Biofilm matrix

Burkholder, J. M., R. G. Wetzel, and K. L. Klomparens. 1990. Direct comparison of phosphate uptake by adnate and loosely attached microalgae within an intact biofilm matrix. Applied and Environmental Microbiology 56 2882-2890. 

Atmosphere-exposed rock as a biofilm substrate environmental prerequisites and biofilm matrix... 

For example, fixed-film bioreactors (using sand as the biofilm matrix, and methane or natural gas as the primary substrate) can remove up to 60% of trichloroethylene (TCE) from polluted water. They can also remove more than 90% of TCE and trichloroacetic acid (TCA) from vapor streams generated by the air stripping of polluted ground-water. 

Although these data show the trends associated with changes in system variables the age and quality of the biofilm will also be a factor, i.e. whether the biofilm is open and "fluffy" or dense and compact. Diffusion of biocide into the biofilm will be facilitated by the existence of "pores" containing water within the biofilm matrix. The quality of the biofilm will be very much a function of the conditions under which it was laid down, particularly in terms of nutrient availability and flow rate (see Chapter 12). Apparent variations in biocidal efficiency reported in the literature may in fact be due to the different morphologies of biofilms of the same strain, but grown under different conditions. 

Extra cellular polymeric substances (EPS) produced by microorganisms are a complex mixture of biopolymers primarily consisting of polysaccharides, as well as proteins, nucleic acids, lipids, and humic substances. EPS make up the intercellular space of microbial aggregates and form the structure and architecture of the biofilm matrix. The key functions of EPS are comprised of the mediation of the initial attachment of cells to different substrate, and protection against environmental stress and dehydration. The latter has a profound impact on an array of biomedical, biotechnical, and industrial fields including pharmaceutical and surgical applications, food engineering, bioremediation. 

Biofllms are complex bacterial commtmities which are encased by a protective exopolysaccharide (EPS) matrix that helps the bacteria thrive in hostile environmental conditions and reduces the efficacy of antibiotics by up to 100-fold relative to planktonic cells/ Briefly, the formation of biofllms can be described as a multistep process. The planktonic bacteria are first attached by strong association of the adherent cells to the surface such as respiratory mucosa and bladder cells in case of lung and urinary tract infections, respectively. Upon attachment, the bacteria multiply to form microcolonies. These microcolonies develop into well-defined mushroom-like three-dimensional structures and eventually produce the EPS coating around them. At times, the biofilm matrix breaks and the bacterial cells disperse, which leads to a spread in infection (Figure 16). ... 

Only recently, however, has spectroelectrochemistry been used for in situ measurements of the redox state of cytochromes in thick, pregrown EABs in which extracellular electron transfer through the biofilm matrix was studied. It was shown that the c-type cytochromes inside thick G. sulfurreducens biofilms probed under nonturnover conditions were completely reduced at polarization potentials below -350 mVsHE and completely oxidized at potentials above -ElOO mVsHE> demonstrating long-range extracellular electron transfer through the cytochrome network [66]. 

What benefit may a biofilm gain by allowing mediators to interact with the conductive biofilm matrix ... 

If the EPS that comprise the biofilm matrix are conductive and this matrix interacts with electron transfer mediators, this interaction should provide an advantage to biofilm growth. The answer to this question can help determine the extent of this advantage. There is strong experimental evidence that EPS contain redox mediators, which can transfer electrons. These mediators can be adsorbed to the EPS surface and transfer electrons by conduction as described in earlier chapters. This is an approach we introduced to model EET in EABs. 

The biofilm in our model is composed of a distribution of biomass (cells and EPS, the biofilm matrix). We assume that the biomass is homogenous in three dimensions and does not change thickness or composition over time. This is a reasonable assumption... 

The biofilm subsists on the oxidation of an organic substrate, S (mM), which is delivered to the biofilm matrix via diffusive mass transport. The substrate is supplied at a constant concentration to a large, well-mixed anodic chamber. This allowed us to assume that the bulk concentration of substrate is constant because of the size of the chamber and the relatively slow consumption rate of substrate by the biofilm. The concentration at the biofilm surface is equal to the bulk concentration because of mixing in the anodic chamber and because of simplification of the model. The substrate utilization rate is controlled by both the substrate (electron donor) concentration and the eleetron acceptor concentration, through multiplicative Monod substrate utilization equations [37, 38]. Equations 9.1 and 9.2 simply state that the biofilm can only metabolize in the presence of both an electron donor and an electron acceptor. The lack of either one prevents biofilm metabolic activity. In our model, we assume that there are two possible electron transfer pathways thus, there are two substrate utilization equations. For diffusion-based EET, substrate utilization is given by ... 

It is assumed that the time required for electron transfer through the biofilm matrix is negligible compared to the time scale of the diffusion of dilute solutes in the biofilm electrons are conducted instantaneously. For simulations considering the isolated-dual and interacting-dual EET cases, the total current density, j (A m ), is the total current derived from both underlying EET mechanisms (diffusion- and conduction-based) ... 

Interacting-Dual Extracellular Electron Transfer Mediator Interactions with a Conductive Biofilm Matrix... 

The aforementioned model formulation represents the standard case. However, we also wanted to explore the hypothesis that mediators are able to interact with, that is, exchange electrons with, a conductive biofilm matrix. This means that reduced mediators may transfer electrons to the matrix, and likewise, oxidized mediators may accept electrons from the conductive matrix. In this case, dubbed interacting-dual EET, the matrix acts as an extension of the electrode and electron exchange can occur between mediators and the matrix, just as it can between mediators and the electrode surface. Mediators may not have to travel the entire distance between the reducing cell and the oxidizing electrode surface to transfer electrons. We wanted to explore this idea because of the mounting evidence of mediator and cytochrome interactions and the critical role cytochromes play in EAB EET [47-51]. In addition, currently, we have strong experimental evidence that this mechanism is actually involved in electron transfer processes. 

The four dependent variables are substrate, 5 oxidized mediator, reduced mediator, and biofilm matrix potential, E. The following are all of the differential equations, initial conditions, and boundary conditions. Each boundary condition is specified as either a Dirichlet (first-type) or a Neumann (second-type) boundary condition. The electrode surface is at x = 0, and the top of the biofilm is at x = L. 

A new variable is defined, the specific electrochemically active surface area per unit volume, (m ), which is a measure of the active surface area available per volume of conductive biofilm matrix with which the mediator species can interact. This is based on the idea that even if the biofilm is highly conductive, generally, only specific sites will be electrochemically active and allow interaction with electron mediators. This is unlike metal conductors, whose entire surface is generally available for electron transfer. An electrochemically active area may include c-type cytochromes, which have been found on nanowires, bound in EPS, and on the outer membrane of 5. oneidensis cells [50,52-54]. By making this assumption, we provide a tool to researchers to check if this is acceptable. 

The following equations and modifications are relevant only to the cases in which mediators are allowed to interact with the matrix. Firstly, the biofilm is now able to oxidize and reduce the mediators on the basis of the local biofilm potential, as defined by Equation 9.21. This leads to a new set of redox reactions for the mediators in the biofilm. Similarly to the redox reactions occurring at the surface of the electrode, it is assumed that the redox reactions occurring in the conductive biofilm matrix will follow Butler-Volmer kinetics. The oxidation rate of Af, in the biofilm due to interaction with the conductive matrix, (mol m s ), is given by ... 

A new standard heterogeneous rate constant, (m s ), and transfer coefficient, (unitless), are used because it is not currently known whether these values will be the same for redox reactions occurring on the conductive biofilm matrix as for those on... 

Figure 9.17 demonstrates the effect of 5 on the local biofilm potential and redox potential profiles. Unlike the case in which interactions are not allowed (see rightmost plot in Fig. 9.15), the redox potential profile is dependent on the local biofilm potential if interactions between the two mechanisms are allowed. This can be observed in the exaggerated case in which 5 is increased 100-fold. The local biofilm potential and redox potential are nearly identical from the middle of the biofilm to the top. This is because the local biofilm potential controls the rate of the mediator reaction at the biofilm matrix surfaces. The mediator concentration defines the redox potential. 

In summary, our simulation results show that interaction between mediators and the conductive biofilm matrix could support higher biofilm metabolic activity. Interaction between mediators and the conductive biofilm matrix may be advantageous for the biofilm because if reduces the requirement for high mediator concentrations, limits mediator losses, and allows for higher biofilm densities. Closely related local biofilm potential and redox potential profiles could be indicative of a strong interaction between mediators and the conductive biofilm mattix. 

Interaction between mediators and the conductive biofilm matrix can support higher biofilm metabolic activity ... 

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