Blog:

Aboard E/V Nautilus Part I: The Marvels of Deep Sea Mud

ML Parker Media

Guest blog by Marley Parker, Video Engineer
Originally posted by ML Parker Media

North Pacific Ocean | 47.7447° N, 124.8836° W | September 25, 2020

Just after 2:00am in the E/V Nautilus Control Van, our team is conducting business as usual: the ROVs are stationed roughly 3,000 feet below the ship, gathering samples of methane-rich mud from the ocean floor. I zoom the camera out to a wide angle view as pilot Dan Cormany skillfully guides a sediment core back into the rack on the front of the ROV.

While Dan secures the tube, Chief Scientist Andrew Thurber provides a running commentary that is both informative and entertaining. He tells us one milliliter of mud contains a billion bacteria. He details the myriad interactions between microbes. And he gives a vivid description of his favorite one, which sounds like something straight out of a science fiction movie:

“Bacteriovorax finds other bacteria that it wants to eat. It rams it, then spins into the cell like drill. Once it gets inside, it eats everything, replicates, and then exits.”

Before this expedition, collecting mud might have sounded a bit mundane. Not anymore.

Andrew’s research career spans the globe, from the Pacific to the Antarctic and many places in between. He has worked on over a dozen different research vessels, carrying with him an infectious enthusiasm to better understand the components that drive life in the deep ocean.

The Thurber Lab at Oregon State University specializes in examining microbial interactions on the sea floor, which can provide a wealth of information related to fisheries, rare earth elements (like those used in cell phones and other mobile devices), advancements in biopharmaceuticals, and natural resources including metals, oil, and gas.

On this expedition, we are collecting sediment cores from methane seeps off the coast of Washington. Amassing data on these unique features can better inform our understanding of how microbial processes sequester methane on the ocean floor, and provide critical insight for our warming planet.

After the dive, I find Andrew and Lila Bellucci (a graduate student in Andrew’s lab) working on the aft deck. While they methodically slice, dice, and bag samples from the sediment cores, I snap photos and ask questions about what they plan to do with all the mud.

Andrew explains they are dividing the samples into three types of containers, and each group will be processed differently. The first are placed in plastic baggies — these will be used for DNA sequencing to determine what microbes are present in the sediment. They will also use these samples to look at the geochemistry.

The second group goes into scintillation vials to be used for “B&B” testing, or potential biotechnological and biopharmaceutical uses, which could eventually lead to new forms of medicine.

For the third group, Andrew and Lila scrape small samples of mud into cryovials, which will be used for RNA analysis. Because RNA gets broken down very easily, it has a short lifespan. The cryovials contain special media to preserve it.

“We use these to glean what is happening at the methane seep,” Andrew says. “What is eating the methane? What is turning sulfide into sulfate or vice versa?”

When all the sequencing is done, the data will be made publicly available.

“Everything we produce will be available to whoever wants it. All of the sequence data will hopefully be used for decades.”

Over lunch, I sit down with Susie Cummings (another grad student in Andrew’s lab) and ask her about a term Andrew mentioned in the control van: metabolomics.

“All omics involve holistically measuring cell processes,” she says. “Genomics is the main one (and the oldest one) and it gives us the big picture. Studying genomes provides a template for all the possible functions cells can have, and who they are.”

Transcriptomics and metabolomics, on the other hand, focus on the here and now. “What is present in a given moment in a certain ecosystem?”

Transcripts act as messengers that cells use to determine which products (for example, proteins) will be produced. Metabolomics is the study of the actual products.

Susie tells me about their lab setup, and the giant freezers (set to -80 degrees Celsius) that house all the mud. The samples collected during his expedition will keep the lab busy for the next few years, as they run hundreds of tests to investigate the intricate, microscopic processes occurring in the deep waters off the Olympic Coast.

I take notes and shake my head in disbelief. “I can’t believe a scoop of mud from the bottom of the ocean can provide so much information.”

Susie chuckles and says, “yeah, you can do a lot with frozen mud.”