One of the many research subjects aboard the R/V Roger Revelle and one of the many components of CCE-LTER is the study of zooplankton. One of the focuses of the Décima lab out of Scripps Institute of Oceanography is the study of mesozooplankton and more specifically mesozooplankton grazing.

What are plankton and what are zooplankton and mesozooplankton?

Plankton are small, even microscopic, organisms that drift in ocean currents. Zooplankton, zoo meaning animal and plankton meaning drifter, are the small animals in the ocean that graze on phytoplankton (essentially small photosynthetic plants, algae, that are the primary producers of the pelagic food web). Mesozooplankton are a specific size class of zooplankton, ranging from 0.2 mm to 20 mm in size.

Why study zooplankton?

The reason that zooplankton are studied is to better understand the flow of energy throughout the pelagic foodweb from phytoplankton, the primary producers, to zooplankton, to fish (such as sardines), to other marine megafauna such as dolphins and whales, and ultimately to us. Understanding the energy flow throughout the pelagic food web by studying the grazing rates and feeding habits of mesozooplankton allows for a better understanding of energy flow to larger organisms, such as fish, that we use as a food source. A better understanding of energy flow through the pelagic food web through studying mesozooplankton helps inform fisheries management practices.

A morning with the Bongo

I usually wake up around 6:30 AM to shower, brush my teeth, and get dressed before meeting the rest of the zooplankton day team in the wet lab around 7:00 AM. From 7:00-7:30, we prepare labels, organize our buckets, and prepare the Bongo Net for sampling. Bongo isn’t an acronym or anything like that—there are two circular nets attached to a frame, making the entire net look like a bongo. We then go to breakfast around 7:30 and meet back in the lab between 8:00 and 8:15 AM. The first Bongo tow of the day happens anywhere between 9:00 AM and 11:00 AM, depending on what the ship’s schedule is for the day and what other operations need to take place. We always have to be ready to put our nets in the water at any time just in case a time slot opens up. We put the Bongo into the water for roughly thirty minutes, descending it to a depth of around 200 meters, towing it for thirty seconds, and then bringing it back up to the surface. The Bongo is typically lowered at thirty meters per minute and raised back up at twenty meters per minute. Once the Bongo is back on board, we process each side of the net, starting with the port (left) side and then the starboard (right) side. We rinse down the nets to collect all of the zooplankton into the codends (containers that collect zooplankton from the nets), transfer the contents of the codends into buckets, and bring them back into the wet lab for processing. When collecting the port side sample, we add a can of seltzer water to the sample to anesthetize the zooplankton so they don’t evacuate their gut content which is used for gut fluorescence processing.

The sample collected from the port side of the net is first poured into the Folsom splitter, an acrylic wheel with an opening at the top and a divider that runs through the middle that splits the sample into two 50% portions. Only the port side sample is split. The entirety of the starboard sample is transferred to a jar and preserved in formalin for later taxonomic identification of the organisms. Once the port sample is in the splitter, we homogenize the sample by mixing it with a ruler before pouring the now-split samples into two basins, making two 50% samples. One of these samples is then placed into a separate bucket and the other is split once more to create two 25% pieces of the original sample. One of these 25% samples is added to the 50% in the bucket to create a 75% sample, and the other 25% sample is transferred to the “gut cup,” where the water is filtered from the sample and the zooplankton are then preserved in a dewar containing liquid nitrogen for later analysis.

The now 75% sample is added again to the splitter, breaking the sample into two 37.5% samples. Both of these 37.5% splits are size fractioned through a series of five decreasing sized (increasing fineness) sieves: >5mm, 2-5mm, 1-2mm, 0.5-1mm, and 0.2-0.5mm to sort through different sized zooplankton within the sample. Each size range is then vacuum filtered over a piece of 202-micron mesh, placed into Petri dishes, labeled, and preserved for later analysis. One of the 37.5% splits is used for gut fluorescence analysis, and the other is used for biomass. The gut fluorescence samples are stored in a dewar containing liquid nitrogen, and the biomass samples are stored in a -80℉ freezer.

The gut fluorescence analysis analyzes the gut content of the zooplankton to calculate the organisms’ grazing rates. This analysis is used to better understand how energy flows from the primary producers throughout the rest of the food web and up different trophic levels, which, again, is useful for fisheries management and understanding how zooplankton communities affect marine megafauna on higher trophic levels. The gut fluorescence samples are also used for DNA analysis to catalog which zooplankton species are present at discreet depths in the water column and to characterize the zooplankton community composition.

The biomass samples are used for determining relative grazing rates for a certain size category of zooplankton and are also used to estimate the relative total biomass of zooplankton for a discreet depth range. For example, biomass samples collected from the Bongo tow would be representative of a depth range of 0-200 meters.

On the left is the Folsom splitter, in the middle are the vacuum pumps, and to the left is the Bongo net.
On the left is the Folsom splitter, in the middle are the vacuum pumps, and to the left is the Bongo net.

An afternoon with the MOCNESS

After the Bongo is fully processed and the nets have been washed down, we usually go to lunch around 11:30 AM, after which we “cock the MOC.” (we’re trying to make “Professional MOC Cocker” t-shirts). When it’s time to tow the MOCNESS (Multiple Opening and Closing Net Environmental Sensing System), we lower the net into the water using two tag liners (people who hold onto ropes wrapped around the MOCNESS to keep it stable and ensure it doesn’t get twisted up or enter the water at the wrong angle), the A-Frame, and the help of a research technician and a winch operator. Depending on the water depth of where we’re located within the California Current, the MOCNESS is towed at a depth of anywhere between 400m and 1100m, which can take anywhere from one-and-a-half to two-and-a-half hours. During the downtime when the net is being towed, we label all of our Petri dishes and our internal and external labels for formalin and ethanol preservations. We also fill our ten buckets a third of the way with seawater and store them in the -40℉ freezer.

Once we retrieve the MOCNESS we rinse the codends down, take them off the nets, and transfer them to the chilled water so that the sample within the codend will not start to rot and decay while it’s waiting to be split. Similar to the Bongo net, we end up splitting the MOCNESS samples, but 50% of the sample is preserved in formalin, 25% is preserved in ethanol, and 25% is size fractionated and used for biomass. The size fractioning always takes the longest, as we have to go through the sieves by hand and pick out all of the plankton that get stuck in the mesh. This can be particularly difficult with transparent-gelatinous zooplankton.

The samples we preserve in ethanol are used for DNA analysis for a similar purpose as the DNA analysis conducted with the gut fluorescence samples: to catalog which species of zooplankton are present at each depth. The samples preserved in formalin are again used for taxonomy and identifying which organisms are present.

Wet lab processing of a MOCNESS sample. In the foreground, you can see the use of the Folsom splitter to split zooplankton samples. To the right, you can see the fractioning and vacuum filtration process for biomass samples. In the background, you can see ethanol sample preservation and label writing. Formalin preservation occurs in the hangar outside of the wet lab.

End of cruise

A month at sea has come and gone. At times it has felt like I’ve been out here for two months, and at others like I’ve only been out here for a day. Maybe a week. The point is, time seems to fluctuate—sometimes it goes real slow out here, and sometimes it seems like it’s going too fast. Right now it feels like the latter. It’s currently the evening of Sunday, March 17, 2024, and we’re due to reach port in San Diego tomorrow evening around 8:00 PM. At this point, the Zooplankton team is done sampling and now all that’s left is to pack up all of our lab equipment before we begin demobilization on Tuesday the 19th. I’m sitting in the hangar watching the winch for our final DPI (deep plankton imager) deployment of the cruise to make sure the tension in the cable doesn’t get too high. The deployment is going to last around twelve hours, but thankfully we’re taking shifts so I’ll only be out here for two hours or so. I’ve got my laptop, a portable radio to communicate with the lab, my phone, a book, and a speaker.

I think the reason time’s gone so fast at points is because of the people we have on the Zooplankton team. With a month at sea, it’s almost impossible not to get to know the people you’re on the boat with, especially those you share twelve-hour shifts with. There’s a lot of work that we have to get done, but there are also moments of calm where we’ve played cards and board games, listened to music, watched movies, shared meals, talked, and gotten to know each other. I’ve been told several times that without a team of volunteers, a lot of the zooplankton samples wouldn’t be able to be collected or processed and I think that if our team was any different, the feeling of the whole cruise would have changed. As I reflect on my whole experience at sea, I’m grateful for this opportunity to participate in CCE-LTER, for everyone I’ve met aboard the R/V Revelle, and I’m incredibly grateful for my lab team. We’re all a part of the Zoop Soup.

Left to right, top to bottom: Jameson Morrin, Sam Culver, Annie Effinger, Ali Appelgate, Jason DeFay, Moira Décima, Marco Moriel, Grace Cawley, and Caro Buck.

Abroad the R/V Revelle

It’s confusing to find your way around at first, but it’s easy to grow familiar with the layout. All of the hallways look the same, but you can tell what level you’re on by the color of the floors. Above the First Platform is the Main Deck where the main lab, computer lab, wet lab, electronics shops, and cardio gym are indoors. Out on the deck is where the bulk of the ship’s operations occur, facilitated by the fantastic crew, and the amazing research technicians of the Revelle, Amber and Andrew, in coordination with the scientists on board. This is where equipment such as the MOCNESS and the DPI (deep plankton imager)  deploy from the stern. Equipment like the bongo net (two large circular nets connected via a frame) and the CTD (conductivity, temperature, and depth—-reads salinity and temperature-depth profiles) are deployed from the starboard side of the ship. There are always operations happening on the main deck, so there’s always something to watch, see, help with, or people to talk to about their projects and research.

Upper left is the Main Lab, upper right is the Computer Lab, bottom left is the Wet Lab, and bottom right is the Cardio Gym.

Above the Main Deck is the First Deck where the ship’s galley/cafeteria, library, lounge, weights gym, and crew staterooms are. In the galley, three meals are served each day by the phenomenal chefs—I may eat better meals on board than I do at home—Jim and Richard, who make sure no one goes hungry. Some of the highlights have been flank steak, pork loin, jambalaya with red beans and rice, tuna poke, cornbread, fried okra, apple fritters, tiramisu, and fresh bread, to name a few. Outside of the meals, coffee and leftovers are available 24/7 for the crew and scientists working around the clock. The Second Deck houses more staterooms, winch controls, the crane, the ship’s hospital, and liferafts. The Third Deck holds the captain’s stateroom, the chief scientist’s stateroom, and more scientific staterooms. And finally, the Fourth Deck is the bridge.

Upper left is the Galley, upper right is the Library, lower left is the Lounge, and upper right is the Weights Gym.
Different views from the bridge of the Revelle. The bridge is the place where the ship is navigated, maneuvered, and managed.

Waking up every day to the rocking of the ship can take a bit of an adjustment period, especially in rougher waters, but there’s no better way to fall asleep than the sound and shaking of the sea and no better view to take in than being on the main deck. I sleep on the top bunk in a stateroom on the first platform, below the water line, hearing the sloshing of the sea and being rocked to sleep each night.

It’s easy to lose track of time while aboard. Most days I have to check my phone to know what day of the week it is, let alone the date. You’re always busy and on a routine that stays largely the same, so the finer details, like what day it is, start to fade away a bit. So far, we haven’t encountered much of any rough waters except for maybe the day after we left port. That was the only time I was acutely aware of just how much the boat was moving. Typically I don’t get seasick, but that was the one day where I had to take some meclizine. I was sitting up in the galley, trying to eat breakfast, and I could just feel waves of nausea washing over me. I figure it’s better to have something in the stomach than nothing when feeling sick, so I finished my meal anyway before making my way to my room to lay down for a bit. If you’re going out on a cruise and aren’t sure how you’ll deal with motion sickness, make sure you bring either meclizine or dramamine and be sure to eat and stay hydrated. If you end up puking, it’s better that you at least have something in your stomach when you do.

In the downtime between operations or when you aren’t supposed to be either working or available for your shift—-I work the day shift for my lab, 7 AM-7 PM—-there are always people to spend time with, or at least be near if you want to be around people but don’t want to socialize, in the library and lounge on board. People are either playing card games like cribbage (which everyone knows how to play) or board games like Seven Wonders or Settlers of Catan. The crew also plays poker every other night on board, but I have no idea how to play and don’t want to lose any money. I spend my free time either sleeping, reading, playing Solitaire, playing Bananagrams, or playing cribbage (I haven’t won once).

Day shift of the Zooplankton Team playing Settlers of Catan. Right to left: Annie Effinger, Jameson Morrin, Ali Appelgate, and Marco Moriel.

The lounge has a communal guitar that I used to play in my downtime, but I somehow broke the E-string (sorry Gomez) and couldn’t fix the thing after a couple of hours of trying. There are no replacements on board, so on top of learning new zooplankton processing methods and how to deploy a range of sampling equipment, I may end up having to learn to play the ukulele, or maybe the spoons.

Being out on the ocean is beautiful. There are a million ways you could describe the experience of being at sea more eloquently, but there’s no other way to put it than the fact that it’s simply breathtaking. Any cliche that can be and has been used to encapsulate it is true and false at the same time. It’s gorgeous and it’s terrifying. It’s treacherous and it’s comfortable. It’s lonely and it’s full of community.

First time on board

I boarded the R/V Roger Revelle around 8:00 PM on Friday the Sixteenth and quickly got lost looking for my room aboard the 273-foot research vessel. I spent nearly twenty minutes wandering the upper decks looking for an entrance into the ship, only to be guided inside after another science crew member arrived and showed me the way. Most of the scientists and volunteers aboard sleep in the staterooms on the First Platform, the floor below the main deck, or in staterooms on the First Deck. The staterooms are comfortable and built for two people with a bunk bed in each room, a desk, storage cabinets for personal belongings, a sink and mirror, and a shared bathroom, equipped with a toilet, shower (with surprisingly good water pressure), and heating lamp between two adjoining staterooms. All the cabinets and drawers on the ship come with a lock or a latch to ensure nothing opens and then slams closed due to the rocking sea.

First Day

My first day aboard the R/V Revelle was hectic and disorienting. I woke in complete darkness and found I was late for a safety meeting. I had to remember my assigned number to make sure everyone was accounted for. I’m number fifty-four. Breakfast was right after and I had no idea where the galley was, so I just followed the herd of people going towards the galley to find my way there. They served omelets, hashbrowns, pancakes, bacon and sausage, and fresh fruit and yogurt. And lots of coffee. Afterward, the Zooplankton lab team, led by Dr. Moira Decima, then did a practice Bongo tow off the starboard side of the ship. The samples collected from the port side of the net are brought into the wet lab for processing. The port side sample is split into three portions. One portion is transferred to the “gut cup,” which is then vacuum filtered and preserved in a dewar containing liquid nitrogen for later analysis. The other two portions are then size fractionated over a series of five sieves with decreasing mesh sizes and vacuum filtered for biomass and gut fluorescent analyses. The biomass samples are then preserved in a -80℃ freezer and the gut fluorescent samples are stored in a dewar containing liquid nitrogen. Each sieve has a corresponding vacuum pump to collect the sample onto a fine mesh filter. The entirety of the starboard sample is preserved in a jar containing a sodium tetraborate buffered 5% formalin solution.

We then all met after lunch in the ship’s library to go over the labeling protocol. Afterward, we did a practice deployment of the MOCNESS: the Multiple Open Closing Net and Environmental Sensing System. Before the net goes into the water, we first have to prepare the net, what we call “cocking the moc,” which involves cocking each of the ten nets of the MOCNESS, a piece of equipment containing ten nets that can be closed while in the water column), by bringing each bar to the top of the rig and latching each metal-wire-trigger into the motor mechanism, making sure that none of the wires are crossed and everything is in its proper order. We then attach the cod ends, where the sample collects, to the bottom of the nets and secure the latches with electrical tape. We bring the net in, take off the cod ends, store them in cooled water, and get to processing the samples, taking anywhere from three to five hours. Half of each net is preserved in formalin, a quarter is preserved in ethanol, and a quarter is size fractioned and kept in Petri dishes for biomass.

When retrieving the MOCNESS we have to scramble to preserve the samples contained in the cod ends in refrigerated buckets and then transfer the samples to a -20℃ freezer. Each bucket corresponds to one of the cod ends of each of the ten nets, each of which can sample a discreet depth of the water column. We then bring the samples back to the wet lab for processing.

We ended the day by having dinner in the galley, served from five to 6:00 PM every day, and going about to different parts of the ship. I ended up reading some of All the Pretty Horses by Cormac McCarthy before heading back to my stateroom to get some sleep—a good contrast to life on the water.

On Feb. 17 CCE will set sail on the R.V. Revelle for a month-long research cruise investigating the processes driving long-term change in the California Current coastal upwelling biome.  Our team of scientists, students, and volunteers will focus on elucidating the impacts of multiple stressors on open-ocean ecosystems during marine heatwave disturbances.  We will also use cutting edge optical imaging approaches to investigate relationships between plankton taxa at high spatial resolution.  This research is built upon, and continues, long-term efforts to quantify the rates underlying long-term change in biogeochemical properties and marine populations in the CCE.