Isolation of gene involved in degradation of carbazole and dibenzothhiophene by marine bacteria

Bioremediation is a technique that has been proven to be an effective way to clean polluted area including heterocyclic compound polluted area such as seawater, marine, lake or estuaries. Thalassospira profundimaris and Pseudomonas stutzeri are known bacteria that can degrade carbazole and dibenzothiophene compound respectively are used in this study. These bacteria utilized compound as a sole of carbon and sulfur compound respectively for their growth, with converting compound into other types of compound by-product which is safer in environment. Total DNA extraction was done to identify the genes responsible in degradation activity, followed by direct Polymerase Chain Reaction (PCR) and DNA sequencing. Specific degenerative primer was designed based on previously reported genes in GenBank to detect carA, carB and carC gene that involved in respective carbazole and DBT-A gene in both heterocyclic compound degrading-bacteria. The most conserve region was chosen as forward and reverse primer during alignment using ClustalW2. Five different strains of carbazole degrading bacteria are chosen to design primer for carbazole gene. Four closely related species are chosen to design primer for DBT gene. Expected PCR product size for CarA, CarB, CarC and DBT-A are 1050 bp-, 700 bp-, 610 bp-and 1200 bp-respectively. Results from PCR showed there are product band for DBTA gene for both primer DBTA-Fl and DBTA-F2. Whereas, no carA, carB and carC gene was detected using all six set of designed primer