Diatom survival: It’s in their genes

March 26, 2013 — 2 Comments

Please welcome Sara Bender to the Science+comics interview series!  This week we’re taking a peek into the world of diatoms, and how they take up nutrients. Check it out!


Diatoms are tiny, single celled organisms that live near the surface of the ocean.  They are a type of phytoplankton, which are small, drifting organisms that form the base of the marine food web.  Many of them are so tiny that they can’t even be seen with the naked eye – even smaller than the width of a human hair.  Although they are not plants, they use photosynthesis to drive their metabolic processes, taking in carbon dioxide and releasing oxygen.  Also, like plants, they need nutrients such as nitrogen and phosphorous to survive.  Because of coastal upwelling and runoff from land, shallow, coastal regions tend to have the highest nutrient concentrations, and also the highest diatom concentrations.

Sara Bender studies phytoplankton ecology with the Armbrust Lab, and is a PhD student in her final year of Biological Oceanography at the University of Washington.  One of the things that Sara has looked at is how diatoms take up nitrogen. How do they do it, and how have they adapted to the conditions that exist at different locations? Sara has looked at three species in particular, all from very different environments. In a way, these species are sort of like the “lab rats” of the diatom research world, and many researchers have used them for experiments in the past and present. Let’s meet Sara’s special “pet diatoms”, shall we?

Diatom-characters

Now, here’s where Sara’s research gets really interesting: she uses cutting edge techniques developed for the medical field, and applies them to her pet diatoms. Her advisor, Ginger, along with a team of researchers, actually sequenced the very first diatom genome (Thaps) in 2004! Since then, both Fracy and Psemu have also had their genomes sequenced, and the number of diatom genomes is on the rise!

So how does Sara use these genetic sequences to learn about diatoms? Well, let’s back up a bit and talk about what is in a genome. DNA is made up of a specific sequence of nucleotides. You can think of these nucleotides as a very short alphabet – one with only four letters: A, T, C, and G. These letters are grouped together into genes that form the genome, which contains information that the cell can use to carry out different operations. Sara is interested in a particular type of operation: she wants to know how diatoms pull nitrogen out of the water. She asks questions like: how have different diatoms adapted to different conditions? And how might diatoms respond if conditions change in the future, as a result of climate change, for example?

diatom-genes

Sara looks for similarities and differences between genes from her three test species. And as it turns out, just because different organisms have some of the same genes, it doesn’t mean that they express them in the same way – or at all. After looking at which genes are present, Sara is able to form hypotheses. For example, let’s say that one diatom has ten of a specific type of nitrogen transporters, and the other two diatoms only have one of those, you might guess that the diatom with the ten transporters had to adapt to some particular condition in its environment.

Diatoms-chat

To test her hypotheses she looks at the next step in the process: the gene transcription step. This is where the information contained in genes gets transcribed into RNA. If this happens, the RNA can be translated into a protein, which can then be used to carry out some cell function. Sara looks at whether particular genes get transcribed in order to better understand how the cell functions under certain conditions. She can simulate different environments in the lab and then look at how the diatoms react based on the level of gene transcription.

Since diatoms play such a significant role in the marine food web, it’s really important to understand how they might be affected by changes in the ocean – whatever happens to them can have cascading effects on other organisms higher up in the food web.

Sara will be graduating this summer, and after that she’s going to the Woods Hole Oceanographic Institution (WHOI) to do a post-doc in Dr. Mak Saito’s lab. While she’s there, Sara will take her knowledge of diatom transcriptomics and translate it into studying phytoplankton proteomics- making the transition from genes to proteins. But fear not, she plans on continuing to unravel the mysteries of phytoplankton nutrient uptake in her future endeavors.

2 responses to Diatom survival: It’s in their genes

  1. ….try.. anaerobic.nitrogenous glyco-protiation. Ain’t phytoplanktonic proteomics a hoot.

  2. you never really said how diatoms take in nitrogen from the water…???

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