soils located within the SRS site. One of the isolated strains, designated as strain SRS-W-2-2016, grew robustly on both U and Ni. To fully understand the arsenal of metabolic functions possessed by this strain, a draft whole genome sequence (WGS) was obtained, assembled, annotated and analyzed. Genome-centric evaluation revealed the isolate to belong to the Burkholderia genus with close affiliation to B. xenovorans LB400, an aggressive polychlorinated biphenyl-degrader. At a coverage of 90×, the genome of strain SRSW-2-2016 consisted of 8,035,584 bases with a total number of 7071 putative genes assembling into 191 contigs with an N50 contig length of 134,675 bases. Several gene homologues coding for resistance to heavy metals/radionuclides were identified in strain SRS-W-2-2016, such as a suite of outermembrane efflux pump proteins similar to nickel/cobalt transporter regulators, peptide/nickel transport substrate and ATP-binding proteins, permease proteins, and a high-affinity nickel-transport protein. Also noteworthy were two separate gene fragments in strain SRS-W-2-2016 homologous to the spoT gene; recently correlated with bacterial tolerance to U. Additionally, a plethora of oxygenase genes were also identified in the isolate, potentially involved in the breakdown of organic compounds facilitating the strain's successful colonization and survival in the SRS co-contaminated soils. The WGS project of Burkholderia sp. strain SRS-W-2-2016 is available at DDBJ/ENA/GenBank under the accession #MSDV00000000.

Keywords: uranium, nickel, biomineralization, metal resistance genes, whole genome sequencing (WGS), Burkholderia

SREL Reprint #3420

Pathak, A., A. Chauhan, P. Stothard, S. Green, M. Maienschein-Cline, R. Jaswal, and J. C. Seaman. 2017. Genome-centric evaluation of Burkholderia sp. strain SRS-W-2-2016 resistant to high concentrations of uranium and nickel isolated from the Savannah River Site (SRS), USA. Genomics Data 12(2017): 62-68.

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).