Literature
Armstrong, R.T., Wildenschild, D., 2012. Microbial enhanced oil recovery in fractional-fet systems: A pore-scale investigation. Transp. Porous Media 92, 819–835. https://doi.org/10.1007/s11242-011-9934-3
Avramov, M., Rock, T.M., Pfister, G., Schramm, K.-W., Schmidt, S.I., Griebler, C., 2013. Catecholamine levels in groundwater and stream amphipods and their response to temperature stress. Gen. Comp. Endocrinol. 194, 110–117. https://doi.org/10.1016/j.ygcen.2013.09.004
Balakotaiah, V., Chang, H.C., 1995. Dispersion of chemical solutes in chromatographs and reactors. Philos. Trans. R. Soc. Lond. Ser. -Math. Phys. Eng. Sci. 351, 39–75.
Baranov, V., Lewandowski, J., Krause, S., 2016. Bioturbation enhances the aerobic respiration of lake sediments in warming lakes. Biol. Lett. 12, 269–281. https://doi.org/10.1098/rsbl.2016.0448
Battiato, I., Tartakovsky, D.M., Tartakovsky, A.M., Scheibe, T.D., 2011. Hybrid models of reactive transport in porous and fractured media. Adv. Water Resour. 34, 1140–1150. https://doi.org/10.1016/j.advwatres.2011.01.012
Bauer, R.D., Maloszewski, P., Zhang, Y., Meckenstock, R.U., Griebler, C., 2008. Mixing-controlled biodegradation in a toluene plume–results from two-dimensional laboratory experiments. J. Contam. Hydrol. 96, 150–68. https://doi.org/10.1016/j.jconhyd.2007.10.008
Bauer, R.D., Rolle, M., Kürzinger, P., Grathwohl, P., Meckenstock, R.U., Griebler, C., 2009. Two-dimensional flow-through microcosms – Versatile test systems to study biodegradation processes in porous aquifers. J. Hydrol. 369, 284–295. https://doi.org/10.1016/j.jhydrol.2009.02.037
Baveye, P., Valocchi, A., 1989. An evaluation of mathematical models of the transport of biologically reacting solutes in saturated soils and aquifers. Water Resour. Res. 25, 1413–1421.
Benioug, F. Golfier, P. Fischer, C. Oltean, M.A. Buès, X. Yang, 2019. Interaction between Biofilm Growth and NAPL Remediation: A Pore-scale Study. Adv. Water Resour. 125. https://doi.org/10.1016/j.advwatres.2019.01.011
Benioug, M., Golfier, F., Oltéan, C., Buès, M.A., Bahar, T., Cuny, J., 2017. An immersed boundary-lattice Boltzmann model for biofilm growth in porous media. Adv. Water Resour. 107, 65–82. https://doi.org/10.1016/j.advwatres.2017.06.009
Benioug, M., Golfier, F., Tinet, A.J., Buès, M.A., Oltéan, C., 2015. Numerical efficiency assessment of IB–LB method for 3D pore-scale modeling of flow and transport. Transp. Porous Media 109, 1–23. https://doi.org/10.1007/s11242-015-0497-6
Bennett, P.C., Hiebert, F.K., Rogers, J.R., 2000. Microbial control of mineral-groundwater equilibria: Macroscale to microscale. Hydrogeol. J. 8, 47–62. https://doi.org/DOI 10.1007/s100400050007
Bergauer, P., Fonteyne, P.-A., Nolard, N., Schinner, F., Margesin, R., 2005. Biodegradation of phenol and phenol-related compounds by psychrophilic and cold-tolerant alpine yeasts. Chemosphere 59, 909–918. https://doi.org/10.1016/j.chemosphere.2004.11.011
Blunt, M.J., 2001. Flow in porous media - Pore-network models and multiphase flow. Curr. Opin. Colloid Interface Sci. 6 6, 197–207.
Brielmann, H., Griebler, C., Schmidt, S.I., Michel, R., Lueders, T., 2009. Effects of thermal energy discharge on shallow groundwater ecosystems. FEMS Microbiol. Ecol. 68, 273–286. https://doi.org/10.1111/j.1574-6941.2009.00674.x
Bucka, F.B., Kölbl, A., Uteau, D., Peth, S., Kögel-Knabner, I., 2019. Organic matter input determines structure development and aggregate formation in artificial soils. Geoderma 354, 113881. https://doi.org/10.1016/j.geoderma.2019.113881
Calabrese, F., Voloshynovska, I., Musat, F., Thullner, M., Schlömann, M., Richnow, H.H., Lambrecht, J., Müller, S., Wick, L.Y., Musat, N., Stryhanyuk, H., 2019. Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations. Front. Microbiol. 10. https://doi.org/10.3389/fmicb.2019.02814
Carrel, M., Morales, V.L., Beltran, M.A., Derlon, N., Kaufmann, R., Morgenroth, E., Holzner, M., 2018. Biofilms in 3D porous media: Delineating the influence of the pore network geometry, flow and mass transfer on biofilm development. Water Res. Water Research, 280–291. https://doi.org/10.1016/j.watres.2018.01.059
Chen, S., Doolen, G.D., 1998. Lattice Boltzmann method for fluid flows. Annu Rev Fluid Mech 30, 329–364.
Coyte, K.Z., Tabuteau, H., Gaffney, E.A., Foster, K.R., Durham, W.M., 2017. Microbial competition in porous environments can select against rapid biofilm growth. Proc. Natl. Acad. Sci. 114, E161–E170. https://doi.org/10.1073/pnas.1525228113
Cuthbert, M.O., Mackay, R., Durand, V., Aller, M.-F., Greswell, R.B., Rivett, M.O., 2010. Impacts of river bed gas on the hydraulic and thermal dynamics of the hyporheic zone. Adv. Water Resour. 33, 1347–1358. https://doi.org/10.1016/j.advwatres.2010.09.014
Davis, C.A., Pyrak‐Nolte, L.J., Atekwana, E.A., Werkema, D.D., Haugen, M.E., 2010. Acoustic and electrical property changes due to microbial growth and biofilm formation in porous media. J. Geophys. Res. Biogeosciences 115. https://doi.org/10.1029/2009JG001143
Davit, Y., Debenest, G., Wood, B.D., Quintard, M., 2010. Modeling non-equilibrium mass transport in biologically reactive porous media. Adv. Water Resour. 33, 1075–1093. https://doi.org/10.1016/j.advwatres.2010.06.013
Dole-Olivier, M.J., Galassi, D.M.P., Marmonier, P., Creuzé des Chatelliers, M., 2000. The biology and ecology of lotic mircrocrustaceans. Freshw. Biol. 44, 63 – 91. https://doi.org/10.1046/j.1365-2427.2000.00590.x
Dong, H., Onstott, T.C., DeFlaun, M.F., Fuller, M.E., Scheibe, T.D., Streger, S.H., Rothmel, R.K., Mailloux, B.J., 2002. Relative dominance of physical versus chemical effects on the transport of adhesion-deficient bacteria in intact cores from South Oyster, Virginia. Environ. Sci. Technol. 36, 891–900. https://doi.org/10.1021/es010144t
Douillet-Grellier, T., Leclaire, S., Vidal, D., Bertrand, F., De Vuyst, F., 2019. Comparison of multiphase SPH and LBM approaches for the simulation of intermittent flows. ArXiv190301168 Phys.
Dufour, S.C., Desrosiers, G., Long, B., Lajeunesse, P., Gagnoud, M., Labrie, J., 2005. A new method for three-dimensional visualization and quantification of biogenic structures in aquatic sediments using axial tomodensitometry. Limnol Ocean. Methods 3, 372–380. https://doi.org/10.4319/lom.2005.3.372
Eberl, H.J., Picioreanu, C., Heijnen, J.J., van Loosdrecht, M.C.M., 2000. A three-dimensional numerical study on the correlation of spatial structure, hydrodynamic conditions, and mass transfer and conversion in biofilms. Chem. Eng. Sci. 55, 6209–6222. https://doi.org/10.1016/S0009-2509(00)00169-X
Esser, D.S., Leveau, J.H.J., Meyer, K.M., 2015. Modeling microbial growth and dynamics. Appl. Microbiol. Biotechnol. 99, 8831–8846. https://doi.org/10.1007/s00253-015-6877-6
Gautreau, E., Volatier, L., Nogaro, G., Gouze, E., Mermillod-Blondin, F., 2020. The influence of bioturbation and water column oxygenation on nutrient recycling in reservoir sediments. Hydrobiologia 847, 1027–1040. https://doi.org/10.1007/s10750-019-04166-0
Gibson, D.T., Koch, R., Kallio, R.E., 1968. Oxidative degradation of aromatic hydrocarbons by microorganisms. Biochemistry 7, 2653–2662. https://doi.org/10.1021/bi00847a031
Griebler, C., Avramov, M., 2015. Groundwater ecosystem services: a review. Freshw. Sci. 34, 355–367. https://doi.org/10.1086/679903
Grösbacher, M., Eckert, D., Cirpka, O.A., Griebler, C., 2018. Contaminant concentration versus flow velocity: drivers of biodegradation and microbial growth in groundwater model systems. Biodegradation 1–22. https://doi.org/10.1007/s10532-018-9824-2
Gruden, C.L., Khijniak, A., Adriaens, P., 2003. Activity assessment of microorganisms eluted from sediments using 5-cyano-2,3-ditolyl tetrazolium chloride: a quantitative comparison of flow cytometry to epifluorescent microscopy. J. Microbiol. Methods 55, 865–874. https://doi.org/10.1016/j.mimet.2003.08.005
Guo, Y., Wen, Z., Zhang, C., Jakada, H., 2020. Contamination and natural attenuation characteristics of petroleum hydrocarbons in a fractured karst aquifer, North China. Environ. Sci. Pollut. Res. 27, 22780–22794. https://doi.org/10.1007/s11356-020-08723-2
Haas, C., Horn, R., 2018. Impact of small-scaled differences in micro-aggregation on physico-chemical parameters of macroscopic biopore walls. Front. Environ. Sci. 6, 1–12. https://doi.org/10.3389/fenvs.2018.00090
Harvey, R.W., Smith, R.L., George, L., 1984. Effect of organic contamination upon microbial distributions and heterotrophic uptake in a Cape Cod, Mass., aquifer. Appl. Environ. Microbiol. 48, 1197–1202. https://doi.org/DOI: 10.1111/j.1574-6941.1999.tb00609.x
Herzyk, A., Fillinger, L., Larentis, M., Qiu, S., Maloszewski, P., Hünniger, M., Schmidt, S.I., Stumpp, C., Marozava, S., Knappett, P.S.K., Elsner, M., Meckenstock, R., Lueders, T., Griebler, C., 2017. Response and recovery of a pristine groundwater ecosystem impacted by toluene contamination – A meso-scale indoor aquifer experiment. J. Contam. Hydrol. 207, 17–30. https://doi.org/10.1016/j.jconhyd.2017.10.004
Hesse, F., Harms, H., Attinger, S., Thullner, M., 2010. Linear exchange model for the description of mass transfer limited bioavailability at the pore scale. Environ. Sci. Technol. 44, 2064–2071. https://doi.org/10.1021/es902489q
Hirt, C.W., Nichols, B.D., 1981. Volume of fluid (VOF) method for the dynamics of free boundaries. J. Comput. Phys. 39, 201–225. https://doi.org/10.1016/0021-9991(81)90145-5
Hölker, F., Vanni, M.J., Kuiper, J.J., Meile, C., Grossart, H.-P., Stief, P., Adrian, R., Lorke, A., Dellwig, O., Brand, A., Hupfer, M., Mooij, W.M., Nützmann, G., Lewandowski, J., 2015. Tube-dwelling invertebrates: tiny ecosystem engineers have large effects in lake ecosystems. Ecol. Monogr. 85, 333–351. https://doi.org/10.1890/07-1861.1
Hose, G.C., Stumpp, C., 2019. Architects of the underworld: bioturbation by groundwater invertebrates influences aquifer hydraulic properties. Aquat. Sci. 81, 20–20. https://doi.org/10.1007/s00027-018-0613-0
Iltis, G.C., Armstrong, R.T., Jansik, D.P., Wood, B.D., Wildenschild, D., 2011. Imaging biofilm architecture within porous media using synchrotron-based X-ray computed microtomography. Water Resour. Res. 47, 1–5. https://doi.org/10.1029/2010WR009410
Jaiswal, P., Al‐Hadrami, F., Atekwana, Estella A., Atekwana, Eliot A., 2014. Mechanistic models of biofilm growth in porous media. J. Geophys. Res. Biogeosciences 119, 1418–1431. https://doi.org/10.1002/2013JG002440
Jayathilake, P.G., Gupta, P., Li, B., Madsen, C., Oyebamiji, O., González-Cabaleiro, R., Rushton, S., Bridgens, B., Swailes, D., Allen, B., McGough, A.S., Zuliani, P., Ofiteru, I.D., Wilkinson, D., Chen, J., Curtis, T., 2017. A mechanistic Individual-based Model of microbial communities. PLoS ONE 12, 1–26. https://doi.org/10.1371/journal.pone.0181965
Jayathilake, P.G., Li, B., Zuliani, P., Curtis, T., Chen, J., 2019. Modelling bacterial twitching in fluid flows: a CFD-DEM approach. Sci. Rep. 9, 14540. https://doi.org/10.1038/s41598-019-51101-3
Jung, H., Meile, C., 2019. Upscaling of microbially driven first-order reactions in heterogeneous porous media. J. Contam. Hydrol. 224, 103483. https://doi.org/10.1016/j.jconhyd.2019.04.006
Kang, Q., Zhang, D., Chen, S., He, X., 2002. Lattice Boltzmann simulation of chemical dissolution in porous media. Phys. Rev. E 65, 036318–036318. https://doi.org/10.1103/PhysRevE.65.036318
Karadimitriou, N.K., Hassanizadeh, S.M., 2012. A review of micromodels and their use in two-phase flow studies. Vadose Zone J. 11, vzj2011.0072. https://doi.org/10.2136/vzj2011.0072
Kechagia, P.E., Tsimpanogiannis, I.N., Yortsos, Y.C., Lichtner, P.C., 2002. On the upscaling of reaction-transport processes in porous media with fast or finite kinetics. Chem. Eng. Sci. 57, 2565–2577. https://doi.org/10.1016/S0009-2509(02)00124-0
Khajepour, H., Mahmoodi, M., Biria, D., Ayatollahi, S., 2014. Investigation of wettability alteration through relative permeability measurement during MEOR process: A micromodel study. J. Pet. Sci. Eng. 120, 10–17. https://doi.org/10.1016/j.petrol.2014.05.022
Kone, T., Golfier, F., Orgogozo, L., Oltéan, C., Lefèvre, E., Block, J.C., Buès, M.A., 2014. Impact of biofilm-induced heterogeneities on solute transport in porous media. Water Resour. Res. 50, 9103–9119. https://doi.org/10.1002/2013WR015213
Kotelnikova, S., 2002. Microbial production and oxidation of methane in deep subsurface. Earth-Sci. Rev. 58, 367–395. https://doi.org/10.1016/S0012-8252(01)00082-4
Kotelnikova, S., Pedersen, K., 1998. Distribution and activity of methanogens and homoacetogens in deep granitic aquifers at Äspö Hard Rock Laboratory, Sweden. FEMS Microbiol Ecol 26, 121–134. https://doi.org/10.1111/j.1574-6941.1998.tb00498.x
Kuzyakov, Y., Blagodatskaya, E., 2015. Microbial hotspots and hot moments in soil: Concept & review. Soil Biol. Biochem. 83, 184–199. https://doi.org/10.1016/j.soilbio.2015.01.025
Lardon, L.A., Merkey, B. V., Martins, S., Dötsch, A., Picioreanu, C., Kreft, J.U., Smets, B.F., 2011. iDynoMiCS: Next-generation individual-based modelling of biofilms. Environ. Microbiol. 13, 2416–2434. https://doi.org/10.1111/j.1462-2920.2011.02414.x
Lechene, C., Hillion, F., Mcmahon, G., Benson, D., Kleinfeld, A.M., Kampf, J.P., Distel, D., Luyten, Y., Hentschel, D., Park, K.M., Ito, S., Benichou, G., Slodzian, G., 2006. High-resolution quantitative imaging of mammalian and bacterial cells using stable isotope mass spectrometry. J. Biol. 5, 20.
Li, L., Peters, C.A., Celia, M.A., 2006. Upscaling geochemical reaction rates using pore-scale network modeling. Adv. Water Resour. 29, 1351–1370. https://doi.org/10.1016/j.advwatres.2005.10.011
Liu, L., De Kock, T., Wilkinson, J., Cnudde, V., Xiao, S., Buchmann, C., Uteau, D., Peth, S., Lorke, A., 2018. Methane Bubble Growth and Migration in Aquatic Sediments Observed by X-ray μCT. Environ. Sci. Technol. 52, 2007–2015. https://doi.org/10.1021/acs.est.7b06061
Luo, H., Quintard, M., Debenest, G., Laouafa, F., 2012. Properties of a diffuse interface model based on a porous medium theory for solid-liquid dissolution problems. Comput. Geosci. 16, 913–932. https://doi.org/10.1007/s10596-012-9295-1
Manz, B., Volke, F., Goll, D., Horn, H., 2003. Measuring local flow velocities and biofilm structure in biofilm systems with Magnetic Resonance Imaging (MRI). Biotechnol. Bioeng. 84, 424–432. https://doi.org/10.1002/bit.10782
Mattison, R.G., Harayama, S., 2001. The predatory soil flagellate Heteromita globosa stimulates toluene biodegradation by a Pseudomonas sp . FEMS Microbiol. Lett. 194, 39–45.
Mehmani, Y., Balhoff, M.T., 2015. Mesoscale and hybrid models of fluid flow and solute transport. Rev. Mineral. Geochem. 80, 433–459.
Mendoza-Lera, C., Mutz, M., 2013. Microbial activity and sediment disturbance modulate the vertical water flux in sandy sediments. Freshw. Sci. 32, 26–38. https://doi.org/10.1899/11-165.1
Mermillod-Blondin, F., Marie, S., Desrosiers, G., Long, B., de Montety, L., Michaud, E., Stora, G., 2003. Assessment of the spatial variability of intertidal benthic communities by axial tomodensitometry: importance of fine-scale heterogeneity. J. Exp. Mar. Biol. Ecol. 287, 193–208. https://doi.org/10.1016/S0022-0981(02)00548-8
Mermillod-Blondin, F., Rosenberg, R., 2006. Ecosystem engineering: the impact of bioturbation on biogeochemical processes in marine and freshwater benthic habitats. Aquat. Sci. 68, 434–442. https://doi.org/10.1007/s00027-006-0858-x
Meyer, K., Hall, G., Offin, D., 2009. Introduction to Hamiltonian Dynamical Systems and the N-Body Problem, Applied Mathematical Sciences. Springer New York, New York, NY. https://doi.org/10.1007/978-0-387-09724-4
Molz, F.J., Widdowson, M.A., Benefield, L.D., 1986. Simulation of microbial growth dynamics coupled to nutrient and oxygen-transport in porous media. Water Resour. Res. 22, 1207–1216.
Neu, T., Woelfl, S., Lawrence, J.R., 2004. Three-dimensional differentiation of photo-autotrophic biofilm constituents by multi-channel laser scanning microscopy (single-photon and two-photon excitation). J. Microbiol. Methods 56, 161–172. https://doi.org/10.1016/j.mimet.2003.10.012
Orgogozo, L., Golfier, F., Buès, M.A., Quintard, M., Koné, T., 2013. A dual-porosity theory for solute transport in biofilm-coated porous media. Adv. Water Resour. 62, 266–279. https://doi.org/10.1016/j.advwatres.2013.09.011
Ostvar, S., Iltis, G., Davit, Y., Schlüter, S., Andersson, L., Wood, B.D., Wildenschild, D., 2018. Investigating the influence of flow rate on biofilm growth in three dimensions using microimaging. Adv. Water Resour. 117, 1–13. https://doi.org/10.1016/j.advwatres.2018.03.018
Pennafirme, S., Machado, A.S., Machado, A.C., Lopes, R.T., Lima, I.C.B., Crapez, M.A.C., 2019. Monitoring bioturbation by a small marine polychaete using microcomputed tomography. Micron 121, 77–83. https://doi.org/10.1016/j.micron.2019.03.004
Peszynska, M., Trykozko, A., Iltis, G., Schlueter, S., Wildenschild, D., 2016. Biofilm growth in porous media: Experiments, computational modeling at the porescale, and upscaling. Adv. Water Resour., Pore scale modeling and experiments 95, 288–301. https://doi.org/10.1016/j.advwatres.2015.07.008
Picioreanu, C., van Loosdrecht, M.C.M., Curtis, T.P., Scott, K., 2010. Model based evaluation of the effect of pH and electrode geometry on microbial fuel cell performance. Bioelectrochemistry 78, 8–24. https://doi.org/10.1016/j.bioelechem.2009.04.009
Picioreanu, C., van Loosdrecht, M.C.M., Heijnen, J.J., 1998. A new combined differential-discrete cellular automaton approach for biofilm modeling: application for growth in gel beads. Biotechnol. Bioeng. 57, 717–730. https://doi.org/DOI: 10.1002/(SICI)1097-0290
Pintelon, T.R.R., Picioreanu, C., van Loosdrecht, M.C.M., Johns, M.L., 2012. The effect of biofilm permeability on bio-clogging of porous media. Biotechnol. Bioeng. 109, 1031–1042. https://doi.org/10.1002/bit.24381
Poonoosamy, J., Westerwalbesloh, C., Deissmann, G., Mahrous, M., Curti, E., Churakov, S.V., Klinkenberg, M., Kohlheyer, D., von Lieres, E., Bosbach, D., Prasianakis, N.I., 2019. A microfluidic experiment and pore scale modelling diagnostics for assessing mineral precipitation and dissolution in confined spaces. Chem. Geol. 528, 119264. https://doi.org/10.1016/j.chemgeo.2019.07.039
Quevauviller, P., 2007. General introduction: the need to protect groundwater, in: Groundwater Science and Policy - An International Overview (Ed. Quevauviller P). RSC Publishing, pp. 3–18.
Raabe, D., 2004. Overview of the lattice Boltzmann method for nano- and microscale fluid. Model. Simul Mater Sci Eng 12, R13–R46.
Rhodes, M., Bijeljic, B., Blunt, M.J., 2009. A rigorous pore-to-field-scale simulation method for single-phase flow based on continuous-time random walks. SPE J. 14, 88–94. https://doi.org/10.2118/106434-PA
Rivett, M.O., Buss, S.R., Morgan, P., Smith, J.W.N., Bemment, C.D., 2008. Nitrate attenuation in groundwater: a review of biogeochemical controlling processes. Water Res. 42, 4215–32. https://doi.org/10.1016/j.watres.2008.07.020
Sahimi, M., 2011. Transport Modeling for Environmental Engineers and Scientists Nonlinear Mesoscopic Elasticity Essentials of Multiphase Flow in Porous Media. Wiley.
Santos, V.L., Linardi, V.R., 2001. Phenol degradation by yeasts isolated from industrial effluents. J Gen Appl Microbiol 47, 213–221. https://doi.org/doi:10.2323/jgam.47.213
Scheibe, T.D., Perkins, W.A., Richmond, M.C., Mckinley, M.I., Romero-Gomez, P.D.J., Oostrom, M., Wietsma, T.W., Serkowski, J.A., Zachara, J.M., 2015. Pore-scale and multiscale numerical simulation of flow and transport in a laboratory-scale column. Water Resour. Res. 51, 10.1002/2014WR015959. https://doi.org/10.1002/2014WR015959
Scheibe, T.D., Tartakovsky, A.M., Tartakovsky, D.M., Redden, G.D., Meakin, P., 2007. Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes. J. Phys. Conf. Ser. 78. https://doi.org/10.1088/1742-6596/78/1/012063
Scheibe, T.D., Wood, B.W., 2003. A particle-based model of size or anion exclusion with application to microbial transport in porous media. Water Resour. Res. 39, 1–10. https://doi.org/10.1029/2001WR001223
Schmidt, S.I., Cuthbert, M.O., Schwientek, M., 2017. Towards an integrated understanding of how micro scale processes shape groundwater ecosystem functions. Sci. Total Environ. 592, 215–227. https://doi.org/10.1016/j.scitotenv.2017.03.047
Schmidt, S.I., Hahn, H.J., Hatton, T.J., Humphreys, W.F., 2007. Do faunal assemblages reflect the exchange intensity in groundwater zones? Hydrobiologia 583, 1–19. https://doi.org/10.1007/s10750-006-0405-8
Schmidt, S.I., Kreft, J.-U., Mackay, R., Picioreanu, C., Thullner, M., 2018. Elucidating the impact of micro-scale heterogeneous bacterial distribution on biodegradation. Adv. Water Resour. 116, 67–76. https://doi.org/10.1016/j.advwatres.2018.01.013
Seymour, J.D., Gage, J.P., Codd, S.L., Gerlach, R., 2007. Magnetic resonance microscopy of biofouling induced scale dependent transport in porous media. Adv. Water Resour. 30, 1408–1420. https://doi.org/10.1016/j.advwatres.2006.05.029
Seymour, J.D., Gage, J.P., Codd, S.L., Gerlach, R., 2004. Anomalous fluid transport in porous media induced by biofilm growth. Phys. Rev. Lett. 93, 198103. https://doi.org/10.1103/PhysRevLett.93.198103
Sheraton, M.V., Melnikov, V.R., Sloot, P.M.A., 2019. Prediction and quantification of bacterial biofilm detachment using Glazier–Graner–Hogeweg method based model simulations. J. Theor. Biol. 482, 109994. https://doi.org/10.1016/j.jtbi.2019.109994
Tang, Y., Liu, H., 2017. Modeling multidimensional and multispecies biofilms in porous media. Biotechnol. Bioeng. 114, 1679–1687. https://doi.org/10.1002/bit.26292
Tang, Y., Valocchi, A.J., Werth, C.J., Liu, H., 2013. An improved pore-scale biofilm model and comparison with a microfluidic flow cell experiment. Water Resour. Res. 49, 8370–8382. https://doi.org/10.1002/2013WR013843
The United Nations - World Water Development, 2009. The United Nations World Water Development Report 3: Water in a Changing World (No. 9789231040955). UNESCO, Paris.
Tierra, G., Pavissich, J.P., Nerenberg, R., Xu, Z., Alber, M.S., 2015. Multicomponent model of deformation and detachment of a biofilm under fluid flow. J. R. Soc. Interface 12, 20150045. https://doi.org/10.1098/rsif.2015.0045
Trucchia, A., Mattei, M.R., Luongo, V., Frunzo, L., Rochoux, M.C., 2019. Surrogate-based uncertainty and sensitivity analysis for bacterial invasion in multi-species biofilm modeling. Commun. Nonlinear Sci. Numer. Simul. 73, 403–424. https://doi.org/10.1016/j.cnsns.2019.02.024
Valladares Linares, R., Wexler, A.D., Bucs, Sz.S., Dreszer, C., Zwijnenburg, A., Flemming, H.-C., Kruithof, J.C., Vrouwenvelder, J.S., 2016. Compaction and relaxation of biofilms. Desalination Water Treat. 57, 12902–12914. https://doi.org/10.1080/19443994.2015.1057036
van Breukelen, B.M., Griffioen, J., 2004. Biogeochemical processes at the fringe of a landfill leachate pollution plume: potential for dissolved organic carbon, Fe(II), Mn(II), NH4, and CH4 oxidation. J. Contam. Hydrol. 73, 181–205.
Wagner, M., Horn, H., 2017. Optical coherence tomography in biofilm research: A comprehensive review. Biotechnol. Bioeng. 114, 1386–1402. https://doi.org/10.1002/bit.26283
Wagner, M., Ivleva, N.P., Haisch, C., Niessner, R., Horn, H., 2009. Combined use of confocal laser scanning microscopy (CLSM) and Raman microscopy (RM): investigations on EPS-Matrix. Water Res. 43, 63–76. https://doi.org/10.1016/j.watres.2008.10.034
Wagner, M., Taherzadeh, D., Haisch, C., Horn, H., 2010. Investigation of the mesoscale structure and volumetric features of biofilms using optical coherence tomography. Biotechnol. Bioeng. 107, 844–853. https://doi.org/10.1002/bit.22864
Werth, C.J., Zhang, C., Brusseau, M.L., Oostrom, M., Baumann, T., 2010. A review of non-invasive imaging methods and applications in contaminant hydrogeology research. J. Contam. Hydrol. 113, 1–24. https://doi.org/10.1016/j.jconhyd.2010.01.001
Wilkens, H., Culver, D., Humphreys, W.F., 2000. Subterranean Ecosystems. Elsevier, Amsterdam.
Wimpenny, J.W.T., Colasanti, R., 1997. A unifying hypothesis structure microbial biofilms cellular automaton models. FEMS Microbioi Ecol 22, 1–16.
Yan, Z., Liu, C., Liu, Y., Bailey, V.L., 2017. Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates. Water Resour. Res. 1–17.
Yang, X., Scheibe, T.D., Richmond, M.C., Perkins, W.A., Vogt, S.J., Codd, S.L., Seymour, J.D., McKinley, M.I., 2013. Direct numerical simulation of pore-scale flow in a bead pack: Comparison with magnetic resonance imaging observations. Adv. Water Resour. 54, 228–241. https://doi.org/10.1016/j.advwatres.2013.01.009
Dr. Susanne Schmidt (Dipl.-Biol.)
http://www.sidata.eu