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This paper highlights the current challenges with quantitative estimation of ammonia‐oxidizing bacteria (AOB) employing quantitative real‐time PCR (qPCR) in diverse natural‐ and engineered‐ environments. In this work we concentrates on: (i) identifying the coverage and specificity of the available primers and TaqMan probes for amoA gene based on current databases; (ii) the development of new primers and TaqMan probes for differential quantification of  N. europaea  and  N. eutropha .

Lost in translation: the quest for Nitrosomonas cluster 7‐specific amoA primers and TaqMan probes