Abstract
The effects of spilled oil on sedimentary bacterial communities were examined in situ at 20 m water depth in a Mediterranean coastal area. Sediment collected at an experimental site chronically subjected to hydrocarbon inputs was reworked into PVC cores with or without a massive addition of crude Arabian light oil (∼20 g kg−1 dry weight). Cores were reinserted into the sediment and incubated in situ at the sampling site (20 m water depth) for 135 and 503 days. The massive oil contamination induced significant shifts in the structure of the indigenous bacterial communities as shown by ribosomal intergenic spacer analysis (RISA). The vertical heterogeneity of the bacterial communities within the sediment was more pronounced in the oiled sediments particularly after 503 days of incubation. Response to oil of the deeper depth communities (8–10 cm) was slower than that of superficial depth communities (0–1 and 2–4 cm). Analysis of the oil composition by gas chromatography revealed a typical microbial alteration of n-alkanes during the experiment. Predominant RISA bands in oiled sediments were affiliated to hydrocarbonoclastic bacteria sequences. In particular, a 395-bp RISA band, which was the dominant band in all the oiled sediments for both incubation times, was closely related to hydrocarbonoclastic sulfate-reducing bacteria (SRB). These bacteria may have contributed to the main fingerprint changes and to the observed biodegradation of n-alkanes. This study provides useful information on bacterial dynamics in anoxic contaminated infralittoral sediments and highlights the need to assess more precisely the contribution of SRB to bioremediation in oil anoxic contaminated areas.
Similar content being viewed by others
References
Aeckersberg, F, Bak, F, Widdel, F (1991) Anaerobic oxidation of saturated hydrocarbons to CO2 by a new type of sulfate-reducing bacterium. Arch Microbiol 156: 5–14
Aller, RC (1982) The effects of macrobenthos on chemical properties of marine sediment and overlying water. In: McCall, PL, Tevesz, MJS (Eds.) Animal–Sediment Relations, Plenum, New York, pp 53–102
Aller, RC (1985) Effects of the marine deposit-feeders Heteromastus filiformis (Polychaeta), Macoma balthica (Bivalvia) and Tellina texana (Bivalvia), on averaged sedimentary solute transport, reaction rates, and microbial distributions. J Mar Res 43: 615–645
Altschul, S, Madden, T, Schaffer, A, Zhang, J, Zhang, Z, Miller, W, Lipman, D (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402
Apitz, SE, Arias, E, Clawson, SA, Lin, EW, Melcher, RJ, Hemmingsen, BB (1999) The development of a sterile, PAH-spiked, aged marine sediment for biodegradation experiments: chemical results. Org Geochem 30: 891–900
Bauer, JE, Capone, DG (1988) Effects of co-occurring aromatic hydrocarbons on degradation of individual aromatic hydrocarbons in marine sediments slurries. Appl Environ Microbiol 54: 1640–1655
Brown, MV, Schwalbach, MS, Hewson, I, Fuhrman, JA (2005) Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to time series. Environ Microbiol 7: 1466–1479
Burns, KA, Saliot, A (1986) Petroleum hydrocarbons in the Mediterranean Sea: a mass balance. Mar Chem 20: 141–157
Burr, MD, Clark, SJ, Spear, CR, Camper, AK (2006) Denaturing gradient gel electrophoresis can rapidly display the bacterial diversity contained in 16S rDNA clone libraries. Microb Ecol 51: 479–486
Caldwell, ME, Garrett, RM, Prince, RC, Suflita, JM (1998) Anaerobic biodegradation of long-chain n-alkanes under sulfate-reducing conditions. Environ Sci Technol 32: 2191–2195
Chakraborty, R, Coates, JD (2004) Anaerobic degradation of monoaromatic hydrocarbons. Appl Microbiol Biotechnol 64: 437–446
Coates, JD, Anderson, RT (2000) Emerging techniques for anaerobic bioremediation of contaminated environments. Trends Biotechnol 18: 408–412
Coates, JD, Woodward, J, Allen, J, Philip, P, Lovley, DR (1997) Anaerobic degradation of polycyclic aromatic hydrocarbons and alkanes in petroleum-contaminated marine harbor sediments. Appl Environ Microbiol 63: 3589–3593
Cravo-Laureau, C, Grossi, V, Raphel, D, Matheron, R, Hirschler-Rea, A (2005) Anaerobic n-alkane metabolism by a sulfate-reducing bacterium, Desulfatibacillum aliphaticivorans strain CV2803T. Appl Environ Microbiol 71: 3458–3467
Cravo-Laureau, C, Matheron, R, Cayol, J-L, Joulian, C, Hirschler-Rea, A (2004) Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 54: 77–83
Cuny, P, Miralles, G, Cornet-Barthaux, V, Acquaviva, M, Stora, G, Grossi, V, Gilbert, F (2006) Influence of bioturbation by the polychaete Nereis diversicolor on the structure of bacterial communities in oil contaminated coastal sediments. Mar Pollut Bull (in press)
De Wit, R, Relexans, J-C, Bouvier, T, Moriarty, DJW (1997) Microbial respiration and diffusive oxygen uptake of deep-sea sediments in the Southern Ocean (ANTARES-I cruise). Deep Sea Res Part II Top Stud Oceanogr 44: 1053–1068
Delille, D, Delille, B (2000) Field observations on the variability of crude oil impact on indigenous hydrocarbon-degrading bacteria from sub-Antartic intertidal sediments. Mar Environ Res 49: 403–417
Dyksterhouse, S, Gray, J, Herwig, R, Lara, J, Staley, J (1995) Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 45: 116–123
Gauthier, MJ, Lafay, B, Christen, R, Fernadez, L, Acquaviva, M, Bonin, P, Bertrand, J-C (1992) Marinobacter hydrocarbonoclasticus gen. nov., sp. nov. a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int J Syst Bacteriol 42: 568–576
Gerino, M, Aller, RC, Lee, C, Cochran, JK, Aller, JY, Green, MA, Hirschberg, D (1998) Comparison of different tracers and methods used to quantify bioturbation during a spring bloom: 234-Thorium, luminophores and chlorophyll a. Estuar Coast Shelf Sci 46: 531–547
Gerino, M, Stora, G, Durbec, J-P (1994) Quantitative estimation of biodiffusive and bioadvective sediment mixing: in situ experimental approach. Oceanol Acta 17: 547–554
Gilbert, F, Rivet, L, Bertrand, J-C (1994) The in vitro influence of the burrowing polychaete Nereis diversicolor on the fate of petroleum hydrocarbons in marine sediments. Chemosphere 29: 1–12
Gilbert, F, Stora, G, Bertrand, J-C (1996) In situ bioturbation and hydrocarbon fate in an experimental contaminated Mediterranean coastal ecosystem. Chemosphere 33: 1449–1458
Gilbert, F, Stora, G, Bonin, P, Le Dréau, Y, Mille, G, Bertrand, J-C (1997) Hydrocarbon influence on denitrification in bioturbated Mediterranean coastal sediments. Hydrobiologia 345: 67–77
Golyshin, PN, Chernikova, TN, Abraham, WR, Lunsdorf, H, Timmis, KN, Yakimov, MM (2002) Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 52: 901–911
Golyshin, PN, Martins Dos Santos, VAP, Kaiser, O, Ferrer, M, Sabirova, YS, Lunsdorf, H, Chernikova, TN, Golyshina, OV, Yakimov, MM, Puhler, A, Timmis, KN (2003) Genome sequence completed of Alcanivorax borkumensis, a hydrocarbon-degrading bacterium that plays a global role in oil removal from marine systems. J Biotechnol 106: 215–220
Gomez, F (2003) The role of the exchanges through the Strait of Gibraltar on the budget of elements in the Western Mediterranean Sea: consequences of human-induced modifications. Mar Pollut Bull 46: 685–694
Goñi-Urriza, M, de Montaudouin, X, Guyoneaud, R, Bachelet, G, de Wit, R (1999) Effect of macrofaunal bioturbation on bacterial distribution in marine sandy sediments, with special reference to sulphur-oxidising bacteria. J Sea Res 41: 269–279
Goréguès, CM, Michotey, VD, Bonin, PC (2005) Molecular, biochemical, and physiological approaches for understanding the ecology of denitrification. Microb Ecol 49: 198–208
Grossi, V, Cuny, P, Caradec, S, Nérini, D, Pancost, R, Gilbert, F (2006) Impact of feeding by Arenicola marina (L.) and ageing of faecal material on fatty acid distribution and bacterial community structure in marine sediments: an experimental approach. J Exp Mar Biol Ecol (in press)
Grossi, V, Massias, D, Stora, G, Bertrand, J-C (2002) Burial, exportation and degradation of acyclic petroleum hydrocarbons following a simulated oil spill in bioturbated Mediterranean coastal sediments. Chemosphere 48: 947–954
Harayama, S, Kishira, H, Kasai, Y, Syutsubo, K (1999) Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol 1: 63–70
Hayes, LA, Nevin, KP, Lovley, DR (1999) Role of prior exposure on anaerobic degradation of naphthalene and phenanthrene in marine harbor sediments. Org Geochem 30: 937–945
Head, IM, Jones, DM, Roling, WFM (2006) Marine microorganisms make a meal of oil. Nat Rev Microbiol 4: 173–182
Head, IM, Swannell, RP (1999) Bioremediation of petroleum hydrocarbon contaminants in marine habitats. Curr Opin Biotechnol 10: 234–239
Hedlund, BP, Geiselbrecht, AD, Bair, TJ, Staley, JT (1999) Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl Environ Microbiol 65: 251–259
Huber, PJ (1981) Robust Statistics. Wiley and Sons, Inc., New York
Jones, DM, Douglas, AG, Parkes, RJ, Taylor, J, Giger, W, Schaffner, C (1983) The recognition of biodegraded petroleum-derived aromatic hydrocarbons in recent marine sediments. Mar Pollut Bull 14: 103–108
Jørgensen, BB (1982) Mineralization of organic matter in the sea bed—The role of sulfate reduction. Nature 377: 223–224
Kasai, Y, Kishira, H, Harayama, S (2002) 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
Kasai, Y, Kishira, H, Sasaki, T, Syutsubo, K, Watanabe, K, Harayama, S (2002) Predominant growth of Alcanivorax strains in oil-contaminated and nutrient-supplemented sea water. Environ Microbiol 4: 141–147
Kasai, Y, Kishira, H, Syutsubo, K, Harayama, S (2001) Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Environ Microbiol 3: 246–255
Kennicutt, II MC, Barker, C, Brooks, JM, DeFreitas, DA, Zhu, GH (1987) Selected organic matter source indicators in the Orinoco, Nile and Changjiang deltas. Org Geochem 11: 41–51
Krzanowski, WJ (1987) Selection of variables to preserve multivariate data structure using principal components. Appl Stat 36: 22–33
Le Dréau, Y, Gilbert, F, Doumenq, P, Asia, L, Bertrand, J-C, Mille, G (1997) The use of hopanes to track in situ variations in petroleum composition in surface sediments. Chemosphere 34: 1663–1672
Le Dréau, Y, Jacquot, F, Doumenq, P, Guiliano, M, Bertrand, JC, Mille, G (1997) Hydrocarbon balance of a site which had been highly and chronically contaminated by petroleum wastes of a refinery (from 1956 to 1992). Mar Pollut Bull 34: 456–468
Macnaughton, SJ, Stephen, JR, Venosa, AD, Davis, GA, Chang, YJ, White, DC (1999) Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microbiol 65: 3566–3574
Maidak, B, Cole, J, Parker, C, Jr, Garrity, G, Larsen, N, Li, B, Lilburn, T, McCaughey, M, Olsen, G, Overbeek, R, Pramanik, S, Schmidt, T, Tiedje, J, Woese, C (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res 27: 171–173
Margesin, R, Labbé, D, Schinner, F, Greer, CW, Whyte, LG (2003) Characterisation of hydrocarbon-degrading microbial populations in contaminated and pristine Alpine soils. Appl Environ Microbiol 69: 3085–3092
Maruyama, A, Ishiwata, H, Kitamura, K, Sunamura, M, Fujita, T, Matsuo, M, Higashihara, T (2003) Dynamics of microbial populations and strong selection for Cycloclasticus pugetii following the Nakhodka oil spill. Microb Ecol 46: 442–453
Mayer, LM, Schick, LL, Self, RFL, Jumars, PA (1997) Digestive environments of benthic macroinvertebrate guts: enzymes, surfactants and dissolved organic matter. J Mar Res 55: 785–812
Melcher, RJ, Apitz, SE, Hemmingsen, BB (2002) Impact of irradiance and polycyclic aromatic hydrocarbon spiking on microbial populations in marine sediment for future aging and biodegradability studies. Appl Environ Microbiol 68: 2858–2868
Muschenheim, DK, Lee, K (2002) Removal of oil from the sea surface through particulate interactions: review and prospectus. Spill Sci Technol Bull 8: 9–18
Normand, P, Ponsonnet, C, Nesme, X, Neyra, M, Simonet, P (1996) ITS analysis of prokaryotes. In: Akkermans, DL, van Elsas, JD, de Bruijn, EI (Eds.) Molecular Microbial Ecology Manual, Kluwer Academic Publishers, Amsterdam, The Netherlands, pp 1–12
O’Rourke, D, Conolly, S (2003) Just oil? The distribution of environmental and social impacts of oil production and consumption. Annu Rev Environ Resour 28: 587–617
Ogino, A, Koshikawa, H, Nakahara, T, Uchiyama, H (2001) Succession of microbial communities during a biostimulation process as evaluated by DGGE and clone library analyses. J Appl Microbiol 91: 625–635
Papaspyrou, S, Gregersen, T, Kristensen, E, Christensen, B, Cox, RP (2006) Microbial reaction rates and bacterial communities in sediment surrounding burrows of two nereidid polychaetes (Nereis diversicolor and N. virens). Mar Biol 148: 541–550
Payne, JR, Clayton, J, John R, Kirstein, BE (2003) Oil/suspended particulate material interactions and sedimentation. Spill Sci Technol Bull 8: 201–221
Perriere, G, Gouy, M (1996) WWW-query: an on-line retrieval system for biological sequence banks. Biochim 78: 364–369
Rahman, KSM, Thahira-Rahman, J, Lakshmanaperumalsamy, P, Banat, IM (2002) Towards efficient crude oil degradation by a mixed bacterial consortium. Bioresour Technol 85: 257–261
Revsbech, NP, Sørensen, J, Blackburn, H (1980) Distribution of oxygen in marine sediments measured with microelectrodes. Limnol Oceanogr 25: 403–411
Röling, WFM, Milner, MG, Jones, DM, Fratepietro, F, Swannell, RPJ, Daniel, F, Head, IM (2004) Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. Appl Environ Microbiol 70: 2603–2613
Röling, WFM, Milner, MG, Jones, DM, Lee, K, Daniel, F, Swannell, RJP, Head, IM (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl Environ Microbiol 68: 5537–5548
Saitou, N, Nei, M (1987) The Neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425
Shen, L, Jaffé, R (2000) Interactions between dissolved petroleum hydrocarbons and pure and humic acid-coated mineral surfaces in artificial seawater. Mar Environ Res 49: 217–231
So, CM, Phelps, CD, Young, LY (2003) Anaerobic transformation of alkanes to fatty acids by a sulfate-reducing bacterium, strain Hxd3. Appl Environ Microbiol 69: 3892–3900
So, CM, Young, LY (1999) Initial reactions in anaerobic alkane degradation by a sulfate reducer, strain AK-01. Appl Environ Microbiol 65: 5532–5540
So, CM, Young, LY (1999) Isolation and characterization of a sulfate-reducing bacterium that anaerobically degrades alkanes. Appl Environ Microbiol 65: 2969–2976
Thompson, J, Higgins, D, Gibson, T (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
Ulses, C, Grenz, C, Marsaleix, P, Schaaff, E, Estournel, C, Meulé, S, Pinazo, C (2005) Circulation in a semi-enclosed bay under influence of strong freshwater input. J Mar Syst 56: 113–132
Volkman, JK, Holdsworth, DG, Neill, GP, Bavor, Jr. HJ (1992) Identification of natural, anthropogenic and petroleum hydrocarbons in aquatic sediments. Sci Total Environ 112: 203–219
Yakimov, M, Golyshin, P, Lang, S, Moore, E, Abraham, W, Lunsdorf, H, Timmis, K (1998) Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 48: 339–348
Yakimov, MM, Denaro, R, Genovese, M, Cappello, S, D’Auria, G, Chernikova, TN, Timmis, KN, Golyshin, PN, Giluliano, L (2005) Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. Environ Microbiol 7: 1426–1441
Yakimov, MM, Giuliano, L, Denaro, R, Crisafi, E, Chernikova, TN, Abraham, W-R, Luensdorf, H, Timmis, KN, Golyshin, PN (2004) Thalassolituus oleivorans gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 54: 141–148
Yakimov, MM, Giuliano, L, Gentile, G, Crisafi, E, Chernikova, TN, Abraham, W-R, Lunsdorf, H, Timmis, KN, Golyshin, PN (2003) Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. Int J Syst Evol Microbiol 53: 779–785
Acknowledgements
We thank Dr. Georges Stora and Dr. Eric Duport for assistance with the luminophore technique. We would also like to thank Dr. Frederic Poitou from Signatures Society, and Laurence Asia for their help in hydrocarbons analyses, Dr. Christelle Goréguès for her skillful technical assistance with DGGE analysis and Elisabeth Brothier, Dr. Franck Poly, and Dr. Lionel Ranjard for their kind advice on the RISA technique. The authors are especially indebted to Michael Paul for careful reading of the English and Dr. Michèle Gilewicz for helpful comments on the paper. Last but not least, we are grateful to Dr. Vincent Grossi, Roland Graille, Frédéric Zuberer and Bernard De Ligondès for their essential work in the field.
This work was carried out in the framework of the program “GDR HYCAR no. 1123: Cycles biogéochimiques des hydrocarbures naturels et anthropiques en milieu marin,” and was supported by the Centre National de la Recherche Scientifique (CNRS) and Total company.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Miralles, G., Nérini, D., Manté, C. et al. Effects of Spilled Oil on Bacterial Communities of Mediterranean Coastal Anoxic Sediments Chronically Subjected to Oil Hydrocarbon Contamination. Microb Ecol 54, 646–661 (2007). https://doi.org/10.1007/s00248-007-9221-6
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00248-007-9221-6