Genome Sequence of Desulfosporosinus sp. OT, an Acidophilic Sulfate-Reducing Bacterium from Copper Mining Waste in Norilsk, Northern Siberia

GENOME ANNOUNCEMENT

Members of the genus Desulfosporosinus are sulfate-reducing bacteria, often found in microbial communities associated with mining environments and involved in the bioremediation of metal-contaminated water and sediments (1, 5–8, 12). In these environments, enriched with SO₄²⁻, sulfate reduction contributes to precipitation of metal sulfides and thereby the immobilization of toxic metals. Recently, Desulfosporosinus bacteria were identified as key players in microbial sulfate reduction in a low-sulfate peatland (13). Here we announce the first draft genome of a member of the genus Desulfosporosinus. Desulfosporosinus sp. OT was isolated from acidic sediment (sample T9) of a copper-mining waste site in Norilsk, Russia (10).

Genomic DNA was isolated by alkaline lysis (4). Sequencing was carried out by pyrosequencing, using an FLX genome sequencer (Roche). A total of 357,734 reads with an average read length of 400 bp resulted in 142,885,740 sequenced bases. Sequence assembly was performed with GS De Novo Assembler version 2.3 software with default settings, yielding 304 contigs with an average size of 22,674 nucleotides and an average of 42% GC content. The number of the bases in all contigs totaled 5,705,508, corresponding to 25-fold sequencing coverage. Identification of open reading frames and annotation were performed by the annotation service for microbial genomes of the Institute for Genome Sciences (IGS), School of Medicine, University of Maryland. The annotation yielded 6,222 open reading frames for proteins, 74 tRNA genes, and 3 rRNA genes. The 16S RNA sequence of Desulfosporosinus sp. OT is 99.4% and 98.1% identical with those of Desulfosporosinus sp. 5apy (GenBank accession no. AF159120) and Desulfosporosinus lacus (GenBank accession no. AJ582757) (14), respectively, which are the most closely related microbial isolates.

Desulfosporosinus sp. OT withstands copper concentrations of up to 236 mM, which is severalfold higher than the concentrations so far reported for other sulfate-reducing bacteria such as Desulfovibrio sp. A2 (genome announcement submitted for publication) or Desulfovibrio sp. R2, also isolated from metal-contaminated habitats (9, 11). Desulfosporosinus sp. OT harbors two CopA-like CPx-type ATPases (see reference 16 for a review), DOT_2451 and DOT_2536, and a polyphosphate kinase-phosphatase couple, DOT_3559 and DOT_4690, as present in Acidithiobacillus ferrooxidans. These systems appear to play a key role in copper tolerance (2). As would be expected for a Gram-positive organism, no CueO-like multicopper oxidase system or cus-like copper efflux system, both of which serve in the control of periplasmic copper in Escherichia coli and other Gram-negative bacteria, is present (15). Also, neither a CopC-like periplasmic copper-binding protein nor a CopD-like integral membrane protein could be found in the genome of Desulfosporosinus sp. OT. These two proteins were first identified as copper resistance determinants carried on a plasmid of Pseudomonas syringae but are also found in the genomes of Gram-negative as well as Gram-positive organisms (3). Based on the genomic information, investigations of the exceptional copper resistance of Desulfosporosinus sp. OT can now be tackled experimentally. Work along these lines in our laboratory is currently proceeding.