Quantifying functional gene populations: comparing gene abundance and corresponding enzymatic activity using denitrification and nitrogen fixation inpulp and paper mill effluent treatment systems

The relationship between the abundance of three functional genes and their corresponding biochemical reaction rates was investigated in several activa ted sludge and mill effluent microbial communities. Gene probes were prepar ed for two key denitrification genes (nirS and nirK) and for one nitrogen-f ixation gene (nifH) and were validated using a variety of strains of known nir and nif genotype. ATP-based measures of viable cell numbers were used t o provide total population sizes. In certain microbial communities (activat ed sludge enrichment cultures and multiple samples taken from the same mill primary clarifier), a strong correlation was observed between gene abundan ce and biochemical activity rates. However, when comparing several differen t nonenriched activated sludge bioreactors and separate primary clarifier m icrobial communities, the ratio of specific gene abundance to biochemical a ctivity rates varied widely. These results suggest that in cases where a mi crobial community is not fully induced for a given biochemical activity or when very different communities are compared, quantitative gene probing can give a better measure of a community's potential to carry out the encoded function than can the relevant biochemical assay. However, the gene quantit ation method employed here probably underestimated the true number of probe d genes present in the microbial communities due to nirS and nifH genes in the communities having reduced DNA sequence similarity with the probes used .