Counting Copepod Eggs

A Calanus pacificus copepod (top right) escapes the grasp of a large ctenophore (photo credit: Mike Stukel)

One of the experiments I am working on during our cruise is measuring the reproductive health of a copepod species, Calanus pacificus, which is one of the dominant zooplankton in our local California Current waters. Copepods are small crustacean zooplankton, which means they have segmented bodies that undergo molting like crabs and lobsters do. They are also very numerous in the ocean (over 13,000 species have been identified!) and generally dominate zooplankton communities.

Calanus pacificus eggs (small white dots).

One overarching question of our CCE-LTER research is how much zooplankton populations change from year to year and between different areas in the California Current (in this case, nearshore newly-upwelled water versus older water farther offshore). One way to quantify zooplankton in the ocean is to measure their biomass, or the total amounts of various species within a sample. Our Bongo and MOCNESS net tows help answer this. A second way to determine zooplankton health and viability is to measure reproductive success. To answer this, I am measuring egg production rates in Calanus pacificus, or the number of eggs that a female copepod produces in a 24 hour period. I also count how many of those eggs successfully hatch into copepod nauplii (larvae).

Egg production rate experiments use a special Bongo net with sealed collecting jars to keep animals alive as we haul them up. We then sort through the samples for mature female Calanus pacificus, placing them in dishes of seawater and incubating them in a cool, dark chamber overnight to mimic in situ ocean conditions. I check the dishes the next day to see if the females have laid eggs, and if they have I incubate the eggs for another day to see if they hatch.

Calanus pacificus nauplii (the newly-hatched stage).

Copepod egg production during this cruise has been quite interesting, likely reflecting the influence of the filament and its evolution over time. During the first two cycles of the cruise (close to shore, in the newly-upwelled filament waters), the copepods were cranking out large numbers of eggs (including one record high of 109!), sometimes laying two clutches a day. The third cycle showed much more variability, perhaps due to older, dying phytoplankton (food) availability, and the fourth cycle showed healthy female copepods but almost zero egg-laying. Further analysis, including quantifying how many nauplii hatched from the eggs, will tell us even more about how reproductively successful female copepods are this year and in relation to the filament.

We have officially ended Cycle 4 (our final cycle of the cruise) and are on to a three-day survey of the filament using our trusty SeaSoar. It will be interesting to see how the filament has evolved since we first surveyed it three weeks ago. While we’re at it, a few more days of sunshine and blue water!

Mark educates about copepods to a microscoping crowd in the main lab


Posted by: Laura Lilly, SIO

Sunshine and SpaceX Satellites

One of the best parts of being at sea is having a clear horizon – especially when the sun finally comes out after a week of clouds! We woke this morning (or were in the middle of working, in some people’s cases) to a beautiful clear sunrise. The whole day has been filled with blue on blue, giving us a boost of energy to finish our cruise out strong.

The SpaceX Iridium satellite launches into the blue (top right)

Clear skies were perfect timing for something else: a front-row view of the SpaceX Iridium satellite launch from Vandenberg Air Force Base this afternoon (here’s a link describing it). At 1:25 p.m., in the midst of our usual afternoon MOCNESS deployment, everyone emerged from the ship’s depths and spread out on the back deck to get a glimpse of the launch. Pretty soon we saw a small fireball shooting up into the sky, followed  by a smoky white trail. Although we are a hundred miles from land, the clear skies gave us the perfect view.

First glimpse of the SpaceX Iridium satellite after its launch from Vandenberg AFB

Sunshine held strong through the evening, when a large pod of dolphins emerged to feed and jump near the ship. They hung around for about 20 minutes, giving us some good shots. Here’s hoping the clear skies hold so we can finally get more satellite images of the ocean filament we are studying!

Dolphin acrobatics
A pod of dolphins does sunset backflips


Posted by: Laura Lilly, SIO

Sharknado 5: Shark vs. Carbon Flux Explorer

Given the record number of shark sightings and attacks off Southern California this spring, it’s about time we had a shark encounter of our own out here! Unfortunately, yesterday marked the first shark-related casualty of the trip: an autonomous carbon flux explorer (CFE) from Jim Bishop’s group at UC Berkeley.

A fully-intact Carbon Flux Explorer (pale blue cylinder with red top) gets deployed during Cycle 2. The sharks hadn’t yet realized how delicious they are!

The CFE was scheduled to surface and be recovered by the ship yesterday afternoon. Around 4:30 p.m., as we neared the bobbing blue cylinder of the CFE, a dark fin appeared on the horizon. It circled a couple of times and then chomped down on the CFE, killing the instrument’s signal and any hope for its recovery. We think the shark was a short-fin mako, but we now know for a fact that CFEs resemble seals bobbing at the surface.

Fortunately Bishop’s team (which also consists of technician Todd Wood,  graduate student Hannah Bourne, and undergraduate assistant Sylvia Targ) has three other CFEs that they will continue to deploy for Cycle 4. CFEs capture and image subsets of sinking particles in the ocean, as a way to determine how much carbon is transported below the ocean’s surface and what kinds of fecal pellets and detrital fluff dominate production. This information helps quantify the ultimate fates of surface-produced phytoplankton carbon and particles, which are important components of the ocean’s essential role as a sink for atmospherically-produced carbon.


Posted by: Laura Lilly, SIO

What does a filament look like?

A cross-section of our filament as depicted by plankton samples. Jars were collected from south to north (right to left) across the filament, approximately every 90 minutes throughout the night. The filament core (middle four jars) produced dense, green, highly-productive waters, with the exception of one lighter sample.

Yesterday we completed our second cross-sectional transect of the upwelling filament we have been studying. This transect complemented the four-day ‘cycle’ we just finished. During cycles, we pick a parcel of ocean water, deploy drifting instruments, and follow those instruments (and the water) for several days, sampling as we go. For transects, we use satellite images of sea surface temperature and phytoplankton chlorophyll to determine the overall extent of the filament, and then draw a line through it and sample along that. Ideally, the midpoint of the line captures the core salty, upwelled, and (presumably) high-productivity waters of the filament, while the endpoints capture lower-productivity waters on either side.

Satellite image of sea surface temperature off California on June 15, 2017. The filament we are studying is visible as the dark blue swirls near the coast extending west as a thick light blue tendril. Our Transect 2 bisected the middle of the light blue filament, around 35N and 122W. Image courtesy of Mati Kahru, SIO.
Stephanie and Laura deploy the vertical Bongo plankton net during Transect 2

Transects are fast-paced, all-night-through-afternoon affairs. This one encompassed a broad section of the filament, which meant 11 sampling stations spaced 5 nautical miles, or about 45 minutes, apart. So by the time we finished collecting water and processing plankton nets from one station, we turned around and sampled at the next station.

Our sampling produced successful and very interesting results! The central part of the transect (filament core) showed cooler temperatures and elevated salinity and fluorescence, consistent with the waters that we measured in Cycle 1, closer to the coast at the newly-upwelled origins of the filament. Plankton samples captured green, phytoplankton-rich waters across the filament, with a notable drop-off to very blue water and reduced biomass at our last station (outside of the filament).

Team Bongo washes down a net (foreground) while Team CTD collects water (background) during Transect 2

We have moved farther west for Cycle 3, to sample the narrow leading tip of the filament – presumably the initial upwelled waters that have since evolved biologically as they have been transported away from shore. We are still seeing lots of big diatoms (a type of phytoplankton that indicates highly-productive waters), but they are mostly dying and sinking, suggesting that they have already bloomed and run their course. The fact that we are finding them offshore provides evidence for exactly the questions we are out here to explore: how much are nearshore upwelling blooms transported offshore, and what does that mean for the ecosystem?

Foam-crested waves breaking off the starboard bow. The ocean holds so many mysteries!


Posted by: Laura Lilly, SIO

Styrofoam CTD

The CTD rosette has an extra-important job today: carrying Styrofoam cups to 3500 meters!

Today we did our first deep CTD cast of the cruise, to 3500 meters below the ocean surface (over 10,000 ft). In addition to sampling important water column properties, we entrusted the CTD with a precious task: transporting decorated Styrofoam cups! No, we didn’t release Styrofoam into the ocean to perpetuate the global marine debris problem; Styrofoam cups make great cruise mementos and oceanographic teaching props!

Since pressure increases with water depth (more water weight sits above something at 3500 meters than at 10 meters depth), and since Styrofoam is compressible, sending cups down into the ocean squeezes them to less than a quarter of their normal size at the surface. This makes them hardly useful for drinking out of, but great for demonstrating how much pressure a fish must adapt to in order to live several thousand meters below the surface.

Filling the cups with paper towels helps maintain their shape
Ben prepares decorated Styrofoam cups for deployment

Our scientific impetus for conducting deep CTD casts is to measure dissolved organic carbon (DOC) in the deep water column. DOC is released into surface waters by animals that produce or take up carbon and then extrude it in dissolved form – usually from phytoplankton that release DOC as they die, or from zooplankton regurgitating bits of carbon as they feed. The pool of DOC in the ocean is similar to the amount of carbon dioxide in the atmosphere, making DOC an important component of the ocean and global carbon cycle.

Brandon Stephens, a Ph.D. candidate in Lihini Aluwihare’s lab at Scripps, is interested in isolating a carbon component known as ‘refractory’ DOC, which is the unpalatable and therefore very old component of organic carbon in the ocean (nothing wants to eat it, so it just cycles around for thousands of years). Stephens is interested in aging DOC and determining the distinct composition of the pool in the California Current System. He also uses deep DOC as a baseline reference for the upper ocean DOC values that he measures during the cruise. His findings suggest, among other things, that deep DOC in the California Current is some of the most carbon-depleted in the world. The ocean in our backyard continues to surprise us!

In other news, the cups all came back successfully! Here is a colorful subset, with an uncompressed cup (plain white) in the background for comparison

Posted by: Laura Lilly, SIO

Birthdays at sea

Ben blows out his birthday candles

June isn’t just a great month for chasing ocean filaments – it’s also a popular birthday month on our Process Cruise! In the past week, we have had three birthdays: Stephanie, Ben, and Cynthia (all, coincidentally, grad students or volunteers in Mark Ohman’s lab).


The science never stops – Ben started his birthday by deploying a midnight MOCNESS tow, and Stephanie and Cynthia each wrangled several Bongo tows and plankton preservationists to celebrate their days – but the chefs baked each of them a birthday cake, and we didn’t let them escape dinner without several rounds of birthday singing. Being at sea is definitely a memorable way to celebrate!

Spotlight: MOCNESS!

The MOCNESS really does look like a creature from the watery depths when it emerges from its tow

When you’ve spent a long time immersed in the world of oceanography, it’s easy to forget that not everyone speaks your lingo in their daily lives. Someone outside of the ship might be surprised to hear us casually mention a monster onboard: the MOCNESS! Fortunately this is one beast we can (mostly) control. The MOCNESS (Multiple Opening/Closing Net and Environmental Sensing System) is a set of ten nets that can be closed at discrete depths, allowing us to sample and compare planktonic organisms from up to ten different parts of the water column. The MOCNESS also has environmental sensors (temperature, salinity, and fluorescence) which collect concurrent physical water measurements to produce a whole picture of the slice of ocean we sample.

NESSy can be a temperamental beast to wrangle back onboard – especially on windy days!

Discrete-depth sampling helps us determine things like: how often and far plankton taxa move up and down in the water column throughout the day (many plankton undergo a daily cycle of vertical migration hundreds of meters up and down), whether certain types of plankton prefer specific water depths, and how plankton distributions change in high- versus low-productivity water masses. In the context of our current cruise to study a newly-upwelled, high-productivity filament off central California, the MOCNESS can also cue us in to how water column distributions change between nearshore and offshore waters, and within the filament as it evolves through time.


Team MOCNESS prep! (left to right) Stephanie, Cynthia, Valeria, and Ben get ready to deploy

This afternoon’s MOCNESS brought up mainly euphausiids (krill) and a few small fishes, but stay tuned for exciting hauls, especially from the night tows! We are halfway through our second cycle, which means we have two more MOCNESS tows for this round (one tonight, one tomorrow afternoon), along with the usual CTDs, Bongo net tows, and various drifter deployments. After a few brushes with the Navy’s missile testing schedule, we have been cleared to keep tracking our filament. Science stands strong!

One of our loyal black-footed albatross followers flies alongside the ship as we deploy the MOCNESS


Posted by: Laura Lilly, SIO

Sunday smokeout


Summer afternoons are always good for grilling – even at sea!

It’s easy to lose track of days at sea, with our constant stream of science and ever-blue horizon. But in some ways, life on the ship is just like a summer afternoon on land: when you smell the barbeque firing up, you know it’s Sunday – steak night!

Chief Engineer Dave and Darlene flip steaks on the back deck

On Sunday evenings (and occasionally other days), the crew will set up a charcoal barbeque on the upper decks and flip steaks and asparagus. It’s a little slice of summer grilling in the park – as long as it doesn’t set off the fire alarms!

In other news, we have finished our first three-day cycle and are now transitting farther offshore to sample the core of our filament. Tonight we will deploy the MVP to survey the area, and will then begin our second cycle. We’ll see if our samples will be as full of green algae as in our first cycle, or if we run into a bloom of something new!

Deploying an instrument that measures carbon fluxes into the ocean


Posted by: Laura Lilly, SIO

Fishing the Filament

Dolphins! A sure sign of a productive ocean

Cynthia, Laura, and Valerie run mddle-of-the-night zooplankton net processing during our first transect (Photo credit: Stephanie Matthews)

Last night we ramped up our sampling in earnest with a marathon cross-filament transect. A beautiful filament of cold, newly-upwelled water emerged off the coast of Morro Bay, California, a few days ago, giving us the perfect feature to begin our first sampling sequence.

A plankton sample from the middle of the filament – lots of green! (Photo credit: Stephanie Matthews)

We started the transect yesterday evening, just in time to catch a pod of whales and flocks of seabirds feeding off the stern – a sure sign that we were in high-productivity waters! Everyone worked through the night to deploy a rapid-fire 11 rounds of CTDs, trace metal water-sampling, and vertical Bongo net tows as we cut a straight line across the filament. We had several new people who had never done this work, but everyone rapidly got up to speed in the flurry of water sampling, filtering, and zooplankton processing. This transect will give us valuable information on the relative productivity within the filament compared to the surrounding waters. Time and data analysis will tell all, but at first glance we saw very green, high-chlorophyll waters (indicating high phytoplankton productivity) and lots of pyrosomes and jellyfish in the plankton samples.

Tonight we begin the second half of this sequence: a four-day cycle in which we deploy various instruments and follow them as they drift for several days in a parcel of ocean water. One piece of equipment is sediment traps, which capture sediments and organic particles as they sink through the water column. Another piece is an in situ incubator that holds phytoplankton as it floats through the ocean, allowing them to grow under real ocean temperature and light conditions. We will retrieve the arrays at the end of four days, but in the meantime, we will be deploying plankton nets and CTDs several times a day. All of this information will help us understand the evolution of the filament of upwelled water as it evolves over time.

Deploying the Moving Vessel Profiler ‘fish’ takes an all-star team! Laura, Kat, and Valerie lead the charge (Photo credit: Shailja Gangrade)


Posted by: Laura Lilly, SIO

Exactly how big is the Revelle?

The R/V Roger Revelle is a big ship! Photo courtesy of Scripps Institution of Oceanography (

When I tell people that I’m going out to sea, they usually ask: “How big is the ship you’ll be on?” When I tell them (something in the 200 ft range), their response is “I have no idea how big that is, but how do you spend a month at sea on a tiny boat without going crazy?”

So how big does the 277 ft Revelle (the largest ship in the Scripps fleet) actually feel? Here’s one useful way to think about it: At home, if you wake up in the middle of the night and want a snack, how many doors and staircases do you have to go through to get to your kitchen? Probably not more than one or two of each. The Revelle has seven decks (levels) and two main internal stairwells (not to mention 2-3 outside staircases between each deck). The ship is also very compartmentalized to conserve air conditioning and contain potential fires, which means that the main hallway alone is divided into five separate sections. Most of the science staterooms are on the lower deck, which means that a midnight trip to the mess deck (kitchen) entails climbing two levels of stairs and going through five doors. Heavy metal doors. Sometimes tilted sideways in the waves. That part of being at sea could make me go crazy.

Sunset is always worth pausing for – even seven flights up!

Even basic science tasks involve a lot of transit. Getting from the from the back deck, where we do most of our sampling, all the way forward to the main lab can involve four doors and a lengthy hallway, which starts to add up when you’re carrying awkward sample bottles. And with five separate labs plus cold rooms and storage spaces, it’s easy to lose your fellow scientists in the maze!

That doesn’t even include trips up to the bridge, which is the uppermost level where the captain and mates steer the ship and the rest of us spot whales in our sporadic free time, or down to the laundry room, which is an essential destination on a month-long voyage. If you were putting your clothes in the dryer after dinner and suddenly realized that you absolutely must go straight up to the bridge to catch the sunset, you would have to sprint up seven levels and open more doors than I can count. If you forgot your binoculars for whale-watching, you would have to do the whole thing again (or borrow from the bridge). Fortunately the sun doesn’t set until after 8 p.m. these days.

We are grateful for all of the space, though, especially the large labs that allow us to spread out our extensive sampling equipment without bumping elbows. We will be finishing our SeaSoar transects tomorrow morning, after which we will head into Santa Barbara to drop off and pick up several people, before heading back out to sea to begin deploying instruments and sampling. Stay tuned for lots of exciting science!

Another stunning sunset over the California Current


Posted by: Laura Lilly, SIO