Bioremediation Of Oil-contaminated Environments Research Articles

Genomic and biotechnological potential of a novel oil-degrading strain Enterobacter kobei DH7 isolated from petroleum-contaminated soil

In this study, a novel oil-degrading strain Enterobacter kobei DH7 was isolated from petroleum-contaminated soil samples from the industrial park in Taolin Town, Lianyungang, China. The whole genome of the strain was sequenced and analyzed to reveal its genomic potential. The oil degradation and growth conditions including nitrogen, and phosphorus sources, degradation cycle, biological dosing, pH, and oil concentration were optimized to exploit its commercial application. The genome of the DH7 strain contains 4,705,032 bp with GC content of 54.95% and 4653 genes. The genome analysis revealed that there are several metabolic pathways and enzyme-encoding genes related to oil degradation in the DH7 genome, such as the paa gene cluster which is involved in the phenylacetic acid degradation pathway, and complete degradation pathways for fatty acid and benzoate, genes related to chlorinated alkanes and olefins degradation pathway including adhP, frmA, and adhE, etc. The strain DH7 under the optimized conditions has demonstrated a maximum degradation efficiency of 84.6% after 14 days of treatment using synthetic oil, which comparatively displays a higher oil degradation efficiency than any Enterobacter species known to date. To the best of our knowledge, this study presents the first-ever genomic studies related to the oil degradation potential of any Enterobacter species. As Enterobacter kobei DH7 has demonstrated significant oil degradation potential, it is one of the good candidates for application in the bioremediation of oil-contaminated environments.

Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains.

A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the carbon-carbon bonds, using the 4S pathway encoded by the dszABC operon-like structure. The genome of the new dibenzothiophene-degrading hydrocarbon-oxidizing bacterial strain Gordonia amicalis 6-1 was completely sequenced and the genes potentially involved in the pathways of DBT desulfurization, oxidation of alkanes and aromatic compounds, as well as in the osmoprotectant metabolism in strain 6-1 and other members of the genus Gordonia, were analyzed. The genome of G. amicalis strain 6-1 consists of a 5,105,798-bp circular chromosome (67.3% GC content) and an 86,621-bp circular plasmid, pCP86 (65.4% GC content). This paper presents a comparative bioinformatic analysis of complete genomes of strain 6-1 and dibenzothiophene-degrading Gordonia strains 1D and 135 that do not have the dsz operon. The assumption is made about the participation in this process of the region containing the sfnB gene. Genomic analysis supported the results of phenomenological studies of Gordonia strains and the possibility of their application in the bioremediation of oil-contaminated environments and in the purification of oil equipment from oil and asphalt-resin-paraffin deposits.

Complete Genome Sequence of Stenotrophomonas maltophilia 1800, a New Bacterial Strain with Potential for Bioremediation of Oil-Contaminated Environments.

ABSTRACTStenotrophomonas maltophilia strain 1800 was isolated from the effluent of an industrial oil refinery in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and assembled using Unicycler. It is composed of one chromosome of 4.83 Mb.

Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications.

Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.

Biodegradation of n-alkanes and polycyclic aromatic hydrocarbons using novel indigenous bacteria isolated from contaminated soils

Oil pollution is a major global environmental concern. Bioremediation is considered as a suitable approach for remediation of oil-contaminated environments. In this study, two crude oil-contaminated soils were collected to isolate and identify some native and active oil-degrading bacteria to be used in remediation of contaminated sites. Five isolates were selected according to “hole-plate diffusion method” and were grown in crude oil. They were cultured in a mineral salt medium in which crude oil was employed as the sole carbon source. Biochemical, morphological and genomic identifications demonstrated the bacteria species as Pseudomonas resinovorans, Plantibacter auratus, Bacillus subtilis, Staphylococcus pasteuri and Bacillus atrophaeus. These bacteria were able to degrade 86.0%, 61.3%, 81.1%, 55.0% and 76.2% of aliphatic compounds and 58.6%, 39.4%, 55.5%, 39.0% and 49.9% of aromatic hydrocarbons in a medium containing crude oil (1% v/v) over 21 days, respectively. The degradation rates of aromatic compounds from 14 to 21 days were higher than of aliphatic hydrocarbons. This rate was 28.4% by Bacillus subtilis, 30.9% by Bacillus atrophaeus, 27.2% by Staphylococcus pasteuri and 21.3% by Pseudomonas resinovorans. In Plantibacter auratus, this rate was 16.19% which is less than aliphatic hydrocarbons. To our knowledge, it seems this is the first time to report Pseudomonas resinovorans and Plantibacter auratus as crude oil degraders. Results of this study indicated that the isolated bacteria could have a high potential to be used in bioremediation of oil-contaminated environments.

Production of a biosurfactant from Bacillus methylotrophicus UCP1616 for use in the bioremediation of oil-contaminated environments.

The aim of the present study was to produce a microbial biosurfactant for use in the bioremediation of environments contaminated with petroleum products. Bacillus methylotrophicus was isolated from seawater taken from a port area and cultivated using industrial waste as substrate (corn steep liquor and sugarcane molasses [both at 3%]). Surface tension measurements and motor oil emulsification capacity were used for the evaluation of the production of the biosurfactant, which demonstrated stability in a broad range of pH and temperature as well as a high concentration of saline, with the reduction of the surface tension of water to 29 mN/m. The maximum concentration of biosurfactant (10.0 g/l) was reached after 144 h of cultivation. The biosurfactant was considered to be a lipopeptide based on the results of proton nuclear magnetic resonance and Fourier transformed infrared spectroscopy. The tests demonstrated that the biosurfactant is innocuous and has potential for the bioremediation of soil and water contaminated by petroleum products. Thus, the biosurfactant described herein has a low production cost and can be used in environmental processes.

Isolation and characterization of different bacterial strains for bioremediation of n-alkanes and polycyclic aromatic hydrocarbons.

Crude oil is a common environmental pollutant composed of a large number of both aromatic and aliphatic hydrocarbons. Biodegradation is carried out by microbial communities that are important in determining the fate of pollutants in the environment. The intrinsic biodegradability of the hydrocarbons and the distribution in the environment of competent degrading microorganisms are crucial information for the implementation of bioremediation processes. In the present study, the biodegradation capacities of various bacteria toward aliphatic and aromatic hydrocarbons were determined. The purpose of the study was to isolate and characterize hydrocarbon-degrading bacteria from contaminated soil of a refinery in Arzew, Algeria. A collection of 150 bacterial strains was obtained; the bacterial isolates were identified by 16S rRNA gene sequencing and their ability to degrade hydrocarbon compounds characterized. The isolated strains were mainly affiliated to the Gamma-Proteobacteria class. Among them, Pseudomonas spp. had the ability to metabolize high molecular weight hydrocarbon compounds such as pristane (C19) at 35.11 % by strain LGM22 and benzo[a] pyrene (C20) at 33.93 % by strain LGM11. Some strains were able to grow on all the hydrocarbons tested including octadecane, squalene, phenanthrene, and pyrene. Some strains were specialized degrading only few substrates. In contrast, the strain LGM2 designated as Pseudomonas sp. was found able to degrade both linear and branched alkanes as well as low and high poly-aromatic hydrocarbons (PAHs). The alkB gene involved in alkane degradation was detected in LGM2 and other Pseudomonas-related isolates. The capabilities of the isolated bacterial strains to degrade alkanes and PAHs should be of great practical significance in bioremediation of oil-contaminated environments.

Structural insights into diversity and n-alkane biodegradation mechanisms of alkane hydroxylases.

Environmental microbes utilize four degradation pathways for the oxidation of n-alkanes. Although the enzymes degrading n-alkanes in different microbes may vary, enzymes functioning in the first step in the aerobic degradation of alkanes all belong to the alkane hydroxylases. Alkane hydroxylases are a class of enzymes that insert oxygen atoms derived from molecular oxygen into different sites of the alkane terminus (or termini) depending on the type of enzymes. In this review, we summarize the different types of alkane hydroxylases, their degrading steps, and compare typical enzymes from various classes with regard to their three-dimensional structures, in order to provide insights into how the enzymes mediate their different roles in the degradation of n-alkanes and what determines their different substrate ranges. Through the above analyzes, the degrading mechanisms of enzymes can be elucidated and molecular biological methods can be utilized to expand their catalytic roles in the petrochemical industry or in bioremediation of oil-contaminated environments.

Isolation and characteristics of a microbial consortium for effectively degrading phenanthrene

A microbial consortium (named W4) capable of aerobic biodegradation of solid phenanthrene as the sole source of carbon and energy was isolated by selective enrichment from petroleum-contaminated soil in the Henan oilfield, China. The strains of the consortium were identified as Sphingomonas cloacae, Rhizobium sp., Pseudomonas aeruginosa and Achromobacter xylosoxidans respectively by means of genetic methods. The major metabolites of phenanthrene were analyzed by gas chromatography-mass spectrometry (GC-MS). The biodegradation percentage of solid phenanthrene at 200 mg/L in liquid medium after 7 days of growth was greater than 99%. The degradation of phenanthrene was compared between individual predominant strains and the microbial consortium in different treatment processes. The microbial consortium showed a significant improvement of phenanthrene degradation rates in either static or shaking culture. The degradation percentage of phenanthrene by the consortium W4 decreased to some degree when C16 coexisted, however it was hardly affected by C30. Furthermore, the ability of consortium W4 to remediate oil sludge from the Dagang oil refinery was studied by composting; and it was found that the consortium W4 could obviously remove polycyclic aromatic hydrocarbons (PAHs) and paraffinic hydrocarbons. All the results indicated that the microbial consortium W4 had a promising application in bioremediation of oil-contaminated environments and could be potentially used in microbial enhanced oil recovery (MEOR).