Descripción
Registros
Los datos en este recurso de registros biológicos han sido publicados como Archivo Darwin Core(DwC-A), el cual es un formato estándar para compartir datos de biodiversidad como un conjunto de una o más tablas de datos. La tabla de datos del core contiene 135.440 registros.
también existen 2 tablas de datos de extensiones. Un registro en una extensión provee información adicional sobre un registro en el core. El número de registros en cada tabla de datos de la extensión se ilustra a continuación.
Este IPT archiva los datos y, por lo tanto, sirve como repositorio de datos. Los datos y los metadatos del recurso están disponibles para su descarga en la sección descargas. La tabla versiones enumera otras versiones del recurso que se han puesto a disposición del público y permite seguir los cambios realizados en el recurso a lo largo del tiempo.
Versiones
La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.
¿Cómo referenciar?
Los usuarios deben citar este trabajo de la siguiente manera:
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
Derechos
Los usuarios deben respetar los siguientes derechos de uso:
El publicador y propietario de los derechos de este trabajo es NOAA Ocean Exploration. En la medida de lo posible según la ley, el publicador ha renunciado a todos los derechos sobre estos datos y los ha dedicado al Dominio público (CC0 1.0). Los usuarios pueden copiar, modificar, distribuir y utilizar la obra, incluso con fines comerciales, sin restricciones.
Registro GBIF
Este recurso ha sido registrado en GBIF con el siguiente UUID: 9806a672-b859-4175-8432-f805b5ce8f30. NOAA Ocean Exploration publica este recurso y está registrado en GBIF como un publicador de datos avalado por GBIF-US.
Palabras clave
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
Contactos
- Originador
- Research Scientist II
- 4301 Rickenbacker Cswy
https://orcid.org/0000-0002-6672-148X
- Originador ●
- Punto De Contacto
- Research Professor
- 4301 Rickenbacker Cswy
- Originador
- NOAA Omics Coordinator
- Originador
- Project Scientist
- 1315 East-West Hwy
- Originador
- Research Associate III
- 1021 Balch Blvd Ste 1003
- Originador
- Operations Support Analyst
- Originador
- Director and Research Zoologist
- MRC 163
- Originador
- Genomics Specialist
- MRC 163
Cobertura geográfica
Northeast Pacific (U.S. West Coast continental margin, northern California to Washington, ~40–48°N, ~125–126°W)
| Coordenadas límite | Latitud Mínima Longitud Mínima [40,133, -126,126], Latitud Máxima Longitud Máxima [48,171, -124,755] |
|---|
Cobertura taxonómica
Marine organisms identified through eDNA metabarcoding
| Reino | Animalia, Bacteria, Chromista, Fungi, Plantae, Protozoa |
|---|
Cobertura temporal
| Fecha Inicial / Fecha Final | 2023-04-15 / 2023-04-26 |
|---|
Datos del proyecto
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.
| Título | NOAA Ocean Exploration seawater eDNA metabarcoding |
|---|---|
| Identificador | noaa-oer-okeanos |
| Fuentes de Financiación | "A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data" (Grant ID NA21OAR4320190-T3-01S040, NOAA Ocean Exploration) |
| Descripción del área de estudio | 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. |
| Descripción del diseño | 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). |
| Subvención al Proyecto |
A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data NOAA Ocean Exploration NA21OAR4320190-T3-01S040 |
Personas asociadas al proyecto:
- Curador
Métodos de muestreo
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.
| Área de Estudio | 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. |
|---|---|
| Control de Calidad | 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. |
Descripción de la metodología paso a paso:
- 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.
Metadatos adicionales
| Propósito | |
|---|---|
| Identificadores alternativos | 9806a672-b859-4175-8432-f805b5ce8f30 |
| https://ipt-obis.gbif.us/resource?r=noaa-oer-okeanos-ex2301 |