(GTG) 5 -PCR analysis and 16S rRNA sequencing of bacteria from Sarawak aquaculture environment

Abstract

(GTG) 5 PCR is a type of repetitive extragenic palindromic (rep)-PCR which amplifies the (GTG) 5 repetitive element that lays throughout the bacterial genome. In this study, fifty, thirtynine and forty-nine unknown bacteria were isolated from aquaculture farms in Miri, Limbang and Lundu, respectively. (GTG) 5 PCR was used to screen for clonal diversity among the isolates according to sampling sites. Banding profiles obtained from electrophoresed (GTG) 5 PCR products were analyzed by RAPDistance Software to generate a dendrogram of neighbor joining tree (NJT) format. Based on the constructed dendrogram, representative isolates were selected for further identification. Conserved 16S rRNA region of the selected bacteria isolates were amplified and purified DNA products were sequenced. (GTG) 5 PCR is useful in differentiation of unknown bacterial isolates and 16S rRNA analysis species identity of the bacteria in Sarawak aquaculture environment. The high diversity of bacteria in aquaculture environment may be caused by contamination from various sources.