Award: OCE-1948025

Biodiversity underpins key ecosystem services like primary production.  In the ocean, phytoplankton account for roughly half of global primary production, cycling on the order of 65 Gt of carbon every year.  Of these phytoplankton, coccolithophores are critically important because of their ability to form blooms and form calcium carbonate plates (calcify) which can drive export of carbon to the deep sea. Numerically, Gephyrocapsa (formerly Emiliania) huxleyi is the most abundant coccolithophore species in the present ocean known for its cosmopolitan distribution. Initial genome sequencing of several G. huxleyi strains suggested that there was gene content variability across strains—termed a ‘pan genome.’ The role of genomic variability in the ecology and biogeography of eukaryotic phytoplankton like G. huxleyi has not been comprehensively examined, and we lack a basic understanding of how the biodiversity of G. huxleyi predicts its distribution across current and future ocean conditions which motivated this research.

This research focused on defining the role of the pan genome in G. huxleyi ecology and biogeography by addressing the following questions with culture experiments, genome sequencing, and field observations:

Q1: How does gene content vary across the genomes of G. huxleyi strains?

Q2: Does the composition of the variable gene set influence G. huxleyi growth under different conditions ?

To address these questions we sequenced and analyzed 16 complete G. huxleyi genomes that span the diversity of this species, providing a new view of the genomic landscape of this important coccolithophore.  From this genome sequencing, a G. huxleyi pan genomic database that defines the core (present in all strains) and variable (present in some strains) portions of the pan genome was constructed. The genomes and the database provide a critical, lasting, resource for further studies on the biodiversity of this organism.  A series of culture experiments showed that the variable gene content, and its expression, is linked to differences in the growth of G. huxleyi strains over different temperatures and resource concentrations.  In short, variation in the variable genes present in different strains appears to drive differences in their success in different environmental conditions.  These findings provide a basis for understanding what environmental factors predict phytoplankton distributions, and the resilience of G. huxleyi populations to shifting conditions.  

In addition to the outcomes noted above, we used the goals of this project to promote awareness that marine microbes play an important role in the habitability of our planet by cycling resources like carbon and nitrogen and other key aspects of the ocean science literacy principles.  To do this, we used a suite of activity platforms to engage the public and diverse learners (e.g., classroom visits, demonstrations, public lectures, etc.).  Some highlights include participation in the Lamont-Doherty Earth Observatory Open House, which attracted thousands of New York City and tri-state families, and in NYC Kids Week on the Intrepid which attracts 25,000 attendees and where this project supported interactive content on the importance of marine phytoplankton to the habitability of our planet and their role in food webs (key ocean science literacy principles).  In addition to these efforts with informal learning, this project also supported formal mentoring of early career researchers in a post-baccalaureate Bridge to Ph.D. program, and provided advanced training on bioinformatics applications in ocean science via an international Genomics Workshop offered annually to roughly 100 participants. Collectively, this project supported a rich set of opportunities to advance ocean literacy, increasing the public’s understanding of oceanography, and providing advancement opportunities for early career researchers.

Last Modified: 06/12/2026
Modified by: Harriet Alexander