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This paper reports on the use of fatty acid analysis for tracking the relative proportion of nitrifiers in reactors treating high strength ammonia wastewater with low carbon to nitrogen ratio. These results suggest the ratio of cis-9-hexadecenoic acid to cis-11-hexadecenoic acid may be useful for a number of acclimation responses including proliferation of small populations and appearance of new genotypes. This method is proposed as a supplement to molecular methods. The fact that fatty acid analysis has a much lower cost per sample and much higher sample throughput relative to most molecular methods makes it particularly suited as a prescreening tool when choosing samples to be submitted for the more costly analysis. Key words: nitrification, fatty acid methyl esters, Nitrospira, free ammonia, nitrite, ammonia inhibition.

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