Mini Sediment Columns and Two-Dimensional Sediment Flow-Through Microcosms: Versatile Experimental Systems for Studying Biodegradation of Organic Contaminants in Groundwater Ecosystems

  • Roland Hofmann
  • Michael Grösbacher
  • Christian Griebler
Part of the Springer Protocols Handbooks book series (SPH)


Groundwater ecosystems are our most important source for drinking water supply. The increasing pressure to our groundwater reservoirs from anthropogenic contamination is a major threat not only to the ecosystem but also to human health. Microbial transformation of quantitatively important organic contaminants, such as petroleum hydrocarbons, in aquifers is an ecosystem service of ecological as well as economic importance. However, key controls and limitations of biodegradation in situ are still poorly understood. Facing the limited accessibility of the subsurface, the complex structural heterogeneity, and the hidden temporal physical–chemical and biotic dynamics, bench-top experimental systems are necessary tools for a systematic and controlled investigation of key variables in contaminant removal processes at appropriate micro- and meso-scales. Here, we introduce mini sediment columns and two-dimensional sediment flow-through microcosms as complementary versatile experimental systems that offer a high degree of simplification, experimental control, and replication.


Biodegradation Contaminant microbiology Flow-through system Groundwater Microcosms Monoaromatic hydrocarbons Sediment columns 


  1. 1.
    Schwarzenbach RP, Egli T, Hofstetter TB et al (2010) Global water pollution and human health. Annu Rev Environ Resourc 35(1):109–136. doi: 10.1146/annurev-environ-100809-125342 CrossRefGoogle Scholar
  2. 2.
    Herman JS, Culver DC, Salzman J (2001) Groundwater ecosystems and the service of water purification. Stanford Environ Law J 20:479Google Scholar
  3. 3.
    Griebler C, Avramov M (2015) Groundwater ecosystem services: a review. Freshwat Sci 34(1):355–367. doi: 10.1086/679903 CrossRefGoogle Scholar
  4. 4.
    Danielopol DL, Griebler C, Gunatilaka A et al (2003) Present state and future prospects for groundwater ecosystems. Environ Conserv 30(2):104–130. doi: 10.1017/S0376892903000109 CrossRefGoogle Scholar
  5. 5.
    Chapelle FH (2001) Ground-water microbiology and geochemistry, 2nd edn. Wiley, New YorkGoogle Scholar
  6. 6.
    Chen CS, Shu Y, Wu S et al (2015) Assessing soil and groundwater contamination from biofuel spills. Environ Sci Process Impacts. doi: 10.1039/c4em00443d Google Scholar
  7. 7.
    Wiedemeier TH (1999) Natural attenuation of fuels and chlorinated solvents in the subsurface. Wiley, New YorkCrossRefGoogle Scholar
  8. 8.
    Foght J (2008) Anaerobic biodegradation of aromatic hydrocarbons: pathways and prospects. J Mol Microbiol Biotechnol 15(2–3):93–120CrossRefPubMedGoogle Scholar
  9. 9.
    Annweiler E, Michaelis W, Meckenstock RU (2001) Anaerobic cometabolic conversion of benzothiophene by a sulfate-reducing enrichment culture and in a tar-oil-contaminated aquifer. Appl Environ Microbiol 67(11):5077–5083. doi: 10.1128/AEM.67.11.5077-5083.2001 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Meckenstock RU, Safinowski M, Griebler C (2004) Anaerobic degradation of polycyclic aromatic hydrocarbons. FEMS Microbiol Ecol 49(1):27–36. doi: 10.1016/j.femsec.2004.02.019 CrossRefPubMedGoogle Scholar
  11. 11.
    Jobelius C, Ruth B, Griebler C et al (2011) Metabolites indicate hot spots of biodegradation and biogeochemical gradients in a high-resolution monitoring well. Environ Sci Technol 45(2):474–481. doi: 10.1021/es1030867 CrossRefPubMedGoogle Scholar
  12. 12.
    Valavanidis A, Vlachogianni T, Fiotakis K et al (2013) Pulmonary oxidative stress, inflammation and cancer: respirable particulate matter, fibrous dusts and ozone as major causes of lung carcinogenesis through reactive oxygen species mechanisms. Int J Environ Res Public Health 10(9):3886–3907. doi: 10.3390/ijerph10093886 CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Gauthier PT, Norwood WP, Prepas EE et al (2014) Metal-PAH mixtures in the aquatic environment: a review of co-toxic mechanisms leading to more-than-additive outcomes. Aquat Toxicol 154:253–269. doi: 10.1016/j.aquatox.2014.05.026 CrossRefPubMedGoogle Scholar
  14. 14.
    Fang J, Barcelona M (1998) Biogeochemical evidence for microbial community change in a jet fuel hydrocarbons-contaminated aquifer. Org Geochem 29(4):899–907. doi: 10.1016/S0146-6380(98)00174-0 CrossRefGoogle Scholar
  15. 15.
    Trautwein K, Kühner S, Wöhlbrand L et al (2008) Solvent stress response of the denitrifying bacterium “Aromatoleum aromaticum” strain EbN1. Appl Environ Microbiol 74(8):2267–2274. doi: 10.1128/AEM.02381-07 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Griebler C, Lueders T (2009) Microbial biodiversity in groundwater ecosystems. Freshwat Biol 54(4):649–677. doi: 10.1111/j.1365-2427.2008.02013.x CrossRefGoogle Scholar
  17. 17.
    Bauer RD, Rolle M, Bauer S et al (2009) Enhanced biodegradation by hydraulic heterogeneities in petroleum hydrocarbon plumes. J Contam Hydrol 105(1–2):56–68CrossRefPubMedGoogle Scholar
  18. 18.
    Jessup CM, Kassen R, Forde SE et al (2004) Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19(4):189–197. doi: 10.1016/j.tree.2004.01.008 CrossRefPubMedGoogle Scholar
  19. 19.
    Alfreider A, Krössbacher M, Psenner R (1997) Groundwater samples do not reflect bacterial densities and activity in subsurface systems. Water Res 31(4):832–840CrossRefGoogle Scholar
  20. 20.
    Griebler C, Mindl B, Slezak D et al (2002) Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microcosm. Aquat Microb Ecol 28:117–129CrossRefGoogle Scholar
  21. 21.
    Zhou Y, Kellermann C, Griebler C (2012) Spatio-temporal patterns of microbial communities in a hydrologically dynamic pristine aquifer. FEMS Microbiol Ecol 81(1):230–242. doi: 10.1111/j.1574-6941.2012.01371.x CrossRefPubMedGoogle Scholar
  22. 22.
    Flynn TM, Sanford RA, Bethke CM (2008) Attached and suspended microbial communities in a pristine confined aquifer. Water Resour Res 44(7), W07425CrossRefGoogle Scholar
  23. 23.
    Anneser B, Pilloni G, Bayer A et al (2010) High resolution analysis of contaminated aquifer sediments and groundwater—what can be learned in terms of natural attenuation? Geomicrobiol J 27(2):130–142. doi: 10.1080/01490450903456723 CrossRefGoogle Scholar
  24. 24.
    Rizoulis A, Elliott DR, Rolfe SA et al (2013) Diversity of planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Microb Ecol 66(1):84–95. doi: 10.1007/s00248-013-0233-0 CrossRefPubMedGoogle Scholar
  25. 25.
    Bauer RD, Rolle M, Kürzinger P et al (2009) Two-dimensional flow-through microcosms – versatile test systems to study biodegradation processes in porous aquifers. J Hydrol 369(3–4):284–295. doi: 10.1016/j.jhydrol.2009.02.037 CrossRefGoogle Scholar
  26. 26.
    Chi F, Amy GL (2004) Transport of anthracene and benz(a)anthracene through iron-quartz and three aquifer materials in laboratory columns. Chemosphere 55(4):515–524CrossRefPubMedGoogle Scholar
  27. 27.
    Jose SC, Cirpka OA (2004) Measurement of mixing-controlled reactive transport in homogeneous porous media and its prediction from conservative tracer test data. Environ Sci Technol 38(7):2089–2096CrossRefPubMedGoogle Scholar
  28. 28.
    Baumann T, Werth CJ (2005) Visualization of colloid transport through heterogeneous porous media using magnetic resonance imaging. Colloids Surf A Physicochem Eng Asp 265(1–3):2–10. doi: 10.1016/j.colsurfa.2004.11.052 CrossRefGoogle Scholar
  29. 29.
    Werth CJ, Zhang C, Brusseau ML et al (2010) A review of non-invasive imaging methods and applications in contaminant hydrogeology research. J Contam Hydrol 113(1–4):1–24. doi: 10.1016/j.jconhyd.2010.01.001 CrossRefPubMedGoogle Scholar
  30. 30.
    Pan B, Tao S, Wu D et al (2011) Phenanthrene sorption/desorption sequences provide new insight to explain high sorption coefficients in field studies. Chemosphere 84(11):1578–1583. doi: 10.1016/j.chemosphere.2011.05.051 CrossRefPubMedGoogle Scholar
  31. 31.
    Higgins CP, Luthy RG (2006) Sorption of perfluorinated surfactants on sediments. Environ Sci Technol 40(23):7251–7256. doi: 10.1021/es061000n CrossRefPubMedGoogle Scholar
  32. 32.
    Burgos WD, Pisutpaisal N (2006) Sorption of naphthoic acids and quinoline compounds to estuarine sediment. J Contam Hydrol 84(3–4):107–126. doi: 10.1016/j.jconhyd.2005.12.008 CrossRefPubMedGoogle Scholar
  33. 33.
    Langenhoff AAM, Zehnder AJB, Schraa G (1996) Behaviour of toluene, benzene and naphthalene under anaerobic conditions in sediment columns. Biodegradation 7(3):267–274. doi: 10.1007/BF00058186 CrossRefGoogle Scholar
  34. 34.
    Hess A, Höhener P, Hunkeler D et al (1996) Bioremediation of a diesel fuel contaminated aquifer: simulation studies in laboratory aquifer columns. J Contam Hydrol 23(4):329–345CrossRefGoogle Scholar
  35. 35.
    Bosma TNP, Marlies E, Ballemans W et al (1996) Biotransformation of organics in soil columns and an infiltration area. Ground Water 34(1):49–56. doi: 10.1111/j.1745-6584.1996.tb01864.x CrossRefGoogle Scholar
  36. 36.
    Haest PJ, Philips J, Springael D et al (2011) The reactive transport of trichloroethene is influenced by residence time and microbial numbers. J Contam Hydrol 119(1–4):89–98. doi: 10.1016/j.jconhyd.2010.09.011 CrossRefPubMedGoogle Scholar
  37. 37.
    Thullner M (2010) Comparison of bioclogging effects in saturated porous media within one- and two-dimensional flow systems. Ecol Eng 36(2):176–196. doi: 10.1016/j.ecoleng.2008.12.037 CrossRefGoogle Scholar
  38. 38.
    Brielmann H, Lueders T, Schreglmann K et al (2011) Oberflächennahe Geothermie und ihre potenziellen Auswirkungen auf Grundwasserökosysteme. Grundwasser 16(2):77–91. doi: 10.1007/s00767-011-0166-9 CrossRefGoogle Scholar
  39. 39.
    Mellage A, Eckert D, Grösbacher M et al (2015) Dynamics of suspended and attached aerobic toluene degraders in small-scale flow-through sediment systems under growth and starvation conditions. Environ Sci Technol 49(12):7161–7169. doi: 10.1021/es5058538 CrossRefPubMedGoogle Scholar
  40. 40.
    Barton JW, Ford RM (1995) Determination of effective transport coefficients for bacterial migration in sand columns. Appl Environ Microbiol 61(9):3329–3335PubMedPubMedCentralGoogle Scholar
  41. 41.
    Mösslacher F, Griebler C, Notenboom J (2001) Biomonitoring of groundwater systems: methods, applications and possible indicators among the groundwater biota. Groundwater ecology: a tool for management of water resources. Office for Official Publications of the European Communities, Luxemburg, pp 132–170Google Scholar
  42. 42.
    Bauer RD, Maloszewski P, Zhang Y et al (2008) Mixing-controlled biodegradation in a toluene plume — results from two-dimensional laboratory experiments. J Contam Hydrol 96(1–4):150–168. doi: 10.1016/j.jconhyd.2007.10.008 CrossRefPubMedGoogle Scholar
  43. 43.
    Werth CJ, Cirpka OA, Grathwohl P (2006) Enhanced mixing and reaction through flow focusing in heterogeneous porous media. Water Resour Res 42(12), W12414. doi: 10.1029/2005wr004511 CrossRefGoogle Scholar
  44. 44.
    Jose SC, Rahman MA, Cirpka OA (2004) Large-scale sandbox experiment on longitudinal effective dispersion in heterogeneous porous media. Water Resour Res 40(12), W12415. doi: 10.1029/2004WR003363 CrossRefGoogle Scholar
  45. 45.
    Huang WE, Smith CC, Lerner DN et al (2002) Physical modelling of solute transport in porous media: evaluation of an imaging technique using UV excited fluorescent dye. Water Res 36(7):1843–1853. doi: 10.1016/S0043-1354(01)00393-1 CrossRefPubMedGoogle Scholar
  46. 46.
    Loveland JP, Bhattacharjee S, Ryan JN et al (2003) Colloid transport in a geochemically heterogeneous porous medium: aquifer tank experiment and modeling. J Contam Hydrol 65(3–4):161–182. doi: 10.1016/S0169-7722(02)00238-3 CrossRefPubMedGoogle Scholar
  47. 47.
    Weisbrod N, Niemet MR, Rockhold ML et al (2004) Migration of saline solutions in variably saturated porous media. J Contam Hydrol 72(1–4):109–133. doi: 10.1016/j.jconhyd.2003.10.013 CrossRefPubMedGoogle Scholar
  48. 48.
    Rahman MM, Liedl R, Grathwohl P (2004) Sorption kinetics during macropore transport of organic contaminants in soils: laboratory experiments and analytical modeling. Water Resour Res 40(1), W01503. doi: 10.1029/2002WR001946 CrossRefGoogle Scholar
  49. 49.
    Cirpka OA, Windfuhr C, Bisch G et al (1999) Microbial reductive dechlorination in large-scale sandbox model. J Environ Eng 125(9):861–870. doi: 10.1061/(ASCE)0733-9372(1999)125:9(861) CrossRefGoogle Scholar
  50. 50.
    Cirpka OA, Valocchi AJ (2007) Two-dimensional concentration distribution for mixing-controlled bioreactive transport in steady state. Adv Water Resour 30(6–7):1668–1679. doi: 10.1016/j.advwatres.2006.05.022 CrossRefGoogle Scholar
  51. 51.
    Chiogna G, Eberhardt C, Grathwohl P et al (2010) Evidence of compound-dependent hydrodynamic and mechanical transverse dispersion by multitracer laboratory experiments. Environ Sci Technol 44(2):688–693. doi: 10.1021/es9023964 CrossRefPubMedGoogle Scholar
  52. 52.
    Cirpka OA, de Barros FPJ, Chiogna G et al (2011) Stochastic flux-related analysis of transverse mixing in two-dimensional heterogeneous porous media. Water Resour Res 47(6), W06515. doi: 10.1029/2010WR010279 CrossRefGoogle Scholar
  53. 53.
    Ballarini E, Beyer C, Bauer RD et al (2014) Model based evaluation of a contaminant plume development under aerobic and anaerobic conditions in 2D bench-scale tank experiments. Biodegradation 25(3):351–371. doi: 10.1007/s10532-013-9665-y CrossRefPubMedGoogle Scholar
  54. 54.
    Cirpka OA, Rolle M, Chiogna G et al (2012) Stochastic evaluation of mixing-controlled steady-state plume lengths in two-dimensional heterogeneous domains. J Contam Hydrol 138–139:22–39. doi: 10.1016/j.jconhyd.2012.05.007 CrossRefPubMedGoogle Scholar
  55. 55.
    Rolle M, Chiogna G, Bauer R et al (2010) Isotopic fractionation by transverse dispersion: flow-through microcosms and reactive transport modeling study. Environ Sci Technol 44(16):6167–6173. doi: 10.1021/es101179f CrossRefPubMedGoogle Scholar
  56. 56.
    Rolle M, Hochstetler D, Chiogna G et al (2012) Experimental investigation and pore-scale modeling interpretation of compound-specific transverse dispersion in porous media. Transp Porous Media 93(3):347–362CrossRefGoogle Scholar
  57. 57.
    Werner D, Karapanagioti HK, Sabatini DA (2012) Assessing the effect of grain-scale sorption rate limitations on the fate of hydrophobic organic groundwater pollutants. J Contam Hydrol 129–130:70–79. doi: 10.1016/j.jconhyd.2011.10.002 CrossRefPubMedGoogle Scholar
  58. 58.
    Zhang C, Werth CJ, Webb AG (2002) A magnetic resonance imaging study of dense nonaqueous phase liquid dissolution from angular porous media. Environ Sci Technol 36(15):3310–3317. doi: 10.1021/es011497v CrossRefPubMedGoogle Scholar
  59. 59.
    Zhang C, Werth CJ, Webb AG (2007) Characterization of NAPL source zone architecture and dissolution kinetics in heterogeneous porous media using magnetic resonance imaging. Environ Sci Technol 41(10):3672–3678. doi: 10.1021/es061675q CrossRefPubMedGoogle Scholar
  60. 60.
    Sharma PK, McInerney MJ (1994) Effect of grain size on bacterial penetration, reproduction, and metabolic activity in porous glass bead chambers. Appl Environ Microbiol 60(5):1481–1486PubMedPubMedCentralGoogle Scholar
  61. 61.
    Strobel KL, McGowan S, Bauer RD et al (2011) Chemotaxis increases vertical migration and apparent transverse dispersion of bacteria in a bench-scale microcosm. Biotechnol Bioeng 108(9):2070–2077. doi: 10.1002/bit.23159 CrossRefPubMedGoogle Scholar
  62. 62.
    Oates PM, Castenson C, Harvey CF et al (2005) Illuminating reactive microbial transport in saturated porous media: demonstration of a visualization method and conceptual transport model. J Contam Hydrol 77(4):233–245. doi: 10.1016/j.jconhyd.2004.12.005 CrossRefPubMedGoogle Scholar
  63. 63.
    Nambi IM, Werth CJ, Sanford RA et al (2003) Pore-scale analysis of anaerobic halorespiring bacterial growth along the transverse mixing zone of an etched silicon pore network. Environ Sci Technol 37(24):5617–5624. doi: 10.1021/es034271w CrossRefPubMedGoogle Scholar
  64. 64.
    Thullner M, Zeyer J, Kinzelbach W (2002) Influence of microbial growth on hydraulic properties of pore networks. Transp Porous Media 49(1):99–122. doi: 10.1023/A:1016030112089 CrossRefGoogle Scholar
  65. 65.
    Thullner M, Mauclaire L, Schroth MH et al (2002) Interaction between water flow and spatial distribution of microbial growth in a two-dimensional flow field in saturated porous media. J Contam Hydrol 58(3–4):169–189. doi: 10.1016/S0169-7722(02)00033-5 CrossRefPubMedGoogle Scholar
  66. 66.
    Thullner M, Schroth MH, Zeyer J et al (2004) Modeling of a microbial growth experiment with bioclogging in a two-dimensional saturated porous media flow field. J Contam Hydrol 70(1–2):37–62. doi: 10.1016/j.jconhyd.2003.08.008 CrossRefPubMedGoogle Scholar
  67. 67.
    Huang WE, Oswald SE, Lerner DN et al (2003) Dissolved oxygen imaging in a porous medium to investigate biodegradation in a plume with limited electron acceptor supply. Environ Sci Technol 37(9):1905–1911. doi: 10.1021/es020128b CrossRefPubMedGoogle Scholar
  68. 68.
    Chu M, Kitanidis PK, McCarty PL (2005) Modeling microbial reactions at the plume fringe subject to transverse mixing in porous media: when can the rates of microbial reaction be assumed to be instantaneous? Water Resour Res 41(6), W06002. doi: 10.1029/2004wr003495 CrossRefGoogle Scholar
  69. 69.
    Rees HC, Oswald SE, Banwart SA et al (2007) Biodegradation processes in a laboratory-scale groundwater contaminant plume assessed by fluorescence imaging and microbial analysis. Appl Environ Microbiol 73(12):3865–3876. doi: 10.1128/AEM.02933-06 CrossRefPubMedPubMedCentralGoogle Scholar
  70. 70.
    Rolle M, Bauer RD, Griebler C et al (2007) Aerobic degradation of toluene plume in homogeneous and heterogeneous porous media. In: Trefry MG (ed) Groundwater quality 2007: securing groundwater quality in urban and industrial environments: program and proceedings of the sixth international IAHS Groundwater Quality conference. International Association of Hydrological Sciences, Wembley, pp 356–363Google Scholar
  71. 71.
    Beyer C, Ballarini E, Bauer RD et al (2012) Interpretation of hydrocarbon plume biodegradation in 2-D bench-scale tank experiments by reactive transport modelling. In: Oswald SE, Kolditz O, Attinger S (eds) Models - repositories of knowledge: proceedings of ModelCARE2011 held at Leipzig, September 2011. IAHS Press, WallingfordGoogle Scholar
  72. 72.
    Eckert D, Kürzinger P, Bauer R et al (2015) Fringe-controlled biodegradation under dynamic conditions: quasi 2-D flow-through experiments and reactive-transport modeling. J Contam Hydrol 172:100–111. doi: 10.1016/j.jconhyd.2014.11.003 CrossRefPubMedGoogle Scholar
  73. 73.
    Anneser B, Einsiedl F, Meckenstock RU et al (2008) High-resolution monitoring of biogeochemical gradients in a tar oil-contaminated aquifer. Appl Geochem 23(6):1715–1730. doi: 10.1016/j.apgeochem.2008.02.003 CrossRefGoogle Scholar
  74. 74.
    Meckenstock RU, Lueders T, Griebler C et al (2010) Microbial hydrocarbon degradation at coal gasification plants. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2293–2312CrossRefGoogle Scholar
  75. 75.
    Klenk I, Grathwohl P (2002) Transverse vertical dispersion in groundwater and the capillary fringe. J Contam Hydrol 58(1–2):111–128. doi: 10.1016/S0169-7722(02)00011-6 CrossRefPubMedGoogle Scholar
  76. 76.
    Herzyk A, Maloszewski P, Qiu S et al (2014) Intrinsic potential for immediate biodegradation of toluene in a pristine, energy-limited aquifer. Biodegradation 25(3):325–336. doi: 10.1007/s10532-013-9663-0 CrossRefPubMedGoogle Scholar
  77. 77.
    Qiu S, Eckert D, Cirpka OA et al (2013) Direct experimental evidence of non-first order degradation kinetics and sorption-induced isotopic fractionation in a mesoscale aquifer: 13C/12C analysis of a transient toluene pulse. Environ Sci Technol 47(13):6892–6899. doi: 10.1021/es304877h CrossRefPubMedGoogle Scholar
  78. 78.
    Ye Y, Chiogna G, Cirpka O et al (2015) Experimental investigation of compound-specific dilution of solute plumes in saturated porous media: 2-D vs. 3-D flow-through systems. J Contam Hydrol 172:33–47. doi: 10.1016/j.jconhyd.2014.11.002 CrossRefPubMedGoogle Scholar
  79. 79.
    Chrysikopoulos CV, Syngouna VI, Vasiliadou IA et al (2012) Transport of Pseudomonas putida in a 3-D bench scale experimental aquifer. Transp Porous Media 94(3):617–642. doi: 10.1007/s11242-012-0015-z CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Roland Hofmann
    • 1
  • Michael Grösbacher
    • 1
  • Christian Griebler
    • 1
  1. 1.Institute of Groundwater Ecology, Helmholtz Zentrum München – German Research Centre for Environmental HealthNeuherbergGermany

Personalised recommendations