Draft Genome Sequence of a Novel Acidophilic Iron-Oxidizing Firmicutes Species, "Acidibacillus ferrooxidans" (SLC66T).

Here, we present the draft genome sequence of the type strain of "Acidibacillus ferrooxidans," a mesophilic, heterotrophic, and acidophilic bacterium that was isolated from mine spoilage subjected to accelerated weathering in humidity cell tests carried out by the former U.S. Bureau of Mines in Salt Lake City, UT.

GENOME ANNOUNCEMENT

Microorganisms that have an optimum pH for growth of <3 are classed as extreme acidophiles; many of these contribute to the biogeochemical cycling of iron and sulfur in these environments. Acidophilic bacteria, as a group, vary significantly in how they assimilate carbon. Many species are obligate autotrophic, others are obligate heterotrophic, and some (facultative autotrophs) fix inorganic carbon (CO2) even though they preferentially assimilate organic carbon (1). Some species of acidophilic prokaryotes, mostly notably iron-oxidizing Acidithiobacillus and Leptospirillum spp. (Proteobacteria), are responsible for the bioleaching of sulfide minerals. Known species of Gram-positive acidophilic bacteria are affiliated with two phyla, Firmicutes and Actinobacteria, and include species that are facultative autotrophs and obligate heterotrophs. Here, we report the draft genome sequence of strain SLC66T, the type strain of the novel species “Acidibacillus ferrooxidans” (2, 3). This acidophile had been isolated from mine waste regolithic material subjected to accelerated weathering in humidity cells at pH 2.9 and 25°C (4, 5). A. ferrooxidans is one of two proposed species of the novel genus “Acidibacillus,” the other being “A. sulfuroxidans.” Acidibacillus is the third genus of acidophilic Firmicutes to be described, the others being Alicyclobacillus and Sulfobacillus. A. ferrooxidans is classified as facultative chemolithoheterotroph and can obtain energy from both inorganic and organic electron donors, but it requires an organic carbon source, with complex organic materials (e.g., yeast extract) being the most effective carbon. A. ferrooxidans is mesophilic and acidophilic (growth optimal at 30°C and pH 2.9), in contrast to the moderate thermophile A. sulfuroxidans (growth optimal at 43°C and pH 1.8). A. ferrooxidans catalyzes the dissimilatory oxidation of ferrous iron (and therefore the oxidative dissolution of sulfidic minerals, such as pyrite), while A. sulfuroxidans oxidizes both reduced iron and sulfur. Both species can couple the oxidation of organic carbon with the reduction of ferric iron in the absence of oxygen.

Sequencing of the genome of SLC66T resulted in 2,122,638 paired-end reads obtained using the Illumina MiSeq platform, with 34.7× coverage of the expected genome size. The reads were trimmed and filtered using the Fastx Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), with a Phred score of 20, resulting in a total of 1,996,872 reads. The assembly of the genome sequence was performed with the Roche Newbler assembler version 2.9, ABySS 1.9 (6), and IDBAUD 1.1.1 (7). The contigs were integrated using the MIX (8) pipeline, resulting in a total of 175 contigs. The draft genome of strain SCL66T comprises a single chromosome of 3.2 Mb, with an overall G+C content of 51.97%. PATRIC (9) was used for automated annotation and identification of rRNA and tRNA, along with RNAmmer (10) and tRNAscan-SE (11), respectively. The draft genome harbored 4 rRNA genes, 53 tRNA genes, and a total of 3,497 protein-coding genes, from which 1,830 are genes with known functions and 1,667 are genes coding for hypothetical proteins.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at GenBank under the accession no. LVKL00000000. The version described in this paper is version LVKL00000000.1.