Skip to main content
Log in

Isolation of a Xanthobacter sp. degrading dichloromethane and characterization of the gene involved in the degradation

  • Original Paper
  • Published:
Biodegradation Aims and scope Submit manuscript

Abstract

A bacterial strain able to degrade dichloromethane (DCM) as the sole carbon source was isolated from a wastewater treatment plant receiving domestic and pharmaceutical effluent. 16S rDNA studies revealed the strain to be a Xanthobacter sp. (strain TM1). The new isolated strain when grown aerobically on DCM showed Luong type growth kinetics, with μmax of 0.094 h−1 and S m of 1,435 mg l−1. Strain TM1 was able to degrade other aromatic and aliphatic halogenated compounds, such as halobenzoates, 2-chloroethanol and dichloroethane. The gene for DCM dehalogenase, which is the key enzyme in DCM degradation, was amplified through PCR reactions. Strain TM1 contains type A DCM dehalogenase (dcmAa), while no product could be obtained for type B dehalogense (dcmAb). The sequence was compared against 12 dcmAa from other DCM degrading strains and 98% or 99% similarity was observed with all other previously isolated DCM dehalogenase genes. This is the first time a Xanthobacter sp. is reported to degrade DCM.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Ames R, Brown J, Wand Y (2000) Public health goals form dichloromethane in drinking water. Office of Environmental Health Hazard Assessment, California Environmental Protection Agency—Pesticide and Environmental Toxicology Section

  • Andrews JF (1968) A mathematical model for the continuous culture of microorganisms utilizing inhibitory substrates. Biotechnol Bioeng 10:707–723. doi:10.1002/bit.260100602

    Article  CAS  Google Scholar 

  • Bader R, Leisinger T (1994) Isolation and characterization of the Methylophilus sp. strain DM11 gene encoding dichloromethane dehalogenase/glutathione S-transferase. J Bacteriol 176:3466–3473

    PubMed  CAS  Google Scholar 

  • Carvalho MF, Alves CC, Ferreira MI, De Marco P, Castro PML (2002) Isolation and initial characterization of bacterial consortia able to mineralize fluorobenzene. Appl Environ Microbiol 68:102–105. doi:10.1128/AEM.68.1.102-105.2002

    Article  PubMed  CAS  Google Scholar 

  • Carvalho MF, Ferreira Jorge R, Pacheco CC, De Marco P, Castro PM (2005) Isolation and properties of a pure bacterial strain capable of fluorobenzene degradation as sole carbon and energy source. Environ Microbiol 7:294–298

    Article  PubMed  CAS  Google Scholar 

  • DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM et al (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34:W394–W399. doi:10.1093/nar/gkl244

    Article  PubMed  CAS  Google Scholar 

  • De Souza M, Seffernick J, Martinez B, Sadowsky MJ, Wackett LP (1998) The atrazine catabolism genes atzABC are widespread and highly conserved. J Bacteriol 180:1951–1954

    PubMed  Google Scholar 

  • Doronina NV, Braus-Stromeyer SA, Leisinger T, Trotsenko YA (1995) Isolation and characterization of a new facultative methylothrophic bacterium: description of Methylorhabdus multivorans gen. nov., sp. nov. Syst Appl Microbiol 18:92–98

    CAS  Google Scholar 

  • Edwards VH (1970) The influence of high substrate concentration on microbial kinetics. Biotechnol Bioeng 12:679–712. doi:10.1002/bit.260120504

    Article  PubMed  CAS  Google Scholar 

  • Evens GJ, Ferguson GP, Booth IR, Vuilleumier S (2000) Growth inhibition of Escherichia coli by dichloromethane dehalogense/glutathione S-transferase. Microbiology 146:2967–2975

    Google Scholar 

  • Ferreira Jorge RM, Livingston AG (1999) Novel method for characterisation of microbial growth kinetics on volatile organic compounds. Appl Microbiol Biotechnol 52:174–178. doi:10.1007/s002530051505

    Article  Google Scholar 

  • Freitas dos Santos LM, Livingston AG (1993) A novel bioreactor system for the destruction of volatile organic compounds. Appl Microbiol Biotechnol 40:151–157. doi:10.1007/BF00170444

    Article  CAS  Google Scholar 

  • Gälli D, Leisinger T (1985) Specialized bacterial strains for the removal of dichloromethane from industrial waste. Conserv Recycl 8:91–100. doi:10.1016/0361-3658(85)90028-1

    Article  Google Scholar 

  • Gisi D, Willi L, Traber H, Leisinger T, Vuilleumier S (1998) Effects of bacterial host and dichloromethane dehalogenase on the competitiveness of methyltrophic bacteria growing with dichloromethane. Appl Environ Microbiol 64:1194–1202

    PubMed  CAS  Google Scholar 

  • Hirano S, Kitauchi F, Haruki M, Imanaka T, Morikawa M, Kanaya S (2004) Isolation and characterization of Xanthobacter polyaromaticivorans sp. no. 127W that degrades polycyclic and heterocyclic aromatic compounds under extremely low oxygen conditions. Biosci Biotechnol Biochem 68:557–564. doi:10.1271/bbb.68.557

    Article  PubMed  CAS  Google Scholar 

  • Howard PH (1990) Handbook of environmental fate of exposure data for organic chemicals, vol 2. Lewis Publishers Inc, Chelsea, MI, pp 176–183

    Google Scholar 

  • Iwasaki I, Utsumi S, Hagino K, Ozawa T (1956) A new spectrophotometric method for the determination of small amounts of chloride using the mercury thiocyanate method. J Chem Soc Jpn 29:860–864. doi:10.1246/bcsj.29.860

    Article  CAS  Google Scholar 

  • Janssen DB, Scheper A, Dijkenhizen L, Witholt B (1985) Degradation of halogenated aliphatic compounds by Xanthobacter autotrophicus GJ10. Appl Environ Microbiol 49:673–677

    PubMed  CAS  Google Scholar 

  • Janssen DB, van den Wijngaard AJ, van der Waarde JJ, Oldenhuis R (1991) Biochemistry and kinetics of aerobic degradation of chlorinated aliphatic hydrocarbons. In: Hinchee RE, Olfenbuttel RF (eds) On-site bioreclamation. Butterworth-Heinmann, Boston, pp 92–112

    Google Scholar 

  • Janssen DB, Dinkla IJ, Poelarends GJ, Terpstra P (2005) Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities. Environ Microbiol 7:1868–1882. doi:10.1111/j.1462-2920.2005.00966.x

    Article  PubMed  CAS  Google Scholar 

  • Kohler-Staub D, Leisinger T (1985) Dichloromethane dehalogenase of Hyphomicrobium sp. strain DM2. J Bacteriol 162:676–678

    PubMed  CAS  Google Scholar 

  • Krausova VI, Robb FT, González JM (2006) Biodegradation of dichloromethane in an estuarine environment. Hydrobiologia 559:77–83. doi:10.1007/s10750-004-0571-5

    Article  CAS  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  • La Roche SD, Leisinger T (1990) Sequence analysis and expression of the bacterial dichloromethane dehalogenase structural gene, a member of the glutathione S-transferase supergene family. J Bacteriol 172:164–171

    PubMed  CAS  Google Scholar 

  • Line DE, Wu J, Arnold JA, Jennings GD, Rubin AR (1997) Water quality of first flush runoff from 20 industrial sites. Water Environ Res 69:305–310. doi:10.2175/106143097X125489

    Article  CAS  Google Scholar 

  • Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar , Buchner A, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüßmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis AP, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer K-H (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371. doi:10.1093/nar/gkh293

    Article  PubMed  CAS  Google Scholar 

  • Luong JHT (1987) Generalization of Monod kinetics for analysis of growth data with substrate inhibition. Biotechnol Bioeng 29:242–248. doi:10.1002/bit.260290215

    Article  PubMed  CAS  Google Scholar 

  • Mägli A, Wendt M, Leisinger T (1996) Isolation and characterization of Dehalobacterium formicoaceticum gen nov. sp. no., a strictly anaerobic bacterium utilizing dichloromethane as source of carbon and energy. Arch Microbiol 166:101–108. doi:10.1007/s002030050362

    Article  Google Scholar 

  • Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3:371–394. doi:10.1146/annurev.mi.03.100149.002103

    Article  CAS  Google Scholar 

  • Nikolausz M, Kappelmeyer U, Nijenhuis I, Ziller K, Kästner M (2005) Molecular characterization of dichloromethane-degrading Hyphomicrobium strain using rDNA and DCM dehalogenase gene sequences. Syst Appl Microbiol 28:582–587. doi:10.1016/j.syapm.2005.03.011

    Article  PubMed  CAS  Google Scholar 

  • Ottengraf SPP, Meesters JJP, van den Oever AHC, Rozema HR (1986) Biological elimination of volatile xenobiotic compounds in biofilters. Bioprocess Eng 1:61–69. doi:10.1007/BF00387497

    Article  Google Scholar 

  • Padden AN, Rainey FA, Kelly DP, Wood AP (1997) Xanthobacter tagetidis sp. nov., an organism associated with Tagetes species and able to grow on substituted thiophenes. Int J Syst Bacteriol 47:394–401

    Article  PubMed  CAS  Google Scholar 

  • Poelarends GJ, Kulakov LA, Larkin MJ, Vlieg JET, Jansson DB (2000) Roles of horizontal gene transfer and gene integration in evolution of 1,3-dichloropropene- and 1,2-dibromoethane-degradative pathways. J Bacteriol 182:2191–2199. doi:10.1128/JB.182.8.2191-2199.2000

    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 

  • Schmid-Appert M, Zoller K, Traber H, Vuilleumier S, Leisinger T (1997) Association of newly discovered IS elements with the dichloromethane utilization genes of methylotrophic bacteria. Microbiology 143:2557–2567

    Article  PubMed  CAS  Google Scholar 

  • Scholtz R, Wackett LP, Egli C, Cook AM, Leisinger T (1988) Dichloromethane dehalogenase with improved catalytic activity isolated from a fast growing dichloromethane-utilizing bacterium. J Bacteriol 170:5698–5704

    PubMed  CAS  Google Scholar 

  • Song J-S, Lee D-H, Lee K, Kim CK (2004) Genetic organization of the dhlA gene encoding 1,2-dichloroethane dechlorinase from Xanthobacter flavus UE15. J Microbiol 42:188–193

    PubMed  CAS  Google Scholar 

  • Spiess E, Sommer C, Görisch H (1995) Degradation of 1,4-dichlorobenzene by Xanthobacter flavus 14p1. Appl Environ Microbiol 61:3884–3888

    PubMed  CAS  Google Scholar 

  • Stubner S, Wind T, Conrad R (1998) Sulfur oxidation in rice field soil: activity, enumeration, isolation and characterization of thiosulphate-oxidizing bacteria. Syst Appl Microbiol 21:569–578

    PubMed  CAS  Google Scholar 

  • Stucki G, Gälli R, Ebersold HR, Leisinger T (1981) Dehalogenation of dichloromethane by cell extracts of Hyphomicrobium DM2. Arch Microbiol 130:366–371. doi:10.1007/BF00414602

    Article  CAS  Google Scholar 

  • Torz M, Wietzes P, Beschkov V, Janssen DB (2007) Metabolism of mono-and dihalogenated C1 and C2 compounds by Xanthobacter autotrophicus growing on 1,2-dichloroethane. Biodegradation 18:145–157. doi:10.1007/s10532-006-9050-1

    Article  PubMed  CAS  Google Scholar 

  • Trotsenko YA, Doronina NV (2003) The biology of methylobacteria capable of degrading halomethanes. Microbiology 72:121–131. doi:10.1023/A:1023218326407

    Article  CAS  Google Scholar 

  • van den Wijngaard AJ, van den Kamp KWHJ, van der Ploeg J, Pries F, Kazemier B, Janssen DB (1992) Degradation of 1,2-dichloroethane by Ancylobacter aquaticus and other facultative methylotrophs. Appl Environ Microbiol 58:976–983

    PubMed  Google Scholar 

  • Vuilleumier S, Leisinger T (1996) Protein engineering studies of dichloromethane dehalogenase/glutathione S-transferase from Methylophilus sp. strain DM11. Ser12 but not Tyr6 is required for enzyme activity. Eur J Biochem 239:410–417. doi:10.1111/j.1432-1033.1996.0410u.x

    Article  PubMed  CAS  Google Scholar 

  • Vuilleumier S, Ivoš N, Dean M, Leisinger T (2001) Sequence variation in dichloromethane dehalogenase/glutathione S-transferases. Microbiology 147:611–619

    PubMed  CAS  Google Scholar 

  • Wayman M, Tseng MC (1976) Inhibition threshold substrate concentrations. Biotechnol Bioeng 18:383–387. doi:10.1002/bit.260180308

    Article  CAS  Google Scholar 

  • Woldringh CL (1973) Effects of toluene and phenethyl alcohol on the ultrastructure of Escherichia coli. J Bacteriol 114:1359–1361

    PubMed  CAS  Google Scholar 

  • Zhou N-Y, Jenkins A, Chan Kwo Chion CKN, Leak DJ (1999) The alkene monooxygenase from Xanthobacter strain Py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. Appl Environ Microbiol 65:1589–1595

    PubMed  CAS  Google Scholar 

  • Zuber L, Dunn IJ, Deshusses MA (1997) Comparative scale-up and cost estimation of a biological trickling filter and a three-phase airlift bioreactor for the removal of methylene chloride from polluted air. J Air Waste Manag Assoc 47:969–975

    CAS  Google Scholar 

Download references

Acknowledgements

This work was supported in part by the European Community’s Human Potential Programme under contract HP-RTH-CT-2002-00213 (BIOSAP). R. Ferreira Jorge would like to thank financial support from Fundação para a Ciência e Tecnologia (SFRH/BPD/18716/2004).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Paula M. L. Castro.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Emanuelsson, M.A.E., Osuna, M.B., Ferreira Jorge, R.M. et al. Isolation of a Xanthobacter sp. degrading dichloromethane and characterization of the gene involved in the degradation. Biodegradation 20, 235–244 (2009). https://doi.org/10.1007/s10532-008-9216-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10532-008-9216-0

Keywords

Navigation