Advertisement

Bioremediation of Hydrocarbons and Chlorinated Solvents in Groundwater: Characterisation, Design and Performance Assessment

  • S. F. ThorntonEmail author
  • P. Morgan
  • S. A. Rolfe
Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

Bioremediation is an accepted and widely implemented technology for the management of groundwater contaminated by hydrocarbon and chlorinated solvent compounds. This chapter reviews the general application of bioremediation processes within a cost–benefit and risk assessment framework, which considers different contaminant types and their properties, release contexts, and the strengths and limitations of available approaches. The pathways, reaction mechanisms and microorganisms responsible for biodegradation of hydrocarbons and chlorinated solvents under aerobic and different anaerobic conditions in groundwater are illustrated. The technical framework and methodology which underpins the characterisation of biodegradation processes for these organic compounds in groundwater is described, including relevant data reduction and interpretation techniques used for the performance assessment of intrinsic and engineered in situ bioremediation. This emphasises the integration of hydrochemical, stable isotope and molecular microbiological analysis with other data in site assessments for in situ bioremediation. Engineering scale-up of bioremediation in groundwater requires knowledge of scale-dependent processes which affect the implementation and performance assessment of this technology. Various methods are described to evaluate these. Comprehensive site investigation is necessary to design in situ bioremediation schemes, with focus on clear definition of the contaminant source and detailed subsurface characterisation of the aquifer geological, hydrogeological and geochemical properties which control groundwater flow and in situ biodegradation potential. This information is needed to develop conceptual site models supporting bioremediation implementation. Enhancement of bioremediation performance using methods based on bioaugmentation and biostimulation, and limitations related to contaminant bioavailability, are critically reviewed. Different design concepts can be devised to enhance and optimise treatment efficiency of engineered in situ bioremediation, by controlling the groundwater flow regime and amendment delivery. The monitoring requirements for process operation and verification are also discussed.

Keywords

Bioremediation Chlorinated solvents Contamination Groundwater Hydrocarbons Microbiology 

References

  1. 1.
    van Liedekerke M, Prokop G, Rabl-Berger S, Kibblewhite M, Louwagie G (2014) Progress in the management of contaminated sites in Europe. Report EUR 26376 EN, Office of the European Union, LuxembourgGoogle Scholar
  2. 2.
    Allen DJ, Darling WG, Davies J, Newell AJ, Gooddy DC, Collins AL (2014) Groundwater conceptual models: implications for evaluating diffuse pollution mitigation measures. Q J Eng Geol Hydrogeol 47:65–80CrossRefGoogle Scholar
  3. 3.
    Alvarez PJJ, Illman WA (2006) Bioremediation and natural attenuation. Process fundamentals and mathematical models. John Wiley & Sons Inc, Hoboken, p 614Google Scholar
  4. 4.
    National Academy of Sciences (1994) Alternatives for ground water clean-up. National Academy Press, Washington, p 336Google Scholar
  5. 5.
    U.S. Environmental Protection Agency (2006) In situ and ex situ biodegradation technologies for remediation of contaminated sites. Engineering issue, solid waste and emergency response, EPA 625/R-06/015, pp 22Google Scholar
  6. 6.
    ITRC (2002) A systematic approach to in situ bioremediation in groundwater including decision trees on in situ bioremediation for nitrates, carbon tetrachloride, and perchlorate. Interstate Technology & Regulatory Council, Washington, p 156, www.itrcweb.org Google Scholar
  7. 7.
    Megharaj M, Ramakrishnan B, Venkateswarlu K, Sethunathan N, Naidu R (2011) Bioremediation approaches for organic pollutants: a critical perspective. Environ Int 37:1362–1375PubMedCrossRefGoogle Scholar
  8. 8.
    Vidali M (2001) Bioremediation an overview. Pure Appl Chem 73:1163–1172CrossRefGoogle Scholar
  9. 9.
    Watanabe K (2001) Microorganisms relevant to bioremediation. Curr Opin Biotechnol 12:237–241PubMedCrossRefGoogle Scholar
  10. 10.
    ASTM (2010) Standard guide for risk-based corrective action. ASTM E2081 - 00(2010)e1Google Scholar
  11. 11.
    DEFRA and Environment Agency (2004) Model procedures for the management of land contamination. Environment Agency, BristolGoogle Scholar
  12. 12.
    Department of Environmental Regulation (2014) Assessment and management of contaminated sites. Contaminated sites guidelines. Department of Environmental Regulation, State of Western Australia, PerthGoogle Scholar
  13. 13.
    NICOLE (2004) Risk assessment comparison study. Network for industrially contaminated land in Europe, Apeldoorn, The Netherlands. http://www.nicole.org/uploadedfiles/2004-Risk-Assessment-Comparison-Study-finalreport.pdf
  14. 14.
    U.S. Environmental Protection Agency (2015) Risk assessment. http://www.epa.gov/risk/
  15. 15.
    ITRC (2008) Enhanced attenuation: chlorinated organics. EACO-1. Interstate Technology & Regulatory Council, Enhanced Attenuation: Chlorinated Organics Team, Washington, pp 109. www.itrcweb.org
  16. 16.
    ITRC (2011a) Green and sustainable remediation: state of the science and practice, GSR-1. Interstate Technology & Regulatory Council, Green and Sustainable Remediation Team, Washington, pp 84. www.itrcweb.org
  17. 17.
    ITRC (2011b) Green and sustainable remediation: a practical framework, GSR-2. Interstate Technology & Regulatory Council, Green and Sustainable Remediation Team, Washington, pp 135. www.itrcweb.org
  18. 18.
    SuRF International (2015) International SuRF groups and partners. www.claire.co.uk/surfinternational
  19. 19.
    Air Force Centre for Environmental Excellence (AFCEE) (1995) Technical protocol for implementing intrinsic remediation with long-term monitoring for natural attenuation of fuel contamination dissolved in groundwater, Vol 1 and 2. AFCEE, Transfer Division, Brooks Air Force Base, San Antonio,Google Scholar
  20. 20.
    ASTM (1998) Standard guide for remediation of ground water by natural attenuation at petroleum release sites. ASTM Standard Guide E1943-98Google Scholar
  21. 21.
    National Academy of Sciences (2000) Natural attenuation for groundwater remediation. Committee on Ground Water Clean-up Alternatives, National Research Council, National Academy Press, WashingtonGoogle Scholar
  22. 22.
    U.S. Environmental Protection Agency (1998) Technical protocol for evaluating natural attenuation of chlorinated solvents in ground water. Office of Research and Development, WashingtonGoogle Scholar
  23. 23.
    Environmental Agency (2000) Guidance on the assessment and monitoring of natural attenuation of contaminants in groundwater. R&D Publication 95, Environment Agency, BristolGoogle Scholar
  24. 24.
    Bardos RP, Morgan P, Swannell RPJ (2000) Application of in situ remediation technologies-1. Contextual framework. Land Contam Reclam 8:301–322Google Scholar
  25. 25.
    CL:AIRE (2010). Contaminated land remediation. DEFRA Research Project Final Report, SP1001, http://randd.defra.gov.uk/Default.aspx?Menu=Menu&Module=More&Location=None&Completed=0&ProjectID=16184#RelatedDocuments
  26. 26.
    Clu-In (2015) About remediation technologies. http://clu-in.org/remediation/
  27. 27.
    Rivett MO, Thornton SF (2008) Monitored natural attenuation of organic contaminants in groundwater: principles and application. Water Manag J 161:381–392Google Scholar
  28. 28.
    Boopathy R (2000) Factors limiting bioremediation technologies. Bioresour Technol 74:63–67CrossRefGoogle Scholar
  29. 29.
    CL:AIRE (2014) An illustrated handbook of LNAPL transport and fate in the subsurface. CL:AIRE, London. ISBN 978-1-905046-24-9. Download at www.claire.co.uk/LNAPL
  30. 30.
    ITRC (2005) Overview of in situ bioremediation of chlorinated ethene DNAPL source zones. BIODNAPL-1. Interstate Technology & Regulatory Council, Bioremediation of Dense Nonaqueous Phase Liquids (Bio DNAPL) Team, Washington, pp 89. www.itrcweb.org
  31. 31.
    Norris RD (1994) In-situ bioremediation of soils and groundwater contaminated with petroleum hydrocarbons. In: Norris RD et al (eds) Handbook of bioremediation. Lewis Publishers, Boca Raton, pp 17–37Google Scholar
  32. 32.
    Singh A, Kuhad RC, Ward OP (2009) Biological remediation of soil: an overview of global market and available technologies. In: Singh A, Kuhad RC, Ward OP (eds) Advances in applied bioremediation. Springer, DordrechtCrossRefGoogle Scholar
  33. 33.
    Sturman PJ, Stewart PS, Cunningham AB, Bouwer EJ, Wolfram JH (1995) Engineering scale-up of in situ bioremediation processes: a review. J Contam Hydrol 19:171–203CrossRefGoogle Scholar
  34. 34.
    Borden RC (1994) Natural bioremediation of hydrocarbon-contaminated ground water. In: Norris RD et al (eds) Handbook of bioremediation. Lewis Publishers, Boca Raton, pp 177–199Google Scholar
  35. 35.
    Vogel TM (1994) Natural bioremediation of chlorinated solvents. In: Norris RD et al (eds) Handbook of bioremediation. Lewis Publishers, Boca Raton, pp 201–225Google Scholar
  36. 36.
    Wiedemeier TH, Rifai HS, Newell CJ, Wilson JT (1999) Natural attenuation of fuels and chlorinated solvents in the subsurface. John Wiley and Sons, New YorkCrossRefGoogle Scholar
  37. 37.
    Williams GM, Pickup RW, Thornton SF, Lerner DN, Mallinson HEH, Moore Y, White C (2001) Biogeochemical characterisation of a coal-tar distillate plume. J Contam Hydrol 53:175–198PubMedCrossRefGoogle Scholar
  38. 38.
    Mattes TE, Alexander AK, Coleman NV (2010) Aerobic biodegradation of the chloroethenes: pathways, enzymes, ecology, and evolution. FEMS Microbiol Rev 34:445–475PubMedCrossRefGoogle Scholar
  39. 39.
    McElroy AE, Farrington JW, Teal JM (1989) Bioavailability of polycyclic aromatic hydrocarbons in the aquatic environment. In: Varanasi U (ed) Metabolism of polycyclic aromatic hydrocarbons in the aquatic environment. CRC Press, Boca RatonGoogle Scholar
  40. 40.
    Mortelmans K, Harworth S, Lawlor T, Speck W, Tainerand B, Zeiger E (1986) Salmonella mutagenicity tests. II. Results from the testing of 270 chemicals. Environ Mutagen 8:1–119PubMedCrossRefGoogle Scholar
  41. 41.
    Environment Agency (2003) An illustrated handbook of DNAPL transport and fate in the subsurface. Environment Agency, Bristol, p 67Google Scholar
  42. 42.
    Chapelle FH (1993) Groundwater microbiology and geochemistry. Wiley, New YorkGoogle Scholar
  43. 43.
    Das N, Chandran P (2011) Microbial degradation of petroleum hydrocarbon contaminants: an overview. Biotechnol Res Int 2011, 941810, 13 pagesPubMedGoogle Scholar
  44. 44.
    Reinhard M (1994) In-situ bioremediation technologies for petroleum-derived hydrocarbons based on alternate electron acceptors (other than molecular oxygen). In: Norris RD (ed) Handbook of bioremediation. Lewis Publishers, Boca Raton, pp 131–147Google Scholar
  45. 45.
    Bombach P, Richnow HH, Kastner M, Fischer A (2010) Current approaches for the assessment of in situ biodegradation. Appl Microbiol Biotechnol 86:839–852PubMedCrossRefGoogle Scholar
  46. 46.
    Banwart SA, Thornton SF (2003) The geochemistry and hydrology of groundwater bioremediation by natural attenuation. In: Head I, Singleton I (eds) Bioremediation: a critical review. Horizon Scientific Press, pp 93–138Google Scholar
  47. 47.
    Banwart SA, Thornton SF (2010) Natural attenuation of hydrocarbons in groundwater. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg, pp 2474–2486Google Scholar
  48. 48.
    Borden RC, Daniel RA, LeBrun LE IV, Davis CW (1997) Intrinsic biodegradation of MTBE and BTEX in a gasoline-contaminated aquifer. Water Resour Res 33:1105–1115CrossRefGoogle Scholar
  49. 49.
    Wilson RD, Thornton SF, Mackay DM (2004) Challenges in monitoring the natural attenuation of spatially variable plumes. Biodegradation 15:359–369PubMedCrossRefGoogle Scholar
  50. 50.
    Thornton SF, Quigley S, Spence M, Banwart SA, Bottrell S, Lerner DN (2001) Processes controlling the distribution and natural attenuation of dissolved phenolic compounds in a deep sandstone aquifer. J Contam Hydrol 53:233–267PubMedCrossRefGoogle Scholar
  51. 51.
    Thornton SF, Lerner DN, Banwart SA (2001) Assessing the natural attenuation of organic contaminants in aquifers using plume-scale electron and carbon balances: model development with analysis of uncertainty and parameter sensitivity. J Contam Hydrol 53:199–232PubMedCrossRefGoogle Scholar
  52. 52.
    Thornton SF, Baker KM, Bottrell SH, Rolfe SA, McNamee P, Forrest F, Duffield P, Wilson RD, Fairburn AW, Cieslak L (2014) Enhancement of in situ biodegradation of organic compounds in groundwater by targeted pump and treat intervention. Appl Geochem 48:28–40CrossRefGoogle Scholar
  53. 53.
    Wilkinson S, Nicklin S, Faull JL (2002) Biodegradation of fuel oils and lubricants: soil and water bioremediation options. In: Singh VR, Stapleton RD (eds) Biotransformations: bioremediation technology for health and environmental protection. Elsevier, Amsterdam, pp 69–100Google Scholar
  54. 54.
    Bouwer EJ, Zehnder AJB (1993) Bioremediation of organic compounds - putting microbial metabolism to work. Trends Biotechnol 11:360–367PubMedCrossRefGoogle Scholar
  55. 55.
    U.S. Environmental Protection Agency (2000) Engineered approaches to in situ bioremediation of chlorinated solvents: fundamentals and field applications. Solid waste and emergency response, EPA 542/R-00-008, pp 144Google Scholar
  56. 56.
    Lu X, Kampbell DH, Wilson JT (2006) Evaluation of the role of Dehalococcoides organisms in the natural attenuation of chlorinated ethylenes in ground water. US EPA/600/R-06/029, pp 121Google Scholar
  57. 57.
    Vogel TM, Criddle CS, McCarty PL (1987) Transformations of halogenated aliphatic compounds. Environ Sci Technol 22:722–736CrossRefGoogle Scholar
  58. 58.
    McCarty PL, Semprini L (1994) Ground-water treatment for chlorinated solvents. In: Norris RD et al (eds) Handbook of bioremediation. Lewis Publishers, Boca Raton, pp 87–116Google Scholar
  59. 59.
    Gerritse J, Drzyzga O, Kloetstra G, Keijmel M, Wiersum LP, Hutson R, Collins MD, Gottschal JC (1999) Influence of different electron donors and acceptors on dehalospiration of tetrachloroethene by Desulfitobacterium frappiere TCE1. Appl Environ Microbiol 65:5212–5221PubMedPubMedCentralGoogle Scholar
  60. 60.
    Leys D, Adrian L, Smidt H (2013) Organohalide respiration: microbes breathing chlorinated molecules. Philos Trans R Soc Lond Ser B Biol Sci 368, 20120316CrossRefGoogle Scholar
  61. 61.
    McCarty PL (1997) Breathing with chlorinated solvents. Science 276:1521PubMedCrossRefGoogle Scholar
  62. 62.
    Bunge M, Adrian L, Kraus A, Opel M, Lorenz WG, Andreesen JR, Gorisch H, Lechner U (2003) Reductive dehalogenation of chlorinated dioxins by an anaerobic bacterium. Nature 421:357–360PubMedCrossRefGoogle Scholar
  63. 63.
    Fennell DE, Nijenhuis I, Wilson SF, Zinder SH, Haggblom MM (2004) Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environ Sci Technol 38:2075–2081PubMedCrossRefGoogle Scholar
  64. 64.
    Poritz M, Schiffmann CL, Hause G, Heinemann U, Seifert J, Jehmlich N, von Bergen M, Nijenhuis I, Lechner U (2015) Dehalococcoides mccartyi strain DCMB5 respires a broad spectrum of chlorinated aromatic compounds. Appl Environ Microbiol 81:587–596PubMedPubMedCentralCrossRefGoogle Scholar
  65. 65.
    Hug LA, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L (2013) Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Philos Trans R Soc Lond B Biol Sci 368, 20120322PubMedPubMedCentralCrossRefGoogle Scholar
  66. 66.
    Löffler FE, Ritalahti KM, Zinder SH (2013) Dehalococcoides and reductive dechlorination of chlorinated solvents. In: Stroo HF, Leeson A, Ward CH (eds) Bioaugmentation for groundwater remediation. Springer, New York, pp 39–88CrossRefGoogle Scholar
  67. 67.
    Gossett JM, Zinder SH (1997) Microbiological aspects relevant to natural attenuation of chlorinated ethenes. In: Proceedings, US EPA symposium in natural attenuation of chlorinated organics in ground water. Dallas, pp 12–15, 11–13 Sept 1996. EPA/540/R-97/504/1997Google Scholar
  68. 68.
    Bradley PM, Chapelle FH (1998) Effect of contaminant concentration on aerobic microbial mineralization of DCE and VC in stream-bed sediments. Environ Sci Technol 32:553–557CrossRefGoogle Scholar
  69. 69.
    Bradley PM, Chapelle FH (1998) Microbial mineralization of VC and DCE under different terminal electron accepting conditions. Anaerobe 4:81–87PubMedCrossRefGoogle Scholar
  70. 70.
    Bradley PM, Chapelle FH, Wilson JT (1998) Field and laboratory evidence for intrinsic biodegradation of vinyl chloride contamination in a Fe III-reducing aquifer. J Contam Hydrol 31:111–127CrossRefGoogle Scholar
  71. 71.
    Bradley PM, Chapelle FH, Lovley DR (1998) Humic acids as electron acceptors for anaerobic microbial oxidation of vinyl chloride and dichloroethene. Appl Environ Microbiol 64:3102–3105PubMedPubMedCentralGoogle Scholar
  72. 72.
    Smits THM, Assal A, Hunkeler D, Holliger C (2011) Anaerobic degradation of vinyl chloride in aquifer microcosms. J Environ Qual 40:915–922PubMedCrossRefGoogle Scholar
  73. 73.
    RTDF (1997) Natural attenuation of chlorinated solvents in groundwater: principles and practices. Version 3.0. Remediation Technologies Development ForumGoogle Scholar
  74. 74.
    Coleman NV, Mattes TE, Gossett JM, Spain JC (2002) Phylogenetic and kinetic diversity of aerobic vinyl chloride-assimilating bacteria from contaminated sites. Appl Environ Microbiol 68:6162–6171PubMedPubMedCentralCrossRefGoogle Scholar
  75. 75.
    McCarty PL, Goltz MN, Hopkins GD, Dolan ME, Allan JP, Kawakami BT, Carrothers TJ (1998) Full-scale evaluation of in situ cometabolic degradation of trichloroethylene in groundwater through toluene injection. Environ Sci Technol 32:88–100CrossRefGoogle Scholar
  76. 76.
    Hunkeler D, Aravena R (2010) Investigating the origin and fate of organic contaminants in groundwater using stable isotope analysis. In: Aelion CM et al (eds) Environmental isotopes in biodegradation and bioremediation. CRC Press, Boca Raton, pp 249–292Google Scholar
  77. 77.
    Wilson JT (1998) Estimating biodegradation and attenuation rate constants. Seminars on monitored natural attenuation for ground water, 5-3 to 5-22. U.S. EPA/625/K-98/001Google Scholar
  78. 78.
    Buscheck T, O’Reilly K (1995) Protocol for monitoring intrinsic bioremediation in groundwater. Chevron Research and Technology Company, Health, Environment and Safety Group, p 20Google Scholar
  79. 79.
    Suarez MP, Rifai HS (1999) Biodegradation rates for fuel hydrocarbons and chlorinated solvents in groundwater. Biorem J 3:337–362CrossRefGoogle Scholar
  80. 80.
    Spence MJ, Bottrell SH, Thornton SF, Richnow HH, Spence KH (2005) Hydrochemical and isotopic effects associated with fuel biodegradation pathways in a chalk aquifer. J Contam Hydrol 79:67–88PubMedCrossRefGoogle Scholar
  81. 81.
    Wealthall GP, Thornton SF, Lerner DN (2002) Assessing the transport and fate of MTBE-amended petroleum hydrocarbons in the UK Chalk aquifer. In: Thornton SF, Oswald SO (eds) GQ2001: Natural and enhanced restoration of groundwater pollution, Sheffield, 16–21 June 2001. IAHS Publ. No. 275, pp 205-212Google Scholar
  82. 82.
    Kao CM, Wang YS (2001) Field investigation of natural attenuation and intrinsic biodegradation rates at an underground storage tank site. Environ Geol 40:622–631CrossRefGoogle Scholar
  83. 83.
    Bockelmann A, Zamfirescu D, Ptak T, Grathwohl P, Teutsch G (2003) Quantification of mass fluxes and natural attenuation rates at an industrial site with a limited monitoring network: a case study. J Contam Hydrol 60:97–121PubMedCrossRefGoogle Scholar
  84. 84.
    Hatfield K, Annable M, Cho J, Rao PSC, Klammler H (2004) A direct passive method for measuring water and contaminant fluxes in porous media. J Contam Hydrol 75:155–181PubMedCrossRefGoogle Scholar
  85. 85.
    Hunkeler D, Höhener P, Bernasconib S, Zeyera J (1999) Engineered in situ bioremediation of a petroleum hydrocarbon-contaminated aquifer: assessment of mineralization based on alkalinity, inorganic carbon and stable carbon isotope balances. J Contam Hydrol 37:201–223CrossRefGoogle Scholar
  86. 86.
    Ptak T, Piepenbrink M, Martac E (2004) Tracer tests for the investigation of heterogeneous porous media and stochastic modelling of flow and transport—a review of some recent developments. J Hydrol 294:122–163CrossRefGoogle Scholar
  87. 87.
    Azizian MF, Istok JD, Semprini L (2007) Evaluation of the in-situ aerobic cometabolism of chlorinated ethenes by toluene-utilizing microorganisms using push-pull tests. J Contam Hydrol 90:105–124PubMedCrossRefGoogle Scholar
  88. 88.
    Gieg LM, Alumbaugh RE, Field J, Jones J, Istok JD, Suflita JM (2009) Assessing in situ rates of anaerobic hydrocarbon bioremediation. Microb Biotechnol 2:222–233PubMedPubMedCentralCrossRefGoogle Scholar
  89. 89.
    Bjerg PL, Rügge K, Corsten J, Nielsen PH, Christensen TH (1999) Degradation of aromatic and chlorinated aliphatic hydrocarbons in the anaerobic part of the Grinsted landfill leachate plume: in situ microcosm and laboratory batch experiments. Ground Water 37:113–121CrossRefGoogle Scholar
  90. 90.
    Mandelbaum RT, Shati MR, Ronen D (1997) In situ microcosms in aquifer bioremediation studies. FEMS Microbiol Rev 20:489–502PubMedCrossRefGoogle Scholar
  91. 91.
    Nielsen PH, Christensen TH, Albrechtsen H-J, Gillham RW (1996) Performance of the in situ microcosm technique or measuring the degradation of organic chemicals in aquifers. Groundw Monit Rem 16:130–140CrossRefGoogle Scholar
  92. 92.
    Kästner M, Fischer A, Nijenhuis I, Geyer R, Stelzer N, Bombach P, Tebbe CC, Richnow HH (2006) Assessment of microbial in situ activity in contaminated aquifers. Eng Life Sci 6:234–251CrossRefGoogle Scholar
  93. 93.
    Stelzer N, Büning C, Pfeifer F, Dohrmann AB, Tebbe CC, Nijenhuis I, Kästner M, Richnow HH (2006) In situ microcosms to evaluate natural attenuation potentials in contaminated aquifers. Org Geochem 37:1394–1410CrossRefGoogle Scholar
  94. 94.
    Hunkeler D, Aravena R, Cox E (2002) Carbon isotopes as a tool to evaluate the origin and fate of vinyl chloride: laboratory experiments and modeling of isotope evolution. Environ Sci Technol 36:3378–3384PubMedCrossRefGoogle Scholar
  95. 95.
    Hunkeler D, Elsner M (2010) Principles and mechanisms of isotope fractionation. In: Aelion CM et al (eds) Environmental isotopes in biodegradation and bioremediation. CRC Press, Boca Raton, pp 43–78Google Scholar
  96. 96.
    Meckenstock RU, Morasch B, Griebler C, Richnow HH (2004) Stable isotope fractionation analysis as a tool to monitor biodegradation in contaminated aquifers. J Contam Hydrol 75:215–255PubMedCrossRefGoogle Scholar
  97. 97.
    Hunkeler D, Morasch B (2010) Isotope fractionation during transformation processes. In: Aelion CM et al (eds) Environmental isotopes in biodegradation and bioremediation. CRC Press, Boca Raton, pp 79–128Google Scholar
  98. 98.
    Chartrand MM, Waller A, Mattes TE, Elsner M, Lacrampe-Couloume G, Gossett JM, Edwards EA, Sherwood Lollar B (2005) Carbon isotopic fractionation during aerobic vinyl chloride degradation. Environ Sci Technol 39:1064–1070PubMedCrossRefGoogle Scholar
  99. 99.
    Chu K, Mahendra S, Song DL, Conrad ME, Alvarez-Cohen L (2004) Stable carbon isotope fractionation during aerobic biodegradation of chlorinated ethenes. Environ Sci Technol 38:3126–3130PubMedCrossRefGoogle Scholar
  100. 100.
    Tiehm A, Schmidt KR, Pfeifer B, Heidinger M, Ertl S (2008) Growth kinetics and stable carbon isotope fractionation during aerobic degradation of cis-1,2-dichloroethene and vinyl chloride. Water Res 42:2431–2438PubMedCrossRefGoogle Scholar
  101. 101.
    Höhener P, Aelion CM (2010) Fundamentals of environmental isotopes and their use in biodegradation. In: Aelion CM et al (eds) Environmental isotopes in biodegradation and bioremediation. CRC Press, Boca Raton, pp 3–22Google Scholar
  102. 102.
    Thornton SF, Bottrell SH, Spence KS, Pickup R, Spence MJ, Shah N, Mallinson HEHM, Richnow HH (2011) Assessment of MTBE biodegradation in contaminated groundwater using 13C and 14C analysis: field and laboratory microcosm studies. Appl Geochem 26:828–837CrossRefGoogle Scholar
  103. 103.
    Abe Y, Aravena R, Zopfi J, Shouakar-Stash O, Cox E, Roberts JD, Hunkeler D (2009) Carbon and chlorine isotope fractionation during aerobic oxidation and reductive dechlorination of vinyl chloride and cis-1,2-dichloroethene. Environ Sci Technol 43:101–107PubMedCrossRefGoogle Scholar
  104. 104.
    Hirschorn SK, Dinglasan MJ, Elsner M, Mancini SA, Lacrampe-Couloume G, Edwards EA, Sherwood Lollar B (2004) Pathway dependent isotopic fractionation during aerobic biodegradation of 1,2-dichloroethane. Environ Sci Technol 38:4775–4781PubMedCrossRefGoogle Scholar
  105. 105.
    Morasch B, Richnow HH, Schink B, Meckenstock R (2001) Stable hydrogen and carbon isotope fractionation during microbial toluene degradation: mechanistic and environmental aspects. Appl Environ Microbiol 67:4842–4849PubMedPubMedCentralCrossRefGoogle Scholar
  106. 106.
    Fischer A, Herklotz I, Herrmann S, Thullner M, Weelink SAB, Stams AJM, Scholmann M, Richnow HH, Vogt C (2008) Combined carbon and hydrogen isotope fractionation investigations for elucidating benzene biodegradation pathways. Environ Sci Technol 42:4356–4363PubMedCrossRefGoogle Scholar
  107. 107.
    Hunkeler D, Aravena R, Berry-Spark K, Cox E (2005) Assessment of degradation pathways in an aquifer with mixed chlorinated hydrocarbon contamination using stable carbon isotope analysis. Environ Sci Technol 39:5975–5981PubMedCrossRefGoogle Scholar
  108. 108.
    Mancini SA, Ulrich AC, Lacrampe-Couloume G, Sleep B, Edwards EA, Sherwood Lollar B (2003) Carbon and hydrogen isotopic fractionation during anaerobic biodegradation of benzene. Appl Environ Microbiol 69:191–198PubMedPubMedCentralCrossRefGoogle Scholar
  109. 109.
    Brungard KL, Munakata-Marr J, Johnson CA, Mandernack KW (2003) Stable carbon isotope fractionation of trans-1,2-dichloroethylene during co-metabolic degradation by methanotropic bacteria. Chem Geol 195:59–67CrossRefGoogle Scholar
  110. 110.
    Carreón-Diazconti C, Santamaría J, Berkompas J, Field JA, Brusseau ML (2009) Assessment of in-situ reductive dechlorination using compound-specific stable isotopes, functional-gene PCR, and geochemical data. Environ Sci Technol 43:4301–4307PubMedPubMedCentralCrossRefGoogle Scholar
  111. 111.
    Lee PKH, Conrad ME, Alvarez-Cohen L (2007) Stable carbon isotope fractionation of chloroethenes by dehalorespiring isolates. Environ Sci Technol 41:4277–4285PubMedCrossRefGoogle Scholar
  112. 112.
    Feisthauer S, Seidel M, Bombach P, Traube S, Knöller K, Wange M, Fachmann S, Richnow HH (2012) Characterization of the relationship between microbial degradation processes at a hydrocarbon contaminated site using isotopic methods. J Contam Hydrol 133:17–29PubMedCrossRefGoogle Scholar
  113. 113.
    Spence MJ, Bottrell S, Thornton SF, Lerner DN (2001) Isotopic modelling of the significance of sulphate reduction for phenol attenuation in a polluted aquifer. J Contam Hydrol 53:285–304PubMedCrossRefGoogle Scholar
  114. 114.
    Fischer A, Theuerkorn K, Stelzer N, Gehre M, Thullner M, Richnow HH (2007) Applicability of stable isotope fractionation analysis for the characterization of benzene biodegradation in a BTEX-contaminated aquifer. Environ Sci Technol 41:3689–3696PubMedCrossRefGoogle Scholar
  115. 115.
    Griebler C, Safinowski M, Vieth A, Richnow HH, Meckenstock RU (2004) Combined application of stable carbon isotope analysis and specific metabolites determination for assessing in situ degradation of aromatic hydrocarbons in a tar oil-contaminated aquifer. Environ Sci Technol 38:617–631PubMedCrossRefGoogle Scholar
  116. 116.
    Hunkeler D, Anderson N, Aravena R, Bernasconi SM, Butler BJ (2001) Hydrogen and carbon isotope fractionation during aerobic biodegradation of benzene. Environ Sci Technol 35:3462–3467PubMedCrossRefGoogle Scholar
  117. 117.
    Mancini SA, Lacrampe-Couloume G, Jonker H, van Breukelen BM, Groen J, Volkering F, Sherwood Lollar B (2002) Hydrogen isotopic enrichment: an indicator of biodegradation at a petroleum hydrocarbon contaminated field site. Environ Sci Technol 36:2464–2470PubMedCrossRefGoogle Scholar
  118. 118.
    Richnow HH, Annweiler E, Michaelis W, Meckenstock RU (2003) Microbial degradation of aromatic hydrocarbons in a contaminated aquifer monitored by 13C/12C isotope fractionation. J Contam Hydrol 64:59–72PubMedCrossRefGoogle Scholar
  119. 119.
    Badin A, Buttet G, Maillard J, Holliger C, Hunkeler D (2014) Multiple dual C-Cl isotope patterns associated with reductive dechlorination of tetrachloroethene. Environ Sci Technol 48:9179–9186PubMedCrossRefGoogle Scholar
  120. 120.
    Audí-Miró C, Cretnik S, Otero N, Palau J, Shouakar-Stash O, Elsner M (2013) Cl and C isotope analysis to assess the effectiveness of chlorinated ethene degradation by zero-valent iron: evidence from dual element and product isotope values. Appl Geochem 32:175–183CrossRefGoogle Scholar
  121. 121.
    Cretnik S, Thoreson KA, Bernstein A, Ebert K, Buchner D, Laskov C, Haderlein S, Shouakar-Stash O, Kliegman S, McNeill K, Elsner M (2013) Reductive dechlorination of TCE by chemical model systems in comparison to dehalogenating bacteria: insights from dual element isotope analysis (13C/12C, 37Cl/35Cl). Environ Sci Technol 47:6855–6863PubMedGoogle Scholar
  122. 122.
    Wiegert C, Mandalakis M, Knowles T, Polymenakou P, Aeppli C, Machackova J, Holmstrand H, Evershed RP, Pancost R, Gustafsson O (2013) Carbon and chlorine isotope fractionation during microbial degradation of tetra- and trichloroethene. Environ Sci Technol 47:6449–6456PubMedGoogle Scholar
  123. 123.
    Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS (2008) Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 11:198–204PubMedPubMedCentralCrossRefGoogle Scholar
  124. 124.
    Bekins BA, Cozzarelli IM, Godsy EM, Warren E, Essaid HI, Tuccillo ME (2001) Progression of natural attenuation processes at a crude oil spill site: II. Controls on spatial distribution of microbial populations. J Contam Hydrol 53:387–406PubMedCrossRefGoogle Scholar
  125. 125.
    Pickup RW, Rhodes G, Alamillo ML, Mallinson HEH, Thornton SF, Lerner DN (2001) Microbiological analysis of multi-level borehole samples from a contaminated groundwater system. J Contam Hydrol 53:269–284PubMedCrossRefGoogle Scholar
  126. 126.
    Holm PE, Nielsen PH, Albrechtsen HJ, Christensen TH (1992) Importance of unattached bacteria and bacteria attached to sediment in determining potentials for degradation of xenobiotic organic contaminants in an aerobic aquifer. Appl Environ Microbiol 58:3020–3026PubMedPubMedCentralGoogle Scholar
  127. 127.
    Rizoulis A, Elliott DR, Rolfe SA, Thornton SF, Banwart SA, Pickup RW, Scholes JS (2013) Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Microb Ecol 66:84–95PubMedCrossRefGoogle Scholar
  128. 128.
    Kovacik WP, Takai K, Mormile MR, McKinley JP, Brockman FJ, Fredrickson JK, Holben WE (2006) Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S°-reducing bacteria in a sulfate-rich environment. Environ Microbiol 8:141–155PubMedCrossRefGoogle Scholar
  129. 129.
    Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321–346PubMedCrossRefGoogle Scholar
  130. 130.
    Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160PubMedPubMedCentralCrossRefGoogle Scholar
  131. 131.
    Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K, Tamaki H, Tanaka M, Nakatsu CH, Kamagata Y (2014) A hidden pitfall in the preparation of agar media undermines microorganism cultivability. Appl Environ Microbiol 80:7659–7666PubMedPubMedCentralCrossRefGoogle Scholar
  132. 132.
    Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schaberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K (2015) A new antibiotic kills pathogens without detectable resistance. Nature 517:455–459PubMedCrossRefGoogle Scholar
  133. 133.
    Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437PubMedCrossRefGoogle Scholar
  134. 134.
    Berney M, Hammes F, Bosshard F, Weilenmann H-U, Egli T (2007) Assessment and interpretation of bacterial viability by using the LIVE/DEAD BacLight Kit in combination with flow cytometry. Appl Environ Microbiol 73:3283–3290PubMedPubMedCentralCrossRefGoogle Scholar
  135. 135.
    Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, VerBerkmoes NC, Hettich RL, Banfield JF (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci 107:8806–8811PubMedPubMedCentralCrossRefGoogle Scholar
  136. 136.
    Gross C, Reddy C, Dazzo F (2010) CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution. Microb Ecol 59:400–414PubMedCrossRefGoogle Scholar
  137. 137.
    Manefield M, Griffiths R, Bailey M, Whiteley A (2006) Stable isotope probing: a critique of its role in linking phylogeny and function, 1st edn. Springer, BerlinGoogle Scholar
  138. 138.
    Frostegård Å, Tunlid A, Bååth E (2011) Use and misuse of PLFA measurements in soils. Soil Biol Biochem 43:1621–1625CrossRefGoogle Scholar
  139. 139.
    Yao H, Chapman S, Thornton B, Paterson E (2015) 13C PLFAs: a key to open the soil microbial black box? Plant Soil 392:3–15CrossRefGoogle Scholar
  140. 140.
    Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4:R54PubMedPubMedCentralCrossRefGoogle Scholar
  141. 141.
    Siggins A, Gunnigle E, Abram F (2012) Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 80:265–280PubMedPubMedCentralCrossRefGoogle Scholar
  142. 142.
    Benndorf D, Balcke GU, Harms H, von Bergen M (2007) Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J 1:224–234PubMedCrossRefGoogle Scholar
  143. 143.
    Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341PubMedPubMedCentralCrossRefGoogle Scholar
  144. 144.
    van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30:418–426PubMedCrossRefGoogle Scholar
  145. 145.
    Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633–D642PubMedCrossRefGoogle Scholar
  146. 146.
    DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072PubMedPubMedCentralCrossRefGoogle Scholar
  147. 147.
    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196PubMedPubMedCentralCrossRefGoogle Scholar
  148. 148.
    Osborn AM, Moore ERB, Timmis KN (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2:39–50PubMedCrossRefGoogle Scholar
  149. 149.
    Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J (2010) Integrated microbial survey analysis of prokaryotic communities for the PhyloChip Microarray. Appl Environ Microbiol 76:5636–5638PubMedPubMedCentralCrossRefGoogle Scholar
  150. 150.
    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336PubMedPubMedCentralCrossRefGoogle Scholar
  151. 151.
    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541PubMedPubMedCentralCrossRefGoogle Scholar
  152. 152.
    Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA Stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68:5367–5373PubMedPubMedCentralCrossRefGoogle Scholar
  153. 153.
    Jeon CO, Park W, Padmanabhan P, DeRito C, Snape JR, Madsen EL (2003) Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment. Proc Natl Acad Sci 100:13591–13596PubMedPubMedCentralCrossRefGoogle Scholar
  154. 154.
    Maphosa F, de Vos WM, Schmidt H (2010) Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria. Trends Biotechnol 28:308–316PubMedCrossRefGoogle Scholar
  155. 155.
    Richardson RE (2013) Genomic insights into organohalide respiration. Curr Opin Biotechnol 24:498–505PubMedCrossRefGoogle Scholar
  156. 156.
    Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechol 31:814–821CrossRefGoogle Scholar
  157. 157.
    Amann R, Fuchs BM (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6:339–348PubMedCrossRefGoogle Scholar
  158. 158.
    Richardson RE, Bhupathiraju VK, Song DL, Goulet TA, Alvarez-Cohen L (2002) Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. Environ Sci Technol 36:2652–2662PubMedCrossRefGoogle Scholar
  159. 159.
    Freeborn RA, West KA, Bhupathiraju VK, Chauhan S, Rahm BG, Richardson RE, Alvarez-Cohen L (2005) Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors. Environ Sci Technol 39:8358–8368PubMedCrossRefGoogle Scholar
  160. 160.
    Muller AL, Kjeldsen KU, Rattei T, Pester M, Loy A (2015) Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases. ISME J 9:1152–1165PubMedCrossRefGoogle Scholar
  161. 161.
    Silva CC, Hayden H, Sawbridge T, Mele P, De Paula SO, Silva LCF, Vidigal PMP, Vicentini R, Sousa MP, Torres APR, Santiago VMJ, Oliveira VM (2013) Identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater. PLoS ONE 8, e61811PubMedPubMedCentralCrossRefGoogle Scholar
  162. 162.
    Tu Q, Yu H, He Z, Deng Y, Wu L, Van Nostrand JD, Zhou A, Voordeckers J, Lee Y-J, Qin Y, Hemme CL, Shi Z, Xue K, Yuan T, Wang A, Zhou J (2014) GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis. Mol Ecol Resour 14:914–928PubMedGoogle Scholar
  163. 163.
    Wu L, Liu X, Schadt CW, Zhou J (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72:4931–4941PubMedPubMedCentralCrossRefGoogle Scholar
  164. 164.
    Liang Y, Li G, Van Nostrand JD, He Z, Wu L, Deng Y, Zhang X, Zhou J (2009) Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field. FEMS Microbiol Ecol 70(2):324–333PubMedCrossRefGoogle Scholar
  165. 165.
    Bell T, Greer C, Yergeau E (2014) Metagenomics potential for bioremediation. In: Nelson KE (ed) Encyclopedia of metagenomics. Springer, New York, pp 1–11Google Scholar
  166. 166.
    Yergeau E, Sanschagrin S, Beaumier D, Greer CW (2012) Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils. PLoS ONE 7, e30058PubMedPubMedCentralCrossRefGoogle Scholar
  167. 167.
    dos Santos HF, Cury JC, do Carmo FL, dos Santos AL, Tiedje J, van Elsas JD, Rosado AS, Peixoto RS (2011) Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLoS ONE 6:e16943Google Scholar
  168. 168.
    Fleming JT, Sanseverino J, Sayler GS (1993) Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites. Environ Sci Technol 27:1068–1074CrossRefGoogle Scholar
  169. 169.
    Huang WE, Ferguson A, Singer AC, Lawson K, Thompson IP, Kalin RM, Larkin MJ, Bailey MJ, Whiteley AS (2009) Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell Raman-fluorescence in situ hybridization. Appl Environ Microbiol 75:234–241PubMedCrossRefGoogle Scholar
  170. 170.
    Huang WE, Stoecker K, Griffiths R, Newbold L, Daims H, Whiteley AS, Wagner M (2007) Raman-FISH: combining stable-isotope Raman spectroscopy and fluorescence in situ hybridization for the single cell analysis of identity and function. Environ Microbiol 9:1878–1889PubMedCrossRefGoogle Scholar
  171. 171.
    Davis C, Cort T, Dai D, Illangasekare TH, Munakata-Marr J (2003) Effects of heterogeneity and experimental scale on the biodegradation of diesel. Biodegradation 14:373–384PubMedCrossRefGoogle Scholar
  172. 172.
    El Fantroussi S, Agathos SN (2005) Is bioaugmentation a feasible strategy for pollutant removal and site remediation? Curr Opin Microbiol 8:268–275PubMedCrossRefGoogle Scholar
  173. 173.
    Sebate J, Vinas M, Solanas AM (2004) Laboratory-scale bioremediation experiments on hydrocarbon-contaminated soils. Int Biodeterior Biodegrad 54:19–25CrossRefGoogle Scholar
  174. 174.
    Cookson JT (1995) Bioremediation engineering: design and application. McGraw Hill, New York, p 524Google Scholar
  175. 175.
    Thomas JM, Ward CH (1994) Introduced organisms for subsurface bioremediation. In: Norris RD et al (eds) Handbook of bioremediation. Lewis Publishers, Boca Raton, pp 227–244Google Scholar
  176. 176.
    Bradley PM, Journey CA, Kirshtein JD, Voytek MA, Lacombe PJ, Imbrigiotta TE, Chapelle FH, Tiedeman CJ, Goode DJ (2012) Enhanced dichloroethene biodegradation in fractured rock under biostimulated and bioaugmented conditions. Remediat J 22:21–32CrossRefGoogle Scholar
  177. 177.
    Romantschuk M, Sarand I, Petänen T, Peltola R, Jonsson-Vihanne M, Koivula T, Yrjälä K, Haahtela K (2000) Means to improve the effect of in situ bioremediation of contaminated soil: an overview of novel approaches. Environ Pollut 107:179–185PubMedCrossRefGoogle Scholar
  178. 178.
    Santharam S, Ibbini J, Davis LC, Erickson LE (2011) Field study of biostimulation and bioaugmentation for remediation of tetrachloroethene in groundwater. Remediat J 21:51–68CrossRefGoogle Scholar
  179. 179.
    Laughlin D, Timmins B (2006) Use of a low-cost substrate in a continuous recirculation process to stimulate plumewide anaerobic dechlorination of chlorinated solvents. Remediation 3:93–107CrossRefGoogle Scholar
  180. 180.
    Cichocka D, Nikolausz M, Haest PJ, Nijenhuis I (2010) Tetrachloroethene conversion to ethene by a Dehalococcoides-containing enrichment culture from Bitterfeld. FEMS Microbiol Ecol 72:297–310PubMedCrossRefGoogle Scholar
  181. 181.
    Lyon DY, Vogel TM (2013) Bioaugmentation for groundwater remediation: an overview. In: Stroo HF, Leeson A, Ward CH (eds) Bioaugmentation for groundwater remediation. Springer, New York, pp 1–37CrossRefGoogle Scholar
  182. 182.
    Boon N, Verstraete W (2010) Bioaugmentation of hydrocarbons. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin/Heidelberg, pp 2532–2538Google Scholar
  183. 183.
    Thompson IP, van der Gast CJ, Ciric L, Singer AC (2005) Bioaugmentation for bioremediation: the challenge of strain selection. Environ Microbiol 7:909–915PubMedCrossRefGoogle Scholar
  184. 184.
    Diaz E (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. Int Microbiol 7:173–180PubMedGoogle Scholar
  185. 185.
    Bouchez T, Patureau D, Dabert P, Juretschko S, Doré J, Delgenès P, Moletta R, Wagner M (2000) Ecological study of a bioaugmentation failure. Environ Microbiol 2:179–190PubMedCrossRefGoogle Scholar
  186. 186.
    Schaefer CE, Lippincott DR, Steffan RJ (2010) Field-scale evaluation of bioaugmentation dosage for treating chlorinated ethenes. Groundw Monit Rem 30:113–124CrossRefGoogle Scholar
  187. 187.
    Greenwood PF, Wibrow S, George SJ, Tibbett M (2009) Hydrocarbon biodegradation and soil microbial community response to repeated oil exposure. Org Geochem 40:293–300CrossRefGoogle Scholar
  188. 188.
    Lamberts RF, Johnsen AR, Andersen O, Christensen JH (2008) Univariate and multivariate characterization of heavy fuel oil weathering and biodegradation in soil. Environ Pollut 156:297–305PubMedCrossRefGoogle Scholar
  189. 189.
    Liu P-WG, Whang LM, Chang TC, Tseng I-C, Pan P-T, Cheng S-S (2009) Verification of necessity for bioaugmentation—lessons from two batch case studies for bioremediation of diesel-contaminated soils. J Chem Technol Biotechnol 84:808–819CrossRefGoogle Scholar
  190. 190.
    Major DW, McMaster ML, Cox EE, Edwards EA, Dworatzek SM, Hendrickson ER, Starr MG, Payne JA, Buonamici LW (2003) Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. Environ Sci Technol 36:5106–5116CrossRefGoogle Scholar
  191. 191.
    Mrozik A, Miga S, Piotrowska-Seget Z (2011) Enhancement of phenol degradation by soil bioaugmentation with Pseudomonas sp JS150. J Appl Microbiol 111:1357–1370PubMedCrossRefGoogle Scholar
  192. 192.
    Hood ED, Major DW, Quinn JW, Yoon W-S, Gavaskar A, Edwards EA (2008) Demonstration of enhanced bioremediation in a TCE source area at Launch Complex 34, Cape Canaveral Air Force Station. Groundw Monit Rem 28:98–107CrossRefGoogle Scholar
  193. 193.
    Lesser LE, Johnson PC, Spinnler GE, Bruce CL, Salanitro JP (2010) Spatial variation in MTBE biodegradation activity of aquifer solids samples collected in the vicinity of a flow-through aerobic biobarrier. Groundw Monit Rem 30:63–72CrossRefGoogle Scholar
  194. 194.
    Lippincott D, Streger SH, Schaefer CE, Hinkle J, Stormo J, Steffan RJ (2015) Bioaugmentation and propane biosparging for in situ biodegradation of 1,4-dioxane. Groundw Monit Rem. doi: 10.1111/gwmr.12093 Google Scholar
  195. 195.
    Takeuchia M, Nanbab K, Iwamotoc H, Nireid H, Kusudae T, Kazaokae O, Owakid M, Furuya K (2005) In situ bioremediation of a cis-dichloroethylene-contaminated aquifer utilizing methane-rich groundwater from an uncontaminated aquifer. Water Res 39:2438–2444CrossRefGoogle Scholar
  196. 196.
    Giddings CGS, Liu F, Gossett JM (2010) Microcosm assessment of Polaromonas sp. JS666 as a bioaugmentation agent for degradation of cis-1,2-dichloroethene in aerobic, subsurface environments. Groundw Monit Rem 30:106–113CrossRefGoogle Scholar
  197. 197.
    Sleep BE, Seepersad DJ, Kaiguo MO, Heidorn CM, Hrapovic L, Morrill PL, McMaster ML, Hood ED, Lebron C, Sherwood Lollar BS, Major DW, Edwards EA (2006) Biological enhancement of tetrachloroethene dissolution and associated microbial community changes. Environ Sci Technol 40:3623–3633PubMedCrossRefGoogle Scholar
  198. 198.
    Paul D, Pandey G, Pandey J, Jain RK (2005) Accessing microbial diversity for bioremediation and environmental restoration. Trends Biotechnol 23:135–142PubMedCrossRefGoogle Scholar
  199. 199.
    Thornton SF, Tobin K, Smith JWH (2013) Comparison of constant and transient-source zones on simulated contaminant plume evolution in groundwater: implications for hydrogeological risk assessment. Groundw Monit Rem 33:78–91Google Scholar
  200. 200.
    Lebrón CA, McHale T, Young R, Williams D, Bogaart MG, Major DW, McMaster ML, Tasker I, Akladiss N (2007) Pilot-scale evaluation using bioaugmentation to enhance PCE dissolution at Dover AFB national test site. Remediat J 17:5–17CrossRefGoogle Scholar
  201. 201.
    Wise DL, Trantolo DJ, Cichon EJ, Inyang HI, Stottmeister U (2000) Bioremediation of contaminated soils. Marcel Dekker Inc, New York, p 920Google Scholar
  202. 202.
    ITRC (2011c) Permeable reactive barrier: technology update. Washington, Interstate Technology & Regulatory Council. Washington, DC, USA, pp 234. www.itrcweb.org
  203. 203.
    Obiri-Nyarko F, Grajales-Mesa SJ, Malina G (2014) An overview of permeable reactive barriers for in situ sustainable groundwater remediation. Chemosphere 111:243–259PubMedCrossRefGoogle Scholar
  204. 204.
    Environment Agency (2002) Guidance on the design, construction, operation and monitoring of permeable reactive barriers. NC/01/51, Environment Agency, BristolGoogle Scholar
  205. 205.
    Anderson RT, Lovley DR (1997) Ecology and biogeochemistry of in situ groundwater remediation. Advances in microbial ecology, vol 15. Plenum Press, New York, pp 289–350Google Scholar
  206. 206.
    Bouwer EJ (1994) Bioremediation of chlorinated solvents using alternate electron acceptors. In: Norris RD, et al (eds) Handbook of bioremediation. Lewis Publishers. Boca Raton, Florida. pp 149–170Google Scholar
  207. 207.
    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 35:1663–1670PubMedCrossRefGoogle Scholar
  208. 208.
    Smith VH, Graham DW, Cleland DD (1998) Application of resource-ratio theory to hydrocarbon biodegradation. Environ Sci Technol 32:3386–3395CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Groundwater Protection and Restoration GroupDept of Civil & Structural Engineering, The University of SheffieldSheffieldUK
  2. 2.Sirius Geotechnical & Environmental LtdThorpe Park, LeedsUK
  3. 3.Dept Animal and Plant SciencesAlfred Denny Building, University of SheffieldSheffieldUK

Personalised recommendations