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Environmental scanning electron microscope images of sand from experimental columns at the end of the experiment. (a) Exopolymeric substance (EPS) connecting two sand grains together, (b) thick gelatinous layer of EPS, and (c) cluster of cells that have colonized a sand grain.
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Flow through sand columns inoculated with Pseudomonas aeruginosa were used to investigate the effect of bioclogging on the complex conductivity and flow and transport properties. Complex conductivity (0.1–1000 Hz), the bulk hydraulic conductivity (K), volumetric flow rate (Q), dispersivity (D), and microbial cell concentrations were monitored over...
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... Figure 4 shows representative ESEM images of sands collected from the experimental columns. Figure 4a shows two sand grains connected by a gelatinous material believed to be an exopolymeric substance (EPS). ...
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... Figure 4 shows representative ESEM images of sands collected from the experimental columns. Figure 4a shows two sand grains connected by a gelatinous material believed to be an exopolymeric substance (EPS). The extracellular polymer produced by P. aeruginosa help the bacterial cells to adhere to the sand grains. ...
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... extracellular polymer produced by P. aeruginosa help the bacterial cells to adhere to the sand grains. Figure 4b shows a thick gelatinous material covering the surface of a sand grain. Figure 4c shows a sand grain colonized by cells of P. aeruginosa. ...
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... 4b shows a thick gelatinous material covering the surface of a sand grain. Figure 4c shows a sand grain colonized by cells of P. aeruginosa. ...
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... The ESEM images presented in Figure 4 show bio- mass on the sands and confirm that biofilms developed in the inoculated sand columns. At the pore scale, clogging can occur either through the formation of continuous biofilms or as isolated colonies that fill the pores [Baveye et al., 1998;Seifert and Engesgaard, 2007;Brovelli et al., 2009]. ...
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... other studies have equally demon- strated that plugs of biomass and not biofilm are responsible for significant clogging of porous media [Seifert and Engesgaard, 2007]. The ESEM images presented in Figure 4 allows us to suggest that both mechanisms of clogging could have occurred in the inoculated columns. Figures 4a and 4b show the presence of gelatinous material or slime (EPS) bridging two sand grains as well as covering the surfaces of grains, whereas, Figure 4c shows clusters/ colonies of cells on the surfaces of grains. ...
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... ESEM images presented in Figure 4 allows us to suggest that both mechanisms of clogging could have occurred in the inoculated columns. Figures 4a and 4b show the presence of gelatinous material or slime (EPS) bridging two sand grains as well as covering the surfaces of grains, whereas, Figure 4c shows clusters/ colonies of cells on the surfaces of grains. Plugs of biomass and biofilm as demonstrated in the ESEM images will constrict pores and cause a reduction in the pore space, leading to the observed decreases in Q (∼28%) and K (∼60%) (Figures 6a and 6b) and F (∼14%) and increases in D (∼27%). ...
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... ESEM images presented in Figure 4 allows us to suggest that both mechanisms of clogging could have occurred in the inoculated columns. Figures 4a and 4b show the presence of gelatinous material or slime (EPS) bridging two sand grains as well as covering the surfaces of grains, whereas, Figure 4c shows clusters/ colonies of cells on the surfaces of grains. Plugs of biomass and biofilm as demonstrated in the ESEM images will constrict pores and cause a reduction in the pore space, leading to the observed decreases in Q (∼28%) and K (∼60%) (Figures 6a and 6b) and F (∼14%) and increases in D (∼27%). ...
Citations
... In contrast, certain biomasses such as biofilms and cells are easily removed by water flows and degrade in nutrient-depleted environments (Taylor and Jaffé, 1990;Hand et al., 2008;Kim and Kwon, 2022). Previous studies investigated bioclogging caused by bacteria in soils (e.g., Cunningham et al., 1991;Seifert and Engesgaard, 2007;Abdel Aal et al., 2010;Xia et al., 2016); however, there is currently no research on utilizing enzymes to produce soft biomasses and induce bioclogging in soils. Additionally, the impact of bacterial cells on biopolymer formation patterns and bioclogging behavior remains poorly examined. ...
This study presents two methods of producing an insoluble biopolymer, the microbially induced biopolymer formation (MIBF) and enzyme-induced biopolymer formation (EIBF) and explores their ability to reduce hydraulic conductivity and cause bioclogging in soil from pore to column scales. The batch experiments confirm that insoluble polysaccharidic biopolymers, dextran, are successfully produced either by the model bacteria or by the extracted cell-free enzyme. The results show that the EIBF method is more efficient in producing biopolymer and reducing hydraulic conductivity compared to the MIBF method. This study also uses microfluidic chips, which reveals the pore-filling behavior of biopolymers produced by both methods. EIBF produces larger dextran flocs than MIBF, and hence EIBF lowers the hydraulic conductivity more than MIBF for a given pore occupancy of dextran. Column experiments demonstrate that both MIBF and EIBF can significantly lower the hydraulic conductivity of coarse sands by two orders of magnitude with only 3% biopolymer pore saturation. The presented results suggest that both methods have the potential to induce well-controlled, engineered bioclogging in coarse-grained soils, and have applications in various geotechnical practices, such as sealing leakage in water-front structures, installing hydraulic barriers, and mitigating soil erosion.
... Self-potential (SP) signals have, under specific conditions, been shown to be sensitive to redox conditions in contaminated groundwater (Naudet et al., 2003;Revil et al., 2009;Arora et al., 2007). Laboratory studies have shown the correlation between SIP and bacteria activity using column experiments (Davis et al., 2006;Abdel Aal et al., 2010;Zhang et al., 2014) and the SIP method has been applied to detect biogeochemical reactions or root activities in the field (Wainwright 280 et al., 2016;Flores Orozco et al., 2012;Ehosioke et al, 2020). However, current interpretations are largely qualitative or empirical through correlation. ...
Essentially all hydrogeological processes are strongly influenced by the subsurface spatial heterogeneity and the temporal variation of environmental conditions, hydraulic properties, and solute concentrations. This spatial and temporal variability needs to be considered when studying hydrogeological processes in order to employ adequate mechanistic models or perform upscaling. The scale at which a hydrogeological system should be characterized in terms of its spatial heterogeneity and temporal dynamics depends on the studied process and it is not always necessary to consider the full complexity. In this paper, we identify a series of hydrogeological processes for which an approach coupling the monitoring of spatial and temporal variability, including 4D imaging, is often necessary: (1) groundwater fluxes that control (2) solute transport, mixing and reaction processes, (3) vadose zone dynamics, and (4) surface-subsurface water interaction occurring at the interface between different subsurface compartments. We first identify the main challenges related to the coupling of spatial and temporal fluctuations for these processes. Then, we highlight some recent innovations that have led to significant breakthroughs in this domain. We finally discuss how spatial and temporal fluctuations affect our ability to accurately model them and predict their behavior. We thus advocate a more systematic characterization of the dynamic nature of subsurface processes, and the harmonization of open databases to store hydrogeological data sets in their four-dimensional components, for answering emerging scientific question and addressing key societal issues.
... Bioclogging is a biologically and hydrologically coupled process, in which microbial biomasses including biofilms cause a significant reduction in hydraulic conductivity or permeability of geologic porous media, such as soils and fractured rocks, altering the fluid flows in the subsurface [1][2][3][4][5]. Biofilms are aggregates of hydrated extracellular polymeric substance (EPS) matrices with embedded bacterial cells. ...
Utilization of bacterial biofilms and extracellular polymeric substances (EPS) for engineered bioclogging has recently garnered increasing attention in various geotechnical practices, such as leakage sealing in water-front structures, soil erosion protection, earthquake-induced liquefaction mitigation, and hydraulic barrier installation. However, the long-term durability is still questioned as to how long the biofilm-associated bioclogging would last as the biofilms readily degrade in nutrient-poor conditions. Therefore, we explore the feasibility of using fine clay particles to enhance the durability of biofilm-induced bioclogging. A series of column experiments were performed to compare the clogging durability of bentonite-associated biofilms against that of biofilms only. The results confirmed that a continuous feed of nutrients to the model bacteria, Bacillus subtilis, stimulated biofilm formation and caused a ~ 99% reduction in hydraulic conductivity of sands. However, nutrient-poor fluid flow caused instantaneous sloughing of biofilms and removal of bioclogging. By contrast, bioclogging associated with bentonite–biofilm aggregates demonstrated enhanced durability against shear detachment by fluid flows in a starved condition. EPS analysis and SEM imaging revealed that bentonite particles in the introduced suspension formed aggregates with biofilms by coating and being embedded within biofilms. This study suggests that the exploitation of bentonite–biofilm aggregations can remarkably enhance bioclogging durability in nutrient-poor conditions. This coupled clay–biofilm clogging approach is expected to provide benefits in developing a strategy for engineered bioclogging in geotechnical practices.
... The inoculum of 150 mL, of which the cell density was ~10 5 -10 6 cells/mL, was initially injected into the specimen at a constant flow rate of 10 mL/min using the syringe pump. The specimen was then left for 12 h to allow the bacteria attachment to the sand grains and further cell growth (Kim and Fogler, 1999;Davis et al., 2009;Abdel et al., 2010). ...
This study investigates changes in low-frequency attenuation responses of sands during microbial formation of soft viscous biofilms, or extracellular polymeric substances (EPS). The resonant column experiments were conducted with two model bacteria Shewanella oneidensis MR1 and Leuconostoc mesenteroides, while monitoring changes in the wave velocities and damping ratios associated with EPS formation in sands. The results show that the accumulation of soft, viscous EPS hardly changes the wave velocities, both the shear and flexural modes. By contrast, the low-frequency attenuations, both torsional and flexural damping ratios, show significant increases with the accumulation of highly viscous EPS. It is found that the contribution of EPS to seismic responses of water-saturated sands is mainly limited to the pore fluid component, causing additional energy dissipation during wave propagation, but with no or minimal impact on skeletal stiffness or no involvement in seismic stress transfer. With these unique and unprecedented low-frequency seismic data of biofilm-associated sands, the results suggest that the formation and accumulation of soft, viscous EPS or biofilms by bacterial activities can be detected by monitoring seismic attenuation and can also alter the seismic attenuation responses of sands, such as the case under earthquake loading or blast-induced compaction.
... Such formation of biofilms is critical in many engineering applications such as wastewater treatment (Miranda et al. 2017), biocatalysis for chemical syntheses (Halan et al. 2012), and enhanced oil recovery (Han et al. 2014;Hosseininoosheri et al. 2016). With sufficient supply of nutrients, biofilm growth can lead to pore clogging that causes significant changes in flow and solute or colloidal transport (Abdel Aal et al. 2010;Baveye et al. 1998;Cunningham et al. 1991). Bioclogging can result in damage to mechanical systems and severe loss of efficiency in bioremediation (Ellis et al. 2000;Lendvay et al. 2003), but it can also be utilized in well-curated engineering strategies. ...
Microorganisms in natural porous media can form biofilms that alter the pore structure and medium permeability. This affects fluid flow and solute transport, with bioclogging shaping the efficiency of, for example, bioremediation and hydrocarbon recovery. Here, we investigate the effect of biofilm growth on fluid flow across a wide range of flow and reaction conditions using pore-scale numerical simulations in idealized porous media. The simulation results show preferential biofilm growth and pore closure near the source of a growth-limiting substrate. This spatially heterogeneous biofilm growth at the pore scale affects the evolution of porosity and permeability. When approaching pore closure, permeability can change significantly without large changes in porosity, differentiating this setting from the empirical porosity–permeability relationships such as the Kozeny–Carman (KC) equation commonly used at the bulk scale. We find for impermeable biofilms that spatially non-uniform biofilm growths depend strongly on Péclet (Pe) and diffusive Damköhler numbers (Da) governing heterogeneous substrate distribution. We also demonstrate that Pe and Da can describe the evolution of porosity and permeability of porous media with various pore geometries, including pore throat size and tortuosity. Finally, the simulations with porous and permeable biofilms reveal significantly different evolution of porosity and permeability compared to non-porous and impermeable biofilms, highlighting the importance of micro-scale biofilm characteristics for macro-scale hydrological properties of porous media.
... This study suggested that the imaginary conductivity could be used as a proxy for microbial growth and biofilm formation in porous media [111]. Gamal and Abdel [112] analyzed the results of hydraulic conductivity measurement, cell count, and environmental scanning electron microscopy (SEM). They concluded that the changes in complex conductivity correspond to different stages of microbial plugging. ...
The development of biofilms and the related changes in porous media in the subsurface cannot be directly observed and evaluated. The primary reason that the mechanism of biofilm clogging in porous media cannot be clearly demonstrated is due to the opacity and structural complexity of three-dimensional pore space. Interest in exploring methods to overcome this limitation has been increasing. In the first part of this review, we introduce the underlying characteristics of biofilm in porous media. Then, we summarize two approaches, non-invasive measurement methods and mathematical simulation strategies, for studying fluid–biofilm–porous medium interaction with spatiotemporal resolution. We also discuss the advantages and limitations of these approaches. Lastly, we provide a perspective on opportunities for in situ monitoring at the field site.
... In geological systems, where the SIP method has been used widely and for decades, the physicochemical mechanisms of polarization for a single grain or pore throat are well understood, but the extrapolation of these mechanisms to a real porous media with heterogeneous characteristics (e.g., grain size, pore size, permeability, tortuosity, chemical heterogeneity, fluid phase distribution, etc.) is still a challenging task that requires theoretical developments . Consequently, interpretation of complex impedance measurements in geosystems may be limited by the need to independently assess or assume the effects of chemical heterogeneity (Vaudelet, Revil, Schmutz, Franceschi, & Bégassat, 2011;Weller, Breede, Slater, & Nordsiek, 2011), temperature (Binley, Kruschwitz, Lesmes, & Kettridge, 2010;Martinez, Batzle, & Revil, 2012), saturation (Breede et al., 2012;Jougnot, Ghorbani, Revil, Leroy, & Cosenza, 2010), multiple fluid phases (Revil, Schmutz, & Batzle, 2011;Schmutz et al., 2010), grain size distribution (Revil & Florsch, 2010), pH (Skold, Revil, & Vaudelet, 2011), soil organic matter (Schwartz & Furman, 2015), or biological processes (Abdel Aal, Atekwana, & Atekwana, 2010;Atekwana & Slater, 2009;Ntarlagiannis, Williams, Slater, & Hubbard, 2005). In the particular case of root systems, interpretation of the complex impedance is difficult due to the complex architecture of roots and the inner root cell distribution and properties. ...
Thorough knowledge of root system functioning is essential to understand the feedback loops between plants, soil, and climate. In situ characterization of root systems is challenging due to the inaccessibility of roots and the complexity of root zone processes. Electrical methods have been proposed to overcome these difficulties. Electrical conduction and polarization occur in and around roots, but the mechanisms are not yet fully understood. We review the potential and limitations of low‐frequency electrical techniques for root zone investigation, discuss the mechanisms behind electrical conduction and polarization in the soil–root continuum, and address knowledge gaps. A range of electrical methods for root investigation is available. Reported methods using current injection in the plant stem to assess the extension of the root system lack robustness. Multi‐electrode measurements are increasingly used to quantify root zone processes through soil moisture changes. They often neglect the influence of root biomass on the electrical signal, probably because it is yet to be well understood. Recent research highlights the potential of frequency‐dependent impedance measurements. These methods target both surface and volumetric properties by activating and quantifying polarization mechanisms occurring at the root segment and cell scale at specific frequencies. The spectroscopic approach opens up a range of applications. Nevertheless, understanding electrical signatures at the field scale requires significant understanding of small‐scale polarization and conduction mechanisms. Improved mechanistic soil–root electrical models, validated with small‐scale electrical measurements on root systems, are necessary to make further progress in ramping up the precision and accuracy of multi‐electrode tomographic techniques for root zone investigation.
... Electrochemical techniques, including EIS, provide useful information regarding metal corrosion behavior and associated biofilm activity on surfaces. Microbial biofilms in the subsurface have been monitored previously with electrochemical impedance techniques [11][12][13] without physically contacting the biofilms. Impedance analysis of biofilms provides a data-rich platform with parameters associated with microbial activity. ...
... Background subtraction of the data from the pristine glass control (Δφ) showed a peak at 1 kHz and is indicative of the increased presence of lipid membranes [14,15]. The imaginary conductivity (σ″) of the biofilms exhibited a peak at 1.26 kHz compared to 2.51 kHz, which was measured under control conditions (Fig. 2c), and is consistent with the presence of attached biofilms, with increased Δσ″ indicative of increased microbial biomass [11][12][13]. ...
... The low biofilm density of B. thuringiensis did not demonstrate Biofilms on glass and glass slides alone were analyzed for IZI (a), phase shift relative to sterile glass controls (Δφ) (b) and imaginary conductivity (σ″) (c) with a relative difference (Δσ″) between control and biofilm, below about 0.5 kHz (inset) any changes to σ″ peak values before or after sonication (data not shown). Increased values for Δσ″ are indicative of increased microbial biomass [11][12][13]. ...
Here, we demonstrate a non-contact technique for electrochemical evaluation of biofilms on surfaces in relation to corrosion. Electrochemical impedance spectrometry was employed, incorporating flat patterned electrodes positioned over the surfaces of aluminum and glass with and without biofilms. Signal communication from the working electrode to the counter electrode followed electric field lines passing tangentially through the biofilms. Electrochemical impedance parameters that were evaluated included complex impedance, phase angle, imaginary (out of phase) conductivity and Cole–Cole plots with a corresponding equivalent circuit. Changes in the impedance properties due to the presence of biofilms were monitored and correlated through microbiological, chemical and electrochemical assays. Impedance parameters associated with microbial activity correlated with biofilms on aluminum and glass surfaces. This technical approach provides impedance information about the biofilm without the signal traveling through the underlying conductive media or disrupting the biofilm. In this way, biological contributions to surface fouling can be evaluated with minimal contribution from the inorganic surface under the biofilm. In addition, this technique can be used to monitor biofilms on electrochemically inert surfaces as well as electrically conductive surfaces.
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... Davis et al. [4] observed that biofilm production in biostimulated samples was detectable when measuring a loss of amplitude of the acoustic waves that crossed the system and when observing a peak in imaginary electrical conductivity. A study by Abdel Aal et al. [18] confirmed the relation between peculiar trends in the imaginary part of electrical conductivity and the clogging of pores by biofilms, and also estimated consequent variations of porosity and hydraulic conductivity of soil. ...
This study aims to monitor the biological processes ongoing in a hydrocarbon polluted soil. The experiments were carried out at a laboratory scale by measuring the evolution of its geophysical electromagnetic parameters. Time-domain reflectometry (TDR) probes were used to measure dielectric permittivity and electrical conductivity in columns of sandy soil artificially contaminated with diesel oil (V oil /V tot = 0.19). To provide aerobic conditions suitable for the growth of microorganisms, they were hydrated with Mineral Salt Medium for Bacteria. One mesocosm was aerated by injecting air from the bottom of the column, while the other had only natural aeration due to diffusion of air through the soil itself. The monitoring lasted 105 days. Geophysical measurements were supported by microbiological, gas chromatographic analyses, and scanning electron microscope (SEM) images. Air injection heavily influenced the TDR monitoring, probably due to the generation of air bubbles around the probe that interfered with the probe-soil coupling. Therefore, the measurement accuracy of geophysical properties was dramatically reduced in the aerated system, although biological analyses showed that aeration strongly supports microbial activity. In the non-aerated system, a slight (2%) linear decrease of dielectric permittivity was observed over time. Meanwhile, the electrical conductivity initially decreased, then increased from day 20 to day 45, then decreased again by about 30%. We compared these results with other researches in recent literature to explain the complex biological phenomena that can induce variations in electrical parameters in a contaminated soil matrix, from salt depletion to pore clogging.
... Pore structure-induced changes, due to processes such as bioclogging, were postulated as the major drivers of biofilmmediated SIP responses (Davis et al. 2006(Davis et al. , 2010Ntarlagiannis and Ferguson 2009;Wu et al. 2014). While bioclogging unequivocally mediates pore geometry and therefore affects current flow and polarization, electromigration and charge storage within the biofilm matrix as well as within the bacterial surfaces concurrently contribute to the measured SIP responses (Abdel Aal et al. 2010). Albrecht et al. (2011) measured a strong correlation between phase shift (as large as 50 mrad, at 4 Hz) and biofilm volume growth in Burkholderia sp. ...
This paper provides an update on the fast‐evolving field of the induced polarization (IP) method applied to biogeophysics. It emphasizes recent advances in the understanding of the IP signals stemming from biological materials and their activity, points out new developments and applications, and identifies existing knowledge gaps. The focus of this review is on the application of IP to study living organisms: soil micro‐organisms and plants (both roots and stems). We first discuss observed links between the IP signal and microbial cell structure, activity and biofilm formation. We provide an up‐to‐date conceptual model of the electrical behavior of the microbial cells and biofilms under the influence of an external electrical field. We also review the latest biogeophysical studies, including work on hydrocarbon biodegradation, contaminant sequestration, soil strengthening and peatland characterization. We then elaborate on the IP signature of the plant root zone, relying on a conceptual model for the generation of biogeophysical signals from a plant root cell. First laboratory experiments show that single roots and root system are highly polarizable. They also present encouraging results for imaging root systems embedded in a medium, and gaining information on the mass density distribution, the structure or the physiological characteristics of root systems. In addition, we highlight the application of IP to characterize wood and tree structures through tomography of the stem. Finally, we discuss up‐ and down‐scaling between laboratory and field studies, as well as joint interpretation of IP and other environmental data. We emphasize the need for intermediate scale studies and the benefits of using IP as a time‐lapse monitoring method. We conclude with the promising integration of IP in interdisciplinary mechanistic models to better understand and quantify subsurface biogeochemical processes. This article is protected by copyright. All rights reserved
