Metagenomics — A Technological Drift in Bioremediation

Abstract

Nature has its ways of resolving imbalances in its environment and microorganisms are one of the best tools of nature to eliminate toxic pollutants. The process of eliminating pollutants using microbes is termed Bioremediation. Metagenomics is a strategic approach for analysing microbial communities at a genomic level. It is one of the best technological upgradation to bioremediation. Identification and screening of metagenomes from the polluted environments are crucial in a metagenomic study. This chapter emphasizes recent multiple case studies explaining the approaches of metagenomics in bioremediation in different contaminated environments such as soil, water etc. The second section explains different sequences and function-based metagenomic strategies and tools starting from providing a detailed view of metagenomic screening, FACS, and multiple advanced metagenomic sequencing strategies dealing with the prevalent metagenomes in bioremediation and giving a list of different widespread metagenomic organisms and their respective projects. Eventually, we have provided a detailed view of different major bioinformatic tools and datasets most prevalently used in metagenomic data analysis and processing during metagenomic bioremediation.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

“…Genomics and metagenomics are powerful tools for analyzing microbial communities at the genomic level from various contaminated environments. This technology gives a new array to environmental microbiologists for understanding unculturable microbiota with a genetic variability of microbial communities (Devarapalli and Kumavnath, 2015 ; Zhu et al, 2018 ; Awasthi et al, 2020 ). It gives more details about the particular degradation potential of microbial communities, as it directly entails the whole-genome sequence from environmental samples ( Table 1 ).…”

“…Thus, modern culture-independent molecular techniques represent a feasible approach to unrevealing the diversity and functional dynamics of microbial population in contaminated environments. Moreover, the advanced innovation in molecular tools and techniques provides new insights and changes the traditional research trend in the field of bioremediation (Malik et al, 2008 ; Shah et al, 2011 ; Devarapalli and Kumavnath, 2015 ; Mahmoud, 2016 ; Biswas and Sarkar, 2018 ; Shakya et al, 2019 ). Omics technologies are the result of advanced molecular techniques, which involved direct characterization of genome structure of microorganisms, devoid of their culture sample (Segata et al, 2013 ; Biswas and Sarkar, 2018 ; Jaiswal et al, 2019 ; Yu K. et al, 2019 ).…”

Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil

“…Metagenomics data can provide a huge amount of information on the genetic potential of microbial communities in soil to degrade a pollutant, allowing researchers to determine which community members are potentially degrading the pollutants at the time of sampling. Detection and characterization of key microbial species pinned to specific physiological pollutantdegrading processes will allow us to discover new metabolic pathways and identify previously unknown or ignored microbes that play critical supporting roles in the metabolism and cometabolism of toxic hydrocarbons in soil (Devarapalli and Kumavath, 2015).…”

Analysis of viral and bacterial communities in groundwater associated with contaminated land

“…Different strategies of bioremediation exist. Particularly, metagenomic-based bioremediation approaches provide a comprehensive and detailed knowledge of endemic uncultured bacterial populations and allow scientists to describe, exploit and monitor the local biodegradative capacity of the local microbial communities (Devarapalli and Kumavath, 2015).…”