From orange to pink, my favorite part of measuring biogenic silica


Kiely Shutt

Diatoms are an extremely common group of phytoplankton and especially important in marine ecosystems. Other than being arguably the most important primary producers in ocean and freshwater systems, diatoms are also thought to be important in carbon export to the deep. With cell walls composed of silica, diatoms are efficient ‘sinkers.’ Sinking within the euphotic zone is beneficial for two reasons: phytoplankton do not want to be burned by the sun and sinking to the ocean bottom is vital for sequestering carbon from the atmosphere. My project at Friday Harbor Labs involves studying how silicification in diatoms may change in acidified waters through measuring biogenic silica (silica produced by biology from dissolved silica in the water column) directly and by attempting to measure these changes using a scanning electron microscope (SEM).

Measuring biogenic silica (often referred to as opal) in the mesocosms involves filtering water, placing said filters in sodium carbonate for hydrolysis (necessary to draw out measurable silica from the filters) in a water bath for two hours, adding hydrochloric acid to lower the pH, and a few more complicated steps that lead to quantifying each samples’ absorbance with a spectrometer.  After absorbance is measured, I do a few tricks on Excel and use this data to convert the absorbance value to biogenic silica in micromoles/liter.


Falcon tubes with filters bathing at 85 degrees C for two hours, a vital step in measuring biogenic silica.


After adding methyl orange to each sample, HCl is added slowly to the point of turning pink. Easily my favorite part of the biogenic silica protocol.

So far, of the three mesocosm treatments, the “high” bags show a higher quantity of biogenic silica. The “high” bags are followed by the “drift” bags and with the control bags having the least amount of biogenic silica. Take a look at the preliminary plot below. The question now is whether or not this trend will stay constant through the remainder of the experiment.


Click to view larger

Using this data along with Amy’s cell counts, I should be able to tell whether or not diatoms silicify more or less in high pCO2 waters. Less silicification could mean decreased carbon export, affecting the biological pump responsible for transporting organic material from the euphotic zone to the deep ocean.

The other part of my project involves using a scanning electron microscope to observe and quantify silicification changes that may occur throughout the experiment. My next blog post will include more information about that aspect and some beautiful pictures. Until then, enjoy this “teaser” picture of a centric diatom taken with the SEM below.


Centric diatom photographed with SEM software from a practice slide.


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