Application of Molecular Techniques for the Assessment of Microbial Communities in Contaminated Sites

The advent of molecular microbial tools has defined the modern era of microbial ecology by paving the way for rapid, high-throughput methods for culture-independent assessment of microbial communities present in complex ecosystems such as contaminated environments, thus overcoming the limitations of cultivation-based approaches. Vast application of molecular techniques in studying the ecology of microorganisms at contaminated sites has led to critical understanding of the structural and functional attributes of complicated, uncultivable microbial communities, providing astounding opportunities for novel bioremediation strategies. A number of microbial community profiling techniques that rely on direct extraction of nucleic acids followed by subsequent de novo amplification of selected markers contribute immensely towards the changes in microbial community structure. In recent years, several novel fields of investigation such as metagenomics, metatranscriptomics, and metaproteomics were developed, largely propelled by the innovation and application of next-generation sequencing methods. The application of these methods allows direct analysis of natural microbial communities in situ, including their genes, transcripts, proteins, and metabolites and how their interactions may impact the attenuation of environmental pollutants leading to restoration of contaminated sites. This chapter discusses the application of traditional as well as recently developed, high-throughput molecular techniques for the characterization of microbial communities, specifically in contaminated environments. © 2014 Elsevier Inc. All rights reserved.