Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media
Abstract
We report that microbial biofilms are ubiquitous within porous media and the dynamics of their growth influence surface and subsurface flow patterns which impacts the physical properties of porous media and large-scale transport of solutes. Here, a two-dimensional pore-scale numerical model was used to evaluate the impact of biofilm-induced flow heterogeneities on conservative transport. Our study integrates experimental biofilm images of Paenibacillus 300A strain in a microfluidic device packed with cylindrical grains in a hexagonal distribution, with mathematical modeling. Biofilm is represented as a synthetic porous structure with locally varying physical properties that honors the impact of biofilm on the porous medium. We find that biofilm plays a major role in shaping the observed conservative transport dynamics by enhancing anomalous characteristics. More specifically, when biofilm is present, the pore structure in our geometry becomes more spatially correlated. We observe intermittent behavior in the Lagrangian velocities that switches between fast transport periods and long trapping events. Our results suggest that intermittency enhances solute spreading in breakthrough curves which exhibit extreme anomalous slope at intermediate times and very marked late solute arrival due to solute retention. The efficiency of solute retention by the biofilm is controlled by a transport regime which canmore »
- Authors:
-
- Desert Research Inst. (DRI), Reno, NV (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Publication Date:
- Research Org.:
- Desert Research Inst. (DRI), Reno, NV (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1854002
- Alternate Identifier(s):
- OSTI ID: 1836639; OSTI ID: 1861891
- Report Number(s):
- PNNL-SA-164581
Journal ID: ISSN 0043-1354
- Grant/Contract Number:
- SC0019437; AC05-76RL01830; DE’SC0019437
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Water Research
- Additional Journal Information:
- Journal Volume: 209; Journal ID: ISSN 0043-1354
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; 58 GEOSCIENCES; 59 BASIC BIOLOGICAL SCIENCES; pore-scale modeling; anomalous transport; biofilm; solute retention
Citation Formats
Perez, Lazaro J., Parashar, Rishi, Plymale, Andrew, and Scheibe, Timothy D. Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media. United States: N. p., 2021.
Web. doi:10.1016/j.watres.2021.117896.
Perez, Lazaro J., Parashar, Rishi, Plymale, Andrew, & Scheibe, Timothy D. Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media. United States. https://doi.org/10.1016/j.watres.2021.117896
Perez, Lazaro J., Parashar, Rishi, Plymale, Andrew, and Scheibe, Timothy D. Thu .
"Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media". United States. https://doi.org/10.1016/j.watres.2021.117896. https://www.osti.gov/servlets/purl/1854002.
@article{osti_1854002,
title = {Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media},
author = {Perez, Lazaro J. and Parashar, Rishi and Plymale, Andrew and Scheibe, Timothy D.},
abstractNote = {We report that microbial biofilms are ubiquitous within porous media and the dynamics of their growth influence surface and subsurface flow patterns which impacts the physical properties of porous media and large-scale transport of solutes. Here, a two-dimensional pore-scale numerical model was used to evaluate the impact of biofilm-induced flow heterogeneities on conservative transport. Our study integrates experimental biofilm images of Paenibacillus 300A strain in a microfluidic device packed with cylindrical grains in a hexagonal distribution, with mathematical modeling. Biofilm is represented as a synthetic porous structure with locally varying physical properties that honors the impact of biofilm on the porous medium. We find that biofilm plays a major role in shaping the observed conservative transport dynamics by enhancing anomalous characteristics. More specifically, when biofilm is present, the pore structure in our geometry becomes more spatially correlated. We observe intermittent behavior in the Lagrangian velocities that switches between fast transport periods and long trapping events. Our results suggest that intermittency enhances solute spreading in breakthrough curves which exhibit extreme anomalous slope at intermediate times and very marked late solute arrival due to solute retention. The efficiency of solute retention by the biofilm is controlled by a transport regime which can extend the tailing in the concentration breakthrough curves. These results indicate that solute retention by the biofilm exerts a strong control on conservative solute transport at pore-scale, a role that to date has not received enough attention.},
doi = {10.1016/j.watres.2021.117896},
journal = {Water Research},
number = ,
volume = 209,
place = {United States},
year = {Thu Nov 25 00:00:00 EST 2021},
month = {Thu Nov 25 00:00:00 EST 2021}
}
Works referenced in this record:
Continuous time random walks for the evolution of Lagrangian velocities
journal, November 2016
- Dentz, Marco; Kang, Peter K.; Comolli, Alessandro
- Physical Review Fluids, Vol. 1, Issue 7
Biofilms: implications in bioremediation
journal, September 2006
- Singh, Rajbir; Paul, Debarati; Jain, Rakesh K.
- Trends in Microbiology, Vol. 14, Issue 9
Modeling the impact of evolving biofilms on flow in porous media inside a microfluidic channel
journal, January 2021
- Karimifard, Shahab; Li, Xu; Elowsky, Christian
- Water Research, Vol. 188
Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms
journal, September 2016
- Ghanbari, Azadeh; Dehghany, Jaber; Schwebs, Timo
- Scientific Reports, Vol. 6, Issue 1
The Bacterial Cell Envelope
journal, April 2010
- Silhavy, T. J.; Kahne, D.; Walker, S.
- Cold Spring Harbor Perspectives in Biology, Vol. 2, Issue 5
Biofilm growth in porous media: Experiments, computational modeling at the porescale, and upscaling
journal, September 2016
- Peszynska, Malgorzata; Trykozko, Anna; Iltis, Gabriel
- Advances in Water Resources, Vol. 95
Peak and tail scaling of breakthrough curves in hydrologic tracer tests
journal, April 2015
- Aquino, T.; Aubeneau, A.; Bolster, D.
- Advances in Water Resources, Vol. 78
Mixing and spreading in stratified flow
journal, January 2007
- Dentz, Marco; Carrera, Jesus
- Physics of Fluids, Vol. 19, Issue 1
Lagrangian Statistical Model for Transport in Highly Heterogeneous Velocity Fields
journal, August 2008
- Le Borgne, Tanguy; Dentz, Marco; Carrera, Jesus
- Physical Review Letters, Vol. 101, Issue 9
Anomalous Fluid Transport in Porous Media Induced by Biofilm Growth
journal, November 2004
- Seymour, Joseph D.; Gage, Justin P.; Codd, Sarah L.
- Physical Review Letters, Vol. 93, Issue 19
Determination of Porosity and Thickness of Biofilm Attached on Irregular-Shaped Media
journal, July 2013
- Hu, Meng; Zhang, Tian C.; Stansbury, John
- Journal of Environmental Engineering, Vol. 139, Issue 7
Current knowledge and perspectives of Paenibacillus: a review
journal, December 2016
- Grady, Elliot Nicholas; MacDonald, Jacqueline; Liu, Linda
- Microbial Cell Factories, Vol. 15, Issue 1
Upscaling and Prediction of Lagrangian Velocity Dynamics in Heterogeneous Porous Media
journal, May 2019
- Hakoun, Vivien; Comolli, Alessandro; Dentz, Marco
- Water Resources Research
PDMS microfluidics: A mini review
journal, January 2020
- Raj M., Kiran; Chakraborty, Suman
- Journal of Applied Polymer Science, Vol. 137, Issue 27
Mixing and Reaction Kinetics in Porous Media: An Experimental Pore Scale Quantification
journal, December 2013
- Anna, Pietro de; Jimenez-Martinez, Joaquin; Tabuteau, Hervé
- Environmental Science & Technology, Vol. 48, Issue 1
Pore‐Scale Hydrodynamics in a Progressively Bioclogged Three‐Dimensional Porous Medium: 3‐D Particle Tracking Experiments and Stochastic Transport Modeling
journal, March 2018
- Carrel, M.; Morales, V. L.; Dentz, M.
- Water Resources Research, Vol. 54, Issue 3
Biotechnology in petroleum recovery: The microbial EOR
journal, December 2008
- Sen, Ramkrishna
- Progress in Energy and Combustion Science, Vol. 34, Issue 6
A web of streamers: biofilm formation in a porous microfluidic device
journal, January 2012
- Valiei, Amin; Kumar, Aloke; Mukherjee, Partha P.
- Lab on a Chip, Vol. 12, Issue 24
Pore-scale simulation of fluid flow and solute dispersion in three-dimensional porous media
journal, July 2014
- Icardi, Matteo; Boccardo, Gianluca; Marchisio, Daniele L.
- Physical Review E, Vol. 90, Issue 1
Biofilm structire and kinetics
journal, July 1997
- Bishop, Paul L.
- Water Science and Technology, Vol. 36, Issue 1
Modeling non-Fickian transport in geological formations as a continuous time random walk
journal, January 2006
- Berkowitz, Brian; Cortis, Andrea; Dentz, Marco
- Reviews of Geophysics, Vol. 44, Issue 2
Effects of Streambed Morphology and Biofilm Growth on the Transient Storage of Solutes
journal, August 2009
- Bottacin-Busolin, Andrea; Singer, Gabriel; Zaramella, Mattia
- Environmental Science & Technology, Vol. 43, Issue 19
Simulation of Flow and Dispersion on Pore-Space Images
journal, December 2012
- Mostaghimi, Peyman; Bijeljic, Branko; Blunt, Martin
- SPE Journal, Vol. 17, Issue 04
Processes in microbial transport in the natural subsurface
journal, August 2002
- Ginn, Timothy R.; Wood, Brian D.; Nelson, Kirk E.
- Advances in Water Resources, Vol. 25, Issue 8-12
Impact of biofilm-induced heterogeneities on solute transport in porous media
journal, November 2014
- Kone, T.; Golfier, F.; Orgogozo, L.
- Water Resources Research, Vol. 50, Issue 11
Lattice Boltzmann simulation of biofilm clogging and chemical oxygen demand removal in porous media
journal, May 2019
- Tian, Zhiwei; Wang, Junye
- AIChE Journal, Vol. 65, Issue 9
Spatial Markov processes for modeling Lagrangian particle dynamics in heterogeneous porous media
journal, August 2008
- Le Borgne, Tanguy; Dentz, Marco; Carrera, Jesus
- Physical Review E, Vol. 78, Issue 2
Upscaling of Mixing‐Limited Bimolecular Chemical Reactions in Poiseuille Flow
journal, January 2019
- Perez, Lazaro J.; Hidalgo, Juan J.; Dentz, Marco
- Water Resources Research, Vol. 55, Issue 1
A dual-porosity theory for solute transport in biofilm-coated porous media
journal, December 2013
- Orgogozo, Laurent; Golfier, Fabrice; Buès, Michel A.
- Advances in Water Resources, Vol. 62
Modeling of Permeability Reduction in Bioclogged Porous Sediments
journal, April 2018
- Abbasi, Babak; Ta, Hien X.; Muhunthan, Balasingam
- Journal of Geotechnical and Geoenvironmental Engineering, Vol. 144, Issue 4
Adhesion and Retention of a Bacterial Phytopathogen Erwinia chrysanthemi in Biofilm-Coated Porous Media
journal, November 2007
- Liu, Yang; Yang, Ching-Hong; Li, Jin
- Environmental Science & Technology, Vol. 42, Issue 1
Biofilms in 3D porous media: Delineating the influence of the pore network geometry, flow and mass transfer on biofilm development
journal, May 2018
- Carrel, Maxence; Morales, Verónica L.; Beltran, Mario A.
- Water Research, Vol. 134
Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems
journal, February 2013
- Drescher, Knut; Shen, Yi; Bassler, Bonnie L.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 11
Microfluidic study of effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength in the flowing and no-flowing microchannels
journal, June 2019
- Liu, Na; Skauge, Tormod; Landa-Marbán, David
- Journal of Industrial Microbiology and Biotechnology, Vol. 46, Issue 6
Stochastic Dynamics of Lagrangian Pore‐Scale Velocities in Three‐Dimensional Porous Media
journal, February 2019
- Puyguiraud, Alexandre; Gouze, Philippe; Dentz, Marco
- Water Resources Research, Vol. 55, Issue 2
A Pore-Scale Model for Permeable Biofilm: Numerical Simulations and Laboratory Experiments
journal, December 2018
- Landa-Marbán, David; Liu, Na; Pop, Iuliu S.
- Transport in Porous Media, Vol. 127, Issue 3
Microbially enhanced geologic containment of sequestered supercritical CO2
journal, February 2009
- Cunningham, A. B.; Gerlach, R.; Spangler, L.
- Energy Procedia, Vol. 1, Issue 1
Semianalytical Computation of Path Lines for Finite-Difference Models
journal, November 1988
- Pollock, David W.
- Ground Water, Vol. 26, Issue 6
Biofilm development and the dynamics of preferential flow paths in porous media
journal, October 2013
- Bottero, Simona; Storck, Tomas; Heimovaara, Timo J.
- Biofouling, Vol. 29, Issue 9
Bacterial floc mediated rapid streamer formation in creeping flows
journal, August 2015
- Hassanpourfard, Mahtab; Nikakhtari, Zahra; Ghosh, Ranajay
- Scientific Reports, Vol. 5, Issue 1
Biofilm enhanced geologic sequestration of supercritical CO2
journal, January 2009
- Mitchell, Andrew C.; Phillips, Adrienne J.; Hiebert, Randy
- International Journal of Greenhouse Gas Control, Vol. 3, Issue 1, p. 90-99
The effect of biofilm permeability on bio-clogging of porous media
journal, December 2011
- Pintelon, Thomas R. R.; Picioreanu, Cristian; van Loosdrecht, Mark C. M.
- Biotechnology and Bioengineering, Vol. 109, Issue 4
Stochastic dynamics of intermittent pore-scale particle motion in three-dimensional porous media: Experiments and theory: PARTICLE MOTION DYNAMICS IN POROUS MEDIA
journal, September 2017
- Morales, V. L.; Dentz, M.; Willmann, M.
- Geophysical Research Letters, Vol. 44, Issue 18
Microfluidic bioanalytical flow cells for biofilm studies: a review
journal, January 2019
- Pousti, Mohammad; Zarabadi, Mir Pouyan; Abbaszadeh Amirdehi, Mehran
- The Analyst, Vol. 144, Issue 1
Applications of biofilms in bioremediation and biotransformation of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals
journal, October 2013
- Edwards, Sarah J.; Kjellerup, Birthe V.
- Applied Microbiology and Biotechnology, Vol. 97, Issue 23
Two-dimensional and three-dimensional dynamic imaging of live biofilms in a microchannel by time-of-flight secondary ion mass spectrometry
journal, May 2015
- Hua, Xin; Marshall, Matthew J.; Xiong, Yijia
- Biomicrofluidics, Vol. 9, Issue 3
Use of tracer tests to investigate changes in flow and transport properties due to bioclogging of porous media
journal, August 2007
- Seifert, Dorte; Engesgaard, Peter
- Journal of Contaminant Hydrology, Vol. 93, Issue 1-4
Anomalous transport in laboratory-scale, heterogeneous porous media
journal, January 2000
- Berkowitz, Brian; Scher, Harvey; Silliman, Stephen E.
- Water Resources Research, Vol. 36, Issue 1
Unraveling the biophysical underpinnings to the success of multispecies biofilms in porous environments
journal, March 2019
- Scheidweiler, David; Peter, Hannes; Pramateftaki, Paraskevi
- The ISME Journal, Vol. 13, Issue 7
Biofilm growth in gravel bed streams controls solute residence time distributions
journal, July 2016
- Aubeneau, A. F.; Hanrahan, Brittany; Bolster, Diogo
- Journal of Geophysical Research: Biogeosciences, Vol. 121, Issue 7
A tensorial approach to computational continuum mechanics using object-oriented techniques
journal, January 1998
- Weller, H. G.; Tabor, G.; Jasak, H.
- Computers in Physics, Vol. 12, Issue 6
Flow Intermittency, Dispersion, and Correlated Continuous Time Random Walks in Porous Media
journal, May 2013
- de Anna, Pietro; Le Borgne, Tanguy; Dentz, Marco
- Physical Review Letters, Vol. 110, Issue 18
Material properties of biofilms—a review of methods for understanding permeability and mechanics
journal, February 2015
- Billings, Nicole; Birjiniuk, Alona; Samad, Tahoura S.
- Reports on Progress in Physics, Vol. 78, Issue 3
Assessment and Prediction of Pore‐Scale Reactive Mixing From Experimental Conservative Transport Data
journal, June 2020
- Perez, Lazaro J.; Hidalgo, Juan J.; Puyguiraud, Alexandre
- Water Resources Research, Vol. 56, Issue 6
Effective dispersion coefficients for the upscaling of pore-scale mixing and reaction
journal, December 2020
- Puyguiraud, Alexandre; Perez, Lazaro J.; Hidalgo, Juan J.
- Advances in Water Resources, Vol. 146
Impact of confined geometries on hopping and trapping of motile bacteria in porous media
journal, January 2021
- Perez, Lazaro J.; Bhattacharjee, Tapomoy; Datta, Sujit S.
- Physical Review E, Vol. 103, Issue 1
Density, porosity, and pore structure of biofilms
journal, November 1994
- Zhang, Tian C.; Bishop, Paul L.
- Water Research, Vol. 28, Issue 11
Mechanisms of dispersion in a porous medium
journal, March 2018
- Dentz, M.; Icardi, M.; Hidalgo, J. J.
- Journal of Fluid Mechanics, Vol. 841
Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network
journal, June 2019
- Aufrecht, Jayde A.; Fowlkes, Jason D.; Bible, Amber N.
- PLOS ONE, Vol. 14, Issue 6
An immersed boundary-lattice Boltzmann model for biofilm growth in porous media
journal, September 2017
- Benioug, M.; Golfier, F.; Oltéan, C.
- Advances in Water Resources, Vol. 107
Morphological analysis of pore size and connectivity in a thick mixed‐culture biofilm
journal, June 2018
- Rosenthal, Alex F.; Griffin, James S.; Wagner, Michael
- Biotechnology and Bioengineering, Vol. 115, Issue 9
Origins of anomalous transport in heterogeneous media: Structural and dynamic controls
journal, February 2014
- Edery, Yaniv; Guadagnini, Alberto; Scher, Harvey
- Water Resources Research, Vol. 50, Issue 2
Relationship between mass transfer coefficient and liquid flow velocity in heterogenous biofilms using microelectrodes and confocal microscopy
journal, December 1997
- Stoodley, Paul; Yang, Shunong; Lappin-Scott, Hilary
- Biotechnology and Bioengineering, Vol. 56, Issue 6