Microbial degradation of petroleum hydrocarbon contaminants: an overview

One of the major environmental problems today is hydrocarbon contamination resulting from the activities related to the petrochemical industry. Accidental releases of petroleum products are of particular concern in the environment. Hydrocarbon components have been known to belong to the family of carcinogens and neurotoxic organic pollutants. Currently accepted disposal methods of incineration or burial insecure landfills can become prohibitively expensive when amounts of contaminants are large. Mechanical and chemical methods generally used to remove hydrocarbons from contaminated sites have limited effectiveness and can be expensive. Bioremediation is the promising technology for the treatment of these contaminated sites since it is cost-effective and will lead to complete mineralization. Bioremediation functions basically on biodegradation, which may refer to complete mineralization of organic contaminants into carbon dioxide, water, inorganic compounds, and cell protein or transformation of complex organic contaminants to other simpler organic compounds by biological agents like microorganisms. Many indigenous microorganisms in water and soil are capable of degrading hydrocarbon contaminants. This paper presents an updated overview of petroleum hydrocarbon degradation by microorganisms under different ecosystems.

1. Introduction

Petroleum-based products are the major source of energy for industry and daily life. Leaks and accidental spills occur regularly during the exploration, production, refining, transport, and storage of petroleum and petroleum products. The amount of natural crude oil seepage was estimated to be 600,000 metric tons per year with a range of uncertainty of 200,000 metric tons per year [1]. Release of hydrocarbons into the environment whether accidentally or due to human activities is a main cause of water and soil pollution [2]. Soil contamination with hydrocarbons causes extensive damage of local system since accumulation of pollutants in animals and plant tissue may cause death or mutations [3]. The technology commonly used for the soil remediation includes mechanical, burying, evaporation, dispersion, and washing. However, these technologies are expensive and can lead to incomplete decomposition of contaminants.

The process of bioremediation, defined as the use of microorganisms to detoxify or remove pollutants owing to their diverse metabolic capabilities is an evolving method for the removal and degradation of many environmental pollutants including the products of petroleum industry [4]. In addition, bioremediation technology is believed to be noninvasive and relatively cost-effective [5]. Biodegradation by natural populations of microorganisms represents one of the primary mechanisms by which petroleum and other hydrocarbon pollutants can be removed from the environment [6] and is cheaper than other remediation technologies [7].

The success of oil spill bioremediation depends on one’s ability to establish and maintain conditions that favor enhanced oil biodegradation rates in the contaminated environment. Numerous scientific review articles have covered various factors that influence the rate of oil biodegradation [7–12]. One important requirement is the presence of microorganisms with the appropriate metabolic capabilities. If these microorganisms are present, then optimal rates of growth and hydrocarbon biodegradation can be sustained by ensuring that adequate concentrations of nutrients and oxygen are present and that the pH is between 6 and 9. The physical and chemical characteristics of the oil and oil surface area are also important determinants of bioremediation success. There are the two main approaches to oil spill bioremediation: (a) bioaugmentation, in which known oil-degrading bacteria are added to supplement the existing microbial population, and (b) biostimulation, in which the growth of indigenous oil degraders is stimulated by the addition of nutrients or other growth-limiting cosubstrates.

The success of bioremediation efforts in the cleanup of the oil tanker Exxon Valdez oil spill of 1989 [13] in Prince William Sound and the Gulf of Alaska created tremendous interest in the potential of biodegradation and bioremediation technology. Most existing studies have concentrated on evaluating the factors affecting oil bioremediation or testing favored products and methods through laboratory studies [14]. Only limited numbers of pilot scale and field trials have provided the most convincing demonstrations of this technology which have been reported in the peer-reviewed literature [15–18]. The scope of current understanding of oil bioremediation is also limited because the emphasis of most of these field studies and reviews has been given on the evaluation of bioremediation technology for dealing with large-scale oil spills on marine shorelines.

This paper provides an updated information on microbial degradation of petroleum hydrocarbon contaminants towards the better understanding in bioremediation challenges.

2. Microbial Degradation of Petroleum Hydrocarbons

Biodegradation of petroleum hydrocarbons is a complex process that depends on the nature and on the amount of the hydrocarbons present. Petroleum hydrocarbons can be divided into four classes: the saturates, the aromatics, the asphaltenes (phenols, fatty acids, ketones, esters, and porphyrins), and the resins (pyridines, quinolines, carbazoles, sulfoxides, and amides) [19]. Different factors influencing hydrocarbon degradation have been reported by Cooney et al. [20]. One of the important factors that limit biodegradation of oil pollutants in the environment is their limited availability to microorganisms. Petroleum hydrocarbon compounds bind to soil components, and they are difficult to be removed or degraded [21]. Hydrocarbons differ in their susceptibility to microbial attack. The susceptibility of hydrocarbons to microbial degradation can be generally ranked as follows: linear alkanes branched alkanes small aromatics cyclic alkanes [6, 22]. Some compounds, such as the high molecular weight polycyclic aromatic hydrocarbons (PAHs), may not be degraded at all [23].

Microbial degradation is the major and ultimate natural mechanism by which one can cleanup the petroleum hydrocarbon pollutants from the environment [24–26]. The recognition of biodegraded petroleum-derived aromatic hydrocarbons in marine sediments was reported by Jones et al. [27]. They studied the extensive biodegradation of alkyl aromatics in marine sediments which occurred prior to detectable biodegradation of n-alkane profile of the crude oil and the microorganisms, namely, Arthrobacter, Burkholderia, Mycobacterium, Pseudomonas, Sphingomonas, and Rhodococcus were found to be involved for alkylaromatic degradation. Microbial degradation of petroleum hydrocarbons in a polluted tropical stream in Lagos, Nigeria was reported by Adebusoye et al. [28]. Nine bacterial strains, namely, Pseudomonas fluorescens, P. aeruginosa, Bacillus subtilis, Bacillus sp., Alcaligenes sp., Acinetobacter lwoffi, Flavobacterium sp., Micrococcus roseus, and Corynebacterium sp. were isolated from the polluted stream which could degrade crude oil.

Hydrocarbons in the environment are biodegraded primarily by bacteria, yeast, and fungi. The reported efficiency of biodegradation ranged from 6% [29] to 82% [30] for soil fungi, 0.13% [29] to 50% [30] for soil bacteria, and 0.003% [31] to 100% [32] for marine bacteria. Many scientists reported that mixed populations with overall broad enzymatic capacities are required to degrade complex mixtures of hydrocarbons such as crude oil in soil [33], fresh water [34], and marine environments [35, 36].

Bacteria are the most active agents in petroleum degradation, and they work as primary degraders of spilled oil in environment [37, 38]. Several bacteria are even known to feed exclusively on hydrocarbons [39]. Floodgate [36] listed 25 genera of hydrocarbon degrading bacteria and 25 genera of hydrocarbon degrading fungi which were isolated from marine environment. A similar compilation by Bartha and Bossert [33] included 22 genera of bacteria and 31 genera of fungi. In earlier days, the extent to which bacteria, yeast, and filamentous fungi participate in the biodegradation of petroleum hydrocarbons was the subject of limited study, but appeared to be a function of the ecosystem and local environmental conditions [7]. Crude petroleum oil from petroleum contaminated soil from North East India was reported by Das and Mukherjee [40]. Acinetobacter sp. was found to be capable of utilizing n-alkanes of chain length C10–C40 as a sole source of carbon [41]. Bacterial genera, namely, Gordonia, Brevibacterium, Aeromicrobium, Dietzia, Burkholderia, and Mycobacterium isolated from petroleum contaminated soil proved to be the potential organisms for hydrocarbon degradation [42]. The degradation of poly-aromatic hydrocarbons by Sphingomonas was reported by Daugulis and McCracken [43].

Fungal genera, namely, Amorphoteca, Neosartorya, Talaromyces, and Graphium and yeast genera, namely, Candida, Yarrowia, and Pichia were isolated from petroleum-contaminated soil and proved to be the potential organisms for hydrocarbon degradation [42]. Singh [44] also reported a group of terrestrial fungi, namely, Aspergillus, Cephalosporium, and Pencillium which were also found to be the potential degrader of crude oil hydrocarbons. The yeast species, namely, Candida lipolytica, Rhodotorula mucilaginosa, Geotrichum sp, and Trichosporon mucoides isolated from contaminated water were noted to degrade petroleum compounds [45].

Though algae and protozoa are the important members of the microbial community in both aquatic and terrestrial ecosystems, reports are scanty regarding their involvement in hydrocarbon biodegradation. Walker et al. [51] isolated an alga, Prototheca zopfi which was capable of utilizing crude oil and a mixed hydrocarbon substrate and exhibited extensive degradation of n-alkanes and isoalkanes as well as aromatic hydrocarbons. Cerniglia et al. [52] observed that nine cyanobacteria, five green algae, one red alga, one brown alga, and two diatoms could oxidize naphthalene. Protozoa, by contrast, had not been shown to utilize hydrocarbons.

3. Factors Influencing Petroleum Hydrocarbon Degradation

A number of limiting factors have been recognized to affect the biodegradation of petroleum hydrocarbons, many of which have been discussed by Brusseau [53]. The composition and inherent biodegradability of the petroleum hydrocarbon pollutant is the first and foremost important consideration when the suitability of a remediation approach is to be assessed. Among physical factors, temperature plays an important role in biodegradation of hydrocarbons by directly affecting the chemistry of the pollutants as well as affecting the physiology and diversity of the microbial flora. Atlas [54] found that at low temperatures, the viscosity of the oil increased, while the volatility of the toxic low molecular weight hydrocarbons were reduced, delaying the onset of biodegradation.

Temperature also affects the solubility of hydrocarbons [62]. Although hydrocarbon biodegradation can occur over a wide range of temperatures, the rate of biodegradation generally decreases with the decreasing temperature. Figure 1 shows that highest degradation rates that generally occur in the range 30–40C in soil environments, 20–30C in some freshwater environments and 15–20C in marine environments [33, 34]. Venosa and Zhu [63] reported that ambient temperature of the environment affected both the properties of spilled oil and the activity of the microorganisms. Significant biodegradation of hydrocarbons have been reported in psychrophilic environments in temperate regions [64, 65].