A Monster of Nets: The MOCNESS

Among the net systems used by biological oceanographers, the MOCNESS ranks among the most involved and invaluable. Our MOCNESS (Multiple Opening and Closing Net and Environmental Sensing System) consists of a 1m2 metal frame with 10 stacked nets nested inside of it. The numerous nets are used to target specific depth ranges for sampling so that scientists can examine what kinds of plankton live within different layers in the ocean. The nets operate in sequence: as one net closes, the net directly above it opens. For instance, in our tows we keep the bottom net open as the net descends to 1000m, then we snap it shut, opening the next net to sample from 1000m-800m and so on. As with the Bongo, the MOCNESS filters water into a cod end, so at the end of each deployment we have 10 cod ends each full of plankton goodies!


The top of the frame is loaded down with sensors that measure the physical environment as the net moves up and down the water column. Data are collected on temperature, salinity, oxygen, fluorescence, transmissometry and more. This allows scientists to place the different organisms in each net in a particular environmental setting. Counter to our land-based intuition, the ocean operates on 3 dimensions and more often the water above and below a single area has distinct properties and animals. In terrestrial ecosystems, a similar parallel would be a rainforest, where the canopy harbors unique fauna and light levels compared to the forest floor.

The beast of scientific innovation is also coupled with the Herculean task of deploying, operating, recovering, and maintaining the MOCNESS and later processing and analyzing the data it collects. Deploying and recovering the MOCNESS requires at least 4 scientists and a marine technician who oversees the process. It all begins with “cocking” the MOCNESS: manually pushing the nets to the top of the frame and securing them to their trip controls so that they are poised to snap shut. Next, cod ends are secured (with some help from electrical tape) and a deck check is performed to ensure all instruments are functional. One scientist remains in the electronic lab to “fly” the MOCNESS and control the software while 3 scientists and the marine tech lower the MOCNESS into the water with the A-frame.

A view of the control room while MOCNESS operations are underway.

The MOCNESS is then dropped to depth and flown for several hours, with the scientists carefully observing and noting the data relayed from the sensors and winch to ensure smooth sailing. When the MOCNESS surfaces, a team of scientists and the marine tech recover the instrument, thoroughly rinse the nets for any plankters stuck in the mesh and begin hauling the cod ends to the lab for processing. Many times nets may become ripped in the process of towing, which requires further work. This cruise we even bathed, scrubbed and soaked in vinegar all the MOCNESS nets in an attempt to remove the booger-like phytoplankton that clogs our mesh.

Recovering the MOCNESS.

Processing the MOCNESS involves each cod end being separated into different splits for preservation or analysis. The preserved splits may be placed in ethanol if the scientist wants to examine the DNA of the organisms, or in formalin if they are more interested in the shape and morphology. Another split is further separated into size classes using sieves and filters to measure biomass and isotopes back on land. Repeating this process for ten nets requires stamina and a positive attitude as we work long and odd hours. Morale boosts through fun playlists, interesting conversations and chocolate-covered treats aid in carrying us through the finish line. 

Despite the time and patience the MOCNESS demands, the excitement and mystery of opening each cod end and discovering what weird creatures we secured never gets old. Furthermore, these data provide an informative snapshot into the complex food web that sustains our coast.

-Dante Capone (Decima lab)

The Deep Cast Chronicles: Colder, Darker, Denser…Smaller

If there’s one thing you can count on as a scientist aboard a research expedition at sea, it is the infamous “Deep Cast”. This is a CTD cast that goes deeper than any other. The Deep Cast is a big deal logistically because it takes over an hour to get to its final depth (4,000m at 60m/min), is interesting scientifically because it samples very old water, and is coveted by all on board because it is the shrinking Styrofoam cast…

Everyone on board partakes in the ritual of decorating anything made of Styrofoam in preparation for the Deep Cast. Our devoted resident marine technician Caitlyn offered her battalion of rainbow sharpies (72 strong!) for us to use, and we got to work. 

Jamee Adams (Diaz lab), Anya Stajner (Decima lab), Rob Lampe (Allen lab), Clay McClure (Bowman lab), and Dante Capone (Decima lab) decorating Styrofoam and staying healthy.
Clay McLure, Dante Capone, and Dante’s creation.

Then, we strapped our creations to the CTD wrapped in layers of mesh bags, and sent the whole package down to 4,000 meters. It took over 2 hours for the CTD to travel down, down, down through layers of cold, dense, dark water, and back up to the surface.

Professors Lihini Aluwihare and Kathy Barbeau packing the cups.
Ralph Torres (Aluwihare lab) securing the mesh bags.
Marine technician Caitlyn sending the CTD down to 4,000 meters.

When the CTD came back to the surface with precious North Pacific deep water, the oldest on Earth, everything had changed. Styrofoam heads were deformed and dense, cups were shrunken, and drawings had taken on a more detailed appearance. The increase in pressure down to 4,000 meters forced the air out of the Styrofoam, and caused each piece to shrink. 

Post Deep Cast Styrofoam. 
A Styrofoam shoutout to California Current Ecosystem Long Term Ecological Research (CCE LTER)!

Aside from our treasured oceanographic samples, anyone who made a Styrofoam creation has a more personal souvenir to take home and gift to friends, family, and loved ones, or to keep for themselves as a reminder of this epic adventure. 

A family of cups.

-Jamee Adams (Diaz lab)

To the Beat of the Bongo

Biological Oceanographers come equipped with an arsenal of nets at their disposal, with some as simple as a ring net and others like the MOCNESS (Multiple Opening and Closing Net Environmental Sensing System) loaded down with sensors and moving parts. Regardless of complexity, each net contains essential core parts including a frame, a mesh and a cod end.

The frame holds the net, which is comprised of a conical mesh with varying size holes. Typically for our plankton sampling we use a 202 um mesh, which is dictated by the particular group of organisms we want to catch. The cod end is a cylindrical plastic bucket secured to the narrow end of the net by a plastic collar. The cod end collects all the plankton, filtering water out of mesh holes (also 202um) in its side as the net is dragged through the water. 

One of our key nets on this cruise is the Bongo Net, which imitates its namesake with a side-by-side two net system. Bongos can be towed through the water obliquely or vertically, but for the CCE cruise protocol we conduct oblique tows twice per day. It is useful to compare day and night tows, because plankton move from shallow water where they feed under cover of darkness during the night, to the deep during the day where they hide from predators, a process called diel vertical migration.

The Bongo net.

The process of deploying the Bongo involves teamwork and communication between scientists and the marine technician. First, the cod ends are secured to the two collars at the ends of the long mesh nets. Next, the Bongo and a weight are connected to a winch and gradually lowered down off the side of the ship at a desired “pay out” speed from the winch. Once the winch has paid out 300m of wire, the net is held at depth for 30 seconds before it is hauled in. Throughout this process we are recording the angles of the winch at certain depths to ensure proper tension on the wire, keeping time, and signaling or shouting to the winch operator and marine technician who runs the operation.

Deploying the Bongo net.
Peter (left, awesome volunteer), Anya (right, Decima lab).

Once the Bongo has surfaced, we spring into action to secure our samples. We quickly but thoroughly rinse down the net so that plankton stuck to its side end up in our cod end. The port side net is used for a range of analyses that demand that the animals stay alive so we must act swiftly. The animals are anesthetized with soda water (unflavoured) and the sample is divided up, processed into size classes, and frozen in liquid nitrogen for measurements of weight and diet back on shore. The starboard net is strained entirely in a glass jar with a formalin (or formaldehyde) solution, which preserves the shape and features of the organisms. Repeating this process at least once per day has allowed us to tune the rhythm of our operation to the beat of the bongo.

Bongos in the water!

-Dante Capone (Decima lab)

Highlight: Big Sur and the Esselen Tribe

Big Sur from the R/V Revelle

Day 18! We have spent several days sampling recently upwelled waters located east of Big Sur, California. This beautiful and pristine mountainous section of the Central Coast is certainly pleasant to gaze at during shipboard operations when we are close to shore, especially when many of our views have been gray and full of fog. This land however, has a dark history. Big Sur is the ancestral homeland of the Esselen Tribe whose people were decimated and whose lands were stolen by Spanish colonial settlement some 250 years ago. While we are trying to better understand how this complex marine food web is impacted by external factors such as warming, it is important to acknowledge the forceful take-over of the coastline occupied by Native Californian tribes. As noted previously, the upwelling in this region results in high productivity and abundant marine foodstocks, which were historically utilized by the Esselen people. 

Historical tribal land along the Central Coast

Recently however, there has been some good news! The Esselen Tribe and the Western Rivers Conservancy (WRC; a non-profit dedicated to environmental conservation and preserving tribal heritage) received a $4.5 million grant from the California Natural Resources Agency to purchase 1,119 acres of land back after 250 years of homelessness. In July 2020, the purchase successfully closed and the land will be used to conduct traditional ceremonies and teach the public about Esselen culture. Furthermore, it will be shared with other Central Coast tribes who were also decimated during the Mission Era. 

Esselen tribe land acquisition

In addition to the tribal significance of this land, the purchased acres host endangered animals including the California spotted owl, California red-legged frog and contains the Little Sur River which is the Central Coast’s most important spawning stream for the threatened south-central coast steelhead. The Esselen tribe are committed to conserving this critical habitat and the species that occupy it. While this land acquisition pales in comparison to the land the Esselen people historically held, this is an excellent start in acknowledging and working to restore ancestral lands back to Native Californian tribes. The CCE LTER acknowledges that we are conducting science near the ancestral home of the Esselen people who we owe honor and gratitude to.

California Steelhead Trout

For more information about the Esselen people, check out the following website. 


-Ralph Torres (Aluwihare lab)

Finding the Upwelling Filament

You may be wondering where the ship is going on this expedition. The answer is that it is always changing! Rather than stationary sampling (Eulerian) we are sailing with one continuous water mass and observing the changes within it through time (Lagrangian). Where we are going depends on finding an upwellingfilament (a special chunk of water that is rich in nutrients) and following that chunk of water wherever it moves. 

So what is upwelling?

Upwelling begins with wind. When strong winds blow North to South along the CA coastline, a process called “Ekman transport,” causes deep water to be brought to the surface and pushed offshore. This water is cold, dense, and rich in nutrients (elements like nitrogen and phosphorous needed to make proteins and DNA). These nutrients can fuel growth of primary producers like microscopic algae. The algae is food for small animals, which become food for bigger fish, dolphins, etc—fueling a productive ecosystem! If this chunk of upwelled water moves westward offshore, we call it a “filament” and follow it with our ship.

Black arrow: Wind direction
Blue arrows: Ekman transport

In Search of a Filament!

We can predict when/where upwelling will occur by looking at wind trajectories, and satellite data.

Wind trajectories

Unfortunately, due to continuous cloud cover, we have been unable to utilize satellite data, including sea surface temperature and sea surface chlorophyll. Instead, we have relied solely on data from wind, deployed instruments, and sampling we do on the ship. When we started, we did not observe upwelling, but by Wednesday, July 21 signs of emerging upwelling were observed: a patch of relatively cold water with a high concentration of nitrogen! We can measure nutrient concentrations in the water by conducting CTD casts (see previous post) that give data that look like this:

The y-axis is depth from 0 to 100 meters, and the x-axis shows temperature, nitrogen, and fluorescence (a proxy for chlorophyll from algae). 

We continue to track the filament once we have found it, and observe the changes to the chemistry and biology as the water mass evolves.

-Monica Thukral (Allen lab)

Searching for Life’s Essential Ingredient in the Benthic Boundary Layer

Last Sunday afternoon, the Revelle’s science party began their Benthic Boundary Layer transect. This set of nine, near-shore stations stretches south from Cambria and wraps around Point Conception to finish just at the northernmost point of the Southern California Bight. These shallow stations allow us to sample water that is close to the seafloor, where the continental shelf provides sedimentary nutrients to upwelled waters on their way to the surface. For a trace metal chemist, this area is particularly interesting, as we suspect the Benthic Boundary Layer (pronounced BBL by busy scientists) is a major source of iron during some of the most productive times of the year.

The path of our BBL transect.

            Iron is an essential and often limiting nutrient for marine primary producers, but its exceptionally low concentrations make it particularly difficult to measure (especially from a big rusty boat). Numerous precautions are taken to assure that our samples avoid contamination during their trip from the ocean back to our lab at Scripps. This starts right when we first collect the water. For BBL sampling, the trace metal team employs a large 30-liter Niskin “GoFlo” bottle that we attach directly to a weighted line. We send it down to as close to the seafloor as possible, then literally throw a heavy Teflon messenger down the line to hit a button that triggers the bottle to close. The design for this bottle was developed over a hundred years ago, and has barely changed since then. To keep our samples free from big-rusty-boat-contamination (BRBC), there is an additional switch on the GoFlo that keeps the bottle closed until it reaches a certain depth. This is important for later.

Sailor with Niskin:
An early, yet shockingly similar version of our Niskin bottles.

            The full GoFlo is likely close to 100 pounds. It may be even more, but as a strapping gentleman, I can’t tell. One of us lugs the GoFlo back into our trace metal clean van (usually one-handed and with little difficulty), where it’s tied into its box and pressurized with high purity nitrogen gas. This allows us to push the water through an in-line filter to get our dissolved metal samples. For the BBL, we took about 6 liters of water at each station, for a variety of iron, mercury, ligand, and nutrient measurements.

            The nine-station transect takes us about 16 hours, so efficiency is key. In the van, the trace metal team becomes one organism with four arms. Some are clean, some are dirty, but they have one mind. The hour is late, the music is loud, and after the fourth or fifth station, the filtering, pressurizing, rinsing, and filling take place with minimal discussion. But there is singing, for the trace metal organism has awoken.

            At the third station, tragedy struck. The GoFlo known as “The Beast” experienced catastrophe. The pressure switch that should have opened the bottle at around 15 meters failed to trigger. The bottle ended up under 100 meters of ocean, still full of air. When we sent down the messenger, the shock imploded the GoFlo, and The Beast was slain. 

The decapitated corpse of The Beast.

            But we are not funded to mourn, and the transect must go on. After switching out The Beast for The Boss (our second “GoFlo” bottle), we were back on track. Efficiency increased throughout the night, and our finish line was marked by a beautiful sunrise over Point Conception. But wait! We do not close our eyes yet, for it’s not a proper BBL transect without a special bonus station in the Santa Barbara Basin, where an underwater sill creates a unique anoxic region. Here, we use our trace metal rosette to get a full depth profile, to see what scientific mysteries lie hidden in this oxygen-deprived water-mass. 

Kiefer with crown:
Kiefer Forsch (Barbeau lab), a veteran trace metal chemist, honors a fallen God.

            We’re very excited to process this data, as we now have six years of BBL measurements. The BBL waters we sampled this transect seem to have noticeably fewer particulates than previous years, so it will be very interesting to start to investigate the phenomena behind this trend, and how it affects the overall micronutrient-dependent behavior of the CCE.

-Max Fenton (Barbeau lab)

Today marks 30 years since Dr. Roger Revelle passed away

We are sailing on the R/V Roger Revelle, so we wanted to take a moment to explain our ship’s namesake and his significance to the world of oceanography. Dr. Roger Revelle was born on March 7th, 1909 in Seattle, WA, and then raised in Pasadena, CA. He completed his undergraduate degree at Pomona College in geology, then he earned his Ph.D. at UC-Berkeley in oceanography. Then, Dr. Revelle started his early work in 1931 at Scripps Institution of Oceanography (SIO). During this time period, he focused on carbon, calcium, and other molecules and their interactions in seawater along with the sea floor. 

During World War II, he left SIO and served as an oceanographer for the United States Navy for 7 years, where he worked on sonar detection of submarines. During his time there, he helped to determine which projects received funding and urged the Navy to support “basic research.” Dr. Revelle’s work with the Navy pushed the Office of Naval Research to fund the work that was occurring at SIO and other oceanographic institutions for years to come. 

Later, Dr. Revelle returned to SIO as a faculty member and eventually the Director of SIO from 1950-1964, where he is credited for leading a new period of oceanographic exploration through major expeditions aimed at studying the sea floor. This period also brought about a major expansion of SIO. At this point in time, UC-San Diego (UCSD) didn’t exist, and his goal was to bring in amazing scientists around the world in hopes to create a UC campus. Dr. Revelle created the center for Atmospheric Carbon Dioxide Program and later recruited Dr. Charles David Keeling (creator of the famous “Keeling Curve”) to SIO. He also recruited Dr. Hans Seuss, and they studied the carbon-14 isotope together to assess how much carbon dioxide was being released into the atmosphere from fossil fuels. In addition to recruiting scientific talent to SIO, Dr. Revelle worked on studying contamination of waters and fisheries by bomb tests and radiation from the war, ocean mixing, oceanic carbonate chemistry, and global warming. Through his efforts in recruitment and major oceanographic discovery, in 1960, Dr. Revelle helped to found UC-San Diego. 

In 1964, Dr. Revelle left UCSD to create the Center for Population Studies at Harvard University, and he became interested in applying science and technology to solving world hunger and other policy issues. One of his students there was Al Gore, who would later become the Vice President of the United States under Bill Clinton. In the late 1970s, he returned to UCSD to teach science and public policy until his death.

In addition to his work as a professor and director, he served as an advisor on various government committees and to the Secretary of the Interior. In 1991, Dr. Revelle received the National Medal of Science from President George Bush.

Portrait of Roger Revelle, UCSD Library

Dr. Revelle passed away on July 15th, 1991. After his death, many awards, research vessels, lecture series, buildings, etc. were named in his honor. Today, he is remembered as one of the main leaders of the early days of the U.S. ocean program that played a large role in discovering the greenhouse effect that would lead to our planet’s warming, among his many other significant discoveries.

-Hannah Adams (Schartup lab)

And We’re Off: CCE Carries Onward!

Hello and welcome to the CCE LTER Process Cruise P2107. We are officially underway! We spent the last three days in MarFac, the Nimitz Marine Facility, loading supplies, securing our gear and equipment, and getting to know each other. P2107 is led by CCE aficionado Mike Stukel, who has participated in 11 CCE sponsored cruises. Wow! This cruise has a science party of 36 (including 3 amazing techs Brent, Kaitlin, and Josh) and a wonderful crew of 21. We are sailing for one month aboard the SIO ocean class vessel the R/V Roger Revelle, whose namesake you will learn more about in a future blog post. Stay tuned… 

The aft view of the R/V Roger Revelle. Pictured, we can see the A-frame, trace-metal van, radio isotope van, incubators, and the MOCNESS.

The first task at hand is calibrating the sensors onboard, including the EK80, our wide-band echo sounder (acoustics) designed to monitor underwater ecosystems, and any other sensors that will travel down with our CTD rosette (Conductivity, Temperature, Depth, nitrate, fluorescence, and an underwater video profiler). Our goal is to measure various aspects of biological production associated with filaments in the CCE region that transport nutrient and organic matter rich water from onshore to offshore. We will be measuring a combination of nutrients that fuel the growth of phytoplankton at the base of the food web, as well as micronekton and zooplankton, and the interactions within the food web to better understand this beautiful ecosystem as a whole.  

The Main Lab space onboard the R/V Revelle. Anissa Garcia (right) is an undergraduate student working under Dr. Darcy Taniguchi at California State University San Marcos. 

Wish us luck as we embark on this journey to explore the CCE region collecting water samples, animals, and testing our seasickness meds!

-Jamee (Diaz lab) and Ralph (Aluwihare lab)

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.

Ocean aggregations

by Laura Lilly

The CTD rosette is a popular aggregating/sampling stop for many of the ship’s scientists during all-night transects.

It’s a well-known fact that, in the ocean’s endless expanses of blue, creatures flock to any semblance of structure. Fishermen will tell you that some of the best places to drop a line are around buoys, kelp patties, and bottom rubble. Divers love oil rigs because they create platforms for mussels, barnacles, and sponges, which in turn attract fish and larger predators. Even seamounts concentrate upwelled nutrients and particles underwater, fueling productive hotspots for migratory fishes and sharks (side note: we just finished sampling in a region near the Davidson Seamount off Central California, which comes up to 1300 m below the ocean’s surface. Our work wasn’t related to the seamount, but perhaps we caught some seamount-related creatures in the MOCNESS). If you’ve been reading the news lately, you may have heard about the giant raft of aggregated pumice pieces that emerged from an underwater volcano near Tonga and is floating toward the Great Barrier Reef off Australia. Scientists believe that the pumice raft may actually help the Great Barrier Reef by collecting marine creatures as it floats, and then depositing them on the GBR, helping to repopulate a reef system that has suffered tremendously from climate change-related coral bleaching.

Zippy reappeared at the surface to an albatross welcoming party.

Yesterday we observed a different example of aggregation when we retrieved Zippy the Zooglider from his two-week excursion! Zippy had been doing continuous underwater up-and-down sampling patterns, so to recover him we had to program him to come up to the surface and float while we tracked down his GPS coordinates and spotted him from the ship (without running him over). But our human party wasn’t the first to spot him. We found Zippy by steaming toward the aggregation of albatrosses we saw sitting in the water nearby. Just like they had when we deployed Zippy, the albatrosses wanted to know why there was a giant orange missile-shaped carrot floating at the surface. We think one even took a bite – Zippy came back missing a small piece of wing! But somehow, even though they weren’t tracking GPS coordinates like we were, those albatrosses spotted Zippy before we did. Aggregation: it’s a marine life instinct.

Zippy gets picked up by the small boat crew.

We all participated in another form of aggregation two days ago: we had our third all-night sampling transect across another part of the (now evolved) ocean filament we are sampling. The transect was a typical all-night party/race of drawing water from CTD casts; filtering rapidly for carbon, nitrogen, and iron; and deploying zooplankton nets and preserving specimens – all before the next station 20 minutes away! We moved through everything successfully, though, and even managed to finish by dawn. Then most people slept all day.

Dolphins sometimes aggregate around our ship, too!