Abstract
The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (<10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. The At. ferrivorans CF27 genome comprises a 3,409,655 bp chromosome and a 46,453 bp plasmid. At. ferrivorans CF27 possesses genes allowing its adaptation to cold, metal(loid)-rich environments, as well as others that enable it to sense environmental changes, allowing At. ferrivorans CF27 to escape hostile conditions and to move toward favorable locations. Interestingly, the genome of At. ferrivorans CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. Furthermore, several genes specific to At. ferrivorans CF27 have been identified that could be responsible for the phenotypic differences of this strain compared to other Acidithiobacillus species. Most genes located inside At. ferrivorans CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups.
Highlights
Acidithiobacillus species are obligately acidophilic, chemolithoautotrophic Gram-negative bacteria, known for their abilities to extract metals such as copper, uranium, cobalt and gold from mineral ores and to remove sulfur compounds from contaminated industrial effluents, liquid wastes or soils (Jerez, 2009; Johnson, 2014)
Similar to At. ferrooxidans ATCC 23270T, At. ferrivorans CF27 has a high number (73 in its chromosome) of tRNA genes, of which 26 are clustered in a specific region (Figure 1, circle 5), which has been acquired through horizontal gene transfer (HGT), possibly from acidophilic Firmicutes, before being subjected to tRNA rearrangements, deletions, insertions, and duplications (Tran et al, 2015)
The gene cluster proposed to be involved in the formation of macroscopic biofilms in At. ferrivorans CF27 (Talla et al, 2014) is located in the GI51, suggesting that these genes have been acquired by HGT
Summary
Acidithiobacillus species are obligately acidophilic, chemolithoautotrophic Gram-negative bacteria, known for their abilities to extract metals such as copper, uranium, cobalt and gold from mineral ores (biomining) and to remove sulfur compounds (bioremediation) from contaminated industrial effluents, liquid wastes or soils (Jerez, 2009; Johnson, 2014). Numerous Acidithiobacillus strains have been isolated from natural and man-made low pH environments in a variety of geo-climatic contexts such as acidic ponds, lakes and rivers, sulfur springs, acid mine/rock drainage waters and mining areas (Nuñez et al, 2016). Based on their 16S rRNA gene sequences, these microorganisms were initially considered to be Gammaproteobacteria (Kelly and Wood, 2000; Garrity et al, 2005) though later, based on comparative multiprotein analysis, they, together with Thermithiobacillus spp., were transferred to a new proteobacterial class, the Acidithiobacillia (Williams and Kelly, 2013). At. ferrivorans [and some strains of At. ferriphilus; (Falagán and Johnson, 2016)] are psychro-tolerant rather than psychrophilic, and grow optimally at temperatures ∼30◦C
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