San Francisco Estuary Institute Phytoplankton eDNA and Toxin Monitoring, San Francisco Bay, CA, 2014-2023

From late 2014-present, San Francisco Estuary Institute has conducted molecular monitoring of phytoplankton in partnership with the US Geological Survey from several stations stretching from Rio Vista in the North Delta to the Lower South Bay, past the Dumbarton Bridge. These samples have been analyzed for 18S eDNA data in partnership with Timothy Otten at Bend Genetics, targeting the V7 region. The included dataset covers the 2014-2023 period, including data up to 2022, conducted with an Illumina MISEQ platform, and from 2022-2023 using a NEXTSEQ platform, which enabled much greater sampling depth.
Two sets of taxonomic assignments are included in this data release, one using the Silva database, and the other using the PR2 database, two of the leading sources of phytoplankton taxonomic data aiding in assignments of OTUs to taxa. Raw sequence data will also be uploaded to NCBI for comparison. Data collection continues and this release will be updated as new time periods are added.