Metagenomic approaches for understanding microbial communities in contaminated environments: Bioinformatic tools, case studies and future outlook

Understanding environmental microbiomes is central to furthering strategies for the restoration of polluted habitats. Such studies allow us to gather important information on the native microbiota, as well as possible microbial responses to remediation procedures. In recent years, metagenomics has emerged as a reliable method to enable the holistic characterization of diverse microbiomes including those from soil, oceans, lakes, and animal gut, among others. Indeed, metagenomics has been used to identify microbial proxies from contaminated environments and elaborate taxonomic and functional changes in microbial communities during pollution events. Coupled with continually decreasing sequencing costs, metagenomics, and associated bioinformatic tools/pipelines now constitute routinely used methods in laboratories worldwide. This necessitates an adequate understanding of metagenomic shotgun sequencing and various other related sequencing applications, as well as the constantly evolving bioinformatic milieu, to ensure proper interpretation of microbiome data. To this end, we review the various massively parallel sequencing-based applications for studying microbiomes in this chapter and discuss the bioinformatic tools, strategies, and approaches available to analyze the sequencing data generated. To provide context, we additionally discuss studies where next-generation sequencing-based applications have been employed in investigating contaminated environments.