Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples

Data stored in a Dryad package (doi:10.5061/dryad.c75sj) associated with the publication:


Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples Authors: Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski, Andrew Davidson. Molecular Ecology Resources.


The Continuous Plankton Recorder (CPR) has been used to characterise zooplankton biodiversity along transects covering hundreds of thousands of kilometres in the Southern Ocean CPR survey. Plankton collected by the CPR is currently identified using is classical taxonomy (i.e. using a microscope and morphological features). We investigated the potential to use DNA metabarcoding (species identification from DNA mixtures using high-throughput DNA sequencing) as a tool for rapid collection of taxonomic data from CPR samples.


In our study, zooplankton were collected on CPR silks along two transects between Tasmania and Macquarie Island. Plankton were identified using standard microscopic methods and by sequencing a mitochondrial COI marker. Data provided in the Dryad Data entry include the DNA sequences (Illumina MiSeq) recovered, the morphological identifications and the R-code used to analyse these data.


The results from our study show that a DNA-based approach increased the number of metazoan species identified and provided high resolution taxonomy of groups problematic in conventional surveys (e.g. larval echinoderms and hydrozoans). Metabarcoding also generally produced more detections than microscopy, but this sensitivity may make cross-contamination during sampling a problem. In some samples, the prevalence of DNA from larger plankton (such as krill) masked the presence of smaller species. Overall, the genetic data represents a substantial shift in perspective, making direct integration into current long-term time-series challenging. We discuss a number of hurdles that exist for progressing this powerful DNA metabarcoding approach from the current snapshot studies to the requirements of a long-term monitoring program.

Simple

Identification info

Alternate title
Data from initial evaluation of DNA metabarcoding for processing continuous plankton recorder samples
Date (Publication)
2017-11-20
Edition
1
Citation identifier
Dataset DOI

Title
Information and documentation - Digital object identifier system
Date (Publication)
2012-04-23
Citation identifier
ISO 26324:2012

Citation identifier
doi:10.5061/dryad.c75sj

Originator

Deagle, B.

Publisher

Australian Antarctic Data Centre

Principal investigator

DEAGLE, BRUCE
Australian Antarctic Division
203
Kingston
Tasmania
7050
Australia

Collaborator

DEAGLE, BRUCE
Australian Antarctic Division
203
Kingston
Tasmania
7050
Australia
Name
CAASM Metadata
Website
https://data.aad.gov.au/metadata/records/AAS_4313_Genetic_CPR

Purpose
Comparison between morphological taxonomy and DNA metabarcoding for processing continuous plankton recorder samples
Status
Completed

Custodian

AU/AADC > Australian Antarctic Data Centre, Australia - AADC, DATA OFFICER (DATA CENTER CONTACT)
Australian Antarctic Division
203 Channel Highway
Kingston
Tasmania
7050
Australia
Topic category
  • Biota
  • Oceans

Extent

N
S
E
W


Extent

Description
Temporal Coverage

Temporal extent

TimePeriod
2015-04-06 2015-04-20
Title
Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples
Date (Publication)
2017
Citation identifier
doi:10.1111/1755-0998.12740

Author

Bruce Deagle , Laurence Clarke , John Kitchener, Andrea Polanowski, Andrew Davidson.
Name
Molecular Ecology Resources
NASA/GCMD Earth Science Keywords
  • EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > AQUATIC ECOSYSTEMS > PLANKTON > ZOOPLANKTON
  • EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ARTHROPODS > CRUSTACEANS > EUPHAUSIIDS (KRILL)
  • EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > ECHINODERMS
  • EARTH SCIENCE > BIOLOGICAL CLASSIFICATION > ANIMALS/INVERTEBRATES > CNIDARIANS > HYDROZOANS
Keywords
  • DNA BARCODING
  • DNA SEQUENCES
NASA/GCMD Earth Science Keywords
  • CPR > Continuous Plankton Recorder
NASA/GCMD Earth Science Keywords
  • R/V AA > R/V Aurora Australis
NASA/GCMD Earth Science Keywords
  • AMD/AU
  • AMD
  • CEOS
NASA/GCMD Earth Science Keywords
  • GEOGRAPHIC REGION > POLAR
  • OCEAN > SOUTHERN OCEAN

Resource constraints

Use limitation
This metadata record is publicly available.

Resource constraints

Access constraints
licence
Other constraints
These data are available from DRYAD at the provided URL.

Resource constraints

File type
Portable Network Graphic
Linkage
Creative Commons by Attribution logo

Title
Attribution 4.0 International (CC BY 4.0)
Website
https://creativecommons.org/licenses/by/4.0/legalcode

Legal code for Creative Commons by Attribution 4.0 International license

Use constraints
licence
Other constraints
This data set conforms to the CCBY Attribution License (http://creativecommons.org/licenses/by/4.0/). Please follow DRAYD guidelines when using these data.
Language
English
Character encoding
UTF8

Distribution Information

Distributor

Distributor

AU/AADC > Australian Antarctic Data Centre, Australia - AADC, DATA OFFICER (DATA CENTER CONTACT)
Australian Antarctic Division
203 Channel Highway
Kingston
Tasmania
7050
Australia

Distributor

Fees
Free
Planned available datetime
2017-11-20T00:00:00
OnLine resource
GET DATA

Access the data at DRYAD.

OnLine resource
PROJECT HOME PAGE

Public information for AAS project AAS_4313

OnLine resource
VIEW RELATED INFORMATION

Citation reference for this metadata record and dataset.

Maintenance and update frequency
As needed
Maintenance note
2017-11-20 - record created by Bruce Deagle. 2018-03-02 - record updated by Dave Connell to update reference information.

Metadata

Metadata identifier
string/AAS_4313_Genetic_CPR

Language
English
Character encoding
UTF8

Author

DEAGLE, BRUCE
Australian Antarctic Division
203
Kingston
Tasmania
7050
Australia

Sponsor

Australian Antarctic Division

Owner

AADC

Type of resource

Resource scope
Dataset

Alternative metadata reference

Title
gov.nasa.gsfc.gcmd
Citation identifier
fbc3f902-2288-42cd-83a7-d40ab31ca5a0

Alternative metadata reference

Title
gov.nasa.gsfc.gcmd
Date (Last Revision)
2021-11-17T12:22:29

Identifier

Description
metadata.extraction_date

Alternative metadata reference

Title
gov.nasa.gsfc.gcmd
Citation identifier
8.6

Metadata linkage
http://data.aad.gov.au/metadata/records/AAS_4313_Genetic_CPR

Point of truth for the metadata record

Date info (Creation)
2017-11-20T00:00:00
Date info (Last Update)
2018-03-02

Metadata standard

Title
ISO 19115-3
Edition
2014
Other citation details
Version 1
Title
DIF to ISO 19115-1 Profile
 
 

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Spatial extent

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