Skip to main content
SpringerLink
Log in

Identification and characterization of o-xylene-degrading Rhodococcus spp. which were dominant species in the remediation of o-xylene-contaminated soils

  • Published:
Biodegradation Aims and scope Submit manuscript

Abstract

Soils contaminated with o-xylene were more difficult to bioremediate than those contaminated with other BTEX hydrocarbons (benzene, toluene, ethylbenzene, m-xylene and p-xylene). In order to identify microorganisms responsible for o-xylene degradation in soil, microbial community structure analyses were carried out with two soil samples in the presence of o-xylene and mineral nutrients. In two different soil samples, Rhodococcus opacus became abundant. We were also able to isolate o-xylene degrading Rhodococcus species from these soil samples. A primer set was developed to specifically detect a cluster of this Rhodococcus group including isolated Rhodococcus strains, Rhodococcus opacus and Rhodococcus koreensis. The growth of this bacterial group in an o-xylene-contaminated soil was followed by competitive PCR (cPCR). The decrease in o-xylene clearly paralleled the growth of the Rhodococcus group.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool J. Mol. Biol. 215: 403–410

    Article  PubMed  CAS  Google Scholar 

  • Baggi G, Barbieri P, Galli E, Tollari S, (1987) Isolation of a Pseudomonas stutzeri strain that degrades o-xylene Appl. Environ. Microbiol. 53: 2129–2132

    PubMed  CAS  Google Scholar 

  • Bickerdike SR, Holt RA, Stephens GM, (1997) Evidence for metabolism of o-xylene by simultaneous ring and methyl group oxidation in a new soil isolate Microbiology 143: 2321–2329

    Article  CAS  Google Scholar 

  • Cavalca L, Di Gennaro P, Colombo M, Andreoni V, Bernasconi S, Ronco I, Bestetti G, (2000) Distribution of catabolic pathways in some hydrocarbon-degrading bacteria from a subsurface polluted soil Res. Microbiol. 151: 877–887

    Article  PubMed  CAS  Google Scholar 

  • Di Gennaro P, Rescalli E, Galli E, Sello G, Bestetti G, (2001) Characterization of Rhodococcus opacus R7, a strain able to degrade naphthalene and o-xylene isolated from a polycyclic aromatic hydrocarbon-contaminated soil Res. Microbiol. 152: 641–651

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J, (1985) Confidence limits on phylogenies: an approach using the bootstrap Evolution 39: 783–791

    Article  Google Scholar 

  • Galli E, Barbieri P, Bestetti G, (1992) Potential of pseudomonads in the degradation of methylbenzenes In Galli E, Silver S, Witholt B, (eds). Pseudomonas: Molecular Biology and Biotechnology American Society for Microbiology Washington, DC pp. 268–276

    Google Scholar 

  • Gibson DT, Subramanian V, (1984) Microbial degradation of aromatic hydrocarbons In Gibson D.T., (ed). Microbial Degradation of Organic Compounds Marcel Dekker New York, NY pp. 181–252

    Google Scholar 

  • Hanson JR, Macalady JL, Harris D, Scow KM, (1999) Linking toluene degradation with specific microbial populations in soil Appl. Environ. Microbiol. 65: 5403–5408

    PubMed  CAS  Google Scholar 

  • Harayama S, Kok M, Neidle EL, (1992) Functional and evolutionary relationships among diverse oxygenases Annu. Rev. Microbiol. 46: 565–601

    Article  PubMed  CAS  Google Scholar 

  • Kasai H, Watanabe K, Gasteiger E, Bairoch A, Isono K, Yamamoto S, Harayama S, (1998) Construction of the gyrB Database for the Identification and Classification of Bacteria Genome Inform. Ser. Workshop Genome Inform. 9: 13–21

    PubMed  CAS  Google Scholar 

  • Kasai Y, Kishira H, Harayama S, (2002a) Bacteria belonging to the genus cycloclasticus play a primary role in the degradation of aromatic hydrocarbons released in a marine environment Appl. Environ. Microbiol. 68: 5625–5633

    Article  CAS  Google Scholar 

  • Kasai Y, Kishira H, Sasaki T, Syutsubo K, Watanabe K, Harayama S, (2002b) Predominant growth of Alcanivorax strains in oil-contaminated and nutrient-supplemented sea water Environ. Microbiol. 4: 141–147

    Article  CAS  Google Scholar 

  • Kim D, Kim YS, Kim SK, Kim SW, Zylstra GJ, Kim YM, Kim E, (2002) Monocyclic aromatic hydrocarbon degradation by Rhodococcus sp strain DK17. Appl. Environ. Microbiol. 68: 3270–3278

    Article  CAS  Google Scholar 

  • Kim D, Chae JC, Zylstra GJ, Kim YS, Kim SK, Nam MH, Kim YM, Kim E., (2004) Identification of a novel dioxygenase involved in metabolism of o-xylene, toluene, and ethylbenzene by Rhodococcus sp strain DKI7. Appl. Environ. Microbiol. 70: 7086–7092

    Article  PubMed  CAS  Google Scholar 

  • Kimura M, (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences J. Mol. Evol. 16: 111–120

    Article  PubMed  CAS  Google Scholar 

  • Klatte S, Kroppenstedt RM, Rainey F, (1994) Rhodococcus opacus sp. nov., An unusual nutritionally versatile Rhodococcus-species Syst. Appl. Microbiol. 17: 355–360

    Google Scholar 

  • Maruyama T, Ishikura M, Taki H, Shindo K, Kasai H, Haga M et al. (2005) Isolation and characterization of o-xylene oxygenase genes from Rhodococcus opacus TKN14. Appl. Environ. Microbiol. in press

  • Mattison RG, Taki H, Harayama S, (2005) The soil flagellate Heteromita globosa accelerates bacterial degradation of alkylbenzenes through grazing and acetate excretion in batch culture Microb. Ecol. 49: 142–150

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, de Waal EC, Uitterlinden AG, (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA Appl. Environ. Microbiol. 59: 695–700

    PubMed  CAS  Google Scholar 

  • Nicholson CA, Fathepure BZ, (2004) Biodegradation of benzene by halophilic and halotolerant bacteria under aerobic conditions Appl. Environ. Microbiol. 70: 1222–1225

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4: 406–425

    PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T, (1989) Molecular Cloning: A Laboratory Manual 2nd ed. Cold Spring Harbor Laboratory Cold Spring Harbor, N.Y

    Google Scholar 

  • Schraa G, Bethe BM, van Neerven AR, Van den Tweel WJ, Van der Wende E, Zehnder AJ, (1987) Degradation 1,2-dimethylbenzene by Corynebacterium strain C125 Antonie Van Leeuwenhoek 53: 159–170

    Article  PubMed  CAS  Google Scholar 

  • Solano-Serena F, Marchal R, Casaregola S, Vasnier C, Lebeault JM, Vandecasteele JP, (2000) A Mycobacterium strain with extended capacities for degradation of gasoline hydrocarbons Appl. Environ. Microbiol. 66: 2392–2399

    Article  PubMed  CAS  Google Scholar 

  • Syutsubo K, Kishira H, Harayama S, (2001) Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains Environ. Microbiol. 3: 371–379

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ, (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22: 4673–4680

    PubMed  CAS  Google Scholar 

  • U.S.EPA (1997) Cleaning up the nation’s waste sites: markets and technology trends, 1996 edition. EPA 542-R-96-005. EPA, Office of Solid Waste and Emergency Response, Washington, D.C

  • van der Meer JR, Bosma TNP, de Bruin WP, Harms H, Holliger C, Rijnaarts HHM, Tros ME, Schraa G, Zehnder JB, (1992) Versatility of soil column experiments to study biodegradation of halogenated compounds under environmental conditions Biodegradation 3: 265–284

    Article  Google Scholar 

  • Vardar G, Wood TK, (2004) Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for synthesizing 4-methylresorcinol, methylhydroquinone, and pyrogallol Appl. Environ. Microbiol. 70: 3253–3262

    Article  PubMed  CAS  Google Scholar 

  • Vogel TM, (1996) Bioaugmentation as a soil bioremediation approach Curr. Opin. Biotechnol. 7: 311–316

    Article  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Williams PA, Sayers JR, (1994) The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas Biodegradation 5: 195–217

    Article  PubMed  CAS  Google Scholar 

  • Yamamoto S, Harayama S, (1995) PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains Appl. Environ. Microbiol. 61: 1104–1109

    PubMed  CAS  Google Scholar 

  • Yamamoto S, Harayama S, (1996) Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products Int. J. Syst. Bacteriol. 46: 506–511

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We are grateful to Yukie Inomata and Reiko Hirano for their technical assistance. We are also grateful to Asaka Matsuura for her advice about DNA extraction methods. This work was supported by the New Energy and Industrial Technology Development Organization (NEDO).

Author information

Authors and Affiliations

  1. Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, Iwate, 026-0001, Japan

    Hironori Taki, Kazuaki Syutsubo, Richard G. Mattison & Shigeaki Harayama

  2. Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama, Kanagawa, 245-0051, Japan

    Hironori Taki

  3. Water and Soil Environment Division, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan

    Kazuaki Syutsubo

  4. Department of Biotechnology, National Institute of Technology and Evaluation, 2-5-8 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan

    Shigeaki Harayama

Authors
  1. Hironori Taki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kazuaki Syutsubo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Richard G. Mattison
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shigeaki Harayama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hironori Taki.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Taki, H., Syutsubo, K., Mattison, R.G. et al. Identification and characterization of o-xylene-degrading Rhodococcus spp. which were dominant species in the remediation of o-xylene-contaminated soils. Biodegradation 18, 17–26 (2007). https://doi.org/10.1007/s10532-005-9030-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10532-005-9030-x

Keywords

Search

Navigation