Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil

Abstract

Rahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface soils that is capable of promoting uranium phosphate mineralization as a result of constitutive phosphatase activity. Here we report the first complete genome sequence of an isolate belonging to the genus Rahnella.

GENOME ANNOUNCEMENT

Rahnella sp. strain Y9602 is a gammaproteobacterium isolated from a mixed-waste-contaminated subsurface (i.e., low pH and high concentrations of nitrate, heavy metals, and radionuclides) at the U.S. Department of Energy (DOE) Oak Ridge Reservation in Oak Ridge, TN (13). Phenotypic characterization of Y9602 indicated resistance to heavy metals, uranium tolerance, and constitutive phosphatase activity. Subsequent studies indicated that the strain precipitated 95% of soluble uranium [U(VI)] as an insoluble autunite mineral during oxic and anoxic growth conditions when supplied with glycerol-3-phosphate as the sole carbon and phosphorus source (1, 2, 12). Additionally, recent microbial ecology studies of metal-, metalloid-, organic-, and radionuclide-contaminated soils have identified enrichments of Rahnella species that show promise for remediation strategies (6, 10, 13, 15). Whole-genome sequencing was thus conducted on Rahnella sp. Y9602 to provide insights into its physiology, which promotes metal and radionuclide sequestration.

The complete genome of Rahnella sp. Y9602 was generated at the DOE Joint Genome Institute (JGI) using a combination of Illumina (3) and 454 (11) technologies. For this genome, an Illumina GAII shotgun library (38,026,764 reads totaling 2,890.0 Mb), a 454 Titanium standard library (260,211 reads), and a paired-end 454 library (269,624 reads totaling 194.8 Mb) were generated and sequenced. All general aspects of library construction and sequencing can be found on the JGI website (http://www.jgi.doe.gov/). The initial draft assembly contained 54 contigs in 3 scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together with Newbler, version 2.3. Illumina sequencing data were assembled with Velvet, version 0.7.63 (16). We integrated the 454 Newbler consensus shreds, the Illumina Velvet consensus shreds, and the read pairs in the 454 paired-end library using parallel Phrap, version SPS-4.24 (High Performance Software, LLC). The software Consed (4, 5, 7) was used in the following finishing process. Illumina data were used to correct potential base errors and increase consensus quality by using the software Polisher, developed at JGI (A. Lapidus, unpublished data). Possible misassemblies were corrected by using GapResolution (C. Han, unpublished data) or Dupfinisher (8) or by sequencing subcloned PCR products. Gaps between contigs were closed by editing in Consed, by PCR, and by Bubble PCR (J.-F. Cheng, unpublished data) primer walks. Protein-encoding genes were determined by Prodigal (9) and GenePrimp (14). The total size of the genome is 5,614,252 bp (chromosome and plasmids), and the final assembly is based on 191.2 Mb of 454 draft data (35× coverage) and 3,166.1 Mb of Illumina draft data (576× coverage).

The Rahnella sp. Y9602 chromosome has a GC content of 52.4%, is 4,864,217 bp in size, and contains two plasmids, pRAHAQ01 and pRAHAQ02, consisting of 616,549 bp (52.1% GC content) and 133,486 bp (48.3% GC content), respectively. The genome contains 5,184 protein-encoding genes, 73 pseudogenes, 76 tRNA genes, and 7 rRNA gene operons.

Nucleotide sequence accession numbers.

The complete genome sequence of Rahnella sp. Y9602 is available in DDBJ/EMBL/GenBank under the accession number CP002505, in the IMG database under accession number 649633088, and in the Genomes OnLine Database under accession number Gc01605. The GenBank accession numbers for plasmids pRAHAQ01 and pRAHAQ02 are CP002506 and CP002507, respectively.