Exploring environmental systems and processes through next-generation sequencing technologies: insights into microbial response to petroleum contamination in key environments

Abstract

Environmental degradation due to petroleum contamination is a widespread phenomenon and can cause irreparable damage to the ecosystem if not contained. Microbial bioremediation has been established as an ecologically and economically viable method for the restoration of environments afflicted with xenobiotic and anthropogenic pollution. Effective execution of bioremediation strategies however, require a thorough understanding of the resident microbial community structure and function along with critical environmental factors. Recent innovative advances such as massively parallel sequencing, coupled with the development of robust bioinformatics tools have provided critical insights into the process of microbial bioremediation in the environment through elucidation of microbial community structures in uncontaminated and contaminated and/or bioaugmented systems with unprecedented efficiency and reproducibility. Aided by next-generation sequencing applications like metagenomics, metatranscriptomics and metagenomic shotgun sequencing, microbiologists have been able to investigate microbial responses to oil pollution with unparalleled completeness, even from extreme environments. The elucidation of the contribution of non-cultivable but viable microbes in oil contaminated sites have furnished us with essential information about the complex microbial associations and interdependencies that are required to facilitate effective remediation of contaminated environments. The current review focuses on microbial responses to oil contamination in various key environments unraveled through the use of NGS technologies, the characteristic features of such responses, and identification of critical factors necessary to facilitate efficient and systemic bioremediation of these polluted environments.