Identification and discrimination of thiobacilli using ARDREA, RAPD and rep-APD

Abstract

S . S EL E NS KA -PO BE L L, A. O TT O A N D S . K U TS CH K E. 1998. A highly reliable procedure for fast identification and taxonomical categorization of thiobacilli is presented. The procedure includes RFLP analysis of PCR amplified 16S rDNA, 23S rDNA, and intergenic spacer rDNA between the 16S and the 23S rRNA-genes (amplified ribosomal DNA restriction enzyme analysis -ARDREA), as well as genomic fingerprinting using random primers (RAPD) and repetitive primers (Rep-APD). The taxonomic and discriminatory power of these three analytical approaches is compared. It is demonstrated that the RAPD and Rep-APD methods provide taxonomic results which are in agreement with the classification based on the RFLP analysis of the highly conservative ribosomal RNA (rrn) operons of the strains studied. Moreover, both kinds of genomic PCR fingerprinting, due to the fact that they derive information from different parts of the whole bacterial genome which may possess different degrees of variability, are more informative than ARDREA. By them, a discrimination of closely related Thiobacillus strains is possible. In addition, they are easier to perform and faster than the ARDREA. Using the method described, it was found that one Thiobacillus isolate recovered from uranium waste heaps described in the literature as Thiobacillus ferrooxidans ATCC 33020 is taxonomically neither closely related to the type strain of the species, Thiobacillus ferrooxidans ATCC23270 T , nor to any other strain of this species analysed in the present work.

The HiPIP from the acidophilic Acidithiobacillus ferrooxidans is correctly processed and translocated in Escherichia coli, in spite of the periplasm pH difference between these two micro-organisms

“…One possibility we cannot exclude is that Iro BRGM was not purified from A. ferrooxidans but from another micro-organism, as strain BRGM, from which the iro BRGM gene and Iro BRGM protein have been analysed (Cavazza et al, 1995 and this paper), is in fact a bacterial consortium (Battaglia-Brunet et al, 2002;Collinet & Morin, 1990). However, A. ferrooxidans strains have been reported by several authors to be physiologically and genomically diverse (Leduc & Ferroni, 1994;Harrison, 1982Harrison, , 1984 and to diverge in different phylogenetic groups (Goebel & Stackebrandt, 1994;Karavaiko et al, 2003;Novo et al, 1996;Selenska-Pobell et al, 1998). In this case, the simplest explanation is that strains Fe-1 and BRGM belong to a different group from the A. ferrooxidans strains analysed in this paper.…”

The iron-oxidizing proteobacteria

“…Harrison (1982) was the first to highlight that major phylogenetic differences existed among many of the 'At. ferrooxidans' strains that he examined, a theme that was later also emphasized by Selenska-Pobell et al (1998) and Karavaiko et al (2003). Hallberg et al (2010) described a novel iron-oxidizing species, Acidithiobacillus ferrivorans (At.…”

Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov.

“…They do, however, exhibit considerable genetic variation (Harrison, 1982 ; Harrison, 1989 ;Goebel et al, 1999). Using PCRbased techniques to assess this genomic variability, similarity coefficients between various isolates were obtained which ranged from almost 0 % to over 98 % (Novo et al, 1996) ; while several culture-collection isolates were very closely related to the type strain (ATCC 23270 T ), one strain (ATCC 33020) was not taxonomically related to the others (Selenska-Pobell et al, 1998). It is inevitable, therefore, that some strains assigned to this species will be reassigned to new species or genera in due course.…”