Modeling multidimensional and multispecies biofilms in porous media

Tang, Youneng; Liu, Haihu

doi:10.1002/bit.26292

Modeling multidimensional and multispecies biofilms in porous media

Journal Article · Tue Apr 18 00:00:00 EDT 2017 · Biotechnology and Bioengineering

DOI:https://doi.org/10.1002/bit.26292· OSTI ID:1401768

^[1]; Liu, Haihu ^[2]

Department of Civil and Environmental Engineering Florida A&,M University‐Florida State University College of Engineering Florida State University Tallahassee Florida
School of Energy and Power Engineering Xi'an Jiaotong University Xi'an Shaanxi 710049 China

ABSTRACT

Modeling multidimensional and multispecies biofilm in porous media at the pore scale is challenging due to the need to simultaneously track the microbial community in the biofilms and the interfaces between the biofilms and the fluid. Therefore, researchers usually assume that the model has only one dimension in space or has only one microbial species. This work uses bioremediation of U(VI)‐contaminated groundwater as the context to develop a two‐dimensional and multispecies biofilm model. The model simulates the transverse mixing zone in which U(VI) is mixed with propionate, a nutrient externally supplied to stimulate the growth of microorganisms. The model considers multiple interactions among fluid flow, transport and reaction of chemical species, and growth of biofilm. The biofilm consists of two types of active biomass (syntrophs and dissimilatory metal reducing bacteria [DMBR]) and inert biomass. The two types of active biomass collaboratively remove U(VI). The model outputs biomass distribution, chemical species concentrations, and fluid flow at the pore scale to fundamentally study the multiple interactions. The model also outputs the contaminant removal rate that can be potentially used for up‐scaling studies. The simulated results are generally consistent with experimental observations from other studies in trend. The trend can be explained by the multiple interactions based on thermodynamics and microbial kinetics. Biotechnol. Bioeng. 2017;114: 1679–1687. © 2017 Wiley Periodicals, Inc.

View Accepted Manuscript (Publisher)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0006771

OSTI ID:: 1401768

Journal Information:: Biotechnology and Bioengineering, Journal Name: Biotechnology and Bioengineering Journal Issue: 8 Vol. 114; ISSN 0006-3592

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United States

Language:: English

References (34)

Effect of diffusive and convective substrate transport on biofilm structure formation: A two-dimensional modeling study Picioreanu, Cristian; Van Loosdrecht, Mark C. M.; Heijnen, Joseph J. Biotechnology and Bioengineering, Vol. 69, Issue 5 https://doi.org/10.1002/1097-0290(20000905)69:5<504::AID-BIT5>3.0.CO;2-S	journal	January 2000
An improved pore-scale biofilm model and comparison with a microfluidic flow cell experiment: A PORE-SCALE BIOFILM MODEL AND COMPARISON WITH AN EXPERIMENT Tang, Youneng; Valocchi, Albert J.; Werth, Charles J. Water Resources Research, Vol. 49, Issue 12 https://doi.org/10.1002/2013WR013843	journal	December 2013
Three-dimensional simulations of biofilm growth in porous media von der Schulenburg, D. A. Graf; Pintelon, T. R. R.; Picioreanu, C. AIChE Journal, Vol. 55, Issue 2 https://doi.org/10.1002/aic.11674	journal	February 2009
Reduction kinetics of Fe(III), Co(III), U(VI), Cr(VI), and Tc(VII) in cultures of dissimilatory metal-reducing bacteria Liu, Chongxuan; Gorby, Yuri A.; Zachara, John M. Biotechnology and Bioengineering, Vol. 80, Issue 6 https://doi.org/10.1002/bit.10430	journal	October 2002
A multispecies biofilm model Wanner, O.; Gujer, W. Biotechnology and Bioengineering, Vol. 28, Issue 3 https://doi.org/10.1002/bit.260280304	journal	March 1986
The Impact of Fe(III)-reducing Bacteria on Uranium Mobility Wilkins, Michael J.; Livens, Francis R.; Vaughan, David J. Biogeochemistry, Vol. 78, Issue 2 https://doi.org/10.1007/s10533-005-3655-z	journal	April 2006
Degradation kinetics of acetate and propionate by immobilized anaerobic mixed cultures Kus, F.; Wiesmann, U. Water Research, Vol. 29, Issue 6 https://doi.org/10.1016/0043-1354(94)00285-F	journal	June 1995
Modeling of biomass-plug development and propagation in porous media Stewart, Terri L.; Kim, Dong-Shik Biochemical Engineering Journal, Vol. 17, Issue 2 https://doi.org/10.1016/S1369-703X(03)00146-3	journal	February 2004
Pore-scale simulation of liquid CO2 displacement of water using a two-phase lattice Boltzmann model Liu, Haihu; Valocchi, Albert J.; Werth, Charles Advances in Water Resources, Vol. 73 https://doi.org/10.1016/j.advwatres.2014.07.010	journal	November 2014
High-resolution monitoring of biogeochemical gradients in a tar oil-contaminated aquifer Anneser, Bettina; Einsiedl, Florian; Meckenstock, Rainer U. Applied Geochemistry, Vol. 23, Issue 6 https://doi.org/10.1016/j.apgeochem.2008.02.003	journal	June 2008
A reactive transport modeling approach to simulate biogeochemical processes in pore structures with pore-scale heterogeneities Gharasoo, Mehdi; Centler, Florian; Regnier, Pierre Environmental Modelling & Software, Vol. 30 https://doi.org/10.1016/j.envsoft.2011.10.010	journal	April 2012
Enhanced biodegradation by hydraulic heterogeneities in petroleum hydrocarbon plumes Bauer, Robert D.; Rolle, Massimo; Bauer, Sebastian Journal of Contaminant Hydrology, Vol. 105, Issue 1-2 https://doi.org/10.1016/j.jconhyd.2008.11.004	journal	February 2009
A thermodynamically-based model for predicting microbial growth and community composition coupled to system geochemistry: Application to uranium bioreduction Istok, J. D.; Park, M.; Michalsen, M. Journal of Contaminant Hydrology, Vol. 112, Issue 1-4 https://doi.org/10.1016/j.jconhyd.2009.07.004	journal	March 2010
Microbial physiology-based model of ethanol metabolism in subsurface sediments Jin, Qusheng; Roden, Eric E. Journal of Contaminant Hydrology, Vol. 125, Issue 1-4 https://doi.org/10.1016/j.jconhyd.2011.04.002	journal	July 2011
An improved cellular automaton method to model multispecies biofilms Tang, Youneng; Valocchi, Albert J. Water Research, Vol. 47, Issue 15 https://doi.org/10.1016/j.watres.2013.06.055	journal	October 2013
Modelling and predicting biofilm structure Picioreanu, Cristian; van Loosdrecht, Mark C. M.; Heijnen, Joseph J. Community Structure and Co-operation in Biofilms https://doi.org/10.1017/CBO9780511754814.009	book	October 2000
Modeling Kinetic Processes Controlling Hydrogen and Acetate Concentrations in an Aquifer-Derived Microcosm Watson, Ian A.; Oswald, Sascha E.; Mayer, K. Ulrich Environmental Science & Technology, Vol. 37, Issue 17 https://doi.org/10.1021/es020242u	journal	September 2003
Simultaneous Utilization of Acetate and Hydrogen by Geobacter sulfurreducens and Implications for Use of Hydrogen as an Indicator of Redox Conditions Brown, Derick G.; Komlos, John; Jaffé, Peter R. Environmental Science & Technology, Vol. 39, Issue 9 https://doi.org/10.1021/es048613p	journal	May 2005
Development and Sensitivity Analysis of a Fully Kinetic Model of Sequential Reductive Dechlorination in Groundwater Malaguerra, Flavio; Chambon, Julie C.; Bjerg, Poul L. Environmental Science & Technology, Vol. 45, Issue 19 https://doi.org/10.1021/es201270z	journal	October 2011
Immobilization of Selenite via Two Parallel Pathways during In Situ Bioremediation Tang, Youneng; Werth, Charles J.; Sanford, Robert A. Environmental Science & Technology, Vol. 49, Issue 7 https://doi.org/10.1021/es506107r	journal	March 2015
Mineral Transformation and Biomass Accumulation Associated With Uranium Bioremediation at Rifle, Colorado Li, Li; Steefel, Carl I.; Williams, Kenneth H. Environmental Science & Technology, Vol. 43, Issue 14 https://doi.org/10.1021/es900016v	journal	July 2009
Effects of Pore-Scale Heterogeneity and Transverse Mixing on Bacterial Growth in Porous Media Zhang, Changyong; Kang, Qinjun; Wang, Xing Environmental Science & Technology, Vol. 44, Issue 8 https://doi.org/10.1021/es903396h	journal	April 2010
Practical Considerations for Measuring Hydrogen Concentrations in Groundwater Chapelle, Francis H.; Vroblesky, Don A.; Woodward, Joan C. Environmental Science & Technology, Vol. 31, Issue 10 https://doi.org/10.1021/es970085c	journal	October 1997
Pore-scale modeling of biological clogging due to aggregate expansion: A material mechanics approach Dupin, Hubert J.; Kitanidis, Peter K.; McCarty, Perry L. Water Resources Research, Vol. 37, Issue 12 https://doi.org/10.1029/2001WR000306	journal	December 2001
Simulations of two-dimensional modeling of biomass aggregate growth in network models Dupin, Hubert J.; Kitanidis, Peter K.; McCarty, Perry L. Water Resources Research, Vol. 37, Issue 12 https://doi.org/10.1029/2001WR000310	journal	December 2001
Pore-scale simulation of biomass growth along the transverse mixing zone of a model two-dimensional porous medium: PORE-SCALE SIMULATION OF BIOMASS GROWTH Knutson, C. E.; Werth, C. J.; Valocchi, A. J. Water Resources Research, Vol. 41, Issue 7 https://doi.org/10.1029/2004WR003459	journal	July 2005
Microbial reduction of uranium Lovley, Derek R.; Phillips, Elizabeth J. P.; Gorby, Yuri A. Nature, Vol. 350, Issue 6317 https://doi.org/10.1038/350413a0	journal	April 1991
Quantitative Cellular Automaton Model for Biofilms Pizarro, Gonzalo; Griffeath, David; Noguera, Daniel R. Journal of Environmental Engineering, Vol. 127, Issue 9 https://doi.org/10.1061/(ASCE)0733-9372(2001)127:9(782)	journal	September 2001
Biofilm development and the dynamics of preferential flow paths in porous media Bottero, Simona; Storck, Tomas; Heimovaara, Timo J. Biofouling, Vol. 29, Issue 9 https://doi.org/10.1080/08927014.2013.828284	journal	October 2013
An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods Scheibe, Timothy D.; Murphy, Ellyn M.; Chen, Xingyuan Groundwater, Vol. 53, Issue 1 https://doi.org/10.1111/gwat.12179	journal	March 2014
Imaging biofilm in porous media using X-ray computed microtomography: IMAGING BIOFILM IN POROUS MEDIA USING X-RAY COMPUTED MICROTOMOGRAPHY Davit, Y.; Iltis, G.; Debenest, G. Journal of Microscopy, Vol. 242, Issue 1 https://doi.org/10.1111/j.1365-2818.2010.03432.x	journal	September 2010
Energy conservation in chemotrophic anaerobic bacteria. Thauer, R. K.; Jungermann, K.; Decker, K. Bacteriological Reviews, Vol. 41, Issue 1 https://doi.org/10.1128/MMBR.41.1.100-180.1977	journal	January 1977
Pore-Scale Model for Reactive Transport and Biomass Growth Tartakovsky, Alexandre M.; Scheibe, Timothy D.; Meakin, Paul Journal of Porous Media, Vol. 12, Issue 5 https://doi.org/10.1615/JPorMedia.v12.i5.30	journal	January 2009
The thermodynamics and kinetics of microbial metabolism Jin, Q.; Bethke, C. M. American Journal of Science, Vol. 307, Issue 4 https://doi.org/10.2475/04.2007.01	journal	April 2007

Similar Records

Microbiological-enhanced mixing across scales during in-situ bioreduction of metals and radionuclides at Department of Energy Sites

Technical Report · Tue Oct 20 00:00:00 EDT 2015 · OSTI ID:1223732

A hybrid pore‐scale and continuum‐scale model for solute diffusion, reaction, and biofilm development in porous media

Journal Article · Mon Mar 30 20:00:00 EDT 2015 · Water Resources Research · OSTI ID:1402156

Biofilm Shows Spatially Stratified Metabolic Responses to Contaminant Exposure

Journal Article · Thu Nov 01 00:00:00 EDT 2012 · Environmental Microbiology, 14(11):2901-2910 · OSTI ID:1054430

Modeling multidimensional and multispecies biofilms in porous media

Citation Formats

References (34)

Similar Records

Related Subjects