Modelling biofilm‐induced formation damage and biocide treatment in subsurface geosystems

Abstract

Biofilm growth in subsurface porous media, and its treatment with biocides (antimicrobial agents), involves a complex interaction of biogeochemical processes which provide non-trivial mathematical modelling challenges. Although there are literature reports of mathematical models to evaluate biofilm tolerance to biocides, none of these models have investigated biocide treatment of biofilms growing in interconnected porous media with flow. In this paper, we present a numerical investigation using a pore network model of biofilm growth, formation damage and biocide treatment. The model includes three phases (aqueous, adsorbed biofilm, and solid matrix), a single growth-limiting nutrient and a single biocide dissolved in the water. Biofilm is assumed to contain a single species of microbe, in which each cell can be a viable persister, a viable non-persister, or non-viable (dead). Persisters describe small subpopulation of cells which are tolerant to biocide treatment. Biofilm tolerance to biocide treatment is regulated by persister cells and includes ‘innate’ and ‘biocide-induced’ factors. Simulations demonstrate that biofilm tolerance to biocides can increase with biofilm maturity, and that biocide treatment alone does not reverse biofilm-induced formation damage. Also, a successful application of biological permeability conformance treatment involving geologic layers with flow communication is more complicated than simply engineering the attachment of biofilm-forming cells at desired sites.

Microbial Dynamics and Control in Shale Gas Production

“…Biofilm formation is a major determinant of biocide resistance. ,,, Some biofilm-associated microbes have been found to resist biocide concentrations approximately 10–20-fold higher than that used to kill planktonic populations. ,, Others have suggested biofilm resistance is increased up to 1000-fold . There may be several reasons for this, including (1) higher cell densities, (2) the presence of persister cells (i.e., dormant cells that resist biocides and other stressors), (3) reduced biocide diffusion due to cohesive interactions within the biofilm matrix, (4) low growth rates, and (5) sequestration of positively charged biocides by negatively charged extracellular polymeric substances (EPS). ,,, Biofilm heterogeneity also creates locally distinct microenvironments that may differentially affect biocide activity. ,, Therefore, minimum inhibitory concentration is much higher not only for biocides tested against biofilms (relative to planktonic populations) but also for most mixed cultures (either planktonic or biofilms) . Further exacerbating the difficulties of treating biofilms is the presence of persister cells .…”

“…There may be several reasons for this, including (1) higher cell densities, (2) the presence of persister cells (i.e., dormant cells that resist biocides and other stressors), (3) reduced biocide diffusion due to cohesive interactions within the biofilm matrix, (4) low growth rates, and (5) sequestration of positively charged biocides by negatively charged extracellular polymeric substances (EPS). ,,, Biofilm heterogeneity also creates locally distinct microenvironments that may differentially affect biocide activity. ,, Therefore, minimum inhibitory concentration is much higher not only for biocides tested against biofilms (relative to planktonic populations) but also for most mixed cultures (either planktonic or biofilms) . Further exacerbating the difficulties of treating biofilms is the presence of persister cells . Persister cells have greatly reduced susceptibility to biocides, although they do not grow or proliferate in their presence.…”

“…102 Biofilm formation is a major determinant of biocide resistance. 93,98,103,104 Some biofilm-associated microbes have been found to resist biocide concentrations approximately 10− 20-fold higher than that used to kill planktonic populations. 93,98,105 Others have suggested biofilm resistance is increased up to 1000-fold.…”

“…93 Further exacerbating the difficulties of treating biofilms is the presence of persister cells. 104 Persister cells have greatly reduced susceptibility to biocides, although they do not grow or proliferate in their presence. Once the biocide is removed, persister cells may revert back to the nonpersister phenotype to begin rapid proliferation and biofilm deposition, which may explain the decreased recovery time needed for biofilms after biocide exposure, 109 especially when slug doses are utilized.…”

A Network Model for the Kinetics of Bioclogged Flow Diversion for Enhanced Oil Recovery

“…Several numerical models have been developed to describe biofilm growth. There exist continuum Darcy models [23], bacterially-based models [12], Lattice-Boltzmann-based simulations [13,17] and Pore Network Models (PNM) [6,22,20,5,7]. Frequently, in biofilm growth models, the porous media consists of three components: the grains, the biofilm which grows on the walls of the solid grains and the liquid in the pore space.…”