18S Monterey Bay Time Series: an eDNA data set from Monterey Bay, California, including years 2006, 2013 - 2016

Latest version published by United States Geological Survey on Jan 18, 2023 United States Geological Survey
Publication date:
18 January 2023
CC-BY 4.0

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 64,903 records in English (2 MB) - Update frequency: unknown
Metadata as an EML file download in English (10 KB)
Metadata as an RTF file download in English (8 KB)


These data are from marine filtered seawater samples collected at a nearshore station in Monterey Bay, CA. They have undergone metabarcoding for the 18S V9 region. A selection of samples from this plate were included in the publication "Environmental DNA reveals seasonal shifts and potential interactions in a marine community" (Djurhuus et al., 2020). Samples were collected by CTD rosette and filtered by a peristaltic pump system.

Illumina MiSeq metabarcoding data was processed in the following steps: (1) primer sequences were removed through atropos (Didion et al., 2017), (2) reads were denoised, ASV sequences inferred, paired reads merged and chimeras removed through Dada2 (Callahan et al., 2016), (3) taxonomic ranks were assigned through blastn searches to NCBI GenBank's non-redundant nucleotide database (nt) with hits filtered by lowest common ancestor algorithm within MEGAN6 (Huson et al., 2016). Furthermore, post-MEGAN6 filtering was performed to ensure only contigs with a hit of ≥97% sequence identity were annotated to the species level and only contigs with a hit of ≥95% sequence identity were annotated to the genus level. Annotations were elevated to the next highest taxonomic level for contigs that failed these conditions.

Data are presented in two comma-separated values files: occurrence.csv, and DNADerivedData.csv. The former contains the taxonomic identification of each ASV observed and its number of reads, in addition to relevant metadata including the location the water sample was taken, references for the identification procedure, and links to archived sequences. The latter contains the DNA sequence of each ASV observed, in addition to relevant metadata including primer information and links to detailed field and laboratory methods. This data set was transformed from its native format into a table structure using Darwin Core and DNA Derived Data Extension term names as column names.


Djurhuus, A, Closek, CJ, Kelly, RP et al. (2020). Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nat Commun 11, 254. https://doi.org/10.1038/s41467-019-14105-1

Didion JP, Martin M, Collins FS. (2017) Atropos: specific, sensitive, and speedy trimming of sequencing reads. PeerJ 5:e3720 https://doi.org/10.7717/peerj.3720

Callahan, B., McMurdie, P., Rosen, M. et al. (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 . https://doi.org/10.1038/nmeth.3869

Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R. (2016) MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS computational biology. Jun 21;12(6):e1004957.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 64,903 records.

1 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

Occurrence (core)

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.


The table below shows only published versions of the resource that are publicly accessible.


Researchers should respect the following rights statement:

The publisher and rights holder of this work is United States Geological Survey. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: e0b59ee7-19ae-4eb0-9217-33317fb50d47.  United States Geological Survey publishes this resource, and is itself registered in GBIF as a data publisher endorsed by U.S. Geological Survey.


Occurrence; Observation


Francisco Chavez
  • Metadata Provider
  • Originator
  • Point Of Contact
Senior Scientist
Monterey Bay Aquarium Research Institute
Kathleen Pitz
  • Metadata Provider
  • Originator
  • Point Of Contact
Research Associate
Monterey Bay Aquarium Research Institute
Diana LaScala-Gruenewald
  • Metadata Provider
  • Point Of Contact
Data Scientist
Monterey Bay Aquarium Research Institute
Abigail Benson
  • Publisher
U.S. Geological Survey
Mathew Biddle
  • Distributor
Physical Scientist
United States Marine Biodiversity Observation Network (US MBON)
1315 East-West Highway
20910 Silver Spring

Additional Metadata

marine, harvested by OBIS

Alternative Identifiers e0b59ee7-19ae-4eb0-9217-33317fb50d47