Back to Land Life

by Laura Lilly

Sailing home past the Channel Islands.

We have safely and successfully returned to land after the end of our 2019 CCE-LTER Process Cruise! On Friday, we sailed back past Point Loma into San Diego Harbor and offloaded our month’s worth of scientific gear and samples. Only time and sample analysis will tell us what we found, but we know we conducted plenty of science! Over the course of 32 days, we did 93 CTD casts (ran out of time for the final 7), 26 MOCNESS tows, 3 SeaSoar deployments, and innumerable Bongo tows and trace metal CTD casts – not to mention Zippy’s solo excursion!

The numbers only capture half the story, though. Going to sea with 57 people on a 280-foot ship inspires you to get to know those around you, and our party bonded across scientific and geographic lines. We look forward to future collaborations around the world! We’ll miss the daily sightings of whales and dolphins, though.

You never forget sunsets (and moonsets) at sea.

Innovation and Sunshine

guest post by Sara Rivera

Sara got crafty with duct tape to protect her water samples from sunlight-induced photo-oxidation. Photo courtesy of Sara Rivera.

Sara Rivera is a graduate student in the Aluwihare Lab at Scripps Institution of Oceanography. Here, she recounts some of her challenges in sampling at sea.

Being at sea for research requires innovative solutions for problems not typically experienced on land.  One of the main issues faced when sampling for microorganisms and organic chemistry is the impact of light on samples.  On land, it is easy to grab a piece of foil to cover a rack of vials.  At sea, it is not so easy because it is fast, windy, and there are limited supplies.  At first, I used foil to cover my tube rack, like I would on land, to block the sunshine.  I found that with the fast pace at sea that I needed to get my samples done, I constantly ripped the foil and needed to get a new piece.  I would also end up chasing pieces of foil as they were blown across the deck.  As my supply of foil dwindled, I contemplated what else would efficiently block the sunshine while allowing easy and efficient access to the sample tubes.

Lo and behold, the answer sat in front of me in an essential piece of cruise equipment: a roll of duct tape.  I created a barn-like structure out of duct tape that would slide over the tube rack and completely block out any sunlight.  It is waterproof and reusable.  It is also removable, allowing me to continue to use the tube rack for other experiments as needed.

Why do I care this much about keeping the samples out of the sunlight?  Sunlight impacts both chemical and biological processes.  The untraviolet (UV) region of sunlight leads to photo-oxidation of organic molecules, changing the chemistry of the sample before I have time to process it.   Recent work by Neal Arakawa (Science Advances, September 2017) demonstrated that a single type of molecule, β-carotene, can photooxidize to generate a slew of carotenoid degradation products that is linked to 4% of the total dissolved organic matter in the ocean.  If one molecule can degrade to such a large number of other molecules, from simply sitting in the sunshine, I do not want that happening in my samples! I want the samples to reflect the chemistry of the sea water from the depth from which I collected it.

Sara’s work involves taking lots of water samples from the ocean. She relies on the CTD and bottle rosette (pictured here) to sample certain depths of the water column. The CTD goes out several times per day and requires careful manhandling to bring back onboard. Photo courtesy of Sara Rivera.

UV also damages biological cells. The biological damage can impact both the biology and chemistry as distressed cells will take up and release different molecules than in their normal state.  Since I measure both the biology and chemistry, this one is doubly bad.

The visible light regions of sunlight are absorbed by the green pigment chlorophyll, found in the organelles called chloroplasts, which is essential to photosynthesis in the majority of marine phytoplankton.  These chloroplasts also give the phytoplankton their green color.  Light is attenuated as you go deeper in the ocean.  We sample at a variety of depths from the surface down to 515 meters (1690 ft).  The organisms below the surface are not acclimated or adapted to the light on the deck of the ship- it is much too bright for them.  It can also lead to fast growth and production from increased photosynthesis.  Because I want to capture the biology at the different depths we sample, I don’t want them to suddenly start growing faster because of the additional light.


by Laura Lilly and Sara Rivera

As the Beatles once said, “It’s been a hard day’s night.”  Once a week, the entire science party on our cruise turns into vampires and samples the ocean all night long, from sunset to sunrise. These marathons are known as transects because the ship sails in a straight line across a gradient between different oceanographic features, and we do a sampling “station” (CTD and water samples, trace metal cast, zooplankton net tow) every hour. We start the transect in lower-productivity waters outside of the filament, cut through the high-productivity filament, and then sail back into low-productivity waters on the other side. The goal of our transects is to measure gradients in water properties (temperature, salinity, oxygen), nutrients and trace metals such as iron, and biological communities (phytoplankton, zooplankton, bacteria) across and outside of the filament. By sunrise on Sunday morning, we had sampled 7 stations and had as many samples from one night as we usually have over a four-day cycle! 

The zooplankton crew brings their Bongo net back onboard after a successful tow. Photo courtesy of Stephanie Sommer.

On transect nights, the entire science party starts their work shift together at sunset and ends in time for breakfast (hopefully). These nights are one of the only times when the whole science party is awake at the same time.  They are intense nights, but are made better by teamwork, positive attitudes, and good music. Some people on the ship claim that the bioanalytical laboratory is the place to be on these nights. Although the people working in that lab have to spend hours filtering the water samples they collect on the transect stations, they also keep a wide variety of snacks in a clean part of the lab. Some of their favorites (that they’ve revealed) include apples, peanut butter pretzels, and chocolate cookies. Both the bioanalytical lab and the wet lab (which processes the zooplankton samples and lays claim to the other funnest place on the ship during transects) often have impromptu 4 a.m. sing-alongs and dance parties in between stations.

Plankton samples from the seven stations on the transect. The left-middle jars are particularly dense with green phytoplankton from the core filament waters. Photo courtesy of Stephanie Sommer.

We conduct the transects entirely at night to avoid changes that can occur in marine plants and animals between day and night. Just like land plants, phytoplankton use chloroplasts filled with chlorophyll to convert sunlight into carbon, and these chloroplasts can get ‘quenched’, or oversaturated, during the day. Measuring phytoplankton at night gives a more accurate indicator of their chlorophyll levels and functionality. Zooplankton also show day/night differences in measurements. One reason is that some zooplankton have surprisingly good eyesight, which allows them to see nets coming in the water and swim away. Nighttime allows us to sneak up on zooplankton, true to our vampiric form. The second reason is that many zooplankton undergo a daily mass migration several hundred meters up and down through the water column (which is quite remarkable considering that many zooplankton are 0.5-2 mm in length!). Scientists believe that this mass migration, called diel vertical migration, is a zooplanktonic attempt to balance feeding opportunities in surface waters against the threat of visually-hunting predators. At night, many zooplankton move up to shallower waters to feed, but when sunrise hits, they move back down to depth to avoid being seen. Sampling the upper 200 meters of the water column during day versus night could therefore give vastly different indications of who is present.

Yesterday we started Cycle 2, which should last several more days. We are back in the core of our upwelled filament, with lots more green, productive waters to sample!

Zippy the Zooglider goes to sea!

by Laura Lilly

Zippy gets deployed over the side of the ship into the ocean. The zooplankton camera is the small grey box attached to the front of the glider’s nose. Photo courtesy of Julie Barrios.

For the first week of our cruise, we were carrying a stowaway science member onboard the Atlantis: Zippy the Zooglider! Zippy is four feet long, orange, and torpedo-shaped, but don’t mistake him for a giant carrot. On Monday, we released Zippy into the ocean to cruise underwater off central California for 20 days while we do our shipboard sampling.

Zippy comes from a class of Spray gliders, which are autonomous underwater vehicles (AUVs) developed by Russ Davis and Jeff Sherman at Scripps Institution of Oceanography. True to their name, AUVs are completely independent, remotely-operated vehicles that can navigate underwater without being tethered to a ship (if you are quick on your nautical literature references, you might recognize the name Spray from the ship that Joshua Slocum single-handedly sailed around the world, as told in his book A Solo Sailing Trip Around the World). The Spray gliders are controlled by engineers on land to ‘fly’ in any underwater pattern we designate. Underwater gliders are gaining popularity for precisely the reason that they can be left out in the ocean for months at a time to record data with no shipboard support. They just need to be launched and recovered! Most Spray gliders are deployed by small dinghys off Scripps, but since we want Zippy to profile the waters that we are sampling on our cruise, we brought him out to deploy at sea.

Zippy gets craned from the upper decks down to the main deck for deployment. Photo courtesy of Julie Barrios.

Similar to the SeaSoar, Spray gliders are equipped with oceanographic sensors to measure water temperature, salinity, oxygen, fluorescence, and biological particles in the ocean. Zippy has an additional characteristic beyond his standard Spray outfit: his “nose” has a shadowgraph plankton camera attached to it, which allows him to image live plankton in their real habitats. This addition was the product of a collaboration between the Instrument Development Group (which runs the Spray program) and Mark Ohman’s lab (also at Scripps), which studies mesozooplankton ecology and behavior. These in situ images give us important insights beyond what our standard shipboard plankton net tows tell us. As with all sampling metrics, plankton nets have advantages and disadvantages. Nets allow us to scoop up an actual sample of ocean plankton in order to visually and genomically identify animals and determine what they feed on, but nets can mangle fragile organisms (long tentacles and watery bodies don’t hold up well against nylon mesh) and they don’t capture animals in their natural habitats. The Zooglider’s camera gives us a literal picture of the natural shapes and orientations of animals, especially features like filamentous antennae and delicate shells. Best of all, it can cover an additional swath of the ocean that our ship won’t have time to sample. The Zooglider still requires land-based image processing, and we can’t always identify individual species, but Zippy does a powerful job of measuring who’s out there.

Shadowgraph images of various zooplankton from previous Zooglider deployments. Many of the animals imaged have long filamentous tentacles and delicate body structures that fall apart in net sampling. Images and composite courtesy of Jeff Ellen.

We hope that Zippy will encounter Hubert the Sea Llama while he is out and about. Hubert is a sharp-witted by elusive fellow who first befriended Steve the SeaSoar when Steve was out cruising last week. We’re looking forward to hearing about that and other adventures when Zippy comes back onboard at the end of our trip! In other news, we are just finishing our first four-day cycle, which sampled the heart of the newly-upwelled water filament we are tracking. The waters have literally been green with phytoplankton, so we are curious to see what our other measurements tell us about the new waters. Stay tuned for more updates.

Zippy was welcomed into the ocean by various emissaries, including black-footed albatrosses and Pacific white-sided dolphins. Photo courtesy of Sven Gastauer.
We think the dolphins might have sampled a bite of Zippy’s fin, but there’s no apparent long-term damage. Photo courtesy of Tristan Biard.
Only one known set of sketches exists of the elusive Hubert the Sea Llama, thanks to Steve the SeaSoar’s adventures last week. Sketches courtesy of Sarah Schwenck, Sara Rivera, Stephanie Sommer, and Jacob Evans.

We are off to sea!

by Laura Lilly

The R/V Atlantis docked in San Diego Harbor

We are officially underway on our 2019 CCE-LTER Process Cruise! We left San Diego Harbor yesterday afternoon under sunny skies and smooth sailing conditions, and we are now heading north toward Monterey, California. We won’t see Point Loma again until September!

The goal of our monthlong cruise is to track water filaments that are upwelled in near-coastal waters off central California and flow out to the open ocean several hundred miles offshore. We are measuring various aspects of the biological production associated with filaments: viruses and bacteria, phytoplankton and zooplankton, along with the nutrients that fuel their growth. Our cruise the latest installment in the California Current Ecosystem Long-Term Ecological Research (CCE-LTER) Program, which was started in 2004. The program consists of a core body of scientists from Scripps Institution of Oceanography and collaborators from numerous other institutions, as well as visiting scientists and volunteers from around the world. Our current cruise includes participants from as far away as Canada, France, Luxembourg, and Ghana! Yesterday evening, we stopped 20 miles offshore to test our scientific sampling equipment. Some of our graduate students and volunteers are out on their first sea trip ever, so they got a glimpse of the deployments we will be doing during the cruise. Stay tuned for future features on our various types of sampling equipment and the scientists who use them.

Gear stowage in the ship’s wet lab. We will be filtering plankton samples and sediment traps in this area.

We are sailing on the Research Vessel (R/V) Atlantis, which is operated by Woods Hole Oceanographic Institution (WHOI) out of Massachusetts. Scripps and WHOI are both members of the University-National Oceanographic Laboratory System (UNOLS), under which ships are built for certain institutions but are shared with other institutions based on where in the ocean the ship is and where a given cruise is going. The Atlantis has a unique claim to fame: it is the mother ship of Alvin, a submersible vehicle that can carry scientists to the seafloor to explore deep-sea communities. The Atlantis and Alvin have been sampling hydrothermal vents in the Pacific Ocean for the past year, so the ship was in the right spot for our cruise. We don’t have plans for Alvin dives on our cruise, but you never know what could come up at sea!

The Atlantis sailing out of San Diego Harbor. Photo. courtesy of Jeff Ellen