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Muccee F, Ejaz S, Riaz N, Iqbal J. Molecular and functional analysis of naphthalene-degrading bacteria isolated from the effluents of indigenous tanneries. J Basic Microbiol 2021; 61:627-641. [PMID: 34197651 DOI: 10.1002/jobm.202100123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/10/2021] [Accepted: 05/23/2021] [Indexed: 11/06/2022]
Abstract
During present study, four naphthalene- metabolizing bacteria were isolated from tanneries effluents through enrichment on naphthalene as sole carbon source in minimal salt medium. The bacteria were analyzed to document growth pattern, naphthalene removal efficiency, biochemical and molecular characteristics, antibiotic sensitivity, and metabolic profile. The 16S ribosomal RNA gene sequences were compared through BLAST (basic local alignment search tool) similarity search tool and three isolates were found homologous to Brevibacillus agri strain NBRC 15538 and one similar to Burkholderia lata strain 383. The naphthalene removal efficiencies ranged from 1.16 ± 0.056 mg/h (IUBN1) to 1.379 ± 0.021 mg/h (IUBN26). All isolates were positive for p-nitrophenyl phosphate (PO4 ), esculin, and inulin fermentation tests. Majority were positive for glucosaminidase (IUBN3, 17, and 26) and a few for mannitol and sorbitol fermentation (IUBN1). Identification of metabolites through gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analysis allowed tracing pathways associated with naphthalene degradation. Intermediates such as cis-dihydrodiolnaphthalene, 2-hydroxychromene-2-carboxylate, 6-hydroxyhexanoic acid, acetyl-CoA confirmed that the present study bacteria can metabolize naphthalene through a pathway which differs from the pathways reported in earlier known bacteria. Due to fast growth rates, high naphthalene removal potentials, and multiple degradation pathways, these bacteria can be exploited for bioremediation of naphthalene.
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Affiliation(s)
- Fatima Muccee
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Samina Ejaz
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Naheed Riaz
- Institute of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jamshed Iqbal
- Department of Pharmacy, Comsats University, Abbottabad, Pakistan
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Muccee F, Ejaz S. Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil. Microbiol Res 2020; 238:126504. [PMID: 32534383 DOI: 10.1016/j.micres.2020.126504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/28/2020] [Accepted: 05/01/2020] [Indexed: 10/24/2022]
Abstract
The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene and petrol) metabolizing bacteria were isolated from tannery effluents and petrol contaminated soil samples by successive enrichment culturing. The taxonomic diversity and gene repertoire conferring POPs degradation ability to the isolated bacterial community were studied through whole genome shotgun sequencing of DNA consortium. The DNA consortium contained equimolar concentration of DNA extracted from each bacterial isolate using organic method. To add a double layer of confirmation the established DNA consortium was subjected to 16S rRNA metagenome sequencing and whole genome shotgun sequencing analysis. Biodiversity analysis revealed that the consortium was composed of phyla Firmicutes (80 %), Proteobacteria (12 %) and Actinobacteria (5%). Genera found included Bacillus (45 %), Burkholderia (25 %), Brevibacillus (9%) and Geobacillus (4%). Functional profiling of consortium helped us to identify genes associated with degradation pathways of a variety of organic compounds including toluene, naphthalene, caprolactam, benzoate, aminobenzoate, xylene, 4-hydroxyphenyl acetic acid, biphenyl, anthracene, aminobenzoate, chlorocyclohexane, chlorobenzene, n-phenylalkanoic acid, phenylpropanoid, salicylate, gentisate, central meta cleavage of aromatic compounds, cinnamic acid, catechol and procatechuate branch of β-ketoadipate pathway, phenyl-acetyl CoA and homogentisate catabolic pathway. The information thus generated has ensured not only biodegradation potential but also revealed many possible future applications of the isolated bacteria.
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Affiliation(s)
- Fatima Muccee
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Samina Ejaz
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
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Anokhina TO, Esikova TZ, Gafarov AB, Polivtseva VN, Baskunov BP, Solyanikova IP. Alternative Naphthalene Metabolic Pathway Includes Formation of ortho-Phthalic Acid and Cinnamic Acid Derivatives in the Rhodococcus opacus Strain 3D. BIOCHEMISTRY (MOSCOW) 2020; 85:355-368. [DOI: 10.1134/s0006297920030116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Miyazawa D, Thanh LTH, Tani A, Shintani M, Loc NH, Hatta T, Kimbara K. Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8. Microorganisms 2019; 8:microorganisms8010044. [PMID: 31878343 PMCID: PMC7023095 DOI: 10.3390/microorganisms8010044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 11/26/2022] Open
Abstract
Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating dioxygenases, respectively. Phylogenetic analysis of amino acid sequences of NahB indicated that it did not belong to the cis-dihydrodiol dehydrogenase group that includes those of classical naphthalene degradation pathways. Downstream of nahB, four open reading frames were found, and their products were predicted as meta-cleavage product hydrolase, monooxygenase, dehydrogenase, and gentisate 1,2-dioxygenase, respectively. A reverse transcriptase-PCR analysis showed that transcription of nahAcAd was induced by naphthalene. These findings indicate that we successfully identified genes involved in the upper pathway of naphthalene degradation from a thermophilic bacterium.
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Affiliation(s)
- Daisuke Miyazawa
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (D.M.); (A.T.)
| | - Le Thi Ha Thanh
- Department of Environment and Energy System, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8011, Japan;
- Institute of Bioactive Compounds, University of Sciences, Hue University, Hue, Thua Thien Hue 530000, Vietnam;
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan; (D.M.); (A.T.)
| | - Masaki Shintani
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
- Correspondence: (M.S.); (K.K.); Tel.: +81-53-478-1181 (M.S.); +81-53-478-1170 (K.K.)
| | - Nguyen Hoang Loc
- Institute of Bioactive Compounds, University of Sciences, Hue University, Hue, Thua Thien Hue 530000, Vietnam;
| | - Takashi Hatta
- Department of Biomedical Engineering, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 703-8232, Japan;
| | - Kazuhide Kimbara
- Department of Environment and Energy System, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8011, Japan;
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
- Correspondence: (M.S.); (K.K.); Tel.: +81-53-478-1181 (M.S.); +81-53-478-1170 (K.K.)
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Abo-State M, Riad B, Bakr A, Abdel Aziz M. Biodegradation of naphthalene byBordetella aviumisolated from petroleum refinery wastewater in Egypt and its pathway. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2019. [DOI: 10.1016/j.jrras.2017.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M.A.M. Abo-State
- Department of Radiation Microbiology, National Center for Radiation Research and Technology (NCRRT), Atomic Energy Authority, Nasr City, Cairo, Egypt
| | - B.Y. Riad
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - A.A. Bakr
- Department of Analysis and Evaluation, Egyptian Petroleum Research Institute (EPRI), Egypt
| | - M.F. Abdel Aziz
- Department of Biochemistry, Faculty of Science, Cairo University, Giza, Egypt
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Current Status of the Degradation of Aliphatic and Aromatic Petroleum Hydrocarbons by Thermophilic Microbes and Future Perspectives. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15122782. [PMID: 30544637 PMCID: PMC6313336 DOI: 10.3390/ijerph15122782] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 01/10/2023]
Abstract
Contamination of the environment by petroleum products is a growing concern worldwide, and strategies to remove these contaminants have been evaluated. One of these strategies is biodegradation, which consists of the use of microorganisms. Biodegradation is significantly improved by increasing the temperature of the medium, thus, the use of thermophiles, microbes that thrive in high-temperature environments, will render this process more efficient. For instance, various thermophilic enzymes have been used in industrial biotechnology because of their unique catalytic properties. Biodegradation has been extensively studied in the context of mesophilic microbes, and the mechanisms of biodegradation of aliphatic and aromatic petroleum hydrocarbons have been elucidated. However, in comparison, little work has been carried out on the biodegradation of petroleum hydrocarbons by thermophiles. In this paper, a detailed review of the degradation of petroleum hydrocarbons (both aliphatic and aromatic) by thermophiles was carried out. This work has identified the characteristics of thermophiles, and unraveled specific catabolic pathways of petroleum products that are only found with thermophiles. Gaps that limit our understanding of the activity of these microbes have also been highlighted, and, finally, different strategies that can be used to improve the efficiency of degradation of petroleum hydrocarbons by thermophiles were proposed.
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Guevara-Luna J, Alvarez-Fitz P, Ríos-Leal E, Acevedo-Quiroz M, Encarnación-Guevara S, Moreno-Godinez ME, Castellanos-Escamilla M, Toribio-Jiménez J, Romero-Ramírez Y. Biotransformation of benzo[a]pyrene by the thermophilic bacterium Bacillus licheniformis M2-7. World J Microbiol Biotechnol 2018; 34:88. [DOI: 10.1007/s11274-018-2469-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
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Minière M, Boutin O, Soric A. Evaluation of degradation and kinetics parameters of acid orange 7 through wet air oxidation process. CAN J CHEM ENG 2018. [DOI: 10.1002/cjce.23195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marine Minière
- Aix Marseille Univ, CNRS; Centrale Marseille, M2P2 Marseille France
| | - Olivier Boutin
- Aix Marseille Univ, CNRS; Centrale Marseille, M2P2 Marseille France
| | - Audrey Soric
- Aix Marseille Univ, CNRS; Centrale Marseille, M2P2 Marseille France
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Guzik U, Hupert-Kocurek K, Sitnik M, Wojcieszyńska D. Protocatechuate 3,4-dioxygenase: a wide substrate specificity enzyme isolated from Stenotrophomonas maltophilia KB2 as a useful tool in aromatic acid biodegradation. J Mol Microbiol Biotechnol 2014; 24:150-60. [PMID: 24970342 DOI: 10.1159/000362791] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Protocatechuate 3,4-dioxygenases (P34Os) catalyze the reaction of the ring cleavage of aromatic acid derivatives. It is a key reaction in many xenobiotic metabolic pathways. P34Os characterize narrow substrate specificity. This property is an unfavorable feature in the biodegradation process because one type of pollution is rarely present in the environment. Thus, the following study aimed at the characterization of a P34O from Stenotrophomonas maltophilia KB2, being able to utilize a wide spectrum of aromatic carboxylic acids. A total of 3 mM vanillic acid and 4-hydroxybenzoate were completely degraded during 8 and 4.5 h, respectively. When cells of strain KB2 were grown on 9 mM 4-hydroxybenzoate, P34O was induced. Biochemical analysis revealed that the examined enzyme was similar to other known P34Os, but showed untypical wide substrate specificity. A high activity of P34O against 2,4- and 3,5-dihydroxybenzoate was observed. As these substrates do not possess ortho configuration hydroxyl groups, it is postulated that their cleavage could be connected with their monodentate binding of substrate to the active site. Since this enzyme characterizes untypical wide substrate specificity it makes it a useful tool in applications for environmental clean-up purposes.
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Affiliation(s)
- Urszula Guzik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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