Draft Genome Sequence of the Extremely Acidophilic BacteriumAcidithiobacillus caldusATCC 51756 Reveals Metabolic Versatility in the GenusAcidithiobacillus

Abstract

Acidithiobacillus caldus is an extremely acidophilic, moderately thermophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and reduced inorganic sulfur compounds. Here we present the draft genome sequence of Acidithiobacillus caldus ATCC 51756 (the type strain of the species), which has permitted the prediction of genes for survival in extremely acidic environments, including genes for sulfur oxidation and nutrient assimilation.Acidothiobacillus caldus is one of the three recognized species of the genus Acidithiobacillus, which also circumscribes A. thiooxidans and A. ferrooxidans. These bacteria live in extremely acidic environments (pH 1 to 3) typically associated with copper mining operations (bioleaching) (15, 17) and natural acid drainage systems (7). All of these bacteria have the capacity to gain energy by the oxidation of sulfur and reduced inorganic sulfur compounds and to thrive in extremely high concentrations of heavy metals (16). Of the three species, A. ferrooxidans is unique in also being able to obtain energy through the oxidation of ferrous iron, as well as being a facultative anaerobe capable of using ferric iron as an alternative electron acceptor. Acidithiobacilli have been shown to be able to fix atmospheric carbon via the Calvin-Benson-Bassham cycle (1,11,21) and to synthesize extracellular polymeric substances that are postulated to promote adhesion to mineral surfaces (3).As opposed to A. ferrooxidans, for which substantial bioinformatic and experimental evidence exists for these and other properties (4,14,19,20), A. caldus is poorly characterized, although it is known that it cannot carry out iron oxidation or nitrogen fixation (13). In contrast to the other two species of the genus, A. caldus thrives at temperatures up to 45 to 50°C. In order to unravel strategies for energy and nutrient assimilation used by A. caldus to survive and proliferate in extremely acidic environments, we have generated and annotated a draft genome sequence of A. caldus and performed a genome-based metabolic reconstruction to address these questions.The draft genome sequence of the type strain of A. caldus, ATCC 51756, was determined by a whole-genome shotgun strategy. Genomic libraries of 4 kb and 40 kb were constructed and sequenced, assembled using the Phred/Phrap programs (5), leading to the generation of a draft assembly based on 41,813 high-quality reads. Using Consed (8), assemblies that contained only contig segments with at least twofold coverage were edited and curated. Gene modeling was performed using CRITICA (2) and Glimmer (6). Predicted coding sequences were annotated based on comparisons with public databases (COG, KEGG, Pfam, TIGRFAMs, Unipprot, and NR-NCBI). Automatic metabolic reconstruction was carried out using the PRIAM and Pathways tools for prediction and curation.The A. caldus ATCC 51756 draft genome sequence has a total of 2,946,159 bp distributed in 139 contigs with an average GC content of 61.4%. Two 5S-16S-23S operons and 47 tRNAs on t...

Draft Genome of the Psychrotolerant Acidophile Acidithiobacillus ferrivorans SS3

“…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 (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).…”

“…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.…”

“…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).…”

Complete Genome Sequence of Temperate Bacteriophage Aca ML1 from the Extreme Acidophile Acidithiobacillus caldus ATCC 51756

“…Several members of this group have recently been sequenced (3,(8)(9)(10). Bioinformatic analysis of the genome sequence of the moderately thermophilic, sulfur-oxidizing acidophile Acidithiobacillus caldus ATCC 51756 predicted the presence of a 59-kb temperate phage located between srrA tmRNA and tRNA Met .…”

“…Assembly of qualified reads, gene modeling, and annotation were performed as previously described (8)(9)(10). Curation of the annotation was carried out using conserved protein motif analyses and motif databases, such as Interproscan (http://www.ebi.ac.uk/Tools/pfa /iprscan) and POG (4), and comparative genomic strategies against viral sequence repositories, such as PhAnToMe (http: //www.phantome.org).…”