Marine zooplankton community structure through environmental DNA metabarcoding in the Florida Keys, collected by the South Florida Program (NOAA/AOML) and the Marine Biodiversity Observation Network (MBON)

Occurrence
Latest version published by United States Geological Survey on Nov 18, 2023 United States Geological Survey
Publication date:
18 November 2023
License:
CC0 1.0

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 3,123 records in English (140 KB) - Update frequency: as needed
Metadata as an EML file download in English (32 KB)
Metadata as an RTF file download in English (12 KB)

Description

This data consists of counts of putative zooplankton OTUs, revealed through metabarcoding of the cytochrome oxidase I (COI) gene extracted from filtered water samples in the Florida Keys National Marine Sanctuary during 2016. It includes results from 95 water samples taken over three days at three coral reef sites. After data processing, a total of 194 taxa were identified; the identification was to the species level, with only a few to the genus level.

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 3,123 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)
3123
dnaDerivedData 
3123

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:

Djurhuus A, Peralta A C, Pitz K, Sawaya N A, Rojas-Marquez J, Michaud B, Montes E, Muller-Karger F, Breitbart M (2023). Marine zooplankton community structure through environmental DNA metabarcoding in the Florida Keys, collected by the South Florida Program (NOAA/AOML) and the Marine Biodiversity Observation Network (MBON). Version 1.3. United States Geological Survey. Occurrence dataset. https://ipt-obis.gbif.us/resource?r=mbonfknmsedna&v=1.3

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is United States Geological Survey. 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: 9d6c78cc-74c6-4a12-b65b-0c9254ddb0b6.  United States Geological Survey publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF-US.

Keywords

Occurrence; zooplankton; DNA sequencing; molecular taxonomy; biodiversity; ocean environment; Occurrence; Observation

Contacts

Anni Djurhuus
  • Metadata Provider ●
  • Originator ●
  • Point Of Contact
  • postdoctoral researcher
College of Marine Science, University of South Florida
US
Ana Carolina Peralta
  • Metadata Provider ●
  • Originator ●
  • Point Of Contact
  • postdoctoral researcher
College of Marine Science, University of South Florida
US
Kathleen Pitz
  • Originator
  • Researcher
Monterey Bay Aquatic Research Institute
California
US
Natalie A. Sawaya
  • Originator
  • Researcher
College of Marine Science, University of South Florida
US
Jaimie Rojas-Marquez
  • Originator
  • Researcher
Fundacion La Salle de Ciencias Naturales, Estacion de Investigaciones Marinas
Margarita
VE
Brianna Michaud
  • Originator
  • Researcher
College of Marine Science, University of South Florida
US
Enrique Montes
  • Originator
  • NOAA Affiliated Researcher
Cooperative Institute for Marine & Atmospheric Studies (CIMAS)
US
Frank Muller-Karger
  • Originator ●
  • Point Of Contact
  • Project Principal Investigator
College of Marine Science, University of South Florida
US
Mya Breitbart
  • Originator
  • Professor and researcher
College of Marine Science, University of South Florida
US
Stephen Formel
  • Reviewer
  • Biologist
U.S. Geological Survey
Mathew Biddle
  • Distributor
  • Physical Scientist
United States Marine Biodiversity Observation Network (US MBON)
  • 1315 East-West Highway
20910 Silver Spring
MD
US
  • 3017134928

Geographic Coverage

Florida Keys: Molasses Reef, Looe Key, and Western Sambo

Bounding Coordinates South West [24.286, -81.654], North East [25.352, -80.228]

Taxonomic Coverage

Zooplankton, including 194 taxa within 37 Classes.

Class Coccolithophyceae, Copepoda, Teleostei, Ascidiacea, Hydrozoa, Sagittoidea, Malacostraca, Gastropoda, Mamiellophyceae, Eurotiomycetes, Chlorarachnea, Bacillariophyceae, Polychaeta, Ostracoda, Palaeonemertea, Anthozoa, Cephalopoda, Pilidiophora, Demospongiae, Ophiuroidea, Thecostraca, Florideophyceae, Cyanophyceae, Holothuroidea, Pyramimonadophyceae, Hexapoda, Homoscleromorpha, Bivalvia, Elasmobranchii, Gymnolaemata, Asteroidea, Dinophyceae, Cryptophyta incertae sedis, Raphidophyce, Echinoidea, Aves, Nuda

Temporal Coverage

Start Date / End Date 2016-03-15 / 2016-05-16

Project Data

A close partnership with NOAA AOML and the FKNMS has focused on periodic MBON surveys of the Florida Keys since 2014. Additional partners now add animal tracking and other dimensions to the Sanctuaries MBON. Specifically, we seek to integrate ground and satellite observations related to biodiversity to inform ecosystem-based management in and around the Florida Keys National Marine Sanctuary (FKNMS). This includes supporting the regional NOAA Integrated Ecosystem Assessment (IEA), the National Marine Fisheries Southeast Fisheries Science Center, the FKNMS, Rookery Bay National Estuarine Research Reserve (NERR), and the State of Florida Fish and Wildlife Commission (FWC) as specific end users of an MBON.

Title South Florida Program (NOAA – AOML) and Marine Biodiversity Observation Network (MBON)
Funding This work is a contribution to the Marine Biodiversity Observation Network (MBON). The MBON project was supported by NASA grant NNX14AP62A ‘National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)’ funded under the National Ocean Partnership Programme (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM and NASA), and the U.S. Integrated Ocean Observing System (IOOS) Programme Office.

The personnel involved in the project:

Frank Muller-Karger
  • Principal Investigator

Sampling Methods

This data represents zooplankton taxonomic composition revealed through metabarcoding of the cytochrome oxidase I (COI) genes. Water samples were collected from three coral reef sites in the Florida Keys National Marine Sanctuary. 1 L surface seawater samples prefiltered through 3 um filters and subsequently collected on 0.22 um filters for eDNA (PF-eDNA). The COI gene metabarcoding of PF-eDNA samples was performed using Illumina MiSeq.

Study Extent Sampling area: Florida Keys - Molasses Reef, Looe Key, and Western Sambo.

Method step description:

  1. https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10237

Additional Metadata

Purpose

MBON cruises have the purpose of collection biological data for biodiversity assessments. Water samples were used to determine dominant copepod survey using eDNA, demonstrating that eDNA metabarcoding is a promising technique for future biodiversity assessments of pelagic zooplankton in marine systems.

Alternative Identifiers 9d6c78cc-74c6-4a12-b65b-0c9254ddb0b6
https://ipt-obis.gbif.us/resource?r=mbonfknmsedna