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Let our powers combine

Five members of the Carbon Flux ecology team onboard the Paragon with a drifting sediment trap in the water behind them.
Members of the Carbon Flux Ecology team. Image: Jared Figurski © 2023 MBARI

Let our powers combine

Written by: Colleen Durkin (team lead, MBARI scientist)

Choosing a “team name” was my first big decision when I started working as a scientist at MBARI. I was warned that these names tend to stick around for a long time, so be careful what you choose. But how can a few short words adequately communicate the entire scope of our work and the variety of our expertise? Our passion for taxonomy spans from microscopic algal cells to deep-sea octopuses. We probe genomes for processes at the molecular scale and satellite images at the global scale. Our team includes oceanographers, biogeochemists, microbiologists, zoologists, engineers, computer vision data analysts, and molecular ecologists. We design new instrumentation, perform our work at sea in all conditions, spend hours at the microscope or the fume hood, and sometimes lose ourselves inside a Python script.  What ties these efforts together is our shared mission to radically advance observations of carbon sequestration in the deep ocean by sinking particles. Okay, so I finally arrived at the “Carbon Flux Ecology” team name.

A map of Monterey Bay, including the bathymetry of the canyon with an animation of the path that our trap took between deployment and recovery.
Drifting path of our sediment trap deployed in Monterey Bay and recovered 24 hours later. Map: Colleen Durkin © 2023 MBARI

We think that major advances in measuring and monitoring the ocean carbon cycle will only be achieved by melding our distinct and very diverse perspectives together. A basic premise of our work is that small-scale ecological interactions matter. These behaviors, adaptations, and minute characteristics control the processes we can feel at the global scale, such as how much climate-warming CO2 is sequestered away from the atmosphere and into the ocean, how much food is fueling deep-sea ecosystems and fisheries, how much primary production fuels surface ecosystems, when will low-oxygen “dead zones” form near the seafloor?

This July, our team had its first opportunity to combine our varied expertise when we deployed a surface-tethered, free-drifting sediment trap to collect sinking particles in Monterey Bay. This type of sinking-particle collector is the established method for quantifying carbon sequestration into the deep ocean, and the samples also allow us to study the biological and genetic composition of sinking particles. Unfortunately, these trap deployments are not scalable and will never provide the observations needed to resolve changes at the global scale. Our team is using sediment traps to ground truth more scalable methods and using the physical samples to probe the otherwise invisible ecological interactions that control carbon export in the ocean.

Underwater cameras that image particles and plankton

Two scientists onboard a small boat preparing the deploy an instrument
Senior Research Specialist Crissy Huffard prepares to deploy the Planktivore underwater microscope camera system. Image: Natalia Llopis Monferrer © 2023 MBARI

On this trip we deployed a new instrument designed by MBARI engineers called Planktivore. This underwater microscope can image plankton and particles as we lower it down from the surface ocean through increasing depths. Crissy Huffard, senior research specialist, has more than a decade of experience deploying underwater camera systems and turning the data generated by these new instruments into valuable discoveries about deep ocean ecosystems.


Probing the molecular physiology of creatures that control carbon export

Scientist looking through a microscope while holding a pipettor toward the sample underneath.
Natalia Llopis Monferrer isolating phaeodarian cells. Image: Colleen Durkin © 2023 MBARI

We also collected physical samples of the plankton populations by pulling a plankton net through the water. We can compare these samples to what the Planktivore underwater microscope detected and also use them for experiments. On this trip, Natalia Llopis Monferrer, MSCA postdoctoral fellow, was excited to detect a large number of phaeodarian heterotrophic protists in the water.

microscope image of a geometrically shaped glass organism
One of the phaeodarian glass protists we collected, imaged under a microscope. Image: Natalia Llopis Monferrer © 2023 MBARI

These single-celled creatures build glass structures that are more than 1 cm wide. They consume sinking marine snow particles and are probably an important control of how much carbon sinks into the deep ocean. Natalia isolated these cells under the microscope and successfully extracted the RNA for transcriptomics which will allow us to probe their physiological adaptations.

Linking our observations to broader time and space scales

A scientist onboard a small boat working at a laptop, sitting next to a black instrument on the floor of the boat
Sasha Kramer preparing the hyperpro instrument for deployment. Image: Colleen Durkin © 2023 MBARI

Our detailed observations from the R/V Paragon, collected at a single location and time, become more valuable when related to observing platforms with a persistent presence or that collect over large spatial scales. Ocean-color satellites have been orbiting the Earth for decades, collecting global-scale observations of phytoplankton communities in the surface ocean. Sasha Kramer, Simons postdoctoral fellow, is exploring how these global observations can be used to better predict carbon export.  On this trip, she deployed a hyperspectral radiometer to quantify surface phytoplankton populations in a way that is comparable to what an ocean-color satellite would detect. Sasha’s work brings together her expertise in ocean optics and our ecologically focused observations of carbon flux in a way that can be applied to the data collected by the next generation of ocean-color satellites. Sasha’s work at sea is already headed into space: NASA’s upcoming PACE mission will use the algorithm she developed to interpret ocean color observations.

Identifying the source of sinking particles that transport carbon to the deep sea

Scientists onboard a small boat holding a metal frame with collection tubes over the side of the boat.
Senior Research Specialist Sebastian Sudek recovering a sediment trap sample. Image: Natalia Llopis Monferrer © 2023 MBARI

Sinking particles form for different reasons, and some particles are more likely to reach the deep ocean than others.  To predict changes in carbon flux, we must know how ecology controls particle formation and export.  Imaging the sinking particles collected in our sediment trap tells us why the particles were formed (Did an animal poop? Which animal? Did the algae die and aggregate?). We can also use the images of our sample to calculate the relative contribution of these different particle categories to carbon export. We can discern so much by only using our eyes (with the help of image-processing computer scripts and machine learning classifiers!). However, some ecological links leave only a forensic trace inside the particles that will never be visible. To reveal these invisible connections, we also isolate individual particles and sequence the genetic contents, though sediment trap particles often present unique challenges when trying to apply typical laboratory protocols. Sebastian Sudek, senior research specialist, is a microbiologist and molecular ecologist with a special talent for making very difficult lab work look easy. His work on extracting the genetic community contents from within sinking particles will identify food-web interactions that drive carbon export that would otherwise remain invisible.

A scientist holding up a glass pill-shaped instrument
Fernanda Lecaros Saavedra with the “MINION” instrument prototype. Image: © 2023 MBARI

One of the most valuable outcomes of this first effort was demonstrating how to deploy and recover this trap array on the R/V Paragon and to successfully collect flux observations in dynamic coastal currents near the shelf break.  In the next few months, we will repeat this deployment in combination with additional autonomous assets. For example, Fernanda Lecaros Saavedra, research technician and engineer, is developing new camera systems that attach to miniature glass floats that will autonomously measure sinking particle fluxes. This is also a collaboration with Melissa Omand at University of Rhode Island. We are excited by the challenge of synthesizing all of these cross-disciplinary data types.

animated gif from the cartoon "Captain Planet"
Image: GIPHY

If you read this far, thank you for your interest in our work. Future posts will highlight the efforts of each of our team members in more detail. Go team!