Evaluation of ribosomal RNA gene restriction patterns for the classification of Bacillus species and related genera

Abstract

Aims: To identify Bacillus species and related genera by ®ngerprinting based on ribosomal RNA gene restriction patterns; to compare ribosomal RNA gene restriction patterns-based phylogenetic trees with trees based on 16S rRNA gene sequences; to evaluate the usefulness of ribosomal RNA gene restriction patterns as a taxonomic tool for the classi®cation of Bacillus species and related genera. Methods and Results: Seventy-eight bacterial species which include 42 Bacillus species, 31 species from ®ve newly created Bacillus-related genera, and ®ve species from ®ve phenotypically related genera were tested. A total of 77 distinct 16S rRNA gene hybridization banding patterns were obtained. The dendrogram resulting from UPGMA analysis showed three distinct main genetic clusters at the 75% banding pattern similarity. A total of 77 distinct 23S and 5S rRNA genes hybridization banding patterns were obtained, and the dendrogram showed four distinct genetic clusters at the 75% banding pattern similarity. A third dendrogram was constructed using a combination of the data from the 16S rRNA gene ®ngerprinting and the 23S and 5S rRNA genes ®ngerprinting. It revealed three distinct main phylogenetic clusters at the 75% banding pattern similarity. Conclusions: The Bacillus species along with the species from related genera were identi®ed successfully and differentiated by ribosomal RNA gene restriction patterns, and most were distributed with no apparent order in various clusters on each of the three dendrograms. Signi®cance and Impact of the Study: Our data indicate that ribosomal RNA gene restriction patterns can be used to reconstruct the phylogeny of the Bacillus species and derived-genera that approximates, but does not duplicate, phylogenies based on 16S rRNA gene sequences.

Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group

“…spizizenii (Nakamura et al, 1999) and Bacillus sonorensis (Palmisano et al, 2001). These taxa can be differentiated from one another by fatty acid composition analysis, restriction digest analysis and DNA-DNA hybridization analysis, but are quite difficult to differentiate by phenotypic characteristics (Roberts et al, 1994;Nakamura et al, 1999).16S rRNA gene sequence analysis is the most commonly used method for identifying bacteria or for constructing bacterial phylogenetic relationships (Woese, 1987;Vandamme et al, 1996;Joung & Cote, 2002); however, its usefulness is limited because of the high percentage of sequence similarity between closely related species (Ash et al, 1991;Martínez-Murcia et al, 1992;Christensen et al, 1998). The use of protein-encoding genes as phylogenetic markers is now a common approach (Yamamoto & Harayama, 1998;Ko et al, 2004;Chelo et al, 2007).…”

“…16S rRNA gene sequence analysis is the most commonly used method for identifying bacteria or for constructing bacterial phylogenetic relationships (Woese, 1987;Vandamme et al, 1996;Joung & Cote, 2002); however, its usefulness is limited because of the high percentage of sequence similarity between closely related species (Ash et al, 1991;Martínez-Murcia et al, 1992;Christensen et al, 1998). The use of protein-encoding genes as phylogenetic markers is now a common approach (Yamamoto & Harayama, 1998;Ko et al, 2004;Chelo et al, 2007).…”

Reassessment of Sequence-Based Targets for Identification of Bacillus Species

“…Molecular procedures are increasingly being used for rapid species identification. However, some methods used for this genus such as restriction digests of a target gene (i.e., 16S rRNA gene) (11) or randomly amplified polymorphic DNA analysis (22) are limiting in discriminating between a large group of species (6). Sequencing of the 16S rRNA gene and select housekeeping genes has shown to be particularly useful, generating large public sequence databases due to the tangible, exact nature of sequence data.…”

Physiological properties of facultative and obligate alkalophilic Bacillus sp. strains isolated from Saudi Arabia

“…They are classified into two groups: alkalophilic bacteria, which are able to grow at pH above 10 and their optimal growth about pH 9 (Xu and Cote, 2003). The other group is called alkalotolerante bacteria, which show optimum growth at pH around 7, but able to grow at pH around 10 (Joung and Cote, 2002). Alkalophilic bacteria can be further divided into obligate and facultative alkaliphilic (Marie et al, 2005).…”