Investigation of the total petroleum hydrocarbon degrading microorganisms in soil and water: a metagenomic approach

Hydrocarbons are relatively recalcitrant compounds and are classified as high priority pollutants. However, these compounds are slowly degraded by a large variety of aerobic and anaerobic microorganisms. Although the corresponding genes in many phylogenetic groups of microbial species show different levels of diversity in terms of the gene sequence, the organisation of the genes in the genome or on plasmids and the activation mode of several microorganisms show identical hydrocarbon degrading genes. Since the majority of microorganisms in natural environments cannot be cultured in laboratory media, culture-based systems are unable to estimate the full microbial diversity of an environment. Metagenomic methods, however, employ sequencing procedures for the determination of the microbial diversity of a community and for examining a particular functional ability of microorganisms in the environment using genomic DNA obtained directly from environmental samples. Application of metagenomic methods provides a huge amount of data that can be analysed only by using powerful computational bioinformatics tools. In this study, we used next generation technology and metagenomic analysis to investigate the microbial diversity in crude oil and crude oil contaminated soils and to find the functional genes involved in the degradation of hydrocarbons in crude oil. The findings from this study can be used for bioremediation of crude oil spills and also for improvement of the quality of crude oil derivatives in terms of removal of sulfur and nitrogen. As a part of this study, we report a list of microorganisms that are abundant in the crude oil and the crude oil contaminated soil. Furthermore, we found a new operon responsible for removal of sulfur from dibenzothiophenes. The three genes in this operon were cloned and their activities measured in cell free condition.