Center for Biofilm Engineering (CBE)
Permanent URI for this communityhttps://scholarworks.montana.edu/handle/1/9334
At the Center for Biofilm Engineering (CBE), multidisciplinary research teams develop beneficial uses for microbial biofilms and find solutions to industrially relevant biofilm problems. The CBE was established at Montana State University, Bozeman, in 1990 as a National Science Foundation Engineering Research Center. As part of the MSU College of Engineering, the CBE gives students a chance to get a head start on their careers by working on research teams led by world-recognized leaders in the biofilm field.
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Item Mathematical model of the effect of electrodiffusion on biomineralization(2011-05) Zhang, Tian-Yu; Klapper, IsaacBiofilm-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.Item An exclusion principle and the importance of mobility for a class of biofilm models(2011-01) Klapper, Isaac; Szomolay, BarbaraMuch 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.Item Models of microbial dormancy in biofilms and planktonic cultures(2012) Ayati, B. P.; Klapper, IsaacWe 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.Item 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.Item 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, FrancescaDespite 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 to—or following—active conservation treatment.Item 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.