View source for Nitrite oxidation (Nxr)

{{BreadcrumbsNutrients}}

* [[Page authors|Page authors]]: [[PRIMO]]
* [[Responsible curator|Responsible curator]]:  [[User:Hagi BucknWise|Hagen Buck-Wiese]]
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! Nitrite oxidation rate (Nxr proteomics)
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| '''Approach:''' targeted proteomics of Nxr + Michaelis–Menten kinetics
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| '''Context:''' environmental collection
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| '''Spatial scale:''' point sample
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| '''Temporal scale:''' hours to days
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| '''Units:''' nmol NO<sub>3</sub><sup>-</sup> d<sup>-1</sup>
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| '''Community captured:''' nitrite-oxidising bacteria (NOB)
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| '''Co-measurements:''' specific activity of purified Nxr; Michaelis–Menten kinetic parameters from whole live cells
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== Method Overview ==

Nitrite oxidation rates are estimated from the concentration of nitrite oxidoreductase (Nxr) enzyme in field samples combined with its kinetic parameters. Nxr is quantified by targeted proteomics: large-volume water samples (300–500 L, typically from pumping systems) are filtered to concentrate NOB biomass, proteins are extracted and digested, and Nxr-specific peptides are quantified by selected-reaction monitoring (SRM) mass spectrometry using isotope-labelled peptide standards. This gives the in situ Nxr concentration. Nitrite oxidation rates are then estimated from the Michaelis–Menten equation using the measured Nxr concentration, in situ [NO<sub>2</sub><sup>-</sup>], and kinetic parameters (V<sub>max</sub>, K<sub>m</sub>) derived from pure-culture or whole-cell experiments<ref name="Saito2020">Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M. R., Rappé, M. S., & Delong, E. F. (2020). Needles in the blue sea: Sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome. ''Nature Microbiology'', 5, 1282–1291. https://doi.org/10.1038/s41561-020-0565-6</ref>.

=== Scale of measurement ===

Very large sample volumes are required (300–500 L) to concentrate sufficient biomass of NOB for protein detection, limiting spatial resolution. Temporal resolution is set by sample collection logistics rather than the incubation itself.

=== Data generated ===

In situ nitrite oxidation rates in nmol NO<sub>3</sub><sup>-</sup> d<sup>-1</sup>, derived from enzyme concentration and kinetic parameters.

=== Units & currency ===

Units are nmol NO<sub>3</sub><sup>-</sup> d<sup>-1</sup>. The currency is nitrogen (gene/transcript/protein abundance; rate estimated from enzyme concentration).

=== Sample size ===

Typical samples are 300–500 L (large-volume pumping).

=== Repositories & databases ===

== Limitations ==

The approach assumes substrate limitation and applies kinetic parameters measured from pure cultures or whole cells to mixed field communities, where the physiological state and kinetic parameters of individual NOB populations may differ substantially. The specific activity of purified Nxr and Michaelis–Menten parameters derived from isolated organisms may not accurately represent the diverse Nxr variants in environmental communities. High sample volume requirements restrict applicability.

== Example Applications & Protocols ==

=== Classic examples ===
*

=== Recent applications ===
* Saito et al. (2020) ''Needles in the blue sea: sub-species specificity in targeted protein biomarker analyses'' <ref name="Saito2020" />

=== Common calculations/conversions ===
* Nitrite oxidation rate = [Nxr] × V<sub>max</sub> × [NO<sub>2</sub><sup>-</sup>] / (K<sub>m</sub> + [NO<sub>2</sub><sup>-</sup>]).

== References ==

[[Category:Main Pages|Model types]]