Thursday, April 14, 2011

Oh, and one more thing

Just about an hour ago I received an email from a fellowship committee that I did not receive a dissertation completion fellowship. While it is possible that my application was sub-par, or that my letter of reference was weak, I can't help but wonder if the committee read my application and thought, "Diatoms? In my entire life I've never heard of such creatures. Why should I care about them now, especially in such dire financial times, when I could fund an applicant who studies something important, like cancer?".

Well, I'm here to set the record straight. Diatom research may not cure cancer (as far as we know), but there are so many applications of diatoms to people's everyday lives.
I'll start with an anecdote. Before I knew anything about diatoms, I took an animal science course at UMass. During one class we visit a farm, where we learned that a popular method for dealing with intestinal parasites was to add diatomaceous earth to the animal's feed. Diatomaceous earth (DE for short) consists of the glass remains of dead diatoms. In some parts of the earth there are huge deposits of DE from highly productive oceans. The DE is inorganic and accumulates in sediments.
The tiny glass bits of broken diatoms act like tiny microbial razors to cut up the offending parasites. From that class on, I knew diatoms were special. Apparently, diatomaceous earth also controls worms in dogs and cats (who knew?!!).

Image: Diatomite mine in Nevada. That white, chalky stuff is all diatoms! (ref 1)

Here's just one more reason people should know and care about diatoms. As I mentioned in the previous post, they are abile to biologically transform silica to from an intricate and repeatable silicate structure, called a frustule. Frustules are amazingly beautiful and have been the object of many artists' attention.

Images: diatom art (ref 2)

Now for the applied part. Humans would really like to capture the inherent ability of diatoms to create this repeatable nanostructure to create highly useful products like semiconductors (ref 3). Current industrial processes are hugely energy intensive, and yet diatoms do it all of the time using proteins. There is also much interest in using diatom frustules for drug delivery (ref 4) and even as an energy harvesting element in solar cells (reviewed in ref 5). The tiny diatom pores in the biological solar cells greatly increases efficiency compared to traditional solar cells.

Image: layout of a diatom-titanium dioxide thin film solar cell (ref 6)

Those are just two HUGE ways that diatoms affect the lives of everyday people. I may not have made that clear enough in my 750-word application, but I hope that I have convinced anyone who reads this that diatoms are worth of our attention.

1. Diatomite image:
2. Diatom art:;
3. Gordon et al. The glass menagerie: diatoms for novel applications in nanotechnology. Trends in Biotechnology 27(2): 116-127.
4. De Stefano et al. Inerfacing the nanostructured biosilica microshells of the marine diatom Coscinodiscus wailesii with biological matter. Acta Biomaterialia 4(1): 126-130.
5. Chapter 35 in: The diatoms: applications for the environmental and earth sciences (vol II). 2010. J. Smol, editor. Cambridge University Press. 686 pages.
6. Greg Rorrer lab, Oregon State University.

Sunday, April 10, 2011



The leader in libations, the king of the kitchen, this tiny organism rises to the top when it comes to making delicious food. Of course, I'm talking about the fomenter of fermentation, Saccharomyces cerevisiae, more commonly known as yeast.

Scanning electron microscope images of yeast cells (source: Yeast cells divide by a process called budding, present on these cells as small round dots.

Under low oxygen conditions, Saccharomyces, or "sugar fungus", can perform a very special form of metabolism called ethanol fermentation. The production of CO2 gas causes bread to rise and gives beer and champagne its fizz. And the ethanol? Well, you know. But, of course, the yeast really care about the energy produced by fermentation that sustains growth and reproduction. I'll note here that yeast grows a lot more efficiently using aerobic respiratory metabolism (like us humans) than anaerobic fermentation.

Making beer is fun! At the Microbial Diversity course in Woods Hole, MA, students learn first-hand about yeast fermentation.

Yeast in the Environment

In the family tree of life, S. cerevisiae belongs to the domain Eukarya (meaning it's more closely related to humans than to bacteria), and the phylum Fungi. While we generally refer to S. cerevisiae as 'yeast', there are many species that belong to this broader yeast group. Some species have real benefits to us (like baker's yeast), while we don't know very much about
many (like most organisms...), and others cause illness (e.g. Candida species). In the environment, fungi play an important role in cycling nutrients by decomposing organic matter so that nutrients become available for plants and micro-organisms. They are the "filters" of the environment, so it's no surprise that they do a great job cleaning up polluted land. S. cerevisiae and other yeasts are known to remediate Chromium (1), a poisonous metal that was made famous in the Julia Roberts film "Erin Brockovich".

Yeast is a relatively simple eukaryotic organism, being single-celled and easy to grow in a laboratory setting. For these reasons, it has become a model organism for scientific research. We have learned a lot about ourselves through understanding the biology of yeast cells. Some truly revolutionary analytical tools were developed using yeast, such as the two-hybrid assay (2), which has revealed insights into cancer biology (3), endocrine disruptors (4), and cell signaling (5), among much more.

We all can appreciate a tiny organism that can make delicious tasting food and beverages. But now that we know that there is so much more to this important microbe, we should all bow down to the king of the kitchen.

1. Ksheminska et al., Process Biochemistry, 2005: 1565-1572.
2. Interested? Check out Wikipedia for more information!
3. Li and Fields, FASEB Journal, 1993: 957-963.
4. Nishihara et al., Journal of Health Science, 2000: 282-298.
5. Staudinger et al., Journal of Cell Biology, 1995: 263-271.

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.