Skip to main content

Modelling the Environmental Fate of Petroleum Hydrocarbons During Bioremediation

  • Protocol
  • First Online:
Hydrocarbon and Lipid Microbiology Protocols

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

  • 771 Accesses

Abstract

This chapter provides the key steps and parameters required for three different numerical modelling approaches to predict the environmental fate of petroleum hydrocarbons in contaminated soils during bioremediation. The first approach is the molecular dynamic simulation which is used to characterise the molecular-scale adsorption, the diffusion and the distribution of the saturate, aromatic, resin and asphaltene (SARA) fractions of oil. Such approach provides insights into the microscopic aggregation, the sequestration and the collision mechanisms which are essential for a better understanding of hydrocarbon bioavailability and biodegradation. The second approach is the use of fugacity modelling to compute the equilibrium distribution of the aliphatic and aromatic hydrocarbons in an environmental matrix composed of four compartments: soil, water, air and nonaqueous phase liquid (NAPL). Further to this, the contribution of the biotic and abiotic processes to the loss of petroleum hydrocarbons including (1) biodegradation in soil and NAPL, (2) advection in air, (3) leaching from soil and (4) diffusion at the soil–air, soil–water and soil–air boundaries can be estimated during biopiling experiments. The third approach is the use of machine learning (ML), an assumption-free data mining method, to predict the changes in the bioavailability of polycyclic aromatic hydrocarbons (PAHs) in contaminated soils. The main advantage of ML models is that they are data-based technique allowing computers to learn and recognise the patterns of the empirical data and work well with highly non-linear systems without relying on prior knowledge on bioremediation processes which make their prediction more realistic than conventional statistical methods. ML outputs can be integrated into microbial degradation models to support decision making for the assessment of bioremediation end points.

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

Access this chapter

eBook
USD 16.99
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

Institutional subscriptions

Similar content being viewed by others

References

  1. Wu G, He L, Chen D (2013) Sorption and distribution of asphaltene, resin, aromatic and saturate fractions of heavy crude oil on quartz surface: molecular dynamic simulation. Chemosphere 92:1465–1471

    Article  CAS  PubMed  Google Scholar 

  2. Viani A, Gualtieri AF, Artioli G (2002) The nature of disorder in montmorillonite by simulation of X-ray powder patterns. Am Mineral 87:966–975

    Article  CAS  Google Scholar 

  3. Teppen BJ, Rasmussen K, Bertsch PM, Miller DM, Schäfer L (1997) Molecular dynamics modeling of clay minerals. 1. Gibbsite, kaolinite, pyrophyllite, and beidellite. J Phys Chem B 101:1579–1587

    Article  CAS  Google Scholar 

  4. Schulten HR, Schnitzer M (1995) Three-dimensional models for humic acids and soil organic matter. Naturwissenschaften 82:487–498

    Article  CAS  Google Scholar 

  5. Sutton R, Sposito G, Diallo MS, Schulten HR (2005) Molecular simulation of a model of dissolved organic matter. Environ Toxicol Chem 24:1902–1911

    Article  CAS  PubMed  Google Scholar 

  6. Niederer C, Goss KU (2007) Quantum chemical modeling of humic acid/air equilibrium partitioning of organic vapors. Environ Sci Technol 41:3646–3652

    Article  CAS  PubMed  Google Scholar 

  7. Sein JLT, Varnum JM, Jansen SA (1999) Conformational modeling of a new building block of humic acid: approaches to the lowest energy conformer. Environ Sci Technol 33:546–552

    Article  CAS  Google Scholar 

  8. Sutton R, Sposito G (2006) Molecular simulation of humic substance–Ca-montmorillonite complexes. Geochim Cosmochim Acta 70:3566–3581

    Article  CAS  Google Scholar 

  9. Zeng QH, Yu AB, Lu GQ, Standish RK (2003) Molecular dynamics simulation of organic–inorganic nanocomposites: layering behavior and interlayer structure of organoclays. Chem Mater 15:4732–4738

    Article  CAS  Google Scholar 

  10. Kuznicki T, Masliyah JH, Bhattacharjee S (2009) Aggregation and partitioning of model asphaltenes at toluene-water interfaces: molecular dynamics simulations. Energy Fuel 23:5027–5035

    Article  CAS  Google Scholar 

  11. Alshareef AH, Scherer A, Tan X, Azyat K, Stryker JM, Tykwinski RR, Gray MR (2012) Effect of chemical structure on the cracking and coking of archipelago model compounds representative of asphaltenes. Energy Fuel 26:1828–1843

    Article  CAS  Google Scholar 

  12. Sjöblom J, Simon S, Xu Z (2015) Model molecules mimicking asphaltenes. Adv Colloid Interface Sci 218:1–16

    Article  PubMed  Google Scholar 

  13. Wu G, Zhu X, Ji H, Chen D (2015) Molecular modeling of interactions between heavy crude oil and the soil organic matter coated quartz surface. Chemosphere 119:242–249

    Article  CAS  PubMed  Google Scholar 

  14. Ren B, Gao H, Cao Y, Jia L (2015) In silico understanding of the cyclodextrin–phenanthrene hybrid assemblies in both aqueous medium and bacterial membranes. J Hazard Mater 285:148–156

    Article  CAS  PubMed  Google Scholar 

  15. Semple KT, Morriss AWJ, Paton GI (2003) Bioavailability of hydrophobic organic contaminants in soils: fundamental concepts and techniques for analysis. Eur J Soil Sci 54:809–818

    Article  CAS  Google Scholar 

  16. Reid BJ, Jones KC, Semple KT (2000) Bioavailability of persistent organic pollutants in soils and sediments – a perspective on mechanisms, consequences and assessment. Environ Pollut 108:103–112

    Article  CAS  PubMed  Google Scholar 

  17. Bru R, Maria Carrasco J, Costa Paraíba L (1998) Unsteady state fugacity model by a dynamic control system. Appl Math Model 22:485–494

    Article  Google Scholar 

  18. Lewis GN (1901) The law of physico-chemical change. Proc Am Acad Arts Sci 37:49–69

    Article  Google Scholar 

  19. Mackay D (2001) Multimedia environmental models: the fugacity approach. Lewis, Chelsea

    Book  Google Scholar 

  20. Pollard SJT, Hoffmann RE, Hrudey SE (1993) Screening of risk management options for abandoned wood-preserving plant sites in Alberta, Canada. Can J Civ Eng 20:787–800

    Article  Google Scholar 

  21. Mills WJ, Bennett ER, Schmidt CE, Thibodeaux LJ (2004) Obtaining quantitative vapor emissions estimates of polychlorinated biphenyls and other semivolatile organic compounds from contaminated sites. Environ Toxicol Chem 23:2457–2464

    Article  CAS  PubMed  Google Scholar 

  22. Coulon F, Whelan MJ, Paton GI, Semple KT, Villa R, Pollard SJT (2010) Multimedia fate of petroleum hydrocarbons in the soil: oil matrix of constructed biopiles. Chemosphere 81:1454–1462

    Article  CAS  PubMed  Google Scholar 

  23. Pollard SJT, Hough RL, Kim KH, Bellarby J, Paton G, Semple KT, Coulon F (2008) Fugacity modelling to predict the distribution of organic contaminants in the soil:oil matrix of constructed biopiles. Chemosphere 71:1432–1439

    Article  CAS  PubMed  Google Scholar 

  24. Shafi S, Sweetman A, Hough RL, Smith R, Rosevear A, Pollard SJT (2006) Evaluating fugacity models for trace components in landfill gas. Environ Pollut 144:1013–1023

    Article  CAS  PubMed  Google Scholar 

  25. Turan NG, Mesci B, Ozgonenel O (2011) Artificial neural network (ANN) approach for modeling Zn (II) adsorption from leachate using a new biosorbent. Chem Eng J 173:98–105

    Article  CAS  Google Scholar 

  26. Giri A, Patel R, Mahapatra S (2011) Artificial neural network (ANN) approach for modelling of arsenic (III) biosorption from aqueous solution by living cells of Bacillus cereus biomass. Chem Eng J 178:15–25

    Article  CAS  Google Scholar 

  27. Turan NG, Mesci B, Ozgonenel O (2011) The use of artificial neural networks (ANN) for modeling of adsorption of Cu (II) from industrial leachate by pumice. Chem Eng J 171:1091–1097

    Article  CAS  Google Scholar 

  28. Inal F (2006) Artificial neural network predictions of polycyclic aromatic hydrocarbon formation in premixed n-heptane flames. Fuel Process Technol 87:1031–1036

    Article  CAS  Google Scholar 

  29. Wu G, Kechavarzi C, Li X, Wu S, Pollard SJ, Sui H, Coulon F (2013) Machine learning models for predicting PAHs bioavailability in compost amended soils. Chem Eng J 223:747–754

    Article  CAS  Google Scholar 

  30. Sun H (1998) COMPASS: an ab initio force-field optimized for condensed-phase applications overview with details on alkane and benzene compounds. J Phys Chem B 102:7338–7364

    Article  CAS  Google Scholar 

  31. Kuznicki T, Masliyah JH, Bhattacharjee S (2008) Molecular dynamics study of model molecules resembling asphaltene-like structures in aqueous organic solvent systems. Energy Fuel 22:2379–2389

    Article  CAS  Google Scholar 

  32. Murgich J, Rodríguez J, Aray Y (1996) Molecular recognition and molecular mechanics of micelles of some model asphaltenes and resins. Energy Fuel 10:68–76

    Article  CAS  Google Scholar 

  33. Verstraete J, Schnongs P, Dulot H, Hudebine D (2010) Molecular reconstruction of heavy petroleum residue fractions. Chem Eng Sci 65:304–312

    Article  CAS  Google Scholar 

  34. Wu G, Kechavarzi C, Li X, Sui H, Pollard SJT, Coulon F (2013) Influence of mature compost amendment on total and bioavailable polycyclic aromatic hydrocarbons in contaminated soils. Chemosphere 90:2240–2246

    Article  CAS  PubMed  Google Scholar 

  35. Risdon GC, Pollard SJT, Brassington KJ, McEwan JN, Paton GI, Semple KT, Coulon F (2008) Development of an analytical procedure for weathered hydrocarbon contaminated soils within a UK risk-based framework. Anal Chem 80:7090–7096

    Article  CAS  PubMed  Google Scholar 

  36. TPHCWG (1998) Total petroleum hydrocarbon criteria working group series volume 2: composition of petroleum mixtures. Amherst Scientific, Amherst

    Google Scholar 

  37. Mitchell T (1997) Machine learning. McGraw Hill, New York

    Google Scholar 

  38. USEPA (1989) Method 610-Polynuclear Aromatic Hydrocarbons, methods for organic chemical analysis of municipal and industrial wastewater. US Environmental Protection Agency, Washington, DC

    Google Scholar 

  39. Cygan RT, Liang JJ, Kalinichev AG (2004) Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field. J Phys Chem B 108:1255–1266

    Article  CAS  Google Scholar 

  40. Lopes PEM, Murashov V, Tazi M, Demchuk E, MacKerell AD (2006) Development of an empirical force field for silica. Application to the quartz-water interface. J Phys Chem B 110:2782–2792

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Jian C, Tang T, Bhattacharjee S (2013) Probing the effect of side-chain length on the aggregation of a model asphaltene using molecular dynamics simulations. Energy Fuel 27:2057–2067

    Article  CAS  Google Scholar 

  42. Bandela A, Chinta JP, Hinge VK, Dikundwar AG, Row TNG, Rao CP (2011) Recognition of polycyclic aromatic hydrocarbons and their derivatives by the 1,3-dinaphthalimide conjugate of calix[4]arene: emission, absorption, crystal structures, and computational studies. J Org Chem 76:1742–1750

    Article  CAS  PubMed  Google Scholar 

  43. Frenkel D, Smit B (2002) Understanding molecular simulation: from algorithms to applications. Academic, San Diego

    Google Scholar 

  44. Brown DG, Knightes CD, Peters CA (1999) Risk assessment for polycyclic aromatic hydrocarbon NAPLs using component fractions. Environ Sci Technol 33:4357–4363

    Article  CAS  Google Scholar 

  45. Haykin S (1999) Neural networks: a comprehensive foundation. Prentice Hall, New York

    Google Scholar 

  46. Fletcher D, Goss E (1993) Forecasting with neural networks. An application using bankruptcy data. Inf Manag 24:159–167

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Frédéric Coulon .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer-Verlag Berlin Heidelberg

About this protocol

Cite this protocol

Wu, G., Coulon, F. (2015). Modelling the Environmental Fate of Petroleum Hydrocarbons During Bioremediation. In: McGenity, T., Timmis, K., Nogales Fernández, B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_121

Download citation

  • DOI: https://doi.org/10.1007/8623_2015_121

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-49309-0

  • Online ISBN: 978-3-662-49310-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics