We use three-dimensional mathematical modeling to represent key substrate phenomena in a prototypical cluster-and-channel biofilm. Clusters are represented as cylinders in which diffusion and reaction occur simultaneously. The geometry of the effective diffusion layer surrounding the cluster is manipulated to simulate different degrees of advection within the channels. The cluster-and-channel configuration can increase the average substrate flux per substratum area only if the channels have advection and the surface coverage is high enough. The modeling also suggests that sub-cluster niches for slower growing species, such as nutrifiers, are reduced in size when substrate penetrates the cluster from all sides. Thus, the cluster-and-channel configuration might create a competitive disadvantage for slow-growing species.

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