Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: Insights into their metabolism and ecophysiology

Draft genome sequences of Acidthiobacillus thiooxidans and A. caldus have been annotated and compared to the previously annotated genome of A. ferrooxidans. This has allowed the prediction of metabolic and regulatory models for each species and has provided a unique opportunity to undertake comparative genomic studies of this group of related bioleaching bacteria. In this paper, the presence or absence of predicted genes for eleven metabolic processes, electron transfer pathways and other phenotypic characteristics are reported for the three acidithiobacilli: CO2 fixation, the TCA cycle, sulfur oxidation, sulfur reduction, iron oxidation, iron assimilation, quorum sensing via the acyl homoserine lactone mechanism, hydrogen oxidation, flagella formation, Che signaling (chemotaxis) and nitrogen fixation. Predicted transcriptional and metabolic interplay between pathways pinpoints possible coordinated responses to environmental signals such as energy source, oxygen and nutrient limitations. The predicted pathway for nitrogen fixation in A. ferrooxidans will be described as an example of such an integrated response. Several responses appear to be especially characteristic of autotrophic microorganisms and may have direct implications for metabolic processes of critical relevance to the understanding of how these microorganisms survive and proliferate in extreme environments, including industrial bioleaching operations.