Comparative genomic characterization of iron oxidizing bacteria isolated from the Tinto River

The genomic organization of different iron oxidizing bacteria belonging to the Thiobacillus and Leptospirillum genus isolated from the Tinto River was studied using pulsed field gel electrophoresis (PFGE). The electrophoretic analysis of intact DNA prepared from different isolates showed that all have a circular chromosome with a variable size, ranging from 2.15 to 2.70 Mb for thiobacilli and 1.64 to 2.53 for leptospirilli. Extrachromosomal elements of important size were only detected in one leptospirilli isolate. The rest of the strains might have supercoiled plasmids of small size, like many of the thiobacilli reference systems or none at all. Low-frequency restriction fragment analysis (LFRFA) was carried out to determine macrorestriction patterns for rare cutters (SpeI, XbaI, SwaI and PmeI), which were used for taxonomic characterization (karyotyping), genome size determination and physical map generation. The results obtained strongly suggest the existence of at least three different clusters in the group of isolates identified phenotypically as T. ferrooxidans strains, while the isolates identified as L. ferrooxidans strains exhibit distinct restriction profiles for different rare cutters, suggesting that they might correspond to different species. A revision of the taxonomic status of these important acidophilic chemolithotrophs is suggested.