Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

Widespread environmental pollution by polycyclic aromatic hydrocarbons (PAHs) poses an immense risk to the environment. Bacteria-mediated attenuation has a great potential for the restoration of PAH-contaminated environment in an ecologically accepted manner. Bacterial degradation of PAHs has been extensively studied and mining of biodiversity is ever expanding the biodegradative potentials with intelligent manipulation of catabolic genes and adaptive evolution to generate multiple catabolic pathways. The present review of bacterial degradation of low-molecular-weight (LMW) PAHs describes the current knowledge about the diverse metabolic pathways depicting novel metabolites, enzyme-substrate/metabolite relationships, the role of oxygenases and their distribution in phylogenetically diverse bacterial species.

Staphylococcus sp. strain PN/Y, capable of utilizing phenanthrene as a sole source of carbon and energy, was isolated from petroleum-contaminated soil. In the degradation of phenanthrene by strain PN/Y, various metabolites, isolated and identified by a combination of chromatographic and spectrometric analyses, revealed a novel phenanthrene assimilation pathway involving 2-hydroxy-1-naphthoic acid. Metabolism of phenanthrene was initiated by the dioxygenation on the 1,2-position of phenanthrene followed by meta-cleavage of phenanthrene-1,2-diol, leading to 2-hydroxy-1-naphthoic acid, which was then processed via a novel meta-cleavage pathway, leading to the formation of trans-2,3-dioxo-5-(29-hydroxyphenyl)-pent-4-enoic acid and subsequently to salicylic acid. In the lower pathway, salicylic acid was transformed to catechol, which was then metabolized by catechol-2,3-dioxygenase to 2-hydroxymuconaldehyde acid, ultimately forming TCA cycle intermediates. The catabolic genes involved in phenanthrene degradation were found to be plasmid-encoded. This detailed study of polycyclic aromatic hydrocarbon (PAH) metabolism by a Gram-positive species involving a unique ring-cleavage dioxygenase in a novel phenanthrene degradation pathway provides a new insight into the microbial degradation of PAHs. INTRODUCTIONPolycyclic aromatic hydrocarbons (PAHs) constitute a group of priority environmental pollutants, which are ubiquitous contaminants in soils and sediments and are of environmental concern because of their toxic, mutagenic and/or carcinogenic effects (Mastrangelo et al., 1996;Marston et al., 2001;Xue & Warshawsky, 2005). In recent years, the biodegradation of PAHs has received considerable attention and a variety of micro-organisms have been reported to play important roles in the process (Pothuluri & Cerniglia, 1994;Shuttleworth & Cerniglia, 1995;Kanaly & Harayama, 2000;Habe & Omori, 2003;Tortella et al., 2005). Bioremediation technologies have increasingly been proposed to decontaminate PAH-contaminated sites (Harayama, 1997;Samanta et al., 2002;Parrish et al., 2004;Vinas et al., 2005).Phenanthrene, a PAH with three condensed rings fused in angular fashion, has a 'bay-region' and a 'K-region' and is often used as a model substrate for studies on the metabolism of carcinogenic PAHs. Over the last 60 years, a number of studies on phenanthrene degradation by several Gram-negative and Gram-positive bacterial species have been reported (Evans et al., 1965;Kiyohara et al., 1976Kiyohara et al., , 1982Kiyohara & Nagao, 1978;Barnsley, 1983;Gibson & Subramanian, 1984;Houghton & Shanley, 1994;Adachi et al., 1999;Samanta et al., 1999), where various pathways and metabolic diversity involved in phenanthrene degradation were documented. In general, the metabolic pathway is initiated by the double hydroxylation of the bay-region of phenanthrene by a dioxygenase enzyme to form cis-3,4-phenanthrenedihydrodiol. The resultant dihydrodiol is then converted by the action of dihydrodiol dehydrogenase to 3,4-dihydroxyphenanthrene, which und...

Time-of-flight mass spectrometry was used for the first time to analyze the hydrocarbons in crude oil. Alkanes in the saturated fraction of a crude oil sample were chemically ionized by the laser desorption of silver nitrate, and the silver-attached C24-C60 alkanes were resolved with mass accuracy below 7 ppm. This technique was used to evaluate the biodegradation of aliphatic hydrocarbons and cycloalkanes by oil-degrading microorganisms resident in seawater. It is shown that the aliphatic hydrocarbons were degraded in the range of 60-80%, while the mono-, di-, tri-, tetra-, and pentacycloalkanes were degraded in the range of 40-55, 20-30, 10-16, 5-9, and <5%, respectively. Its high sensitivity and speed of application could result in an analysis by laser desorption silver chemical ionization time-of-flight mass spectrometry being the method of choice for determining high-molecular-weight hydrocarbons in various petroleum products.

Photooxidation and biodegradation are the two most important factors involved in the transformation of crude oil or its products that are released into a marine environment. Natural microbial populations in seawater biodegraded 28% of crude oil within 8 weeks at 20 °C when sufficient nutrients were supplied to the seawater. Photooxidation mainly affected the aromatic compounds in crude oil and converted them to polar species. This treatment increased the amount of crude-oil components susceptible to biodegradation, and 36% of photooxidized crude oil could be degraded in 8 weeks at 20 °C. It is concluded that the susceptibility of crude oil to biodegradation is increased by its photooxidation.