Phylogenetics of an antibiotic producing Streptomyces strain isolated from soil

Abstract

Traditional methods of species classification and identification of the organism are based on morphological, physiological, biochemical, developmental and nutritional characteristics. Accurate assignment of taxonomic status to the new biologically active microbial isolates through existing bioinformatics methods is now very essential and also helpful in chemical characterization of the active molecule produced by microorganisms. The bacterial strain M4 (ckm7) was isolated from the pre-treated soil sample collected from the agricultural field of Eastern Uttar Pradesh (U.P.), India and was found to be producing antibacterial and antifungal antibiotics. Taxonomic identification of the isolate belongs to the genus Streptomyces which was done with the help of sequence analysis and later confirmed by biological activity. Sequence comparison study of ckm7 showed 98% identical similarity with 16S rRNA gene sequences of Streptomyces spinichromogenes, Streptomyces triostinicus and Streptomyces capoamus. On the basis of both biological activity and phylogenetic analysis of ckm7, it was concluded that the isolated strain is a new variant of S. triostinicus.

Keywords: 16S rRNA gene; Phylogenetics; Streptomyces; antibacterial; antifungal antibiotics; biological activity study; ckm7.

Figure 1

Antibacterial activity (A), antifungal activity (B) and morphological appearance through light microscopy (C) of the producer strain.

Figure 2

Partial gene sequence of 16S rRNA gene of ckm7, sequenced from Microbial Type Culture Collection (MTCC), IMTECH, Chandigarh, India. The length of nucleotide sequence is 1424 base pair.

Figure 3

Conservation of nucleotides in the 16S rRNA sequences of S. spinichromogenes, S. capoamus, S. triostinicus and ckm7. In the diagram arabic numbers i.e. 1 to 14 indicates range of nucleotides from 100 to 1400 while roman numbers on the top of each row except ckm7 indicates difference in number of nucleotides with ckm7 sequence.

Figure 4

Unrooted phylogenetic tree showing evolutionary relationship of ckm7 with other members of Streptomyces along with their evolutionary distances.