Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics

Abstract

Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.

High‐throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments

“…The unprecedented advances in these areas represent a valuable source of information that is increasingly being incorporated into the improvement of bioprocesses and environmental engineering applications (e.g. wastewater treatment, bioremediation) to achieve a more sustainable environment (Czaplicki and Gunsch, 2016;Techtmann and Hazen, 2016). compilation of the application of HTS technologies to microbial water quality assessment.…”

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

“…Similar studies were carried out by Joshi et al ( 2014 ) that investigated the metagenomes isolated from petroleum muck, which revealed the indigenous microbial communities inhabiting the petroleum-contaminated sites. Recently, a number of research papers (George et al, 2011 ; Kumavath and Deverapalli, 2013 ; Bell et al, 2014 ; Pushpanathan et al, 2014 ; Ufarté et al, 2015 ; Czaplicki and Gunsch, 2016 ; Chistoserdova, 2017 ) have been published wherein different authors have emphasized individual genomic or transcriptomic approaches in bioremediation of environment. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation.…”

Bacteria, Fungi and Microalgae for the Bioremediation of Marine Sediments Contaminated by Petroleum Hydrocarbons in the Omics Era

“…Our ability to identify microbes capable of degrading contaminants or reducing their toxic effects has been boosted by the development of next generation sequencing (NGS) techniques and in silico analyses [ 176 ]. Technologies based on high-throughput analysis are very useful in shedding light on microbial community diversity, otherwise not accessible using culture dependent methods.…”