Karen's Daily Blog

In a Sedimental Mood

Thing One and Thing Two came back all yellow and brown and disgusting.

The Main Lab smells like sulfur and oil and something worse.

Alvin needs its windows washed every time it comes up.

And Eric Wommack is holding a contest for naming the smell emanating from the Wet Lab where the LVWS water samples are processed. The only suggestion so far is “Rather Pooey.”

In other words, P.U.!  But follow the smell to where science is getting done!

Deep down below the cloudy blue waves of Guaymas Basin, Alvin pilot Mark Spear uses the manipulator claw to grip a corer and plant it firmly into the bacterial mat at Rebecca’s Roost. He jams the corer through the mat and into the mud beneath and sucks up a “core” -- a long sausage of sediment. Then he places the corer back into the milk crate fastened to Alvin’s basket and pulls out another. By the end of the day Mark will have gathered 12 cores at three different locations along Alvin’s route. Aboard Atlantis, scientists in long white coats (to keep the smelly mud off their clothes) spend their night processing their samples, storing some and examining others.

In the Main Lab, Diane Kim carefully sections a sample by cutting a 1 cm slice with a small flat square of metal. She places her slice in a petrie dish, stirs it, and spoons it carefully into a storage tube Amy Koid holds. The tube is labeled with the Alvin dive number and the coring site, and the section’s “horizon” -- the location of the slice in the sausage. When I comment that the consistency of the mud reminds me of cake icing, an amused look crosses Diane’s face. “You know, I spent a year and a half icing ice cream cakes for Baskin-Robbins,” she says. She’s got the skills to prove it!

Doug Fadrosh holds up the lid of Thing One, after it has gathered water from Guaymas Basin.

Like most of the scientists working with core sediment samples, Diane is interested in making comparisons between the mat, the sediment at the edge, and the sediment farther from the edge, as well as comparing several different sections of the core, as well as comparing cores from bacterial mats of white, yellow, and orange. 

Here on the ship, she’ll be looking at sample sediment under the environmental scanning electron microscope, as well as under the light microscope. She’ll preserve some samples and take them home for further testing. As with the water samples they’re analyzing, the Caron lab wants to find the total diversity of protists living in the sediment at the Guaymas vents.

In Hydro Lab, Kathy Coyne tells me her plans for her cores. She’s taking samples from two cores per bacterial mat, one taken from the center and one from the outer edge, as well as a core of the sediment farther away. Kathy is using only the top centimeter of her core, because she wants to know about the ciliates living on the mats. Her goal is to determine what diversity of ciliates (single-celled organisms that feed on bacteria) live in the mats and to learn the relationship between the color of the mats and the kind of ciliates found there.

Dave Walter washes the oil from the Guaymas Basin sea floor from Alvin’s window.

In Main Lab, Fanny Reisman Moussan and Ruth Villanueva Estrada are, like the others, working with cores from all three colors of bacterial mats. Like Kathy, they’re looking at three cores from each mat -- inside the mat, at the edge, and a few meters away. They’ll study the top segment and another slice 10 cm down. Fanny is looking for infaunal compounds, those related to the animals that live on the seafloor. Fanny will begin some DNA extractions aboard Atlantis, and freeze others to work on in her home lab. Ruth’s specialty is assessing the trace metals in the sediment, using microscopy and x-ray.

The Wommack lab is also going to do some core work, since there is so much sediment on tap. They’ll syringe out a subcore and culture it, waiting to see if bacteria grow. Bekki  Helton and Lisa Zeigler will be counting bacteria and viruses present throughout the core.

The Wommack lab is mainly trying to get rid of the mud and oil in their water samples.  Through a nine-step process of filtration, he will reduce his large volumes of water samples to samples of about a cup’s worth. Then he’ll analyze the viruses within. Bekki has spent many hours of this week watching old movies in the lounge while painstakingly handstitching nylex filters in ever-decreasing mesh sizes, to make filter sleeves designed to separate the muck from the microbes.

Out on the deck, where the air smells clean, I check in with Pat Hennessy to see how the fishing is going.  Nothing biting, he says. But today he did see something interesting – big dollops of oil that floated up from the bottom of the sea and bubbled – glug – when they got to the surface.

Today's Extreme Blogger:
Amy Koid

How being on a research cruise
transforms you into a nocturnal creature

When I woke up this morning from a deep and dreamless REM cycle, my cell phone told me that it was a whopping 11:30 in the morning. I had missed breakfast and was about to miss lunch as well. Feeling like I was in high school and about to miss the school bus all over again, I quickly showered and rushed up to the lab to begin my day.

I blame my tardiness on Dave, the principal investigator of my lab group. Today is his day to dive, and last night, he told us, with compassion in his eyes, to not worry about waking up early to send him off. Thus, I took the liberty of not setting my phone to ring at 7:45 a.m., fifteen minutes before the submersible deploys.

It turns out that this leg of the cruise is a heavily nocturnal one. Typically, Alvin comes up at approximately 5 p.m. The first thing that happens when the two observers emerge from the belly of Alvin is the hazing of the scientist, if she is a first-time Alvin diver. The lab group that she belongs to would have an elaborate torture plan prepared, usually involving buckets of ice-cold water (one of the primary uses of our -20 degree freezer) and squishy things in shoes.

Then, after Alvin is returned to the hangar, the feeding frenzy begins. Everyone attempts to retrieve and put away their samples as quickly as possible to ensure that the samples remain in good condition. A quick dinner follows, but we do linger a little longer in the mess if the dessert is especially good.

Last night was special, though. Craig, the chief scientist, planted the notion of a cookout in Chef Mark’s head, so a barbeque pit was set up on the back deck. It was framed by two tables draped in white tablecloth laden with cocktail shrimp, a potato salad, grilled steak and chicken, and a gorgeous sunset in the background.

This dinner took a little longer than usual and the “core team” did not get started processing the cores until 8 p.m. The core team consists of Diane and me; Pete and Karen were the auxiliary members whose primary function was to give us moral support and entertain us with their antics.

When we get a core, we attach it to a harness on the side of a low bench to extrude it centimeter by centimeter. The extruder is a simple hydraulic jack, similar to one you would use to change a car tire.

First, we remove the core top water using a 25- milliliter pipette, and we save this water in a culture flask for use later. If the core has a microbial mat, we put some of that on a microscope cover slip for electron microscopy. Then, we extrude the first centimeter of the core into a Petri dish. After homogenizing the sediment, we divide it up into subsamples, for different methods of sample processing and analysis. Each of these subsamples has to be labeled carefully to avoid confusion down the road; when we have literally hundreds of samples, it is imperative to know where each sample came from, and what it is for.

In fact, most of my energy last night was spent labeling tubes, cryovials and culture flasks. “4477, #5, 0-1, DNA”. Each label had the dive number, core number, horizon in centimeters, and sample type.

We repeated the same thing three times, for three cores, each horizon one centimeter high, for electron and light microscopy, cell counts, DNA and RNA, as well as culturing.

In between each core, we try to tidy up the work area, put away samples in the fridge or freezer, label tubes for the next core, and clean out the PVC pipes used for the coring.

It’s little wonder that by the time we were done, it was close to midnight.

While we were all really tired working that late into the night, we had one major impetus to keep us going: PB&J party when we were done with the last core. So Diane and I kept at it while Pete told us funny stories about his two-year-old son Garrett, and Karen said funny things until we were done with the last subsample for the last horizon on the last core.

Then, we all went upstairs to the mess, busted out the fluffy sourdough bread, peanut butter, butter, honey, three different kinds of jam from Knotts Berry Farm and hot chocolate and had a jolly good party.

As far as the at-sea lab environment goes, there is something special about 12 a.m. that isn’t true about 12 p.m. There is a certain camaraderie among the scientists, a feeling of “We’re in this together, looking bleary-eyed together” that makes working at God-forsaken hours that much more comfortable.

It was at this PB&J party that Dave said that we should sleep in the next day; I took his advice quite literally and am beginning to embrace the nocturnal lifestyle of the Guaymas leg of the Extreme 2008 Deep- Sea Cruise.

It is 5 p.m. right now; the submersible is about to come back on deck with more cores, and I say bring it on! Tonight, we’ll have another party. Or maybe we’ll watch a movie when we’re all done.

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