AmoA gene or transcript abundance
| Ammonia oxidiser abundance (amoA) |
|---|
| Approach: qPCR / RT-qPCR of amoA gene and transcripts |
| Context: in situ, incubation, lab |
| Spatial scale: point sample |
| Temporal scale: hours to days (DNA); minutes (RNA snapshot) |
| Units: copies L-1 |
| Community captured: ammonia-oxidising archaea (AOA) and bacteria (AOB) |
| Co-measurements: volume filtered, cell abundance |
Method Overview
The amoA gene encodes the alpha-subunit of ammonia monooxygenase (AMO), the enzyme catalyzing the first step of nitrification (NH3 → NH2OH). It is the primary molecular marker for ammonia-oxidizing archaea (AOA) and bacteria (AOB). Water samples are filtered onto membranes, nucleic acids are extracted, and amoA gene copies (from DNA) or transcripts (from RNA via RT-qPCR) are quantified by qPCR or ddPCR using lineage-specific primers. Separate primer sets target AOA-amoA (crenarchaeotal/thaumarchaeotal) and AOB-amoA (betaproteobacterial), enabling their independent quantification[1].
Scale of measurement
Point sample; DNA provides a snapshot of ammonia-oxidizer abundance. RNA captures transcriptional activity at the moment of sampling. Filter volumes of 1–100 L are used depending on cell densities.
Data generated
amoA gene or transcript copies per liter, resolved into AOA and AOB contributions. When combined with nitrification rate measurements, per-cell nitrification rates can be calculated.
Units & currency
Units are copies L-1. The currency is cDNA (RNA assay) or DNA copies.
Sample size
Typical samples are 1–100 L in volume.
Repositories & databases
Limitations
Gene copies indicate the presence of ammonia oxidizers but not necessarily their activity. Transcript abundance can be more informative but changes rapidly (timescale of minutes) with light and substrate fluctuations, requiring standardized sampling times. A single copy of amoA per genome is assumed; polyploidy would cause overestimation.
Example Applications & Protocols
Classic examples
- Carini et al. (2018) Patterns of thaumarchaeal gene expression in culture and diverse marine environments [1]
Recent applications
- Santoro et al. (2021) Nitrification and nitrous oxide production in the offshore waters of the eastern tropical South Pacific [2]
Common calculations/conversions
- Per-cell nitrification rate = nitrification rate (nmol N L-1 d-1) / amoA gene copies L-1.
References
- ↑ 1.0 1.1 Carini, P., Dupont, C. L., & Santoro, A. E. (2018). Patterns of thaumarchaeal gene expression in culture and diverse marine environments. Environmental Microbiology, 20(6), 2112–2124. https://doi.org/10.1111/1462-2920.14107
- ↑ Santoro, A. E., Buchwald, C., Knapp, A. N., Berelson, W. M., Capone, D. G., & Casciotti, K. L. (2021). Nitrification and nitrous oxide production in the offshore waters of the eastern tropical South Pacific. Global Biogeochemical Cycles, 35, e2020GB006716. https://doi.org/10.1029/2020GB006716