My research focuses on how phytoplankton, fecal pellets, and other detrital particles influence carbon export out of the surface ocean through a process called “the biological pump”.  Currently, I am motivated by three major question:

  1. Which particles and cells are transporting carbon through the water column?
  2. What physical and biological processes can explain or predict why these particles and cells sink?
  3. How are (genetic) adaptations and diversity in phytoplankton linked with the carbon cycle?
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Collage of diverse diatom species

I use a variety of methods to study phytoplankton, including microscopy and gene expression.  I use these techniques to observe natural communities.  Laboratory experiments with cultured isolates help interpret what we are observing in the field.

To determine the consequence of surface phytoplankton biology on biogeochemistry, I use sediment traps to collect particles sinking out of the surface.  Sediment traps are upward-facing tubes that collect sinking material and they come in a variety of models.  Here are the types I have used along with my collaborators:


Usually, we include clear gel layers on the bottom of trap tubes to collect sinking particles and make sure they remain intact and distinctly separated from each other.  These particles can be analyzed in more detail by microscopy.

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example of cells (left) and particles (right) imaged in sediment trap gel layers

Current Projects

NASA EXPORTS: Linking satellite observations of surface plankton with carbon export into the deep ocean

collaborators: Margaret Estapa (Skidmore College), Melissa Omand (University of Rhode Island), Ken Buesseler (Woods Hole Oceanographic Institution)
NASA project title: Linking sinking particle chemistry and biology with changes in the magnitude and efficiency of carbon export into the deep ocean (link to NASA project)

The NASA EXPORTS project is a comprehensive process study that brings together a large, collaborative team of scientists to measure every component of the biological pump.  The first field campaign occured the North Pacific in the summer of 2018.  The synthesis of these quantitative measurements will lead to the development of more accurate models of carbon uptake by the ocean based on satellite observations.  Our team deployed a suite of sediment traps at multiple depths to capture the particles and organisms that are sinking over the course of the process study.  We will also deployed a water column profiling Wire Walker to measure water column properties highly resolved in depth and time.  The Moss Landing Lab team is specifically responsible for quantifying the flux of different particle types (aggregate, fecal pellets, organis

imaging gels during EXPORTS

ms) collected in sediment traps and the genetic composition of those particles (18S and 16S rRNA sequence identities).  Our team is testing 3 specific hypotheses: 1) Key organisms drive the magnitude of elemental fluxes from the base of the euphotic zone, 2) Key organisms and their organic matter are transported by distinct export pathways, which determine the transfer efficiency of elemental fluxes through the water column, 3) Different export pathways are associated with specific temporal scales in flux (e.g. steady vs. episodic flux).

Linking surface phytoplankton with sinking particles to resolve mechanisms of the biological pump

collaborators: Melissa Omand (University of Rhode Island), Margaret Estapa (Skidmore College)
NSF project title: Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump (link to NSF)

The goals of this project are to :

1) Observationally resolve which organisms are exported from the surface ocean and the mechanisms that lead to their transport.
2) Develop a new particle-specific DNA sequencing approach to link specific organisms with sinking particle types and constrain sources of uncertainty.

particles that sank into a polyacrylamide gel layer inside a sediment trap tube

Carbon is fixed into organic matter by phytoplankton growing in the surface ocean, and is naturally sequestered in the ocean interior when particles and organisms sink: a process called the “biological pump.”Accurate prediction of the global carbon cycle requires an understanding of the specific processes that link surface plankton communities and sinking particulate carbon flux (export) out of the surface ocean,  but this process is still very difficult to quantify and predict.  We must resolve the underlying mechanisms that produce and transport sinking particles to better quantify carbon export in the ocean. We deployed a suite of drifting instrument platforms to fully resolve upper water column physical and chemical properties and to quantify the particles sinking below this surface environment. We conducted 2 pilot studies in November 2015 and June 2016 at the New England shelf break, where we deployed a surface profiling Wire Walker and multiple sediment traps that contain polyacrylamide gel layers on the bottom.  These initial cruises taught us how to coordinate these platform deployments and how the data sets collected by each platform can be integrated to create a more complete picture of carbon export.  Microscopic examination of these particles, combined with the high resolution optical and chemical measurements made by Melissa Omand and Meg Estapa, will enable us to characterize how and what types of particles are exported.

In February 2017 we sailed on the R/V Falkor from Hawaii to Portland, OR during the “Sea to Space” research cruise.  On this cruise, we added DNA sequencing to our suite of particle-resolving observations.  By sequencing the DNA contents of individually isolated particles collected in the gel trap layers, we will identify direct linages between specific phytoplankton in the surface and the mechanisms of carbon export.  Our hypothesis is that different members of the surface phytoplankton community are transported out of the surface ocean by distinct export pathways which occur over a range of timescales.

This work is supported by the National Science Foundation Biological Oceanography “EAGER” program (Early-concept Grants for Exploratory Research).

related publications:
Durkin et al. 2015. Observations of carbon export by small sinking particles in the upper mesopelagic. Marine Chemistry 175: 72-81 (link)
Estapa et al. 2015. Carbon flux from bio-optical profiling floats: calibrating transmissometers for use as optical sediment traps. Deep Sea
Research I
. 120:100-111 (link)

Phytoplankton and particle export to the abyssal seafloor

collaborators: Ken Smith (MBARI), Crissy Huffard (MBARI), Chris Preston (MBARI)
California Sea Grant project title: How does climate change affect the export of phytoplankton to the seafloor? (link to Sea Grant project)

Rapidly settling particles can effectively transport surface phytoplankton and other organic matter to the abyssal seafloor (4000 m), fueling deep sea ecosystems and also leading to long-term carbon sequestration.  Ken Smith (Monterey Bay Aquarium Research Institute) has been observing the flux of organic carbon to the seafloor in the California Current for nearly 30 years, over which time carbon export has increased.  In this project, we look for clues about why these changes have occured in the quantity and composition of phytoplankton cells present in these archived sediment trap samples (example of what we see).  Previous microscopic analysis of these samples suggest that the increases can not be attributed to an increase in the supply of fecal material from above.  We think that changes in the surface ocean environment may have lead to greater or more efficient transport of phytoplankton/phyto-detritus to the seafloor.  We are testing the following hypotheses: 1) Different phytoplankton compositions are associated with sinking particles during high POC flux periods compared to low POC flux periods, 2) High POC flux events are caused by an increase in the supply of fresh phytodetritus to the seafloor, 3) Variability in phytoplankton flux is correlated with climate-related indices and surface production, 4) Benthic community composition changes and carbon consumption increases when food supplied by sinking particles is composed of fresh phytoplankton cells.

This work is the focus of MLML student Cynthia Michaud’s masters thesis.


Automated identification of sinking particles images using machine learning

collaborators: Jessica Sheu, recent graduate from San Jose State University masters in Computer Science

Advancement in oceanographic imaging-based methods has increased our ability to observe individually-resolved marine particles and organisms from many locations, across space, and over time. Analyzing these large imaging datasets has required the development of computational tools to rapidly categorize images. We have been training and testing models on datasets from 2 separate sources: images collected by a deep ocean imaging sediment trap moored off coastal California (the sediment event sensor, SES), and micrographs of gel layers deployed in mesopelagic-drifting sediment traps in 6 different coastal and open ocean environments.  We believe that this image classification model and library of categorized particle images will be useful for future image-based particle studies and will enable large image datasets to be analyzed in greater biological detail.