Effects of Temperature and pH on the Activities of Catechol 2,3-dioxygenase Obtained from Crude Oil Contaminated Soil in Ilaje, Ondo State, Nigeria

Assay Development for Metal-Dependent Enzymes-Influence of Reaction Buffers on Activities and Kinetic Characteristics

Buffers are often thought of as innocuous components of a reaction, with the sole task of maintaining the pH of a system. However, studies had shown that this is not always the case. Common buffers used in biochemical research, such as Tris (hydroxymethyl) aminomethane hydrochloride (Tris-HCl), can chelate metal ions and may thus affect the activity of metalloenzymes, which are enzymes that require metal ions for enhanced catalysis. To determine whether enzyme activity is influenced by buffer identity, the activity of three enzymes (BLC23O, Ro1,2-CTD, and trypsin) was comparatively characterized in N-2- hydroxyethylpiperazine-N'-2-ethanesulfonic acid (HEPES), Tris-HCl, and sodium phosphate buffer. The pH and temperature optima of BLC23O, a Mn2+-dependent dioxygenase, were first identified, and then the metal ion dissociation constant (Kd) was determined in the three buffer systems. It was observed that BLC23O exhibited different Kd values depending on the buffer, with the lowest (1.49 ± 0.05 μM) recorded in HEPES under the optimal set of conditions (pH 7.6 and 32.5 °C). Likewise, the kinetic parameters obtained varied depending on the buffer, with HEPES (pH 7.6) yielding overall the greatest catalytic efficiency and turnover number (kcat = 0.45 ± 0.01 s-1; kcat/Km = 0.84 ± 0.02 mM-1 s-1). To corroborate findings, the characterization of Fe3+-dependent Ro1,2-CTD was performed, resulting in different kinetic constants depending on the buffer (Km (HEPES, Tris-HCl, and Na-phosphate) = 1.80, 6.93, and 3.64 μM; kcat(HEPES, Tris-HCl, and Na-phosphate) = 0.64, 1.14, and 1.01 s-1; kcat/Km(HEPES, Tris-HCl, and Na-phosphate)= 0.36, 0.17, and 0.28 μM-1 s-1). In order to determine whether buffer identity influenced the enzymatic activity of nonmetalloenzymes alike, the characterization of trypsin was also carried out. Contrary to the previous results, trypsin yielded comparable kinetic parameters independent of the buffer (Km (HEPES, Tris-HCl, and Na-Phosphate) = 3.14, 3.07, and 2.91 mM; kcat(HEPES, Tris-HCl, and Na-phosphate) = 1.51, 1.47, and 1.53 s-1; kcat/Km (HEPES, Tris-HCl, and Na-phosphate) = 0.48, 0.48, and 0.52 mM-1 s-1). These results showed that the activity of tested metalloenzymes was impacted by different buffers. While selected buffers did not influence the tested nonmetalloenzyme activity, other research had shown impacts of buffers on other enzyme activities. As a result, we suggest that buffer selection be optimized for any new enzymes such that the results from one lab to another can be accurately compared.

Attenuation of petroleum hydrocarbon fractions using rhizobacterial isolates possessing alkB, C23O, and nahR genes for degradation of n-alkane and aromatics

This work assessed the catabolic versatility of functional genes in hydrocarbon-utilizing bacteria obtained from the rhizosphere of plants harvested in aged polluted soil sites in Ogoni and their attenuation efficacy in a bioremediation study. Rhizosphere soil was enumerated for its hydrocarbon-utilizing bacteria. The bacteria were in-vitro screened and selected through the quantification of their total protein and specific intermediate pathway enzyme (catechol 2,3-dioxygenase) activity in the metabolism of hydrocarbon. Thereafter, agarose gel electrophoresis technique was deployed to profile the genome of the selected strains for catechol 2,3-dioxygenase (C23O), 1,2-alkane monooxygenase (alkB), and naphthalene dioxygenase (nahR). Four rhizobacterial isolates namely Pseudomonas fluorescens (A3), Achromobacter agilis (A4), Bacillus thuringiensis (D2), and Staphylococcus lentus (L1) were selected based on the presence of C23O, alkB, and nahR genes. The gel electrophoresis results showed an approximate molecular weight of 200 bp for alkB, 300 bp for C23O, and 400 bp for nahR. The gas chromatogram for residual total petroleum hydrocarbon (TPH) revealed mineralization of fractions C₈-C₁₇, phytane, C₁₈-C₃₀. TPH for in-vitro bioremediation of crude oil-polluted soil was observed to have an optimal reduction/loss of 97% within the 56th day of the investigation. This study has further revealed that the microbiome of plants pre-exposed to crude oil pollution could serve as a reservoir for mining group of bacterial with broad catabolic potentials for eco-recovery and waste treatment purposes.

An insight into the current oil spills and on-site bioremediation approaches to contaminated sites in Nigeria

Land oil spills in Nigeria have a long history of contaminating the soil, groundwater, vegetation, and streams with spill extension being the primary of numerous ordeals. These have left the host communities of oil fields and pipelines in crucial need of soil rehabilitation. Thus, this review provides insights into the current state of land oil spills and the effectiveness of on-site remediation approaches across communities. A total of 44 incidents of land oil spills of ≥ 500 bbl, amounting to 53,631 bbl between 2011 and 2019, was recorded by the Shell Petroleum Development Company, which primarily attributed to 83% of the total sabotage. Over 73% of the 53,631 bbl spills were unrecovered from the spill areas, which had deleterious impacts on farmlands, fishponds, rivers, and residential areas. Remediation by enhanced natural attenuation (RENA) is a feasible technique for restoring petroleum hydrocarbon-contaminated sites, but it might be ineffective when limited to tiling, windrows, and fertilizer applications due to the presence of non-biodegradable residues and contaminants beyond the aeration depth. However, bioremediation techniques ranging from non-supplemented in-situ and fertilizer supplemented in-situ to mixed in-situ and ex-situ bio-cells supplemented RENA are feasible approaches for spill sites. However, challenging limitations with regard to RENA application failures in the region include delayed responses to spill emergency, large amounts of un-recovered spilled oil, and un-implemented legislative guidelines for spill cleanup. Nevertheless, the temperature, moisture, nutrient, oxygen, and pH of the soil are essential parameters to be considered when implementing a landfarming remediation approach.

The genomic attributes of Cd-resistant, hydrocarbonoclastic Bacillus subtilis SR1 for rhizodegradation of benzo(a)pyrene under co-contaminated conditions

Bacillus subtilis SR1 is a metal resistant, polyaromatic hydrocarbon-degrading bacterium isolated from petroleum contaminated sites. This study reports the characteristics of the genome of the isolate containing one circular chromosome (4,093,698 bp) annotated into 4155 genes and 4095 proteins. The genome analysis confirmed the presence of multiple catabolic genes: aromatic ring-hydroxylating dioxygenase (COG2146), aromatic ring hydroxylase (COG2368), catechol 2, 3 dioxygenase (COG2514), 4-hydroxybenzoate decarboxylase (COG0043), carboxymuconolactone decarboxylase (COG0599) responsible for the catabolism of aromatic hydrocarbons along with the genes for biosurfactant production and functional genes (czcD and cadA) for resistance to cadmium, zinc, and cobalt. Gas Chromatography-Mass spectroscopy analysis revealed up to 35% in-vitro degradation of benzo(a)pyrene after 21 days of growth along with the production of different intermediate metabolites. The pot trial analysis in the greenhouse condition validated the rhizodegradation of BaP, which was significantly higher in the presence of plant-microbe association (85%) than degradation in bulk soil (68%).

Functional Gene Diversity of Selected Indigenous Hydrocarbon-Degrading Bacteria in Aged Crude Oil

Crude oil pollution has consistently deteriorated all environmental compartments through the cycle of activities of the oil and gas industries. However, there is a growing need to identify microbes with catabolic potentials to degrade these pollutants. This research was conducted to identify bacteria with functional degradative genes. A crude oil-polluted soil sample was obtained from an aged spill site at Imo River, Ebubu, Komkom community, Nigeria. Bacteria isolates were obtained and screened for hydrocarbon degradation potential by turbidometry assay. Plasmid and chromosomal DNA of the potential degraders were further screened for the presence of selected catabolic genes (C230, Alma, Alkb, nahAC, and PAHRHD_(GP)) and identified by molecular typing. Sixteen (16) out of the fifty (50) isolates obtained showed biodegradation activity in a liquid broth medium at varying levels. Bacillus cereus showed highest potential for this assay with an optical density of 2.450 @ 600 nm wavelength. Diverse catabolic genes resident in plasmids and chromosomes of the isolates and, in some cases, both plasmid and chromosomes of the same organism were observed. The C230 gene was resident in >50% of the microbial population tested, while other genes occurred in lower proportions with the least observed in nahAC and PAHRHD. These organisms can serve as potential bioremediation agents.

Insights into the binding interaction of substrate with catechol 2,3-dioxygenase from biophysics point of view

This study aims to clarify the interaction mechanism of substrate with catechol 2,3-dioxygenase (C23O) through multi-technique combination. A novel C23O (named C23O-2G) was cloned, heterogeneously expressed, and identified as a new member in subfamily I.2 of extradiol dioxygenases. Based on the simulations of molecular docking and dynamics, the exact binding sites of catechol on C23O-2G were identified, and the catalytic mechanism mediated by key residues was proposed. The roles of the predicted residues during catalysis were confirmed by site-directed mutagenesis, and the mutation of Thr254 could significantly increase catalytic efficiency and substrate specificity of C23O-2G. The binding and thermodynamic parameters obtained from fluorescence spectra suggested that catechol could effectively quench the intrinsic fluorescence of C23O-2G via static and dynamic quenching mechanisms and spontaneously formed C23O-2G/catechol complex by the binding forces of hydrogen bond and van der Waals force. The results of UV-vis spectra, synchronous fluorescence, and CD spectra revealed obvious changes in the microenvironment and conformation of C23O-2G, especially for the secondary structure. The atomic force microscope images further demonstrated the changes from an appearance point of view. This study could improve our mechanistic understanding of representative dioxygenases involved in aromatic compound degradation.

Optimization of bioremediation-cocktail for application in the eco-recovery of crude oil polluted soil

Background: Environmental sustainability is the driver for finding the optimal bioremediation cocktail with the combination of highly potent hydrocarbonoclastic strains and the nutrient additives that significantly enhance mineralization of crude oil in polluted soil in order to mitigate its deleterious effects on the environment. In this study, four hydrocarbon-degrading bacterial strains were pre-selected from mined rhizobacterial isolates in aged crude oil-contaminated soil.  Method: Agrowaste residues of poultry-droppings, corn chaff, and plantain peel were selected among others for their ability to support high biomass of selected bacterial strains. Baseline proximate analysis was performed on the agrowaste residues. Simplified, one variable at a time (OVAT) was employed in the validation of the variables for optimization using the Multivariate analysis tool of Response Surface Methodology (RSM). To test the significant formulation variables, the Box-Behnken approach using 15 runs design was adopted. Results:  The rate of contaminant removal was observed to fit into a quadratic function. For optimal rate or contaminant removal, the fitted model predicted the optimal formulation cocktail condition to be within 0.54 mg/kg (Corn steep liquor), phosphate 137.49 mg/kg (poultry droppings) and 6.4% inocula for initial TPH of 9744 mg kg -1 and THC of 9641 mg kg -1 contaminant level. The model for the application of the bioremediation product and the variables evaluated had a significant p-value < 0.005 for the attainment of 85 to 96 % of TPH and THC removal after 56 days of treatment. Conclusions:  This study has shown the need to harness the abundant agrowaste nutrients in supporting high throughput rhizobacteria in the formulation of a bioremediation agent suitable for use in the reclamation of oil spill sites in the Niger Delta oil-producing region.

Phenol hydroxylase from Pseudomonas sp. KZNSA: Purification, characterization and prediction of three-dimensional structure

A 61.3 kDa Phenol hydroxylase (PheA) was purified and characterized from Pseudomonas sp. KZNSA (PKZNSA). Cell free extract of the isolate grown in mineral salt medium supplemented with 600 ppm phenol showed 21.58 U/mL of PheA activity with a specific activity of 7.67 U/mg of protein. The enzyme was purified to 1.6-fold with a total yield of 33.6%. The purified PheA was optimally active at pH 8 and temperature 30 °C, with ≈95% stability at pH 7.5 and temperature 30 °C after 2 h. The Lineweaver-Burk plot showed the v_max and K_m values of 4.04 µM/min and 4.03 µM, respectively, for the substrate phenol. The ES-MS data generated from the tryptic digested fragments of pure protein and PCR amplification of a ≈600 bp gene from genomic DNA of PKZNSA lead to the determination of complete amino acid and nucleotide sequence of PheA. Bioinformatics tools and homology modelling studies indicated that PheA from PKZNSA is likely a probable protein kinase UbiB (2-octaprenylphenol hydroxylase) involving Lys and Asp at positions 153 and 288 for binding and active site, respectively. Characterization and optimization of PheA activity may be useful for a better understanding of 2,4-dichlorophenol degradation by this organism and for potential industrial application of the enzyme.