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Monitoring nutrient impact on bacterial community composition during bioremediation of anoxic PAH-contaminated sediment

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Abstract

Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.

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References

  • Bach, Q.D., S.J. Kim, S.C. Choi, and Y.S. Oh. 2005. Enhancing the intrinsic bioremediation of PAH-contaminated anoxic estuarine sediments with biostimulating agents. J. Microbiol. 43, 319–324.

    PubMed  CAS  Google Scholar 

  • Biddle, J.F., J.S. Lipp, M.A. Lever, K.G. Lloyd, K.B. Sørensen, R. Andersonc, H.F. Fredricks, M. Elvert, T.J. Kelly, D.P. Schrag, M.L. Sogin, J.E. Brenchley, A. Teske, C.H. House, and K.U. Hinrichs. 2006. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci. USA 103, 3846–3851.

    Article  PubMed  CAS  Google Scholar 

  • Campbell, B.J. and S.C. Cary. 2001. Characterization of a novel Spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana. Appl. Environ. Microbiol. 67, 110–117.

    Article  PubMed  CAS  Google Scholar 

  • Chang, B.V., L.C. Shiung, and S.Y. Yuan. 2002. Anaerobic bio-degradation of polycyclic aromatic hydrocarbon in soil. Chemosphere 48, 717–724.

    Article  PubMed  CAS  Google Scholar 

  • Chang, W., Y. Um, B. Hoffman, and T.R.P. Holoman. 2005. Molecular characterization of polycyclic aromatic hydrocarbon (PAH)-degrading methanogenic communities. Biotechnol. Prog. 21, 682–688.

    Article  PubMed  CAS  Google Scholar 

  • Chang, W., Y. Um, and T.R.P. Holoman. 2006. Polycyclic aromatic hydrocarbon (PAH) degradation coupled to methanogenesis. Biotechnol. Lett. 28, 425–430.

    Article  PubMed  CAS  Google Scholar 

  • Coates, J.D., J. Woodward, J. Allen, P. Philp, and D.R. Lovley. 1997. Anaerobic degradation of polycyclic aromatic hydrocarbons and alkanes in petroleum-contaminated marine harbor sediments. Appl. Environ. Microbiol. 63, 3589–3593.

    PubMed  CAS  Google Scholar 

  • Connon, S.A., A. Tovanabootr, M. Dolan, K. Vergin, S.J. Giovan-noni, and L. Semprini. 2005. Bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. Environ. Microbiol. 7, 165–178.

    Article  PubMed  CAS  Google Scholar 

  • Cullen, D.W. and P.R. Hirsch. 1998. Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol. Biochem. 30, 983–993.

    Article  CAS  Google Scholar 

  • Cuypers, M.P., T.C. Grotenhius, and W.H. Rulkens. 1998. Characterization of PAH contaminated sediments in a remediation perspective. Water Sci. Technol. 37, 157–164.

    Article  CAS  Google Scholar 

  • Delong, E. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685–5689.

    Article  PubMed  CAS  Google Scholar 

  • Dojka, M.A., P. Hugenholtz, S.K. Haack, and N.R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64, 3869–3877.

    PubMed  CAS  Google Scholar 

  • Ellis, R.J., P. Morgan, A.J. Weightman, and J. Fry. 2003. Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal contaminated soil. Appl. Environ. Microbiol. 69, 3223–3230.

    Article  PubMed  CAS  Google Scholar 

  • Elshahed, M.S., F.Z. Najar, B.A. Roe, A. Oren, T.A. Dewers, and L.R. Krumholz. 2004. Survey of archaeal diversity reveals an abundance of halophilic archaea in a low-salt, sulfide-, and sulfur-rich spring. Appl. Environ. Microbiol. 70, 2230–2239.

    Article  PubMed  CAS  Google Scholar 

  • Ferrarese, E., G. Andreottola, and I.A. Oprea. 2008. Remediation of PAH-contaminated sediments by chemical oxidation. J. Hazard. Mater. 152, 128–139.

    Article  PubMed  CAS  Google Scholar 

  • Giovannoi, S.J. 1991. The polymerase chain reaction, p. 177–201. In E. Stackebrandt and M. Goodfellow (eds.), Nucleic acid techniques in bacterialsystematics. John Wiley & Sons, New York, N.Y., USA.

    Google Scholar 

  • Gray, J.P. and R.P. Herwig. 1996. Phylogenetic analysis of the bacterial communities in marine sediment. Appl. Environ. Microbiol. 62, 4049–4059.

    PubMed  CAS  Google Scholar 

  • Haapea, P. and T. Tuhkanen. 2006. Integrated treatment of PAH contaminated soil by soil washing, ozonation, and biological treatment. J. Hazard. Mater. 136, 244–250.

    Article  PubMed  CAS  Google Scholar 

  • Hayes, L.A., K.P. Nevin, and D.R. Lovley. 1999. Role of prior exposure on anaerobic degradation of naphthalene and phenanthrene in marine harbor sediments. Org. Geochem. 30, 937–945.

    Article  CAS  Google Scholar 

  • Henner, P., M. Schiavon, J.L. Morel, and E. Lichtfouse. 1997. Polycyclic aromatic hydrocarbon (PAH) occurrence and remediation methods. Anal. Mag. 25, 56–59.

    Google Scholar 

  • Higashi, Y., M. Sunamura, K. Kitamura, K.I. Nakamura, Y. Kurusu, J.I. Ishibashi, T. Urabe, and A. Maruyama. 2004. Microbial diversity in hydrothermal surface to subsurface environments of Suiyo Seamount, Izu-Bonin Arc, using a catheter-type in situ growth chamber. FEMS Microbiol. Ecol. 47, 327–336.

    Article  CAS  PubMed  Google Scholar 

  • Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M. Delwiche, F.S. Colwell, K.H. Nealson, K. Horikoshi, S. D’Hondt, and B.B. Jørgensen. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. USA 103, 2815–2820.

    Article  PubMed  CAS  Google Scholar 

  • Jukes, T.H. and C.R. Canter. 1969. Evolution of protein molecules, p. 21–132. In H.N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y., USA.

    Google Scholar 

  • Karthikeyan, R. and A. Bhandari. 2001. Anaerobic biotransformation of aromatic and polycyclic aromatic hydrocarbons in soil microcosms: a review. J. Hazard. Subst. Res. 3, 1–19.

    Google Scholar 

  • Kim, B., H.M. Oh, H.K. Kang, and J. Chun. 2005. Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. J. Microbiol. 43, 144–151.

    PubMed  CAS  Google Scholar 

  • Long, E.R., D.D. MacDonald, S.L. Smith, and F.D. Calder. 1995. Incidence of adverse biological effects within ranges of chemical concentrations in marine and estuary sediments. Environ. Manage. 19, 81–97.

    Article  Google Scholar 

  • Madigan, M.T., J.M. Martinko, and J. Parker. 2003. Biology of microorganisms, 10th ed., p. 453–455. Pearson Education, Inc., Upper Saddle River, NJ, USA.

    Google Scholar 

  • Mai, B.S., J.M. Fu, G.Y. Sheng, Y.H. Kang, Z. Lin, and G. Zhang. 2002. Chlorinated and polycyclic aromatic hydrocarbons in riverine and estuarine sediments from Pearl River Delta, China. Environ. Pollut. 117, 457–474.

    Article  PubMed  CAS  Google Scholar 

  • O’Mahony, M.M., A.D.W. Dobson, J.D. Barnes, and I. Singleton. 2006. The use of ozone in the remediation of polycyclic aromatic hydrocarbon contaminated soil. Chemosphere 63, 307–314.

    Article  PubMed  CAS  Google Scholar 

  • Parkes, R.J., G. Webster, B.A. Cragg, A.J. Weightman, C.J. New-berry, T.G. Ferdelman, J. Kallmeyer, B.B. Jørgensen, I.W. Aiello, and J.C. Fry. 2005. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436, 390–394.

    Article  PubMed  CAS  Google Scholar 

  • Reed, D.W., Y. Fujita, M.E. Delwiche, D.B. Blackwelder, P.P. Sheridan, T. Uchida, and F.S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68, 3759–3770.

    Article  PubMed  CAS  Google Scholar 

  • Rothermich, M.M., L.A. Hayes, and D.R. Lovley. 2002. Anaerobic, sulfate-dependent degradation of polycyclic aromatic hydrocarbons in petroleum-contaminated harbor sediment. Environ. Sci. Technol. 36, 4811–4817.

    Article  PubMed  CAS  Google Scholar 

  • Saul, D.J., J.M. Aislabie, C.E. Brown, L. Harris, and J.M. Foght. 2005. Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol. Ecol. 53, 141–155.

    Article  PubMed  CAS  Google Scholar 

  • Sekiguchi, Y., Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura. 1998. Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology 144, 2655–2665.

    Article  PubMed  CAS  Google Scholar 

  • Takai, K., T. Komatsu, F. Inagaki, and K. Horikoshi. 2001a. Distribution of archaea in a black smoker chimney structure. Appl. Environ. Microbiol. 67, 3618–3629.

    Article  PubMed  CAS  Google Scholar 

  • Takai, K., D.P. Moser, M. Deflaun, T.C. Onstott, and J.K. Fredrickson. 2001b. Archaeal diversity in waters from deep South African gold mines. Appl. Environ. Microbiol. 67, 5750–5760.

    Article  PubMed  CAS  Google Scholar 

  • Taylor, L.T. and D.M. Jones. 2001. Bioremediation of coal tar PAH in soils using biodiesel. Chemosphere 44, 1131–1136.

    Article  PubMed  CAS  Google Scholar 

  • Watanabe, K., Y. Kodama, N. Hamamura, and N. Kaku. 2002. Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Appl. Environ. Microbiol. 68, 3899–3907.

    Article  PubMed  CAS  Google Scholar 

  • Wild, S.R. and K.C. Jones. 1995. Polynuclear aromatic hydrocarbons in the United Kingdom Environment: a preliminary source inventory and budget. Environ. Pollut. 88, 91–108.

    Article  PubMed  CAS  Google Scholar 

  • Yuan, S.Y. and B.V. Chang. 2007. Anaerobic degradation of five polycyclic aromatic hydrocarbons from river sediment in Taiwan. J. Environ. Sci. Health B. 42, 63–69.

    PubMed  CAS  Google Scholar 

  • Zucchi, M., L. Angiolini, S. Borin, L. Brusetti, N. Dietrich, C. Gigliotti, P. Barbieri, and D. Daffonchio. 2003. Response of bacterial community during bioremediation of an oil-polluted soil. J. Appl. Microbiol. 94, 248–257.

    Article  PubMed  CAS  Google Scholar 

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Kim, M., Bae, S.S., Seol, M. et al. Monitoring nutrient impact on bacterial community composition during bioremediation of anoxic PAH-contaminated sediment. J Microbiol. 46, 615–623 (2008). https://doi.org/10.1007/s12275-008-0097-z

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