Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs

Due to continuous anthropogenic activities and other natural changes, aquatic ecosystems are under increasing stress. Metagenomics aided by next-generation sequencing techniques provides in-depth insights into microbiome dynamics from multitude of aquatic resources thus contributes in understanding the physiological, metabolic, and ecological roles of microbial assemblies. Monitoring of diverse aquatic resources using metagenomics has the potential to efficiently characterize diverse range of microbiomes with relevant functional pathways. Contributions made by high-throughput second and third generation sequencing platforms are noteworthy in monitoring aquatic microbial biodiversity through characterization of genetic variations which is indicative of changing environmental adaptations. Analysis of sequence and function driven metagenomics enable elucidation of enzymatic pathways leading to the discovery of novel gene sequences with desired functions having ecological, industrial and pharmaceutical importance. This review seeks to define the role of metagenomics in exploring aquatic microbiota in terms of toxicological exposure, genome heterogeneity, assessment, and the management of aquatic ecosystem by utilizing microbial bio-indicators. We have also enlisted various high-throughput computational biology packages and tools exclusively used to handle metagenomic data along with the challenges and future perspectives. Owing to global climate change and massive human-induced alterations in aquatic ecosystems, we expect that the on-going whole-genome metagenomics studies in combination with “meta-OMICS” approaches would transform our comprehension of microbiome community structure, function and ecology at high resolution.