Description
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 135,440 records.
2 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.
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.
Versions
The table below shows only published versions of the resource that are publicly accessible.
How to cite
Researchers should cite this work as follows:
Coclet C, Thompson L, Miller N, Marranzino A, Green J, Kline L, Collins A, Auscavitch S (2026). NOAA Ocean Exploration seawater eDNA metabarcoding (EX2301). Version 1.4. NOAA Ocean Exploration. Occurrence dataset. https://ipt-obis.gbif.us/resource?r=noaa-oer-okeanos-ex2301&v=1.4
Rights
Researchers should respect the following rights statement:
The publisher and rights holder of this work is NOAA Ocean Exploration. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.
GBIF Registration
This resource has been registered with GBIF, and assigned the following GBIF UUID: 9806a672-b859-4175-8432-f805b5ce8f30. NOAA Ocean Exploration publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF-US.
Keywords
marine biome; marine epipelagic zone; marine mesopelagic zone; marine bathypelagic zone; seawater; Pacific Ocean; 18S rRNA (SSU eukaryote); 12S rRNA (SSU mitochondria); COI (cytochrome oxidase I); eDNA; metabarcoding; marine biodiversity; environmental DNA; Occurrence
Contacts
- Originator
- Research Scientist II
- 4301 Rickenbacker Cswy
https://orcid.org/0000-0002-6672-148X
- Originator ●
- Point Of Contact
- Research Professor
- 4301 Rickenbacker Cswy
- Originator
- NOAA Omics Coordinator
- Originator
- Project Scientist
- 1315 East-West Hwy
- Originator
- Research Associate III
- 1021 Balch Blvd Ste 1003
- Originator
- Operations Support Analyst
- Originator
- Director and Research Zoologist
- MRC 163
- Originator
- Genomics Specialist
- MRC 163
Geographic Coverage
Northeast Pacific (U.S. West Coast continental margin, northern California to Washington, ~40–48°N, ~125–126°W)
| Bounding Coordinates | South West [40.133, -126.126], North East [48.171, -124.755] |
|---|
Taxonomic Coverage
Marine organisms identified through eDNA metabarcoding
| Kingdom | Animalia, Bacteria, Chromista, Fungi, Plantae, Protozoa |
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Temporal Coverage
| Start Date / End Date | 2023-04-15 / 2023-04-26 |
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Project Data
The mission of NOAA Ocean Exploration is to explore the ocean for national benefit, including discovery and characterization of deep-sea environments and biodiversity. This project provides preliminary environmental DNA metabarcoding data from plankton, metazoa, cnidaria, and fish collected aboard NOAA Ship Okeanos Explorer, operated by NOAA Ocean Exploration. Sample archiving and management, wet lab processing, and sequencing was conducted by the Smithsonian National Museum of Natural History and the NOAA National Systematics Laboratory. DNA sequence analysis was performed by the NOAA Atlantic Oceanographic and Meteorological Laboratory.
| Title | NOAA Ocean Exploration seawater eDNA metabarcoding |
|---|---|
| Identifier | noaa-oer-okeanos |
| Funding | "A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data" (Grant ID NA21OAR4320190-T3-01S040, NOAA Ocean Exploration) |
| Study Area Description | Atlantic (SE U.S., Gulf of America, Puerto Rico/Puerto Rico Trench, Azores) and Pacific (U.S. West Coast) from 2021-10-27 to 2023-04-26. |
| Design Description | To characterize biodiversity in sampled ocean environments using eDNA metabarcoding data from NOAA Ship Okeanos Explorer expeditions, with emphasis on deep-sea communities in the abyssal zone (depths below 4,000 m). |
| Project Award |
A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data NOAA Ocean Exploration NA21OAR4320190-T3-01S040 |
The personnel involved in the project:
- Curator
Sampling Methods
Seawater samples were collected aboard NOAA Ship Okeanos Explorer during ROV dives and CTD casts. Water was drawn from Niskin bottles mounted on either the Deep Discoverer ROV or a CTD rosette. Standard collection volumes were 1.7 L for water samples and 2.0 L for distilled water blanks. Samples were filtered through 0.45 um or 0.22 um membrane filters. Sample and environmental metadata - including dive or CTD cast ID, date, time, location, in-situ measurements (salinity, temperature, dissolved oxygen), and estimated bottom depth - were recorded electronically and transferred to the Sample Operator User Portal (SOUP). Laboratory procedures followed documented protocols (https://github.com/aomlomics/protocols). DNA was extracted from filters and amplified by PCR targeting three metabarcoding markers: 18S rRNA (protists/eukaryotes), COI (metazoa), and 12S rRNA (fish). Sequencing was performed on the Illumina NextSeq platform at the NOAA National Systematics Laboratory. Bioinformatic processing was performed on the Northern Gulf Institute's Orion computing cluster using the Tourmaline 2 pipeline. Steps included adapter trimming and quality filtering (Cutadapt), denoising and representative sequence determination (DADA2), and taxonomic assignment using a naive Bayes classifier and consensus VSEARCH (QIIME 2). Raw sequence data in FASTQ format were submitted to the NCBI Sequence Read Archive (SRA). FAIRe-formatted sample metadata were submitted to NCBI BioSample. Taxonomic occurrence data were formatted for submission to OBIS.
| Study Extent | Northeast Pacific (U.S. West Coast continental margin, northern California to Washington, ~40–48°N, ~125–126°W) from 2023-04-15 to 2023-04-26. |
|---|---|
| Quality Control | Quality control measures were implemented across all stages of the workflow. During sample collection, laboratory errors and deviations from standard operating procedures (NOAA Ocean Exploration eDNA Sample Workflow, Revision 2.3) were recorded per sample in a physical notebook and transferred to the Sample Operator User Portal (SOUP). Negative controls (distilled water blanks, extraction blanks, PCR blanks, and sequencing blanks) were included throughout sampling and processing to monitor for contamination. Control samples were excluded from the final published dataset but are archived in NCBI SRA and BioSample records for transparency. Raw sequence data were processed using the Tourmaline 2 pipeline. Low-quality bases and adapters were trimmed using Cutadapt, and sequences were denoised using DADA2 to generate representative sequences. Taxonomic assignments were made using a naive Bayes classifier and consensus VSEARCH, with confidence thresholds applied to ensure reliable identifications. Post-assignment filters were applied to remove sequences associated with domestic or human taxa (Bovidae, Suidae, Felidae, Canidae, Primates, Homo sapiens), unresolved assignments (Unassigned), and terrestrial organisms as flagged by WoRMS habitat classifications. |
Method step description:
- DNA was extracted from seawater filters, amplified by PCR for 18S, COI, and 12S metabarcoding markers, sequenced on Illumina, and analyzed with the Tourmaline 2 pipeline. Field sampling design and detailed procedures are described under sampling; bioinformatic QC and filtering are described under quality control.
Additional Metadata
| Purpose | |
|---|---|
| Alternative Identifiers | 9806a672-b859-4175-8432-f805b5ce8f30 |
| https://ipt-obis.gbif.us/resource?r=noaa-oer-okeanos-ex2301 |