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

Advances in Water Resources

Volumn 59, Issue , 2013, Pages 256-270

  Tartakovsky, G D ^a   Tartakovsky, A M ^a   Scheibe, T D ^a   Fang, Y ^a   Mahadevan, R ^b   Lovley, D R ^c  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

Biogeochemistry; Genome scale model; Geobacter; Metal reduction; Pore scale; Simulation

Indexed keywords

GENOME-SCALE MODEL; GEOBACTER; METAL REDUCTION; PORE-SCALE; SIMULATION;

BIOGEOCHEMISTRY; BIOMASS; FORECASTING; GENES; GRAIN GROWTH; GROWTH KINETICS; IRON; METABOLISM; NAVIER STOKES EQUATIONS; NUTRIENTS; REACTION RATES; SOLUTE TRANSPORT; STOICHIOMETRY; VOLATILE FATTY ACIDS;

COMPUTER SIMULATION;

BIOGEOCHEMISTRY; DARCY LAW; GROWTH; MICROBIOLOGY; REACTION RATE; REACTIVE TRANSPORT;

EID: 84881525046     PISSN: 03091708     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.advwatres.2013.05.007     Document Type: Article

References (68)

1. Lovley D., Phillips E. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 1998, 54(6):1472-1480.
2. Lovley D., Phillips E., Gorby Y., Landa E. Microbial reduction of uranium. Nature 1991, 350:413-416.
3. Lovley D. Bioremediation of organic and metal contaminants with dissimilatory metal reduction. J Ind Microbiol 1995, 14:85-93.
4. Anderson R., Vrionis H., Ortiz-Bernad I., Resch C., Peacock A., Dayvault R., et al. Stimulating the in situ activity of geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl Environ Microbiol 2003, 69:58845891.
5. Wu W., Carley J., Gentry T., Ginder-Vogel M., Fienen M., Mehlhorn T., Yan H., Carroll S., Nyman J., Luo J., Gentile M., Fields M., Hickey R., Watson D., Cirpka O., Fendorf S., Zhou J., Kitanidis P., Jardine P., Criddle C. 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 2006, 40(12):3986-3995.
6. Holmes D., Nevin K., ONeil R., Ward J., Adams L., Woodard T., Vrionis H., Lovley D. 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 2005, 71:6870-6877.
7. Holmes D., ONeil R., Vrionis H., NGuessan L., Ortiz-Bernad I., Larrahondo M., Adams L., Ward J., Nicoll J., Nevin K., Chavan M., Johnson J., Long P., Lovley D. Subsurface clade of geobacteraceae that predominates in a diversity of fe(iii)-reducing subsurface environments. ISME J 2007, 1:663-677.
8. Roden E., Scheibe T. Conceptual and numerical model of uranium(vi) reductive immobilization in structured subsurface sediments. Chemosphere 2005, 59(5):617-628.
9. Scheibe T., Fang Y., Murray C., Roden E., Chen J., Chien Y.-J., Brooks S., Hubbard S. Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer. Geosphere 2006, 2(4):220-235.
10. Yabusaki S., Fang Y., Long P., Resch C., Peacock A., Komlos J., Jaffe P., Morrison S., Dayvault R., White D., Anderson R. Uranium removal from groundwater via in situ biostimulation: field-scale modeling of transport and biological processes. J Contam Hydrol 2007, 93:216-235.
11. Fang Y., Yabusaki S., Morrison S., Amonette J., Long P. Multicomponent reactive transport modeling of uranium bioremediation field experiments. Geochim Cosmochim Acta 2009, 73:6029-6051.
12. Li L., Steefel C., Williams K., Wilkins M., Hubbard S. Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during uranium bioremediation at rifle, colorado. J Contamin Hydrol 2010, 112:45-63.
13. Zhao J., Scheibe T., Mahadevan R. Model-based analysis of the role of biological, hydrological and geochemical factors affecting uranium bioremediation. Biotechnol Bioeng 2011, 108(7):1537-1548.
14. Ramkrishna D., Song H.-S. A rational for monods biochemical growth kinetics. Ind Eng Chem Res 2008, 47:9090-9098.
15. Bazylinski D., Dean A., Schuler D., Phillips E., Lovley D. N-2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, geobacter and magnetospirillum species. Environ Microbiol 2000, 2:266-273.
16. Methe B., Webster J., Nevin K., Butler J., Lovley D. Dna microarray analysis of nitrogen fixation and fe(iii) reduction in geobacter sulfurreducens. Appl Environ Microbiol 2005, 71:2530-2538.
17. Lovley D. Minimum threshold for hydrogen metabolism in methanogenic bacteria. Appl Environ Microbiol 1985, 49:1530-1531.
18. Lovley D. Cleaning up with genomics: applying molecular biology to bioremediation. Nat Rev Microbiol 2003, 1:35-44.
19. Lovley D., Mahadevan R., Nevin K. Systems biology approach to bioremediation with extracellular electron transfer. Microbial Biodegradation: Genomics and Molecular Biology 2008, 71-96. Caister Academic Press, Norfolk, UK. E. Daz (Ed.).
20. Mahadevan R., Palsson B., Lovley D. In situ to in silico and back: elucidating the physiology and ecology of geobacter spp. using genome-scale modeling. Nat Rev Microbiol 2011, 9(1):39-50.
21. Mahadevan R., Bond D., Butler J., Esteve-Nunez A., Coppi M., Palsson B., et al. Characterization of metabolism in the fe(iii)-reducing organism geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol 2006, 72:1558-1568.
22. Scheibe T., Mahadevan R., Fang Y., Garg S., Long P., Lovely D. Coupling a genome scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb Biotechnol 2009, 2(2):274-286.
23. Gramling C.M., Harvey C.F., Meigs L.C. Reactive transport in porous media: a comparison of model prediction with laboratory visualization. Environ Sci Technol 2002, 36(11):2508-2514.
24. Meile C., Tuncay K. Scale dependence of reaction rates in porous media. Adv Water Resour 2006, 29(1):62-71.
25. Li L., Steefel C.I., Yang L. Scale dependence of mineral dissolution rates within single pores and fractures. Geochimica et Cosmochimica Acta 2008, 72(2):360-377.
26. Ryan E., Tartakovsky A.M., Amon C. Pore-scale modeling of competitive adsorption in porous media. J Contam Hydrol 2011, 120-121:56-78.
27. 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.
28. Morris J., Zhu Y., Fox P. Parallel simulations of pore-scale flow through porous media. Comput Geotech 1999, 25(4):227-246.
29. Tartakovsky A., Meakin P. Modeling of surface tension and contact angles with smoothed particle hydrodynamics. Phys Rev E 2005, 72:026301.
30. Tartakovsky A., Meakin P. Simulation of unsaturated flow in complex fractures using smoothed particle hydrodynamics. Vadose Zone J 2005, 4(3):848-855.
31. Tartakovsky A., Meakin P. A smoothed particle hydrodynamics model for miscible flow in three-dimensional fractures and the two-dimensional Rayleigh-Taylor instability. J Comput Phys 2005, 207:610-624.
32. Tartakovsky A., Meakin P. Pore-scale modeling of immiscible and miscible flows using smoothed particle hydrodynamics. Adv Water Resour 2006, 29:1464-1478.
33. Tartakovsky A.M., Neuman S. Effects of peclet number on pore-scale mixing and channeling of a tracer and on directional advective porosity. Geophys Res Lett 2008, 35:L21401.
34. 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.
35. Zhu Y., Fox P. Smoothed particle hydrodynamics model for diffusion through porous media. Transp Porous Media 2001, 43(3):441-471.
36. Tartakovsky A., Meakin P., Scheibe T., West R.E. Simulations of reactive transport and precipitation with smoothed particle hydrodynamics. J Comput Phys 2007, 222:654-672.
37. Tartakovsky A., Meakin P., Scheibe T., Wood B. A smoothed particle hydrodynamics model for reactive transport and mineral precipitation in porous and fractured porous media. Water Resour Res 2007, 43:W05437.
38. Tartakovsky A., Tartakovsky D., Scheibe T., Meakin P. Hybrid simulations of reaction-diffusion systems in porous media. SIAM J Sci Comput 2007, 30(6):2799-2816.
39. Tartakovsky A, Tartakovsky D, Meakin P, Stochastic langevin model for flow and transport in porous media, Phys Rev Lett 2008;101(4).
40. Tartakovsky A.M., Scheibe T., Meakin P. Pore-scale model for reactive transport and biomass growth. J Porous Media 2009, 12(5):417-434.
41. Childers S., Ciufo S., Lovley D. Geobacter metallireducens accesses insoluble fe(iii) oxide by chemotaxis. Nature 2002, 416(6882):767-769.
42. Vrionis H.A., Anderson R.T., Ortiz-Bernad I., O'Neill K.R., Resch C.T., Peacock A.D., Dayvault R., White D.C., Long P.E., Lovley D.R. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl Environ Microbiol 2005, 71(10):6308-6318.
43. Zhao J., Fang Y.L., Scheibe T.D., Lovley D.R., Mahadevan R. Modeling and sensitivity analysis of electron capacitance for geobacter in sedimentary environments. J Contam Hydrol 2010, 112(1-4):30-44.
44. Luef B., Fakra S.C., Csencsits R., Wrighton K.C., Williams K.H., Wilkins M.J., Downing K.H., Long P.E., Comolli L.R., Banfield J.F. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. ISME J 2013, 7(2):338-350.
45. Ma H., Pazmino E., Johnson W. 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 2011, 27(4):14982-14994.
46. Rittmann B., McCarty P. Environmental biotechnology 2001, McGraw-Hill, Boston, MA, USA.
47. Reed J., Famili I., Thiele I., Palsson B. Towards multidimensional genome annotation. Nat Rev Genet 2006, 7:130-141.
48. Feist A., Palsson B.O. The growing scope of applications of genome-scale metabolic reconstructions using escherichia coli. Nat Biotechnol 2008, 26:659-667.
49. Ibarra R., Edwards J., Palsson B. Escherichia coli k-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189.
50. Fong S., Palsson B. Metabolic gene-deletion strains of escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 2004, 36:1056-1058.
51. Varma A., Boesch B., Palsson B. Stoichiometric interpretation of escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol 1993, 59:2465-2473.
52. Schuetz R., Kuepfer L., Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in escherichia coli. Mol Syst Biol 2007, 3:119.
53. Fang Y., Scheibe T., Mahadevan R., Garg S., Long P., Lovley D. Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model. J Contam Hydrol 2011, 122:96-103.
54. Fang Y., Wilkins M.J., Yabusaki S.B., Lipton M.S., Long P.E. Evaluation of a genome-scale in silico metabolic model for geobacter metallireducens by using proteomic data from a field biostimulation experiment. Appl Environ Microbiol 2012, 78(24):8735-8742.
55. Palmer B., Gurumoorthi V., Tartakovsky A., Scheibe T. A component based framework for smoothed particle hydrodynamics simulations of reactive fluid flow in porous media. Int J High Perform Comput Appl 2010, 24(2):228-239.
56. Sayyar B, Thermodynamic electron equivalent modeling of metal reducing bacteria, Master's thesis, University of Toronto, 2008.
57. Roden E., Jin Q. Thermodynamics of microbial growth coupled to metabolism of glucose, ethanol, short-chain organic acids, and hydrogen. Appl Environ Microbiol 2011, 77(5):1907-1909.
58. Stolpovsky K., Martinez-Lavanchy P., Heipieper H.J., Cappellen P.V., Thullner M. Incorporating dormancy in dynamic microbial community models. Ecol Model 2011, 222(17):3092-3102.
59. Stolpovsky K., Gharasoo M., Thullner M. The impact of pore-size heterogeneities on the spatiotemporal variation of microbial metabolic activity in porous media. Soil Sci 2012, 177(2):98-110.
60. King E.I., Tuncay K., Ortoleva P., Meile C. In silico geobacter sulfurreducens metabolism and its representation in reactive transport models. Appl Environ Microbiol 2009, 75(1):83-92.
61. Thullner M. Comparison of bioclogging effects in saturated porous media within one- and two-dimensional flow systems. Ecol Eng 2010, 36(2):176-196.
62. Yabusaki S., Fang Y., Williams K.H., Muray C.J., Ward A.L., Dayvault R.D., Waichler S.R., Newcomer D.R., Spane F.A., Long P.E. Variably saturated flow and multicomponent biogeochemical reactive transport modeling of a uranium bioremediation field experiment. J Contam Hydrol 2011, 126(3-4):271-290.
63. Hesse F., Harms H., Attinger S., Thullner M. Linear exchange model for the description of mass transfer limited bioavailability at the pore scale. Environ Sci Technol 2010, 44(6):2064-2071.
64. Bolster D., Valdes-Parada F.J., LeBorgne T., Dentz M., Carrera J. Mixing in confined stratified aquifers. J Contam Hydrol 2011, 120-21:198-212.
65. Chiogna G., Hochstetler D.L., Bellin A., Kitanidis P.K., Massimo R. Mixing, entropy and reactive solute transport. Geophy Res Lett 2012, 39:L20405.
66. de Dreuzy J.-R., Carrera J., Dentz M., Borgne T.L. Time evolution of mixing in heterogeneous porous media. Water Resour Res 2012, 48:W06511.
67. Tartakovsky A.M., de Anna P., Borgne T.L., Balter A., Bolster D. Effect of spatial concentration fluctuations on effective kinetics in diffusion-reaction systems. Water Resour Res 2012, 48:W02526.
68. Tartakovsky A., Scheibe T. Dimension reduction method for advection-diffusion-reaction systems. Adv Water Resour 2011, 34(12):1616-1626.