Biofilm reactors, such as rotating biological contactors (RBCs) and trickling filters, have been used to treat both municipal and industrial waste streams. One fundamental property of biofilms which may affect their performance is surface roughness, or the magnitude of variability in height over the structure's profile. This property has an effect on the rate of diffusion of nutrients into the biofilm for degradation through its influence on the thickness of the concentration boundary layer.

The method presented here to quantify the surface characteristics of a biofilm involves the in situ analysis of biofilm surface profile data collected at discrete points. For each point, a microprobe is lowered from some datum above the surface, and the distance down to the biofilm surface is measured at that point. Statistical analysis performed on the data set produces the correlation coefficient between heights on the biofilm surface at various separation intervals. A graph relating the correlation coefficient to the separation interval between heights is constructed from many points to determine the length over which points with low correlation can be collected. A set of nearly independent height data collected at that length interval is then analyzed for mean and standard deviation. The resulting statistics are characteristic of the magnitude of the variability between independent heights on the surface profile, and can be used to compare and contrast the roughness of biofilm surfaces.

This method was used to define the roughness of artificial and real biofilm surfaces. Artificial biofilms, which were made from agar roughed with sand paper of varying grit size, were found to have distinct and consistent roughness, as determined by this method. It was useful to compare the standard deviation (roughness) of real biofilms to these values, because the roughness of sand paper is easily observable, and standardized.

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