BATS, Big Data, and the Base of the Marine Food Web

The collaborative BIOS-SCOPE project brings together researchers from around the world to study the microbial processes of the Sargasso Sea, with the goal of understanding how carbon is cycled through the marine environment. Doctoral student Fabian Wittmers (right) and his mentor, ocean ecosystems biologist Alexandra Worden, both at the GEOMAR Helmholz Centre for Ocean Research Kiel, Germany, are tracking the movement of carbon within the base of the marine food web (phytoplankton). On a recent BIOS-SCOPE cruise, Wittmers and Michelle Michelson, lab manager of the Temperton research group from the University of Exeter (U.K.), stood aboard the deck of R/V Atlantic Explorer after finishing a cast of the CTD, a large piece of oceanographic equipment which is used to collect samples of seawater. Photo by Noah Germolus.

In mid-November, the BIOS-operated research vessel Atlantic Explorer headed into the Sargasso Sea for the eighth research cruise as part of the multi-year, multi-institutional BIOS-SCOPE (Bermuda Institute of Ocean Sciences - Simons Collaboration on Ocean Processes and Ecology) project. Since 2015, scientists from Bermuda, Germany, the United Kingdom, and the United States have converged at BIOS to investigate the microbial ecology of the Sargasso Sea and understand how organic matter (carbon) cycles within the marine environment.

To prepare for the cruise, more than a dozen scientists readied for four days at sea by packing scientific equipment and labeling chemical reagents. Doctoral student Fabian Wittmers, from the GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany, carefully washed and rinsed many bottles and labeled 300 cyrovials for preserving samples in liquid nitrogen.

“The bottles were used in other experiments, so there may be traces of organic material left in them,” explained Wittmers. “We needed them to be clean, because we were using them to collect samples of seawater for experiments with various species of phytoplankton.”

Any leftover organic matter could contaminate the results, potentially undoing all of the hard work that goes into an international scientific excursion at sea, particularly one conducted during a global pandemic.

Agents of Mortality

Wittmers is a student in the laboratory of Alexandra Worden, a BIOS-SCOPE investigator and GEOMAR professor of ocean ecosystems biology. Worden joined the BIOS-SCOPE project during its renewal phase in 2020, when the Simons Foundation International gave the green light for five more years of funding. Together, Wittmers and Worden are using the information they obtain from samples and experiments on BIOS-SCOPE research cruises and combine it with data from the Bermuda Atlantic Time-series Study (BATS).

Worden was excited to join the effort, in part due to its connection to BATS, which she sees as “an outstanding global resource for examining ocean change, being one of the few long-term open ocean research programs.” BATS is run 50 miles (80 kilometers) off Bermuda and has been collecting biological, chemical, and physical oceanographic data on a monthly basis since 1988. By combining these two data streams into larger data sets, or big data, Wittmers and Worden hope to understand what they refer to as “agents of mortality.”

Every BIOS-SCOPE cruise involves the coordination of at least a dozen scientists and technicians. And while each researcher is there to conduct their own study, there is also a strong sense of teamwork. Here, Wittmers (left) and Craig Carlson, BIOS-SCOPE program director and co-principal investigator, “take five” before in-situ pumps were retrieved from the Sargasso Sea. Wittmers and Carlson assisted BIOS-SCOPE investigator Hilary Close, assistant professor at the Rosenstiel School of Marine and Atmospheric Sciences (U.S.) and doctoral student Lillian Henderson with demounting the pumps from the wire after they arrived on the back deck of R/V Atlantic Explorer. Photo by Henderson.

As Wittmers and Worden explain, the way an individual phytoplankton meets its demise impacts the way an atom of carbon moves up the food chain. If the phytoplankton is grazed on by another plankton, such as zooplankton or protists, the carbon moves up the food chain. However, if the phytoplankton is infected by a marine virus, the former organism can explode, releasing dissolved and particulate carbon back into the water column—and fueling growth of other organisms such as bacteria.

“Combining the grazing mortality and phytoplankton growth rates with other BIOS-SCOPE core sampling such as nutrients and dissolved organic carbon gives us an amazing baseline of data on the movement of carbon in the base of the food web at BATS,” Wittmers said.

Their research will answer one small part of the larger question that BIOS-SCOPE scientists are trying to figure out: what is the fate of organic matter in the water column, and what organisms (or mechanisms) affect its quality (transformation) and which organisms (mechanisms) are responsible for recycling it or moving it up the food web?

The Mystery of Mixotrophs

Worden and Wittmers are also interested in uncovering more information about the rates of grazing by mixotrophic protists on the phytoplankton species (and other microbes) at BATS. Protists are primarily microscopic and unicellular, and mixotrophic protists occupy a unique place in the natural community at BATS, as they are able to derive their energy and carbon from a combination of photosynthesis (autotrophy) and consuming other organisms (heterotrophy), such as bacteria.

By taking advantage of a natural property of certain elements called stable isotopes, the team can “label” marine organisms to keep track of who eats whom. For example, the most abundant form of carbon is called 12C and has six protons and six neutrons. By adding another neutron, scientists can make 13C, which acts the same as 12C for the most part, but can be “traced” when it is incorporated into living organisms.

Because phytoplankton operate in a similar manner to plants, they play a key role in taking up take up carbon dioxide during the process of photosynthesis, and generating the base food resource in the ocean. The team is able to grow phytoplankton in the lab in a manner such that the organisms incorporate stable isotopes. Their fate becomes traceable when they are incubated with the 13C and released into the natural community at sea, where the 13C can be followed through the food web.

Since 13C is heavier than 12C, molecules with this isotopic carbon are heavier and can be separated out, resulting in a process called stable isotope probing (SIP). In this process the separated DNA and RNA molecules are sequenced, allowing identification of which protists consumed the cells that had been labelled in the lab and incubated in the washed bottles at sea.

Experimental work using the SIP process with cultured strains of marine cyanobacteria (a group of small phytoplankton) and other common species of phytoplankton found at BATS will help Worden, Wittmers, and their BIOS-SCOPE collaborators estimate how much carbon is moving through the food web from phytoplankton to higher trophic levels such as mixotrophic protists.

“The oceans are changing fast, and BIOS-SCOPE is positioned to elucidate basic aspects of ocean food webs that are still not known,” Worden said. “It is incredibly exciting to be able to make the connections between different members of the microbial community and their ultimate fate with all the context that BIOS-SCOPE is pursuing, and in such an important ecosystem.”

"Fabian and Alex have been great additions to the BIOS-SCOPE team that has brought a new dimension to studying carbon biogeochemistry and tracking carbon flow within the microbial food web at BATS,” said Craig Carlson, professor at the University of California at Santa Barbara, BIOS adjunct professor, and the BIOS-SCOPE program director and co-principal investigator.