Common Threads

Bacteria genes, microscale turbulence and ocean optics, pteropod species and distributions, salp physiology, anoxic basins, internal waves, iron complexes and oxidation, amphipods in oxygen minimum zones, nitrous oxide in water and sediments, pore water radon, phosphorites, viruses.

Over the past week the participants of NH1212 have gathered samples and data, discussed and linked these research areas. They have shared the latest ideas and methods, statistical packages, pictures, stories, lack of sleep and close quarters.  What are the common threads?

I can think of many.  First, the scientists aboard are accomplishing new research on diverse questions from a single research vessel.  We call these vessels multi-purpose for good reason.  This week R/V New Horizon has towed multiple opening and closing nets, hosted atmospheric gas sensors, pumped ocean surface water to filters and sensors, lowered novel current meters, triggered rosette samplers, cored the seafloor, and been a laboratory for complex sample processing and measurements.  Second, and more importantly all these activities concern the ocean, that 70% of our planet that has evolved life and climate, and continues to influence where we live, our atmosphere and weather, and what we eat. I’m excited we have many bright minds studying our oceans.  I will wager many in this group will work together again and find many of the hidden threads that are essential to the fabric of Earth’s ocean.

Mentor Clare- waxing poetic

The command center

In the main lab on the New Horizon is nested the brain center of deck operations. Several monitors hover above a desk spouting various information streams: ship location, speed, ETA, time to station, information on currents, the output from the CTD, the depth of the water based on the several sources, the amount of cable out on the various winches, and a monitor with cc tv on four separate deck cameras. There are other instruments here too, such as specialized computers for controlling the MOCNESS and any other specific equipment brought on for a given group. It is the job of the chief scientist, or the res tech, (or whomever’s experiment it happens to be at the time) to sit in this location to monitor and even control certain aspects of the operation. Importantly, there is an open line to the winch operator and bridge. Throughout a deployment, many commands are called out and affirmed. Questions are asked and answered. Occasionally, late into a shift, the odd joke might be told to keep everyone awake. The command center is thus the hub of all communication- between humans and machines, and humans and other humans- all over the ship.

Jen Jackson playing the wizard of the New Horizon command center

Catching Critters

On this trip we are using two types of nets to collected critters. One is called a Bongo net. This is actually two nets connected side by side in a metal frame. The connected round frames look like bongo drums. This design allows the nets to attach to the wire without it going through the middle of the net opening, which could damage organisms going into the net. Bongo nets are done in oblique tows, where the net is open on the way down and back up.

A salp collected with the bongo net

The other net we are using is a MOCNESS, known as the MOCNESS monster to the midnight to noon crew. It stands for Multiple Open Closing Net Environmental Sensing System. There are 9 nets stacked on top of one another in a rectangular frame. It is equipped with a temperature and salinity probe, and can have other probes such as oxygen sensors. There are electronics on the net that allow the person running it to use a computer program to close the nets, and get real time readings of information such as temperature and volume of water filtered. The bottom bar of one net is the top bar of the net below it, so when one net opens it is closing the net below it. The MOCNESS is deployed with the lowest net in the stack, net 0, open the entire way down in an oblique tow. Once the net reaches the deepest depth net 1 is open, which closes net 0. The MOCNESS then carries out discrete tows on the way up. An example tow is to send the net down to 400m, and open net 1, towing it at 400m, then the net is brought up to 350 meters and net 2 is open, net 3 is open at 300, net 4 at 250 meters etc, with the final net, net 9 remaining open as it is pulled out of the water. All this is done while paying careful attention to the speed of the boat, the speed of the net coming up, the angle of the net and a few other variables to ensure it is fishing effectively and there is no risk of blowing out one of the nets. The two resident technicians on board, Meghan and Rob have done a wonderful job teaching us how to “fly” the MOCNESS.

The MOCNESS net being recovered. The bars on the bottom of the square are the stacked net bars, with the top net open as it comes out of the water.

Each net has a plastic cod end that everything caught washes into. When we recover the MOCNESS we put each cod end in a labeled bucket and sort them quickly, then put them in the cold room at 8C to ensure the organisms are still in good condition. The nets are small enough so larger organisms are able to avoid it. The critters we are fishing for are zooplankton. Some of the zooplankton we caught so far includes lots of krill, copepods, salps, hatchling squid and others.

Lloyd and Stephanie sorting through a MOCNESS code end, which includes a large pyrosome (midwater tunicate)

Post and pictures by Leanne Elder

The 1980s called. They want their modem back.

Instant communication could, for all practical purposes, be described as the defining characteristic of the early 21st Century. We live in an age where we can access scientific literature from all over the world at the push of a button, keep up with the current intellectual debates via twitter and watch an army of cats playing a plethora of pianos on YouTube.  As a direct consequence of high-throughput data transfer, the rate of scientific discovery has accelerated to unprecedented levels via global collaborations involving large datasets, teleconferencing, email and shared manuscript editing. Of course, the cost of instant communication is that everyone expects you to communicate instantly. Not so long ago, going on a cruise provided the scientist with an opportunity to ignore the expanding inbox and enjoy uninterrupted contemplation (unless of course the seas are unkind. It’s hard to read a statistics paper whilst hanging over a railing enjoying your dinner in reverse).

Nowadays, recognizing that digital communication is at the heart of all science, satellite networks such as HiSeasNet provide research vessels with internet access even in the remotest parts of the ocean. You can now find yourself in the middle of an ocean gyre, hundreds of miles off shore fielding email requests from collaborators to comment on manuscripts or re-run computational analyses. But, the Land Internet we know and love is fast because information can be beamed at the speed of light down fibre-optic cables. Beaming your information into space and back is a different matter and transfer speeds less than 64-512kbs are common. The last time most people dealt with an internet running at such speed, Vanilla Ice was still growing his ridiculous hair and MC Hammer had just started making his extraordinary trousers.

As a newbie seagoing scientist, initial seasickness is soon replaced by data sickness, as you come to terms with the idea that you can’t just grab a reference or download a bunch of genes for multiple sequence alignment. After a while, clarity sets in and you realize that the fact that you can communicate electronically at all when there is no land in sight is a testament to just how awesome technology is.

There’s little doubt that globally availability of the high bandwidth we have  become accustomed to is both necessary and imminent. Sending people to sea is expensive and the increasing use of automated buoys, underwater vehicles and remote sensors shows a long-term move towards unmanned stations and devices beaming back information to scientists on shore. Once they figure out how to build automated DNA sequencers that can survive a storm, the amount of data being transmitted will increase exponentially and will undoubtedly create sufficient adaptive pressure to implement newer and faster communication at sea. Until such time, I am going to embrace the digital bottleneck and stand on the deck and look for charismatic megafauna while this post uploads.

Filtering in the wet lab

I know you will have read the scientist’s statements by now (wink wink, nudge nudge), and thus be completely up to date on what we are all trying to do and how. Ben Temperton and I are utilizing the same samples to accomplish different goals. The bulk of our work from metagenomics and single-cell genomics will come much later, after we sequence the DNA from our filters and our isolated cells. Our ship time is thankfully pretty straightforward, by design. While the ship has traveled all around the Southern California bight to serve the varied needs of the science team, we are taking samples specifically along a coastal to deep-water transect using sites from the CalCOFI surveys to improve our metadata.

Some of the initial sketches for our cruise plan

Our ideas for this sampling opportunity started in the same way as many, literally sketched out on a piece of paper, which turned into a proposal, and has landed us here on the ship, carrying out the work. An amazing opportunity, to be sure. Our sampling plan is simple: take several discrete water samples using the CTD from each site, filter some of the water for later DNA extraction and metagenomic sequencing, concentrate cells from the remaining water for later cell-sorting and single-cell genome amplification/sequencing. Because we’re filtering large volumes of water, we’re in the wet lab. Most ships have one- a place usually near a deck where water can get spilled and it’s not the end of the world. Ours is set up for use with 142mm filter units and a small tangental flow filtration system. After filtering, everything goes in a liquid N2 dewar to keep it cold. Simple enough. For now. Post-sequencing, the workload explodes.

The New Horizon wet lab, CTD outside on the starboard deck

Prayers, Rituals, and Superstitions

Sediment core sectioning by Melissa Madison and Ben Temperton on deck of the New Horizon.

No matter how many times you throw an instrument overboard, there is always a chance that it’s just not going to work.  Whether it’s ripping a hole in a net, a misfire on a bottle trigger, or any of hundreds of other scenarios, there are many ways in which oceanographers try to deal with these problems.

Typically, scientists will first try logic and reason to determine what might have happened to make the instrument malfunction beneath 1000 meters of water and suggest a feasible “fix” for the possible problem.  Sometimes this “fix” works wonders and the instrument responds, but many times the “fix” just doesn’t seem to work.  In all cases we can always come up with ideas for new gadgets or toys that we just know will fix all our future worries, but alas we are restricted to items that we have on board.  In terms of the multicorer (my personal flavor of instrument used for sampling ocean sediments) we try adjusting impact speeds, line settling times, adding or subtracting weights from the frame (etc..), but sometimes no matter what we do things just don’t always go our way and samples are just unattainable.

So as logical, brilliant scientists that we are we eventually resort to the old adage of prayers, rituals, or superstitions.  When all hope seems lost and we are in desperate need of a success and have no further ideas to better our sampling events sometimes we just have to send up a prayer, create some good luck ritual, or wear a certain piece of clothing to tempt fortune in our favor.  On this particular voyage, after 22 casts of our trusty multicorer, only 7 have come up successfully and we have tried every fix we can come up with to improve the success of our coring attempts.  Therefore, we have started to look to other powers that be to help us collect our samples.  For this sleep deprived crew we have developed our own multicore dance to go along with every cast and recovery for the teams on deck to perform. Does this ritual work??? Well on three casts accompanied by this new 2:30 am choreography, we still only had one successfully recovered set of cores.  So not any improvement yet, but for the sediment group we have here on the Horizon, we still have hope of better coring rates in our upcoming stations.

Dropping the bucket…

On this research cruise, we are deploying many types of instrumentation to collect samples and data. The most frequently deployed instrument in known as the CTD – an acronym that stands for conductivity, temperature, and depth. These are the primary ocean parameters measured by the device – but it can measure other properties as well, such as chlorophyll concentration. In addition to taking measurements of the ocean water as it is lowered through the water column, the CTD is carried on a frame that also houses large bottles (known as Niskin bottles) that are used for the collection of seawater. These bottles can be  triggered from the ship to collect water from specific depths. The water collected on this cruise is used by cruise participants to study various biological and chemical properties of the water column. In the photo below, the science party, the crew, and the restech work together to deploy one of the day’s many CTD casts.


Science gets gritty…

…or muddy, or sandy, or really any sort of dirty if you’re lucky. By lucky, I mean that the multi-corer recovers usable cores for sampling. This sampling can include sectioning, profiling, squeezing, and pressing. Whatever you’re interested in, it’s a pretty safe bet that you won’t end up being clean.
The first few coring casts we did came up with great cores! All four tubes with sediment and the ever important sediment-water interface, and on the first try to boot! It would seem that our luck is on empty (pun intended), as many of our more recent casts have been unsuccessful for a variety of reasons. Yesterday the sediment was too soft and we had no interface; today the sediment was too sandy and we would lose the core on the way back to the surface.
Thankfully, with the help of good research techs and dedicated winch drivers, usable cores were taken from almost every site of interest. I spent most of yesterday (Monday) sampling sediment cores, and maybe part of it playing in them. I section at least two cores from each station for microbial community assessment and porosity. I am interested in identifying pollutant-resistance genes that I may be able to link to historical pollution data. I also squeezed a third from one station for porewater. I stripped the porewater for radon and saved it for nutrient analyses. As you can see, I did not end up clean- but that’s where the fun is. (Photos will be up soon.)

-Shelby LaBuhn


The whole science party was out on deck to watch as we left port Saturday morning, but for many of us, excitement changed to dismay as soon as we got past Point Loma into open water. As we had learned in our pre-cruise workshop, the New Horizon’s design is top-heavy; even with concrete ballast below, whenever the seas are at all rough, the ship still tends to roll. And roll. And roll. With predictable results. Clare Reimers, one of our mentors on this cruise, has an iron stomach, but just about everyone else in the science party got walloped by seasickness for a few hours. A few of us had trouble for longer; I started to feel human again about 18 hours after we got underway, when I could keep water down for the first time, and I was relieved to be up and around again in time to collect and process my samples early Sunday afternoon.

At least it was a pretty day

We’ve heard a lot on the ship about the importance of safety in all our operations, both in the lab and out on deck, but I got a new perspective on the commitment to safety when I was sick. If you need to stand at the rail, you’ve got to have a buddy the whole time; goodness only knows how much work I kept our restech Robb from getting done on Saturday, because I was at the rail for hours. It’s not just concern about man-overboard situations, either; the restechs, the co-chief scientists, and the captain all kept tabs on me, making sure I had enough water to drink and enough Saltines to—well, not to eat, but to imagine someday being able to eat.

By now, the haze of seasickness has long since been replaced for most of the science party by the haze of long and unpredictable hours. As Cameron mentioned, we’re divided into two 12-hour watches. But we also all have samples coming in from a number of stations; nearly all our samples demand immediate attention, often requiring many hours to process and log, and nothing says we’ll reach your station during your watch. So the days blur together, and our progress through time has already come to seem much less relevant than our progress through the cruise plan.

Working the night watch

Deploying the bongo nets, Dave Checkley looks on.

It is not unusual for oceanographic research cruises to have a watch schedule. This cruise is no exception. We have two watches, noon to midnight and midnight to noon. Yours truly, Cameron Thrash, is on the night watch. It’s a crazy thing to try and adapt to. Yesterday, being the first day, I didn’t sleep much. We started with CTD casts, multi-corer casts, bongo net casts, MOCNESS casts and just went all through the night (more on these later). It was a productive time. I got off watch at noon, took a shower, did some laundry, and promptly slept for several hours. I got up at 9pm for what is now my morning before work! Ben saved me a dinner plate of lamb and prime rib. Breakfast of champions. Now, we’re at it again, working under the stars. There are several good things about working the night watch- you get to have coffee all night long, and the sunrises are gorgeous.

The moon, Venus, and CTD at sunrise. Catalina Island in the background