Biodegradation of pyrene by Mycobacterium frederiksbergense in a two-phase partitioning bioreactor system

A Review of Pyrene Bioremediation Using Mycobacterium Strains in a Different Matrix

Polycyclic aromatic hydrocarbons are compounds with 2 or more benzene rings, and 16 of them have been classified as priority pollutants. Among them, pyrene has been found in higher concentrations than recommended, posing a threat to the ecosystem. Many bacterial strains have been identified as pyrene degraders. Most of them belong to Gram-positive strains such as Mycobacterium sp. and Rhodococcus sp. These strains were enriched and isolated from several sites contaminated with petroleum products, such as fuel stations. The bioremediation of pyrene via Mycobacterium strains is the main objective of this review. The scattered data on the degradation efficiency, formation of pyrene metabolites, bio-toxicity of pyrene and its metabolites, and proposed degradation pathways were collected in this work. The study revealed that most of the Mycobacterium strains were capable of degrading pyrene efficiently. The main metabolites of pyrene were 4,5-dihydroxy pyrene, phenanthrene-4,5-dicarboxylate, phthalic acid, and pyrene-4,5-dihydrodiol. Some metabolites showed positive results for the Ames mutagenicity prediction test, such as 1,2-phenanthrenedicarboxylic acid, 1-hydroxypyrene, 4,5-dihydropyrene, 4-phenanthrene-carboxylic acid, 3,4-dihydroxyphenanthrene, monohydroxy pyrene, and 9,10-phenanthrenequinone. However, 4-phenanthrol showed positive results for experimental and prediction tests. This study may contribute to enhancing the bioremediation of pyrene in a different matrix.

Interfacial biodegradation of phenanthrene in bacteria-carboxymethyl cellulose-stabilized Pickering emulsions

The limited bioavailability of PAHs in non-aqueous phase liquid (NAPL) limits their degradation. The biodegradation of phenanthrene in n-tetradecane by hydrophilic bacterium Moraxella sp. CFP312 was studied with the assistance of two polymers, chitosan and carboxymethyl cellulose (CMC). Both chitosan and CMC improved the cell hydrophobicity of CFP312 and increased the contact angle of CFP312 cells from 30.4 to 78.5 and 88.5, respectively. However, CMC increased the degradation ratio of phenanthrene from 45 to nearly 100%, while chitosan did not cause any improvement. We found that CMC was more effective than chitosan in promoting CFP312 to stabilize Pickering emulsion. In the bacteria-CMC complex system, oil was dispersed into small droplets to obtain a high emulsification index and large specific surface area. Moreover, according to the microscopic image of the bacteria-CMC emulsion droplet, we observed that the droplet surface was tightly covered by the CFP312 cells. Therefore, CFP312 cells joined with CMC can utilize phenanthrene in oil phase at the oil-water interface. This study will offer a new strategy for effective microbial degradation of hydrophobic compounds in NAPLs by hydrophilic bacteria. KEY POINTS: • Biodegradation of phenanthrene in Pickering emulsions • Pickering emulsions stabilized by hydrophilic CFP312 joined with CMC. • Phenanthrene was degraded by CFP312 at oil-water interface.

Synergistic degradation of pyrene by Pseudomonas aeruginosa PA06 and Achromobacter sp. AC15 with sodium citrate as the co-metabolic carbon source

Two pyrene-degrading strains, Pseudomonas aeruginosa PA06 and Achromobacter sp. AC15 were co-incubated in equal proportions as a microbiological consortium and could enhance the degradation of pyrene. The enzymatic activities of the catechol 1,2-dioxygenase (C12O) and 2,3-dioxygenase activities (C23O) were produced complementary expression by P. aeruginosa PA06 and Achromobacter sp. AC15, respectively. Meanwhile, results showed that pyrene degradation was sufficiently promoted in the presence of sodium citrate as a co-metabolic carbon source, likely a result of enhanced biomass and biosurfactant production. The optimized dosage and ideal initial pHs were 1.4 g L^-1 and 5.5, respectively. We also analyzed the rate constant of pyrene degradation, cell growth, and enzyme activity. Results show that P. aeruginosa PA06 had a better effect than Achromobacter sp. AC15 in bacterial growth. However, the C23O or C12O activity produced by Achromobacter sp. AC15 continued at a similar or even faster than that of P. aeruginosa PA06. The mixed bacteria had a better effect than any single bacteria, suggesting the strains worked synergistically to enhance the degradation efficiency. In the co-metabolism system of 600 mg/L pyrene and 1.4 g/L sodium citrate, pyrene degradation reached 74.6%, was 1.57 times, 2.06 times, and 3.89 times that of the mix-culture strains, single PA06 and single AC15 without sodium citrate, respectively. Overall, these findings are valuable as a potential tool for the bioremediation of high-molecular-weight PAHs.

Enhancing Chlorobenzene Biodegradation by Delftia tsuruhatensis Using a Water-Silicone Oil Biphasic System

In this study, a water-silicone oil biphasic system was developed to enhance the biodegradation of monochlorobenzene (CB) by Delftia tsuruhatensis LW26. Compared to the single phase, the biphasic system with a suitable silicone oil fraction (v/v) of 20% allowed a 2.5-fold increase in the maximum tolerated CB concentration. The CB inhibition on D. tsuruhatensis LW26 was reduced in the presence of silicone oil, and the electron transport system activity was maintained at high levels even under high CB stress. Adhesion of cells to the water-oil interface at the water side was observed using confocal laser scanning microscopy. Nearly 75% of cells accumulated on the interface, implying that another interfacial substrate uptake pathway prevailed besides that initiated by cells in the aqueous phase. The 8-fold increase in cell surface hydrophobicity upon the addition of 20% (v/v) silicone oil showed that silicone oil modified the surface characteristics of D. tsuruhatensis LW26. The protein/polysaccharide ratio of extracellular polymeric substances (EPS) from D. tsuruhatensis LW26 presented a 3-fold enhancement. These results suggested that silicone oil induced the increase in the protein content of EPS and rendered cells hydrophobic. The resulting hydrophobic cells could adhere on the water-oil interface, improving the mass transfer by direct CB uptake from silicone oil.

Co-biodegradation of pyrene and other PAHs by the bacterium Acinetobacter johnsonii

Polycyclic aromatic hydrocarbons (PAHs) usually co-exist in environment with interactional effects. Currently, Acinetobacter johnsonii was employed to degrade 400 mg L^-1 of pyrene (PYR) and kinetic modeling indicated substrate inhibition over 76 mg L^-1 by introducing an inhibition constant parameter. In PAHs co-biodegradation, naphthalene (NAP) dominated biodegradation processes through the preferential utilization as growth substrate. The peak biodegradation of PYR increased to 415 mg L^-1 with 65 mg L^-1 of NAP. Furthermore, phenanthrene (PHE), PYR and anthracene (ANT) were degraded in turn and ended in reverse order. When the concentrations reached their respective limiting concentration of 22%, ANT could not be degraded and PHE and PYR biodegradations also respectively terminated at 66 and 45 h later with a removal rate of 40% and 26% due to very low specific activities of salicylate hydroxylase and catechol 2,3-dioxygenase. However, by introducing 125-133 mg L^-1 of NAP, the bacterial potential was effectively enhanced to 29% after cell underwent a re-stimulation stage with the exhaustion of NAP. NAP prominently contributed to cell growth to stimulate secretion of key enzymes, but the advantage would gradually get lost with the decline of its titer. To research the interplay of PAHs is conducive to targeted decontamination.

Comparative proteomic analysis and characterization of benzo(a)pyrene removal by Microbacterium sp. strain M.CSW3 under denitrifying conditions

High-molecular-weight polycyclic aromatic hydrocarbons are persistent organic pollutants with great environmental and human health risks and the associated bioremediation activities have always been hampered by the lack of powerful bacterial species under redox conditions. A Microbacterium sp. strain capable of using benzo(a)pyrene as sole carbon and energy sources under denitrifying conditions was isolated. The difference in protein expression during BaP removal and removal characterization were investigated. A total of 146 proteins were differentially expressed, 44 proteins were significantly up-regulated and 102 proteins were markedly down-regulated. GO and COG analysis showed that BaP removal inhibited the expression of proteins related to glucose metabolism at different levels and activated other metabolic pathway. The proteins associated with catalytic activity and metabolic process were altered significantly. Furthermore, the BaP removal might be occurred in certain organelle of M.CSW3. The strain removed BaP with a speed of 0.0657-1.0072 mg/L/day over the concentrations range 2.5-100 mg/L. High removal rates (>70%) were obtained over the range of pH 7-11 in 14 days. Carbohydrates and organic acids which could be utilized by the strain, as well as heavy metal ions, reduced BaP removal efficiency. However, phenanthrene or pyrene addition enhanced the removal capability of M.CSW3. The strain was proved to have practical potential for bioremediation of PAHs-contaminated soil and this study provided a powerful platform for further application by improving production of associated proteins.

Removal Capacities of Polycyclic Aromatic Hydrocarbons (PAHs) by a Newly Isolated Strain from Oilfield Produced Water

The polycyclic aromatic hydrocarbon (PAH)-degrading strain Q8 was isolated from oilfield produced water. According to the analysis of a biochemical test, 16S rRNA gene, house-keeping genes and DNA-DNA hybridization, strain Q8 was assigned to a novel species of the genus Gordonia. The strain could not only grow in mineral salt medium (MM) and utilize naphthalene and pyrene as its sole carbon source, but also degraded mixed naphthalene, phenanthrene, anthracene and pyrene. The degradation ratio of these four PAHs reached 100%, 95.4%, 73.8% and 53.4% respectively after being degraded by Q8 for seven days. A comparative experiment found that the PAHs degradation efficiency of Q8 is higher than that of Gordonia alkaliphila and Gordonia paraffinivorans, which have the capacities to remove PAHs. Fourier transform infrared spectra, saturate, aromatic, resin and asphaltene (SARA) and gas chromatography-mass spectrometry (GC-MS) analysis of crude oil degraded by Q8 were also studied. The results showed that Q8 could utilize n-alkanes and PAHs in crude oil. The relative proportions of the naphthalene series, phenanthrene series, thiophene series, fluorene series, chrysene series, C21-triaromatic steroid, pyrene, and benz(a)pyrene were reduced after being degraded by Q8. Gordonia sp. nov. Q8 had the capacity to remediate water and soil environments contaminated by PAHs or crude oil, and provided a feasible way for the bioremediation of PAHs and oil pollution.

Remediation of PAH-contaminated soil at a gas manufacturing plant by a combined two-phase partition system washing and microbial degradation process

The aim of this study was to design a remediation technique using both soil washing and microbial degradation to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soil. PAH biodegradation by inoculation of Mycobacterium sp. was first tested. The effectiveness of washing agents (Tween 80 solution, biodiesel, and a two-phase partition system (TPPS)) was then evaluated with column experiments. Third, the combination of TPPS washing and microbial degradation was studied. PAH bioavailability before and after biodegradation and the joint remediation was also assessed using hydroxypropyl-β-cyclodextrin (HPCD) extraction. Only phenanthrene and anthracene were noticeably biodegradable when the soil was inoculated with Mycobacterium sp. TPPS containing 2% (v/v) biodiesel and 2.5% (w/v) Tween 80 was used as the washing agent for the joint remediation test because it gave higher PAH extractions than Tween 80 solution with lower doses, and there was less residue in the soil. Joint TPPS washing and microbial degradation gave a total PAH removal of 92.6%, which was much higher than the results from either the biodegradation or washing experiments alone. Removals of all high molecular weight (HMW) PAHs were improved. Bioavailable concentrations of all PAHs decreased significantly after the joint remediation process, indicating that there were reduced risks from all PAHs. The results demonstrate that the combination of TPPS washing and microbial degradation is a useful and innovative process for remediation of PAH-contaminated soils.

Biosorption and biodegradation of pyrene by Brevibacillus brevis and cellular responses to pyrene treatment

Biodegradation has been proposed as an effective approach to remove pyrene, however, the information regarding cellular responses to pyrene treatment is limited thus far. In this study, the biodegradation and biosorption of pyrene by Brevibacillus brevis, along with cellular responses caused by pollutant were investigated by means of flow cytometry assay and scanning electron microscopy. The experimental results showed that pyrene was initially adsorbed by B. brevis and subsequently transported and intracellularly degraded. During this process, pyrene removal was primarily dependent on biodegradation. Cell invagination and cell surface corrugation occurred due to pyrene exposure. Nevertheless, cell regrowth after 96h treatment was observed, and the proportion of necrotic cell was only 2.8% after pyrene exposure for 120h, confirming that B. brevis could utilize pyrene as a sole carbon source for growth. The removal and biodegradation amount of pyrene (1mg/L) at 168h were 0.75 and 0.69mg/L, respectively, and the biosorption amount by inactivated cells was 0.41mg/L at this time.

A catheter-related bloodstream infection with Mycobacterium frederiksbergense in an immunocompromised child

We report a case of a catheter-related bloodstream infection with Mycobacterium frederiksbergense in an immunocompromised child with acute lymphoblastic leukemia. Nontuberculous mycobacteria have been implicated in central venous catheter infections in immunosuppressed individuals, however, to our knowledge this is the first reported case of invasive infection with this organism.

Biodegradation of pyrene by a Pseudomonas aeruginosa strain RS1 isolated from refinery sludge

High molecular weight (HMW) polynuclear aromatic hydrocarbons (PAHs) with more than three rings are inherently difficult to degrade. Degradation of HMW PAHs is primarily reported for actinomycetes, such as, Rhodococcus and Mycobacterium. This study reports pyrene degradation by a Pseudomonas aeruginosa strain isolated from tank bottom sludge in a refinery. High cell surface hydrophobicity induced during growth on pyrene facilitated its utilization as sole carbon source. Specific growth rate (μ) in the range of 0.03-0.085 h(-1) could be achieved over the concentration range 25-500 mg/L. The specific growth rate and specific pyrene utilization rate increased linearly with increase in total pyrene concentration. Although various degradation intermediates were identified in the aqueous phase, accumulation of total organic carbon (TOC) in the aqueous phase was only a small fraction of TOC equivalents of pyrene lost from the cultures. The degradation pathway appears to be similar to that reported for Mycobacterium sp. PYR-I.

Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge

The abundance, diversity, and distribution of biodegradation genes (BDGs) and phenol degradation genes (PDGs) in activated sludge (AS) from two wastewater treatment plants (WWTPs) at different sampling times were assessed by metagenomic analysis using a total of 15 datasets derived from Illumina high-throughput sequencing and BLAST comparisons to BDGs and PDGs databases. The results showed that the abundance (0.015-0.030%) and diversity of BDGs in AS varied with the WWTP and the sampling times. The p450 and pmo genes were the most abundant genes in the BDGs and PDGs subgroups, respectively. MG-RAST analysis revealed that 87 detected bacterial genera potentially capable of degrading pollutants were mostly affiliated with Proteobacteria (59.8%), Bacteroidetes (17.2%), and Actinobacteria (9.2%). Mycobacterium, belonging to Actinobacteria, was found to be the most abundant genus (23.4%). This method could be used to monitor an AS's biodegradation ability for organic pollutants and to evaluate its wastewater treatment efficiency.

Enhanced anoxic bioremediation of PAHs-contaminated sediment

In this study, the biodegradation of 16 polycyclic aromatic hydrocarbons (PAHs) in marine sediment was investigated under three different anoxic conditions, i.e. sulfate-only, nitrate-only and mixed nitrate/sulfate as electron acceptors. All two-, three- and four-ring PAHs showed significant biodegradation with the removal efficiencies ranging from 42% to 77%, while five- and six-ring PAHs showed little degradation. The results illustrated that two- to three-ring PAHs could be degraded at a rate of 4.01×10(-2)-6.42×10(-2) d(-1) under nitrate-reducing condition, faster than that of under sulfate-reducing condition. Biodegradation of two- and three-ring PAHs followed first-order model well with the rate constants of 1.62×10(-2)-6.42×10(-2) d(-1). The biodegradation of four ring PAHs followed the zero-order kinetic model with the rate constants of 1.26×10(-2)-2.22×10(-2) mg/kg/d. Molecular analysis indicated that nahAc gene increased by two orders of magnitude during the biodegradation and served as a good indicator of PAHs-degrading bacterial population and biodegradation process.

Isolation and characterization of a novel pyrene-degrading Bacillus vallismortis strain JY3A

The PAHs-degrading bacterium strain JY3A was newly isolated from the polluted soil in the Jinan Oil Refinery Factory, Shandong Province of China. The isolate was identified as Bacillus vallismortis with respect to its 16S rDNA sequence, DNA-DNA relatedness and fatty acid profiles, as well as various physiological characteristics. The strain was Gram-positive, motile, endospore forming, aerobic, oxidase and catalase-positive. The cells were 0.8-1.0μm wide and 2.0-2.5μm long, single or in pairs and sometimes in chains. Bacillus vallismortis strain JY3A could utilize naphthalene, phenanthrene, anthracene, pyrene, fluorene, benzene, toluene, phenol, methanol, ethanol, Tween 80, cyclohexane or catechol as sole carbon source. The strain alone removed 90.5% of pyrene at an initial concentration of 150ppm in 15days in the presence of 0.5% (w/w) Tween 80. However, in co-culture with Phanerochaete chrysosporium, JY3A reduced the concentration of pyrene by nearly 55.4% after 7days of incubation.

Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem

High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) are pollutants that persist in the environment due to their low solubility in water and their sequestration by soil and sediments. Although several PAH-degrading bacterial species have been isolated, it is not expected that a single isolate would exhibit the ability to degrade completely all PAHs. A consortium composed of different microorganisms can better achieve this. Two-liquid phase (TLP) culture systems have been developed to increase the bioavailability of poorly soluble substrates for uptake and biodegradation by microorganisms. By combining a silicone oil-water TLP system with a microbial consortium capable of degrading HMW PAHs, we previously developed a highly efficient PAH-degrading system. In this report, we characterized the bacterial diversity of the consortium with a combination of culture-dependent and culture-independent methods. Polymerase chain reaction (PCR) of part of the 16S ribosomal RNA gene (rDNA) sequences combined with denaturing gradient gel electrophoresis was used to monitor the bacterial population changes during PAH degradation of the consortium when pyrene, chrysene, and benzo[a]pyrene were provided together or separately in the TLP cultures. No substantial changes in bacterial profiles occurred during biodegradation of pyrene and chrysene in these cultures. However, the addition of the low-molecular-weight PAHs phenanthrene or naphthalene in the system favored one bacterial species related to Sphingobium yanoikuyae. Eleven bacterial strains were isolated from the consortium but, interestingly, only one-IAFILS9 affiliated to Novosphingobium pentaromativorans-was capable of growing on pyrene and chrysene as sole source of carbon. A 16S rDNA library was derived from the consortium to identify noncultured bacteria. Among 86 clones screened, 20 were affiliated to different bacterial species-genera. Only three strains were represented in the screened clones. Eighty-five percent of clones and strains were affiliated to Alphaproteobacteria and Betaproteobacteria; among them, several were affiliated to bacterial species known for their PAH degradation activities such as those belonging to the Sphingomonadaceae. Finally, three genes involved in the degradation of aromatic molecules were detected in the consortium and two in IAFILS9. This study provides information on the bacterial composition of a HWM PAH-degrading consortium and its dynamics in a TLP biosystem during PAH degradation.

Batch growth kinetics of an indigenous mixed microbial culture utilizing m-cresol as the sole carbon source

An indigenous mixed microbial culture, isolated from a sewage treatment plant located in Guwahati was used to study biodegradation of m-cresol in batch shake flasks. m-Cresol concentration in the growth media was varied from 100mg/L to 900mg/L. The degradation kinetics was found to follow a three-half-order model at all initial m-cresol concentrations with regression values greater than 0.97. A maximum observed specific degradation rate of 0.585h(-1) was observed at 200mg/L m-cresol concentration in the medium. In the range of m-cresol concentrations used in the study, specific growth rate of the culture and specific degradation rates were observed to follow substrate inhibition kinetics. These two rates were fitted to kinetic models of Edward, Haldane, Luong, Han-Levenspiel, and Yano-Koga that are used to explain substrate inhibition on growth of microbial culture. Out of these models Luong and Han-Levenspiel models fitted the experimental data best with lowest root mean square error values. Biokinetic constants estimated from these two models showed good potential of the indigenous mixed culture in degrading m-cresol in wastewaters.