Inter- and intraspecific genomic variability of the 16S–23S intergenic spacer regions (ISR) in representatives ofAcidithiobacillus thiooxidansandAcidithiobacillus ferrooxidans

Abstract

The complete sequences of 32 intergenic spacer regions (ISR) from Acidithiobacillus strains, including 29 field strains isolated from coal, copper, molybdenum mine wastes or sediment of different geoclimatic regions in China, reference strain ATCC19859 and the type strains of the two species were determined. These data, together with other sequences available in the GenBank database, were used to carry out the first detailed assessment of the inter- and intraspecific genomic variability of the ISR sequences and to infer phylogenetic relationships within the genus. The total length of the 16S-23S rRNA intergenic spacer regions of the Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans strains ranged from 451 to 490 bp, and from 434 to 456 bp, respectively. The degree of intrageneric ISR sequence similarity was higher than the degree of intergeneric similarity, and the overall similarity values of the ISRs varied from 60.49% to 84.71% between representatives of different species of the genus Acidithiobacillus. Sequences from the spacer of the A. thiooxidans and A. ferrooxidans strains ranged from 86.71% to 99.56% and 92.36% to 100% similarity, respectively. All Acidithiobacillus strains were separated into three phylogenetic major clusters and seven phylogenetic groups. ISR may be a potential target for the development of in situ hybridization probe aimed at accurately detecting acidithiobacilli in the various acidic environments.

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.…”

Diversity and Ecophysiology of New Isolates of Extremely Acidophilic CS 2 -Converting Acidithiobacillus Strains

“…The genus Acidithiobacillus comprises a physiologically and genetically heterogeneous group of microorganisms (39,40), despite the often low sequence diversity in the 16S rRNA gene. For that reason, the 16S-23S ISR is used to discriminate at the intra species level (41,42).…”

Arsenic bioleaching in medical realgar ore and arsenicbearing refractory gold ore by combination of <i>Acidithiobacillus ferrooxidans</i> and <i>Acidithiobacillus thiooxidans</i>

“…Isolation and identification of these acidophilic micro-organism strains have been reported in the previous work of our laboratory [16]. After adaptation to inorganic arsenic, all of them could resist soluble arsenic compounds of high concentrations [15].…”