Phylogenetic and genetic characterization of Acidithiobacillus strains isolated from different environments

Abstract

To study the phylogenetic relationships and genetic heterogeneity of 21 Acidithiobacillus strains isolated from different environments, we amplified and sequenced the 16S-23S rRNA gene intergenic spacers (ITS) of all these strains. These sequence data, combined with related sequences available from GenBank, were divided into six phylogenetic groups by 16S rRNA gene and by 16S-23S rRNA gene sequence analysis. The results of phylogenetic analysis were consistent with those obtained by repetitive element PCR and arbitrarily primed PCR. In this research, the Acidithiobacillus ferrooxidans (A. ferrooxidans) strains were always separated into two groups in phylogenetic and cluster analyses. Genotypic analyses of the genes rusA, rusB, hip and iro suggest that these two groups may have different biochemical mechanisms for oxidizing ferrous iron. Strains in one A. ferrooxidans group were detected with rusA gene that encodes rusticyanin A which plays a very important role in the iron respiratory chain. The second A. ferrooxidans group was found to contain rusB gene which encode a homologous protein (RusB). The data suggested that ITS-based phylogeny is an effective tool to elucidate the relationships of Acidithiobacillus and that a different iron oxidation pathway may exist in different A. ferrooxidans groups.

Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon

“…However, a number of additional lineages (phylotypes) with statistically well-supported nodes also became apparent in either, or in both, analyses, uncovering further inherent diversity for this taxon. This is in agreement with evidence derived from phylogenetic studies encompassing more restricted sets of strains, mostly focused on iron-oxidizing strains of the group (Amouric et al, 2011; Wu et al, 2014 and references therein), which have resulted in recent reclassification of a number of strains of A. ferrooxidans into the new species referred to above. In this work a total of 6 new phylotypes (16S rRNA clades 1B, 1C, 1D, 2B, 3A, 4B, Supplementary Table 4) were identified that are readily distinguishable by phylogenetic clustering and important levels of sequence divergence.…”

“…However, in the last two decades, a variety of molecular tools suited for typing and identification of bacteria have been applied to further revise the taxon (reviewed in Nuñez et al, 2016). Acidithiobacillus strains of diverse origins have since been assigned to distinct phylogenetic subgroups and/or genomovars, thought to represent a number of unidentified cryptic species (e.g., Luo et al, 2009; Amouric et al, 2011; Wu et al, 2014). Based on a careful re-evaluation of phenotypic characteristics (e.g., capacity to oxidize molecular hydrogen, temperature, and pH tolerance profiles, tolerance to elevated concentrations of transition metals and chloride, presence of flagella, etc.)…”