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.

Wrangling the MOCNESS monster

by Laura Lilly

Recovering MOCNESS nets can be exciting in rough seas. They really do look like creatures from the watery depths!

When you do zooplankton tows, you bring a lot of monstrous-looking creatures onboard. Sometimes we get Phronima hyperiid amphipods, which were the inspiration for the 1979 movie Alien; occasionally we pull up red tuna crabs, small lobster-like crustaceans with very sharp claws; and the other day we caught two vampire squids, small purple creatures with big black eyes, Dumbo ears, and tissues between their tentacles that resemble vampire cloaks. But one of the craziest monsters we have is the net we use to capture and sample these organisms: the MOCNESS!

A Phronima hyperiid amphipod curled up in a hollow salp ‘barrel’ (body case). Phronima carves a salp’s body out and uses the barrel as a house – like a slightly morbid version of a hermit crab. Photo courtesy of Pierre Chabert.

Assuming you haven’t been living under a rock for the past hundred years, you will probably recognize MOCNESS as a play on Scotland’s Loch Ness Monster. MOCNESS stands for Multiple Opening/Closing Net and Environmental Sampling System, and was developed by Peter Wiebe at Woods Hole Oceanographic Institution. If you can process that behemoth of a name, you will get clues about what the MOCNESS does. Most of our plankton nets have simple circular ‘mouths’ that stay open for the whole net deployment: they go down to depth open and come back up still open, so if we sample down to 200 meters we are actually collecting animals everywhere between the surface and 200 meters. That comprehensive sampling is fine for a lot of the research questions we ask (aka: “Who is present in the upper ocean off San Diego versus Monterey?”), but sometimes we want more information about which animals live at specific depths. As its name implies, the MOCNESS has multiple nets (10 on our current setup!) attached to one frame, and they can be opened and closed in sequence to sample different depths. If you want to compare the zooplankton living at 1000 meters versus 100 meters, you can program separate nets to close at each of those depths. The MOCNESS also has oceanographic instruments to measure water temperature, salinity, oxygen, and fluorescence, so we can get information about the physical water profile in addition to zooplankton specimens.

A vampire squid underwater in Monterey Bay. The squids we pulled up in our nets were on their last legs (tentacles), but they had the same distinct Dumbo ears. Photo: MBARI.

Most of our MOCNESS tows on this cruise sample down to 450 meters, although occasionally we sample to 1000 meters. Those deep tows can last over three hours, which doesn’t even include the net washdowns afterward! The majority of the sample from each net filters down to a plastic jar attached to the end of the net, but once the nets come back on deck, we hose them down to make sure we collect all the animals that may have gotten stuck in the net mesh. Net washdowns sometimes feel like they go on forever, but they can be very important: one of the vampire squids we caught a couple of days ago was stuck halfway down the net, and we wouldn’t have collected it if we hadn’t done the net washdown.

Getting the MOCNESS overboard can be quite a process! Fortunately we’ve had mostly calm seas and a very helpful deck crew. Photo courtesy of Lance Wills.
Each of the ten MOCNESS nets has a plastic ‘cod end jar’ attached to the end. These jars collect most of the organisms that get caught in the nets, and bring them back to the surface for us to sample. Four cod end jars are visible here as the grey cylinders with drainage holes and duct tape bumpers. Photo courtesy of Lance Wills.

Net washing time is also essential for taking in the afternoon sun (or sometimes early morning pre-dawn air) out on deck, and for keeping an eye and ear open for passing whales. Today we started our third cycle, and we were graced all day by the presence of several fin whales. Their broad backs and deep exhales were sometimes just 50 feet from our ship. The sound of a fellow mammal emerging from the depths of the ocean to release a breath of air never gets old. Plus, all those whales are a sure sign that there are zooplankton around to feed on!

The cloudy skies finally parted for a brief sunset. Our red drift array buoy is visible in the foreground, flashing its red light. During each cycle, we follow this drift array as it floats around in the ocean, which allows us to track the same single water parcel for several days.

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.

SeaSoaring with sea creatures off Monterey

by Laura Lilly

The SeaSoar gets launched off the back of the Atlantis through the large blue A-frame. Photo credit: Julie Barrios

We have officially begun our cruise’s scientific measurements! Tuesday evening, we deployed the SeaSoar, a small yellow airplane-shaped vehicle about the size of a bicycle. We will tow the SeaSoar behind the ship for three days as we sail in a radiator grid pattern (long lines from south to north and back south) off Monterey, California. The SeaSoar descends from the surface down to 300 meters and then back up, changing the pitch of its wings to control its direction. It will repeat this yo-yo pattern continuously the whole time it is deployed. SeaSoar measures water temperature, salinity, oxygen, fluorescence (an indicator of how much chlorophyll is produced by phytoplankton), and several other biogeochemical variables. We combine the SeaSoar dives into cross-sectional profiles to give us an image of what the subsurface waters off central California look like.

We do this profiling transect at the beginning of our cruise to identify and determine the water ‘feature’ that we will sample throughout the month. Our goal is to find a newly-upwelled water filament (think a triangular-shaped parcel of water, with the wide base along the coast and the tip pointing offshore) and to follow that filament as it moves progressively offshore. We have identified a potential filament off Monterey using satellite measurements of sea surface temperature and water currents, so we are cruising through the area with the SeaSoar to get additional information about the subsurface structure of the feature. We hope that this emerging filament continues to grow and move offshore, so that we have time to sample various areas of it!

A mola mola (“ocean sunfish”) drifted by the ship while we were deploying the SeaSoar on Tuesday evening! We considered it a good luck symbol for the cruise. And no, it’s not a giant plastic bag. Photo courtesy of Rob Lampe.

We have been graced by lots of animal sightings while we do the SeaSoar survey. As we were preparing to deploy the SeaSoar on Tuesday evening, a mola mola floated by at the surface! Molas are oval-shaped bony fish with very flat bodies. They often float on their sides at the surface of the ocean, resembling large pancakes. Sharks and killer whales have been known to sample them (or perhaps use them as frisbees), but overall they are rather unpalatable. We have also seen albatrosses and other seabirds. Wednesday afternoon the sky cleared for a beautiful sunset with pods of dolphins and whales cruising alongside the ship!

A black-footed albatross – the ocean’s true sea soarer
A trio of dolphins – we never get tired of seeing them!