The Mycobacterium genus is often associated with HMW PAH biodegradation

In the absence of major decomposition pathways, PAHs are removed from the atmosphere by dry and wet deposition, which is considered the major source of PAHs in soil . Although PAHs are considered amongst the most widespread organic pollutants in numerous environmental matrices such as soils, sediments, water, and wastewater, the ultimate sink of atmospheric PAHs is soil . Wild and Jones conducted an investigation to quantify the production, cycling, and storage of PAHs in the United Kingdom and determined that more than 90% of the total PAH burden resided in the surface soil. In addition to atmospheric deposition, PAHs can also enter soil systems through disposal of waste materials, creosote use, road runoff, and fossil fuel spills . The fate of PAHs in soil systems is primarily influenced by PAH hydrophobicity and the physicochemical properties of the soil. Due to their strong hydrophobicity and environmental recalcitrance, PAHs are typically associated with nonaqueous phases in soil where they associate into four main compartments: 1) organic matter; 2) the mineral compartment, which includes exposed soil surfaces and surfaces within pore spaces; 3) nonaqueous-phase liquids; and 4) combustion residues such as soot . The degree to which PAHs are retained within the soil system is controlled primarily by soil properties such as organic matter and soil texture as well as the PAH physicochemical properties.

Because of the nonpolar, hydrophobic nature of PAHs, soil organic matter is considered the most important sorbent of PAHs . The organic matter or total organic carbon can also act as a carrier for the vertical migration of PAHs from the soil surface .Polycyclic aromatic hydrocarbons have a very strong affinity for soil organic matter via π-π interactions between the aromatic structure of PAHs and aromatic moieties of organic matter . In soils with low amounts of organic matter or total organic carbon content,fodder systems for cattle the soil texture plays a critical role in the environmental fate of PAHs. For example, Karickhoff et al. reported an increase in pyrene adsorption coefficients with an increasing clay content . In addition, decreasing particle size is typically associated with concomitant increases in the proportion of HMW and decrease in the proportion of LMW PAHs . The greatest PAH soil concentrations in numerous studies have been observed in the silt-sized soil fraction, which was potentially due to the silt fraction containing the greatest concentration of soil organic matter and its associated aromatic structures for binding . In addition, clay fractions are characterized by a very high specific surface area, abundant surface charge, and a high organic matter density, all of which provide a large number of sorption sites for PAHs . Sorption of PAHs to soils generally entails an initially rapid and reversible phase followed by a period of slow sorption occurring over a period ranging from weeks to years, and this slow sorption leads to a chemical fraction that resists desorption and biodegradation . Increasing contact times between PAHs and soil organic matter or fine soil fractions can also result in the “aging” effect or sequestration of PAHs . This process involves the continuous diffusion and retention of PAHs within the solid phase of organic matter and also in nanopores or voids in the organic matrix, thus blocking PAHs from abiotic and biotic loss processes.

As a result of the strong association of PAHs with the nonpolar soil organic fractions, PAH bioavailability, or PAH concentrations in the aqueous phase that are directly available to soil microbes for degradation, is generally low . The bioavailability of PAHs is determined by two main factors, which are the rate of transfer of PAHs from the soil to the living cell and the rate of uptake and metabolism . Bio-availability is an important concept with regards to PAH-contaminated soil remediation and risk assessment as microbial degradation constitutes the major dissipation pathway for PAHs compared to other processes such as evaporation, photolysis, and plant uptake . The extent and rate of microbial degradation of PAHs in the terrestrial environment is influenced by a variety of abiotic and biotic factors which include temperature, pH, aeration, accessibility ofactors, which are the rate of transfer of PAHs from the soil to the living cell and the rate of uptake and metabolism . Bio-availability is an important concept with regards to PAH-contaminated soil remediation and risk assessment as microbial degradation constitutes the major dissipation pathway for PAHs compared to other processes such as evaporation, photolysis, and plant uptake .f nutrients, microbial population, contaminant bio-availability, and physicochemical properties of the PAH . Typically, the rate of PAH biodegradation is inversely proportional to the number of aromatic rings or molecular weight of the PAH . For example, half-lives of phenanthrene in soil may range from 16 to 126 days, while half-lives of HMW PAHs such as benzo[a]pyrene may Mansour, 2016. Some of the major PAH-degrading genera in soils include Mycobacterium, Sphingomonas, Bacillus, Pseudomonas, and Rhodococcus . The ability of soil microbes to degrade PAHs is determined by 1) the ability of bacteria to transport the PAH into the cell, 2) the physicochemical properties of the PAH as a substrate for available microbial enzymes, and 3) the suitability of the PAH as an inducer for the appropriate transport or degradative enzymes .

As shown in Figure 1.3, there are two primary mechanisms involved in the aerobic metabolism of PAHs by soil bacteria . The principal mechanism for aerobic PAH degradation by soil bacteria involves the dioxygenase/monooxygenase enzymes, which incorporates a hydroxyl group derived from molecular oxygen into the aromatic nucleus, resulting in the oxidation of the aromatic ring to form cis-dihydrodiols . This initial ring oxidation is considered to be the rate limiting step of the PAH bio-degradation process in soil systems . The cis-dihydrodiols are stereoselectively dehydrogenated by cisdihydrodiol dehydrogenases to form dihydroxylated intermediates, called catechols . Subsequently, the catechol may then be cleaved by intradiol or extradiol ring-cleaving dioxygenases through the ortho or meta-cleavage pathway to tricarboxylic acid intermediates such as succinic, fumaric, pyruvic, and acetic acids and acetaldehyde. These TCA intermediates are utilized for cell-protein synthesis and energy by microorganisms with the final production of carbon dioxide and water . Soil bacteria can also degrade PAHs via the cytochrome P450-mediated pathway to form transdihydrodiols . Polycyclic aromatic hydrocarbons are biodegraded by soil microbes in one of two ways, either as the sole carbon and energy source or by cometabolism . Because PAHs occur in the environment as complex mixtures of LMW and HMW PAHs, cometabolism is an important interaction that transforms non-growth substrate PAHs, particularly HMW PAHs, in the presence of growth substrates to enhance PAH degradation . Numerous soil microbes have been isolated that utilizeLMW PAHs such as naphthalene and phenanthrene as their sole carbon source and throughout the past decade, multiple soil bacteria have been discovered and isolated that are capable of utilizing HMW PAHs as sole carbon sources . For example, Mycobacterium vanbaalenii PYR-1, an isolate from an oil-contaminated estuary near the Gulf of Mexico,fodder sprouting system has been utilized to determine the complete pyrene degradation pathway using various metabolic, genomic, and proteomic approaches.Pyrene is often used as a model compound for HMW PAH biodegradation because it is structurally similar to several carcinogenic HMW PAHs.The primary pathway for pyrene degradation by M. vanbaalenii PYR-1 is deoxygenation by dioxygenase and monooxygenase at the C-4 and C-5 positions to produce both cis– and trans-4,5-pyrenedihydrodiol, respectively. The metabolite undergoes further metabolization involving more than 20 enzymatic steps utilizing rearomatization, decarboxylation, and oxygenation to produce phthalate that is further transformed to the TCA cycle via the β-ketoadipate pathway . Another pyrene degradation pathway exists for M. vanbaalenii PYR-1 that involves the oxidation of pyrene at the C-1 and C-2 positions to form O-methylated derivatives of pyrene-1,2-diol as a detoxification step . Mycobacterium vanbaalenii PYR-1 is also capable of degrading or transforming biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, benzo[a]anthracene, and benzo[a]pyrene, thus making this bacterium an effective candidate for the  bio-remediation of PAH-contaminated soils. Because PAHs are toxic, ubiquitous pollutants that are highly resistant to degradation in contaminated soils, remediation of PAH-contaminated sites is critical for protecting human health and the environment. Several physical and chemical PAH remediation technologies such as incineration, excavation and land filling, UV oxidation, and solvent extraction have been used to clean up PAH-contaminated soils.

However, these remediation methods have several negative aspects including cost, regulatory burden, and that some of these conventional methods do not result in PAH dissipation, but rather transfer from one environmental compartment or form to another . These limitations of conventional treatment methods have led to the increased use of bio-remediation techniques at PAH-contaminated sites as they are considered to be safe, environmentally-friendly, and cost-effective . Bio-remediation involves the utilization of biological processes or activity of microorganisms to remove pollutants from contaminated matrices to achieve concentrations that are acceptable according to health and regulatory standards. Bio-remediation technologies can be classified into two main categories, in situ or ex situ. In situ bio-remediation technologies target contaminant removal or attenuation under natural environmental conditions without the need for excavation, whereas ex situ bio-remediation processes involve the physical removal of the contaminated material for remediation off-site . Therefore, in situ remediation practices are particularly effective for widely dispersed contaminants and are typically less expensive than ex situ approaches. Additionally, exposure to site workers to hazardous pollutants is minimal and in situ treatments also allow for remediation in inaccessible environments . Because of these advantages, in situ bio-remediation constitutes approximately 25% of all remediation projects for contaminated sites . However, because in situ bio-degradation does not disturb the contaminated soil, remediation has been found to be more variable due to the natural environmental conditions . Although ex situ bio-remediation is less economical compared to in situ treatments, ex situ bio-remediation methods are less limited by environmental factors that could adversely affect the remediation efficacy and the physical and chemical conditions can be manipulated before and during degradation . Ex situ bio-remediation generally requires less time to achieve efficient contaminant remediation since optimal remediation conditions can be monitored and modified as needed . The successful implementation of PAH-contaminated soil  bio-remediation treatments depends on a multitude of factors that can be categorized into three main domains encompassing PAHs, environmental conditions, and soil microbial communities . Factors involving PAHs include the physicochemical properties of PAHs, concentration and toxicity, and the length of time the PAHs have been in contact with the soil and their associated bio-availability. Because in situ bio-degradation treatments are currently a common type of remediation practice, environmental conditions in soil that must be evaluated for effective PAH bio-degradation include soil type, organic matter content, nutrient availability, moisture, temperature, pH, and presence of oxygen or alternative electron acceptors. Soil microbial transformations are the major process governing degradation of PAHs in contaminated soil, and therefore critical factors related to soil microbes include the presence of a soil microbial community capable of degrading PAHs, which encompasses microbial type, abundance, distribution, acclimation or previous exposure, and metabolic rate. Natural or bio-attenuation is an in situ  bio-remediation technique that involves passive remediation of a PAH-contaminated site without any external alterations . Because there are no site modifications, natural attenuation is considerably cheaper than other  bio-remediation methods. However, one of the major limitations of bio-attenuation is that the process can take extended periods of time to achieve appreciable levels of PAH dissipation. Bio-degradation is especially slow in PAH contaminated sites that have been in contact with non-polar soil domains for a prolonged duration, resulting in decreased PAH bio-availability.Due to the environmental stability of PAHs, the majority of PAH-contaminated sites undergo engineered or enhanced bio-remediation, which involves site modifications to enhance the extent and rate of PAH degradation . Typically, enhanced bio-remediation techniques for PAH-contaminated soils involve bio-augmentation, bio-stimulation, surfactant amendment, phytoremediation, or an integrated combination of bio-remediation techniques.Bio-augmentation is the process in which contaminant-degrading microorganisms are introduced into the soil as single strains or bacterial consortia to increase the rate of PAH bio-degradation. The main advantage of bio-augmentation is the relatively low cost of inoculating soil microorganisms into the soil system.Bio-augmentation is an effective method to increase bio-remediation efficacy for PAH-contaminated soils that possess low numbers of native PAH-degrading soil microbes or when the native soil microbial population does not exhibit sufficient metabolic activity to result in PAH dissipation.