Skip to main content
Log in

Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil

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

Abstract

The indigenous microbiota of polluted coastal seawater in Tunisia was enriched by increasing the concentration of zarzatine crude oil. The resulting adapted microbiota was incubated with zarzatine crude oil as the only carbon and energy source. Crude oil biodegradation capacity and bacterial population dynamics of the microbiota were evaluated every week for 28 days (day 7, day 14, day 21, and day 28). Results show that the percentage of petroleum degradation was 23.9, 32.1, 65.3, and 77.8%, respectively. At day 28, non-aromatic and aromatic hydrocarbon degradation rates reached 92.6 and 68.7%, respectively. Bacterial composition of the adapted microflora was analysed by 16S rRNA gene cloning and sequencing, using total genomic DNA extracted from the adapted microflora at days 0, 7, 14, 21, and 28. Five clone libraries were constructed and a total of 430 sequences were generated and grouped into OTUs using the ARB software package. Phylogenetic analysis of the adapted microbiota shows the presence of four phylogenetic groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Diversity indices show a clear decrease in bacterial diversity of the adapted microflora according to the incubation time. The Proteobacteria are the most predominant (>80%) at day 7, day 14 and day 21 but not at day 28 for which the microbiota was reduced to only one OTU affiliated with the genus Kocuria of the Actinobacteria. This study shows that the degradation of zarzatine crude oil components depends on the activity of a specialized and dynamic seawater consortium composed of different phylogenetic taxa depending on the substrate complexity.

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

Abbreviations

AH:

Aromatic hydrocarbon

AM:

Adapted Microbiota

NAH:

Non-aromatic hydrocarbon

TPH:

Total Petroleum Hydrocarbon

UCM:

Unresolved complex mixture

ZCO:

Zarzatine crude oil

References

  • Abed RM, Safi NM, Köster J, de Beer D, El-Nahhal Y, Rullkötter J, Garcia-Pichel F (2002) Microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. Appl Environ Microbiol 68:1674–1683. doi:10.1128/AEM.68.4.1674-1683.2002

    Article  PubMed  CAS  Google Scholar 

  • Ahn IS, Ghiorse WC, Lion LW, Shuler ML (1998) Growth kinetics of Pseudomonas putida G7 on naphthalene and occurrence of naphthalene toxicity during nutrient deprivation. Biotechnol Bioeng 59(5):587–594. doi:10.1002/(SICI)1097-0290(19980905)59:5<587::AID-BIT9>3.0.CO;2-6

    Article  PubMed  CAS  Google Scholar 

  • Aislabiea JM, Chhourb KL, Saulb DJ, Miyauchib S, Aytonb J, Paetzoldc RF, Balksd MR (2006) Dominant bacteria in soils of Marble Point and Wright Valley, Victoria Land, Antarctica. Soil Biol Biochem 38(10):3041–3056. doi:10.1016/j.soilbio.2006.02.018

    Article  CAS  Google Scholar 

  • Alekhina IA, Marie D, Petit JR, Lukin VV, Zubkov VM, Bulat SA (2007) Molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at Vostok, East Antarctica. FEMS Microbiol Ecol 59(2):289–299. doi:10.1111/j.1574-6941.2006.00271.x

    Article  PubMed  CAS  Google Scholar 

  • Alvarez HM, Souto MF, Viale A, Pucci OH (2001) Biosynthesis of fatty acids and triacylglycerols by 2, 6, 10, 14-tetramethyl pentadecane-grown cells of Nocardia globerula 432. FEMS Microbiol Lett 200(2):195–200. doi:10.1111/j.1574-6968.2001.tb10715.x

    Article  PubMed  CAS  Google Scholar 

  • Atlas RM (1981) Microbial degradation of petroleum hydrocarbons: an environmental perspective. Microbiol Rev 45(1):180–209

    PubMed  CAS  Google Scholar 

  • Bartha R (1977) The microbiology of aquatic oil spills. Adv Appl Microbiol 22:225–266. doi:10.1016/S0065-2164(08)70164-3

    Article  PubMed  CAS  Google Scholar 

  • Bertrand JC, Mille G (1989) Devenir de la matière organique exogène. Un modèle: les hydrocarbures. In: Bianchi M, Marty D, Bertrand JC, Caumette P, etGauthier MJ (eds) Microorganismes dans les écosystèmes océaniques, Chapitre 13. Masson, Paris, pp 85–343

    Google Scholar 

  • Bertrand JC, Rambeloarisoa JF, Rontani JF, Giusti G, Mattei G (1983) Microbial degradation of crude oil in sea water in continuous culture. Biotechnol Lett 5:567–572. doi:10.1007/BF01184950

    Article  Google Scholar 

  • Brakstad OG, Lødeng AGG (2004) Microbial diversity during biodegradation of crude oil in seawater from the North Sea. Microb Ecol 49(1):94–103. doi:10.1007/s00248-003-0225-6

    Article  PubMed  CAS  Google Scholar 

  • Brakstad OG, Bonaunet K, Nordtug T, Johansen O (2004) Biotransformation and dissolution of petroleum hydrocarbons in natural flowing seawater at low temperature. Biodegradation 15(5):337–346. doi:10.1023/B:BIOD.0000042189.69946.07

    Article  PubMed  CAS  Google Scholar 

  • Chaîneau CH, Morel J, Dupont J, Bury E, Oudot J (1999) Comparison of the fuel oil biodegradation potential of hydrocarbon-assimilating microorganisms isolated from a temperate agricultural soil. Sci Total Environ 227(2–3):237–247. doi:10.1016/S0048-9697(99)00033-9

    Article  PubMed  Google Scholar 

  • Chang YJ, Stephen JR, Richter AP, Venosa AD, Brüggemann J, Macnaughton SJ, Kowalchuk GA, Haines JR, Kline E, White DC (2000) Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method. J Microbiol Methods 40(1):19–31. doi:10.1016/S0167-7012(99)00134-7

    Article  PubMed  CAS  Google Scholar 

  • Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2003) Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. Appl Environ Microbiol 69(12):7354–7363. doi:10.1128/AEM.69.12.7354-7363.2003

    Article  PubMed  CAS  Google Scholar 

  • Chouari R, Le Paslier D, Daegelen P, Ginestet P, Weissenbach J, Sghir A (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ Microbiol 7(8):1104–1115. doi:10.1111/j.1462-2920.2005.00795.x

    Article  PubMed  CAS  Google Scholar 

  • Gallego JL, García-Martínez MJ, Llamas JF, Belloch C, Peláez AI, Sánchez J (2007) Biodegradation of oil tank bottom sludge using microbial consortia. Biodegradation 18(3):269–281. doi:10.1007/s10532-006-9061-y

    Article  PubMed  Google Scholar 

  • Ghosh W, Roy P (2006) Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant. Int J Syst Evol Microbiol 56:91–97. doi:10.1099/ijs.0.63967-0

    Article  PubMed  CAS  Google Scholar 

  • Good IJ (1953) The population frequencies of species and the estimation of population parameters. Biometrika 40:237–264

    Google Scholar 

  • Hara A, Syutsubo K, Harayama S (2003) Alcanivorax which prevails in oil-contaminated seawater exhibits broad substrate specificity for alkane degradation. Environ Microbiol 5(9):746–753. doi:10.1046/j.1468-2920.2003.00468.x

    Article  PubMed  CAS  Google Scholar 

  • Harayama S, Kishira H, Kasai Y, Shutsubo K (1999) Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol 1(1):63–70

    PubMed  CAS  Google Scholar 

  • Hernandez-Raquet G, Budzinski H, Caumette P, Dabert P, Le Ménach K, Muyzer G, Duran R (2006) Molecular diversity studies of bacterial communities of oil polluted microbial mats from the Etang de Berre (France). FEMS Microbiol Ecol 58(3):550–562. doi:10.1111/j.1574-6941.2006.00187.x

    Article  PubMed  CAS  Google Scholar 

  • Hicks RE, Amann RI, Stahl DA (1992) Dual staining of natural bacterioplankton with 4′, 6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Appl Environ Microbiol 58(7):2158–2163

    PubMed  CAS  Google Scholar 

  • Hill TCJ, Walsh KA, Harris JA, Moffett BF (2003) Using ecological diversity measures with bacterial communities. FEMS Microbiol Ecol 43:1–11. doi:10.1111/j.1574-6941.2003.tb01040.x

    Article  CAS  PubMed  Google Scholar 

  • Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJ (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67(10):4399–4406. Erratum in: Appl Environ Microbiol. 68. 1: 448. doi:10.1128/AEM.67.10.4399-4406.2001

    Google Scholar 

  • Juck D, Charles T, Whyte LG, Greer CW (2000) Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities. FEMS Microbiol Ecol 33(3):241–249. doi:10.1111/j.1574-6941.2000.tb00746.x

    Article  PubMed  CAS  Google Scholar 

  • Kaplan CW, Kitts CL (2004) Bacterial–bacterial succession in a petroleum land treatment unit. Appl Environ Microbiol 70(3):1777–1786. doi:10.1128/AEM.70.3.1777-1786.2004

    Article  PubMed  CAS  Google Scholar 

  • 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(4):246–255. doi:10.1046/j.1462-2920.2001.00185.x

    Article  PubMed  CAS  Google Scholar 

  • Kasai Y, Takahata Y, Hoaki T, Watanabe K (2005) Physiological and molecular characterization of a microbial community established in unsaturated petroleum-contaminated soil. Environ Microbiol 7(6):806–818. doi:10.1111/j.1462-2920.2005.00754.x

    Article  PubMed  CAS  Google Scholar 

  • Kim JS, Crowley DE (2007) Microbial diversity in natural asphalts of the Rancho La Brea Tar Pits. Appl Environ Microbiol 73(14):4579–4591. doi:10.1128/AEM.01372-06

    Article  PubMed  CAS  Google Scholar 

  • Ko SH, Lebeault JM (1999) Effect of mixed culture on co-oxidation during the degradation of saturated hydrocarbon mixture. J Appl Microbiol 87:72–79. doi:10.1046/j.1365-2672.1999.00797.x

    Article  PubMed  CAS  Google Scholar 

  • Labbé N, Parent S, Villemur R (2002) Nitratireductor aquibiodomus gen. nov., sp., a novel α-protebacterium fom the marine denitrication system of the Montreal Biodome (Canada). Int J Syst Evol Microbiol 54(1):269–273. doi:10.1099/ijs.0.02793-0

    Article  CAS  Google Scholar 

  • Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54:305–315

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Marc V, Sabaté J, Espuny MJ, Solanas AM (2005) Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 71(11):7008–7018. doi:10.1128/AEM.71.11.7008-7018.2005

    Article  CAS  Google Scholar 

  • McKenna EJ, Kallio RE (1971) Microbial metabolism of the isoprenoid alkane pristine. Proc Natl Acad Sci USA 68:1552–1554. doi:10.1073/pnas.68.7.1552

    Article  PubMed  CAS  Google Scholar 

  • McKew BA, Coulon F, Osborn AM, Timmis KN, McGenity TJ (2007) Determining the identity and roles of oil-metabolizing marine bacteria from the Thames estuary, UK. Environ Microbiol 9(1):165–176. doi:10.1111/j.1462-2920.2006.01125.x

    Article  PubMed  CAS  Google Scholar 

  • Minamisawa K, Nishioka K, Miyaki T, Ye B, Miyamoto T, You M, Saito A, Saito M, Barraquio WL, Teaumroong N, Sein T, Sato T (2004) Anaerobic nitrogen-fixing consortia consisting of clostridia isolated from gramineous plants. Appl Environ Microbiol 70(5):3096–3102. doi:10.1128/AEM.70.5.3096-3102.2004

    Article  PubMed  CAS  Google Scholar 

  • Oudot J, Merlin FX, Pinvidic P (1998) Weathering rate of oil components in a bioremediation experiment in Estuarine sediments. Mar Environ Res 45(2):113–125. doi:10.1016/S0141-1136(97)00024-X

    Article  CAS  Google Scholar 

  • Ozaki S, Fujita KishimotoT (2006) Isolation and phylogenetic characterization of microbial consortia able to degrade aromatic hydrocarbons at high rates. Microbes Environ 21(1):44–52. doi:10.1264/jsme2.21.44

    Article  Google Scholar 

  • Pedrós-Alió C (2006) Marine microbial diversity: can it be determined? Trends Microbiol 14(6):257–263. doi:10.1016/j.tim.2006.04.007

    Article  PubMed  CAS  Google Scholar 

  • Penet S, Marchal R, Sghir A, Monot F (2004) Biodegradation of hydrocarbon cuts used for diesel oil formulation. Appl Microbiol Biotechnol 66(1):40–47. doi:10.1007/s00253-004-1660-0

    Article  PubMed  CAS  Google Scholar 

  • Pineda-Flores G, Ball-Arguello G, Lira-Galeana C, Mesta-Howard MA (2004) A microbial consorptium isolated from a crude oil sample that uses asphaltenes as a carbon and energy source. Biodegradation 15:145–151. doi:10.1023/B:BIOD.0000026476.03744.bb

    Article  PubMed  CAS  Google Scholar 

  • Pirnik MP, Atlas RM, Bartha R (1974) Metabolism by Brevibacterium erythrogenes: normal and branched alkanes. J Bacteriol 119(3):868–878

    PubMed  CAS  Google Scholar 

  • Popp N, Schlömann M, Mau M (2006) Bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils. Microbiology 152(11):3291–3304. doi:10.1099/mic.0.29054-0

    Article  PubMed  CAS  Google Scholar 

  • Prince RC (2005) Petroleum microbiology. In: Ollivier B, Magot M (eds) The microbiology of marine oil spill bioremediation. American Society for Microbiology Press, Washington DC, pp 317–336

    Google Scholar 

  • Reddy GS, Prakash JS, Prabahar V, Matsumoto GI, Stackebrandt E, Shivaji S (2003) Kocuria polaris sp. nov., an orange-pigmented psychrophilic bacterium isolated from an Antarctic cyanobacterial mat sample. Int J Syst Evol Microbiol 53(1):183–187. doi:10.1099/ijs.0.02336-0

    Article  PubMed  CAS  Google Scholar 

  • Rehmann K, Hertkorn N, Kettrup AA (2001) Fluoranthene metabolism in Mycobacterium sp. strain KR20: identity of pathway intermediates during degradation and growth. Microbiology 147(10):2783–2794

    PubMed  CAS  Google Scholar 

  • Reid BJ, Fermor TR, Semple KT (2002) Induction of PAH-catabolism in mushroom compost and its use in the biodegradation of soil-associated phenanthrene. Environ Pollut 118(1):65–73. doi:10.1016/S0269-7491(01)00239-1

    Article  PubMed  CAS  Google Scholar 

  • Reisfeld A, Rosenberg E, Gutnick D (1972) Microbial degradation of crude oil: factors affecting the dispersion in sea water by mixed and pure cultures. Appl Microbiol 24(3):363–368

    PubMed  CAS  Google Scholar 

  • Röling WF, Milner MG, Jones DM, Lee K, Daniel F, Swannell RJ, Head IM (2002) Robust hydrocarbon degradation and dynamics of bacterial communities during nutrient-enhanced oil spill bioremediation. Appl Environ Microbiol 68(11):5537–5548

    Article  PubMed  CAS  Google Scholar 

  • Rontani JF, Giusti G (1986) Study of the biodegradation of poly-branched alkanes by a marine bacterial community. Mar Chem 20:197–205. doi:10.1016/0304-4203(86)90039-3

    Article  CAS  Google Scholar 

  • Saliot A (1981) Natural hydrocarbons in sea water. In: Duursma EK, Dawson R (eds) Marine organic chemistry. Elsevier, Amsterdam, pp 327–374

    Google Scholar 

  • Saul DJ, Aislabie JM, Brown CE, Harris L, Foght JM (2005) Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. FEMS Microbiol Ecol 53(1):141–155. doi:10.1016/j.femsec.2004.11.007

    Article  PubMed  CAS  Google Scholar 

  • Schaeffer TL, Cantwell SG, Brown JL, Watt DS, Fall RR (1979) Microbial growth on hydrocarbons: terminal branching inhibits biodegradation. Appl Environ Microbiol 38:742–746

    PubMed  CAS  Google Scholar 

  • Schloss PD, Handelsman J (2006) Introducing TreeClimber, a test to compare microbial community structures. Appl Environ Microbiol 72(4):2379–2384. doi:10.1128/AEM.72.4.2379-2384.2006

    Article  PubMed  CAS  Google Scholar 

  • Sharma SL, Pant A (2000) Biodegrdation and conversion of alkanes and crude oil by marine Rhododcoccus sp. Biodegradation 11(5):289–294. doi:10.1023/A:1011185806974

    Article  PubMed  CAS  Google Scholar 

  • Sikorski J, Mohle M, Wackernagel W (2002) Identification of complex composition, strong strain diversity and directional selection in local Pseudomonas stutzeri populations from marine sediment and soils. Environ Microbiol 4(8):465–476. doi:10.1046/j.1462-2920.2002.00325.x

    Article  PubMed  CAS  Google Scholar 

  • Syutsubo K, Kishira H, Harayama S (2001) Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains. Environ Microbiol 3(6):371–379. doi:10.1046/j.1462-2920.2001.00204.x

    Article  PubMed  CAS  Google Scholar 

  • Trabelsi S, Driss MR (2005) Polycyclic aromatic hydrocarbons in superficial coastal sediments from Bizerte Lagoon, Tunisia. Mar Pollut Bull 50:344–359. doi:10.1016/j.marpolbul.2004.11.031

    Article  PubMed  CAS  Google Scholar 

  • Viñas M, Grifoll M, Sabaté J, Solanas AM (2002) Biodegradation of a crude oil by three microbial consortia of different origins and metabolic capabilities. J Ind Microbiol Biotechnol 28:252–260. doi:10.1038/sj.jim.7000236

    Article  PubMed  Google Scholar 

  • Viñas M, Sabaté J, Espuny MJ, Solanas AM (2005) Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. Appl Environ Microbiol 71(11):7008–7018. doi:10.1128/AEM.71.11.7008-7018.2005

    Article  PubMed  CAS  Google Scholar 

  • Walker JD, Colwell RR (1974) Microbial petroleum degradation: use of mixed hydrocarbon substrates. Appl Microbiol 27(6):1053–1060

    PubMed  CAS  Google Scholar 

  • Wang RF, Cao WW, Cerniglia CE (1995a) Phylogenetic analysis of polycyclic aromatic hydrocarbon degrading mycobacteria by 16S rRNA sequencing. FEMS Microbiol Lett 130(1):75–80

    PubMed  CAS  Google Scholar 

  • Wang ZD, Fingas M, Sergy G (1995b) Chemical characterization of crude oil residues from an arctic beach by GC/MS and GC/FID. Environ Sci Technol 29:2622–2631. doi:10.1021/es00010a025

    Article  CAS  Google Scholar 

  • Weissenfels WD, Beyer M, Klein J (1990) Degradation of phenanthrene, fluorene and fluoranthene by pure bacterial cultures. Appl Microbiol Biotechnol 32(4):479–484. doi:10.1007/BF00903787

    Article  PubMed  CAS  Google Scholar 

  • Wilson MM, Metcalf WW (2005) Genetic diversity and horizontal transfer of genes involved in oxidation of reduced phosphorus compounds by Alcaligenes faecalis WM2072. Appl Environ Microbiol 71(1):290–296. doi:10.1128/AEM.71.1.290-296.2005

    Article  PubMed  CAS  Google Scholar 

  • Winderl C, Schaefer S, Lueders T (2007) Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker. Environ Microbiol 9(4):1035–1046. doi:10.1111/j.1462-2920.2006.01230.x

    Article  PubMed  CAS  Google Scholar 

  • Zheng D, Alm EW, Stahl DA, Raskin L (1996) Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62:4504–4513

    PubMed  CAS  Google Scholar 

  • Zobell CE (1946) Action of microorganisms on hydrocarbons. Bacteriol Rev 10:1–49

    PubMed  CAS  Google Scholar 

  • Zrafi-Nouira I, Khedir-Ghenim Z, Zrafi F, Bahri R, Cheraeif I, Rouabhia M, Saidane-Mosbahi D (2008) Hydrocarbon pollution in the sediment from the Jarzouna-Bizerte coastal area of Tunisia (Mediterranean Sea). Bull Environ Contam Toxicol 80(6):566–572. doi:10.1007/s00128-008-9421-x

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank STIR refinery employees of Bizerte for their help in seawater sampling. Chromatography analyses were performed in the laboratory of Biochemistry and Mass spectrometry at the Monastir Medical School Tunisia. We thank Sebastien Chaussonnerie for his help in sequence analyses and the CEA-Genoscope sequencing team for their technical assistance. We thank Suzan Cure for the reading of the manuscript. We are grateful to Rémy Marchal, Institut Français de Pétrole, France, for his help and his continuous encouragement. This study was partly supported by grants from the Ministry of Education, Scientific Research and Biotechnology of Tunisia and the University of Monastir.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ines Zrafi-Nouira.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zrafi-Nouira, I., Guermazi, S., Chouari, R. et al. Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil. Biodegradation 20, 467–486 (2009). https://doi.org/10.1007/s10532-008-9235-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10532-008-9235-x

Keywords

Navigation