Use of rpoB Sequences and rep-PCR for Phylogenetic Study of Anoxybacillus Species

Kadriye Inan; Yusuf Bektas; Sabriye Canakci; Ali Osman Belduz

doi:10.1007/s12275-011-1136-8

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Use of rpoB Sequences and rep-PCR for Phylogenetic Study of Anoxybacillus Species: Kadriye Inan ¹, Yusuf Bektas ², Sabriye Canakci ¹, Ali Osman Belduz ¹; Journal of Microbiology 2011;49(5):782-790.
DOI: https://doi.org/10.1007/s12275-011-1136-8
Published online: November 9, 2011

¹Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey, ²Faculty of Fisheries and Aquatic Sciences, Rize University, 53100 Rize, Turkey

Corresponding author: Ali Osman Belduz , Tel: +90-462-377-2522,

Received: 17 March 2011 • Accepted: 7 June 2011

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Abstract

This study was conducted to investigate the applicability of rpoB, which encodes the β subunit of RNA polymerase, to be used as an alternative to 16S rRNA gene sequence similarity analysis in the thermophilic genus Anoxybacillus. Partial rpoB sequences were generated for the 14 type strains of Anoxybacillus species and 6 other strains of four Anoxybacillus species. The sequences and the phylogenetic tree of rpoB were compared with those obtained from 16S rRNA gene analysis. The rpoB gene was found to provide a better resolution for Anoxybacillus species, with lower interspecies sequence similarities. The rpoB sequence similarity analysis permitted a more accurate discrimination of the species within the Anoxybacillus genus than the more commonly used 16S rRNA gene. Furthermore, rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (REP-, ERIC-, and BOX-PCR) were employed for the specimens of genus Anoxybacillus. Through comparison of the three methods, it was found that the BOX-PCR method generated more informative results than REP-PCR for the studied strains; BOX-PCR profiles were more distinct for the different strains, including a higher number of bands. Rapid and reproducible repetitive extragenic palindromic fingerprinting techniques (rep-PCR) constitute a suitable molecular approach for the validation and maintenance of taxonomy within the Anoxybacillus genus. The results of this study show that rpoB and rep-PCR provide rapid and reliable methods for molecular typing of Anoxybacillus species.

Keywords: Anoxybacillus;16S rRNA;rpoB;REP-PCR;BOX-PCR;ERIC-PCR

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Use of rpoB Sequences and rep-PCR for Phylogenetic Study of Anoxybacillus Species

J. Microbiol. 2011;49(5):782-790. Published online November 9, 2011

DOI: https://doi.org/10.1007/s12275-011-1136-8

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