Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

Lovley, 1998, Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese, Appl Environ Microbiol, 54, 1472, 10.1128/AEM.54.6.1472-1480.1988 Lovley, 1991, Microbial reduction of uranium, Nature, 350, 413, 10.1038/350413a0 Lovley, 1995, Bioremediation of organic and metal contaminants with dissimilatory metal reduction, J Ind Microbiol, 14, 85, 10.1007/BF01569889 Anderson, 2003, Stimulating the in situ activity of geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer, Appl Environ Microbiol, 69, 58845891, 10.1128/AEM.69.10.5884-5891.2003 Wu, 2006, Pilot-scale bioremediation of uranium in a highly contaminated aquifer ii: Evidence of u(vi) reduction and geochemical control of u(vi) bioavailability, Environ Sci Technol, 40, 3986, 10.1021/es051960u Holmes, 2005, Potential for quantifying expression of the geobacteraceae citrate synthase gene to assess the activity of geobacteraceae in the subsurface and on current-harvesting electrodes, Appl Environ Microbiol, 71, 6870, 10.1128/AEM.71.11.6870-6877.2005 Holmes, 2007, Subsurface clade of geobacteraceae that predominates in a diversity of fe(iii)-reducing subsurface environments, ISME J, 1, 663, 10.1038/ismej.2007.85 Roden, 2005, Conceptual and numerical model of uranium(vi) reductive immobilization in structured subsurface sediments, Chemosphere, 59, 617, 10.1016/j.chemosphere.2004.11.007 Scheibe, 2006, Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer, Geosphere, 2, 220, 10.1130/GES00029.1 Yabusaki, 2007, Uranium removal from groundwater via in situ biostimulation: field-scale modeling of transport and biological processes, J Contam Hydrol, 93, 216, 10.1016/j.jconhyd.2007.02.005 Fang, 2009, Multicomponent reactive transport modeling of uranium bioremediation field experiments, Geochim Cosmochim Acta, 73, 6029, 10.1016/j.gca.2009.07.019 Li, 2010, Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during uranium bioremediation at rifle, colorado, J Contamin Hydrol, 112, 45, 10.1016/j.jconhyd.2009.10.006 Zhao, 2011, Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation, Biotechnol Bioeng, 108, 1537, 10.1002/bit.23096 Ramkrishna, 2008, A rational for monods biochemical growth kinetics, Ind Eng Chem Res, 47, 9090, 10.1021/ie800905d Bazylinski, 2000, N-2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, geobacter and magnetospirillum species, Environ Microbiol, 2, 266, 10.1046/j.1462-2920.2000.00096.x Methe, 2005, Dna microarray analysis of nitrogen fixation and fe(iii) reduction in geobacter sulfurreducens, Appl Environ Microbiol, 71, 2530, 10.1128/AEM.71.5.2530-2538.2005 Lovley, 1985, Minimum threshold for hydrogen metabolism in methanogenic bacteria, Appl Environ Microbiol, 49, 1530, 10.1128/AEM.49.6.1530-1531.1985 Lovley, 2003, Cleaning up with genomics: applying molecular biology to bioremediation, Nat Rev Microbiol, 1, 35, 10.1038/nrmicro731 Lovley, 2008, Systems biology approach to bioremediation with extracellular electron transfer, 71 Mahadevan, 2011, In situ to in silico and back: elucidating the physiology and ecology of geobacter spp. using genome-scale modeling, Nat Rev Microbiol, 9, 39, 10.1038/nrmicro2456 Mahadevan, 2006, Characterization of metabolism in the fe(iii)-reducing organism geobacter sulfurreducens by constraint-based modeling, Appl Environ Microbiol, 72, 1558, 10.1128/AEM.72.2.1558-1568.2006 Scheibe, 2009, Coupling a genome scale metabolic model with a reactive transport model to describe in situ uranium bioremediation, Microb Biotechnol, 2, 274, 10.1111/j.1751-7915.2009.00087.x Gramling, 2002, Reactive transport in porous media: a comparison of model prediction with laboratory visualization, Environ Sci Technol, 36, 2508, 10.1021/es0157144 Meile, 2006, Scale dependence of reaction rates in porous media, Adv Water Resour, 29, 62, 10.1016/j.advwatres.2005.05.007 Li, 2008, Scale dependence of mineral dissolution rates within single pores and fractures, Geochimica et Cosmochimica Acta, 72, 360, 10.1016/j.gca.2007.10.027 Ryan, 2011, Pore-scale modeling of competitive adsorption in porous media, J Contam Hydrol, 120–121, 56, 10.1016/j.jconhyd.2010.06.008 Gouet-Kaplan M, Tartakovsky A, Berkowitz B, Simulation of the interplay between resident and infiltrating water in partially saturated porous media, Water Resour Res 2009;45:W05416. http://dx.doi.org/10.1029/2008WR007350. Morris, 1999, Parallel simulations of pore-scale flow through porous media, Comput Geotech, 25, 227, 10.1016/S0266-352X(99)00026-9 Tartakovsky, 2005, Modeling of surface tension and contact angles with smoothed particle hydrodynamics, Phys Rev E, 72, 026301, 10.1103/PhysRevE.72.026301 Tartakovsky, 2005, Simulation of unsaturated flow in complex fractures using smoothed particle hydrodynamics, Vadose Zone J, 4, 848, 10.2136/vzj2004.0178 Tartakovsky, 2005, A smoothed particle hydrodynamics model for miscible flow in three-dimensional fractures and the two-dimensional Rayleigh–Taylor instability, J Comput Phys, 207, 610, 10.1016/j.jcp.2005.02.001 Tartakovsky, 2006, Pore-scale modeling of immiscible and miscible flows using smoothed particle hydrodynamics, Adv Water Resour, 29, 1464, 10.1016/j.advwatres.2005.11.014 Tartakovsky, 2008, Effects of peclet number on pore-scale mixing and channeling of a tracer and on directional advective porosity, Geophys Res Lett, 35, L21401, 10.1029/2008GL035895 Tartakovsky A, Ward A, Meakin P, Pore-scale simulations of drainage of heterogeneous and anisotropic porous media, Phys Fluids 2007;19(10):103301. http://dx.doi.org/10.1063/1.2772529. Zhu, 2001, Smoothed particle hydrodynamics model for diffusion through porous media, Transp Porous Media, 43, 441, 10.1023/A:1010769915901 Tartakovsky, 2007, Simulations of reactive transport and precipitation with smoothed particle hydrodynamics, J Comput Phys, 222, 654, 10.1016/j.jcp.2006.08.013 Tartakovsky, 2007, A smoothed particle hydrodynamics model for reactive transport and mineral precipitation in porous and fractured porous media, Water Resour Res, 43, W05437, 10.1029/2005WR004770 Tartakovsky, 2007, Hybrid simulations of reaction–diffusion systems in porous media, SIAM J Sci Comput, 30, 2799, 10.1137/070691097 Tartakovsky A, Tartakovsky D, Meakin P, Stochastic langevin model for flow and transport in porous media, Phys Rev Lett 2008;101(4). Tartakovsky, 2009, Pore-scale model for reactive transport and biomass growth, J Porous Media, 12, 417, 10.1615/JPorMedia.v12.i5.30 Childers, 2002, Geobacter metallireducens accesses insoluble fe(iii) oxide by chemotaxis, Nature, 416, 767, 10.1038/416767a Vrionis, 2005, Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site, Appl Environ Microbiol, 71, 6308, 10.1128/AEM.71.10.6308-6318.2005 Zhao, 2010, Modeling and sensitivity analysis of electron capacitance for geobacter in sedimentary environments, J Contam Hydrol, 112, 30, 10.1016/j.jconhyd.2009.10.002 Luef, 2013, Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth, ISME J, 7, 338, 10.1038/ismej.2012.103 Ma, 2011, Surface heterogeneity on hemispheres-in-cell model yields all experimentally-observed non-straining colloid retention mechanisms in porous media in the presence of energy barriers, Langmuir, 27, 14982, 10.1021/la203587j Rittmann, 2001 Reed, 2006, Towards multidimensional genome annotation, Nat Rev Genet, 7, 130, 10.1038/nrg1769 Feist, 2008, The growing scope of applications of genome-scale metabolic reconstructions using escherichia coli, Nat Biotechnol, 26, 659, 10.1038/nbt1401 Ibarra, 2002, Escherichia coli k-12 undergoes adaptive evolution to achieve in silico predicted optimal growth, Nature, 420, 186, 10.1038/nature01149 Fong, 2004, Metabolic gene-deletion strains of escherichia coli evolve to computationally predicted growth phenotypes, Nat Genet, 36, 1056, 10.1038/ng1432 Varma, 1993, Stoichiometric interpretation of escherichia coli glucose catabolism under various oxygenation rates, Appl Environ Microbiol, 59, 2465, 10.1128/AEM.59.8.2465-2473.1993 Schuetz, 2007, Systematic evaluation of objective functions for predicting intracellular fluxes in escherichia coli, Mol Syst Biol, 3, 119, 10.1038/msb4100162 Fang, 2011, Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model, J Contam Hydrol, 122, 96, 10.1016/j.jconhyd.2010.11.007 Fang, 2012, Evaluation of a genome-scale in silico metabolic model for geobacter metallireducens by using proteomic data from a field biostimulation experiment, Appl Environ Microbiol, 78, 8735, 10.1128/AEM.01795-12 Palmer, 2010, A component based framework for smoothed particle hydrodynamics simulations of reactive fluid flow in porous media, Int J High Perform Comput Appl, 24, 228, 10.1177/1094342009358415 Sayyar B, Thermodynamic electron equivalent modeling of metal reducing bacteria, Master’s thesis, University of Toronto, 2008. Roden, 2011, Thermodynamics of microbial growth coupled to metabolism of glucose, ethanol, short-chain organic acids, and hydrogen, Appl Environ Microbiol, 77, 1907, 10.1128/AEM.02425-10 Stolpovsky, 2011, Incorporating dormancy in dynamic microbial community models, Ecol Model, 222, 3092, 10.1016/j.ecolmodel.2011.07.006 Stolpovsky, 2012, The impact of pore-size heterogeneities on the spatiotemporal variation of microbial metabolic activity in porous media, Soil Sci, 177, 98, 10.1097/SS.0b013e318241105d King, 2009, In silico geobacter sulfurreducens metabolism and its representation in reactive transport models, Appl Environ Microbiol, 75, 83, 10.1128/AEM.01799-08 Thullner, 2010, Comparison of bioclogging effects in saturated porous media within one- and two-dimensional flow systems, Ecol Eng, 36, 176, 10.1016/j.ecoleng.2008.12.037 Yabusaki, 2011, Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment, J Contam Hydrol, 126, 271, 10.1016/j.jconhyd.2011.09.002 Hesse, 2010, Linear exchange model for the description of mass transfer limited bioavailability at the pore scale, Environ Sci Technol, 44, 2064, 10.1021/es902489q Bolster, 2011, Mixing in confined stratified aquifers, J Contam Hydrol, 120–21, 198, 10.1016/j.jconhyd.2010.02.003 Chiogna, 2012, Mixing, entropy and reactive solute transport, Geophy Res Lett, 39, L20405, 10.1029/2012GL053295 de Dreuzy, 2012, Time evolution of mixing in heterogeneous porous media, Water Resour Res, 48, W06511, 10.1029/2011WR011360 Tartakovsky, 2012, Effect of spatial concentration fluctuations on effective kinetics in diffusion-reaction systems, Water Resour Res, 48, W02526, 10.1029/2011WR010720 Tartakovsky, 2011, Dimension reduction method for advection–diffusion–reaction systems, Adv Water Resour, 34, 1616, 10.1016/j.advwatres.2011.07.011