Tuesday, March 29, 2011


For my graduate work, I have been studying a diverse group of microbes called diatoms. You may know of them as the greenish-brown slimy layer that grows on the bottoms of rivers or, maybe, your swimming pool. The word diatom is derived from the Greek work diatomos meaning "cut in two", an apt name for creatures living in a glass box. Literally! Diatoms take in silica (glass) present in water, store it in compartments called silica-deposition vesicles (ref 1), and then transport it outside the cell to form intricately patterned shells called frustules. Like a snowflake, the shape and features of the frustule are unique for nearly all species.

Scanning electron microscope
image of a diatom showing the
glass frustule.The top and bottom
fit together like a Petri dish (ref 2)

Diatoms are phototrophs, meaning that they live by the sun's energy and eat carbon dioxide. Ecologists often refer to phototrophs as primary producers because they are at the bottom of the food chain, similar to plants.

And, man! Are there a LOT of species! There are estimated to be between 100,000 and 200,000 diatom species (ref 3). They live in nearly every aquatic environment on the planet, from the open ocean to hot springs to swimming pools, sometimes to our chagrin. But even though we sometimes consider diatoms as pond scum when it turns our swimming pools green, we all owe a huge debt of gratitude to these feisty creatures. Nearly 1/4 of all oxygen in the atmosphere is produced by diatoms: for every fourth breath you take, be sure to thank the diatoms! They might be small, but their ubiquity in oceans, lakes and streams scales up to a hugely important impact on the earth's atmosphere (ref 4).

Scientists love to study diatoms for lots of reasons, and I'll give just a few examples here. As I mentioned earlier, diatoms produce glass frustules. When the individual dies, it's frustule remains intact for a really long time, as in millions of years. The frustule sinks to the bottom of a lake or ocean and accumulates in layers in the sediments.

Example sediment cores. Going deeper
into the core takes you deeper in time.
Note the distinct layers, reflecting
different environmental conditions (ref 5)

Once these sediment layers are separated, researchers look for changes in the diatom species found in different layers and can relate changes in the composition of diatoms to climate and many other environmental changes.

Many diatoms are very sensitive to habitat conditions and we can track changes in a particular species to changes in habitat, and for this reason we call them ecological indicators. For example, in modern times many studies use diatoms to determine how eutrophication (e.g. human input of nutrients) affects aquatic ecosystems. Over longer time scales, we can track changes in habitat-sensitive species to infer climate changes, such as glaciation or deglaciation events (ref 6).

The value of diatoms as ecological indicators has formed the basis of my graduate research on diatoms living in Antarctic streams. Intense! These diatoms have adapted to the extreme cold and icy conditions that prevail for most of the year. Despite these harsh conditions, diatoms seem to thrive: at least 40 different species are known to exist there! My goal is to determine the habitat preferences of these different species so that we can use these diatoms as ecological indicators of climate change in the Antarctic.

An exciting field of diatom research involves growing diatoms and other algae for producing biofuels. While everyone has heard of alternative energy sources such as solar and wind power, algal biofuels has been underrepresented as a viable alternative to fossil fuels, but I look forward to its continued progress. The idea behind using algae to grow energy is that they produce less CO2 than fossil fuels as well as other biomass feedstocks, such as corn and soy. They have an advantage over biomass feedstocks as well because they don't affect our food supply, a problem inherent in corn and soy. The algae produce large amounts of lipids, which are used to make hydrocarbons that we find in

Turn that pond scum into something
useful! Here an open raceway pond is
growing algaefor biofuels production
(ref 7)

I have only scraped the surface of the ecology and history of these amazing organisms. For more information, check out these other sources:

A) Pennsylvania Academy of Natural Sciences: one of the oldest diatom herbariums in the United States. Lots of interesting historical facts about the pioneers of American diatom research.
B) University College London: good overview of systematics, biology, life cycle, and applications of diatoms.
C) National Renewable Energy Lab's Biomass Research Project: current algal biofuels development projects underway.
D) Oilgae: good resource for all things related to algal biofuels

1. Schmid A-M, Schulz D (1979) Wall morhpogenesis in diatoms: deposition of silica by cytoplasmic vesicles. Protoplasma 100: 267-288
2. Antarctic freshwater diatoms database
3. Mann DG, Droop SJM (1996) Biodiversity, biogeography and conservation of diatoms. Hydrobiologia
4. Nelson DM, P Treguer, MA Brzesinski, A Leynaert, B Queguiner (1995) Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation. Global Biogeochemical Cycles 9: 359-372
5. Center for Advanced Marine Core Research, Kochi University
6. Seltzer GO, DT Rodbell, PA Baker, SC Fritz, PM Tapia, HD Rowe, RB Dunbar (2002) Early warming of tropical South America at the last glacial-interglacial transition. Science 296: 1685-1686
7. Make Biofuel: the ultimate biofuel resource.


Welcome to the first installment of my "Microbe of the week" post! My goal is to provide interesting tidbits of information on members of the microbial world to a diverse audience. I want everyone to appreciate microbes the way I do! Maybe even love them :) Feel free to leave comments or suggestions.