Biodegradation of n-hexadecane by bacterial strains B1 and B2 isolated from petroleum-contaminated soil

Spatial distribution characteristics and degradation mechanism of microorganisms in n-hexadecane contaminated vadose zone

The damage caused by petroleum hydrocarbon pollution to soil and groundwater environment is becoming increasingly significant. The vadose zone is the only way for petroleum hydrocarbon pollutants to leak from surface into groundwater. The spatial distribution characteristics of indigenous microorganisms in vadose zone, considering presence of capillary zones, have rarely been reported. To explore the spatial distribution characteristics of indigenous microorganisms in vadose zone contaminated by petroleum hydrocarbons, a one-dimensional column migration experiment was conducted using n-hexadecane as characteristic pollutant. Soil samples were collected periodically from different heights during experiment. Corresponding environmental factors were monitored online. The microbial community structure and spatial distribution characteristics of the cumulative relative abundance were systematically analyzed using 16S rRNA sequencing. In addition, the microbial degradation mechanism of n-hexadecane was analyzed using metabolomics. The results showed that presence of capillary zone had a strong retarding effect on n-hexadecane infiltration. Leaked pollutants were mainly concentrated in areas with strong capillary action. Infiltration and displacement of NAPL-phase pollutants were major driving force for change in moisture content (θ) and electric conductivity (EC) in vadose zone. The degradation by microorganisms results in a downward trend in potential of hydrogen (pH) and oxidation-reduction potential (ORP). Five petroleum hydrocarbon-degrading bacterial phyla and 11 degradable straight-chain alkane bacterial genera were detected. Microbial degradation was strong in the area near edge of capillary zone and locations of pollutant accumulation. Mainly Sphingomonas and Nocardioides bacteria were involved in microbial degradation of n-hexadecane. Single-end oxidation involved microbial degradation of n-hexadecane (C16H34). The oxygen consumed, hexadecanoic acid (C16H32O2) produced during this process, and release of hydrogen ions (H+) were the driving factors for reduction of ORP and pH. The vadose zone in this study considered presence of capillary zone, which was more in line with actual contaminated site conditions compared with previous studies. This study systematically elucidated vertical distribution characteristics of petroleum hydrocarbon pollutants and spatiotemporal variation characteristics of indigenous microorganisms in vadose zone considered presence of capillary zone. In addition, the n-hexadecane degradation mechanism was elucidated using metabolomics. This study provides theoretical support for development of natural attenuation remediation measures for petroleum-hydrocarbon-contaminated soil and groundwater.

Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil

The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.

Isolation and characterization of a novel hydrocarbonoclastic and biosurfactant producing bacterial strain: Fictibacillus phosphorivorans RP3

In this study, an indigenous novel hydrocarbonoclastic (kerosene and diesel degrading) and biosurfactant producing strain Fictibacillus phosphorivorans RP3 was identified. The characteristics of bacterial strain were ascertained through its unique morphological and biochemical attributes, 16S rRNA sequencing, and phylogenetic analysis. The degradation of hydrocarbons by F. phosphorivorans RP3 was observed at Day 7, Day 10 and Day 14 of the experimental duration. GC-FID chromatograms demonstrated a significant increase in hydrocarbon degradation (%) with progressing days (from 7 to 14). The bacterium exhibited capability to utilize and degrade n-hexadecane (used for primary screening) and petroleum hydrocarbons (kerosene and diesel; by ≥ 90%). With increase in the number of experimentation days, the optical density of the culture medium increased, whereas pH declined (became acidic) for both Kerosene and Diesel. Absence of resistance to routinely used antibiotics makes it an ideal candidate for future field application. The study is, thus, significant in view of toxicological implications of hydrocarbons and their degradation using environmentally safe techniques so as to maintain ecological and human health.

Microbial Biodegradation of Paraffin Wax in Malaysian Crude Oil Mediated by Degradative Enzymes

The deposition of paraffin wax in crude oil is a problem faced by the oil and gas industry during extraction, transportation, and refining of crude oil. Most of the commercialized chemical additives to prevent wax are expensive and toxic. As an environmentally friendly alternative, this study aims to find a novel thermophilic bacterial strain capable of degrading paraffin wax in crude oil to control wax deposition. To achieve this, the biodegradation of crude oil paraffin wax by 11 bacteria isolated from seawater and oil-contaminated soil samples was investigated at 70°C. The bacteria were identified as Geobacillus kaustophilus N3A7, NFA23, DFY1, Geobacillus jurassicus MK7, Geobacillus thermocatenulatus T7, Parageobacillus caldoxylosilyticus DFY3 and AZ72, Anoxybacillus geothermalis D9, Geobacillus stearothermophilus SA36, AD11, and AD24. The GCMS analysis showed that strains N3A7, MK7, DFY1, AD11, and AD24 achieved more than 70% biodegradation efficiency of crude oil in a short period (3 days). Notably, most of the strains could completely degrade C₃₇–C₄₀ and increase the ratio of C₁₄–C₁₈, especially during the initial 2 days incubation. In addition, the degradation of crude oil also resulted in changes in the pH of the medium. The degradation of crude oil is associated with the production of degradative enzymes such as alkane monooxygenase, alcohol dehydrogenase, lipase, and esterase. Among the 11 strains, the highest activities of alkane monooxygenase were recorded in strain AD24. A comparatively higher overall alcohol dehydrogenase, lipase, and esterase activities were observed in strains N3A7, MK7, DFY1, AD11, and AD24. Thus, there is a potential to use these strains in oil reservoirs, crude oil processing, and recovery to control wax deposition. Their ability to withstand high temperature and produce degradative enzymes for long-chain hydrocarbon degradation led to an increase in the short-chain hydrocarbon ratio, and subsequently, improving the quality of the oil.

Pseudomonas fluorescens: A Bioaugmentation Strategy for Oil-Contaminated and Nutrient-Poor Soil

Bioremediation technology is one of the most profitable and sustainable strategies for remediating soils contaminated with hydrocarbons. This study focuses on assessing the influence of biostimulation and bioaugmentation with Pseudomonas fluorescens to contribute to the removal of total petroleum hydrocarbons (TPHs) of a soil. Laboratory studies were carried out (measurements of emitted CO₂, surface tension, and residual TPH) to select the best bioaugmentation and biostimulation treatment. The sources of C, N, and P were glucose–yeast extract, NH₄Cl–NaNO₃, and K₂HPO₄–K₃PO₄, respectively. The effect of culture conditions on the reduction of TPH and respiratory activity was evaluated through a factorial design, 2³, in a solid culture system. After 80 days of incubation, it was observed that treatments of yeast extract–NH₄Cl–K₂HPO₄ (Y4) and glucose–NaNO₃–K₃PO₄ (Y5) presented a higher level of TPH removal (20.91% and 20.00% degradation of TPH, respectively). Biostimulation favors the production of biosurfactants, indirectly measured by the change in surface tension in the soil extracts. The treatments Y4 and Y5 showed a lower change value of the surface tension (23.15 and 23.30 mN·m⁻¹ at 25 °C). A positive correlation was determined between the change in surface tension and the removal of TPH; hence there was a contribution of the biosurfactants produced to the removal of hydrocarbons.

Biodegradation of Petroleum Hydrocarbons by Bacillus subtilis BL-27, a Strain with Weak Hydrophobicity

The biodegradation of petroleum hydrocarbons has many potential applications and has attracted much attention recently. The hydrocarbon-degrading bacterium BL-27 was isolated from petroleum-polluted soil and was compounded with surfactants to improve biodegradation. Its 16S rDNA and rpoD gene sequences indicated that it was a strain of Bacillus subtilis. Strain BL-27 had extensive adaptability and degradability within a broad range of temperatures (25–50 °C), pH (4.0–10.0) and salinity (0–50 g/L NaCl). Under optimal conditions (45 °C, pH 7.0, 1% NaCl), the strain was able to degrade 65% of crude oil (0.3%, w/v) within 5 days using GC-MS analysis. Notably, strain BL-27 had weak cell surface hydrophobicity. The adherence rate of BL-27 to n-hexadecane was 29.6% with sucrose as carbon source and slightly increased to 33.5% with diesel oil (0.3%, w/v) as the sole carbon source, indicating that the cell surface of BL-27 is relatively hydrophilic. The strain was tolerant to SDS, Tween 80, surfactin, and rhamnolipids at a concentration of 500 mg/L. The cell surface hydrophobicity reduced more with the addition of surfactants, while the chemical dispersants, SDS (50–100 mg/L) and Tween 80 (200–500 mg/L), significantly increased the strain’s ability to biodegrade, reaching 75–80%. These results indicated that BL-27 has the potential to be used for the bioremediation of hydrocarbon pollutants and could have promising applications in the petrochemical industry.

Biofilm mediated synergistic degradation of hexadecane by a naturally formed community comprising Aspergillus flavus complex and Bacillus cereus group

BACKGROUND

The hydrophobic nature of hydrocarbons make them less bioavailable to microbes, generally leading to low efficiency in biodegradation. Current bioremediation strategies for hydrocarbon contamination, uses induced mixed microbial cultures. This in-vitro study demonstrates the utilization of naturally occurring communities in suitable habitats for achieving highly efficient, synergistic degradation of hydrocarbons in a simple community structure without additives.

METHODS

Enrichment media supplemented with 1% (7652.53 mg/L) hexadecane (HXD) as the sole carbon source were inoculated with samples of soil with waste polythene, collected from a municipal landfill in order to isolate microbial communities. Gas Chromatography-Mass Spectrometry (GC-MS) analysis was performed on HXD grown co-cultures and individual counterparts after 14 days incubation and percentage degradation was calculated. Microbes were identified using 16S rRNA gene and Internal Transcribed Spacer region sequencing. Biofilm formation was confirmed through scanning electron microscopy, in the most efficient community.

RESULTS

Three mixed communities (C1, C2 and C3) that demonstrated efficient visual disintegration of the HXD layer in the static liquid cultures were isolated. The C1 community showed the highest activity, degrading > 99% HXD within 14 days. C1 comprised of a single fungus and a bacterium and they were identified as a Bacillus sp. MM1 and an Apsergillus sp. MM1. The co-culture and individual counterparts of the C1 community were assayed for HXD degradation by GC-MS. Degradation by the fungal and bacterial monocultures were 52.92 ± 8.81% and 9.62 ± 0.71% respectively, compared to 99.42 ± 0.38% by the co-culture in 14 days. This proved the synergistic behavior of the community. Further, this community demonstrated the formation of a biofilm in oil-water interface in the liquid medium. This was evidenced from scanning electron microscopy (SEM) showing the Bacillus cells attached on to Aspergillus mycelia.

CONCLUSIONS

This study demonstrates the utilization of naturally formed fungal-bacterial communities for enhanced biodegradation of hydrocarbons such as hexadecane and reports for the first time, synergistic degradation of hexadecane through biofilm formation, by a community comprising of Bacillus cereus group and Aspergillus flavus complex.

Biodegradation of n-hexadecane by Aspergillus sp. RFC-1 and its mechanism

Fungi can use n-hexadecane (HXD) as a sole carbon source. But the mechanism of HXD degradation remains unclear. This work mainly aimed to study the degradation of HXD by Aspergillus sp. RFC-1 obtained from oil-contaminated soil. The HXD content, medium acidification and presence of hexadecanoic acid in the medium were determined by gas chromatography-mass spectrometry, and fungal growth was observed. Enzyme and gene expression assays suggested the involvement of an alkane hydroxylase, an alcohol dehydrogenase, and a P450 enzyme system in HXD degradation. A biosurfactant produced by the strain RFC-1 was also characterized. During 10 days of incubation, 86.3% of HXD was degraded by RFC-1. The highest activities of alkane hydroxylase (125.4 µmol mg^-1 protein) and alcohol dehydrogenase (12.5 µmol mg^-1 proteins) were recorded. The expression level of cytochrome P450 gene associated with oxidation was induced (from 0.94-fold to 5.45-fold) under the HXD condition by Real-time PCR analysis. In addition, HXD accumulated in inclusion bodies of RFC-1with the maximum of 5.1 g L^-1. Results of blood agar plate and thin-layer chromatography analysis showed RFC-1 released high lipid and emulsification activity in the fungal culture. Induced cell surface hydrophobicity and reduced surface tension also indicated the RFC-1-mediated biosurfactant production, which facilitated the HXD degradation and supported the degradation process.

Assessment of three approaches of bioremediation (Natural Attenuation, Landfarming and Bioagumentation - Assistited Landfarming) for a petroleum hydrocarbons contaminated soil

Contamination with total petroleum hydrocarbons (TPH) subsequent to refining activities, is currently one of the major environmental problems. Among the biological remediation approaches, landfarming and in situ bioremediation strategies are of great interest. Purpose of this study was to verify the feasibility of a remediation process wholly based on biological degradation applied to contaminated soils from a decommissioned refinery. This study evaluated through a pot experiment three bioremediation strategies: a) Natural Attenuation (NA), b) Landfarming (L), c) Bioaugmentation-assisted Landfarming (LB) for the treatment of a contaminated soil with petroleum hydrocarbons (TPHs). After a 90-days trial, Bioagumentation - assistited Landfarming approach produced the best results and the greatest evident effect was shown with the most polluted samples reaching a reduction of about 86% of total petroleum hydrocarbons (TPH), followed by Landfarming (70%), and Natural Attenuation (57%). The results of this study demonstrated that the combined use of bioremediation strategies was the most advantageous option for the treatment of contaminated soil with petroleum hydrocarbons, as compared to natural attenuation, bioaugmentation or landfarming applied alone. Besides, our results indicate that incubation with an autochthonous bacterial consortium may be a promising method for bioremediation of TPH-contaminated soils.

Comparative bioremediation of heavy metals and petroleum hydrocarbons co-contaminated soil by natural attenuation, phytoremediation, bioaugmentation and bioaugmentation-assisted phytoremediation

Biological remediation technologies are an environmentally friendly approach for the treatment of polluted soils. This study evaluated through a pot experiment four bioremediation strategies: a) natural attenuation, b) phytoremediation with alfalfa (Medicago sativa L.), c) bioaugmentation with Pseudomonas aeruginosa and d) bioaugmentation-assisted phytoremediation, for the treatment of a co-contaminated soil presenting moderate levels of heavy metals (Cu, Pb and Zn at 87, 100 and 110mgkg(-1) DW, respectively) and petroleum hydrocarbons (3800mgkg(-1) DW). As demonstrated by plant biomass and selected physiological parameters alfalfa plants were able to tolerate and grow in the co-contaminated soil, especially when soil was inoculated with P. aeruginosa, which promoted plant growth (56% and 105% increase for shoots and roots, respectively) and appeared to alleviate plant stress. The content of heavy metals in alfalfa plants was limited and followed the order: Zn>Cu>Pb. Heavy metals were mainly concentrated in plant roots and were poorly translocated, favouring their stabilization in the root zone. Bioaugmentation of planted soil with P. aeruginosa generally led to a decrease of plant metal concentration and translocation. The highest degree of total petroleum hydrocarbon removal was obtained for bioaugmentation-assisted phytoremediation treatment (68%), followed by bioaugmentation (59%), phytoremediation (47%) and natural attenuation (37%). The results of this study demonstrated that the combined use of plant and bacteria was the most advantageous option for the treatment of the present co-contaminated soil, as compared to natural attenuation, bioaugmentation or phytoremediation applied alone.

Systematic investigations on the biodegradation and viscosity reduction of long chain hydrocarbons using Pseudomonas aeruginosa and Pseudomonas fluorescens

The use of microorganisms has been researched extensively for possible applications related to hydrocarbon degradation in the petroleum industry. However, attempts to improve the effect of microorganisms on the viscosity of hydrocarbons, which find potential use in the development of robust models for biodegradation, have been rarely documented. This study investigates the degradation of long chain hydrocarbons, such as hexadecane and eicosane using Pseudomonas fluorescens PMMD3 (P. fluorescens) and Pseudomonas aeruginosa CPCL (P. aeruginosa). P. aeruginosa used here is isolated from petroleum contaminated sediments and the P. fluorescens is from the coastal area, and both have hydrocarbon degrading genes. The degradation of hydrocarbons is studied using carbon profiling and reduction in viscosity pre- and post-degradation of hydrocarbons. The carbon profiling has been obtained using gas chromatography-mass spectroscopy (GC-MS), and Fourier transform infrared spectrometer (FTIR) results. GC-MS results have indicated an improved biodegradation of hydrocarbons by 77-93% in one day. The yield coefficients of biomass (YX/S) for P. aeruginosa and P. fluorescens using hexadecane as a carbon source are 1.35 and 0.81 g g(-1), and the corresponding values with eicosane are 0.84 and 0.88 g g(-1). The viscosity of hexadecane is reduced by the order of 53 and 47%, while that of eicosane was reduced by 53 and 65%, using P. aeruginosa and P. fluorescens, respectively. This study also presents information on the activity of enzymes responsible for the hydrocarbon degradation. Pseudomonas species have shown their use in potential applications for bioremediation, oil-spill treatment, and flow assurance. We believe that this study will also provide stringent tests for possible model development for the bioremediation of long chain paraffins suitable for oilfield applications.

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

Microbial interactions have a key role in global geochemical cycles. Although we possess significant knowledge about the general biochemical processes occurring in microbial communities, we are often unable to decipher key functions of individual microorganisms within the environment in part owing to the inability to cultivate or study them in isolation. Here, we circumvent this shortcoming through the use of single-cell genome sequencing and a novel low-input metatranscriptomics protocol to reveal the intricate metabolic capabilities and microbial interactions of an alkane-degrading methanogenic community. This methanogenic consortium oxidizes saturated hydrocarbons under anoxic conditions through a thus-far-uncharacterized biochemical process. The genome sequence of a dominant bacterial member of this community, belonging to the genus Smithella, was sequenced and served as the basis for subsequent analysis through metabolic reconstruction. Metatranscriptomic data generated from less than 500 pg of mRNA highlighted metabolically active genes during anaerobic alkane oxidation in comparison with growth on fatty acids. These data sets suggest that Smithella is not activating hexadecane by fumarate addition. Differential expression assisted in the identification of hypothetical proteins with no known homology that may be involved in hexadecane activation. Additionally, the combination of 16S rDNA sequence and metatranscriptomic data enabled the study of other prevalent organisms within the consortium and their interactions with Smithella, thus yielding a comprehensive characterization of individual constituents at the genome scale during methanogenic alkane oxidation.