Differentiation of Acidithiobacillus ferrooxidans and A. thiooxidans strains based on 16S–23S rDNA spacer polymorphism analysis

Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways

“…The genus Acidithiobacillus has generally been considered to be a member of the Gammaproteobacteria, though recent phylogenetic analysis suggests it arose after divergence from the Alphaproteobacteria but before the Betaproteobacteria/Gammaproteobacteria split (Williams et al, 2010). There have been numerous reports suggesting that Fe(II)-oxidizing acidithiobacilli are a heterogeneous collection of bacteria with sufficient genetic variability to warrant classification as more than one species (Harrison, 1982(Harrison, , 1984Novo et al, 1996;Amils et al, 1998;Selenska-Pobell et al, 1998;Paulino et al, 2001;Karavaiko et al, 2003;Mitchell et al, 2003;Bergamo et al, 2004; Akbar et al, 2005;Waltenbury et al, 2005;Peng et al, 2006;Ni et al, 2007Ni et al, , 2008a. For instance, a Abbreviations: BV, bootstrap value; HiPIP, high potential iron-sulfur protein; MLSA, multilocus sequence analysis; PP, posterior probability; RISC, reduced inorganic sulfur compound.…”

16S rDNA and 16S–23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Acidithiobacillus phylogeny

“…Bacterial cells were harvested by centrifugation at 15 000 g for 10 min and washed with acid water (pH 1.2) to remove ferric iron precipitate. Genomic DNA was isolated from the tested strains as described by Novo et al (1996) and Bergamo et al (2004), with modifications. After treatment with 10 ml RNase (20 mg ml 21 ), DNA concentrations and purity were determined by spectrophotometric readings.…”

“…The cycling programme when using longer (.17 nt) primers was as described by Williams et al (1990), with minor modifications. Each amplification was done in triplicate and results were reproducible when DNA obtained by different extraction procedures of the same strain was used (Novo et al, 1996;Bergamo et al, 2004). The amplification products (10 ml) were separated by electrophoresis on 1.5 % agarose 0.56 TBE gels.…”

“…While ITS sequence similarity levels between members of the two A. thiooxidans groups were only 88-90 %, the two groups showed more than 98 % identity in their 16S rRNA gene sequence. A. thiooxidans strain CASQ22, described by Bergamo et al (2004), which possessed an ITS with a smallest size of 409 bp, and fell into none of groups, showed only ITS sequence similarity on average of less than 87 % to other A. thiooxidans strains, suggesting that this strain might correspond to a different genospecies or genomovar from the remaining A. thiooxidans strains. Consequently, the ITS could also be used as a tool to clarify controversial strains.…”

“…These bacteria appear to be present in a wide range of environments, especially in sites where pH is low, such as mining areas, hot sulfur springs and bioleaching operations. Many attempts have been made to describe a large number of Acidithiobacillus strains (Harrison, 1982;Karavaiko et al, 2003;Bergamo et al, 2004). More recently, bacteria of the genus Acidithiobacillus have been widely studied for bioleaching, biodegradation and desulfurization of coal and natural gas (Acharya et al, 2004;Rawlings & Johnson, 2007).…”