USC Microbial Observatory at the San Pedro Ocean Time series (SPOT)

Running since 2000, the USC Microbial Observatory (MO) and the related Dimensions of Biodiversity (DOBD) projects focus on time-dependent changes in prokaryotic and unicellular eukaryotic community composition in relation to environmental parameters. These projects occur within the context of the San Pedro Ocean Time Series , a monthly time series since 1998 run by the Wrigley Institute for Environmental Studies.

SPOT and other sampling sites

Map of Study Sites: The Port of Los Angeles (POLA, 33°42.75’N, 118°15.55’W), the San Pedro Ocean Time series station (SPOT, 33°33′N, 118°24′W), and a site off of Santa Catalina Island (CAT, 33°27.17’N, 118°28.51’W).

Our primary sampling site (SPOT) is located midway between Los Angeles and the USC Wrigley Marine Laboratory on Santa Catalina Island in approximately 900 m of water (33°33′N, 118°24′W). This site is visited monthly by ship for sampling to 890 m depth.

From 2012-2014, quarterly sampling also took place at two other locations, one off the coast of Santa Catalina Island (CAT, 33°27.17’N, 118°28.51’W) and one within the Port of Los Angeles (POLA, 33°42.75’N, 118°15.55’W). These other locations help us to elucidate patterns in biodiversity related to anthropogenic impacts.

Routinue monthly measurements (SPOT)

As part of the San Pedro Ocean Time Series, basic oceanographic parameters are measured monthly by the Wrigley Institute for Environmental Studies. Continuous measurements are made with various sensors fixed to a Conductivity/Temperature/Depth (CTD) profiler. These include temperature, salinity, PAR, chlorophyll, CDOM fluorescence, dissolved oxygen. Bottle measurements are also taken at discrete depths from water collected in niskin bottles fixed to the CTD (nitrate, nitrite, phosphate, silicate, dissolved oxygen, chlorophyll-a, salinity). These are measured at the following depths (in meters) 2, 10, 20, 30, 40, 50, 60, 100, 250, 500, 750, and 885.

For the Microbial Observatory, routine monthly sampling includes monitoring the following at 5 m, the chlorophyll maximum (CMAX or DCM), 150 m, 500 m, and 885 m:

  • the abundance of the microbial assemblages by flow cytometry (Synechococcus, Prochlorococcus, total prokaryotes, phototrophic picoeukaryotes),
  • microscopic enumeration (phototrophic and heterotrophic nanoplankton, microplankton, prokaryotes, viruses),
  • prokaryotic activity by incorporation of labeled leucine and thymidine
  • microbial diversity, genomics (prokaryotes, protists, and viruses), gene expression (protists, prokaryotes), and viral gene activity by an array of molecular-based techniques including:
    • Historically: ARISA (Automated Ribosomal Intergenic Spacer Analysis) and TRFLP
    • Now (and retrospective re-analysis): Tag sequencing (16S and 18S rRNA gene fragment sequencing)
    • Some date ranges: g23 sequencing (myoviruses), cyanobacterial internal transcribed spacer (ITS) sequencing, SAR11 ITS sequencing
    • some dates:SAG analysis (Single Amplified Genomes)
    • Recent: Shotgun metagenomics of bacterial and viral size fractions
    • Recent: Shotgun metatranscriptomics of protists (polyA selected) and also the entire commmunity (sometimes rRNA depleted)

These techniques provide abundance and activity measures of the entire microbial community, including bacteria, archaea, viruses and eukaryotes. Molecular biological analyses of these samples provide culture-independent estimates of microbial diversity, pathways, and processes.

These monthly measurements make up the core data set for the project. An important part of the project is to use these data to determine the time-dependent changes in microbial community composition and to try to learn what physical, chemical, and biological factors regulate that composition. While most of the microbial work is broad-based, meaning it looks at the entire community, we also have studies that focus on particular taxa or functional groups. For example, we use genetic analysis to examine the time-dependent change in cyanobacteria and their viruses, the SAR11 group, aerobic anoxygenic photosynthetic bacteria, and bacteria that possess genes for nitrogen fixation. Culture efforts with eukaryotes are focused on obtaining representative protistan taxa in laboratory culture, and linking genetic signatures to morphotypes of these species.

Quarterly Sampling (POLA, SPOT, CAT)

From 2012-2014, quarterly sampling was performed by taking surface samples at POLA, SPOT, and CAT, and samples were analyzed in a manner similar to that for monthly sampling. In addition, grazing experiments were performed.

Finding connections and microbial interactions

Our collaboration with Dr. Fengzhu Sun in the USC computational biology program uses our sequence and othe rmicrobial data to develop statistical and networking tools for data analysis and interpretation.


Fuhrman Lab
University of Southern California
3616 Trousdale Parkway, AHF 230
Los Angeles, CA 90089-0371


Caron Lab
University of Southern California
3616 Trousdale Parkway, AHF 301
Los Angeles, CA 90089-0371



The USC Microbial Observatory is currently supported by the National Science Foundation under Grant No. 1737409 and by the Moore Foundation grant 3779 and and Simons Foundation grant 549943. Past support has been through NSF grants  0084231 (from 2000-2007), 0703159 (from 2007-2013), and 1136818 (2011-2016)