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Markale I, Carrel M, Kurz DL, Morales VL, Holzner M, Jiménez-Martínez J. Internal Biofilm Heterogeneities Enhance Solute Mixing and Chemical Reactions in Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:8065-8074. [PMID: 37205794 DOI: 10.1021/acs.est.2c09082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Bacterial biofilms can form in porous media that are of interest in industrial applications ranging from medical implants to biofilters as well as in environmental applications such as in situ groundwater remediation, where they can be critical locations for biogeochemical reactions. The presence of biofilms modifies porous media topology and hydrodynamics by clogging pores and consequently solutes transport and reactions kinetics. The interplay between highly heterogeneous flow fields found in porous media and microbial behavior, including biofilm growth, results in a spatially heterogeneous biofilm distribution in the porous media as well as internal heterogeneity across the thickness of the biofilm. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore-scale fluid flow and solute transport by considering multiple equivalent stochastically generated internal permeability fields for the biofilm. We show that the internal heterogeneous permeability mainly impacts intermediate velocities when compared with homogeneous biofilm permeability. While the equivalent internal permeability fields of the biofilm do not impact fluid-fluid mixing, they significantly control a fast reaction. For biologically driven reactions such as nutrient or contaminant uptake by the biofilm, its internal permeability field controls the efficiency of the process. This study highlights the importance of considering the internal heterogeneity of biofilms to better predict reactivity in industrial and environmental bioclogged porous systems.
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Affiliation(s)
- Ishaan Markale
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Dorothee L Kurz
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Verónica L Morales
- Department of Civil and Environmental Engineering, University of California Davis, Davis, California 95616-5270, United States
| | - Markus Holzner
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- WSL, Swiss Federal Institute of Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland
| | - Joaquín Jiménez-Martínez
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland
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Kurz DL, Secchi E, Stocker R, Jimenez-Martinez J. Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5666-5677. [PMID: 36976631 DOI: 10.1021/acs.est.2c08890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The functioning of natural and engineered porous media, like soils and filters, depends in many cases on the interplay between biochemical processes and hydrodynamics. In such complex environments, microorganisms often form surface-attached communities known as biofilms. Biofilms can take the shape of clusters, which alter the distribution of fluid flow velocities within the porous medium, subsequently influencing biofilm growth. Despite numerous experimental and numerical efforts, the control of the biofilm clustering process and the resulting heterogeneity in biofilm permeability is not well understood, limiting our predictive abilities for biofilm-porous medium systems. Here, we use a quasi-2D experimental model of a porous medium to characterize biofilm growth dynamics for different pore sizes and flow rates. We present a method to obtain the time-resolved biofilm permeability field from experimental images and use the obtained permeability field to compute the flow field through a numerical model. We observe a biofilm cluster size distribution characterized by a spectrum slope evolving in time between -2 and -1, a fundamental measure that can be used to create spatio-temporal distributions of biofilm clusters for upscaled models. We find a previously undescribed biofilm permeability distribution, which can be used to stochastically generate permeability fields within biofilms. An increase in velocity variance for a decrease in physical heterogeneity shows that the bioclogged porous medium behaves differently than expected from studies on heterogeneity in abiotic porous media.
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Affiliation(s)
- Dorothee L Kurz
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
- Department Water Resources and Drinking Water, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
| | - Joaquin Jimenez-Martinez
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland
- Department Water Resources and Drinking Water, Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
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Wu T, Yang Z, Hu R, Chen YF. Three-Dimensional Visualization Reveals Pore-Scale Mechanisms of Colloid Transport and Retention in Two-Phase Flow. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1997-2005. [PMID: 36602921 DOI: 10.1021/acs.est.2c08757] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Colloids are ubiquitous in the natural environment, playing an important role in facilitating the transport of absorbed contaminants. However, due to the complexities arising from two-phase flow and difficulties in three-dimensional observations, the detailed mechanisms of colloid transport and retention under two-phase flow are still not well understood. In this work, we visualize the colloid transport and retention during immiscible two-phase flow based on confocal microscopy. We find that the colloid transport and retention behaviors depend strongly on the flow rate and pore/grain size. At low levels of saturation (high flow rate) with the wetting liquid mainly present as pendular rings, the colloids can aggregate at the liquid filaments in small-grain packings and are uniformly distributed in large-grain packings. Through theoretical analysis of the pendular ring geometry, we elucidate the mechanism responsible for the strong dependence of colloid clogging behavior on solid grain size. Our results further demonstrate that even at dilute concentrations, colloids can alter the flow paths and the wetting fluid topology, suggesting a strong two-way coupling dynamics between immiscible two-phase flow and colloid transport and calling for improved predictive models to incorporate the overlooked clogging behavior.
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Affiliation(s)
- Ting Wu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan430072, China
- Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan430072, China
- Nanjing Hydraulic Research Institute, Nanjing210029, China
| | - Zhibing Yang
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan430072, China
- Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan430072, China
| | - Ran Hu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan430072, China
- Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan430072, China
| | - Yi-Feng Chen
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan430072, China
- Key Laboratory of Rock Mechanics in Hydraulic Structural Engineering of the Ministry of Education, Wuhan University, Wuhan430072, China
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Anomalous transport of colloids in heterogeneous porous media: A multi-scale statistical theory. J Colloid Interface Sci 2022; 617:94-105. [DOI: 10.1016/j.jcis.2022.02.127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 11/24/2022]
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5
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Perez LJ, Parashar R, Plymale A, Scheibe TD. Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media. WATER RESEARCH 2022; 209:117896. [PMID: 34922103 DOI: 10.1016/j.watres.2021.117896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/13/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
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. 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.
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Affiliation(s)
| | | | - Andrew Plymale
- Pacific Northwest National Laboratory, Richland, WA, USA
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Reactive Transport: A Review of Basic Concepts with Emphasis on Biochemical Processes. ENERGIES 2022. [DOI: 10.3390/en15030925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reactive transport (RT) couples bio-geo-chemical reactions and transport. RT is important to understand numerous scientific questions and solve some engineering problems. RT is highly multidisciplinary, which hinders the development of a body of knowledge shared by RT modelers and developers. The goal of this paper is to review the basic conceptual issues shared by all RT problems, so as to facilitate advancement along the current frontier: biochemical reactions. To this end, we review the basic equations to indicate that chemical systems are controlled by the set of equilibrium reactions, which are easy to model, but whose rate is controlled by mixing. Since mixing is not properly represented by the standard advection-dispersion equation (ADE), we conclude that this equation is poor for RT. This leads us to review alternative transport formulations, and the methods to solve RT problems using both the ADE and alternative equations. Since equilibrium is easy, difficulties arise for kinetic reactions, which is especially true for biochemistry, where numerous challenges are open (how to represent microbial communities, impact of genomics, effect of biofilms on flow and transport, etc.). We conclude with the basic eleven conceptual issues that we consider fundamental for any conceptually sound RT effort.
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Nguyen VT, Papavassiliou DV. Velocity Magnitude Distribution for Flow in Porous Media. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.1c02474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vi T. Nguyen
- School of Chemical Biological and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Dimitrios V. Papavassiliou
- School of Chemical Biological and Materials Engineering, The University of Oklahoma, Norman, Oklahoma 73019, United States
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8
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Flow Path Resistance in Heterogeneous Porous Media Recast into a Graph-Theory Problem. Transp Porous Media 2021. [DOI: 10.1007/s11242-021-01671-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
This work aims to describe the spatial distribution of flow from characteristics of the underlying pore structure in heterogeneous porous media. Thousands of two-dimensional samples of polydispersed granular media are used to (1) obtain the velocity field via direct numerical simulations, and (2) conceptualize the pore network as a graph in each sample. Analysis of the flow field allows us to distinguish preferential from stagnant flow regions and to quantify how channelized the flow is. Then, the graph’s edges are weighted by geometric attributes of their corresponding pores to find the path of minimum resistance of each sample. Overlap between the preferential flow paths and the predicted minimum resistance path determines the accuracy in individual samples. An evolutionary algorithm is employed to determine the “fittest” weighting scheme (here, the channel’s arc length to pore throat ratio) that maximizes accuracy across the entire dataset while minimizing over-parameterization. Finally, the structural similarity of neighboring edges is analyzed to explain the spatial arrangement of preferential flow within the pore network. We find that connected edges within the preferential flow subnetwork are highly similar, while those within the stagnant flow subnetwork are dissimilar. The contrast in similarity between these regions increases with flow channelization, explaining the structural constraints to local flow. The proposed framework may be used for fast characterization of porous media heterogeneity relative to computationally expensive direct numerical simulations.
Article Highlights
A quantitative assessment of flow channeling is proposed that distinguishes pore-scale flow fields into preferential and stagnant flow regions.
Geometry and topology of the pore network are used to predict the spatial distribution of fast flow paths from structural data alone.
Local disorder of pore networks provides structural constraints for flow separation into preferential v stagnant regions and informs on their velocity contrast.
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Jung H, Meile C. Pore-Scale Numerical Investigation of Evolving Porosity and Permeability Driven by Biofilm Growth. Transp Porous Media 2021. [DOI: 10.1007/s11242-021-01654-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Puyguiraud A, Gouze P, Dentz M. Pore-Scale Mixing and the Evolution of Hydrodynamic Dispersion in Porous Media. PHYSICAL REVIEW LETTERS 2021; 126:164501. [PMID: 33961446 DOI: 10.1103/physrevlett.126.164501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/09/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
We study the interplay of pore-scale mixing and network-scale advection through heterogeneous porous media, and its role for the evolution and asymptotic behavior of hydrodynamic dispersion. In a Lagrangian framework, we identify three fundamental mechanisms of pore-scale mixing that determine large scale particle motion, namely, the smoothing of intrapore velocity contrasts, the increase of the tortuosity of particle paths, and the setting of a maximum time for particle transitions. Based on these mechanisms, we derive a theory that predicts anomalous and normal hydrodynamic dispersion in terms of the characteristic pore length, Eulerian velocity distribution, and Péclet number.
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Affiliation(s)
- Alexandre Puyguiraud
- Spanish National Research Council (IDAEA-CSIC), 08034, Barcelona, Spain and Geoscience Montpellier, CNRS, Université de Montpellier, 34090, Montpellier, France
| | - Philippe Gouze
- Spanish National Research Council (IDAEA-CSIC), 08034, Barcelona, Spain and Geoscience Montpellier, CNRS, Université de Montpellier, 34090, Montpellier, France
| | - Marco Dentz
- Spanish National Research Council (IDAEA-CSIC), 08034, Barcelona, Spain and Geoscience Montpellier, CNRS, Université de Montpellier, 34090, Montpellier, France
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Karimifard S, Li X, Elowsky C, Li Y. Modeling the impact of evolving biofilms on flow in porous media inside a microfluidic channel. WATER RESEARCH 2021; 188:116536. [PMID: 33125999 DOI: 10.1016/j.watres.2020.116536] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/22/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
This study integrates microfluidic experiments and mathematical modeling to study the impacts of biofilms on flow in porous media and to explore approaches to simplify modeling permeability with complicated biofilm geometries. E. coli biofilms were grown in a microfluidic channel packed with a single layer of glass beads to reach three biofilm levels: low, intermediate, and high, with biofilm ratios (βr) of 2.7%, 17.6%, and 55.2%, respectively. Two-dimensional biofilm structures and distributions in the porous medium were modeled by digitizing confocal images and considering broad ranges of biofilm permeability (kb) (from 10-15 m2 to 10-7 m2) and biofilm porosity (εb) (from 0.2 to 0.8). The overall permeability of the porous medium (k), the flow pathways and the overall/local pressure gradients were found to be highly dependent on βr and kb but were moderately impacted by εb when the biofilm levels were high and intermediate with kb>10-11 m2. When biofilm structures are well developed, simplified biofilm geometries, such as uniform coating and symmetric contact filling, can provide reasonable approximations of k.
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Affiliation(s)
- Shahab Karimifard
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States
| | - Christian Elowsky
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, United States
| | - Yusong Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States.
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Sherman T, Engdahl NB, Porta G, Bolster D. A review of spatial Markov models for predicting pre-asymptotic and anomalous transport in porous and fractured media. JOURNAL OF CONTAMINANT HYDROLOGY 2021; 236:103734. [PMID: 33221038 DOI: 10.1016/j.jconhyd.2020.103734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 10/02/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
Heterogeneity across a broad range of scales in geologic porous media often manifests in observations of non-Fickian or anomalous transport. While traditional anomalous transport models can successfully make predictions in certain geological systems, increasing evidence suggests that assumptions relating to independent and identically distributed increments constrain where and when they can be reliably applied. A relatively novel model, the Spatial Markov model (SMM), relaxes the assumption of independence. The SMM belongs to the family of correlated continuous time random walks and has shown promise across a wide range of transport problems relevant to natural porous media. It has been successfully used to model conservative as well as more recently reactive transport in highly complex flows ranging from pore scales to much larger scales of interest in geology and subsurface hydrology. In this review paper we summarize its original development and provide a comprehensive review of its advances and applications as well as lay out a vision for its future development.
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Affiliation(s)
- Thomas Sherman
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, South Bend, IN, USA
| | - Nicholas B Engdahl
- Department of Civil and Environmental Engineering, Washington State University, Pullman, WA, USA
| | - Giovanni Porta
- Dipartimento di Ingegneria Civile ed Ambientale, Politecnico di Milano, Piazza L. Da Vinci, 32, 20133 Milano, Italy
| | - Diogo Bolster
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, South Bend, IN, USA.
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Bolster D, Roche KR, Morales VL. Recent advances in anomalous transport models for predicting contaminants in natural groundwater systems. Curr Opin Chem Eng 2019. [DOI: 10.1016/j.coche.2019.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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