Interspecies electron transfer (IET) is important for many anaerobic processes, but is critically dependent on mode of transfer. In particular, direct IET (DIET) has been recently proposed as a metabolically advantageous mode compared with mediated IET (MIET) via hydrogen or formate. We analyse relative feasibility of these IET modes by modelling external limitations using a reaction-diffusion-electrochemical approach in a three-dimensional domain. For otherwise identical conditions, external electron transfer rates per cell pair (cp) are considerably higher for formate-MIET (317 × 10 3 e − cp − 1 s − 1 ) compared with DIET (44.9 × 10 3 e − cp − 1 s − 1 ) or hydrogen-MIET (5.24 × 10 3 e − cp − 1 s − 1 ). MIET is limited by the mediator concentration gradient at which reactions are still thermodynamically feasible, whereas DIET is limited through redox cofactor (for example, cytochromes) activation losses. Model outcomes are sensitive to key parameters for external electron transfer including cofactor electron transfer rate constant and redox cofactor area, concentration or count per cell, but formate-MIET is generally more favourable for reasonable parameter ranges. Extending the analysis to multiple cells shows that the size of the network does not strongly influence relative or absolute favourability of IET modes. Similar electron transfer rates for formate-MIET and DIET can be achieved in our case with a slight (0.7 kJ mol − 1 ) thermodynamic advantage for DIET. This indicates that close to thermodynamic feasibility, external limitations can be compensated for by improved metabolic efficiency when using direct electron transfer.

An individual-based, mass-spring modeling framework has been developed to investigate the effect of cell properties on the structure of biofilms and microbial aggregates through Lagrangian modeling. Key features that distinguish this model are variable cell morphology described by a collection of particles connected by springs and a mechanical representation of deformable intracellular, intercellular, and cell-substratum links. A first case study describes the colony formation of a rod-shaped species on a planar substratum. This case shows the importance of mechanical interactions in a community of growing and dividing rod-shaped cells (i.e., bacilli). Cell-substratum links promote formation of mounds as opposed to single-layer biofilms, whereas filial links affect the roundness of the biofilm. A second case study describes the formation of flocs and development of external filaments in a mixed-culture activated sludge community. It is shown by modeling that distinct cell-cell links, microbial morphology, and growth kinetics can lead to excessive filamentous proliferation and interfloc bridging, possible causes for detrimental sludge bulking. This methodology has been extended to more advanced microbial morphologies such as filament branching and proves to be a very powerful tool in determining how fundamental controlling mechanisms determine diverse microbial colony architectures.

A two-dimensional pore-scale numerical model was developed to evaluate the dynamics of preferential flow paths in porous media caused by bioclogging. The liquid flow and solute transport through the pore network were coupled with a biofilm model including biomass attachment, growth, decay, lysis, and detachment. Blocking of all but one flow path was obtained under constant liquid inlet flow rate and biomass detachment caused by shear forces only. The stable flow path formed when biofilm detachment balances growth, even with biomass weakened by decay. However, shear forces combined with biomass lysis upon starvation could produce an intermittently shifting location of flow channels. Dynamic flow pathways may also occur when combined liquid shear and pressure forces act on the biofilm. In spite of repeated clogging and unclogging of interconnected pore spaces, the average permeability reached a quasi-constant value. Oscillations in the medium permeability were more pronounced for weaker biofilms.

Microbial interactions play an important role in environmental processes, both beneficial (e.g., production of methane through anaerobic digestion) and detrimental (e.g., bulking of sludge). By better understanding microbial interactions, conditions can be optimised to either make the microbial processes more effective or limit the negative effects caused by the microbial community. This thesis mathematically investigates physical and chemical microbial interspecies interactions in order to determine the impact of elementary controlling mechanisms. Research is focused on basic mechanical interactions and chemical-electrochemical interspecies interactions, with application to key systems where the physical, electrical, and chemical elements are linked. To enable description of the physical components, an extendible individual-based modelling framework is presented that predicts the movement, growth and development of single cells, as well as their interactions with surfaces and other cells in the microbial community (chapter 2). This extends previous approaches to consider physics at the level of individual cells and enables the use of non-spherical cell geometries. Using this model it is shown that (i) in a biofilm consisting of rod-shaped cells, inclusion of cell-substratum anchoring links cause biofilms to rapidly grow in thickness instead of surface area, and (ii) interfloc bridging in activated sludge is related to the relative growth rates of floc forming and filament forming microorganisms. A microbial community where direct interspecies electron transfer occurs is evaluated by modelling both the physical organisation of cells and interspecies links, along with diffusion-migration transport, electrochemistry and biochemical reactions. This allows comparison of the external limitations of a recently reported direct interspecies electron transfer (IET) mechanism to classical, mediated IET through formate or hydrogen (chapter 3). This work shows that direct IET through nanowires is more strongly limited by thermodynamics than formate-mediated IET. Redox complex activation losses encountered during cell-nanowire transfer govern the system (93% of total losses). A sensitivity analysis shows that only when the redox complex transfer rate is an order of magnitude higher or the redox complex count is five times higher does nanowire resistance play a role, yet the feasibility of direct IET remains lower than formate-mediated IET. However, a minor metabolic advantage, as reported in recent literature, is sufficient to explain why direct IET can outcompete formate-mediated IET in some systems despite the limitations governing electron transfer. The techniques developed in chapter 2, as well as reaction-diffusion as applied in chapter 3 are further developed to consider the shell-shaped aggregates mediating anaerobic oxidation of methane in deep sea sediments (chapter 4). Extremely low reaction rates, acid dissociation and polysulfide precipitation cause diffusion to be non-limiting even in the largest reporte...