DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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 » 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.« less

Authors:
 [1];  [1];  [2];  [2]
  1. Desert Research Inst. (DRI), Reno, NV (United States)
  2. 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


Biofilms: implications in bioremediation
journal, September 2006


Modeling the impact of evolving biofilms on flow in porous media inside a microfluidic channel
journal, January 2021


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
  • DOI: 10.1038/srep32097

The Bacterial Cell Envelope
journal, April 2010


Biofilm growth in porous media: Experiments, computational modeling at the porescale, and upscaling
journal, September 2016


Peak and tail scaling of breakthrough curves in hydrologic tracer tests
journal, April 2015


Mixing and spreading in stratified flow
journal, January 2007

  • Dentz, Marco; Carrera, Jesus
  • Physics of Fluids, Vol. 19, Issue 1
  • DOI: 10.1063/1.2427089

Lagrangian Statistical Model for Transport in Highly Heterogeneous Velocity Fields
journal, August 2008


Anomalous Fluid Transport in Porous Media Induced by Biofilm Growth
journal, November 2004


Determination of Porosity and Thickness of Biofilm Attached on Irregular-Shaped Media
journal, July 2013


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
  • DOI: 10.1186/s12934-016-0603-7

Upscaling and Prediction of Lagrangian Velocity Dynamics in Heterogeneous Porous Media
journal, May 2019

  • Hakoun, Vivien; Comolli, Alessandro; Dentz, Marco
  • Water Resources Research
  • DOI: 10.1029/2018WR023810

PDMS microfluidics: A mini review
journal, January 2020

  • Raj M., Kiran; Chakraborty, Suman
  • Journal of Applied Polymer Science, Vol. 137, Issue 27
  • DOI: 10.1002/app.48958

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
  • DOI: 10.1021/es403105b

Biotechnology in petroleum recovery: The microbial EOR
journal, December 2008


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
  • DOI: 10.1039/c2lc40815e

Pore-scale simulation of fluid flow and solute dispersion in three-dimensional porous media
journal, July 2014


Biofilm structire and kinetics
journal, July 1997


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
  • DOI: 10.1029/2005RG000178

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
  • DOI: 10.1021/es900852w

Simulation of Flow and Dispersion on Pore-Space Images
journal, December 2012

  • Mostaghimi, Peyman; Bijeljic, Branko; Blunt, Martin
  • SPE Journal, Vol. 17, Issue 04
  • DOI: 10.2118/135261-PA

Processes in microbial transport in the natural subsurface
journal, August 2002


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
  • DOI: 10.1002/2013WR015213

Lattice Boltzmann simulation of biofilm clogging and chemical oxygen demand removal in porous media
journal, May 2019


Spatial Markov processes for modeling Lagrangian particle dynamics in heterogeneous porous media
journal, August 2008


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
  • DOI: 10.1029/2018WR022730

A dual-porosity theory for solute transport in biofilm-coated porous media
journal, December 2013


Modeling of Permeability Reduction in Bioclogged Porous Sediments
journal, April 2018


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
  • DOI: 10.1021/es071698k

Biofilms in 3D porous media: Delineating the influence of the pore network geometry, flow and mass transfer on biofilm development
journal, May 2018


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
  • DOI: 10.1073/pnas.1300321110

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
  • DOI: 10.1007/s10295-019-02161-x

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
  • DOI: 10.1029/2018WR023702

A Pore-Scale Model for Permeable Biofilm: Numerical Simulations and Laboratory Experiments
journal, December 2018


Microbially enhanced geologic containment of sequestered supercritical CO2
journal, February 2009


Semianalytical Computation of Path Lines for Finite-Difference Models
journal, November 1988


Biofilm development and the dynamics of preferential flow paths in porous media
journal, October 2013


Bacterial floc mediated rapid streamer formation in creeping flows
journal, August 2015

  • Hassanpourfard, Mahtab; Nikakhtari, Zahra; Ghosh, Ranajay
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep13070

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
  • DOI: 10.1016/j.ijggc.2008.05.002

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
  • DOI: 10.1002/bit.24381

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
  • DOI: 10.1039/C8AN01526K

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
  • DOI: 10.1007/s00253-013-5216-z

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
  • DOI: 10.1063/1.4919807

Use of tracer tests to investigate changes in flow and transport properties due to bioclogging of porous media
journal, August 2007


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
  • DOI: 10.1029/1999WR900295

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
  • DOI: 10.1038/s41396-019-0381-4

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
  • DOI: 10.1002/2016JG003333

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
  • DOI: 10.1063/1.168744

Flow Intermittency, Dispersion, and Correlated Continuous Time Random Walks in Porous Media
journal, May 2013


Material properties of biofilms—a review of methods for understanding permeability and mechanics
journal, February 2015


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
  • DOI: 10.1029/2019WR026452

Effective dispersion coefficients for the upscaling of pore-scale mixing and reaction
journal, December 2020


Impact of confined geometries on hopping and trapping of motile bacteria in porous media
journal, January 2021


Density, porosity, and pore structure of biofilms
journal, November 1994


Mechanisms of dispersion in a porous medium
journal, March 2018

  • Dentz, M.; Icardi, M.; Hidalgo, J. J.
  • Journal of Fluid Mechanics, Vol. 841
  • DOI: 10.1017/jfm.2018.120

Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network
journal, June 2019


An immersed boundary-lattice Boltzmann model for biofilm growth in porous media
journal, September 2017


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
  • DOI: 10.1002/bit.26729

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
  • DOI: 10.1002/2013WR015111