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

Anila Fariq,Youjun Deng,Terry J Gentry,John C Blazier,Azra Yasmin

doi:10.1038/s41598-019-49213-x

Anila Fariq, Youjun Deng + Show 3 more

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https://doi.org/10.1038/s41598-019-49213-x

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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.

Highlights

IntroductionOxidation of sulphur results in production of sulphuric acid and ferrous ion is oxidized to ferric
Diverse acidic environments with a wide range of acidity are found in natural and man-made settings on Earth
A bulk of genes associated with carbon dioxide and dinitrogen fixation, pH resistance, oxidative stress, and heavy metal detoxification have been identified in whole genome sequence of A. ferrooxidans YQH-14

Summary

Introduction

Oxidation of sulphur results in production of sulphuric acid and ferrous ion is oxidized to ferric Acidophiles accelerate this oxidation process up to 106 times[1]. Acidithiobacilli are a group of sulphur-oxidizing acidophilic bacteria that exist in low pH environments. They are involved in acid mine drainage formation and have been used for the processing of different minerals. Another study demonstrated sulphur oxidation in the extremophile Acidithiobacillus thiooxidans through whole-genome sequence analysis using a bioinformatic approach[5]. The microflora responsible for the oxidation of pyrite in these seeps have yet to be explored To this end, we have isolated the pyrite oxidizing bacterium i.e. Acidithiobacillus ferrooxidans IO-2C, from acid seep soil and investigated its iron oxidation potential. IO-2C genome was compared with other related species genomes to elucidate the degrees of genetic heterogeneity and gene conservation in Acidithiobacillus ferrooxidans

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