Project: Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series

Acronym/Short Name:SPOT
Project Duration:2017-08 - 2021-07
Geolocation:San Pedro Channel off the coast of Los Angeles

Description

Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.

This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.


DatasetLatest Version DateCurrent State
Environmental data, nutrients, and leucine and thymidine bacterial production from samples collected by CTD during cruises in the San Pedro Channel on R/V Yellowfin from 2005 to 20182022-12-29Final no updates expected
A characterization of microbes at the San Pedro Ocean Time-series (SPOT) from 2005 to 2018, using SSU rRNA gene sequencing from two size fractions, with a universal primer set that amplifies from prokaryotes and eukaryotes2022-12-29Final no updates expected
Nutrients (phosphate and nitrite+nitrate) from daily sampling at the Santa Monica Pier (SMP), Santa Monica Bay, CA from 2018 to 20192022-11-17Data not available
Sampling information and sequence accessions for 18S-V4 sequences from surface water collected at the Santa Monica Pier (SMP) Santa Monica Bay, CA from 2018 to 20192022-11-17Data not available
CTD data from daily sampling at the Santa Monica Pier (SMP), Santa Monica Bay, CA from 2018 to 20192022-11-17Preliminary and in progress
Nutrient concentrations and cell/virus-like particles counts2022-09-21Final no updates expected
Chlorophyll data from daily sampling at the Santa Monica Pier, CA from April to May of 20192019-10-03Preliminary and in progress
DNA and cDNA (RNA) V4 tag sequence genetic accessions from microbial eukaryotes sampled in the upper euphotic zone of the eastern North Pacific during R/V Yellowfin cruises from 2003-20182019-06-07Final no updates expected
Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 20142018-10-15Final no updates expected
Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 20152018-10-15Final no updates expected
Daily RBRconcerto data from surface waters off of the Santa Monica Pier, California from April 16-25th, 2018 as part of the San Pedro Ocean Time-series (SPOT)2018-09-18Under revision
NCBI accession metadata for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 20142018-09-04Final no updates expected

People

Principal Investigator: Jed A. Fuhrman
University of Southern California (USC-WIES)

Co-Principal Investigator: David Caron
University of Southern California (USC-WIES)

Contact: Jed A. Fuhrman
University of Southern California (USC-WIES)


Data Management Plan

DMP_OCE-1737409_Fuhrman.pdf (139.08 KB)
07/30/2018