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, Ϸ25°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.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 g proteinase K ml Ϫ1 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 ϳ10-fold coverage) and Illumina draft sequencing (ϳ50-fold coverage). Finally, 454 paired-end libraries were constructed with a nominal insert size of 8 kb (sequenced to ϳ15-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 (Ն10 reads and Ն2 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 CO 2 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 p...

Acidithiobacillus ferriphilus sp. nov., a facultatively anaerobic iron- and sulfur-metabolizing extreme acidophile

“…All strains grew at 10 8C (five very slowly) and three strains (including the type strain) at 5 8C. From this it was concluded that A. ferriphilus is mesophilic, but that some strains are psychrotolerant, a feature that has only previously been reported for A. ferrivorans among the ironoxidizing acidithiobacilli (Hallberg et al, 2010;Liljeqvist et al, 2011). All strains were acidophilic and grew at pH 1.8, although two strains did not grow at pH 1.5, and none at pH 1.25.…”

Tetrathionate-Forming Thiosulfate Dehydrogenase from the Acidophilic, Chemolithoautotrophic Bacterium Acidithiobacillus ferrooxidans

“…The Sox complex is widely distributed in bacteria (23). Genes encoding sox homologs have been found in acidophilic sulfur oxidizers Acidithiobacillus caldus (24,25) and Acidithiobacillus thiooxidans (26), the neutrophilic sulfur oxidizer Thiobacillus denitrificans (27), and the iron-and/or sulfur-oxidizer Acidithiobacillus ferrivorans (28), although the sox genes are not necessarily complete. However, homologous genes have not been found in the A. ferrooxidans ATCC 23270 genome.…”

“…Although a suite of genes potentially encoding TQO has been identified in A. ferrooxidans (5), A. caldus (24,25), A. thiooxidans (26), and A. ferrivorans (28), the biochemical function of TQOs in these bacterial species remains elusive.…”

Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the Evolution of the Acidithiobacillus Genus

“…Together with other members of the genus Acidithiobacillus (10), this bacterium has the capacity to obtain energy from inorganic sulfur compounds (ISCs) and survive in extremely high concentrations of heavy metals. A. thiooxidans is one of four members of the genus Acidithiobacillus characterized to date (6,15,16,18) whose shared metabolic and functional capabilities allow them to survive in extremely acidic environments. Little is known about the genomic and functional properties of this microbe, and most information regarding this genus comes from experimental and genome-based analyses of Acidithiobacillus ferrooxidans and Acidithiobacillus caldus (7,8,15,12).…”