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