title: In silico approach to study adaptive divergence in nucleotide composition of the 16S rRNA gene among bacteria thriving under different temperature regimes.
abstract: Bacteria exist in a wide range of habitats ranging from psychrophilic through mesophilic to thermophilic. These different habitats have distinct environmental restriction for their existence. These microorganisms evolve themselves to survive in a specific habitat through the phenotypic and genotypic changes. In the bacterial domain, in silico analysis of 16S rRNA gene sequences using Mega 5.2 software by computing nucleotide composition, and evaluating their significance by statistical analysis using analysis of variance through Statistical Package for the Social Sciences (SPSS) version 16.0, revealed the habitat-specific bias in the occurrence of four types of nucleosides (A, T, C, and G) in the 16S rRNA gene. This hypothesis is also supported by Duncan's multiple range significance test at p=0.05 and also by the clustering of bacterial species of the same habitat group in the neighbor-joining tree of 150 different bacterial species of different psychrophilic, mesophilic, and thermophilic habitats (50 from each). The results on the probability of substitution (transition and transversion) in 16S rRNA gene sequences suggest that there is a habitat-specific selection pressure that possibly happens at the level of replication and repair process that results in a decreasing frequency of occurrence of adenine and thymine in the order psychrophilic>mesophilic>thermophilic species, and in an increasing frequency of occurrence of cytosine and guanine in the order psychrophilic<mesophilic<thermophilic species of bacteria.
authors.affiliation: Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India .
authors.forename: Hari
authors.initials: H
authors.lastname: Ram
authors.forename: Alok
authors.initials: A
authors.lastname: Kumar
authors.forename: Lebin
authors.initials: L
authors.lastname: Thomas
authors.forename: Ved Pal
authors.initials: VP
authors.lastname: Singh
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D003198:Computer Simulation; D017753:Ecosystem; D005798:Genes, Bacterial; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013696:Temperature
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: database; genetic analysis; genetic variation; multiple alignments; phylogenetic analysis