View source for Functional gene quantification (hzs, hzo)

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* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]:  [[User:Hagi BucknWise|Hagen Buck-Wiese]]
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! Anammox marker genes (hzs, hzo)
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| '''Approach:''' qPCR quantification of anammox-specific functional genes
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| '''Context:''' lab, environmental collection
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| '''Spatial scale:''' point sample
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| '''Temporal scale:''' days (DNA)
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| '''Units:''' gene copy number L<sup>-1</sup>
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| '''Community captured:''' anammox bacteria
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| '''Co-measurements:''' O<sub>2</sub>, NO<sub>2</sub><sup>-</sup>, NH<sub>4</sub><sup>+</sup>
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== 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 NH<sub>4</sub><sup>+</sup> to form hydrazine (N<sub>2</sub>H<sub>4</sub>), and hydrazine dehydrogenase oxidizes hydrazine to N<sub>2</sub>. 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<sup>-1</sup>), 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<sup>-1</sup>. 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<sup>-1</sup> × cell-specific anammox rate (nmol N<sub>2</sub> cell<sup>-1</sup> d<sup>-1</sup>), where cell-specific rate is taken from culture data or co-measured by isotope pairing.

== References ==

[[Category:Main Pages|Model types]]