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Open Access Publications from the University of California

Scholarly Works (2 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2019)

Marine microbial communities consist of millions of species engaging in complex interactions with one another and with their environments over a variety of time scales. The field of marine microbial ecology has only begun to understand the true extent of the diversity – both of species themselves (which include members of the bacteria, archaea, and eukaryotic protists) and the ways they interact with one another. Many studies of marine species diversity represent snapshots of a community but do not capture the temporal dynamics of its members. In this dissertation I illustrate how the microbial community at a single site changes over time by collecting high-frequency samples at the Scripps Pier (La Jolla, CA, USA). I leverage amplicon sequencing to describe the bacterial and eukaryotic communities and find there to be detectable, occasionally very large, fluctuations, some with seasonal patterns and others on the order of days. I use this high-resolution sequence data to: identify putative grazers of the marine cyanobacteria Synechococcus (Chapter 1), characterize fine-scale changes in Synechococcus microdiversity over the course of blooms (Chapter 2), and suggest new Syndiniales parasite-host interactions at our site (Chapter 3).

    Cover page: Temporal Dynamics of Marine Microbial Communities at the SIO Pier
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2025)
    The diversity of the marine cyanobacterium Synechococcus can be broadly separated into clades, with clade II typically present in warm oligotrophic water, and clades I and IV found in cooler coastal water. We found amplicon sequence variants (ASVs) belonging to clade II in the nutrient-replete waters of San Diego Bay (SDB). Using the 16S rRNA gene, 18S rRNA gene and internal transcribed spacer region sequencing, we analysed multiple locations in SDB monthly for over a year, with additional samples dating back to 2015. Synechococcus community composition differed from the nearby coast into SDB in terms of dominant clade and ASVs. Specific clade II ASVs became relatively more abundant towards the back of the bay and showed seasonality, with higher relative abundance in the warm months. Select ASVs group phylogenetically and show similar seasonal and spatial distribution patterns, indicating these ASVs have adapted to SDB. Isolates matching clade II ASVs from SDB show pigment composition that is better adapted to the green light available in SDB, further supporting our findings. Other microbial taxa also show SDB enrichment, providing evidence that SDB is a chemostat-like environment where circulation, temperature, light and other environmental conditions create a zone for microbial evolution and diversification.
      Cover page: Temporal and Spatial Dynamics of Synechococcus Clade II and Other Microbes in the Eutrophic Subtropical San Diego Bay.
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