GeneCount® Nitrifiers Collection

Quantitatively detect and estimate the abundance of 5 key nitrifying microbial groups: AOB, AOA, NOB (including Nitrospira), NOB (including Nitrobacter) and Comammox.

Requires GeneCount® Voyager or GeneCount® Q-96 thermocycler.

Our team responds to quote requests within 1 business day.


The GeneCount® Nitrifiers Collection qPCR assay panel is designed to quantitatively detect and estimate the abundance of key nitrifying microbial groups:

  • Ammonia-Oxidizing Bacteria (AOB)
  • Ammonia-Oxidizing Archaea (AOA)
  • Nitrite-Oxidizing Bacteria (NOB) Group 1 (including Nitrospira)
  • Nitrite-Oxidizing Bacteria (NOB) Group 2 (including Nitrobacter)
  • Comammox

The assay panel consists of five different assays that can be run on the same sample and provide an overview of the abundance of the major contributors to the process. The effectiveness of the qPCR method is achieved through the design and validation of specific primers and probes targeting unique genetic markers associated with each group of nitrifying microorganisms.

Assay design and optimization

Each assay within the panel is optimized to achieve high specificity and sensitivity for its target microorganism group. This involves the selection of primers and probes that are highly specific to the target genes, minimizing cross-reactivity with non-target DNA. The optimization process also includes determining the appropriate annealing temperatures, primer concentrations, and cycle conditions to maximize amplification efficiency.

Application and data interpretation

The nitrification qPCR assay panel can be applied to environmental monitoring, wastewater treatment troubleshooting/optimization, and ecological research to quantify the abundance of nitrifying microorganisms. It’s particularly useful in assessing the nitrification process in industrial and municipal wastewater treatment systems where the complete conversion of ammonia to nitrate is critical to meeting regulated discharge permits, for monitoring treatment of recycled water for industrial reuse and maintaining the health of the local ecosystem.

Understanding nitrification dynamics

Quantitative data obtained from the qPCR assays allows for better insight into the nitrification processes and provides visibility on the abundance of the key microbial populations responsible for treatment process. Increases or decreases in the abundance of specific nitrifying groups can indicate changes in nitrogen availability, the health of the populations or impacts from environmental conditions that are harmful or beneficial for the organisms. When changes are observed, actions can be taken to remediate and optimize the process based on these key process indicators.

Quantitative insights that complement 2nd Generation ATP and NGS

Combined with regular ATP measurements (which provide overall microbial population activity and health levels) and DNA sequencing analysis (a snapshot of which organisms are present), the nitrification qPCR assay panel is a powerful tool for monitoring and studying the key players in the nitrogen cycle. By providing quantitative insights into the abundance of specific nitrifying microorganisms, it helps elucidate the dynamics of nitrification in various environments.


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