Sydney Greenlee
I have wanted to be a marine biologist since I was two years old, so it should be no surprise that working at Bigelow this summer with Dr. Pete Countway is my dream job! In fact, I love it here so much that I’m continuing on to participate in the Colby-Bigelow Changing Oceans semester this fall. I’ll be working with Dr. Doug Rasher to document changes in Maine’s oceans through scuba diving! And in January, I received the opportunity to work with Dr. Barney Balch on his upcoming Southern Ocean research expedition. There’s so much to learn about the ocean from many different fields of research here at Bigelow!
I originally wanted to work with animals, like stingrays or corals, but I fell in love with bacteria and phytoplankton not too long after arriving in East Boothbay. Pete collected all our samples from Palmer Station, Antarctica (I didn’t get to go this time!). If you want to learn more about life in Antarctica in comic form, check out illustrator and author Karen Romano Young’s AntarcticLog. She accompanied Pete and several other Bigelow scientists to document their research in a fun, accessible way.
This summer, Pete and I are looking at how dimethylsulfoniopropionate (DMSP) affects Antarctic bacterial and microalgal community structuring and DMSP-degrading functional gene abundance using quantitative real-time PCR.
That’s a mouthful, right? I’ll admit I didn’t understand all of that before I got to Bigelow. It isn’t as scary as it sounds!
Microbial ecology is the study of how environmental factors, like temperature or chemicals, change the types and numbers of bacteria, phytoplankton (tiny algae), and other small organisms. DMSP is a compound that some phytoplankton make to regulate how much water they take up and that some bacteria consume for nutrients. A functional gene is a DNA sequence that actually gets coded and performs a function. For example, a functional gene in humans would be one that produces your eye color or determines your skin color. Most of our DNA and the DNA of all living things is made up of nonsense genes that have no purpose and don’t get coded. So, a DMSP-degrading functional gene would be a gene that bacteria have to break down DMSP to access its nutrients.
An important part of my project is being able to measure the abundance, or amount, of functional genes in these bacterial communities. So how can I count what I can’t see, even with a microscope? I use PCR! PCR stands for “polymerase chain reaction,” which is a technique used to amplify, or increase replication of, DNA strands by changing the temperature of the reaction in a specific way. We heat up or denature the DNA so it unravels, then cool it slightly to extend it so it can be cut and amplified, then anneal or cool it. We repeat this cycle over 30 times.
PCR can be used to isolate genes for cloning, but it can also be used to quantify the amount of a gene in a sample. Pete has a real-time PCR machine in his lab, which takes a reading of the samples after every cycle. The machine also records the relative fluorescence of each sample, so it creates a graph of the amplification. When you have known amounts of a gene in a sample, you can create standards. Using these standards, you can estimate the amount of the same gene in your own sample!
Maybe one day, everyone will be able to do PCR right at home thanks to companies like Biomeme, who are working on creating a PCR iPhone app! Pete is helping test the device, both in the lab and in the field. I’ve gotten to run it a few times too. Right now, it’s still pretty expensive, but the hope is that it will be both financially accessibly and user-friendly to non-scientists.
But most importantly, why should we care about what kinds of genes bacteria in Antarctica have? It doesn’t directly appear to affect our lives here in the U.S., either economically or environmentally, right? Actually, some of the DMSP-degradation functional genes create a by-product called dimethyl sulfide (DMS) gas. DMS gas forms clouds, so if these bacteria produce more DMS, we’ll have increased cloud cover, and increased cloud cover means atmospheric cooling. So in other words, these bacteria have the potential to mitigate some of the effects of climate change! Additionally, DMSP-producing phytoplankton and DMSP-degrading bacteria are found all over the world — even in coral reefs! My project could help inform other scientists about bacteria in other non-polar systems around the globe. All research is important, but not all of it seems important on a huge scale. In reality, most scientific projects are smaller steps towards a greater understanding of the world around us.
Sydney Greenlee is a Colby College student in Bigelow Laboratory for Ocean Science’s Research Experience for Undergraduates program. This intensive experience provides an immersion in ocean research with an emphasis on hands-on, state-of-the-art methods and technologies.