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{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Ammonia oxidiser abundance (amoA) |- | '''Approach:''' qPCR / RT-qPCR of amoA gene and transcripts |- | '''Context:''' ''in situ'', incubation, lab |- | '''Spatial scale:''' point sample |- | '''Tempo..."

2026-05-12T17:58:25Z

Created page with "{{BreadcrumbsNutrients}} * Page authors: PRIMO * Responsible curator: Hagen Buck-Wiese ---- __TOC__ <div class="model-box"> {| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;" ! Ammonia oxidiser abundance (amoA) |- | '''Approach:''' qPCR / RT-qPCR of amoA gene and transcripts |- | '''Context:''' ''in situ'', incubation, lab |- | '''Spatial scale:''' point sample |- | '''Tempo..."

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{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Hagi BucknWise|Hagen Buck-Wiese]]
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<div class="model-box">
{| class="model-ib" style="float:right; margin-left:1em; margin-bottom:1em;"
! 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<sup>-1</sup>
|-
| '''Community captured:''' ammonia-oxidising archaea (AOA) and bacteria (AOB)
|-
| '''Co-measurements:''' volume filtered, cell abundance
|}
</div>
<div style="clear:both"></div>

== Method Overview ==

The amoA gene encodes the alpha-subunit of ammonia monooxygenase (AMO), the enzyme catalyzing the first step of nitrification (NH<sub>3</sub> → NH<sub>2</sub>OH). 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<ref name="Carini2018">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</ref>.

=== 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<sup>-1</sup>. 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'' <ref name="Carini2018" />

=== Recent applications ===
* Santoro et al. (2021) ''Nitrification and nitrous oxide production in the offshore waters of the eastern tropical South Pacific'' <ref name="Santoro2021">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</ref>

=== Common calculations/conversions ===
* Per-cell nitrification rate = nitrification rate (nmol N L<sup>-1</sup> d<sup>-1</sup>) / amoA gene copies L<sup>-1</sup>.

== References ==

[[Category:Main Pages|Model types]]

AmoA gene or transcript abundance - Revision history