Table 3.

Genomics tools for studying bioremediation of different contaminants.

S. no.	Tool	Purpose	Microorganisms involved	Contaminant	Reference
1	Cloning and sequencing of ribosomal DNA	Identification of #BGD genes in community members of contaminated sites	Stenotrophomonas maltophilia	Pesticides, Heavy metals, Acid mine drainage	Raman et al., 2018; Simfukwe and Tindwa, 2018; Shukla et al., 2018
2	Second generation sequencing	Identification of community members having #BGD genes	Cycloclasticus, Pseudomonas, Halomonas, Pseudoalteromonas, Marinomonas, Bacillus, Dietzia, Colwellia, Acinetobacter, Alcanivorax, Salinisphaera, and Shewanella	Polycyclic aromatic hydrocarbons (PAHs)	Dong et al., 2015; Lozada and Dionisi, 2016
3	Quantitative PCR (polymerase chain reaction), RT-qPCR (real time quantitative PCR)	Quantification of #BGD genes and their expression	Pseudomonas and Rhodococcus	Diesel	Yergeau et al., 2012; Denaro et al., 2014
4	RFLP (restriction fragment length polymorphism), fingerprinting methods	Bacterial communities involved in biodegradation of persistent compounds	Thermoanaerobacteraceae, Desulfobulbaceae	Naphthalene	Marozava et al., 2018
5	FISH (fluorescent in situ hybridization)	In situ identification of metabolites involved in bioremediation	Dehalococcoides	Chlorinated solvents	Matturro et al., 2012
6	SIP (stable isotope probing)	Uptake of labeled compounds as substrate under defined conditions	Rhodoplanes, Kaistobacter, Pseudomonas, Flavobacterium, Mycobacterium	Naphthenic acids, phenanthrene, and atrazine	Fenner et al., 2013; Ahad et al., 2018; Lin et al., 2018; Subashchandrabose et al., 2018

^#BGD, biodegradation.