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Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics
derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief
discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.
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Fluorene having three rings is a major constituent of fossil fuels and coal derivatives. Several bacteria able to use fluorene as their sole source of carbon and energy have been isolated and are in the genera of Arthrobacter, Brevibacterium, Burkholderia, Mycobacterium, Pseudomonas and Sphingomonas.
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Phenanthrene, a three aromatic ring system, is found in high concentrations in PAH-contaminated sediments, surface soils, and waste sites [49]. Bacterial degradation of phenanthrene has been extensively studied. A variety of bacterial strains in Acidovorax, Arthrobacter, Brevibacterium, Burkholderia, Comamonas, Mycobacterium, Pseudomonas, and Sphingomonas have been isolated and have the ability to utilize phenanthrene as a sole carbon and energy source.
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Proteomics and metabolomics have been recently employed in studies of environmental microbiology and have shown their high impact on the field of biodegradation and bioremediation [158, 159]. Proteomics is an effective technique to identify proteins and their functions involved in the biodegradation of aromatics while metabolomics can be used to profile degradation products of PAHs and primary metabolites in response to PAH exposures. Intent of a brief discussion of proteomics and metabolomics here is to bring attention to these emerging fields rather than offering a comprehensive review and a long list of references. A good number of genomic sequences or expressed sequence tags (ESTs) of bacteria are currently available. These include several PAH degrading bacteria in the genus of Mycobacterium, Acinetobacter, Arthrobacter, and Burkholderia.
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