to monitor and evaluate microbes in environmental samples and to assist in bioremediation techniques [14]. Microbes can be screened through metagenomics for potential genes that can be used as biomarkers for pollution [16] or for the production of novel biomolecules for environmental management.
Biosurfactants are key agents in the remediation of persistent heavy metals in soil. They have been found to be effective in the remediation of heavy metals contaminated soil by the formation of a surfactant‐associated complex which has already been established [3]. Metagenomics figure centrally in this context as well. For instance, metallothionein (MT) genes have been discovered from soil microbiomes using this approach. MT genes from novel metal‐tolerant bacterial strains that confer Cu/Cd resistance and biosorption have been used for the development of metal bioremediation tools [13]. Similarly, metagenomics can help isolate genes that specifically target the degradation of PAHs in contaminated soil. This is crucial in the context of producing biosurfactants since they play a significant role in the biodegradation of polyaromatic hydrocarbons (PAHs) from soil. Biosurfactants increase the mobility of PAHs by reducing surface and interface stresses [17] and reduce the half‐life of three‐ and five‐ring PAHs by accelerating the degradation process of contaminated soil PAHs [4]. In addition to PAH degradation, biosurfactants are used to clean oil sludge from storage tanks, enhance oil recovery from refinery sludge and reservoirs, and mobilize oil flow through pipelines [4, 5, 18].
Metagenomics is used to identify genes from an environmental sample that have the potential to produce enzymes of industrial importance. Several enzymes, such as lipase, β‐glucosidase, amylase, proteases, and esterases, have been described to have been investigated using metagenomics approaches [19]. They have also been used successfully in the creation of novel products for drug molecules [15]. Recent research has expanded our knowledge in the field of biomedicine by showing that both terrestrial and aquatic environments harbor microorganisms involved in the production of drug molecules [20]. Several microbial metabolites with antibacterial, antiviral, and antifungal properties have been screened through functional metagenomics [21]. In the field of health care, an individual’s clinical diagnosis for pathogenic organisms can be traced with the help of metagenomics. Since most pathogens can be grown in selective media and are difficult to cultivate, metagenomics offers the screening of the individuals’ microbiome as a whole [14].
Metagenomics is further employed in a range of other diverse sectors. In the food sector, it can be used in the detection of potential microbes for biosurfactant production for use in food industries. While the use of biosurfactants has not been very common in the food industry, they are being used to stabilize the agglomeration of fat globules and to improve the quality of foods based on fat [3]. In the field of agriculture, they are mainly used to monitor plant pathogens. Early detection of pathogens may help prevent plant diseases and minimize the loss of economically important crop plants [14]. They can also be used to successfully track viral pathogens, which often pose difficulties in screening using other conventional methods.
From this, it becomes evident that metagenomics has become an integral technique with multiple uses, from the detection of new molecules to advanced medical technology. Enzymes and other industrially important bioactive compounds, such as biosurfactants, have led to sustainable industrial growth through metagenomics. This technology also greatly contributes to the environmental monitoring of microbes and toxins, leading to the identification, treatment, and prevention of many diseases, and to the prevention of epidemics. Early identification with microbial metagenomics contributes to the reduction and elimination of health threats. Bioremediation and innovation of new drugs also help to improve the quality of life. Given the novelty of this technique, however, many other aspects of metagenomics are yet to be explored.
2.3 Hydrocarbon‐Degrading Bacteria and Genes
Exploration of crude oil often results in accidental spillage and environmental contamination due to its various toxic components [22, 23]. Crude oil exploration fields are also home to oil‐degrading microbes that are capable of using spilled oil as their carbon source and can remove crude oil from contaminated sites [24]. Numerous oil‐degrading bacteria strains have been isolated from both cold [9] and hot [25] environments. Microbe‐enhanced oil recovery tests performed using biosurfactant‐producing microorganisms are briefly described in Chapter 5.
In the last few years, attempts have been made to identify possible biosurfactant‐producing microorganisms [4]. Some of the key genera that make biosurfactants are Acinetobacter, Bacillus, Azotobacter, Candida [18], Enterobacter, Micrococcus, Oceanobacillus, Pseudomonas, Rhodococcus, Serratia and Stenotrophomonas [18, 26]. Rhodococcus sp. HL‐6 reported from petroleum‐contaminated soil produces glycolipid biosurfactants and has been successfully exploited for the remediation of crude oil contaminated sites [27]. Pseudomonas is one of the most widely described genera for the production of biosurfactants [28]. Bacillus subtilis and Pseudomonas aeruginosa have also been reported from oil‐contaminated soils and have been shown to be a potential candidate for the degradation of petroleum hydrocarbons [18, 28, 29]. Similarly, biosurfactants derived from the consortium of P. aeruginosa and Rhodococcus strains have been reported to degrade more than 90% of oil sludge [30]. P. aeruginosa RS29 isolated from crude oil‐contaminated sites has been reported to produce potent biosurfactants with enhanced foaming and emulsifying properties [28]. The thermophilic hydrocarbon‐degrading bacteria P. aeruginosa AP02‐1 are known to produce biosurfactants using hydrocarbon as the sole source of carbon [31]. Biosurfactant BSW10 derived from P. aeruginosa W10 has been successful in phenanthrene and fluoranthene biodegradation from oil‐contaminated sites [32].
The marine microbiome is a global collective of all microorganisms. This is a good source of useful microbes for use in bioproducts. Specific microbial communities living in marine and coral reefs have been reported to be beneficial to humans. Acinetobacter, Alteromonas, Azotobacter, Corynebacteria, and Myroids are some marine microorganisms that have been reported to produce biosurfactants [12], while Alcanivorax and Halomonas have also been reported to produce biosurfactants in marine environments and to degrade hydrocarbons [33]. Alcanivorax uses n‐alkanes from oil‐contaminated sites producing glycolipid biosurfactants [34]. Species of Halobacterium viz. Haloferax, Halovivax, and Haloarcula have been described as biosurfactant producers and are known to utilize different hydrocarbons [35]. Marinobacter, Methylophagia, Roseovarius, Thalassospria, Rheinheimera, and Sphingomonas are the other genera known to produce biosurfactants and have been able to degrade aliphatic and aromatic hydrocarbons [36].
Many potential genes that are responsible for biosurfactant production have now been identified and described. Leite et al. [37] describe the presence of rhlAB and alkB genes from bacterial genomes isolated from soil contaminated with crude oil. The main pollutants of crude oil are alkanes and aromatic hydrocarbons. These bacterial genomes contain RhlAB genes and are responsible for the production of rhamnolipid biosurfactants and the alkB gene (alkane mono‐oxygenase) mediates the degradation of petroleum hydrocarbons by the alkane mono‐oxygenase enzyme system. Similarly, another gene reported from oil‐contaminated soil is the naphthalene dioxygenase (Nah) gene, which contributes to the degradation of both alkanes and aromatic hydrocarbons [38]. Likewise, a lipopeptide biosurfactant surfactin is produced by three genes, srfA, srfB, and srfC, present in srfA operon [35, 39].
All the results reported in this section provide scientific evidence that oil‐contaminated soil and marine environment are good sources of potential microbes that produce biosurfactants and degrade hydrocarbons. Microbial genes from contaminated environments could be used to produce environmentally safe biosurfactants that help with bioremediation and at the same time reduce production costs involved in the process.
2.4 Metagenomic Approaches in the
