Southern Ocean GasEx Blog

Dispatches from the Southern Ocean Gas Exchange Experiment

The Importance of Quenching

Posted by sogasex on March 27, 2008

By Bob Vaillancourt, LDEO

The most common measurement to make for a biological oceanographer is for chlorophyll a (abbreviated “Chl a”). This is the pigment that is common to all phytoplankton, so is a convenient proxy for the size of the plant crop in the ocean at a given time. We have two ways of measuring Chl a: by direct measurement of its concentration on discrete water samples captured in a bottle, or indirectly, by measuring the amount of fluorescent light the plants emit.

Fluorescence is a phenomenon by which a material (in this case, Chl a) absorbs light energy, then re-emits a portion of this energy as light at a lower energy. In the case of phytoplankton, their Chl a (and other pigments) absorb energy in the more energetic blue-green portion of the spectrum, and re-emit (or “fluoresce”) in the less energetic red portion. This light is too weak to observe with the human eye, so we use special instrument called fluorometers to measure it.

Typically, we lower a submersible fluorometer over the side of the ship to measure the “vertical profile” of Chl a fluorescence. If we don’t have time to stop the ship, then we can make “underway” measurements by piping surface seawater into the ship’s lab and running it through benchtop fluorometers. We then look at this profile (or time-series) as a “proxy” or suitable substitute, for phytoplankton concentration. As chlorophyll concentration increases, generally so does the level of fluorescence- but not always. So it is important to realize the situations when chlorophyll fluorescence is not a good proxy for concentration. We most often see this in surface waters where light levels are highest.

Figure 1 shows a time series of surface sunlight (upper graph, blue line) measured on the deck of the ship, and Chl a (lower graph, green and black symbols) measured at a depth of 3 meters, near the surface. As sunlight increased throughout the day, we observe a suppression, or “quenching” of Chl a fluorescence by about a factor of nearly two between early morning and mid-afternoon (approx 15:00 GMT). We see this happening on rather short time scales too, as dips in sunlight, perhaps caused by the passing of clouds overhead, cause momentary relaxation of quenching in the fluorescence traces at approximately 1200 and 1700 hrs (red arrows). The Chl a concentration, meanwhile, showed a nearly constant level throughout the day. Quenching of Chl a fluorescence causes a huge departure from the normal co-variation between concentration and fluorescence. But does this happen at all depths?

The next figure shows similar data, but taken on two vertical profiles: one during mid-day (Station 7, left graph), and the other near mid-night (Station 4, right graph). You see that during the daytime, quenching of fluorescence occurs down to about 20 meters depth, and decreases fluorescence by a factor of about ten, when compared to Chl a concentration measurements made on captured samples. During night-time, however (right graph), the Chl a concentration data (green symbols) and Chl a fluorescence track each other nicely.

Another way of viewing these data is by property-property plots (see figure 3). Here we see that when plotted this way, the night-time data show a nice linear relationship (although over a limited range), but the day-time data, corrupted by fluorescence quenching show no such correlation. So, if one were to use the Chl a concentration data to calibrate their chlorophyll fluorometers, it makes sense to use nighttime data only.


Solar Irradiance (upper) and corresponding Chl a (lower) level changes through the day on March 16. Green symbols are concentration values (units of micrograms per liter) and black dots are fluorescence values (units of voltage). As sunlight increases through day, the fluorescence from chlorophyll is quenched, without a corresponding decrease in concentration.


Two vertical profiles of Chla fluorescence (black symbols) and corresponding concentration values (green symbols) for mid-day station 7 (left graph) and mid-night station 4 (right graph). During daytime, Chl a fluorescence in the upper 20 meters is quenched and does not track Chl a concentration. The quenching phenomenon disapears during the night-time.


Property-property plots of Chl a concentration (x-axis) versus Chl a fluorescence (y-axis) for mid-day (black symbols) and mid-night (red symbols) from Figure 2. Night-time fluorescence, devoid of quenching, shows linear relationship to Chl a concentration.

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