**3. Metagenomic bioremediation of different contaminations**

The environment where human activity abounds is being more polluted and contaminated by different kinds of toxic contaminants [18-20]. The contaminations are diverse and cover almost all sources of life including water, soil, and air which are considered the most important sources of life [21-23]. Metagenomic analysis is applied to multiple kinds of polluted environments primarily soil- and water-contaminated environments [24, 25].

#### **3.1. Metagenomic bioremediation of soil contaminations**

tools to reduce pollutants in different ways, and bioremediation is considered to be the best way to neutralise polluted environments on Earth [1, 2]. In this genomic era, metagenomic approaches have been developed and are known as effective methods of removing various kinds of pollutants [3, 4]. Metagenomics is a strategic approach of analyzing microbial communities at a genomic level. This provides a glimpse of the microbial community view of "Uncultured Microbiota". Recent studies suggest that microbial communities are the potential alternatives to eliminate toxic contaminants from our environment [5-8]. The term metage‐ nomics was coined by Jo Handelsman et al. in 1998. They have accessed the collective genomes and the biosynthetic machinery of soil microflora during a study of cloning the metagenome [9]. Bioremediation has always been adapting new advances in science and technology for establishing better environments. Compared with the previous years, there has been a gradual increase of interest in metagenomics-based bioremediation studies [10-12]. These studies can prove that metagenomics is one of the best adaptations of bioremediation leading to the

In this chapter, we discussed recent approaches of metagenomics in bioremediation with the help of recent multiple case studies. Preliminarily, we explained the methodology behind metagenomic analysis, starting from the sample screening and ending up with metagenomic analysis with respect to bioremediation. Metagenomic bioremediation reviews and extracts microbial communities applying their extensive biochemical pathways in degrading toxic pollutants. A part of our study aims to emphasize multiple case studies of metagenomic applications on air, water, and soil contaminations. Our analysis provided a topic-specific landscape with respect to metagenomic bioremediation of water contaminations, soil contam‐ inations, and followed by air contaminations. The following part of our study focuses on recently developed sequence and function-based metagenomic strategies to analyze metage‐ nomes from contaminated environments. In addition to this, our study explains the highly prevalent metagenomes derived from metagenomic communities which are also highly capable of degrading contaminations and toxins in the environment. Finally, we provided a landscape view of multiple bioinformatic tools used in the processing and analysis of meta‐

Environmental scientists consider metagenomic bioremediation as one of the potential tools to remove contaminants from the environment [13-15]. As cited earlier, recent multiple studies have reported metagenomic approaches in bioremediation. When this was compared with the other approaches of bioremediation, metagenomic bioremediation provided best outcomes with better degrading ratios. The results of a recent study emphasized the potential of metagenomic bacteria derived from petroleum reservoirs [16]. In this study, microbial strains and metagenomic clones have been isolated from petroleum reservoirs, and petroleum degradation abilities were evaluated either individually or in pools using seawater artificial ecosystems. The results showed that metagenomic clones were able to biodegrade up to 94% of phenanthrene and methyl phenanthrenes with rates ranging from 55% to 70% after 21 days

establishment of a pure nontoxic environment.

74 Advances in Bioremediation of Wastewater and Polluted Soil

genomic bioremediation data.

**2. Applications of metagenomics in bioremediation**

Soil contamination is a serious contamination [26, 27] as soil is considered as one of the major sources of life [28]. Compared with other approaches of bioremediation, microbial and environmental researches are more inclined in applying metagenomic approaches to biore‐ mediation [10, 29, 30]. A recent case study discusses the metagenomic analysis of arctic soils contaminated by high concentration of diesel in Canada [31]. As this study was on arctic soils, the objective framed was to trace out microorganisms and their functional genes which are abundant and active during hydrocarbon degradation at cold temperature. In this study, scientists have sequenced the soil metagenome and performed reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudo‐ monas species were detected as the most abundant organisms in diesel-contaminated soils at cold environments. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in arctic biopile soils. The results of this study indicated that biopile treatment leads to major shifts in soil microbial communities which favors aerobic bacteria to degrade hydrocarbons [31].

#### **3.2. Metagenomic bioremediation of water contaminations**

Water pollution has dramatically increased in comparison with the conditions of the 20th century [32, 33]. Metagenomic application in the bioremediation of water contamination is one of the best ways to reduce water contaminations [34-37]. Recent multiple case studies suggest that metagenomic applications have been widely used for the identification and treatment of pollutants and contaminations in the sea, ground water, and drinking water [34-37]. A recent research performed at the Gulf of Mexico beaches precisely talks about the longitudinal metagenomic analysis of water and soil affected by deepwater horizon oil spill [34]. Approx‐ imately 7×105 cubic meters of crude oil were released into the Gulf of Mexico as a consequence of deepwater horizon drilling rig explosion, where thousands of square miles of the earth's surface were covered in crude oil. During this study, researchers performed high throughput DNA sequencing of close-to-shore water and beach soil samples before and during the appearance of oil in Louisiana and Mississippi. The sequencing results have identified an unusual increase in the human pathogen *Vibrio cholera*, a sharp increase in *Rickettsiales sp.*, and decrease of *Synechococcus sp.* in water samples [34]. In addition, a metagenomic analysis was also performed for the bioremediation of hexavalent chromium-contaminated water that existed in fixed-film bioreactor [38]. This study talks about hexavalent chromium (Cr6+) contamination from a dolomite stone mine in Limpopo Province, South Africa, causing extensive groundwater contamination. To restrict any further negative environmental impact at the site, an effective and sustainable treatment strategy for the removal of up to 6.49 mg/l Cr6+ from the groundwater was developed. The microbial community shifted in relative dominance during operation to establish an optimal metal-reducing community, including *Enterobactercloacae*, *Flavobacterium sp.* and *Ralstonia sp.,* which achieved 100% reduction. This study provides a glimpse of effective demonstration of a biological chromium (VI) bioreme‐ diation system [38].
