1
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Song Q, Li X, Hou N, Pei C, Li D. Chemotaxis-mediated degradation of PAHs and heterocyclic PAHs under low-temperature stress by Pseudomonas fluorescens S01: Insights into the mechanisms of biodegradation and cold adaptation. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133905. [PMID: 38422734 DOI: 10.1016/j.jhazmat.2024.133905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/06/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
As wellknown persistent contaminants, polycyclic aromatic hydrocarbons (PAHs) and heterocyclic polyaromatic hydrocarbons (Heterocyclic PAHs)'s fates in cryogenic environments are remains uncertain. Herein, strain S01 was identified as Pseudomonas fluorescens, a novel bacterium tolerant to low temperature and capable of degrading PAHs and heterocyclic PAHs. Strain S01 exhibited growth at 5-40 ℃ and degradation rate of mixed PAHs and heterocyclic PAHs reached 52% under low-temperature. Through comprehensive metabolomic, genomic, and transcriptomic analyses, we reconstructed the biodegradation pathway for PAHs and heterocyclic PAHs in S01 while investigating its response to low temperature. Further experiments involving deletion and replacement of methyl-accepting chemotaxis protein (MCP) confirmed its crucial role in enabling strain S01's adaptation to dual stress of low temperature and pollutants. Additionally, our analysis revealed that MCP was upregulated under cold stress which enhanced strain S01's motility capabilities leading to increased biofilm formation. The establishment of biofilm promoted preservation of distinct cellular membrane stability, thereby enhancing energy metabolism. Consequently, this led to heightened efficiency in pollutant degradation and improved cold resistance capabilities. Our findings provide a comprehensive understanding of the environmental fate of both PAHs and heterocyclic PAHs under low-temperature conditions while also shedding light on cold adaptation mechanism employed by strain S01.
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Affiliation(s)
- Qiuying Song
- Northeast Agricultural University, School of Resources and Environment, China
| | - Xianyue Li
- Northeast Agricultural University, School of Resources and Environment, China
| | - Ning Hou
- Northeast Agricultural University, School of Resources and Environment, China.
| | - Chenghao Pei
- Northeast Agricultural University, School of Resources and Environment, China
| | - Dapeng Li
- Northeast Agricultural University, School of Resources and Environment, China.
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2
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Nemoto Y, Ozawa K, Mori JF, Kanaly RA. Nondesulfurizing benzothiophene biotransformation to hetero and homodimeric ortho-substituted diaryl disulfides by the model PAH-degrading Sphingobium barthaii. Biodegradation 2023; 34:215-233. [PMID: 36808269 DOI: 10.1007/s10532-023-10014-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/06/2023] [Indexed: 02/21/2023]
Abstract
Understanding the biotransformation mechanisms of toxic sulfur-containing polycyclic aromatic hydrocarbon (PASH) pollutants such as benzothiophene (BT) is useful for predicting their environmental fates. In the natural environment, nondesulfurizing hydrocarbon-degrading bacteria are major active contributors to PASH biodegradation at petroleum-contaminated sites; however, BT biotransformation pathways by this group of bacteria are less explored when compared to desulfurizing organisms. When a model nondesulfurizing polycyclic aromatic hydrocarbon-degrading soil bacterium, Sphingobium barthaii KK22, was investigated for its ability to cometabolically biotransform BT by quantitative and qualitative methods, BT was depleted from culture media but was biotransformed into mostly high molar mass (HMM) hetero and homodimeric ortho-substituted diaryl disulfides (diaryl disulfanes). HMM diaryl disulfides have not been reported as biotransformation products of BT. Chemical structures were proposed for the diaryl disulfides by comprehensive mass spectrometry analyses of the chromatographically separated products and were supported by the identification of transient upstream BT biotransformation products, which included benzenethiols. Thiophenic acid products were also identified, and pathways that described BT biotransformation and novel HMM diaryl disulfide formation were constructed. This work shows that nondesulfurizing hydrocarbon-degrading organisms produce HMM diaryl disulfides from low molar mass polyaromatic sulfur heterocycles, and this may be taken into consideration when predicting the environmental fates of BT pollutants.
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Affiliation(s)
- Yuki Nemoto
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Kohei Ozawa
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Jiro F Mori
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan
| | - Robert A Kanaly
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama, Kanagawa, 236-0027, Japan.
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3
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Wang H, Qi X, Zhang L, Zhang X, Xu P, Wang X. Efficient bioelectricity generation and carbazole biodegradation using an electrochemically active bacterium Sphingobium yanoikuyae XLDN2-5. CHEMOSPHERE 2022; 307:135986. [PMID: 35970217 DOI: 10.1016/j.chemosphere.2022.135986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/04/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
Carbazole and its derivatives are polycyclic aromatic heterocycles with unusual toxicity and mutagenicity. However, disposal of these polycyclic aromatic heterocycles remains a significant challenge. This study focused on efficient resource recovery from carbazole using an obligate aerobe, Sphingobium yanoikuyae XLDN2-5, in microbial fuel cells (MFCs). S. yanoikuyae XLDN2-5 successfully achieved carbazole degradation and simultaneously electricity generation in MFCs with a maximum power density of 496.8 mW m-2 and carbazole degradation rate of 100%. It is the first time that S. yanoikuyae XLDN2-5 was discovered as an electrochemically active bacterium with high extracellular electron transfer (EET) capability. Redox mediator analysis indicated that no self-produced redox mediators were found for S. yanoikuyae XLDN2-5 under analysis conditions, and the exogenous redox mediators used in this study did not promote its EET. The nanowires produced by S. yanoikuyae XLDN2-5 cells were found in the biofilm by morphology characterization and the growth process of the nanowires was consistent with the discharge process of the MFC. Conductivity determination further verified that the nanowires produced by S. yanoikuyae XLDN2-5 cells were electrically conductive. Based on these results, it is speculated that S. yanoikuyae XLDN2-5 may mainly utilize conductive nanowires produced by itself rather than redox mediators to meet the requirements of normal energy metabolism when it grows in the low dissolved oxygen zone of the anodic biofilm. These novel findings on the EET mechanism of S. yanoikuyae XLDN2-5 lay a foundation for further exploration of polycyclic aromatic heterocyclic pollutants treatment in electrochemical devices, which may create new biotechnology processes for these pollutants control.
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Affiliation(s)
- Huimin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China; Department of Microbiology, College of Life Science, Key Laboratory for Agriculture Microbiology, Shandong Agricultural University, Taian, 271018, PR China
| | - Xiaoyan Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Lei Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Xueli Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xia Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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4
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Shen X, Li M, Zhou T, Huang J. Benzo[
b
]naphtho[1,2‐
d
]thiophene Sulfoxides: Biomimetic Synthesis, Photophysical Properties, and Applications. Angew Chem Int Ed Engl 2022; 61:e202203908. [DOI: 10.1002/anie.202203908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Xian‐Yan Shen
- School of Pharmacy Tongji Medical College Huazhong University of Science and Technology Wuhan 430030, Hubei Province China
| | - Man Li
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education School of Chemistry and Chemical Engineering Huazhong University of Science and Technology Wuhan 430030, Hubei Province China
| | - Tai‐Ping Zhou
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education School of Chemistry and Chemical Engineering Huazhong University of Science and Technology Wuhan 430030, Hubei Province China
| | - Ji‐Rong Huang
- School of Pharmacy Tongji Medical College Huazhong University of Science and Technology Wuhan 430030, Hubei Province China
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5
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Shen XY, Li M, Zhou TP, Huang JR. Benzo[b]naphtho[1,2‐d]thiophene Sulfoxides: Biomimetic Synthesis, Photophysical Properties, and Applications. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xian-Yan Shen
- Huazhong University of Science and Technology Tongji Medical College School of Pharmacy CHINA
| | - Man Li
- Huazhong University of Science and Technology School of Chemistry and Chemical Engineering CHINA
| | - Tai-Ping Zhou
- Huazhong University of Science and Technology School of Chemistry and Chemical Engineering CHINA
| | - Ji-Rong Huang
- Huazhong University of Science and Technology Tongji Medical College School of Pharmacy 13 Hangkong Road 430030 Wuhan CHINA
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6
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Monooxygenase- and Dioxygenase-Catalyzed Oxidative Dearomatization of Thiophenes by Sulfoxidation, cis-Dihydroxylation and Epoxidation. Int J Mol Sci 2022; 23:ijms23020909. [PMID: 35055091 PMCID: PMC8777831 DOI: 10.3390/ijms23020909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Enzymatic oxidations of thiophenes, including thiophene-containing drugs, are important for biodesulfurization of crude oil and drug metabolism of mono- and poly-cyclic thiophenes. Thiophene oxidative dearomatization pathways involve reactive metabolites, whose detection is important in the pharmaceutical industry, and are catalyzed by monooxygenase (sulfoxidation, epoxidation) and dioxygenase (sulfoxidation, dihydroxylation) enzymes. Sulfoxide and epoxide metabolites of thiophene substrates are often unstable, and, while cis-dihydrodiol metabolites are more stable, significant challenges are presented by both types of metabolite. Prediction of the structure, relative and absolute configuration, and enantiopurity of chiral metabolites obtained from thiophene enzymatic oxidation depends on the substrate, type of oxygenase selected, and molecular docking results. The racemization and dimerization of sulfoxides, cis/trans epimerization of dihydrodiol metabolites, and aromatization of epoxides are all factors associated with the mono- and di-oxygenase-catalyzed metabolism of thiophenes and thiophene-containing drugs and their applications in chemoenzymatic synthesis and medicine.
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7
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Ghosh P, Mukherji S. Environmental contamination by heterocyclic Polynuclear aromatic hydrocarbons and their microbial degradation. BIORESOURCE TECHNOLOGY 2021; 341:125860. [PMID: 34614557 DOI: 10.1016/j.biortech.2021.125860] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Heterocyclic polynuclear aromatic hydrocarbons (PAHs) have been detected in all environmental matrices at few ppb to several ppm concentrations and they are characterized by high polarity. Some heterocyclic PAHs are mutagenic and carcinogenic to humans and various organisms. Despite being potent environmental pollutants, these compounds have received less attention. This paper focuses on the sources and occurrence of these compounds and their microbial degradation using diverse species of bacteria, fungi, and algae. Complete removal of 1.8 to 2614 mg/L of nitrogen heterocyclic PAH (PANH), 0.27 to 184 mg/L of sulfur heterocyclic PAH (PASH), and 0.6 to 120 mg/L of oxygen heterocyclic PAH (PAOH) compounds by various microbial species was observed between 3 h and 18 days, 8 h to 6 days, and 4 h to 250 h, respectively under aerobic condition. Strategies for enhancing the removal of heterocyclic PAHs from aquatic systems are also discussed along with the challenges.
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Affiliation(s)
- Prasenjit Ghosh
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Department of Civil Engineering, NIT Tiruchirappalli, Tiruchirappalli, Tamil Nadu 620015, India
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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8
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Huang J. Organic Transformation of Benzothiophenes by C−S Bond Cleavage Beyond Reductive Desulfurization. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jirong Huang
- School of Pharmacy Tongji Medical College Huazhong University of Science and Technology Wuhan 430030 Hubei Province People's Republic of China
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9
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Ghosh P, Mukherji S. Elucidation of substrate interaction effects in multicomponent systems containing 3-ring homocyclic and heterocyclic polynuclear aromatic hydrocarbons. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:1394-1404. [PMID: 34382630 DOI: 10.1039/d1em00140j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial growth and degradation experiments were conducted on carbazole (CBZ), fluorene (FLU) and dibenzothiophene (DBT) individually and in various mixture combinations using an efficient polynuclear aromatic hydrocarbon (PAH) degrading bacterial strain, Pseudomonas aeruginosa RS1. In single component systems, bacterial growth on CBZ (specific growth rate, μ = 0.99 day-1) was much higher compared to that on FLU (μ = 0.38 day-1) and DBT (μ = 0.33 day-1) and bacterial growth was inhibited in the presence of FLU and DBT in binary (μ = 0.64 day-1) and ternary (μ = 0.75 day-1) mixtures. Multisubstrate additive modelling indicated growth inhibition in all the systems. The degradation of the compounds was significantly inhibited in binary mixtures. While the degradation of the compounds in binary mixtures varied from 35 ± 4% to 73 ± 3%, their degradation varied from 61 ± 5% to 91 ± 4%, when applied as sole substrates and from 77 ± 3% to 96 ± 3%, when applied in a ternary mixture. Degradation experiments were also conducted in ternary mixtures using a 23 full factorial design and the results were examined using analysis of variance (ANOVA) and Tukey's honest significant difference (HSD) tests. At a low concentration of the heterocyclics, CBZ and DBT (5 mg L-1 each), the degradation of the PAH, FLU, was significantly enhanced (from 81 ± 1% to 93 ± 0.3%) when its concentration was increased from 5 to 30 mg L-1. The full factorial design can provide valuable insights into substrate interaction effects in mixtures.
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Affiliation(s)
- Prasenjit Ghosh
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Department of Civil Engineering, National Institute of Technology Goa, Farmagudi, Ponda, Goa 403401, India.
| | - Suparna Mukherji
- Environmental Science and Engineering Department (ESED), Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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10
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Mukherjee AK, Chanda A, Mukherjee I, Kumar P. Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation. J Appl Microbiol 2021; 132:1062-1078. [PMID: 34415661 DOI: 10.1111/jam.15258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/28/2022]
Abstract
AIM Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium. METHODS AND RESULTS The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole. CONCLUSION The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.
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Affiliation(s)
- Ashis K Mukherjee
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India.,Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path Garchuk, Paschim, Boragaon, Guwahati, Assam, India
| | - Abhishek Chanda
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Indrajit Mukherjee
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Pawan Kumar
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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11
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Mitra M, Nguyen KMAK, Box TW, Gilpin JS, Hamby SR, Berry TL, Duckett EH. Isolation and characterization of a novel Sphingobium yanoikuyae strain variant that uses biohazardous saturated hydrocarbons and aromatic compounds as sole carbon sources. F1000Res 2020; 9:767. [PMID: 32934808 PMCID: PMC7477647 DOI: 10.12688/f1000research.25284.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/14/2020] [Indexed: 01/09/2023] Open
Abstract
Background: Green micro-alga,
Chlamydomonas reinhardtii (a Chlorophyte), can be cultured in the laboratory heterotrophically or photo-heterotrophically in
Tris-
Phosphate-
Acetate (TAP) medium, which contains acetate as the carbon source.
Chlamydomonas can convert acetate in the TAP medium to glucose via the glyoxylate cycle, a pathway present in many microbes and higher plants. A novel bacterial strain, CC4533, was isolated from a contaminated TAP agar medium culture plate of a
Chlamydomonas wild type strain. In this article, we present our research on the isolation, and biochemical and molecular characterizations of CC4533. Methods: We conducted several microbiological tests and spectrophotometric analyses to biochemically characterize CC4533. The 16S rRNA gene of CC4533 was partially sequenced for taxonomic identification. We monitored the growth of CC4533 on Tris-Phosphate (TP) agar medium (lacks a carbon source) containing different sugars, aromatic compounds and saturated hydrocarbons, to see if CC4533 can use these chemicals as the sole source of carbon. Results: CC4533 is a Gram-negative, non-enteric yellow pigmented, aerobic, mesophilic bacillus. It is alpha-hemolytic and oxidase-positive. CC4533 can ferment glucose, sucrose and lactose, is starch hydrolysis-negative, resistant to penicillin, polymyxin B and chloramphenicol. CC4533 is sensitive to neomycin. Preliminary spectrophotometric analyses indicate that CC4533 produces b-carotenes. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of CC4533 show 99.55% DNA sequence identity to that of
Sphingobium yanoikuyae strain PR86 and
S. yanoikuyae strain NRB095. CC4533 can use cyclo-chloroalkanes, saturated hydrocarbons present in car motor oil, polyhydroxyalkanoate, and mono- and poly-cyclic aromatic compounds, as sole carbon sources for growth. Conclusions: Taxonomically, CC4533 is very closely related to the alpha-proteobacterium
S. yanoikuyae, whose genome has been sequenced. Future research is needed to probe the potential of CC4533 for environmental bioremediation. Whole genome sequencing of CC4533 will confirm if it is a novel strain of
S. yanoikuyae or a new
Sphingobium species.
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Affiliation(s)
- Mautusi Mitra
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Kevin Manoap-Anh-Khoa Nguyen
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA.,Department of Mechanical Engineering, Kennesaw State University, Marietta, GA, 30060, USA
| | - Taylor Wayland Box
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Jesse Scott Gilpin
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Seth Ryan Hamby
- Biology Department, University of West Georgia, Carrollton, GA, 30118, USA
| | - Taylor Lynne Berry
- Carrollton High School, Carrollton, GA, 30117, USA.,Department of Chemistry and Biochemistry, University of North Georgia, Dahlonega, GA, 30597, USA
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12
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Marques Netto CGC, Palmeira DJ, Brondani PB, Andrade LH. Enzymatic reactions involving the heteroatoms from organic substrates. AN ACAD BRAS CIENC 2018; 90:943-992. [PMID: 29742205 DOI: 10.1590/0001-3765201820170741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/01/2018] [Indexed: 11/22/2022] Open
Abstract
Several enzymatic reactions of heteroatom-containing compounds have been explored as unnatural substrates. Considerable advances related to the search for efficient enzymatic systems able to support a broader substrate scope with high catalytic performance are described in the literature. These reports include mainly native and mutated enzymes and whole cells biocatalysis. Herein, we describe the historical background along with the progress of biocatalyzed reactions involving the heteroatom(S, Se, B, P and Si) from hetero-organic substrates.
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Affiliation(s)
| | - Dayvson J Palmeira
- Departamento de Química Fundamental, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Patrícia B Brondani
- Departamento de Ciências Exatas e Educação, Universidade Federal de Santa Catarina, Blumenau, SC, Brazil
| | - Leandro H Andrade
- Departamento de Química Fundamental, Universidade de São Paulo, São Paulo, SP, Brazil
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13
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Zhao Q, Yue S, Bilal M, Hu H, Wang W, Zhang X. Comparative genomic analysis of 26 Sphingomonas and Sphingobium strains: Dissemination of bioremediation capabilities, biodegradation potential and horizontal gene transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 609:1238-1247. [PMID: 28787798 DOI: 10.1016/j.scitotenv.2017.07.249] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 05/12/2023]
Abstract
Bacteria belonging to the genera Sphingomonas and Sphingobium are known for their ability to catabolize aromatic compounds. In this study, we analyzed the whole genome sequences of 26 strains in the genera Sphingomonas and Sphingobium to gain insight into dissemination of bioremediation capabilities, biodegradation potential, central pathways and genome plasticity. Phylogenetic analysis revealed that both Sphingomonas sp. strain BHC-A and Sphingomonas paucimobilis EPA505 should be placed in the genus Sphingobium. The bph and xyl gene cluster was found in 6 polycyclic aromatic hydrocarbons-degrading strains. Transposase and IS coding genes were found in the 6 gene clusters, suggesting the mobility of bph and xyl gene clusters. β-ketoadipate and homogentisate pathways were the main central pathways in Sphingomonas and Sphingobium strains. A large number of oxygenase coding genes were predicted in the 26 genomes, indicating a huge biodegradation potential of the Sphingomonas and Sphingobium strains. Horizontal gene transfer related genes and prophages were predicted in the analyzed strains, suggesting the ongoing evolution and shaping of the genomes. Analysis of the 26 genomes in this work contributes to the understanding of dispersion of bioremediation capabilities, bioremediation potential and genome plasticity in strains belonging to the genera Sphingomonas and Sphingobium.
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Affiliation(s)
- Qiang Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shengjie Yue
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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14
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Visible-light-induced synthesis of benzothiophenes and benzoselenophenes via the annulation of thiophenols or 1,2-diphenyldiselane with alkynes. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Oberoi AS, Philip L. Variation in toxicity during the biodegradation of various heterocyclic and homocyclic aromatic hydrocarbons in single and multi-substrate systems. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 135:337-346. [PMID: 27770649 DOI: 10.1016/j.ecoenv.2016.10.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 06/06/2023]
Abstract
In the present study, an attempt was made to understand the variation in the toxicity during the biodegradation of aromatic hydrocarbons in single and multi-substrate system. The bacterial bioassay based on the inhibition of dehydrogenase enzyme activity of two different bacterial sp. E.coli and Pseudomonas fluorescens was used for toxicity assessment. Amongst the chosen pollutants, the highest acute toxicity was observed for benzothiophene followed by benzofuran having EC50 value of 16.60mg/L and 19.30mg/L respectively. Maximum residual toxicity of 30.8% was observed at the end during the degradation of benzothiophene. Due to the accumulation of transitory metabolites in both single and multisubstrate systems, reduction in toxicity was not proportional to the decrease in pollutant concentration. In multi-substrate system involving mixture of heterocyclic hydrocarbons, maximum residual toxicity of 39.5% was observed at the end of biodegradation. Enhanced degradation of benzofuran, benzothiophene and their metabolic intermediates were observed in the presence of naphthalene resulting in significant reduction in residual toxicity. 2 (1H) - quinolinone, an intermediate metabolite of quinoline was observed having significant eco-toxicity amongst all other intermediates investigated.
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Affiliation(s)
- Akashdeep Singh Oberoi
- Environmental and Water Resources Engineering Division, Department of Civil Engineering, IIT Madras, Chennai 600 036, India
| | - Ligy Philip
- Environmental and Water Resources Engineering Division, Department of Civil Engineering, IIT Madras, Chennai 600 036, India.
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Saeb ATM. Presence of Bacterial Virulence Gene Homologues in the dibenzo-p-dioxins degrading bacterium Sphingomonas wittichii. Bioinformation 2016; 12:241-248. [PMID: 28197061 PMCID: PMC5290665 DOI: 10.6026/97320630012241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/28/2022] Open
Abstract
Sphingomonas wittichii, a close relative of the human pathogen Sphingomonas paucimobilis, is a microorganism of great interest to the bioremediation community for its ability of biodegradation to a large number of toxic polychlorinated dioxins. In the present study we investigated the presence of different virulence factors and genes in S. wittichii. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of S. wittichii as a potential virulent pathogen. The 16SrDNA phylogenetic tree showed that the closest bacterial taxon to S. wittichii is Brucella followed by Helicobacter, Campylobacter, Pseudomonas then Legionella. Despite their close phylogenetic relationship, S. wittichii did not share any virulence factors with Helicobacter or Campylobacter. On the contrary, in spite of the phylogenetic divergence between S. wittichii and Pseudomonas spp., they shared many major virulence factors, such as, adherence, antiphagocytosis, Iron uptake, proteases and quorum sensing. S. wittichii contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp. and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. S. wittichii is a potential virulent bacterium. Another possibility is that reductive evolution process attenuated S. wittichii pathogenic capabilities. Thus plenty of care must be taken when using this bacterium in soil remediation purposes.
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Affiliation(s)
- Amr T. M. Saeb
- Biotechnology Department, Strategic Center for Diabetes Research, College of medicine, King Saud University, Saudi Arabia
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Biodegradation of Various Aromatic Compounds by Enriched Bacterial Cultures: Part B—Nitrogen-, Sulfur-, and Oxygen-Containing Heterocyclic Aromatic Compounds. Appl Biochem Biotechnol 2015; 176:1746-69. [DOI: 10.1007/s12010-015-1692-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
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18
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Ming W, Liu X, Wang L, Liu J, Wang M. Tandem Thien- and Benzannulations of α-Alkenoyl-α-alkynyl Ketene Dithioacetals with Cyanoacetates: Synthesis of Functionalized Benzo[b]thiophenes. Org Lett 2015; 17:1746-9. [DOI: 10.1021/acs.orglett.5b00523] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenbo Ming
- Department of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Xiaocui Liu
- Department of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Lianjie Wang
- Department of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Jun Liu
- Department of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Mang Wang
- Department of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
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19
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Khedkar S, Shanker R. Degradation of dibenzothiophene and its metabolite 3-hydroxy-2-formylbenzothiophene by an environmental isolate. Biodegradation 2014; 25:643-54. [DOI: 10.1007/s10532-014-9688-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/19/2014] [Indexed: 11/29/2022]
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20
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Hari DP, Hering T, König B. Visible light photocatalytic synthesis of benzothiophenes. Org Lett 2012; 14:5334-7. [PMID: 23039199 DOI: 10.1021/ol302517n] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The photocatalytic reaction of o-methylthio-arenediazonium salts with alkynes yields substituted benzothiophenes regioselectively through a radical annulation process. Green light irradiation of eosin Y initiates the photoredox catalysis. The scope of the reaction was investigated by using various substituted diazonium salts and different alkynes.
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Affiliation(s)
- Durga Prasad Hari
- Institut für Organische Chemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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21
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Genome sequence of Sphingomonas wittichii DP58, the first reported phenazine-1-carboxylic acid-degrading strain. J Bacteriol 2012; 194:3535-6. [PMID: 22689229 DOI: 10.1128/jb.00330-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas wittichii DP58 (CCTCC M 2012027), the first reported phenazine-1-carboxylic acid (PCA)-degrading strain, was isolated from pimiento rhizosphere soils. Here we present a 5.6-Mb assembly of its genome. This sequence would contribute to the elucidation of the molecular mechanism of PCA degradation to improve the antifungal's effectiveness or remove superfluous PCA.
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Liu X, Gai Z, Tao F, Tang H, Xu P. Carotenoids play a positive role in the degradation of heterocycles by Sphingobium yanoikuyae. PLoS One 2012; 7:e39522. [PMID: 22745775 PMCID: PMC3380023 DOI: 10.1371/journal.pone.0039522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/22/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Microbial oxidative degradation is a potential way of removing pollutants such as heterocycles from the environment. During this process, reactive oxygen species or other oxidants are inevitably produced, and may cause damage to DNA, proteins, and membranes, thereby decreasing the degradation rate. Carotenoids can serve as membrane-integrated antioxidants, protecting cells from oxidative stress. FINDINGS Several genes involved in the carotenoid biosynthetic pathway were cloned and characterized from a carbazole-degrading bacterium Sphingobium yanoikuyae XLDN2-5. In addition, a yellow-pigmented carotenoid synthesized by strain XLDN2-5 was identified as zeaxanthin that was synthesized from β-carotene through β-cryptoxanthin. The amounts of zeaxanthin and hydrogen peroxide produced were significantly and simultaneously enhanced during the biodegradation of heterocycles (carbazole < carbazole + benzothiophene < carbazole + dibenzothiophene). These higher production levels were consistent with the transcriptional increase of the gene encoding phytoene desaturase, one of the key enzymes for carotenoid biosynthesis. CONCLUSIONS/SIGNIFICANCE Sphingobium yanoikuyae XLDN2-5 can enhance the synthesis of zeaxanthin, one of the carotenoids, which may modulate membrane fluidity and defense against intracellular oxidative stress. To our knowledge, this is the first report on the positive role of carotenoids in the biodegradation of heterocycles, while elucidating the carotenoid biosynthetic pathway in the Sphingobium genus.
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Affiliation(s)
- Xiaorui Liu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Zhonghui Gai
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People′s Republic of China
- * E-mail:
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23
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Comprehensive GC2/MS for the monitoring of aromatic tar oil constituents during biodegradation in a historically contaminated soil. J Biotechnol 2012; 157:460-6. [DOI: 10.1016/j.jbiotec.2011.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 07/28/2011] [Accepted: 08/08/2011] [Indexed: 11/18/2022]
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24
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Boyd DR, Sharma ND, McMurray B, Haughey SA, Allen CCR, Hamilton JTG, McRoberts WC, More O'Ferrall RA, Nikodinovic-Runic J, Coulombel LA, O'Connor KE. Bacterial dioxygenase- and monooxygenase-catalysed sulfoxidation of benzo[b]thiophenes. Org Biomol Chem 2012; 10:782-90. [DOI: 10.1039/c1ob06678a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Kannel PR, Gan TY. Naphthenic acids degradation and toxicity mitigation in tailings wastewater systems and aquatic environments: a review. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2012; 47:1-21. [PMID: 22217078 DOI: 10.1080/10934529.2012.629574] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Naphthenic acids, NAs (classical formula C(n)H(2n+z)O(2), where n is the carbon numbers, z represents zero or negative even integers), found in oil sands process waters (OSPWs), are toxic to aquatic environments depending upon several factors such as pH, salinity, molecular size and chemical structure of NAs. Among various available methods, biodegradation seems to be generally the most cost-effective method for decreasing concentrations of NAs (n ≤ 21) and reducing their associated toxicity in OSPW, however the mechanism by which the biodegradation of NAs occurs are poorly understood. Ozonation is superior over biodegradation in decreasing higher molecular weight alkyl branched NAs (preferentially, n ≥ 22, -6 ≥ z ≥ -12) as well as enabling accelerated biodegradation and reducing toxicity. Photolysis (UV at 254 nm) is effective in cleaving higher molecular weight NAs into smaller fragments that will be easier for microorganisms to degrade, whereas photocatalysis can metabolize selective NAs (0 ≥ z ≥ -6) efficiently and minimize their associated toxicity. Phytoremediation is applicable for metabolizing specific NAs (O(2), O(3), O(4), and O(5) species) and minimizing their associated toxicities. Petroleum coke (PC) adsorption is effective in reducing the more structurally complex NAs (preferentially 12 ≥ n ≥ 18 and z = -10, -12) and their toxicity in OSPWs, depending upon the PC content, pH and temperature. Several factors have influence on the degradation of NAs in OSPWs and aquatic environments, which include molecular mass and chemical structure of NAs, sediment structure, temperature, pH, dissolved oxygen, nutrients, and bacteria types.
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Affiliation(s)
- Prakash R Kannel
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
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Genome sequence of Sphingobium yanoikuyae XLDN2-5, an efficient carbazole-degrading strain. J Bacteriol 2011; 193:6404-5. [PMID: 22038966 DOI: 10.1128/jb.06050-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingobium yanoikuyae XLDN2-5 is an efficient carbazole-degrading strain. Carbazole-degrading genes are accompanied on both sides by two copies of IS6100 elements. Here, we describe the draft genome sequence of strain XLDN2-5, which may provide important clues as to how it recruited exogenous genes to establish pathways to degrade the xenobiotics.
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Blum P, Sagner A, Tiehm A, Martus P, Wendel T, Grathwohl P. Importance of heterocylic aromatic compounds in monitored natural attenuation for coal tar contaminated aquifers: A review. JOURNAL OF CONTAMINANT HYDROLOGY 2011; 126:181-194. [PMID: 22115084 DOI: 10.1016/j.jconhyd.2011.08.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 08/12/2011] [Accepted: 08/15/2011] [Indexed: 05/31/2023]
Abstract
NSO heterocycles (HET) are typical constituents of coal tars. However, HET are not yet routinely monitored, although HET are relatively toxic coal tar constituents. The main objectives of the study is therefore to review previous studies and to analyse HET at coal tar polluted sites in order to assess the relevance of HET as part of monitored natural attenuation (MNA) or any other long-term monitoring programme. Hence, natural attenuation of typical HET (indole, quinoline, carbazole, acridine, methylquinolines, thiophene, benzothiophene, dibenzothiophene, benzofuran, dibenzofuran, methylbenzofurans, dimethylbenzofurans and xanthene) were studied at three different field sites in Germany. Compound-specific plume lengths were determined for all main contaminant groups (BTEX, PAH and HET). The results show that the observed plume lengths are site-specific and are above 250m, but less than 1000m. The latter, i.e. the upper limit, however mainly depends on the level of investigation, the considered compound, the lowest measured concentration and/or the achieved compound-specific detection limit and therefore cannot be unequivocally defined. All downstream contaminant plumes exhibited HET concentrations above typical PAH concentrations indicating that some HET are generally persistent towards biodegradation compared to other coal tar constituents, which results in comparatively increased field-derived half-lives of HET. Additionally, this study provides a review on physicochemical and toxicological parameters of HET. For three well investigated sites in Germany, the biodegradation of HET is quantified using the centre line method (CLM) for the evaluation of bulk attenuation rate constants. The results of the present and previous studies suggest that implementation of a comprehensive monitoring programme for heterocyclic aromatic compounds is relevant at sites, if MNA is considered in risk assessment and for remediation.
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Affiliation(s)
- Philipp Blum
- Karlsruhe Institute of Technology, Institute for Applied Geosciences (AGW), Kaiserstraße 12, 76131 Karlsruhe, Germany.
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Heaven MW, Wild K, Verheyen V, Cruickshank A, Watkins M, Nash D. Seasonal and wastewater stream variation of trace organic compounds in a dairy processing plant aerobic bioreactor. BIORESOURCE TECHNOLOGY 2011; 102:7727-7736. [PMID: 21704516 DOI: 10.1016/j.biortech.2011.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/13/2011] [Accepted: 06/01/2011] [Indexed: 05/31/2023]
Abstract
Bioreactors are often an integral part of dairy factory efforts to reduce the biological oxygen demand of their wastewater. In this study, infeed, mixed liquor and supernatant samples of an aerobic bioreactor used by a dairy factory in South-Eastern Australia were analyzed for nutrients and organic compounds using gas chromatography-mass spectrometry and physicochemical analyses. Despite different concentrations of organic inputs into the bioreactor, nutrients and trace organic compounds were reduced significantly (i.e. average concentration of trace organic compounds: infeed=1681 μg/L; mixed liquor=257 μg/L; supernatant=23 μg/L). However, during one sampling period the bioreactor was adversely affected by the organic loading. Trace organic compounds in the samples were predominantly fatty acids associated with animal products. The analyses suggest that it is possible to trace a disruptive input (i.e. infeed with high organic carbon concentrations) into an aerobic bioreactor by measuring concentrations of fatty acids or ammonia.
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Affiliation(s)
- Michael W Heaven
- Future Farming Systems Research Division, Department of Primary Industries, 1301 Hazeldean Road, Ellinbank, Victoria 3821, Australia
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Shyam Prasad G, Girisham S, Reddy SM. Potential of Thermophilic Fungus Rhizomucor pusillus NRRL 28626 in Biotransformation of Antihelmintic Drug Albendazole. Appl Biochem Biotechnol 2011; 165:1120-8. [DOI: 10.1007/s12010-011-9329-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 07/27/2011] [Indexed: 10/17/2022]
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The genes coding for the conversion of carbazole to catechol are flanked by IS6100 elements in Sphingomonas sp. strain XLDN2-5. PLoS One 2010; 5:e10018. [PMID: 20368802 PMCID: PMC2848856 DOI: 10.1371/journal.pone.0010018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/15/2010] [Indexed: 11/24/2022] Open
Abstract
Background Carbazole is a recalcitrant compound with a dioxin-like structure and possesses mutagenic and toxic activities. Bacteria respond to a xenobiotic by recruiting exogenous genes to establish a pathway to degrade the xenobiotic, which is necessary for their adaptation and survival. Usually, this process is mediated by mobile genetic elements such as plasmids, transposons, and insertion sequences. Findings The genes encoding the enzymes responsible for the degradation of carbazole to catechol via anthranilate were cloned, sequenced, and characterized from a carbazole-degrading Sphingomonas sp. strain XLDN2-5. The car gene cluster (carRAaBaBbCAc) and fdr gene were accompanied on both sides by two copies of IS6100 elements, and organized as IS6100::ISSsp1-ORF1-carRAaBaBbCAc-ORF8-IS6100-fdr-IS6100. Carbazole was converted by carbazole 1,9a-dioxygenase (CARDO, CarAaAcFdr), meta-cleavage enzyme (CarBaBb), and hydrolase (CarC) to anthranilate and 2-hydroxypenta-2,4-dienoate. The fdr gene encoded a novel ferredoxin reductase whose absence resulted in lower transformation activity of carbazole by CarAa and CarAc. The ant gene cluster (antRAcAdAbAa) which was involved in the conversion of anthranilate to catechol was also sandwiched between two IS6100 elements as IS6100-antRAcAdAbAa-IS6100. Anthranilate 1,2-dioxygenase (ANTDO) was composed of a reductase (AntAa), a ferredoxin (AntAb), and a two-subunit terminal oxygenase (AntAcAd). Reverse transcription-PCR results suggested that carAaBaBbCAc gene cluster, fdr, and antRAcAdAbAa gene cluster were induced when strain XLDN2-5 was exposed to carbazole. Expression of both CARDO and ANTDO in Escherichia coli required the presence of the natural reductases for full enzymatic activity. Conclusions/Significance We predict that IS6100 might play an important role in the establishment of carbazole-degrading pathway, which endows the host to adapt to novel compounds in the environment. The organization of the car and ant genes in strain XLDN2-5 was unique, which showed strong evolutionary trail of gene recruitment mediated by IS6100 and presented a remarkable example of rearrangements and pathway establishments.
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