Aboard the R/V Sikuliaq we often run around-the-clock operations and do our best to collect every last bit of data. Not only is our time limited, but ship time is valuable—really valuable. Even if you did manage to make the absolute most of the available ship time, there are inevitably gaps when the vessel is transiting from station to station, the equipment requires attention, or the weather limits safe science operations. This is where instruments that sample continuously come in handy. They record data all the time regardless of what the ship is or isn’t doing. Another benefit is the flow-through data is collected at no added cost to the science party since the ship records the data anyway.

I am particularly interested in using the seawater intake and flow-through systems to measure a variety of ocean parameters. The flow-through system pumps seawater from an intake on the hull and carries it through a series of different sensors. On the Sikuliaq, the flow-through system measures temperature, salinity and amount of Chlorophyll in the seawater. It does this 60 times a minute, nonstop, throughout the entire cruise. For our cruise that’s almost 1.3 million data points per sensor!

The flow through system is suitable for only some types of science because it measures seawater parameters at just one depth. However it does provide nice contextual information that can help frame the results of the other science happening on the ship. For example, consider this plot that shows the amount of Chlorophyll measured by the ship over the course of our cruise.

Figure 1. Plot showing the amount of Chlorophyll in the water over the course of our cruise. The ship set sail from Hawai’i on December 2 and arrives in San Diego December 17th.

Chlorophyll in aquatic systems, just like on land, is a rough measure of the amount of plants in the area. The figure above shows there was a substantial increase in Chlorophyll during the latter part of our cruise, which corresponds with our arrival to coastal California waters. Nutrient waters are present throughout this region, leading to blooms of phytoplankton (marine plants) such as the one we measured here.

High chlorophyll events like the one on December 12th occur frequently off of the coast of California, however it is not only is the water column that is packed full of organic matter (consider the large fishing industry here) but the sediments are as well. You can actually see the difference in the color of the cores we collected in the North Pacific Gyre (far from the coast) and in the California borderlands (near the coast).

This sediment core sample was collected off the coast of California. It is green because of organic material. Photo by Megan Roberts.

This sediment core was collected in the middle of the North Pacific Gyre and consists almost entirely of mineral dust. Photo by Jake Beam.

The flow-through system is one of a number of systems onboard that helps us to understand the world around us; in other words, helps us to do science.

Relaxing on the bow of the ship brings a fresh breeze, plenty of sunshine, and a fine mist from the waves. When the waves on the open ocean break, small droplets of salt, water and biological material are lofted into the air. These droplets are transported vertically by the wind and may become seed particles for clouds or drift over continents. We call these droplets aerosols.

Waves breaking on the side of the ship create small droplets of salt, water and biological material called aerosols. Photo by Lauren Frisch.

Aerosol particles, depending on their size and likelihood to be absorbed by a cloud, can travel globally to impact foreign regions of the Earth. Some parts of the Amazon are fertilized by African desert dust, and wildfires in Canada generate soot that’s easily detected in Europe. All kinds of particles make it into the atmosphere, from organic bacteria to solid quartz. Volcanoes contribute significant amounts of sulfur and glass to the atmosphere. Particles that transport globally are usually in the 10s to 100s of nanometers range, which means they’re too small to see with the eye. However, they can still scatter ultraviolet light and small amounts of visible light, which has an effect on the radiation balance of the atmosphere.

Aboard the R/V Sikuliaq, I’m attempting to measure how much sea spray aerosol is generated by wave activity. This involves walking around the deck and waving my aerosol spectrometer in the air. It counts and measures the sizes of particles, because number and size are relatively easy quantities to measure. With this knowledge, we can make some good guesses about where the particles will go, and how much light it will scatter from the sun.

Joseph Niehaus uses a spectrometer to measure the number and size of aerosol particles. Photo by Lauren Frisch.

The size and amount of aerosol in the atmosphere may also affect human health. Lots of glassy particles can be scarring to lungs, and significant amounts of micron-sized aerosol causes the condition known as Black Lung. Because of this, the Environmental Protection Agency (EPA) regulates the concentration of aerosol particles (PM10 and PM2.5) that are safe in the atmosphere. PM2.5 is the particulate matter larger than 2.5 micrometers, about the size of flour dust. PM10 is the particulate matter larger than 10 micrometers. For reference, a strand of hair is about 100 micrometers wide. Typically, you would not notice breathing in PM2.5, but inhaling PM10 can make you cough. Thankfully the air out here is very clean, with virtually no particles larger than 5 micrometers.

Back in the lab, we have a mesocosm tank to test the amount of aerosol spray being produced by waves in the Pacific. The mesocosm is basically an aquarium with attachments that we fill with artificial seawater. We can generate aerosols with a waterfall which causes bubble bursting. The amount and type is very similar to ocean waves breaking, where trapped air generates bubbles which rise to the surface and burst. Using the same instruments on the voyage, we’re hoping to close the circle on how sea spray enters the atmosphere, altering weather patterns and climate conditions across all continents.

While taking break from shift and expecting to see nothing but water and maybe some clouds in either direction, I could not help but notice plastic trash littering the ocean. Where did all this garbage come from?

A piece of plastic seen off the side of the ship, the inspiration for this post. Photo by Anastasia Yanchilina.

We are currently working our way through the North Pacific Gyre, a region of the ocean known as the “Horse latitudes”. This area is characterized by calmer winds which could trap ships in the pioneer days of sailing and maritime voyaging for days or even weeks. The name “Horse latitudes” potentially originates from Spanish sailors who had to ditch their horses overboard during transit because of water shortages after their ship became becalmed in the middle of the ocean.

Today, instead of trapping ships, the gyre traps plastic, where it is fast becoming a potential hazard to sea life and navigation. A gyre is a region of the ocean where currents move in a circular formation. This water can draw objects inward. When garbage works its way into the gyre, it can easily get trapped. This is because the rotational currents surrounding the garbage keep it from working its way out.

Plastic trash is sourced from the overuse and improper disposal of plastics. Over time, debris captured in currents makes its way into the North Pacific Gyre and begins to accumulate. Plastics are not biodegradable, and only a portion of these plastics will begin the very slow process of degradation into the smaller pieces called “microplastics.”

The area in the North Pacific where plastic has been accumulating was named the Great Pacific Garbage Patch. This area is defined by high concentrations of plastic particles and other debris. The exact size of the patch is unknown since many of the particles are too small to see and are suspended at or just below the surface. Some estimates show a geographic coverage twice the size of France. It was first discovered in the late 1990’s by a racing boat Captain Charles Moore who was sailing between Hawaii to California, a route not too different than the one we are taking on the R/V Sikuliaq.

This discovery led Capt. Moore on the quest to quantify the amount of plastic in the North Pacific Gyre. Researchers have collected ~750,000 bits of microplastic in just 1 km² of the patch. This problem is not limited to the open ocean, the amount of microplastic in coastal waters has also increased since this is one place where the trash may originate.

In addition, similar patches also exist in the Western Pacific Gyre, Atlantic, and Indian Oceans created under similar ocean current conditions.

The plastic is not just unappealing to the eye but may cause insurmountable harm to marine mammals and turtles that mistake the plastic for some of their favorite food. Ingesting plastic can cause ruptured organs and introduces plastics into the food chain. Large marine mammals like whales that consume large volumes of water to filter out plankton may unknowingly be consuming many microplastics as well. However, marine mammals aren’t the only ones affected. Microplastics can be ingested by small marine organisms at the bottom of the food chain. This may eventually affect organisms higher up on the food chain and may even make it to the local dinner table.

Ships like the R/V Sikuliaq take certain precautions to ensure we do not contribute to the plastic problem. There are many national and international maritime laws that dictate waste management, air quality management and oil pollution protocols to protect the marine environment, air and water.

Finding a permanent solution to the plastic problem may take some time. However, we can begin to alleviate this problem by recycling, using more biodegradable products, and being conscious of daily garbage disposal.

There are over 100 million bacterial cells in every liter of seawater from the open ocean, but we know very little about these organisms. Most ocean bacteria behave differently from common bacteria, such as E. coli or Salmonella, which are the source of most scientific knowledge on bacteria. Sequencing DNA of bacteria in ocean water allows scientists to see which bacteria are present and to gain a glimpse into the potential behavior of these bacteria with relative ease.

However, DNA is only an indicator of potential bacterial activities. To learn what these bacteria actually do, including the chemical reactions they facilitate, scientists must use other methods. One of the best ways to study growth and metabolic processes of bacterial cells is to grow them in the laboratory.

Tom Lankiewicz works in one of Sikuliaq’s temperature controlled rooms to add bacterial cells into the growth medium he created from ALOHA station seawater. Photo by Joseph Niehaus.

My task onboard R/V Sikuliaq is to isolate some of these previously uncultivated bacterial cells from the ocean. After isolating these bacterial cells, I will grow them in my lab to better understand their growth rates, metabolisms, and ultimately their roles in nutrient cycling in the ocean.

Cultivating bacteria from the open ocean is a challenging task that, in many ways, can be thought of as a game of matching. To succeed, I must match the conditions these bacteria live in while in the ocean so I can ensure the cells I am trying to grow have everything they might need to survive and flourish. The best way to go about matching these ocean conditions is to grow the cells in a liquid, called a growth medium that was created using the actual seawater they came from.

To get seawater and bacterial cells from the same water mass in the ocean requires a two-step (and two research cruise) process that began two weeks ago. I first collected approximately 200 liters of seawater from Station ALOHA (A Long-term Oligotrophic Habitat Assessment), a study site about 100 kilometers north of the Hawaiian Island of Oahu. This study site is part of the Hawaii Ocean Time-series program, or HOT, which has been taking biological and chemical measurements at a monthly frequency since 1988 to develop better understanding of chemistry and microbiology in the open ocean. We used Sikuliaq’s CTD rosette to collect this water at specific depth intervals. Using a CTD and other instruments that attach to it, we can collect information on several important water characteristics including salinity (conductivity), temperature, and depth, as well as concentrations of oxygen, chlorophyll, and particles.

The HOT team graciously allowed me to participate in their research cruise from November 25^th through November 29^th on Sikuliaq. During this HOT cruise and onshore, with generous resources lent to me by the Center for Microbial Oceanography Research and Education (C-MORE) at the University of Hawaii, I filtered and sterilized my collected seawater in preparation for my cultivation effort and to create the growth medium. After filtration and sterilization, I added various food sources for bacteria to the growth medium and returned to Sikuliaq.

Upon re-boarding Sikuliaq, we returned immediately to Station ALOHA and I collected another 300 liters of seawater using the ship’s CTD rosette to start my new cultures of marine bacteria. I took several subsamples of water at Station ALOHA to measure concentrations of dissolved organic carbon, nutrients, and bacterial cells. Additionally, I took samples of bacterial DNA for sequencing. Between my samples and the information gathered from Sikuliaq’s instrumentation I should be able to gain a well-rounded picture of the microbial community that my new cultures were taken from.

Starting my new bacterial cultures was then simply a matter of diluting bacterial cells from my new seawater into the growth medium I had previously created. This process must be done in the cold and dark to match the temperature and light conditions that these cells normally live in. I spent lot of time in Sikuliaq’s walk-in refrigerator to keep my bacterial cultures cold and dark!

This is only the beginning of this cultivation effort. From here on out I will need to let these new cultures sit for more than a month before checking them to see if cells have grown in the medium. I have around 1200 new cultures to check. I will count the cells from each culture with an instrument called a flow cytometer, which uses a laser to count microscopic cells that have been stained with a fluorescent dye. After seeing which cultures have successfully grown, I will need to transfer them into new growth medium and allow them to continue to multiply before characterizing the cells using controlled experiments. I will also sequence the DNA of the new cultures to identify them and to further study their genomes.

I owe a big thank you to the entire crew of Sikuliaq, but especially our marine technicians Steve Hartz and Bern McKiernan, who have made my operations onboard run exceptionally smoothly. Thanks, All!

With his remarkable beard, positive attitude and colorful shirts, Bern McKiernan is a pleasure to sail with on the R/V Sikuliaq.

Bern has been working as a marine technician on the R/V Sikuliaq since operations started in 2014. A marine technician is the liaison between the ship’s crew and the scientists. He is responsible for facilitating the science party’s needs based on the ship capabilities. Bern makes sure the scientists can access the Sikuliaq network, data and instruments while out at sea. His familiarity with the ship and the crew is extremely helpful for the scientists on board.

Bern McKiernan, a marine technician for the R/V Sikuliaq, is hard at work on an icy day. Photo courtesy of Bern McKiernan.

Before working on the Sikuliaq, Bern spent a total of 12 years working for Columbia University. The last 6 of those years he spent working as a marine technician on the R/V Marcus Langseth, a research vessel operated by Columbia. The similarity between equipment on the Marcus Langseth and the Sikuliaq, as well as the opportunity to work on a brand new ship, made the opening with Sikuliaq very appealing.

Unlike Bern’s previous ship, the Sikuliaq is ice capable, so the ship is best at conducting scientific research in cold weather regions. Bern explained that working in a cold weather environment can be challenging.

One of the largest differences between working in the open ocean and in areas with ice is the sea state. Unlike the open ocean, areas with ice are relatively calm due to the dampening effect of the ice cover. As the ship approaches iced covered areas, waves are not able to grow so the sea state becomes calmer. Bern describes sailing in ice-covered regions “like riding on a train”, which is smoother than the open ocean.

Despite the usually calmer sailing, working at higher latitudes presents unique obstacles related to the cold temperatures. For scientists and the crew, the cold brings higher personal risk and requires proper clothing when working outside. Likewise, the instruments also face a risk of getting too cold and even freezing when working in the ice. Sometimes sea ice can close over the deployed underwater instruments. Deploying instruments on the ice is even more hazardous and great safety precautions need to be taken.

In addition to working in Alaska, Bern has sailed to several exotic locations including Tahiti, Easter Island and Antarctica over the past 25 years (working for the Navy and on research vessels). While out at sea, he has seen a fair amount of sea life including Mola mola, killer whales, sharks, and flying fish. Although he has traveled to many places, he finds some of the most picturesque locations to be near his home port in Alaska. In particular, he described sailing by the Alaska coast as “just beautiful”.

Bern was hired before the ship was launched, and is a plank owner of the ship. This means he will get a physical piece of the ship once it is retired. This honor is only granted to the original crew of a ship.

Jake Beam shows off his sediment core sample. Photo by Lauren Frisch.

I want to understand how microbes are relevant to the carbon cycle in energy-limited, deep-sea muds, and what they are eating down in the eternal darkness of the abyss.

After a few days steaming from Honolulu across the wide expanse that is the Pacific Ocean, we had the chance to grab a mud sample 3 miles below the sea surface in a region called the North Pacific Gyre.

This is no ordinary mud, however. Actually, it is quite extraordinary. At this location the rate at which new sediment is added to the mud is extremely slow. About 4 feet of new sediment is added every 1 million years. So we are looking at mud that has been around well before modern humans first appeared on Earth (not out of thin air, of course).

So this is what I’m thinking about as I hold these mud samples in my hand. Human hands have probably never touched them. It’s almost a feeling of reverence for this mud, it is really special.

Okay, this mud is really old, that’s cool, but what do we want to know about it in particular?

Prior work has shown that these muds accumulate new sediment at extremely slow rates. These slow rates tells us that there probably isn’t a lot of food (organic carbon) around for microbes to eat. This is also evident when we look at oxygen in these muds. Oxygen penetrates many feet below the seafloor (Røy et al., 2012)—this tells us that the microbes lack the food necessary to consume all the oxygen. This type of system is what is referred to as energy-limited or oligotrophic. Oligotrophic oceanic regions cover about 42 % of the seafloor, but only contain 10 % of the total amount of microbes in the seafloor (Kallmeyer et al., 2012). So the big question here is: how do microbes under extreme energy limitation make a living?

We sent this gravity core 3 miles below the surface to collect our sample. Photo by Jake Beam.

Microorganisms from the environment are notoriously difficult to grow in the laboratory, especially ones that come up from 3 miles below the sea surface and live in energy-limited mud. However, we have a way around this problem. We can sequence the genomes (DNA) of individual microbes and reconstruct their metabolisms to understand what they are actually eating.

There are several ways to accomplish this. First we can extract all the DNA from the mud and sequence it, then attempt to reconstruct all the DNA fragments to different populations of microbes. Reconstructing one microbe’s DNA is kind like putting together the pieces of a jigsaw puzzle. Attempting to reconstruct the DNA fragments from different microbial populations is more like mixing about a million different jigsaw puzzles together without the nice picture on the front of the box to help decode the correct answer. This can be problematic, but modern computers and programs are getting better every day at accomplishing this task.

Rhizons attached to the cores extract ancient water in the mud for analysis. Beam will use these water samples to see how much iron is in pore water. Photo by Jake Beam.

Single cell genomics is a clever way around trying to reconstruct microbial DNA. Like before, we start with millions of jigsaw puzzles, but this time the pieces stay in their individual boxes and don’t get mixed together. Individual microbial cells from the sample are sorted into tiny wells on a plate by a machine called a fluorescence-activated cell sorter. Next, we can break open the cells and sequence their individual DNA without mixing it with the DNA from other cells. This allows us to definitively link pieces of DNA to a specific microbe and a specific metabolic function, giving us insight into what the organism is eating and doing in its environment.

Although DNA provides us the potential for what a microbe can do, it doesn’t reveal any information about its activity in the environment. But it can lead us down the right road, instead of driving blindly in the dark.

Ben Urann and Thomas Kelly retrieve the gravity core as it comes out of the water. Photo by Jake Beam.

It shouldn’t be understated how awesome the Sikuliaq crew was during this operation, and how well everyone (science team included) came together to accomplish grabbing over 3 feet of mud from 3 miles below the sea. This may sound easy, but it is very difficult to accomplish. We don’t work in isolated islands, and it really showed during this recent coring operation. The science is great, but what’s really important are the people involved (crew and science team). I think the more you communicate with everyone on the ship, the more you come to appreciate the experience and the science.

Kallmeyer, J et al. (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. Proceeding of the National Academy of Sciences, 109, 16213-16216. doi: 10.1073/pnas.1203849109

Røy H et al. (2012) Aerobic Microbial Respiration in 86-Million-Year-Old Deep-Sea Red Clay. Science, 336, 992-995. doi:10.1126/science.1219424

We are starting our trip across the Pacific from Hawaii to San Diego aboard the R/V Sikuliaq [see-KOO-lee-auk]. Sikuliaq is an Inupiaq name meaning ‘young sea ice that is safe to walk on’. This is an appropriate name for this 261 foot, Polar Class 5 research vessel as it is built to break through about a meter of first year sea ice. The new research vessel is owned by the National Science Foundation and operated by the University of Alaska Fairbanks College of Fisheries and Ocean Sciences. It was launched in 2012 and began science operations in 2014. The ship has travelled around the world and conducts scientific surveys in the open seas, near shore and in single-year sea ice regions. The ship berths up to 26 scientists along with 20 crew and 2 marine technicians.

The R/V Sikuliaq can cut through about one meter of first year sea ice. Photo by Mark Teckenbrock.

A number of features on the Sikuliaq were designed to work at high latitudes where ice may be present. The ship has an ice knife in the front to help break through ice cover. The propulsion on this ship is specially designed for handling ice. The thrusters pull the ship through the water chewing and chipping the ice, like a margarita maker, before the ice can hit the more sensitive pod. This means the propellers are facing to the direction the vessel is moving. In addition, the Sikuliaq has broad shoulders and narrow waist to reduce ice resistance.

For our travels we won’t be utilizing the ice-cutting capabilities of this ship, but we will be using many of the pieces of equipment the Sikuliaq offers. The main tools we will use are an echosounding instrument to map the bottom of the ocean floor, seismic reflection to view the sediment and rock layers beneath the seafloor, and a gravity corer to collect seafloor sediments.

We will post more details about our specific projects when we reach our stations of interest. For now, we are enjoying getting to know the capabilities of the ship, and learning how to use the monitoring systems onboard.