Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms

Naproxen ecotoxicity and biodegradation by Bacillus thuringiensis B1(2015b) strain

High level of naproxen consumption leads to the appearance of this drug in the environment but its possible effects on non-target organisms together with its biodegradation are not well studied. The aim of this work was to evaluate naproxen ecotoxicity by using the Microbial Assay for Risk Assessment. Moreover, Bacillus thuringiensis B1(2015b) was tested for both ecotoxicity and the ability of this strain to degrade naproxen in cometabolic conditions. The results indicate that the mean value of microbial toxic concentration estimated by MARA test amounts to 1.66 g/L whereas EC₅₀ of naproxen for B1(2015b) strain was 4.69 g/L. At toxic concentration, Bacillus thuringiensis B1(2015b) showed 16:0 iso 3OH fatty acid presence and an increase in the ratio of total saturated to unsaturated fatty acids. High resistance of the examined strain to naproxen correlated with its ability to degrade this drug in cometabolic conditions. The results of bacterial reverse mutation assay (Ames test) revealed that naproxen at concentrations above 1 g/L showed genotoxic effect but the response was not dose-dependent. Maximal specific naproxen removal rate was observed at pH 6.5 and 30 °C, and in the presence of 0.5 g/L glucose as a growth substrate. Kinetic analysis allowed estimation of the half saturation constant (K_s) and the maximum specific naproxen removal rate (q_max) as 6.86 mg/L and 1.26 mg/L day, respectively. These results indicate that Bacillus thuringiensis B1(2015b) has a high ability to degrade naproxen and is a potential tool for bioremediation.

Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1

The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C₁₄) or long-chain (n-C₂₈) alkanes. During growth on n-C₁₄, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C₂₈), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C₁₄ but not on n-C₂₈ also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C₁₀ up to n-C₃₂. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.

Petroleum Hydrocarbon-Degrading Bacteria for the Remediation of Oil Pollution Under Aerobic Conditions: A Perspective Analysis

With the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.

The Impact of Biosurfactants on Microbial Cell Properties Leading to Hydrocarbon Bioavailability Increase

The environment pollution with hydrophobic hydrocarbons is a serious problem that requires development of efficient strategies that would lead to bioremediation of contaminated areas. One of the common methods used for enhancement of biodegradation of pollutants is the addition of biosurfactants. Several mechanisms have been postulated as responsible for hydrocarbons bioavailability enhancement with biosurfactants. They include solubilization and desorption of pollutants as well as modification of bacteria cell surface properties. The presented review contains a wide discussion of these mechanisms in the context of alteration of bioremediation efficiency with biosurfactants. It brings new light to such a complex and important issue.

Oil type and temperature dependent biodegradation dynamics - Combining chemical and microbial community data through multivariate analysis

BACKGROUND

This study investigates a comparative multivariate approach for studying the biodegradation of chemically dispersed oil. The rationale for this approach lies in the inherent complexity of the data and challenges associated with comparing multiple experiments with inconsistent sampling points, with respect to inferring correlations and visualizing multiple datasets with numerous variables. We aim to identify novel correlations among microbial community composition, the chemical change of individual petroleum hydrocarbons, oil type and temperature by creating modelled datasets from inconsistent sampling time points. Four different incubation experiments were conducted with freshly collected Norwegian seawater and either Grane and Troll oil dispersed with Corexit 9500. Incubations were conducted at two different temperatures (5 °C and 13 °C) over a period of 64 days.

RESULTS

PCA analysis of modelled chemical datasets and calculated half-lives revealed differences in the biodegradation of individual hydrocarbons among temperatures and oil types. At 5 °C, most n-alkanes biodegraded faster in heavy Grane oil compared to light Troll oil. PCA analysis of modelled microbial community datasets reveal differences between temperature and oil type, especially at low temperature. For both oils, Colwelliaceae and Oceanospirillaceae were more prominent in the colder incubation (5 °C) than the warmer (13 °C). Overall, Colwelliaceae, Oceanospirillaceae, Flavobacteriaceae, Rhodobacteraceae, Alteromonadaceae and Piscirickettsiaceae consistently dominated the microbial community at both temperatures and in both oil types. Other families known to include oil-degrading bacteria were also identified, such as Alcanivoracaceae, Methylophilaceae, Sphingomonadaceae and Erythrobacteraceae, but they were all present in dispersed oil incubations at a low abundance (< 1%).

CONCLUSIONS

In the current study, our goal was to introduce a comparative multivariate approach for studying the biodegradation of dispersed oil, including curve-fitted models of datasets for a greater data resolution and comparability. By applying these approaches, we have shown how different temperatures and oil types influence the biodegradation of oil in incubations with inconsistent sampling points. Clustering analysis revealed further how temperature and oil type influence single compound depletion and microbial community composition. Finally, correlation analysis of degraders community, with single compound data, revealed complexity beneath usual abundance cut-offs used for microbial community data in biodegradation studies.

Biodegradation of marine oil spills in the Arctic with a Greenland perspective

New economic developments in the Arctic, such as shipping and oil exploitation, bring along unprecedented risks of marine oil spills. Microorganisms have played a central role in degrading and reducing the impact of the spilled oil during past oil disasters. However, in the Arctic, and in particular in its pristine areas, the self-cleaning capacity and biodegradation potential of the natural microbial communities have yet to be uncovered. This review compiles and investigates the current knowledge with respect to environmental parameters and biochemical constraints that control oil biodegradation in the Arctic. Hereby, seawaters off Greenland are considered as a case study. Key factors for biodegradation include the bioavailability of hydrocarbons, the presence of hydrocarbon-degrading bacteria and the availability of nutrients. We show how these key factors may be influenced by the physical oceanographic conditions in seawaters off Greenland and other environmental parameters including low temperature, sea ice, sunlight regime, suspended sediment plumes and phytoplankton blooms that characterize the Arctic. Based on the acquired insights, a first qualitative assessment of the biodegradation potential in seawaters off Greenland is presented. In addition to the most apparent Arctic characteristics, such as low temperature and sea ice, the impact of typical Arctic features such as the oligotrophic environment, poor microbial adaptation to hydrocarbon degradation, mixing of stratified water masses, and massive phytoplankton blooms and suspended sediment plumes merit to be topics of future investigation.

The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp

Citrobacter sp. has been shown to degrade 2,4,6-trinitrotoluene (TNT). However, the mechanism of its TNT biodegradation is poorly understood. An integrated proteome and transcriptome analysis was performed for investigating the differential genes and differential proteins in bacterial growth at the onset of experiments and after 12 h treatment with TNT. With the RNA sequencing, we found a total of 3792 transcripts and 569 differentially expressed genes (≥2 fold, P < 0.05) by. Genes for amino acid transport, cellular metabolism and stress-shock proteins were up-regulated, while carbohydrate transport and metabolism were down-regulated. A total of 42 protein spots (≥1.5 fold, P < 0.05) showed differential expression on two-dimensional gel electrophoresis and these proteins were identified by mass spectrometry. The most prominent proteins up-regulated were involved in energy production and conversion, amino acid transport and metabolism, posttranslational modification, protein turnover and chaperones. Proteins involved in carbohydrate transport and metabolism were down-regulated. Most notably, we observed that nemA encoding N-ethylmaleimide reductase was the most up-regulated gene involved in TNT degradation, and further proved that it can transform TNT to 4-amino-2,6-dinitrotoluene (4-ADNT) and 2-amino-4,6-dinitrotoluene (2-ADNT). This study highlights the molecular mechanisms of Citrobacter sp. for TNT removal.

Theoretical Insight into the Biodegradation of Solitary Oil Microdroplets Moving through a Water Column

In the aftermath of oil spills in the sea, clouds of droplets drift into the seawater column and are carried away by sea currents. The fate of the drifting droplets is determined by natural attenuation processes, mainly dissolution into the seawater and biodegradation by oil-degrading microbial communities. Specifically, microbes have developed three fundamental strategies for accessing and assimilating oily substrates. Depending on their affinity for the oily phase and ability to proliferate in multicellular structures, microbes might either attach to the oil surface and directly uptake compounds from the oily phase, or grow suspended in the aqueous phase consuming solubilized oil, or form three-dimensional biofilms over the oil–water interface. In this work, a compound particle model that accounts for all three microbial strategies is developed for the biodegradation of solitary oil microdroplets moving through a water column. Under a set of educated hypotheses, the hydrodynamics and solute transport problems are amenable to analytical solutions and a closed-form correlation is established for the overall dissolution rate as a function of the Thiele modulus, the Biot number and other key parameters. Moreover, two coupled ordinary differential equations are formulated for the evolution of the particle size and used to investigate the impact of the dissolution and biodegradation processes on the droplet shrinking rate.

Oil biodegradation: Interactions of artificial marine snow, clay particles, oil and Corexit

During the Deepwater Horizon (DwH) oil spill, interactions between oil, clay particles and marine snow lead to the formation of aggregates. Interactions between these components play an important, but yet not well understood, role in biodegradation of oil in the ocean water. The aim of this study is to explore the effect of these interactions on biodegradation of oil in the water. Laboratory experiments were performed, analyzing respiration and n-alkane and BTEX biodegradation in multiple conditions containing Corexit, alginate particles as marine snow, and kaolin clay. Two oil degrading bacterial pure cultures were added, Pseudomonas putida F1 and Rhodococcus qingshengii TUHH-12. Results show that the presence of alginate particles enhances oil biodegradation. The presence of Corexit alone or in combination with alginate particles and/or kaolin clay, hampers oil biodegradation. Kaolin clay and Corexit have a synergistic effect in increasing BTEX concentrations in the water and cause delay in oil biodegradation.

Single-Cell Real-Time Visualization and Quantification of Perylene Bioaccumulation in Microorganisms

Bioaccumulation of perylene in Escherichia coli and Staphylococcus aureus was visualized and quantified in real time with high sensitivity at high temporal resolution. For the first time, single-molecule fluorescence microscopy (SMFM) with a microfluidic flow chamber and temperature control has enabled us to record the dynamic process of perylene bioaccumulation in single bacterial cells and examine the cell-to-cell heterogeneity. Although with identical genomes, individual E. coli cells exhibited a high degree of heterogeneity in perylene accumulation dynamics, as shown by the high coefficient of variation (C.V = 1.40). This remarkable heterogeneity was exhibited only in live E. coli cells. However, the bioaccumulation of perylene in live and dead S. aureus cells showed similar patterns with a low degree of heterogeneity (C.V = 0.36). We found that the efflux systems associated with Tol C played an essential role in perylene bioaccumulation in E. coli, which caused a significantly lower accumulation and a high cell-to-cell heterogeneity. In comparison with E. coli, the Gram-positive bacteria S. aureus lacked an efficient efflux system against perylene. Therefore, perylene bioaccumulation in S. aureus was simply a passive diffusion process across the cell membrane.

Biodegradation of malodorous thiols by a Brevibacillus sp. strain isolated from a Tunisian phosphate factory

Hydrogen sulfide (H2S) and thiols (RSH) generated by the phosphate industry cause harmful effects on human health and quality of life. The present study aims to investigate and evaluate a bacterial strain CAT37 isolated from gas-washing wastewaters in terms of its properties and ability to degrade malodorous thiols. Gas-washing wastewater samples were submitted to physicochemical analyses and used for the isolation of thiol-degrading bacteria. The results from gas chromatography-mass spectrometry (GC-MS) analysis revealed that the isolated strain CAT37 was able to oxidize ∼99% of each thiol, decanethiol and dodecanethiol used as sole carbon and energy sources after 30 days of incubation at 37°C. The strain CAT37 displayed a biodegradative potential on several thiols known by their toxicity and odors. The results from phylogenetic and phenotypic analysis revealed that the CAT37 isolate belonged to the genus Brevibacillus, showing the highest sequence similarity to Brevibacillus agri. Overall, the results indicated that the strain CAT37 exhibited a number of attractive biodegradation abilities against thiols and could be considered a promising candidate for industrial application in future thiol biodeodorization strategies.