What diatomists do to diatoms

My research is on the diatom communities of the Everglades. To study how the communities respond to environmental changes, I have to identify and count each of the diatom species I encounter under the microscope. To do that though, the diatoms have to be stripped clean of any organic material and other 'junk' in the sample. The diatoms go through a harsh bath of acid and heat, until all that is left of them are their empty but beautiful cell walls. This is possible because diatom cell walls are essentially glass.

Beakers of diatom samples mixed with hydrogen peroxide and nitric acid boiling away on a hot plate. Different amounts of organic matter (like peat or plants) and inorganic matter (like sand or clay) result in different colors and reactions.

In the Everglades, the limestone bedrock adds a lot of calcium carbonate into the soil and periphyton. Some components of periphyton (especially mucilage-producing filamentous algae) attract calcite crystals like a magnet. The addition of calcium carbonate, an inorganic substance, makes Everglades periphyton a bit more difficult to process all the junk away. That's because inorganic things don't really dissolve with the normal chemicals we use to get rid of organic stuff. But we don't want to try to dissolve too much of the inorganic material either, because we don't want to damage the diatom cells! Everglades samples go through an intense process including sulfuric acid, potassium permanganate, and oxalic acid. Check out this animation that shows how Everglades periphyton is transformed into a bubbly and acidic concoction, then into a white powdery layer of clean diatom cells at the bottom of the beaker:

Here are some before and after processing images of periphyton and diatoms under the microscope:


  1. Thanks for posting this, Sylvia! It's really interesting for me to see what the diatoms look like and to learn more about what you do with them. My daughter is doing a project that includes, in a minor way, Everglades periphyton, and I was excited to find your images to show her of the diatoms! Good luck with your research.

    1. Thanks for your comment Hilary! I am glad the pictures came in handy. I hope your daughter's project is going well/was successful! Great to hear about young people getting involved in science.

  2. Thanks for posting this. I recently started cleaning diatoms myself with a view to making permanent mounts of selected frustrules (eventually). I'm just doing a few strews to start with though - learning gradually...

    You mention that you get a lot of calcium carbonate in your samples from the Everglades. Most of the protocols I've read (and tried) use a hydrochloric acid wash to get rid of carbonates before processing with sulphuric acid; else you get insoluble calcium sulphate (is that gypsum?) in your final sample.

    Doesn't appear to be much of a problem though (from looking at your "after" pics). Have you tried this - or don't you get an issue with it?


    1. Hi Beatsy, sorry for the delayed response. I just saw your comment. We have not had any problem with insoluble materials with our procedure, except when we get samples with a lot of sand. My advisor was working on some samples from Canada in areas with dolomite bedrock that was not reacting as well as Everglades calcareous periphyton. So, she added additional HCl and this seemed to work well enough. I am not sure if it would have been better to add the HCl before the procedure as you mentioned. Our procedure is based on Hasle and Fryxell 1970 paper. I can email this to you if you'd like. Best wishes, Sylvia


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