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.

自2014年末至今，旧金山河口研究所（San Francisco Estuary Institute）联合美国地质调查局（US Geological Survey），在北三角洲里奥维斯塔至南湾下游、跨越登巴顿大桥的多个监测站点，系统性开展浮游植物的分子监测工作。本次监测采集的样本由本德遗传学（Bend Genetics）的蒂莫西·奥滕（Timothy Otten）合作完成18S环境DNA（18S eDNA）测序分析，测序靶向18S rRNA基因的V7可变区。本次公开的数据集涵盖2014至2023年的监测数据（含截至2022年的历史观测数据）：2022年之前采用因美纳MiSeq（Illumina MISEQ）测序平台，2022至2023年则升级使用因美纳NextSeq（NEXTSEQ）测序平台，后者可实现更高的测序覆盖深度。本次数据发布包含两套分类注释方案：一套采用席尔瓦（Silva）数据库，另一套采用PR2数据库；二者均为当前浮游植物分类学研究的主流参考数据库，可辅助完成操作分类单元（Operational Taxonomic Units，OTU）的物种分类指派。原始测序数据也将上传至美国国家生物技术信息中心（NCBI），以供学界进行比对验证。目前监测数据采集工作仍在持续推进，后续将随着新时段观测数据的补充，对本次公开数据集进行更新。