Potential of hexadecane-utilizing soil-microorganisms for growth on hexadecanol, hexadecanal and hexadecanoic acid as sole sources of carbon and energy

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.

Characteristics of organic carbon metabolism and bioremediation of petroleum-contaminated soil by a mesophilic aerobic biopile system

An innovative mesophilic aerobic biopile technology was explored to improve the bioremediation efficiency of petroleum-contaminated soil. Under the suitable soil conditions (C:N:P at 100:5:1 and soil moisture content at 18%), the soil pH was hold in the range of 7.4 to 6.8 throughout the bioremediation process, the mesophilic (30 °C-40 °C) and forced aeration (3 h-on/1 h-off) conditions were the critical factors to enhancing petroleum biodegradation. The consumption of bioavailable organic carbon (BAC) which was one of the most important factors regulating microbial metabolism, was positively related (R² = 0.85, 40 °C) with the rate of petroleum removal. The 50% threshold of BAC could be regarded as the signal for supplementing the soil nutrients in the mesophilic aerobic biopiles to favor petroleum removal. The optimal conditions (40 °C, 3 h-on/1 h-off) maximized the utilization of BAC, promoted the petroleum degradation, and remained the microbial abundance and community composition stable to the greatest extent. In addition, the accumulation of aliphatic acids affected the microbial activity, which limited the efficiency of petroleum degradation to a certain extent. Jointly considering the energy consumption, time cost and soil conditions maintenance, a cost-effective biopile technology was obtained by temperature and aeration regulation and BAC supplementation, which could be applied to engineering application.

Cultivable fungi from deep-sea oil reserves in the Gulf of Mexico: Genetic signatures in response to hydrocarbons

The estimation of oil spill effects on marine ecosystems is limited to the extent of our knowledge on the autochthonous biota. Fungi are involved in key ecological marine processes, representing a major component of post-spill communities. However, information on their functional capacities remains lacking. Herein we analyzed cultivable fungi from sediments in two oil-drilling regions of the Gulf of Mexico for their ability to tolerate and use hexadecane and 1-hexadecene as the sole carbon sources; and to evaluate gene expression profiles of key hydrocarbonoclastic taxa during utilization of these hydrocarbons. The isolated fungi showed differential sensitivity patterns towards the tested hydrocarbons under three different concentrations. Remarkably, six OTUs (Aureobasidium sp., Penicillium brevicompactum, Penicillium sp., Phialocephala sp., Cladosporium sp. 1 and 2) metabolized the tested alkane and alkene as the sole carbon sources, confirming that deep-sea fungal taxa are valuable genetic resources with potential use in bioremediation. RNA-seq results revealed distinctive gene expression profiles in the hydrocarbonoclastic fungus Penicillium sp. when using hexadecane and 1-hexadecene as the sole carbon sources, with up-regulation of genes involved in transmembrane transport, metabolism of six-carbons carbohydrates, and nitric oxide pathways.

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.

Highly Active and Stable Large Catalase Isolated from a Hydrocarbon Degrading Aspergillus terreus MTCC 6324

A hydrocarbon degrading Aspergillus terreus MTCC 6324 produces a high level of extremely active and stable cellular large catalase (CAT) during growth on n-hexadecane to combat the oxidative stress caused by the hydrocarbon degrading metabolic machinery inside the cell. A 160-fold purification with specific activity of around 66 × 10⁵ U mg⁻¹ protein was achieved. The native protein molecular mass was 368 ± 5 kDa with subunit molecular mass of nearly 90 kDa, which indicates that the native CAT protein is a homotetramer. The isoelectric pH (pI) of the purified CAT was 4.2. BLAST aligned peptide mass fragments of CAT protein showed its highest similarity with the catalase B protein from other fungal sources. CAT was active in a broad range of pH 4 to 12 and temperature 25°C to 90°C. The catalytic efficiency (K_cat/K_m) of 4.7 × 10⁸ M⁻¹ s⁻¹ within the studied substrate range and alkaline pH stability (half-life, t_1/2 at pH 12~15 months) of CAT are considerably higher than most of the extensively studied catalases from different sources. The storage stability (t_1/2) of CAT at physiological pH 7.5 and 4°C was nearly 30 months. The haem was identified as haem b by electrospray ionization tandem mass spectroscopy (ESI-MS/MS).

Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms

Petroleum-based products are a primary energy source in the industry and daily life. During the exploration, processing, transport and storage of petroleum and petroleum products, water or soil pollution occurs regularly. Biodegradation of the hydrocarbon pollutants by indigenous microorganisms is one of the primary mechanisms of removal of petroleum compounds from the environment. However, the physical contact between microorganisms and hydrophobic hydrocarbons limits the biodegradation rate. This paper presents an updated review of the petroleum hydrocarbon uptake and transport across the outer membrane of microorganisms with the help of outer membrane proteins.

Isolation and characterization of alkane degrading bacteria from petroleum reservoir waste water in Iran (Kerman and Tehran provenances)

Petroleum products spill and leakage have become two major environmental challenges in Iran. Sampling was performed in the petroleum reservoir waste water of Tehran and Kerman Provinces of Iran. Alkane degrading bacteria were isolated by enrichment in a Bushnel-Hass medium, with hexadecane as sole source of carbon and energy. The isolated strains were identified by amplification of 16S rDNA gene and sequencing. Specific primers were used for identification of alkane hydroxylase gene. Fifteen alkane degrading bacteria were isolated and 8 strains were selected as powerful degradative bacteria. These 8 strains relate to Rhodococcus jostii, Stenotrophomonas maltophilia, Achromobacter piechaudii, Tsukamurella tyrosinosolvens, Pseudomonas fluorescens, Rhodococcus erythropolis, Stenotrophomonas maltophilia, Pseudomonas aeruginosa genera. The optimum concentration of hexadecane that allowed high growth was 2.5%. Gas chromatography results show that all strains can degrade approximately half of hexadecane in one week of incubation. All of the strains have alkane hydroxylase gene which are important for biodegradation. As a result, this study indicates that there is a high diversity of degradative bacteria in petroleum reservoir waste water in Iran.

Relative quantitative PCR to assess bacterial community dynamics during biodegradation of diesel and biodiesel fuels under various aeration conditions

The degradation of diesel fuel, B20 blend and biodiesel in liquid cultures by a seven-member bacterial consortium was compared under conditions with full aeration or with limited aeration with nitrate added as main electron acceptor. Community dynamics was assessed employing real-time PCR and the ddCt method for relative quantification. Biodegradation rates increased with increasing biodiesel content, but were significantly reduced under conditions with nitrate. Despite large variations in biodegradation rates, magnitude changes in population numbers were typically observed only from zero to one order, regardless the type of fuel and electron acceptor. Only Comamonadaceae and Variovorax sp. distinctly preferred aerobic conditions, and during aerobic growth showed suppression as fuel contained more biodiesel. Thus, the consortium is relatively stable and most of the degraders can shift their metabolism from hydrocarbons to biodiesel. The stability of the consortium is of interest in the context of biodiesel-mediated biodegradation of petroleum hydrocarbons.

Carbon content reduction in a model reluctant clayey soil: slurry phase n-hexadecane bioremediation

Clayey soils contaminated with organic pollutants are nowadays one of the important environmental issues as they are highly reluctant to conventional bioremediation techniques. In this study, biodegradability of n-hexadecane as a model contaminant in oil polluted clayey soil by an indigenous bacterium was investigated. Maximal bacterial growth was achieved at 8% (v/v) n-hexadecane as sole carbon and energy sources in aqueous phase. The predominant n-hexadecane uptake mechanism was identified to be biosurfactant-mediated using bacterial adhesion to hydrocarbon (BATH) test and surface tension measurements. The effect of n-hexadecane concentration, soil to water ratio, inoculum concentration and pH on total organic carbon (TOC) reduction from kaolin soil in slurry phase was investigated at two levels in shake flasks using full factorial experimental design method where 10,000 (mg n-hexadecane)(kg soil)(-1), soil-water ratio of 1:3, 10% (v/w) inoculum and pH of 7 resulted in the highest TOC reduction of 70% within 20 days. Additionally, slurry bioreactor experiments were performed to study the effect of various aeration rates on n-hexadecane biodegradation during 9 days where 2.5 vvm was found as an appropriate aeration rate leading to 54% TOC reduction. Slurry phase bioremediation is shown to be a successful method for remediation of clayey reluctant soils.