Skip to main content
Log in

Naphthalene-utilizing and mercury-resistant bacteria isolated from an acidic environment

  • Original Paper
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript


Soil samples were taken from areas of low pH (2.5–3.5) surrounding an outdoor coal storage pile. These samples were added to medium with naphthalene as the sole carbon source to enrich for organisms capable of degrading polycyclic aromatic hydrocarbons (PAH) at low pH. Five such bacterial strains were isolated. Sequencing of the 16S rDNA showed them to be members of the genera Clavibacter, Arthrobacter and Acidocella. These organisms were all capable of growth with naphthalene as a sole carbon source at low pH. The genes nahAc, nahAd, phnAc, nahH, xylE or GST, which are known to be associated with PAH degradation were not detected. Isolate 10, the Acidocella strain, tolerated high levels of mercury. PCR amplification and sequencing of genes from the mer operon from isolate 10 DNA suggested that mercury is transported into the bacterial cell and subsequently detoxified since the enzymes encoded by genes in this operon are involved in these processes.

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


  • Bacelar-Nicolau P, Johnson DB (1999) Leaching of pyrite by acidophilic heterotrophic iron-oxidizing bacteria in pure and mixed cultures. Appl Environ Microbiol 65:585–590

    CAS  PubMed  Google Scholar 

  • Banerjee PC, Ray MK, Koch C, Bhattacharyya S, Shivaji S, Stackebrandt E (1996) Molecular characterization of two acidophilic heterotrophic bacteria isolated from a copper mine of India. Syst Appl Microbiol 19:78–82

    CAS  Google Scholar 

  • Cerniglia CE (1984) Microbial metabolism of polycyclic aromatic hydrocarbons. In: Laskin A (ed) Advances in applied microbiology, vol 30. Academic Press, New York, pp 31–71

  • Curran KJ, Irvine KN, Droppo IG, Murphy TP (2000) Suspended solids, trace metal and PAH concentrations and loadings from coal pile runoff to Hamilton Harbour, Ontario. J Great Lakes Res 26:18–30

    CAS  Google Scholar 

  • De-Silóniz MI, Lorenzo P, Murua M, Perera J (1993) Characterization of a new metal-mobilizing Thiobacillus isolate. Arch Microbiol 159:237–243

    Google Scholar 

  • Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16Sribosomal RNA. Nucleic Acids Res 17:7843–7851

    CAS  PubMed  Google Scholar 

  • Ghosh S, Mahapatra NR, Banerjee PC (1997) Metal resistance in Acidocella strains and plasmid-mediated transfer of this characteristic to Acidiphilium multivorum and Escherichia coli. Appl Environ Microbiol 63:4523–4527

    CAS  PubMed  Google Scholar 

  • Grosser R, Warshawsky D, Vestal J (1995) Mineralization of polycyclic and n-heterocyclic aromatic compounds in hydrocarbon-contaminated soils. Environ Toxicol Chem 14:375–382

    CAS  Google Scholar 

  • Hobman JL, Wilson JR, Brown NL (2000) Microbial mercury reduction. In: Lovley DR (ed) Environmental microbe-metal interactions. ASM Press, Washington, D.C., pp 177–197

  • Ibeanusi VM, Wilde EW (1998) Bioremediation of coal pile run off waters using an integrated microbial ecosystem. Biotechnol Lett 20:1077–1079

    Article  CAS  Google Scholar 

  • Insam H, Hutchinson TC, Reber HH (1996) Effects of heavy metal stress of the metabolic quotient of the soil microflora. Soil Biol Biochem 28:691–694

    Article  CAS  Google Scholar 

  • Johnson DB, Rolfe S, Hallberg KB, Iversen E (2001) Isolation and phylogenetic characterization of acidophilic microorganisms indigenous to acidic drainage waters at an abandoned Norwegian copper mine. Environ Microbiol 3:630–637

    CAS  PubMed  Google Scholar 

  • Keane A, Phoenix P, Ghoshal S, Lau PCK (2002) Exposing culprit organic pollutants: a review. J Microbiol Methods 49:103–119

    Article  CAS  PubMed  Google Scholar 

  • Kishimoto N, Kosako Y, Wakao N, Tano T, Hiraishi A (1995) Transfer of Acidiphilium facilis and Acidiphilium animolytica to the genus Acidocella gen. nov., and emendation of the genus Acidiphilium system. Appl Microbiol 18:85–91

    Google Scholar 

  • Kiyohara H, Torigoe S, Kaida N, Asaki T, Iida T, Hayashi H, Takizawa N (1994) Cloning and characterization of a chromosomal gene cluster, pah that encodes the upper pathway for phenanthrene and naphthalene utilization by Pseudomonas putida OUS82. J Bacteriol 176:2439–2443

    CAS  PubMed  Google Scholar 

  • Laurie AD, Lloyd-Jones G (1999) The phn genes of Burkholderia sp. Strain RP007 constitute a divergent gene cluster for polycyclic aromatic hydrocarbon catabolism. J Bacteriol 181:531–540

    CAS  PubMed  Google Scholar 

  • Laurie AD, Lloyd-Jones G (2000) Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl Environ Microbiol 66:1814–1817

    Article  CAS  PubMed  Google Scholar 

  • Lloyd-Jones G, Lau PCK (1997) Glutathione S-transferase-encoding gene as a potential probe for environmental bacterial isolates capable of degrading polycyclic aromatic hydrocarbons. Appl Environ Microbiol 63:3286–3290

    CAS  PubMed  Google Scholar 

  • Mahapatra NR, Banerjee PC (1996) Extreme tolerance to cadmium and high resistance to copper, nickel and zinc in different Acidiphilium strains. Lett Appl Microbiol 23:393–397

    CAS  Google Scholar 

  • Mason JR, Halder I, Henkler C, Fenwick C (1998) Assessment of biodegradative potential and activity in contaminated sites: molecular approaches to environmental monitoring. Biochem Soc Trans 26:694–697

    CAS  PubMed  Google Scholar 

  • Misra TK, Brown NL, Fritzinger DC, Pridmore RD, Barnes WM, Haberstroh L, Silver S (1984) Mercuric ion-resistance operons of plasmid R100 and transposon Tn501: the beginning of the operon including the regulatory region and the first two structural genes. Proc Natl Acad Sci USA 81:5975–5979

    CAS  PubMed  Google Scholar 

  • Muyzer G, De Waal ED, 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  Google Scholar 

  • Reniero D, Mozzon E, Galli E, Barbieri P (1998) Two aberrant mercury resistance transposons in the Pseudomonas stutzeri plasmid pPB Gene 208:37–42

    Article  CAS  Google Scholar 

  • Stapleton RD, Savage DC, Sayler GS, Stacey G (1998) Biodegradation of aromatic hydrocarbons in an extremely acidic environment. Appl Environ Microbiol 64:4180–4184

    CAS  PubMed  Google Scholar 

  • Swofford D (1993) PAUP (phylogenetic analysis using parsimony), version 4.0 beta. Laboratory of Molecular Systematics, Smithsonian Institution, Washington, D.C.

  • Takizawa N, Naofumi K, Torigoe S, Moritani T, Sawada T, Satoh S, Kiyohara H (1994) Identification and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase and polycyclic aromatic hydrocarbon dihydrodiol dehydrogenase in Pseudomonas putida OUS82. J Bacteriol 176:2444–2449

    CAS  PubMed  Google Scholar 

  • Thirukkumaran CM, Morrison I (1996) Impact of simulated acid rain on microbial respiration, biomass and metabolic quotient in a mature sugar maple Acer saccharum forest floor. Can J For Res 26:1446–1453

    CAS  Google Scholar 

  • Trajanovska S, Britz ML, Bhave M (1997) Detection of heavy metal ion resistance genes in Gram-positive and Gram-negative bacteria isolated from a lead-contaminated site. Biodegradation 8:113–124

    Article  CAS  PubMed  Google Scholar 

  • Wang R-F, Luneau A, Cao W-W, Cerniglia C (1996) PCR detection of polycyclic aromatic hydrocarbon-degrading mycobacteria. Environ Sci Technol 30:307–311

    Article  Google Scholar 

  • Wild SR, Obbard JP, Munn CI, Berrow ML, Jones KC (1991) The long-term persistence of polynuclear aromatic hydrocarbons (PAHs) in an agricultural soil amended with metal-contaminated sewage sludges. Sci Total Environ 101:235–253

    CAS  Google Scholar 

  • You I-S, Ghosal D, Gunsalus IC (1988) Nucleotide sequence of plasmid NAH7 gene nahR and DNA binding of the nahR product. J Bacteriol 170:5409–5415

    CAS  PubMed  Google Scholar 

  • Zelmanowitz S, WC Boyle, Member ASCE, Armstrong DE, Park JK (1995) Ability of subsoils to buffer extremely acidic simulated coal-pile leachates. J Environ Eng 121:816–823

    Article  CAS  Google Scholar 

Download references


We acknowledge the help and advice of Drs. Andrew Laursen, Peter Blair, Mark Schneegurt, Uwe Stolz and Jason Wilder in performing this study and Dennis Birdsell and Rian Grant for technical support with the ICP-OES. Financial support was provided by the Department of Biological Sciences, University of Notre Dame, the Bayer Predoctoral Fellowship and Chevron Research and Technology Corporation. These experiments comply with current laws of the United States of America.

Author information

Authors and Affiliations


Corresponding author

Correspondence to C. F. Kulpa Jr.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dore, S.Y., Clancy, Q.E., Rylee, S.M. et al. Naphthalene-utilizing and mercury-resistant bacteria isolated from an acidic environment. Appl Microbiol Biotechnol 63, 194–199 (2003).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: