Browsing by Author "Klapper, Isaac"

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Adaptive responses to antimicrobial agents in biofilms
(2005-08) Szomolay, Barbara; Klapper, Isaac; Dockery, Jack D.; Stewart, Philip S.
Bacterial biofilms demonstrate adaptive resistance in response to antimicrobial stress more effectively than corresponding planktonic populations. We propose here that, in biofilms, reaction-diffusion limited penetration may result in only low levels of antimicrobial exposure to deeper regions of the biofilm. Sheltered cells are then able to enter an adapted resistant state if the local time scale for adaptation is faster than that for disinfection. This mechanism is not available to a planktonic population. A mathematical model is presented to illustrate. Results indicate that, for a sufficiently thick biofilm, cells in the biofilm implement adaptive responses more effectively than do freely suspended cells. Effective disinfection requires applied biocide concentration that increases quadratically or exponentially with biofilm thickness.
Analysis of adaptive response to dosing protocols for biofilm control
(2010-01) Szomolay, Barbara; Klapper, Isaac; Dindos, Martin
Biofilms are sessile populations of microbes that live within a self-secreted matrix of extracellular polymers. They exhibit high tolerance to antimicrobial agents, and experimental evidence indicates that in many instances repeated doses of antimicrobials further reduce disinfection efficiency due to an adaptive stress response. In this investigation, a mathematical model of bacterial adaptation is presented consisting of an adapted-unadapted population system embedded within a moving boundary problem coupled to a reaction-diffusion equation. The action of antimicrobials on biofilms under different dosing protocols is studied both analytically and numerically. We find the limiting behavior of solutions under periodic and on-off dosing as the period is made very large or very small. High dosages often carry undesirable side effects so we specially consider low dosing regimes. Our results indicate that on-off dosing for small doses of biocide is more effective than constant dosing. Moreover, in a specific case, on-off dosing for short periods is again more effective regardless of the biocide dose. We also provide sufficient conditions for the eradication of biofilms under a constant dosing regime.
Biofilm material properties as related to shear-induced deformation and detachment phenomena
(2002-12) Stoodley, Paul; Cargo, R.; Rupp, Cory J.; Wilson, Suzanne; Klapper, Isaac
Biofilms of various Pseudomonas aeruginosa strains were grown in glass flow cells under laminar and turbulent flows. By relating the physical deformation of biofilms to variations in fluid shear, we found that the biofilms were viscoelastic fluids which behaved like elastic solids over periods of a few seconds but like linear viscous fluids over longer times. These data can be explained using concepts of associated polymeric systems, suggesting that the extracellular polymeric slime matrix determines the cohesive strength. Biofilms grown under high shear tended to form filamentous streamers while those grown under low shear formed an isotropic pattern of mound-shaped microcolonies. In some cases, sustained creep and necking in response to elevated shear resulted in a time-dependent fracture failure of the "tail" of the streamer from the attached upstream "head." In addition to structural differences, our data suggest that biofilms grown under higher shear were more strongly attached and were cohesively stronger than those grown under lower shears.
Commonality of elastic relaxation times in biofilms
(2004-08) Shaw, T.; Winston, Matthew T.; Rupp, Cory J.; Klapper, Isaac; Stoodley, Paul
Biofilms, sticky conglomerations of microorganisms and extracellular polymers, are among the Earth's most common life forms. One component for their survival is an ability to withstand external mechanical stress. Measurements indicate that biofilm elastic relaxation times are approximately the same (about 18 min) over a wide sample of biofilms though other material properties vary significantly. A possible survival significance of this time scale is that it is the shortest period over which a biofilm can mount a phenotypic response to transient mechanical stress.
Description of mechanical response including detachment using a novel particle model of biofilm/flow interaction
(2007-05) Alpkvist, Erik; Klapper, Isaac
Bacterial biofilms, while made up of microbial-scale objects, also function as meso- and macroscale materials. In particular, macro-scale material properties determine how biofilms respond to large-scale mechanical stresses, e.g. fluid shear. Viscoelastic and other constitutive properties influence biomass structure (through growth and fluid shear stresses) by erosion and sloughing detachment. In this paper, using the immersed boundary method, biofilm is modelled by a system of viscoelastic, breakable springs embedded in a fluid flow, evolving according to the basic physical laws of conservation of mass and momentum. We demonstrate in the context of computer simulation biofilm deformation and detachment under fluid shear stress.
Diffusive transport through a model host-biofilm system
(2015-08) Aristotelous, A. C.; Klapper, Isaac; Grabovsky, Y.; Pabst, Breana; Pitts, Betsey; Stewart, Philip S.
Free-living biofilms have been subject to considerable attention, and basic physical principles for them are generally accepted. Many host-biofilm systems, however, consist of heterogeneous mixtures of aggregates of microbes intermixed with host material and are much less studied. Here we analyze a key property, namely reactive depletion, in such systems and argue that two regimes are possible: (1) a homogenizable mixture of biofilm and host that in important ways acts effectively like a homogeneous macrobiofilm and (2) a distribution of separated microbiofilms within the host with independent local microenvironments.
Estimation of a biofilm-specific reaction rate: kinetics of bacterial urea hydrolysis in a biofilm
(2015-09) Connolly, James M.; Jackson, Benjamin; Rothman, Adam P.; Klapper, Isaac; Gerlach, Robin
Background/Objectives: Biofilms and specifically urea-hydrolysing biofilms are of interest to the medical community (for example, urinary tract infections), scientists and engineers (for example, microbially induced carbonate precipitation). To appropriately model these systems, biofilm-specific reaction rates are required. A simple method for determining biofilm-specific reaction rates is described and applied to a urea-hydrolysing biofilm. Methods: Biofilms were grown in small silicon tubes and influent and effluent urea concentrations were determined. Immediately after sampling, the tubes were thin sectioned to estimate the biofilm thickness profile along the length of the tube. Urea concentration and biofilm thickness data were used to construct an inverse model for the estimation of the urea hydrolysis rate. Results/Conclusions: It was found that urea hydrolysis in Escherichia coli MJK2 biofilms is well approximated by first-order kinetics between urea concentrations of 0.003 and 0.221 mol/l (0.186 and 13.3 g/l). The first-order rate coefficient (k1) was estimated to be 23.2±6.2 h−1. It was also determined that advection dominated the experimental system rather than diffusion, and that urea hydrolysis within the biofilms was not limited by diffusive transport. Beyond the specific urea-hydrolysing biofilm discussed in this work, the method has the potential for wide application in cases where biofilm-specific rates must be determined.
An exclusion principle and the importance of mobility for a class of biofilm models
(2011-01) Klapper, Isaac; Szomolay, Barbara
Much of the earth’s microbial biomass resides in sessile, spatially structured communities such as biofilms and microbial mats, systems consisting of large numbers of single-celled organisms living within self-secreted matrices made of polymers and other molecules. As a result of their spatial structure, these communities differ in important ways from well-mixed (and well-studied) microbial systems such as those present in chemostats. Here we consider a widely used class of 1D biofilm models in the context of a description of their basic ecology. It will be shown via an exclusion principle resulting from competition for space that these models lead to restrictions on ecological structure. Mathematically, this result follows from a classification of steady-state solutions based on a 0-stability condition: 0-stable solutions are in some sense determined by competitive balance at the biofilm base, whereas solutions that are not 0-stable, while less dependent on conditions at the biofilm base, are unstable at the base. As a result of the exclusion principle, it is argued that some form of downward mobility, against the favorable substrate gradient direction, is needed at least in models and possibly in actuality.
General theory for integrated analysis of growth, gene, and protein expression in biofilms
(2013-12) Zhang, Tian-Yu; Pabst, Breana; Klapper, Isaac; Stewart, Philip S.
A theory for analysis and prediction of spatial and temporal patterns of gene and protein expression within microbial biofilms is derived. The theory integrates phenomena of solute reaction and diffusion, microbial growth, mRNA or protein synthesis, biomass advection, and gene transcript or protein turnover. Case studies illustrate the capacity of the theory to simulate heterogeneous spatial patterns and predict microbial activities in biofilms that are qualitatively different from those of planktonic cells. Specific scenarios analyzed include an inducible GFP or fluorescent protein reporter, a denitrification gene repressed by oxygen, an acid stress response gene, and a quorum sensing circuit. It is shown that the patterns of activity revealed by inducible stable fluorescent proteins or reporter unstable proteins overestimate the region of activity. This is due to advective spreading and finite protein turnover rates. In the cases of a gene induced by either limitation for a metabolic substrate or accumulation of a metabolic product, maximal expression is predicted in an internal stratum of the biofilm. A quorum sensing system that includes an oxygen-responsive negative regulator exhibits behavior that is distinct from any stage of a batch planktonic culture. Though here the analyses have been limited to simultaneous interactions of up to two substrates and two genes, the framework applies to arbitrarily large networks of genes and metabolites. Extension of reaction-diffusion modeling in biofilms to the analysis of individual genes and gene networks is an important advance that dovetails with the growing toolkit of molecular and genetic experimental techniques.
Hypoxia arising from concerted oxygen consumption by neutrophils and microorganisms in biofilms
(2018-06) Wu, Yilin; Klapper, Isaac; Stewart, Philip S.
Infections associated with microbial biofilms are often found to involve hypoxic or anoxic conditions within the biofilm or its vicinity. To shed light on the phenomenon of local oxygen depletion, mathematical reaction-diffusion models were derived that integrated the two principal oxygen sinks, microbial respiration and neutrophil consumption. Three simple one-dimensional problems were analyzed approximating biofilm near an air interface as in a dermal wound or mucus layer, biofilm on an implanted medical device, or biofilm aggregates dispersed in mucus or tissue. In all three geometries considered, hypoxia at the biofilm–neutrophil interface or within the biofilm was predicted for a subset of plausible parameter values. The finding that oxygen concentration at the biofilm–neutrophil juncture can be diminished to hypoxic levels is biologically relevant because oxygen depletion will reduce neutrophil killing ability. The finding that hypoxia can readily establish in the interior of the biofilm is biologically relevant because this change will alter microbial metabolism and persistence.
Mathematical model of biofilm induced calcite precipitation
(2010-08) Zhang, Tian-Yu; Klapper, Isaac
Microbially modulated carbonate precipitation is a fundamentally important phenomenon of both engineered and natural environments. In this paper, we propose a mixture model for biofilm induced calcite precipitation. The model consists of three phasesâ€”calcite, biofilm and solventâ€”which satisfy conservation of mass and momentum laws with addition of a free energy of mixing. The model also accounts for chemistry, mechanics, thermodynamics, fluid and electrodiffusion transport effects. Numerical simulations qualitatively capturing the dynamics of this process and revealing effects of kinetic parameters and external flow conditions are presented.
Mathematical model of the effect of electrodiffusion on biomineralization
(2011-05) Zhang, Tian-Yu; Klapper, Isaac
Biofilm-induced mineral precipitation is a fundamentally important phenomenon with many potential applications including carbon sequestration and bioremediation. Based on a mixture model consisting of three phases (calcite, biofilm, and solvent) and also accounting for chemistry, mechanics, thermodynamics, fluid, and electrodiffusive transport effects, we describe the self-induced generation of an electric field due to different diffusivities of different ion species and study the effects of this field on ionic transport and calcite precipitation. Numerical simulations suggest that one of these effects is enhanced precipitation.
Measurements of accumulation and displacement at the single cell cluster level in Pseudomonas aeruginosa biofilms
(2008-09) Klayman, Benjamin J.; Klapper, Isaac; Stewart, Philip S.; Camper, Anne K.
Quantitative descriptions of biofilm growth and dynamics at the individual cell level are largely missing from the literature. To fill this gap, research was done to describe growth, accumulation and displacement patterns in developing Pseudomonas aeruginosa biofilms. A parent strain of PAO1 was labelled with either a cyan or yellow fluorescent protein. These were then grown in a flow cell biofilm together so that pockets of dividing cells could be identified and their accumulation and displacement tracked. This analysis revealed a pattern of exponential accumulation for all clusters followed by a stationary accumulation phase. A background ‘carpet’ layer of cells uniformly colonizing the surface exhibited zero net accumulation of bio-volume. The individual clusters were found to have a mean accumulation rate of 0.34 h-1 with a range of 0.28–0.41 h-1. Cluster accumulation rates were negatively correlated with cluster size; larger clusters accumulated volume at a slower rate (P < 0.001). Pockets of cells on the inside of clusters initially accumulated at a comparable rate to the cluster within which they resided, but later invariably exhibited zero to slightly negative accumulation despite continued exponential (positive) accumulation of the cluster. Expanding clusters were able to displace neighbouring cells from the surface, and larger clusters displaced smaller clusters. This work provides a more detailed quantitative experimental observation of biofilm behaviour than has been described previously.
Models of microbial dormancy in biofilms and planktonic cultures
(2012) Ayati, B. P.; Klapper, Isaac
We present models of dormancy in planktonic cultures and in biofilm, and a new numerical technique for solving the model equations. We use this modeling framework to examine the relative advantage of short dormancy versus long dormancy times in planktonic cultures and biofilms under some basic assumptions. Simulations and asymptotic analyses indicate that in planktonic batch cultures and in chemostats, live biomass is maximized by the fastest possible exit from dormancy. The lower limit of time to reawakening is thus perhaps governed by physiological, biochemical, or other constraints within the cells. In biofilm we see, in contrast, that the slower waker may have an advantage over the faster waker.
A multidimensional multispecies continuum model for heterogeneous biofilm development
(2007-01) Alpkvist, Erik; Klapper, Isaac
We propose a multidimensional continuum model for heterogeneous growth of biofilm systems with multiple species and multiple substrates. The new model provides a deterministic framework for the study of the interactions between several species and their effects on biofilm heterogeneity. It consists of a system of partial differential equations derived on the basis of conservation laws and reaction kinetics. The derivation and key assumptions are presented. The assumptions used are a combination of those used in the established one dimensional model, due to Wanner and Gujer, and for the viscous fluid model, of Dockery and Klapper. The work of Wanner and Gujer in particular has been extensively used through the years, and thus this new model is an extension to several spatial dimensions of an already proven working model. The model equations are solved using numerical techniques, for purposes of simulation and verification. The new model is applied to two different biofilm systems in several spatial dimensions, one of which is equivalent to a system originally studied by Wanner and Gujer. Dimensionless formulations for these two systems are given, and numerical simulation results with varying initial conditions are presented.
A multiscale model of biofilm as a senescence-structured fluid
(2007-01) Ayati, B. P.; Klapper, Isaac
We derive a physiologically structured multiscale model for biofilm development. The model has components on two spatial scales, which induce different time scales into the problem. The macroscopic behavior of the system is modeled using growth-induced flow in a domain with a moving boundary. Cell-level processes are incorporated into the model using a so-called physiologically structured variable to represent cell senescence, which in turn affects cell division and mortality. We present computational results for our models which shed light on modeling the combined role senescence and the biofilm state play in the defense strategy of bacteria.
Niche partitioning of a pathogenic microbiome driven by chemical gradients
(2018-09) Quinn, Robert A.; Comstock, William; Zhang, Tian-yu; Morton, James T.; da Silva, Ricardo; Tran, Alda; Aksenov, Alexander; Nothias, Louis-Felix; Wangpraseurt, Daniel; Melnik, Alexey V.; Ackermann, Gail; Conrad, Douglas; Klapper, Isaac; Knight, Rob; Dorrestein, Pieter C.
Environmental microbial communities are stratified by chemical gradients that shape the structure and function of these systems. Similar chemical gradients exist in the human body, but how they influence these microbial systems is more poorly understood. Understanding these effects can be particularly important for dysbiotic shifts in microbiome structure that are often associated with disease. We show that pH and oxygen strongly partition the microbial community from a diseased human lung into two mutually exclusive communities of pathogens and anaerobes. Antimicrobial treatment disrupted this chemical partitioning, causing complex death, survival, and resistance outcomes that were highly dependent on the individual microorganism and on community stratification. These effects were mathematically modeled, enabling a predictive understanding of this complex polymicrobial system. Harnessing the power of these chemical gradients could be a drug-free method of shaping microbial communities in the human body from undesirable dysbiotic states.
Senescence can explain microbial persistence
(2007-11) Klapper, Isaac; Gilbert, P.; Ayati, B. P.; Dockery, Jack D.; Stewart, Philip S.
It has been known for many years that small fractions of persister cells resist killing in many bacterial colony–antimicrobial confrontations. These persisters are not believed to be mutants. Rather it has been hypothesized that they are phenotypic variants. Current models allow cells to switch in and out of the persister phenotype. Here, a different explanation is suggested for persistence, namely senescence. Using a mathematical model including age structure, it is shown that senescence provides a natural explanation for persistence-related phenomena, including the observations that the persister fraction depends on growth phase in batch culture and dilution rate in continuous culture.
Subaerial biofilms on outdoor stone monuments: changing the perspective towards an ecological framework
(2016-04) Villa, Federica; Stewart, Philip S.; Klapper, Isaac; Jacob, J. M.; Cappitelli, Francesca
Despite the appreciation of the role played by outdoor stone heritage in societal well-being and sustainable urban development, research efforts have not been completely successful in tackling the complex issues related to its conservation. One of the main problems is that we are continuously underestimating the role and behavior of microorganisms in the form of biofilm (subaerial biofilms, SABs) in the management of stone artifacts. To this end, we discuss the necessity of approaching the topic from an ecological perspective through an overview of the characteristics of SABs that mediate different ecological interactions. Furthermore, we explore the application of functional-traits ecology to unravel the mechanisms by which SABs might respond to a changing environment. Finally, we guide and prioritize further research in order to inform policymakers and to develop management strategies for protection prior toâ€”or followingâ€”active conservation treatment.
Viscoelastic fluid description of bacterial biofilm material properties
(2002-09) Klapper, Isaac; Rupp, Cory J.; Cargo, R.; Purevdorj, B.; Stoodley, Paul
A mathematical model describing the constitutive properties of biofilms is required for predicting biofilm deformation, failure and detachment in response to mechanical forces. Laboratory observations indicate that biofilms are viscoelastic materials. Likewise, current knowledge of biofilm internal structure suggests modeling biofilms as associated polymer viscoelastic systems. Supporting experimental results and a system of viscoelastic fluid equations with a linear Jeffreys viscoelastic stress-strain law are presented here. This system of equations is based on elements of associated polymer physics and is also consistent with presented and previous experimental results. A number of predictions can be made. One particularly interesting result is the prediction of an elastic relaxation time on the order of a few minutes: biofilm disturbances on shorter time scales produce an elastic response, biofilm disturbances on longer time scales result in viscous flow, i.e., non-reversible biofilm deformation. Although not previously recognized, evidence of this phenomenon is in fact present in recent experimental results.