Functional gene quantification (hzs, hzo)
| Anammox marker genes (hzs, hzo) |
|---|
| Approach: qPCR quantification of anammox-specific functional genes |
| Context: lab, environmental collection |
| Spatial scale: point sample |
| Temporal scale: days (DNA) |
| Units: gene copy number L-1 |
| Community captured: anammox bacteria |
| Co-measurements: O2, NO2-, NH4+ |
Method Overview
The genes hzs (hydrazine synthase) and hzo (hydrazine dehydrogenase) encode the two key enzymes of the anammox pathway: hydrazine synthase condenses NO and NH4+ to form hydrazine (N2H4), and hydrazine dehydrogenase oxidizes hydrazine to N2. Both genes are unique to anammox bacteria and serve as highly specific molecular markers for this group. Water samples are filtered onto membranes, DNA is extracted, and hzs and hzo gene copies are quantified by qPCR using anammox-specific primers. When paired with cell-specific anammox rates from isotope experiments or literature values, the gene copy data can constrain community-level anammox rates.
Scale of measurement
DNA provides a snapshot of anammox cell abundance at the time of collection.
Data generated
hzs and hzo gene copy concentrations (copies L-1), which serve as a proxy for anammox cell abundance. When combined with cell-specific anammox rates, volumetric anammox rates can be estimated.
Units & currency
Units are gene copy number L-1. The currency is gene copy number.
Sample size
Typical samples are < 1 L in volume.
Repositories & databases
Limitations
Gene copy number and anammox rate are only loosely correlated — the metabolic activity per cell varies with environmental conditions (substrate availability, temperature) independent of gene abundance. The number of gene copies per genome must be assumed (typically 1), which may not hold for all anammox lineages. Extraction efficiency varies and is rarely 100%.
Example Applications & Protocols
Classic examples
Recent applications
Common calculations/conversions
- Estimated anammox rate = hzs copy number L-1 × cell-specific anammox rate (nmol N2 cell-1 d-1), where cell-specific rate is taken from culture data or co-measured by isotope pairing.