Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C

Abstract

Acidithiobacillus ferrooxidans, a chemolithoautotrophic bacterium, is well known for its mineral oxidizing properties. The current study combines experimental and whole genome sequencing approaches to investigate an iron oxidizing, extreme acidophilic bacterium, A. ferrooxidans isolate (IO-2C) from an acid seep area near Carlos, TX, USA. Strain IO-2C was capable of oxidizing iron i.e. iron sulphate and iron ammonium sulphate yielding shwertmannite and jarosite minerals. Further, the bacterium's genome was sequenced, assembled and annotated to study its general features, structure and functions. To determine genetic heterogeneity, it was compared with the genomes of other published A. ferrooxidans strains. Pan-genome analysis displayed low gene conservation and significant genetic diversity in A. ferrooxidans species comprising of 6926 protein coding sequences with 23.04% (1596) core genes, 46.13% (3195) unique and 30.82% (2135) accessory genes. Variant analysis showed >75,000 variants, 287 of them with a predicted high impact, in A. ferrooxidans IO-2C genome compared to the reference strain, resulting in abandonment of some important functional key genes. The genome contains numerous functional genes for iron and sulphur metabolism, nitrogen fixation, secondary metabolites, degradation of aromatic compounds, and multidrug and heavy metal resistance. This study demonstrated the bio-oxidation of iron by newly isolated A. ferrooxidans IO-2C under acidic conditions, which was further supported by genomic analysis. Genomic analysis of this strain provided valuable information about the complement of genes responsible for the utilization of iron and tolerance of other metals.

Figure 1

Bio-oxidation of (a) FeSO₄ and (b) Fe(NH₄)₂SO₄ by Acidithiobacillus ferrooxidans IO-2C.

Figure 2

XRD spectra of iron oxides produced by Acidithiobacillus ferrooxidans IO-2C using (a) FeSO₄ (b) Fe(NH₄)₂SO₄ as substrates.

Figure 3

Heat map representing average pairwise nucleotide identity of Acidithiobacillus ferrooxidans IO-2C with other genomes of the same genus.

Figure 4

Circular genome map of Acidithiobacillus ferrooxidans IO-2C. Contigs represented in blue color; CDS-FWD in green; CDS-REV in purple; Non-CDS features in light blue; GC content in violet and GC skew in brown color.

Figure 5

Phylogenetic analysis of the Acidithiobacillus ferrooxidans based on (a) pan and (b) core-genome similarity.

Figure 6

(a) Core-pan plot of genomes under study (b) COG and (c) KEGG distribution of the genes forming core, accessory and unique portion of genomes under study.

Figure 7

Multiple sequence alignments depicting (a) Gene apparatus encoding iron-sulfur cluster assembly (b) Mercury resistant gene cluster I (c) Mercury resistant gene cluster II in different Acidithiobacillus ferrooxidans species.