Single Turnover Chlorophyll Fluorescence

2026-02-21T10:43:32Z

Michiel Perneel: Created page with "{{BreadcrumbsPhotoautotrophy}} * Page authors: Michiel Perneel, PRIMO * Responsible curator: Kate Evans ---- Photosynthetic primary productivity is the light-driven process of extracting reducing power from water to drive CO<sub>2</sub> reduction to carbohydrates (i.e. CO<sub>2</sub> ‘fixation’). Global primary productivity is a critical source of O<sub>2</sub> for the atmosphere and oceans. Marin..."

{{BreadcrumbsPhotoautotrophy}}

* [[Page authors|Page authors]]: [[Michiel Perneel]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Kate Evans|Kate Evans]]
----
Photosynthetic primary productivity is the light-driven process of extracting reducing power from water to drive CO<sub>2</sub> reduction to carbohydrates (i.e. CO<sub>2</sub> ‘fixation’). Global primary productivity is a critical source of O<sub>2</sub> for the atmosphere and oceans. Marine primary productivity also plays an important role in carbon sequestration to the deep ocean through the biological pump, while providing a critical source of organic matter to support aquatic food webs and metabolism.

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<div class="model-box">
{| class="model-ib"
! What is being measured in 1 - 3 words
|-
| '''Photosynthetic electron transport'''
|-
| '''Approach:''' active chlorophyll fluorescence (single turnover), optical photophysiology
|-
| '''Context:''' ''in situ'', underway, incubation, autonomous platforms
|-
| '''Spatial scale:''' mL to km<sup>2</sup> (point measurements to transects)
|-
| '''Temporal scale:''' milliseconds to seasons (instantaneous to long-term monitoring)
|-
| '''Units:''' electrons m<sup>-3</sup> s<sup>-1</sup>, e<sup>-</sup> PSII<sup>-1</sup> s<sup>-1</sup>, derived C or O<sub>2</sub> units
|-
| '''Community captured:''' target species culture experiments, bulk phytoplankton community; taxon-weighted signal
|-
| '''Co-measurements:''' irradiance, temperature, salinity, nutrient concentrations, chlorophyll a, light history
|}
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== Method Overview ==
Single Turnover Active Chlorophyll Fluorescence (ST-ChlF) is an optical technique used to quantify photosynthetic activity in aquatic primary producers by resolving rapid fluorescence induction and relaxation transients following short excitation flashes. These transients reflect the opening and closure of Photosystem II (PSII) reaction centres and downstream electron transport processes.

By fitting photophysiological models to fluorescence transients, ST-ChlF enables estimation of photosynthetic electron transfer rates (ETR), which scale stoichiometrically with gross oxygen evolution and are closely linked to primary productivity. The method provides rapid, non-invasive measurements and can be applied across laboratory, ship-based, and autonomous observing platforms.

== Output ==

=== Scale of measurement ===
*Cellular to community-integrated photosynthesis
*Short- and long temporal scales

=== Data generated ===
*Raw fluorescence induction-relaxation transients
*Primary photophysiological parameters (e.g. Fo, Fm, σPSII, τ)
*Electron transfer rates (ETR)
*Light-response (ETR–E) curves and derived parameters (α, Ek, ETRmax)
*Ancillary stress and efficiency metrics (e.g. NPQ-related indices)

=== Units & currency ===
*ETR reported as electrons per unit volume or per PSII reaction centre per second
*Can be converted to O<sub>2</sub> or carbon-based primary productivity using stoichiometric or empirical relationships
*Represents gross photosynthetic activity on instantaneous time scales

=== Sample size ===
*Typically mL per measurement
*Not necessarily needing sample destruction
*Compatible with continuous flow-through systems

=== Repositories & databases ===

== Limitations ==
*ETR is not a direct measure of carbon fixation and requires conversion assumptions
*Relationships between ETR, O<sub>2</sub>, and carbon vary with taxonomy and environmental conditions
*Sensitive to non-photochemical quenching (NPQ) and light history
*Requires careful calibration, spectral correction, and baseline fluorescence treatment
*Community-weighted signal may mask taxon-specific responses

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

=== Common calculations/conversions ===
*Conversion of ETR to gross O<sub>2</sub> production (4 e- per O<sub>2</sub>)
*Empirical ETR–C relationships calibrated against 14C incubations
*Light-response curve fitting (ETR vs irradiance)

== References ==
SCOR Working Group 156 (2021). A User Guide for the Application of Single Turnover Active Chlorophyll Fluorescence for Phytoplankton Productivity Measurements. Version 1.0.

[[Category:Main Pages|Model types]]

Bulk RNA-sequencing (whole transcriptome)

2026-02-21T10:24:04Z

Michiel Perneel: Created page with "* Page authors: Michiel Perneel, PRIMO * Responsible curator: Kate Evans ---- __TOC__ <div class="model-box"> {| class="model-ib" High-throughput sequencing of RNA transcribed by an individual or population of a given organism, or a community of species. |- | '''Approach:''' filtering, RNA extraction, sequencing, bioinformatics |- | '''Context:''' ''in situ'', culturing, incubations |- | '''Spatial s..."

* [[Page authors|Page authors]]: [[Michiel Perneel]], [[PRIMO]]
* [[Responsible curator|Responsible curator]]: [[User:Kate Evans|Kate Evans]]
----

__TOC__
<div class="model-box">
{| class="model-ib"
High-throughput sequencing of RNA transcribed by an individual or population of a given organism, or a community of species.
|-
| '''Approach:''' filtering, RNA extraction, sequencing, bioinformatics
|-
| '''Context:''' ''in situ'', culturing, incubations
|-
| '''Spatial scale:''' L
|-
| '''Temporal scale:''' seconds, days, seasons
|-
| '''Units:''' gene expression, e.g. TPM
|-
| '''Community captured:''' size-fractioned, e.g. 0.2 - 250 µm, cultured or target species
|-
| '''Co-measurements:''' Other measurements required for interpretation of results e.g., temperature, salinity, nutrients, physiological data
|}
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<div style="clear:both"></div>

== Method Overview ==

== Output ==

=== Scale of measurement ===

=== Data generated ===

=== Units & currency ===

=== Sample size ===

=== Repositories & databases ===

== Limitations ==

== Example Applications & Protocols ==

=== Classic examples ===

=== Recent applications ===

=== Common calculations/conversions ===
* Normalised expression, for example transcripts per million (TPM)
* Quantitative estimates, for example transcripts per L (TPL)

== References ==

[[Category:Main Pages|Model types]]

Grazing

2026-02-21T10:07:33Z

Michiel Perneel:

===Microzooplankton on phyto loss process===
*[[Incubation dilution experiments]]
*[[Incubation dilution experiments]]
*[[Cell abundance]]
*[[Gut-fluorescence]]

===Bacterivory & Mixotrophy===
*[[Fluorescently labeled prey surrogates]]
*[[Radioactively labeled prey surrogates]]
*[[Pulse-chase labeling of bacterial prey]]
*[[Stable isotope-labelled prey]]

===Life Cycles===
*[[Bulk RNA-sequencing (whole transcriptome)]]

OceanWiki - User contributions [en]

Single Turnover Chlorophyll Fluorescence

Bulk RNA-sequencing (whole transcriptome)

Grazing