International Journal of Genetics and Genomics

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Isolation and Genetic Characterization of Phenol-Utilizing Marine Bacteria and Their Phenol Degradation Pathway

Received: 26 November 2014    Accepted: 09 December 2014    Published: 27 February 2015
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Abstract

Phenolic compounds are widely distributed toxic pollutants in seawater, and their effective degradation is very important for bioremediation programs. In this study, nine phenol-degrading bacteria were isolated from seawater samples, which were collected from the coastal areas of Japan. Besides the enrichment substrate phenol, all isolates could utilize at least one isomer of cresol as the sole source of carbon. A 16S rRNA gene sequence analysis indicated that all strains were affiliated with the class Gammaproteobacteria, four strains were closely related to Spongiibacter, four were closely related to Marinobacter, and one was closely related to Photobacterium. During growth on phenol, all isolates produced a yellow product, and a whole-cell study indicated that it was an extradiol meta-ring cleavage product of catechol, 2-hydroxymuconate semialdehyde. Phylogenetic analysis revealed that the partial gene encoding the largest subunit of the multicomponent phenol hydroxylase of the isolates was similar to that of terrestrial bacteria, thereby suggesting that phenol is converted into catechol by marine bacteria. We also suggest that horizontal transfer of the gene may occur not only among marine bacteria but also between the genera Marinobacter and Pseudomonas.

DOI 10.11648/j.ijgg.20150302.11
Published in International Journal of Genetics and Genomics (Volume 3, Issue 2, April 2015)
Page(s) 20-25
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Phenol Degradation, Marine Bacteria, Multicomponent Phenol Hydroxylase, Catechol 2, 3-Dioxygenase, Isolation, Marinobacter, Spongiibacter, Photobacterium

References
[1] Michałowicz J, Duda W (2007) Phenols – Sources and Toxicity. Polish Environ Stud 16:347-362
[2] vanSchie PM, Young LY (2000) Biodegradation of phenol: mechanisms and applications. Bioremed J 4:1-18
[3] Nair CI, Jayachandran K, Shashidhar S (2008) Biodegradation of phenol. African J Biotechnol 7:4951-4958
[4] Iwaki H, Fujioka M, Hasegawa Y (2014) Isolation and characterization of marine nonylphenol-degrading bacteria and description of Pseudomaricurvus alkylphenolicus gen. nov., sp. nov. Curr Microbiol 68:167-173
[5] Iwaki H, Takada K, Hasegawa Y (2012) Maricurvus nonylphenolicus gen. nov., sp. nov., a nonylphenol‐degrading bacterium isolated from seawater. FEMS Microbiol Lett 327:142-147
[6] Moxley K, Schmidt S (2012). Isolation of a phenol-utilizing marine bacterium from Durban Harbour (South Africa) and its preliminary characterization as Marinobacter sp. KM2. Water Sci Technol 65:932-939
[7] Iwaki H, Nishimura A, Hasegawa Y (2012) Isolation and characterization of marine bacteria capable of utilizing phthalate. World J Microbiol Biotechnol 28:1321–1325
[8] Iwaki H, Hasegawa Y, Wang S, Kayser MM, Lau PC (2002) Cloning and characterization of a gene cluster involved in cyclopentanol metabolism in Comamonas sp. strain NCIMB 9872 and biotransformations effected by Escherichia coli-expressed cyclopentanone 1,2-monooxygenase. Appl Environ Microbiol 68:5671-5684
[9] Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 30:2725-2729
[10] Junca H, Pieper DH (2003) Amplified functional DNA restriction analysis to determine catechol 2,3-dioxygenase gene diversity in soil bacteria. J Microbiol Meth 55:697–708
[11] Futamata H, Harayama S, Watanabe K (2001) Group-specific monitoring of phenol hydroxylase genes for a functional assessment of phenol-stimulated trichloroethylene bioremediation. Appl Environ Microbiol 67:4671–4677
[12] Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
[13] Duran R (2010) Marinobacter, in Handbook of Hydrocarbon and Lipid Microbiology, ed K. N. Timmis (Berlin, Heidelberg: Springer-Verlag), 1725–1735
[14] Hernandez-Raquet G, Budzinski H, Caumette P, Dabert P, Le Ménach K, Muyzer G, Duran R (2006) Molecular diversity studies of bacterial communities of oil polluted microbial mats from the Etang de Berre (France). FEMS Microbiol Ecol 58:550-562
[15] Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M (2011) Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Appl Environ Microbiol 77:7962-7974
[16] Nicholson CA, Fathepure BZ (2004) Biodegradation of benzene by halophilic and halotolerant bacteria under aerobic conditions. Appl Environ Microbiol 70:1222-1225
[17] Yakimov MM, Denaro R, Genovese M, Cappello S, D’Auria G, Chernikova TN, Timmis KN, Golyshin PN, Giluliano L (2005) Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environ Microbiol 7:1426-1441
[18] Zhao C, Ruan L (2011) Biodegradation of Enteromorpha prolifera by mangrove degrading micro-community with physical–chemical pretreatment. Appl Microbiol Biotechnol 92:709-716
[19] Kojima Y, Itada N, Hayaishi O (1961) Metapyrocatachase: a new catechol-cleaving enzyme. J Biol Chem 236:2223-2228
[20] Watanabe K, Teramoto M, Futamata H, Harayama S (1998) Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl Environ Microbiol 64:4396–4402
[21] Cafaro V, Izzo V, Scognamiglio R, Notomista E, Capasso P, Casbarra A, Pucci P, DiDonato A (2004) Phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1: interplay between two enzymes. Appl Environ Microbiol 70:2211-2219
[22] Izzo V, Leo G, Scognamiglio R, Troncone L, Birolo L, DiDonato A (2011) PHK from phenol hydroxylase of Pseudomonas sp. OX1. Insight into the role of an accessory protein in bacterial multicomponent monooxygenases. Arch Biochem Biophys 505:48-59
[23] McCormick MS, Lippard SJ (2011) Analysis of substrate access to active sites in bacterial multicomponent monooxygenase hydroxylases: X-ray crystal structure of xenon-pressurized phenol hydroxylase from Pseudomonas sp. OX1. Biochemistry 50:11058-11069
[24] Sazinsky MH, Dunten PW, McCormick MS, DiDonato A, Lippard SJ (2006) X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase. Biochemistry 45:15392-15404
[25] Tinberg CE, Song WJ, Izzo V, Lippard SJ (2011) Multiple roles of component proteins in bacterial multicomponent monooxygenases: phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas sp. OX1. Biochemistry 50:1788-1798
[26] Shingler V, Powlowski J, Marklund U (1992) Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J Bacteriol 174:711-724
[27] Hugo N, Meyer C, Armengaud J, Gaillard J, Timmis KN, Jouanneau Y (2000) Characterization of three XylT-like [2Fe-2S] ferredoxins associated with catabolism of cresols or naphthalene: evidence for their involvement in catechol dioxygenase reactivation. J Bacteriol 182:5580-5585
[28] Ochman H,Wilson AC (1987) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26:74-86
[29] Hedlund BP, Geiselbrecht AD, Staley JT (2001) Marinobacter strain NCE312 has a Pseudomonas–like naphthalene dioxygenase. FEMS Microbiol lett 201:47-51
Author Information
  • Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan

  • Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan

  • Department of Life Science & Biotechnology, Kansai University, 3-3-35 Yamate-Cho, Suita, Osaka 564-8680, Japan

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  • APA Style

    Hiroaki Iwaki, Kengo Takada, Yoshie Hasegawa. (2015). Isolation and Genetic Characterization of Phenol-Utilizing Marine Bacteria and Their Phenol Degradation Pathway. International Journal of Genetics and Genomics, 3(2), 20-25. https://doi.org/10.11648/j.ijgg.20150302.11

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    ACS Style

    Hiroaki Iwaki; Kengo Takada; Yoshie Hasegawa. Isolation and Genetic Characterization of Phenol-Utilizing Marine Bacteria and Their Phenol Degradation Pathway. Int. J. Genet. Genomics 2015, 3(2), 20-25. doi: 10.11648/j.ijgg.20150302.11

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    AMA Style

    Hiroaki Iwaki, Kengo Takada, Yoshie Hasegawa. Isolation and Genetic Characterization of Phenol-Utilizing Marine Bacteria and Their Phenol Degradation Pathway. Int J Genet Genomics. 2015;3(2):20-25. doi: 10.11648/j.ijgg.20150302.11

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  • @article{10.11648/j.ijgg.20150302.11,
      author = {Hiroaki Iwaki and Kengo Takada and Yoshie Hasegawa},
      title = {Isolation and Genetic Characterization of Phenol-Utilizing Marine Bacteria and Their Phenol Degradation Pathway},
      journal = {International Journal of Genetics and Genomics},
      volume = {3},
      number = {2},
      pages = {20-25},
      doi = {10.11648/j.ijgg.20150302.11},
      url = {https://doi.org/10.11648/j.ijgg.20150302.11},
      eprint = {https://download.sciencepg.com/pdf/10.11648.j.ijgg.20150302.11},
      abstract = {Phenolic compounds are widely distributed toxic pollutants in seawater, and their effective degradation is very important for bioremediation programs. In this study, nine phenol-degrading bacteria were isolated from seawater samples, which were collected from the coastal areas of Japan. Besides the enrichment substrate phenol, all isolates could utilize at least one isomer of cresol as the sole source of carbon. A 16S rRNA gene sequence analysis indicated that all strains were affiliated with the class Gammaproteobacteria, four strains were closely related to Spongiibacter, four were closely related to Marinobacter, and one was closely related to Photobacterium. During growth on phenol, all isolates produced a yellow product, and a whole-cell study indicated that it was an extradiol meta-ring cleavage product of catechol, 2-hydroxymuconate semialdehyde. Phylogenetic analysis revealed that the partial gene encoding the largest subunit of the multicomponent phenol hydroxylase of the isolates was similar to that of terrestrial bacteria, thereby suggesting that phenol is converted into catechol by marine bacteria. We also suggest that horizontal transfer of the gene may occur not only among marine bacteria but also between the genera Marinobacter and Pseudomonas.},
     year = {2015}
    }
    

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  • TY  - JOUR
    T1  - Isolation and Genetic Characterization of Phenol-Utilizing Marine Bacteria and Their Phenol Degradation Pathway
    AU  - Hiroaki Iwaki
    AU  - Kengo Takada
    AU  - Yoshie Hasegawa
    Y1  - 2015/02/27
    PY  - 2015
    N1  - https://doi.org/10.11648/j.ijgg.20150302.11
    DO  - 10.11648/j.ijgg.20150302.11
    T2  - International Journal of Genetics and Genomics
    JF  - International Journal of Genetics and Genomics
    JO  - International Journal of Genetics and Genomics
    SP  - 20
    EP  - 25
    PB  - Science Publishing Group
    SN  - 2376-7359
    UR  - https://doi.org/10.11648/j.ijgg.20150302.11
    AB  - Phenolic compounds are widely distributed toxic pollutants in seawater, and their effective degradation is very important for bioremediation programs. In this study, nine phenol-degrading bacteria were isolated from seawater samples, which were collected from the coastal areas of Japan. Besides the enrichment substrate phenol, all isolates could utilize at least one isomer of cresol as the sole source of carbon. A 16S rRNA gene sequence analysis indicated that all strains were affiliated with the class Gammaproteobacteria, four strains were closely related to Spongiibacter, four were closely related to Marinobacter, and one was closely related to Photobacterium. During growth on phenol, all isolates produced a yellow product, and a whole-cell study indicated that it was an extradiol meta-ring cleavage product of catechol, 2-hydroxymuconate semialdehyde. Phylogenetic analysis revealed that the partial gene encoding the largest subunit of the multicomponent phenol hydroxylase of the isolates was similar to that of terrestrial bacteria, thereby suggesting that phenol is converted into catechol by marine bacteria. We also suggest that horizontal transfer of the gene may occur not only among marine bacteria but also between the genera Marinobacter and Pseudomonas.
    VL  - 3
    IS  - 2
    ER  - 

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