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

Abstract

In order to contribute to our understanding of Acidithiobacillus taxonomy, we determined 16S rDNA sequences and the 16S-23S internally transcribed spacer (ITS) sequence of 35 Chinese Acidithiobacillus isolates and three reference strains representing three validly described species and used them to construct phylogenetic trees. The two phylogenetic trees were roughly similar topologically, and Acidithiobacillus strains were assigned to eight phylogenetic groups. In addition, the results of phylogenetic analysis were consistent with those obtained by randomly amplified polymorphic DNA (RAPD) cluster analysis. Compared with a phylogenetic tree based on the 16S rRNA sequences, the ITS tree showed more clearly the inter-and intraspecific genealogical relationships of the genus Acidithiobacillus. Similarity values of the ITSs varied from 60.5 % to 84.7 % between representative strains of different species, and the maximum level of ITS divergence between strains belonging to the same species was 13 %. Coupling phylogenetic analysis and phenotypic characteristics, we concluded that at least each of the three Acidithiobacillus ferrooxidans phylogenetic groups should be considered a separate subspecies, and that five sulfur-oxidizing Chinese Acidithiobacillus-like isolates represent one or two new species of the genus Acidithiobacillus. The ITS may be a potential target for the development of fluorescent in situ hybridization probes for more accurately detecting distinct ecotypes of Acidithiobacillus strains and other closely related sulfur-oxidizing bacteria.

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

“…3b). Interestingly, in the ITS1 tree, the grouping of the strains correlated with sequence lengths, as observed by Ni et al (2007Ni et al ( , 2008a. The size of the ITS1 was 441, 454, 442-443 and 452 bp for strains from Groups I-IV, respectively.…”

“…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 recent study using microarrays of the whole genome of the At.…”

Characterization of diverse natural variants of CYP102A1 found within a species of Bacillus megaterium

“…The amplification of partial 16S rRNA genes was carried out using the primers 9F (5'-GAGTTTGATCCTGGCTCAG-3') and 1512R (5'-ACGGCTACCTTGTTACGACTT-3') (Ni et al 2008). The amplification reaction (25 μl) contained 50 ng DNA, 0.50 μM of each primer, 250 μM dNTPs, 1.5 mM MgCl 2 , and 1.25 U pfu polymerase in the buffer supplied by the manufacturer.…”

Use of LSPR Spectroscopy Biosensing for In Situ Identification of Arsenic from Bioleaching of Realgar by Acidithiobacillus ferrooxidans

“…is strain was selected based on its growth and physical and chemical properties. e strain was entered into GenBank after 16S rRNA nucleic acid sequencing (DQ676505) [20]. e culture medium for strain A. ferrooxidans BY-3 (CCTCC-M203071) was 9K culture medium containing 44.69 g/L ferrous sulfate [21].…”