Skip to main content
SpringerLink
Log in
Book cover

Hydrocarbon and Lipid Microbiology Protocols pp 131–152Cite as

Protocols for Harvesting a Microbial Community Directly as a Biofilm for the Remediation of Oil Sands Process Water

  • Protocol
  • First Online:

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

The prevalence of inorganic pollutants co-contaminating sites with multiple organic pollutants complicates bioremediation efforts. For this reason, new methods are needed for bioremediation of co-contaminated sites. One strategy being explored is the use of microbial community biofilms. Biofilms offer advantages in bioremediation that their planktonic counterparts don’t. These advantages include: (1) the biofilm matrix provides protection from the rapid diffusion and penetration of toxins; (2) biofilms exist as a community with diverse metabolic potentials, increasing their ability to degrade a variety of xenobiotics; and (3) biofilm formation is an effective way to retain biomass in a bioreactor.

Here, we describe a robust method for harvesting and applying environmentally derived mixed-species biofilms for the remediation of contaminants – namely, naphthenic acids – from Oil sands process water (OSPW). OSPW is an alkaline mixture of clay, sand, and residual hydrocarbons. In addition, OSPW is rife with acutely and chronically toxic levels of heavy metals, polyaromatic hydrocarbons, and naphthenic acids.

Currently, we have established facile methods for harvesting a microbial mixed-species biofilm in a high-throughput device – the Calgary Biofilm Device (CBD) – and on various wastewater treatment support materials using a modified CBD. We have observed that the established biofilm can then be used to inoculate an ex situ bioreactor. To date, we have established that our biofilm-inoculated bioreactor maintains the capacity to degrade a mixture of commercially available naphthenic acids at concentrations exceeding those found in OSPW over a 30-day period.

Altogether, this chapter will provide a template for an easy and effective example of how biofilms can be used to remediate organic pollutants in co-contaminated sites.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Atlas RM (1995) Bioremediation of petroleum pollutants. Int Biodeter Biodegr 35:317–327

    Article  CAS  Google Scholar 

  2. Farhadian M, Vachelard C, Duchez D, Larroche C (2008) In situ bioremediation of monoaromatic pollutants in groundwater: a review. Bioresour Technol 99:5296–5308

    Article  CAS  PubMed  Google Scholar 

  3. Chen K-F, Kao C-M, Chen C-W, Surampalli RY, Lee M-S (2010) Control of petroleum-hydrocarbon contaminated groundwater by intrinsic and enhanced bioremediation. J Environ Sci 22:864–871

    Article  CAS  Google Scholar 

  4. Kao C, Chien H, Surampalli R, Chien C, Chen C (2009) Assessing of natural attenuation and intrinsic bioremediation rates at a petroleum-hydrocarbon spill site: laboratory and field studies. J Environ Eng 136:54–67

    Article  Google Scholar 

  5. Kostka JE, Prakash O, Overholt WA et al (2011) Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater horizon oil spill. Appl Environ Microbiol 77:7962–7974

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lu Z, Deng Y, Van Nostrand JD et al (2012) Microbial gene functions enriched in the deepwater horizon deep-sea oil plume. ISME J 6:451–460

    Article  CAS  PubMed  Google Scholar 

  7. Pritchard PH, Mueller JG, Rogers JC, Kremer FV, Glaser JA (1992) Oil spill bioremediation: experiences, lessons and results from the Exxon Valdez oil spill in Alaska. Biodegradation 3:315–335

    Article  CAS  Google Scholar 

  8. Prince RC, Bragg JR (1997) Shoreline bioremediation following the Exxon Valdez oil spill in Alaska. Bioremediat J 1:97–104

    Article  Google Scholar 

  9. Liang X, Devine CE, Nelson J, Sherwood Lollar B, Zinder S, Edwards EA (2013) Anaerobic conversion of chlorobenzene and benzene to CH4 and CO2 in bioaugmented microcosms. Environ Sci Technol 47:2378–2385

    Article  CAS  PubMed  Google Scholar 

  10. Richardson RE (2013) Genomic insights into organohalide respiration. Curr Opin Biotechnol 24:498–505

    Article  CAS  PubMed  Google Scholar 

  11. Perelo LW (2010) Review: in situ and bioremediation of organic pollutants in aquatic sediments. J Hazard Mater 177:81–89

    Article  CAS  PubMed  Google Scholar 

  12. Lors C, Damidot D, Ponge J-F, Périé F (2012) Comparison of a bioremediation process of PAHs in a PAH-contaminated soil at field and laboratory scales. Environ Pollut 165:11–17

    Article  CAS  PubMed  Google Scholar 

  13. Tyagi M, da Fonseca MM, de Carvalho CCR (2011) Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation 22:231–241

    Article  CAS  PubMed  Google Scholar 

  14. Demeter MA, Lemire J, George I, Yue G, Ceri H, Turner RJ (2014) Harnessing oil sands microbial communities for use in ex situ naphthenic acid bioremediation. Chemosphere 97:78–85

    Article  CAS  PubMed  Google Scholar 

  15. McKenzie N, Yue S, Liu X, Ramsay BA, Ramsay JA (2014) Biodegradation of naphthenic acids in oils sands process waters in an immobilized soil/sediment bioreactor. Chemosphere 109:164–172

    Article  CAS  PubMed  Google Scholar 

  16. Cunningham JA, Rahme H, Hopkins GD, Lebron C, Reinhard M (2001) Enhanced in situ bioremediation of BTEX-contaminated groundwater by combined injection of nitrate and sulfate. Environ Sci Technol 35:1663–1670

    Article  CAS  PubMed  Google Scholar 

  17. Ramos D, da Silva M, Chiaranda H, Alvarez PJ, Corseuil H (2013) Biostimulation of anaerobic BTEX biodegradation under fermentative methanogenic conditions at source-zone groundwater contaminated with a biodiesel blend (B20). Biodegradation 24:333–341

    Article  CAS  PubMed  Google Scholar 

  18. Liao C-S, Chen L-C, Chen B-S, Lin S-H (2010) Bioremediation of endocrine disruptor di-n-butyl phthalate ester by Deinococcus radiodurans and Pseudomonas stutzeri. Chemosphere 78:342–346

    Article  CAS  PubMed  Google Scholar 

  19. He Z, Xiao H, Tang L, Min H, Lu Z (2013) Biodegradation of di-n-butyl phthalate by a stable bacterial consortium, HD-1, enriched from activated sludge. Bioresour Technol 128:526–532

    Article  CAS  PubMed  Google Scholar 

  20. Amor L, Kennes C, Veiga MC (2001) Kinetics of inhibition in the biodegradation of monoaromatic hydrocarbons in presence of heavy metals. Bioresour Technol 78:181–185

    Article  CAS  PubMed  Google Scholar 

  21. Sandrin TR, Maier RM (2003) Impact of metals on the biodegradation of organic pollutants. Environ Health Perspect 111:1093–1101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Olaniran AO, Balgobind A, Pillay B (2013) Bioavailability of heavy metals in soil: impact on microbial biodegradation of organic compounds and possible improvement strategies. Int J Mol Sci 14:10197–10228

    Article  PubMed  PubMed Central  Google Scholar 

  23. Galarneau E, Hollebone BP, Yang Z, Schuster J (2014) Preliminary measurement-based estimates of PAH emissions from oil sands tailings ponds. Atmos Environ 97:332–335

    Article  CAS  Google Scholar 

  24. Kannel PR, Gan TY (2012) Naphthenic acids degradation and toxicity mitigation in tailings wastewater systems and aquatic environments: a review. J Environ Sci Health A Tox Hazard Subst Environ Eng 47:1–21

    Article  CAS  PubMed  Google Scholar 

  25. Armstrong SA, Headley JV, Peru KM, Mikula RJ, Germida JJ (2010) Phytotoxicity and naphthenic acid dissipation from oil sands fine tailings treatments planted with the emergent macrophyte Phragmites australis. J Environ Sci Health A Tox Hazard Subst Environ Eng 45:1008–1016

    Article  CAS  PubMed  Google Scholar 

  26. Quesnel DM, Bhaskar IM, Gieg LM, Chua G (2011) Naphthenic acid biodegradation by the unicellular alga Dunaliella tertiolecta. Chemosphere 84:504–511

    Article  CAS  PubMed  Google Scholar 

  27. Han X, MacKinnon MD, Martin JW (2009) Estimating the in situ biodegradation of naphthenic acids in oil sands process waters by HPLC/HRMS. Chemosphere 76:63–70

    Article  CAS  PubMed  Google Scholar 

  28. Del Rio LF, Hadwin AK, Pinto LJ, MacKinnon MD, Moore MM (2006) Degradation of naphthenic acids by sediment micro-organisms. J Appl Microbiol 101:1049–1061

    Article  PubMed  Google Scholar 

  29. Clemente JS, MacKinnon MD, Fedorak PM (2004) Aerobic biodegradation of two commercial naphthenic acids preparations. Environ Sci Technol 38:1009–1016

    Article  CAS  PubMed  Google Scholar 

  30. Lu X-Y, Zhang T, Fang H-P (2011) Bacteria-mediated PAH degradation in soil and sediment. Appl Microbiol Biotechnol 89:1357–1371

    Article  CAS  PubMed  Google Scholar 

  31. Fernández-Luqueño F, Valenzuela-Encinas C, Marsch R, Martínez-Suárez C, Vázquez-Núñez E, Dendooven L (2011) Microbial communities to mitigate contamination of PAHs in soil—possibilities and challenges: a review. Environ Sci Pollut Res Int 18:12–30

    Article  PubMed  Google Scholar 

  32. Saidi-Mehrabad A, He Z, Tamas I et al (2013) Methanotrophic bacteria in oilsands tailings ponds of northern Alberta. ISME J 7:908–921

    Article  CAS  PubMed  Google Scholar 

  33. Gargouri B, Karray F, Mhiri N, Aloui F, Sayadi S (2014) Bioremediation of petroleum hydrocarbons-contaminated soil by bacterial consortium isolated from an industrial wastewater treatment plant. J Chem Technol Biotechnol 89:978–987

    Article  CAS  Google Scholar 

  34. Wang X-B, Chi C-Q, Nie Y et al (2011) Degradation of petroleum hydrocarbons (C6–C40) and crude oil by a novel Dietzia strain. Bioresour Technol 102:7755–7761

    Article  CAS  PubMed  Google Scholar 

  35. Bruins MR, Kapil S, Oehme FW (2000) Microbial resistance to metals in the environment. Ecotoxicol Environ Saf 45:198–207

    Article  CAS  PubMed  Google Scholar 

  36. Harrison JJ, Ceri H, Turner RJ (2007) Multimetal resistance and tolerance in microbial biofilms. Nat Rev Microbiol 5:928–938

    Article  CAS  PubMed  Google Scholar 

  37. Hall-Stoodley L, Costerton JW, Stoodley P (2004) Bacterial biofilms: from the natural environment to infectious diseases. Nat Rev Microbiol 2:95–108

    Article  CAS  PubMed  Google Scholar 

  38. Stewart PS (2003) Diffusion in biofilms. J Bacteriol 185:1485–1491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Fang L, Wei X, Cai P et al (2011) Role of extracellular polymeric substances in Cu(II) adsorption on Bacillus subtilis and Pseudomonas putida. Bioresour Technol 102:1137–1141

    Article  CAS  PubMed  Google Scholar 

  40. d’Abzac P, Bordas F, Joussein E, van Hullebusch ED, Lens PN, Guibaud G (2013) Metal binding properties of extracellular polymeric substances extracted from anaerobic granular sludges. Environ Sci Pollut Res Int 20:4509–4519

    Article  PubMed  Google Scholar 

  41. Klapper I, Rupp CJ, Cargo R, Purvedorj B, Stoodley P (2002) Viscoelastic fluid description of bacterial biofilm material properties. Biotechnol Bioeng 80:289–296

    Article  CAS  PubMed  Google Scholar 

  42. Stoodley P, Cargo R, Rupp CJ, Wilson S, Klapper I (2002) Biofilm material properties as related to shear-induced deformation and detachment phenomena. J Ind Microbiol Biotechnol 29:361–367

    Article  CAS  PubMed  Google Scholar 

  43. Todhanakasem T, Sangsutthiseree A, Areerat K, Young GM, Thanonkeo P (2014) Biofilm production by Zymomonas mobilis enhances ethanol production and tolerance to toxic inhibitors from rice bran hydrolysate. N Biotechnol 31:451–459

    Article  CAS  PubMed  Google Scholar 

  44. Hansen SK, Rainey PB, Haagensen JA, Molin S (2007) Evolution of species interactions in a biofilm community. Nature 445:533–536

    Article  CAS  PubMed  Google Scholar 

  45. Burmolle M, Ren D, Bjarnsholt T, Sorensen SJ (2014) Interactions in multispecies biofilms: do they actually matter? Trends Microbiol 22:84–91

    Article  PubMed  Google Scholar 

  46. Elias S, Banin E (2012) Multi-species biofilms: living with friendly neighbors. FEMS Microbiol Rev 36:990–1004

    Article  CAS  PubMed  Google Scholar 

  47. Schwering M, Song J, Louie M, Turner RJ, Ceri H (2013) Multi-species biofilms defined from drinking water microorganisms provide increased protection against chlorine disinfection. Biofouling 29:917–928

    Article  CAS  PubMed  Google Scholar 

  48. McBain AJ (2009) In vitro biofilm models: an overview. In: Allen IL, Sima S, Geoffrey MG (eds) Advances in applied microbiology. Academic, San Diego, pp 99–132

    Google Scholar 

  49. Pham VHT, Kim J (2012) Cultivation of unculturable soil bacteria. Trends Biotechnol 30:475–484

    Article  CAS  PubMed  Google Scholar 

  50. Golby S, Ceri H, Gieg LM, Chatterjee I, Marques LLR, Turner RJ (2012) Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond. FEMS Microbiol Ecol 79:240–250

    Article  CAS  PubMed  Google Scholar 

  51. Gavrilescu M, Macoveanu M (2000) Attached-growth process engineering in wastewater treatment. Bioprocess Eng 23:95–106

    Article  CAS  Google Scholar 

  52. Nicolella C, van Loosdrecht MC, Heijnen JJ (2000) Wastewater treatment with particulate biofilm reactors. J Biotechnol 80:1–33

    Article  CAS  PubMed  Google Scholar 

  53. Wilderer PA, McSwain BS (2004) The SBR and its biofilm application potentials. Water Sci Technol 50:1–10

    CAS  PubMed  Google Scholar 

  54. Sundar K, Sadiq IM, Mukherjee A, Chandrasekaran N (2011) Bioremoval of trivalent chromium using Bacillus biofilms through continuous flow reactor. J Hazard Mater 196:44–51

    Article  CAS  PubMed  Google Scholar 

  55. Chang WC, Hsu GS, Chiang SM, Su MC (2006) Heavy metal removal from aqueous solution by wasted biomass from a combined AS-biofilm process. Bioresour Technol 97:1503–1508

    Article  CAS  PubMed  Google Scholar 

  56. Costley SC, Wallis FM (2001) Bioremediation of heavy metals in a synthetic wastewater using a rotating biological contactor. Water Res 35:3715–3723

    Article  CAS  PubMed  Google Scholar 

  57. Quagraine EK, Peterson HG, Headley JV (2005) In situ bioremediation of naphthenic acids contaminated tailing pond waters in the athabasca oil sands region—demonstrated field studies and plausible options: a review. J Environ Sci Health A Tox Hazard Subst Environ Eng 40:685–722

    Article  CAS  PubMed  Google Scholar 

  58. Harrison JJ, Ceri H, Yerly J et al (2006) The use of microscopy and three-dimensional visualization to evaluate the structure of microbial biofilms cultivated in the Calgary Biofilm Device. Biol Proc Online 8:194–215

    Article  CAS  Google Scholar 

  59. Ritalahti KM, Amos BK, Sung Y, Wu Q, Koenigsberg SS, Loffler FE (2006) Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl Environ Microbiol 72:2765–2774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Harrison JJ, Stremick CA, Turner RJ, Allan ND, Olson ME, Ceri H (2010) Microtiter susceptibility testing of microbes growing on peg lids: a miniaturized biofilm model for high-throughput screening. Nat Protoc 5:1236–1254

    Article  CAS  PubMed  Google Scholar 

  61. Harrison JJ, Turner RJ, Ceri H (2005) High-throughput metal susceptibility testing of microbial biofilms. BMC Microbiol 5:53

    Article  PubMed  PubMed Central  Google Scholar 

  62. O’Toole GA (2011) Microtiter dish biofilm formation assay. J Vis Exp. doi:10.3791/2437

    PubMed  PubMed Central  Google Scholar 

  63. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    Article  CAS  PubMed  Google Scholar 

  64. Ceri H, Olson ME, Stremick C, Read RR, Morck D, Buret A (1999) The Calgary biofilm device: new technology for rapid determination of antibiotic susceptibilities of bacterial biofilms. J Clin Microbiol 37:1771–1776

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Rogers VV, Liber K, MacKinnon MD (2002) Isolation and characterization of naphthenic acids from Athabasca oil sands tailings pond water. Chemosphere 48:519–527

    Article  CAS  PubMed  Google Scholar 

  66. Scott AC, Young RF, Fedorak PM (2008) Comparison of GC–MS and FTIR methods for quantifying naphthenic acids in water samples. Chemosphere 73:1258–1264

    Article  CAS  PubMed  Google Scholar 

  67. Yen T-W, Marsh WP, MacKinnon MD, Fedorak PM (2004) Measuring naphthenic acids concentrations in aqueous environmental samples by liquid chromatography. J Chromatogr A 1033:83–90

    Article  CAS  PubMed  Google Scholar 

  68. Clemente JS, Fedorak PM (2005) A review of the occurrence, analyses, toxicity, and biodegradation of naphthenic acids. Chemosphere 60:585–600

    Article  CAS  PubMed  Google Scholar 

  69. Merlin M, Guigard SE, Fedorak PM (2007) Detecting naphthenic acids in waters by gas chromatography–mass spectrometry. J Chromatogr A 1140:225–229

    Article  CAS  PubMed  Google Scholar 

  70. Headley JV, Peru KM, Barrow MP (2009) Mass spectrometric characterization of naphthenic acids in environmental samples: a review. Mass Spectrom Rev 28:121–134

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada, T2N 1N4

    Joe Lemire, Marc Demeter & Raymond J. Turner

  2. Biofilm Research Group, University of Calgary, Calgary, AB, Canada

    Joe Lemire, Marc Demeter & Raymond J. Turner

Authors
  1. Joe Lemire
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marc Demeter
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Raymond J. Turner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Raymond J. Turner .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Essex , Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer-Verlag Berlin Heidelberg

About this protocol

Cite this protocol

Lemire, J., Demeter, M., Turner, R.J. (2015). Protocols for Harvesting a Microbial Community Directly as a Biofilm for the Remediation of Oil Sands Process Water. In: McGenity, T., Timmis, K., Nogales, B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_55

Download citation

  • DOI: https://doi.org/10.1007/8623_2015_55

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-53110-5

  • Online ISBN: 978-3-662-53111-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation