17 August 2023: Processing Samples
The Thompson is one of a fleet of four research vessels, which are owned by the US Navy and under charter to the Woods Hole Ocean Institute (WHOI), the Scripps Institute, the University of Washington, and NOAA. All are equipped with science labs containing fume hoods, cold rooms and freezers at -80⁰C so samples can be processed live onboard.
My purpose here, alongside Dr. Rika Anderson and Max Borden, is to collect and process samples of hot fluid emanating from hydrothermal vents at Axial Caldera. Once on-shore, these will be analyzed to characterize the unusual microbial and viral communities that live there.
The ocean is full of microscopic bacteria and archaea, so it’s important for us to know which strains thrive in hydrothermal vents and which have drifted there on the back of ocean currents. To distinguish them apart, we collect a background sample of plain seawater from a similar depth at a different location. In our case, this depth is around 1,500 m below the surface. Temperatures down here are cold, just a couple of degrees warmer than the kitchen fridge, so when our bottle of water returns to the ship, it’s cool to the touch with beads of water condensing on the outside like raindrops.
Our first port of call is to decant exactly 3.92 ml of this deep-sea fluid into two cryovials, ready to fix with glutaraldehyde from the fridge in the lab. Wearing gloves, we carefully pipette the samples and their fixing agents into their containers, seal them shut inside parafilm and whirlpack bags and place them in the ship’s chest freezer which sits at a chilly -80⁰C.
Similar temperatures were used to store and transport some of the coronavirus vaccines. Like our samples, they contain viruses which need to be cold to stay preserved. Bacteria, just like people, can be infected and killed by viruses, but viruses also do useful things like transferring genes from one strain to another or keeping the population of an overpowering strain under control, so it doesn’t outnumber the others.
For many years, people weren’t aware of the diversity of bacterial viruses because they are difficult to see and hard to sequence. Advances in sequencing technology of the past twenty years have vastly improved this, enabling us to find and sequence the DNA of even small populations of viruses hidden amongst swathes of bacteria and archaea. They still need a little help though. To capture the rarest viruses of all, we remove all the micro-organisms from litres of water using sterilized filters and precipitate out the remaining viruses using iron chloride. What’s left after this process is a delicate piece of filter paper covered in a layer of virus-filled rusty orange “dust”. Our precious cargo from a 12-day research expedition in the Pacific Ocean.
15 August 2023: First Day at Sea
It’s 06:55 am in the NorthEast Pacific Ocean. The Sun has risen, and all that remains of the night is a pale orange hue in the skyline. A few people are tucked away, feeling queasy due to the rhythmic rocking of the ocean below us. Word on the street (or should I say boat!) is that we’ll get used to it within a day or two, but until then we’ll take our travel sickness pills and munch lightly on crackers, hoping we won’t become one of the poor souls that has to sleep next to a bucket.
Jason the remotely operated vehicle (ROV) is sitting neatly on deck. It’s already dove two or three times since we set sail from Newport twenty hours ago. It is one of the oldest ROVs in the US, having been built in the 1980s, around the same time as ROPOS, the Canadian ROV. Both have two large manipulator arms which are capable of crushing with hundreds of pounds worth of strength. Jason used them yesterday for one of the most delicate of jobs – cleaning a camera on the seabed which had been encrusted with algae! The waters here are productive, so when Jason submerges underwater, its robotic eyes are filled with a haze of green. Inside this haze are a wealth of phytoplankton: Organisms like diatoms, cyanobacteria and coccolithophores which bloom during the summer months, creating food for herbivorous zooplankton like copepods and crab larvae.
Cal and I just returned from our first night watch, where we log events that happen during Jason’s dives. They vary from things like “Entering water” and “Touching Bottom” to taking ultra-high-definition videos of the wildlife. During the last dive, which lasted from 4 am to around 6:30 am, we watched as Jason descended 500m to land on the seafloor. A large shoal of tiny silver fish seemed to follow Jason down to the bottom as he descended. Their bodies shimmered as they passed through. Then as we reached the bottom, larger fish appeared. Just like a scuba diver landing on a sandy seafloor, Jason kicked up a cloud of silt which obscured most of what we saw on camera in a yellowish-brown haze until the operators moved Jason sideways and away. How strange Jason must seem to the creatures that swim by, with his bright lights illuminating the pitch-black, and the gentle rhythm of the thrusters which propel him forwards and backwards. The ocean beneath us is a weird and wonderful place.
14 August 2023
Today, the ship sets sail out of Newport, Oregon.
We have been waiting in the dock for a day or so due to high winds which make
it difficult to deploy ROV Jason. They look better now, but the chief science
officer has had to change plans slightly to avoid the worst of the weather.
This means we won’t be heading straight out to Axial Seamount which is ~200
miles offshore and a 24-hour journey. Instead, we’ll go to a site closer to
shore to maintain the cabled array. It’s probably going to be a bumpy ride!