Comparison of molecular and phenetic typing methods to assess diversity of selected members of the genus Bacillus

Abstract

A comparison of different molecular typing methods viz. ERIC-PCR, BOX-PCR and ARDRA along with carbohydrate utilization pattern was carried out to analyze their discriminatory power and suitability for assessing diversity of selected Bacillus isolates. ERIC-PCR generated 61 bands ranging from 0.56 to 3.9 kb while BOX-PCR resulted in 127 bands ranging from 0.16 to 3.9 kb. Restriction analysis of 16S rDNA with AluI and HaeIII produced 56 and 67 bands ranging from 0.14 to 0.54 and 0.12 to 0.96, respectively. Clustering of isolates based on the ERIC, BOX and ARDRA pattern clearly showed the superiority of the former two methods to reveal the intrageneric and intraspecific diversity. Carbohydrate utilization pattern showed that most preferred sugar was Fructose while Xylose, Rhamnose and D-Arabinose were least preferred by the isolates used for the study. Clustering based on carbohydrate utilization was also able to differentiate among the isolates which showed 100% similarity based on ARDRA profiles. This study clearly shows that typing methods exploiting the repetitive elements distributed over the genome are more useful for assessing genetic diversity. Moreover, metabolic diversity of the bacterial groups may also be useful instead of using single locus specific marker systems for revealing the diversity.