Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

Monthly San Pedro Ocean Time-series (SPOT) cruises on R/V Yellowfin were conducted in the San Pedro Channel, off the coast of Los Angeles, California, USA (33 N, 118 W). Samples were collected monthly from five depths, including 5 meters (m), deep chlorophyll maximum (DCM), 150m, 500m, and 890 m, between the years 2005 and 2018. Ten to fifteen liters of seawater was sequentially filtered through an 80-micrometer (μm) mesh, a 1-μm A/E filter (Pall, Port Washington, NY), and a 0.2-μm Durapore filter (ED Millipore, Billerica, MA). Filters were stored at -80° Celsius (C) until DNA extraction. Durapore filters (collecting material 0.2 to 1 μm) were used for free-living prokaryotic community analysis, and A/E filters (collecting material between 1 to 80 μm) were used to analyze phytoplankton, microzooplankton, and particle-associated or larger prokaryotic communities. DNA was extracted from the Durapore filters using a hot SDS, phenol/chloroform/isoamyl alcohol, ethanol precipitation extraction protocol as described by Fuhrman et al. (1988). DNA on the A/E filters was extracted using a NaCl/CTAB bead-beating extraction protocol as described by Lie et al. (2013) with slight modification by adding an ethanol precipitation step after lysis to reduce the volume of crude extract, which helps minimize DNA loss during the subsequent purification.

The V4-V5 hyper-variable region of the 16S and 18S rRNA genes were amplified simultaneously using a universal primer set 515Y (GTGYCAGCMGCCGCGGTAA) and 926R (CCGYCAATTYMTTTRAGTTT). All DNA samples were amplified and purified using the same conditions described in Yeh et al. 2021). Purified PCR products were pooled in equal amount and then sequenced on Illumina HiSeq 2500 in PE250 mode or MiSeq PE300.

The code used for processing the raw sequence data and getting the reads into ASVs that can be used for downstream community composition analyses has been saved in Zenodo with DOI 10.5281/zenodo.7340378.

BCO-DMO Processing:
- concatenated two separate .csv files (one per BioProject) into one dataset.

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.