Why Am I Here?

Post by: Dalton Hardisty, Michigan State University

Why am I here? This is a question any oceanographer may find themselves thinking during a research expedition at sea. Days from land and working around the clock, rain or shine, where uncertainty of success, waves of thrill, and simply feeling out of whack (sea sickness?) are part of the routine. “Why am I here?” is also the most important question any researcher should ask well before the work starts, and certainly before the ship leaves port.

At sea, it helps to know your equipment inside and out. Here, Dalton Hardisty from Michigan State University, Alysia Cox from Montana Tech, and Drew Syverson from Yale University test a hydrothermal fluid sampler known as a “major” that they disassembled, cleaned, and reassembled. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

A research expedition is typically preceded by months to years of preparation—funding, experimental methods, training, etc. In my case, this will be followed by additional months to years of follow-up work in the lab before I see the results of shipboard experiments.

Ultimately, understanding why we are here is at the core of why I am on the ship. My research is directly focused on understanding the chemistry of the oceans on early Earth and, more specifically, how oxygen produced by photosynthetic organisms shaped that world into the landscape we know today. The hydrothermal vents of the East Pacific Rise provide an amazing opportunity to better understand how the geologic record of oxygen in the ocean relates to the history of life on Earth. Hydrothermal vents are one of the many environments that may have hosted Earth’s first life, and that we also know had a very different impact on ocean chemistry in Earth’s ancient past compared to today.

Scientists often find they have to modify their equipment to the requirements of deep-sea research. Here, Carolyn Tepolt from the Woods Hole Oceanographic Institution converts a crab trap so that it will fit on Alvin science basket. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

This is evident to anyone from Michigan, my recently adopted home state, which hosts some the largest records of ancient hydrothermal activity—the banded iron formations in the Upper Peninsula. These and other geologic records uncommonly found in today’s oxic ocean, but prevalent in the past, are a testament to the persistence of low-oxygen conditions in the oceans for billions of years of Earth history. This permitted the widespread accumulation of oxygen-sensitive chemicals like iron on the seafloor.

Dalton Hardisty from Michigan State University and Alysia Cox from Montana Tech get a quick tutorial in the operation of “major” fluid samplers from Alvin pilot Mike Skowronski. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

In my work, the abundance of these oxygen-sensitive elements in the vent fluids and the reactions that occur upon exposure to our oxygen-rich ocean will provide a window into changes that occurred on our planet nearly 2.4 billion years ago during the Great Oxidation Event, when evidence shows that low-oxygen conditions in the ocean began to disappear.

The Early Career Scientist Cruise provides an incredible opportunity to learn the details of planning and implementing oceanographic research from a legendary group of senior scientists and to gain new collaborations with a group of eager, interdisciplinary scientists. My research objectives include evaluations of the chemistry in the vent plumes and relies heavily on the use of the human-occupied vehicle (HOV) Alvin and Nisken bottles lowered from the research vessel Atlantis itself for sample collection.

Members of the science team wait for the signal that Alvin has been secured before they claim their samples off the sub’s front science basket. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

As we approach our sampling sites and finalize our scientific and logistical plans, I can feel the excitement and realization rising: This is actually happening! The chance to work onboard the R/V Atlantis and visit the almost alien world of the seafloor and hydrothermal vents via HOV Alvin is like a dream come true, one that merges my love for geology and my childhood (and adult) dreams of expeditions and discovery. I both can and can’t wait to report home on our findings and to see what new breakthroughs will arise from this amazing opportunity.

Going Viral

Post by:  Rika Anderson of Carleton College

Atlantis technician Emily Shimada (left) signals the winch operator while Rika Anderson from Carleton College keeps tension on a tag line to prevent the CTD (conductivity, temperature, depth) rosette from swinging during deployment. Anderson later filtered water from the CTD to collect microbes and viruses to analyze later as part of her research related to the cruise. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

Let’s start with some numbers. Consider the number 10-7 (0.0000001). That’s the approximate length, in meters, of a single virus. Just for scale, more than 5,000 viruses could fit across the width of your fingernail. We can’t see that with the naked eye.

Now consider the number 10 million (10,000,000,000). That’s the number of viruses in a single teaspoon of seawater. Another number: there are 1023 (that’s a one followed by 23 zeroes or 100,000,000,000,000,000,000,000) teaspoons of water in our oceans. That means there are about 1030 viruses in our oceans.

To give you a sense of the sheer size of that number, if you were to line up all those viruses end-to-end, stretching out into a thin, delicate strand, that strand would span the Milky Way galaxy 100 times. (See here for citations for these numbers!)

Alvin expedition leader Todd Litke (left) and pilot Danik Forsman prepare the sub to make its first dive of the expedition. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

Most of these viruses can’t make us sick—instead, their victims of choice are mostly single-celled microbes, which merely number in the millions in a single teaspoon of seawater. I study the viruses that live in the darkest, hottest places in our oceans—deep-sea hydrothermal vents. Not only do viruses live in hydrothermal vents, but we think those viruses manipulate microbes by hiding in their genomes.

Ken Kostel and Elizabeth Trembath-Reichert from the Woods Hole Oceanographic Institution and Matt Smith from the University of Florida (left to right) take part in a live discussion with 200 elementary, middle, and high school students from the U.S. and Canada during transit to the first dive site. (Photo by Mike Perfit, University of Florida)

One of the best-known examples of viral manipulation of a host microbe occurs with the disease cholera. This disease is caused by drinking water contaminated with the bacterium Vibrio cholerae, and can lead to severe vomiting and diarrhea or even death. However, the symptoms of cholera are not caused by the bacterium, but by a portion of a viral genome tucked inside the genome of Vibrio cholerae. It is this viral genome that carries a gene encoding a toxin that causes the symptoms of cholera.

Ronnie Whims, bosun on Atlantis watches the ocean prior to deploying the autonomous underwater vehicle Sentry on an overnight mission. As bosun, Whims is responsible for the safety and success of deck operations. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

Some viruses are beneficial, often in surprising ways. Millions of years ago, a virus infected a mammalian ancestor, delivering a gene that allowed it to form a placenta. Without a virus, you wouldn’t have been born. (See here for more info on that story.)

Viruses similar to the cholera virus reside inside the genomes of hydrothermal vent microbes, as well. I want to know whether they carry genes encoding toxins or if they carry other types of genes.

My goal on this cruise is to collect viruses and microbes from deep-sea hydrothermal vents and then peer into their genomes to find out what kinds of viruses are there, who infects whom, and what genes the viruses carry. In the past, we’ve seen evidence of some viruses enabling their microbial hosts to obtain energy from different chemicals within the hydrothermal vent fluid than they usually do. This gives the microbes an additional tool in their genetic toolkit that helps them survive when the need arises.

Sunset always draws a crowd to the west-facing rail. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

We usually think of viruses as parasites in that the virus gets some benefit out of the relationship, but not the host. But if a virus is hiding inside a microbe, then helping the microbe also helps the virus by ensuring that it has a safe place to live. In cases like this, viruses can become beneficial symbionts—at least for a while. Eventually, that virus will eventually leave its safe haven. It will start making new viruses and then burst the host microbe open to go off in search of new victims.

Viruses are messing around with the genomes of their hosts in just about any environment on Earth, but I’m interested in deep-sea hydrothermal vents because I think viruses have been playing this game for billions of years. Some scientists think that deep-sea hydrothermal vents were important sites for the origin and early evolution of life on Earth, and I think this virus-host relationship was key to that success. If we can understand how evolution operates in these places, we might better understand how microbes and viruses evolved together on the early Earth—and whether life might exist elsewhere in the universe.

It Begins

Co-chief scientists Mike Perfit (left) from the University of Florida and Dan Fornari from the Woods Hole Oceanographic Institution held a quick meeting on the plane to Manzanillo to plan Alvin and Sentry dives on the seamounts at 8°20’N. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

How does a research expedition begin? With the submission of the proposal? With its acceptance? With the first meeting of the team? When everyone arrives on the ship? Or when the ship finally casts off?

Matt Smith from the University of Florida is a marine geologist by trade, but takes a moment to practice his craft on an outcrop along a street in Manzanillo. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

There are many beginnings to something as complicated as this. We have passed many of them and are now making final preparations on the ship before we leave Manzanillo at 8:00 a.m. Monday, December 3. I almost wrote, “And then the real work begins,” but in reality, this team has been hard at work planning and organizing for months, if not years.

Drew Syverson from Yale University gets his first glimpse of Atlantis in Manzanillo, Mexico. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

And that, perhaps, is the first and most important lesson for the early-career scientists on board Atlantis—that a complicated, multi-disciplinary expedition like this, one that involves a limited number of dives by the submersible Alvin and autonomous underwater vehicle Sentry in several locations spread over hundreds of miles, is only going to succeed with careful, detailed planning and organization.

We’ll get to all of that in future posts. First, a road map of the next two weeks:

This expedition will unfold in two parts. When we leave port Monday morning, we’ll head first to a chain of seamounts south of Manzanillo and west of the East Pacific Rise at 8°20’ N to complete the 2016 OASIS expedition with four Alvin and three Sentry dives. After that, we steam 100 miles north to the East Pacific Rise at 9°50’ N to do four more dives with Alvin and Sentry. The latter part is official the Early-Career Scientist (ECS) portion of the expedition, but in fact, the entire trip is a learning experience.

Today (Sunday) was our first full day on the ship and we spent transforming it to meet our needs—which are very different from those of the previous science party. Fortunately, Atlantis, like all the ships in the UNOLS fleet, is built to be flexible and we gradually reconfigured the lab spaces into a shape that will permit microbiologists to work alongside geologists and fluid chemists to share space with macro biologists. Meetings were also a big part of our day, including a quick tutorial from WHOI geologist Dan Fornari on the nuances of arranging the equipment and sample containers on the science basket mounted to the front of Alvin.

R/V Atlantis at sunrise in Manzanillo. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)

Tonight, we’ll finish securing all of our gear for sea by tying down computers and monitors and strap and We’ll continue preparing as we transit from Manzanillo to our first dive site on Thursday morning. Keep following along to learn more about what we’re doing and to hear from each of the early-career scientists on board. You can also keep up with us on the UNOLS Chief Scientist Training Facebook page (@UNOLSCSW) or by following the hashtag #ECS2018 on Twitter or Instagram.

Valentina Romano from the University of Illinois gets fitted for an emergency rebreather mask in anticipation of a possible Alvin dive later in the cruise. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)
Dan Fornari holds a master class in the planning and organization of Alvin’s science basket. (Photo by Ken Kostel, Woods Hole Oceanographic Institution)