Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3

Abstract

Acidithiobacillus ferrivorans SS3 is a psychrotolerant acidophile capable of growth in the range of 5° to 30°C (optimum, ≈25°C). It gains energy from the oxidation of ferrous iron and inorganic sulfur compounds and obtains organic carbon from carbon dioxide. Here, we present the draft genome sequence of A. ferrivorans SS3 that will permit investigation of genes involved in growth in acidic environments at low temperatures.

GENOME ANNOUNCEMENT

Psychrotolerant acidophiles from the Acidithiobacillus genus constitute a new species, Acidithiobacillus ferrivorans (4). This sequenced strain, A. ferrivorans SS3 (originally named Acidithiobacillus ferrooxidans SS3), was isolated from Norilsk, Russia, and was noted for its growth and oxidation of ferrous iron and inorganic sulfur compounds (ISCs) at low temperatures (2, 7, 8). Strains of A. ferrivorans catalyze low-temperature metal solubilization in the biotechnological process “bioleaching,” and it is the dominant species during complex multi-metal sulfide mineral dissolution at 7°C (2). In addition, a mixed culture dominated by A. ferrivorans is being investigated for low-temperature ISC removal from mining process waters (9).

DNA preparation, genome sequencing, and draft assembly.

A. ferrivorans SS3 was colony streaked 3 times on agarose plates (5), and a single colony was inoculated into pH 2.5 mineral salts medium (3) and incubated at 6°C. Cells were pretreated with 200 μg proteinase K ml⁻¹ in Tris buffer for 10 min at 50°C and lysed with 2% (wt/vol) sodium dodecyl sulfate. High-quality DNA was prepared and then checked via the genomic DNA QC protocol (http://my.jgi.doe.gov/general/). Libraries were constructed for 454 (standard libraries sequenced to ∼10-fold coverage) and Illumina draft sequencing (∼50-fold coverage). Finally, 454 paired-end libraries were constructed with a nominal insert size of 8 kb (sequenced to ∼15-fold sequence depth). Gene prediction and annotation was performed as described previously (11, 12).

Genome analysis.

The A. ferrivorans SS3 draft genome is 3,152,659 bp distributed in 61 contigs (≥10 reads and ≥2 kbp), with an average coverage of 30-fold. The sequence has a GC content of 56.5% and, according to the JGI sequence annotation pipeline, contains 3,257 candidate protein-encoding gene models. The genome exhibits genes potentially encoding CO₂ fixation by the Calvin-Benson-Bassham cycle, rus and petI operons involved in iron oxidation, genes for assimilatory sulfur reduction, and a complete repertoire of genes for nitrogen metabolism. A suite of genes potentially encoding ISC metabolizing enzymes were identified (also present in other acidithiobacilli), including tetrathionate hydrolase (tth), sulfide quinone reductase (sqr), and thiosulfate quinone oxidoreductase (doxD). However, in contrast to sequenced A. ferrooxidans strains, A. ferrivorans SS3 contains genes potentially encoding the sulfur oxidation complex SOX (soxYZ-hypB) and a sulfur oxygenase:reductase gene (sor) similar to those in Acidithiobacillus caldus (10, 12). Unexpectedly, a full set of genes is predicted for uptake and reduction of nitrate (nitrate reductase [nar], nitrite reductase [nir], and nitric oxide reductase [nor]). This suggests that A. ferrivorans SS3 can oxidize thiosulfate under denitrifying conditions, as observed for Thiobacillus denitrificans (1). Genes potentially encoding trehalose biosynthesis that are not present in the other sequenced acidithiobacilli and that could help in conferring psychrotolerance were identified (6). These findings aid investigations into the origin and evolution of genomic and metabolic diversity in acidithiobacilli and help unveil the underlying biology of psychrotolerance, vital for understanding bioleaching operations in cold climates.

Nucleotide sequence and accession number.

The draft sequence is available at http://genome.jgi-psf.org/acifs/acifs.home.html and is deposited in GenBank (accession number AFJD00000000).