Spectra of microbial fatty acid methyl esters were used to assess the influence of pH on the biofilm and suspended biomass populations within bench scale moving bed bioreactors treating bleached kraft mill effluent. The fatty acid spectral data were reduced by logcontrast canonical component analysis. The first canonical component differentiated biofilm from suspended populations and the second two appeared to indicate an influence of pH on microbial ecology. Thus, the biofilm and suspended microbial communities were distinct, as were the populations acclimated at pH 6 and pH 8. Experimental data for total organic carbon removal suggested that the more recalcitrant fraction of the influent was consumed by the slower growing, high SRT biofilm fraction of the biomass. Since the biofilm ecology was sensitive to pH within typical pH operating limits of full-scale systems, tighter pH control might improve treatment reliability in the event of process transients.

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