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Metagenomic approaches for the selection of biosurfactants producing genes are scanty, and few studies have been conducted to detect commercially important biosurfactants using metagenomic tools [40, 41]. In view of the enormous diversity of microbes in oil‐contaminated soil, the search for novel biosurfactant molecules should be stepped up [42, 43].

Standard cultivation techniques do not encourage the isolation and screening of novel biosurfactant producers due to the diverse culture requirements of the microbial population. Moreover, due to structural and molecular diversity, the vast majority of them remain uncultured [43–45]. Metagenomics is an excellent way to bypass traditional cultivation techniques and to explore the undiscovered microbial population from oil‐contaminated soil [44, 46, 47]. Metagenomic tools make it easier to isolate DNA and diverse microbial populations from environmental samples for potential uses [48–50].

Isolated metagenomic DNA is subjected to DNA sequencing or screening for functional activity [51, 52]. Metagenomic DNA sequencing involves next generation sequencing (NGS) and polymerase chain reaction (PCR) amplification. NGS allows the identification of coding sequences based on the homology of known genes [53]. The screening process is based on previously designed probes and primers based on sequences of known gene coding for an enzyme or bioactive compound [14].

Shotgun metagenomic sequencing is normally used to acquire a gene pool from a sample of environmental DNA [13]. Metagenomic sequence homology to reference sequence database is performed through similarity search tools such as BLAST (basic local alignment search tool), KEGG (Kyoto Encyclopedia of Genes and Genomes), COG (clusters of orthologous droups of proteins), etc. [46]. A software tool such as antiSMASH (antibiotic and secondary metabolite analysis shell) enables the identification of gene clusters linked to important biosynthetic pathways such as biosurfactant production [52]. Furthermore, screening for other related genes parallel to known genes for biosynthetic pathways may help to explore new structural compounds with improved biosurfactant properties from oil‐contaminated soil.

Functional metagenomics involves the cloning of environmental DNA into a suitable vector and the heterologous expression of genes of interest. This technique allows the detection and testing of heterologous biomolecules and bioactivity using high‐throughput monitoring systems [46, 51]. Functional screening aids in the identification of genes or new biomolecules from the Environmental Clone Library without prior knowledge of sequence isolation [14, 54, 55].

The construction of a metagenomics library for the desired gene expression is based on the precise selection of DNA fragments from the DNA pool extracted. The ideal vectors and hosts are then selected for target gene expression. Various vectors, such as plasmids, cosmids, fosmids, and bacterial artificial chromosomes (BAC), are used based on the size of the DNA fragment. Both single‐host and multiple‐host expression systems are used for gene expression systems [19].

Although functional metagenomics has made significant progress in the last few years, it has some limitations. Environmental DNA expression depends on the heterologous expression system of choice. Expressions of foreign genes in heterologous hosts may be hindered by host transcription machinery, which leads to low targeted gene expression. In contrast, the screening method may not be sufficiently sensitive to detect gene expression [56]. In addition, the proteins expressed may have a toxic effect on the host and the desired number of new biomolecules may not be achieved. [46]. Another caveat for functional metagenomics is searching for the targeted novel genes or its functional products from the large community DNA pool. To overcome this limitation, recent research has come to focus on ecological enhancement, i.e. enhancement of in situ environmental conditions by addition of specific substrates or altering the microhabitat for targeted microbial communities so that the desired functions from the extracted metagenome is achieved [56].

Thus, at present, metagenomics could be considered to be a powerful molecular technique for the detection of both bacterial and gene‐producing biosurfactants. However, the efficacy of metagenomics can be improved by the use of the stable isotope probe (SIP) discussed in the next section.