Abstract
The degradation of polycyclic aromatic compounds (PACs) has been widely studied. Knowledge of the degradation of PACs by microbial populations can be utilized in the remediation of contaminated sites. To isolate and identify PAC-degrading bacteria for potential use in future bioremediation programmes, we established a series of PAC enrichments under the same experimental conditions from a single sediment sample taken from a highly polluted estuarine site. Enrichment cultures were established using the pollutants: anthracene, phenanthrene and dibenzothiophene as a sole carbon source. The shift in microbial community structure on each of these carbon sources was monitored by analysis of a time series of samples from each culture using 16S rRNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Significantly, our findings demonstrate that shifts in the constituent species within each degradative community are directly attributable to enrichment with different PACs. Subsequently, we characterized the microorganisms comprising the degradative communities within each enrichment using 16S rRNA sequence data. Our findings demonstrate that the ability to degrade PACs is present in five divisions of the Proteobacteria and Actinobacteria. By determining the precise identity of the PAC-degrading bacterial species isolated from a single sediment sample, and by comparing our findings with previously published research, we demonstrate how bacteria with similar PAC degrading capabilities and 16S rRNA signatures are found in similarly polluted environments in geographically very distant locations, e.g., China, Italy, Japan and Hawaii. Such a finding suggests that geographical barriers do not limit the distribution of key PAC-degrading bacteria; this finding is in accordance with the Baas-Becking hypothesis “everything is everywhere; the environment selects” and may have significant consequences for the global distribution of PAC-degrading bacteria and their use in bioremediation.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Ahn Y, Sanseverino J, Sayler GS (1999) Analyses of polycyclic aromatic hydrocarbon-degrading bacteria isolated from contaminated soils. Biodegradation 10:149–157. doi:10.1023/A:1008369905161
Andreoni V, Cavalca L, Roa MA, Nocerino G, Bernasconi S, Dell’Amico E, Colombo M, Gianfreda L (2004) Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere 57:401–412. doi:10.1016/j.chemosphere.2004.06.013
Baas-Becking LGM (1934) Geobiologie of Inleiding Tot de Milieukunde. Van Stockkum & Zoon, The Hague
Boopathy R (2000) Factors limiting bioremediation technologies. Bioresour Technol 74:63–67. doi:10.1016/S0960-8524(99)00144-3
Cerniglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351–368. doi:10.1007/BF00129093
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequences alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500. doi:10.1093/nar/gkg500
Cho JC, Tiedje JM (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66:5448–5456. doi:10.1128/AEM.66.12.5448-5456.2000
Crump BC, Hopkinson CS, Sogin ML, Hobbie JE (2004) Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time. Appl Environ Microbiol 70:1494–1505. doi:10.1128/AEM.70.3.1494-1505.2004
Daane LL, Harjono I, Zylstra GJ, Haggblom MM (2001) Isolation and characterization of polycyclic aromatic hydrocarbon-degrading bacteria associated with the rhizophere of salt marsh plants. Appl Environ Microbiol 67:2683–2691. doi:10.1128/AEM.67.6.2683-2691.2001
Dean-Ross D, Moody JD, Freeman JP, Doerge DR, Cerniglia CE (2001) Metabolism of anthracene by Rhodococcus species. FEMS Microbiol Lett 204:205–211. doi:10.1111/j.1574-6968.2001.tb10886.x
Denome SA, Stanley DC, Olson ES, Young KD (1993) Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway. J Bacteriol 175:6890–6901
Edwards U, Rogall T, Blocker H, Emde M, Bottger EC (1989) Isolation and direct complete nucleotide determination entire genes. Characterisation of a gene encoding 16S ribosomal RNA. Nucleic Acids Res 17:7843–7853
Environment Agency, Severn River Basin District Liaison Panel (2008) River basin planning: summary of significant water management issues. http://www.environment-agency.gov.uk/static/documents/Research/sev_swmi_consult_1954048.pdf
Graff A, Stubner S (2003) Isolation and molecular characterization of thiosulfate-oxidizing bacteria from an Italian rice field soil. Syst Appl Microbiol 26:445–452. doi:10.1078/072320203322497482
Habe H, Omori T (2003) Genetics of polycyclic aromatic hydrocarbon metabolism in diverse aerobic bacteria. Biosci Biotechnol Biochem 67:225–243. doi:10.1271/bbb.67.225
Hamann C, Hegemann J, Hildebrandt A (1999) Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol Lett 173:255–263. doi:10.1111/j.1574-6968.1999.tb13510.x
Herrick JB, Stuart-Keil KG, Ghiorse WC, Madsen EL (1997) Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native to a coal tar-contaminated field site. Appl Environ Microbiol 63:2330–2337
Hirano S, Haruki M, Takano K, Imanaka T, Morikawa M, Kanaya S (2006) Gene cloning and in vivo characterization of dibenzothiophene dioxygenase from Xanthobacter polyaromaticivorans. Appl Environ Biotechnol 69:672–681
Hughes Martiny JB, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Adams Krumins J, Kuske CR, Morin PJ, Naeem S, Ovreas L, Reysenbach A, Smith VH, Staley JT (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4:102–112. doi:10.1038/nrmicro1341
Johnsen AR, Wick LY, Harms H (2005) Principles of microbial PAH-degradation in soil. Environ Pollut 133:71–84. doi:10.1016/j.envpol.2004.04.015
Joint Nature Conservation Committee (2001) SPA review site accounts. http://www.jncc.gov.uk/default.aspx?page=2066. Accessed 2001
Jukes TH, Cantor T (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic Press, New York, pp 21–132
Kropp KG, Andersson JT, Fedorak PM (1997) Bacterial transformations of 1, 2, 3, 4-tetrahydrodibenzothiophene and dibenzothiophene. Appl Environ Microbiol 63:3032–3042
Launen LA, Dutta J, Turpeinen R, Eastep ME, Dorn R, Buggs VH, Leonard JW, Haggblom MM (2008) Characterization of the indigenous PAH-degrading bacteria of Spartina dominated salt marshes in the New York/New Jersey Harbor. Biodegradation 19:347–363. doi:10.1007/s10532-007-9141-7
Lloyd-Jones G, Laurie AD, Hunter DWF, Fraser R (1999) Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol Ecol 29:69–79. doi:10.1111/j.1574-6941.1999.tb00599.x
Muller JG, Devereux R, Santavy DL, Lantz SE, Willis SG, Pritchard PH (1997) Phylogenetic and physiological comparisons of PAH-degrading bacteria from geographically diverse soils. Antonie Van Leeuwenhoek 71:329–343. doi:10.1023/A:1000277008064
Muyzer G, Waal E, 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
Ni Chadhain SM, Norman RS, Pesce KV, Kukor JJ, Zylstra GJ (2006) Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol 72:4078–4087. doi:10.1128/AEM.02969-05
Omori T, Monna L, Saiki Y, Kodama T (1992) Desulfurization of dibenzothiophene by Corynebacterium sp. Appl Environ Microbiol 58:911–915
Royal Haskoning/The Bristol Port Company (2008) Environmental statement. http://e2edocs.bristol-city.gov.uk/WAM/doc/Report-414531.pdf. Cited July 2008
Sho M, Hamel C, Greer CW (2004) Two distinct gene clusters encode pyrene degradation in Mycobacterium sp. strain S65. FEMS Microbiol Ecol 48:209–220. doi:10.1016/j.femsec.2004.01.011
Stingley RL, Khan AA, Cerniglia CE (2004) Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1. Biochem Biophys Res Commun 322:133–146. doi:10.1016/j.bbrc.2004.07.089
Stoffels M, Amann R, Ludwig W, Hekmat D, Schleifer KH (1998) Bacterial community dynamics during start-up of a trickle-bed reactor degrading aromatic compounds. Appl Environ Microbiol 64:930–939
Tett VA, Willetts AJ, Lappin-Scott HM (1994) Enantioselective degradation of the herbicide mecoprop [2-(2-methyl-4-chlorophenoxy) propionic acid] by mixed and pure bacterial cultures. FEMS Microbiol Ecol 14:191–199. doi:10.1111/j.1574-6941.1994.tb00105.x
Van Hamme JD, Singh A, Ward OP (2003) Recent advances in petroleum microbiology. Microbiol Mol Biol Rev 67:503–549. doi:10.1128/MMBR.67.4.503-549.2003
Vinas M, Sabate J, Espunny MJ, Solanas AM (2005) Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 71:7008–7018. doi:10.1128/AEM.71.11.7008-7018.2005
Whyte LG, Bourbonniere L, Greer CW (1997) Biodegradation of petroleum hydrocarbons by psychotrophic Pseudomonas strains possessing both alkane (alk) and naphthalene (nah) catabolic pathways. Appl Environ Microbiol 63:3719–3723
Widada J, Kasuga HK, Nojiri , Yoshida T, Habe H, Omori T (2002) Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl Microbiol Biotechnol 58:202–209. doi:10.1007/s00253-001-0880-9
Wilson MS, Herrick JB, Jeon CO, Hinman DE, Madsen EL (2003) Horizontal transfer of phnAc dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adajacent soil environments. Appl Environ Microbiol 69:2172–2181. doi:10.1128/AEM.69.4.2172-2181.2003
Yang GP, Zhang ZB (1997) Adsorption of dibenzothiophene on marine sediments treated by a sequential procedure. J Colloid Interface Sci 192:398–407. doi:10.1006/jcis.1997.4998
Yang GP, Lui XL, Zhang JW (1998) Distribution of dibenzothiophene in the sediment of the South China Sea. Environ Pollut 101:405–414. doi:10.1016/S0269-7491(98)00020-7
Acknowledgments
We gratefully acknowledge funding from Schlumberger Cambridge Research Ltd. Thanks to Dr. Corinne Whitby (Essex, UK) and Dr. Dalia Zakaria for helpful discussions. Many thanks also to Peter Splatt for excellent technical assistance.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Long, R.M., Lappin-Scott, H.M. & Stevens, J.R. Enrichment and identification of polycyclic aromatic compound-degrading bacteria enriched from sediment samples. Biodegradation 20, 521–531 (2009). https://doi.org/10.1007/s10532-008-9241-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10532-008-9241-z