Metagenomics: An Emerging Novel Approach to Assess Microbial Diversity in the Riverine Ecosystem

Abstract

At the beginning of the 21st century, the scientific communities witnessed the emergence of metagenomics as an innovative technology to visualize the communities of the microorganisms in the river ecosystem. Metagenomics has bought a revolutionary change in deciphering microbial diversity in a culture-independent manner. This technology paves the way for analyzing genetic material obtained directly from river water and has provided a new direction into studying the overall microbial communities of river water. The biodiversity of the river environment is exceptionally diverse, with a considerable variation exerted mainly by anthropic activities. Now it is possible to unlock the massive uncultured microbial load dominated in the river water. The microbes in the river water perform crucial activity in the biogeochemical cycle. Thus, analysis of microbial composition by metagenomic approaches has accelerated the way to study microbial diversity as well as detecting pathogenic contamination. Furthermore, a metagenome based study is also of great significance as it significantly impacts routine monitoring of river water for hazardous microbial pathogens, which is of great significance in protecting human health. The various sequencing platforms have changed the entire chronology of studying microbial diversity. The large scale DNA based sequencing approaches targeting the 16S rRNA gene has revolutionized the abysmal study of microbial diversity in the river water. Thus, the innovation of NGS techniques, including 16S rRNA has made it easy for bacterial identification in river water samples. The metagenome study has gained applause since only 1% of microbes can be cultured under standard biosafety conditions. There is less knowledge about freshwater bacteria and the pathogenic bacteria affecting human health directly. Also, the rivers are the shield of climate and environmental change but they are primarily affected by various anthropogenic activities. The outcome of which is irretrievable damage to the ecosystem of the river. Thus, the metagenomics technologies are innovating the microbial world and pathogen dissemination in the river ecosystem. This review highlights the metagenomic potentialities and challenges to study the microbial world in the river water ecosystem. We will be discussing the challenges, benefits and importance of metagenomics in the study of microbial communities in the river water. Therefore, this study will significantly enhance our knowledge to understand rivers better in terms of microbial biodiversity, various interactions within the microbial communities, and public health concerns.