Crude Oil Bioremediation: History
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Contributor:
Rosa Paola Radice
,
Vincenzo De Fabrizio
,
Antonietta Donadoni
,
Antonio Scopa
,
Giuseppe Martelli

Crude oil is one of the major pollutants present. Its extraction and processing generate processing waters contaminated by hydrocarbons which are harmful to both human health and the flora and fauna that come into contact with it. Hydrocarbon contamination can involve soil and water, and several technologies are used for recovery. The most used techniques for the recovery of spilt oil involve chemical-physical methods that can remove most of the pollutants. Among these, must consider the bioremediation by microorganisms, mostly bacterial capable of degrading many of the toxic compounds contained within the petroleum. Microalgae participate in bioremediation indirectly, supporting the growth of degrading bacteria, and directly acting on contaminants. Their direct contribution is based on the activation of various mechanisms ranging from the production of enzymes capable of degrading hydrocarbons, such as lipoxygenases, to the attack through the liberation of free radicals. 

  • microalgae
  • petroleum
  • hydrocarbons
  • bioremediation

1. Current Bioremediation Techniques

1.1. Bacteria Biodegradation

The bacteria are also used in the recovery of the crude oil lost during the extraction process, exploiting the ability of various species of bacteria and archaea to metabolise organic carbon and to produce biosurfactant solvents which improve the chemical-physical characteristics of the oil to recover [1][2]. The most used bacterial strains are Clostridium, Zymomonas, Klebsiella, Enterobacter and the archaeon Methanobacterium [3]. Oil and its constituents have existed in nature for millions of years, and consequently, there are organisms capable of using them as a source of nourishment and energy. Among the microorganisms that can grow in the presence of hydrocarbons, there are about 175 bacterial genera, many archaea and some eukaryotic microorganisms [4]. However, the bioremediation implemented by microorganisms is a complex mechanism that requires numerous steps and cooperation between different species capable of acting on hydrocarbons synergistically. Furthermore, it must be considered that there are numerous factors such as temperature and nutrient concentration that play a fundamental role in the remediation process [5]. Bioremediation generally begins with some bacterial genera capable of attacking straight-chain and branched alkanes present in high quantities. Between these Oceanispirillales order (class gammaproteobacteria; phylum proteobacteria), and specifically the genre Alcanivorax spp. intervene on n-alkanes and cycloalkanes [6]. To generate energy from alkanes, Alcanivorax spp. uses different hydrolases (a non-haem diiron monooxygenase AlkB1 and AlkB2) and three cytochrome P450-dependent alkane monooxygenases [7]. Given the different conditions in which these bacteria operate, some gammaproteobacteria activate special monooxygenases to survive in the presence of ultraviolet light. For example, they use the monooxygenase capable of binding flavin (AlmA) to metabolize the long-chain C22 and C36 n-alkanes as an energy source [8], instead Cycloclasticus spp., Colwellia and Pseudoalteromonas (class gammaproteobacteria; phylum proteobacteria), degrade aromatic hydrocarbons when, in a second phase, they are found in larger quantities [9][10]. Heterotrophic bacteria degrade exopolymer by-products thanks to peptidase and hydrolase. These enzymes are more expressed in contaminated environments. Halomonas bacteria fall into this category by producing exopolysaccharides. They reduce the solubilization of PAHs in an aqueous environment, making them more vulnerable to biodegradation and the formation of aggregates. [2][11]. However, the bioremediation processes mediated by microorganisms are in the balance between the increase of bacteria due to the degradation of toxic compounds and the lack of nutrients which decrease indirectly in proportion to the growth of bacterial biomass [12]. For this reason, it is sometimes necessary to add nutrients, and in particular, nitrogen, to improve performance. In a protected environment, this aspect is easy to solve, but in nature, the consumption of hydrocarbons by microorganisms causes a high degradation of the oxygen necessary for the sustenance of the other species present in the environment [13].

1.2. Different Bacteria Consortium

It is evident that there is a collaboration between the different domains for the bioremediation process. In fact, in contaminated waters, phytoplankton and zooplankton collaborate synergistically due to the degradation of hydrocarbons, very often forming agglomerates that settle on the seabed. These agglomerates are rich in crude oil and are formed thanks to the coagulation of phytoplankton, which incorporates oil droplets and precipitates on the seabed. [14]. In the vicinity of oil spills, the indigenous microbial community increases the expression of genes, which are involved in the biodegradation process. It improves bacterial motility, chemotaxis and enzymes involved in aliphatic degradation. Even the very action of the currents favors bacterial blooms and accelerate the degradation [15]. Furthermore, the degradation of the various oil components involves different plasmid genes, depending on the hydrocarbons involved. For the metabolism of alkanes, aerobic microorganisms mainly use various monooxygenases, rubredoxin and rubredoxin reductase to convert alkanes into alcohol by increasing the expression of several alk genes. The PAHs metabolism, on the other hand, is more complex given the size of the hydrocarbons. The genes involved are mainly naphthalene dioxygenase (nah) genes [16], naphthalene dioxygenase (ndo) [17], doxycycline-inducible system (dox) [18].

2. Microalgae and Petroleum Bioremediation

Microalgae constitute a fundamental element in the treatment of water contaminated by crude oil and hydrocarbons. Ugya et al. evaluated the ability of some microalgae grown on a biofilm to remove contaminants of petroleum origin, including PAHs and total petroleum hydrocarbon (TPH). The results showed a significant reduction of phytochemical parameters such as sulphate −17.5%, chloride −14.65%, nitrates −33% total suspended solids (TSS) −26%, total dissolved solids (TDS) −7.9%, and chemical oxygen demand (COD) and biochemical oxygen demand (BODs) reduced by 8% and 16.7% respectively. Although not in high percentages, the removal of TPH was equal to 15% after 14 days of exposure [19]. Kuttiyathil et al., on the other hand, analysed not only the removal of crude oil by the microalga Chlorella spp. but also how, in nature, the mechanical action of sea waves contributes to creating an emulsion of water and crude oil that could favour the removal of pollutants making them more available. Their results show that following an initial period of adaptation, the Total Organic Carbon (TOC) of the solution was drastically reduced and that, after 5 days, Chlorella removed 80% of the emulsified oil [20]. Water mixing and how it can alter bioremediation was also studied in 2014 by Özhan et al., which demonstrated how the bioavailability of crude oil is altered by physical mixing applied in the laboratory. The mixing of the water column containing crude oil does not significantly affect the concentration of total petroleum hydrocarbons (TPH) but increases the concentration of some alkanes and PAHs and causes the formation of colloidal micro-particles (1–70 μm), which improve the degradation of hydrocarbons. [21]. Chlorella spp. has been the subject of several studies precisely because of its ability to survive in contaminated media. Znad et al., reported that the treatment of petroleum effluent (PE) with Chlorella spp. completely removed phosphorus after 13 days, reduced nitrogen by 78% and reduced COD from 504 mg/L to 144 mg/L. However, treatment of petroleum effluent with Chlorella spp. initially increased the biomass, but in the long term, start to be toxic and inhibites cell growth [22]. The nature and concentration of the crude oil, and its constituents, greatly influence the growth and removal of Chlorella. For example, the use of Water-Accommodated Fraction (WAF) deriving from diesel is more toxic for Chlorella than diesel as it is containing many low molecular weight hydrocarbons (LMW-HC), which can cause damage to cell membranes and affect the production of protective pigments, as reported by Ramadass et al. in its 2017 study [23]. Further studies carried out on Chlorella have confirmed its ability to remove various compounds contained in crude oil. For example, Xaaldi Kalhor et al., in both of their studies [24][25] tested different concentrations of crude oil (10 and 20 g/L) on Chlorella vulgaris for two intervals (7 and 14 days). The results were encouraging, and the best removal of low molecular weight hydrocarbons (LW), equal to 100%, was achieved with 10 g/L for 14 days, while at higher concentrations (20 g/L), after 14 days, the LW were reduced by 82%. The removal of heavy molecular weight hydrocarbons (HW) followed the same trend as the light ones, reaching higher values for the 14-day intervals and at a concentration of 10 g/L (reduction of HW equal to approximately 78%) [24]. Hamouda et al. (2016) and El-Sheekh et al. (2013) evaluated how the addition of crude oil to the Chlorella culture affected its metabolism and, specifically, whether the microalgae preferred a mixotrophic and heterotrophic mechanism rather than the classic autotrophic one. Hamouda et al. tested the growth of Chlorella in mixotrophic conditions using 1% crude oil, and the results on the hydrocarbons concentrations, present after 30 days of incubation, showed that the following aliphatic compounds: 3-methyl decane, heptadecane, octadecane, nonadecane, docosane, and tetracosane were removed, while decane, undecane, tridecane, hexadecane, tricosane were significantly reduced compared to the control [26]. El-Sheekh et al. instead, tested Chlorella’s bioremediation capacity using up to 2% crude oil. The results obtained by gas chromatography-mass spectrometry (GC-MS) showed that, after 15 days of incubation, Indole-3-acetic acid was removed at all tested concentrations, while decane, Indole-3-acetic acid, p-Phenyltoluene, Naphthalene, 3-ethyl, Tridecane, phenanthracene, 1-methyl, Benzene, decyl, phenanthracene, 2-methyl, cyclohexane undecyl, b-pregnane and Octacosane were removed at a concentration of 2% crude oil [27]. One of the most interesting aspects concerning the El-Sheekh study is that PAHs were reduced more efficiently in heterotrophic conditions. This supports the hypothesis that eukaryotic microalgae, such as Chlorella, use organic carbon, present in solution, improving their growth range and biomass using a heterotrophic metabolism that allows them to use, split and/or convert hydrocarbons into intermediate metabolites. Confirming this hypothesis is also the study conducted by Das et al. in 2019, which demonstrated how Chlorella reached the highest biomass yield (1.72 g/L) in mixotrophic conditions with the addition of pre-treated produced water (PPW) of petroleum origin and removed 92% of the total nitrogen (TN) and 73% of the TOC [28].

3. Consortium Microalgae and Bacteria

Nowadays, bacteria are widely studied as bioremediators, and several species suitable for this process are known. On the other hand, microalgae could be valid substitutes. For this reason, many studies have focused on bacteria and microalgae collaboration to degrade crude oil and its pollutants. This collaboration can be of various types, but the basic principle sees the microorganisms work synergistically to obtain a better result. For example, Ashwaniy et al. found that the microalga grown in petroleum refinery effluent (PRE) can reduce the concentration of COD, 81% of BOD, 61% of sulphide, 61% of TSS by 70%. 67% phosphorous and TDS and can act as a substrate for bacterial growth in a microbial desalination cell (MDC) to produce clean energy [29]. Chernikova et al. described how microalgae and bacteria collaborate continuously in nature. The microalgae provide oxygen, exopolymers and organic-material useful for bacterial growth. In turn, bacteria support microalgae growth, producing vitamins, micronutrients, iron and carbon dioxide. Furthermore, Chernikova et al., in their work, demonstrated that in two petroleum-enriched microalgae cultures, P. lutheri and N. oculata, there was a selection of hydrocarbonoclastic alpha and gammaproteobacteria, especially Alcanivorax and Marinobacter spp., identifying in total 48 non-redundant bacterial strains also belonging to the genera Thalassospira, Hyphomonas, Halomonas, Marinovum and Roseovarius. These results are interesting as they candidate microalgae as possible host organisms for these bacteria whose housing niches are ignored [30]. Das et al. found that the ability of Chlorella spp. to remove various contaminants supported the growth of aerobic bacteria present in the unsterilized pretreated waters deriving from petroleum processing (PPW). In addition, the bacteria made nitrogen more available by promoting the microalgae biomass [23]. These results confirm the studies conducted by Mahdavi et al. in 2015 where algae produce oxygen through photosynthesis, which is necessary for aerobic bacteria for toxic compounds biodegradation. But the results support the ability of some algal strains to degrade directly and completely, some compounds such as naphthenic acids. In their study, a sample of freshwater taken directly from a pond in northern Alberta was tested for removal. Various conditions were tested, such as the absence of oxygen, presence of a Navicula pelliculosa diatom, and light variations. Only bacteria were tested, and bacteria with algae. The results showed how the algae-bacteria consortium led to an increase in the removal of toxic compounds given by the increase in microbial biomass in the algae-bacteria consortium. The higher rate of detoxification, obtained with bacteria alone, was improved by microalgae, which improved bacterial growth [31]. The coexistence of bacteria and microalgae was also observed by Hodges et al. where filamentous cyanobacteria dominated the reactor used for the decontamination and bio-removal of nutrients and suspended solids petrochemical wastewater [32]. So far, it has been analyzed how algae have been supporting bacterial growth in bioremediation, but Abid et al. have conducted a study in which the opposite occurs. A double-chamber bioreactor was built in which in one the bacteria biodegraded petroleum wastewater and the CO2 produced was channelled into the chamber containing the microalga Spongiochloris sp, which used it to increase its growth, sequestering the CO2 produced by the bacteria from the atmosphere [33]. However, these two paths of mutual exchange are accompanied by a third possibility. Tang demonstrated how a microalgae-bacteria consortium, artificially created, can optimize the removal of different petroleum constituents. In his study conducted in 2010, he separately tested four bacterial strains known for their ability to degrade PAHs (Shingomonas GY2B, Burkholderia capacia GS3C, Pseudomonas GP3A and Pandoraea pnomenusa GP3B) and the microalga Scenedesmus obliquus GH2, both as unialgal and axenic algae. Unialgal GH2 alone was able to remove various contaminants even with high percentages, such as 46% of alkanes and 51% of alkylcycloalkanes, or by reducing PAHs and alkylated naphtalenes by 81%, while axenic GH2 did not show potential for removal. However, these results were disproved by the union of microalgae with bacterial strains. Unialgal GH2, added with the various strains, has not increased its degradative properties, indeed in some cases, it has reduced its efficiency; axenic GH2 in conjunction with the different bacteria, on the other hand, has shown an increase in all degradation rates, completely removing toxic compounds such as PAHs, naphthalene, fluorene and phenanthrene [34]. Although there are not many studies in this regard, Ozhan et al., have shown how the oil spill in southern Louisiana has created dysfunctions in the phytoplankton, which is a valid indicator of toxicity for the health of the compromised marine ecosystem [21]. Jung et al. confirm this and argues that the dose of oil with which the phytoplankton comes into contact is responsible for the imbalance between bacteria and microalgae, reporting that concentrations greater than 1000 ppm inhibit the growth of microalgae by stimulating the bacterial one instead [35].

This entry is adapted from the peer-reviewed paper 10.3390/pr11020442

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