There are two really cool things about this research cruise: time and scale. The researchers are going from satellite images taken from far above the Earth, all the way down to the lipids and proteins found within individual Ehux cells, bridging a huge range of scales. They’re also using today’s observations to tell them about what happened thousands of years ago, and what might happen thousands of years from now, so they’re jumping through time as well.
Today and tomorrow we’re going to meet the two PI’s whose work really epitomizes these two distinct parts of the cruise. Today: time. This is Marco Coolen:
Marco is a researcher at the Woods Hole Oceanographic Institution in Massachusetts. His work focuses on paleo-genetics — using genetic signatures preserved in rocks and sediments to tell us about what was alive at different time periods. Usually, that means taking sediment cores and doing DNA sequencing on the material to see what genetic material is there. So, for example, last year he published a paper in the journal Science chronicling 7000 years of Ehux viruses in the Black Sea. They found that the coccolithovirus, the one that we talked about in an earlier post, has been attacking Ehux for a very long time.
On board the Knorr, Marco and his student Cherel Balkema have been serving as a rapid response team. We pull up to a spot that looks good on the satellites, grab some water, and Marco and Cherel use genetic techniques to quickly tell the rest of the team what’s there. They do so by isolating the genetic material in the water and then amplifying the virus and Ehux DNA, using something called quantitative polymerase chain reaction, or qPCR. So our workflow often looks like this. Go to a spot, dunk the CTD, analyze the water for DNA and then decide whether to stay.
Marco and Cherel did hit a road bump recently — the primers they use for pulling out and amplifying the desired genes got contaminated. At sea, contamination is a real problem. Scientists are working in a very small space with lots of other people doing experiments, using equipment that isn’t necessarily theirs. Sometimes, if they run out of items, they have to wash and reuse things they would normally throw out, which could introduce contamination as well.
Despite their contamination issues, Marco and Cherel have been collecting samples and helping other people with their work. At home they’ll be able to analyze the samples in the lab where they have uncontaminated primers, and get the information they’re looking for.
And Marco has a new interest: fecal pellets. Two of the other scientists on board – Miguel Frada and Daniella Schatz from the Weizmann lab (more on them later) - had wondered whether copepods – small zooplankton that often wind up on the filters – were eating infected Ehux cells. They collected copepods and analyzed them (and therefore, their stomachs) for DNA to see whether Ehux and the virus were inside. Miguel also showed Marco how to find and suck up copepod fecal pellets, and together they analyzed the DNA present in those as well. Sure enough, the copepods and the pellets have DNA from both Ehux and the virus.
Between sampling and helping, Marco tells funny stories about weird dreams, errant contractors, traveling and life at Woods Hole and Cherel kicks everyone’s butt at Pictionary. Together, they marvel at the oddities of Americans. “If someone can sue McDonalds for burning their mouth on coffee, can I sue my contractor for making bad steps?” asked Marco. ”Why do you say ‘how are you?’ when you don’t actually want to know the answer?” Cherel asked us one day. The people on the boat from the South said “we do want to know!” The people on the boat from New England said, “it’s just a common greeting.” The people from New York City said “we don’t ask.” Cherel said “Americans are weird.”
During this trip, I’ll be answering your questions about the science, this ship, and life onboard. Want to know how we search for plankton, why we’re here, or what the food is like? Just ask me! And if you’re wondering how I got here, check out the groups that made this adventure possible: Mind Open Media and COSEE NOW.
Previously in this series:
All Aboard: how you can be a part of our research blog
You wanted to know: what are these phytoplankton?
You wanted to know: what am I bringing to sea?
Greetings from Ponta Delgada! We set sail tomorrow.
Steaming North: how the scientists are trying to find plankton
The superstar sensor: what is a CTD?
Status Update: Day 3 at the Cyclonic Eddy
You wanted to know: what is this virus that infects the phytoplankton (Part One)
You wanted to know: what is this virus that infects the phytoplankton (Part Two)
Plankton hunting: Part art, Part science
You wanted to know: what’s the food like on board?
Jumborizing: a brief history of the R/V Knorr
On the importance of names. Or, “are we at the hump or the hole?”
Arts and crafts day on the Knorr
On the importance of names, part two. What’s the difference between a boat and a ship?
How to stay sane on a ship in the middle of the ocean
A graphical representation of the cruise so far
You wanted to know: who are these scientists? Introducing: Kay Bidle
You wanted to know: who are these scientists? Introducing: Jack DiTullio