Research in the Time of COVID-19

Despite a deserted campus, some essential Scripps research programs carry on

The onset of the coronavirus has put research on hold for a wide swath of the science community, but several programs are continuing at the Scripps Institution of Oceanography at UC San Diego. Many are automated and not subject to the restrictions their operators face, but others continue with human intervention: keeping critical specimens alive, taking measurements in solitude, and in one case, continuing on with shipboard work because there is no option to leave. 

One project has gone on so long that it was disrupted not just by this pandemic but also the influenza pandemic of 1918.

While much of the campus is working remotely, select groups were granted exceptions pending the ability to maintain physical distancing guidelines. Some dispatches collected from Scripps Oceanography researchers still at work:

For the Second Time, a Pandemic Disrupts Temperature Readings

It’s rare for the Shore Stations Program to skip a beat in taking daily temperature and salinity samples from the end of Scripps Pier. These important seawater measurements have been collected since 1916, providing researchers with critical information about changes in the coastal Pacific Ocean.

One significant pause occurred during another severe pandemic—the Spanish flu of 1918—as records indicate five days of missed measurements in the fall of 1918, when San Diego was under quarantine.

Now, more than a century later, the program is again facing the challenges of a global health crisis. Shore Stations Program Manager Melissa Carter said they missed six sampling days at Scripps Pier due to COVID-19 impacts, but that operations would carry on now that protective measures, such as an enhanced cleaning protocol and wearing gloves during sampling, have been put in place.

“Our priority has been ensuring the health and safety of all personnel, meeting CDC and UC San Diego health standards, and getting proper authorizations for access to campus,” said Carter.

Carter and two other members of the Shore Stations team, Jimmy Fumo and Kristi Seech, will be collecting daily samples from the pier during the campus closure. Historically, Birch Aquarium aquarists are responsible for this task, but with the aquarium’s temporary closure and reduced staff, the Shore Stations team will be filling in to keep the daily observations going. This effort will ensure that the beat goes on for the longest continuous measurement program at Scripps.

The Shore Stations Program is part of a larger statewide network with nine other stations along the coast. Most of the stations include city and county observers such as lifeguards or Harbor Patrol; these stations are continuing to collect daily samples while other stations affiliated with universities are missing more days due to limited staff, said Carter.

Travel Plans on Ice

An icebreaker in the ocean

MOSAiC, the Multidisciplinary Drifting Observatory for the Study of Arctic Climate, takes place on a German icebreaker deliberately frozen into Arctic sea ice. One Scripps Oceanography scientist, biological oceanographer Jeff Bowman, is on board R/V Polarstern at the moment. For reasons only partly related to coronavirus, he can’t leave.

Bowman is managing multiple projects in the mission led by Germany’s Alfred Wegener Institute. To chip away at the global carbon budget question, he needs pristine, year-long data on the microbiology of the surface Arctic ocean. He uses an instrument called a membrane inlet mass spectrometer to “sip out” dissolved gases like argon and oxygen from the ocean water stream. Calculations applied to the gas contents can then tell scientists the rate at which the microbes are photosynthesizing or respiring carbon.

The science has been continuing apace, which is good because there is no way for anyone to get off the ship except for medical emergencies. For starters, the cruise itself is bearing out the phenomenon its scientists want to study: the rapid change in the Arctic because of climate change. The sea ice into which the ship is embedded is moving and breaking up so fast, it hasn’t been possible to establish a landing strip for the fixed-wing aircraft that were planned to be used to transport people to and from the ship, Bowman said. In one recent 24-hour period, the ship drifted 30 kilometers (19 miles) southward.

Even if the ice were sufficiently intact to accommodate a plane, “none of the providers of fixed-wing aircraft or long-haul helicopters are able to fly due to various airport closures and restrictions in Norway, Canada, and Russia,” said Bowman.

The same goes for other icebreakers that might go meet Polarstern. “Most of these vessels are under restrictions that prevent them from carrying passengers at this time,” said Bowman.

The project is an international effort and many researchers can’t easily travel to Germany to stage for transport to the vessel because of coronavirus-related restrictions. Even if they could, they would likely need to be quarantined for a period to make sure they would not deliver the virus to Polarstern. Currently cruise organizers are considering all avenues to continue the expedition, including returning the ship to port until it can be repositioned further north, Bowman said.

Keeping Eyes on the Oceans

The Argo network of robotic floats spread through the world’s oceans represents the most comprehensive study of the oceans in history.  Argo teams, including Scripps Oceanography, are working to maintain as many of the 4,000 floats in the Argo network as possible. This involves deploying new floats at a rate sufficient to balance the loss of old ones. With production capacities impacted, researchers are first drawing on the inventory of floats that are finished or nearly finished held by global Argo partners. Argo is a multinational effort, with each national program doing what it can to sustain the global network through acquisition and deployment of floats.

Argo floats measure fundamental ocean conditions such as temperature, salinity, and current speed and direction to depths of 2,000 meters (6,560 feet). Some in the network are designed to travel to 6,000 meters (20,000 feet) and others are outfitted with extra sensors that measure what scientists call biogeochemical variables to estimate the ocean’s carbon cycle and acidification, and give a sense of the activity of marine organisms in a given area. Among its many applications, Argo is the primary source of ocean data for assessing the increasing heat content of the climate system. 

Upkeep requires deployments from ships and relies heavily on the research fleet. Most research vessel operations worldwide are presently suspended but may be resumed in the coming months. All Argo teams, nationally and internationally, are positioning themselves for resumption of deployments when conditions permit, to avoid a major hiatus and gaps in the Argo time-series. By assessing present float inventories worldwide, adding to the stock of deployable floats, and liaising with ship operators, the disruption to Argo’s critical ocean and climate time-series will be minimized, said Scripps Oceanography Argo Principal Investigator Dean Roemmich.

The California Current Ecosystem Long-Term Ecological Research (LTER) program monitors the productivity of and changes to the California Current, an upwelling ecosystem responsible for the abundance of life off the Pacific Coast. 

Mark Ohman, professor of biological oceanography at Scripps and lead principal investigator of the LTER, has shifted the focus of the program to analysis for the time being.

Most of the team is working remotely, delving into extensive data from research cruises, satellite remote sensing, glider and Zooglider deployments, and moorings at sea. The program relies heavily on collaborations at Scripps Oceanography, especially with numerical modeling groups, and this work continues from home. The lab is still staffed by graduate students finishing crucial DNA extractions, and by the lab director, who ensures the security of crucial freezers, plankton sample archives, and computer resources.

Despite this continued work, Ohman stresses that the program is likely to experience major interruptions of important ocean time series collections. One of these is the CalCOFI cruise scheduled for April.

“If it does not occur, this will be the first time in nearly 50 years that this program has not sampled the California Current System in springtime, a biologically and oceanographically important season,” said Ohman. “Once sampling is missed, those ocean observations are lost forever.”

An additional cruise scheduled for April to service three moorings will also likely be cancelled. Ohman worries that if delayed too long, the mooring batteries will die and data acquisition will stop, interrupting another important time series.

Keeping Cultures Alive

cultures in flasks in a lab

Several labs around Scripps Oceanography must continue to keep organisms being cultured on campus alive – for the sake of the organisms and to prevent the loss of records that have taken months or years to compile.

Lisa Levin, a biological oceanographer at Scripps, had to close down her lab almost entirely.

“We have been forced to shut down everything but feeding oysters,” said Levin, who studies deep-sea communities and low oxygen levels in various ecosystems. “It’s easy to sense my frustration, with the losses and the effects on the careers of those in my lab.”

Postdoctoral researcher Lilly McCormick—who received her PhD from Scripps with Levin as her advisor—has had to put on hold physiology, metabolic, and behavior experiments on larval fish for National Science Foundation (NSF)-funded research that is determining the effects of changing oxygen conditions on sensory systems in early life stages of marine organisms. McCormick is in the final stretch of the award, creating added pressure on her experiments.

Scripps Oceanography is also home to one of the largest collections of marine cyanobacteria in the world. Scientists with the Center for Marine Biotechnology and Biomedicine have spent decades collecting these chemically-rich marine bacteria from around the globe to investigate them for anti-cancer, anti-parasitic, and antimicrobial properties. 

“It’s really an unmatched collection unlike anything else in the world, especially since we have already sequenced many of the genomes of these bacteria,” said Wiliam Gerwick, a biochemist who holds a joint professorship with the UC San Diego’s Skaggs School of Pharmacy and Pharmaceutical Sciences.

While some specimens can be stored via cryopreservation in freezers at minus-80 degrees Celsius, most cannot, and must be maintained in petri dishes or flasks that must be refreshed weekly by trained technicians to keep the bacteria alive. 

Gerwick’s Lab, which manages the marine cyanobacteria collection, also stores human cancer cell lines that they use to test the cancer-fighting potential of the cyanobacteria. These cells must continue to be maintained in liquid nitrogen, which would slowly evaporate without occasional replenishment. The lab will be doing monthly replenishment of the liquid nitrogen, he said.

Scripps coral ecologist Jennifer Smith has been working on a multiyear project to cultivate a marine algae called Asparagopsis taxiformis, which produces a compound that could halt bovine production of methane, a powerful greenhouse gas that is 30 times more potent than CO2. This is significant because more than half of all methane emissions in California come from livestock, primarily from the state’s 1.8 million dairy cows as they burp, exhale, experience flatulence, and produce manure.

“We collected these algae from more than 10 different places and have painstakingly cultured, sequenced, and analyzed this methane-halting compound,” said Smith. “If we were to lose those, we’d lose all that time and effort.”

To keep the algae maintained, Smith and postdoctoral researcher Gal Dishon alternate days when they go to the lab. These cultures must be checked every day, as living cultures could easily become compromised due to disconnected tubes, leaks, or pathogens in the samples.

“It’s not just about keeping them alive, it’s about thinking of them as a living library,” said Smith. “We searched long and hard for these particular strains, the ones that are hardiest for cutting methane emissions.”

Cliffs Still Crumble

While people have cleared out of Southern California beaches, that does not stop coastal cliff erosion. Given the erosion activity of cliffs in Del Mar, Calif., and ongoing cliff stabilization efforts, weekly surveys contribute to an important data set to improve understanding of changing terrain.

Scientists from the Center for Climate Change Impacts and Adaptation at Scripps will continue to conduct high-resolution LIDAR surveys of cliffs and beaches in Del Mar to monitor changes, continuing surveys that began in 2001.

These two-person surveys have been altered to enforce distancing guidelines. The LIDAR is typically mounted on a truck. Scientists have now reconfigured the LIDAR to an all-terrain vehicle (ATV) that better allows for distancing.

“Maintaining this long record is of great importance to the state, allowing the state to assess the safety of projects along the coast,” said Adam Young, the project scientist overseeing the surveys.

Scripps Oceanography Program Keeps Supply Chain Afloat

The Coastal Data Information Program (CDIP) at Scripps measures, analyzes, and disseminates coastal environment data for use by coastal engineers, planners and managers, as well as scientists and mariners. Data on wave height and direction is critical for safe maritime navigation, particularly for shipping, and long-term sea-surface temperature readings provide important information on ocean warming trends. 

CDIP has research continuity plans in place for all of its operations and projects. While working from home, team members are managing nearly 70 active buoy stations around the world, each of which transmits data every 30 minutes. 

“In many locations the buoy data are critical for maritime safety, domestic security, and national defense,” said CDIP manager Jim Behrens. “We are still responding to the need to replace buoys and moorings, both on regular maintenance schedules, and in response to ship strikes and mooring failures.”

Testing and refurbishing buoys between deployments also needs to continue, as does assembling the moorings, so the team has a social distancing plan in place to allow critical buoy shop operations to proceed at the Scripps facility, Behrens said.

All CDIP buoys will eventually run out of batteries if they aren't recovered first. A deployment life span is from 18-36 months, depending on buoy configuration. The team can dial back the data call rate and data transfer volume to buy some extra battery endurance, and is doing so for buoys that are within a few months of battery depletion. Behrens said a worst-case scenario is that they may have to start hiring boats to tow the buoys in to shore to prevent power loss at sea, with no operational capacity to re-instrument the moorings.

“Environmental data sets increase in value with both length and continuity, of course,” said Behrens. “CDIP's mission continues to be to provide both aspects to the best of our ability.”

A Silver Lining in Cleaner Skies

The Advanced Global Atmospheric Gases Experiment (AGAGE) and the Los Angeles Megacities project are two trace-gas measurement networks with hubs at Scripps Oceanography. A skeleton crew of researchers keeps on-campus instruments running, supporting the maintenance of AGAGE instruments around the world, and of L.A. Megacities instruments in Southern California. They also perform some data quality control and data processing that cannot be done remotely, working under social distancing protocols established by UC San Diego, but most of this work is now done remotely from makeshift home offices.

To date, all AGAGE stations around the world are operational, but access to some of them is limited and this puts the work at added risk, said Scripps Oceanography geochemist Ray Weiss, a lead scientist in both programs. For instance, an AGAGE station in American Samoa could soon be without its manager. Commercial flights to American Samoa have been suspended at least for several more weeks. The manager might have to be evacuated by military flight, depending on the progress of the COVID-19 crisis on the island.  Meanwhile one instrument in American Samoa is already shut down and awaiting repair that cannot be carried out because of travel restrictions. 

Stations in both networks will help to tell the story of how the atmosphere responded to the slowdown in greenhouse and pollutant gas emissions due to the present crisis. AGAGE measures more than 50 different environmentally important human-caused atmospheric gases, including a wide range of potent industrial greenhouse gases and substances that deplete the stratospheric ozone layer. Only certain sectors of global activity are being curtailed by the crisis, such as transportation and some construction and manufacturing, while other activities such as refrigeration, air conditioning and power generation are continuing.

For L.A. Megacities, researchers are beginning to look for signals in the data of changes in emissions of carbon dioxide, carbon monoxide and methane across the greater Los Angeles area that may be associated with reductions in some fossil fuel burning activities such as transportation. From initial looks, it does appear that there have been measurable reductions in emissions, with the largest signal likely being in carbon monoxide, Weiss said.

Global carbon dioxide operations managed by several agencies including Scripps Oceanography continue unabated with appropriate social distancing. Media attention has turned to whether COVID-19 will have an appreciable effect on global carbon dioxide levels that have broken their upward trend only slightly a few times during the most significant global events—including world wars, depressions, and recessions—of the last three centuries.

In response, Scripps Oceanography geochemist Ralph Keeling and other climate scientists suggest it might take a year of prolonged downturn for the drop in CO2 emissions to show up clearly at remote stations such as Mauna Loa. Assuming the economy rebounds after the COVID-19 crisis, emissions will almost certainly rebound. To have a significant impact on the climate problem, the crisis would need to lead to permanent changes in human behavior such as reductions in reliance on fossil fuels,  more telecommuting or less long-distance travel, Keeling said.

The Oceans Get Quieter

Researchers in the Scripps Whale Acoustics Lab study the ecology of marine animals and the impact of anthropogenic sounds on them using acoustic techniques and technology. Due to coronavirus impacts, most of the lab’s field operations have been suspended because the research vessels they typically use are not allowed to operate at this time.

In the meantime, the researchers have a trove of previously collected data that can be analyzed remotely.

“We have a large archive of recordings collected over the past twenty-plus years and we will continue to analyze these for marine mammal presence and ocean noise,” said John Hildebrand, distinguished professor of oceanography and director of the Scripps Whale Acoustics Lab.

Many of the lab’s instruments are still in the ocean collecting data, but as time goes on their batteries and data storage will be exhausted and they will stop collecting data. When field operations resume, however, data from these instruments may give researchers a glimpse of what the ocean sounds like during a pandemic-driven slowdown in commerce. Hildebrand recalls that in 2008, during the financial crisis, there was a decline in the number of commercial ships at sea and his lab documented an associated decline in ocean noise levels.

“We expect that this will also be the case during the COVID-19 shutdown,” he said. “In addition to commercial shipping, we expect that there also may be a decline in sonar usage, but study of this must wait until we can recover the data currently being collected. It will then be important to see if marine mammals and other organisms behave differently in a quiet ocean.”

Wildfire Readiness

ALERTWildfire‘s network of 350 cameras throughout California provide early confirmation of fires for officials and first responders, and will remain operational during this time as an essential public safety tool. The cameras, all viewable at, are routinely monitored by first responders.

While the state isn’t currently experiencing any of the “red flag” dangerous fire conditions that come in fall, there are still fires to look out for, including a recent fire spotted on the cameras in the Mojave desert.

Scripps geoscientist Neal Driscoll leads the effort for UC San Diego. Driscoll said that installation of new cameras has slowed down significantly since the stay-at-home order went into place. 

“We had been installing 20-30 new cameras per week, but our subcontractors doing the installation have slowed that to about five to ten cameras per week to maintain physical distancing for the crews working on installation,” said Driscoll.

ALERTWildfire scientists are  hoping to install another 300 cameras once the stay-at-home order has been lifted, to ensure more complete coverage of fire-prone areas of the state. The challenge will be to complete the installation in a compressed timeline before next fall.

For those who need a dose of the outdoors, the cameras provide beautiful views from California’s mountaintops.

– Reported by Brittany Hook, Chase Martin, Robert Monroe, and Lauren Fimbres Wood

About Scripps Oceanography

Scripps Institution of Oceanography at the University of California San Diego is one of the world’s most important centers for global earth science research and education. In its second century of discovery, Scripps scientists work to understand and protect the planet, and investigate our oceans, Earth, and atmosphere to find solutions to our greatest environmental challenges. Scripps offers unparalleled education and training for the next generation of scientific and environmental leaders through its undergraduate, master’s and doctoral programs. The institution also operates a fleet of four oceanographic research vessels, and is home to Birch Aquarium at Scripps, the public exploration center that welcomes 500,000 visitors each year.

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