This is a test site. The production site with full data is available at GBIF.org
{{nav.loginGreeting}}
  • Get data
      • Occurrences
      • GBIF API
      • Species
      • Datasets
      • Occurrence snapshots
      • Hosted portals
      • Trends
  • How-to
    • Share data

      • Quick-start guide
      • Dataset classes
      • Data hosting
      • Standards
      • Become a publisher
      • Data quality
      • Data papers
    • Use data

      • Featured data use
      • Citation guidelines
      • GBIF citations
      • Citation widget
      • Guides and documentation
  • Tools
    • Publishing

      • IPT
      • Data validator
      • GeoPick
      • New data model
      • GRSciColl
      • Suggest a dataset
      • Metabarcoding data toolkit
    • Data access and use

      • Hosted portals
      • Scientific collections
      • Data processing
      • Derived datasets
      • rgbif
      • pygbif
      • MAXENT
      • Tools catalogue
    • GBIF labs

      • Species matching
      • Name parser
      • Sequence ID
      • Relative observation trends
      • GBIF data blog
  • Community
    • Network

      • Participant network
      • Nodes
      • Publishers
      • Network contacts
      • Community forum
      • alliance for biodiversity knowledge
    • Volunteers

      • Mentors
      • Ambassadors
      • Translators
      • Citizen scientists
    • Activities

      • Capacity development
      • Programmes & projects
      • Training and learning resources
      • Data Use Club
      • Living Atlases
  • About
    • Inside GBIF

      • What is GBIF?
      • Become a member
      • Governance
      • Strategic framework
      • Work Programme
      • Funders
      • Partnerships
      • Release notes
      • Contacts
    • News & outreach

      • News
      • Subscribe
      • Events
      • Awards
      • Science Review
      • Data use
      • Thematic communities
  • User profile

A metagenetic approach for revealing community structure of marine planktonic copepods

Dataset homepage

Citation

MGnify (2019). A metagenetic approach for revealing community structure of marine planktonic copepods. Sampling event dataset https://doi.org/10.15468/hqedjb accessed via GBIF.org on 2025-06-21.

Description

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We developed a method for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) through analysis of an artificial copepod community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads per MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. MOTUs were successfully classified at the family level at 97% similarity; similar patterns of species richness and biomass within families were revealed with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.

Sampling Description

Sampling

Marine planktonic copepods are an ecologically important group with high species richness and abundance. Here, we propose a new metagenetic approach for revealing the community structure of marine planktonic copepods using 454 pyrosequencing of nuclear large subunit ribosomal DNA. We developed a method for clustering pyrosequencing data into molecular operational taxonomic units (MOTUs) through analysis of an artificial copepod community containing 33 morphologically identified species. The 99% similarity threshold had high species-level resolution for MOTU clustering but overestimated species richness. The artificial community was appropriately clustered into MOTUs at 97% similarity, with little inflation in MOTU numbers and with relatively high species-level resolution. The number of sequence reads per MOTU was correlated with dry weight of that taxon, suggesting that sequence reads could be used as a proxy for biomass. Next, we applied the method to field-collected samples, and the results corresponded reasonably well with morphological analysis of these communities. Numbers of MOTUs were well correlated with species richness at 97% similarity, and large numbers of sequence reads were generally observed in MOTUs derived from species with large biomass. MOTUs were successfully classified at the family level at 97% similarity; similar patterns of species richness and biomass within families were revealed with metagenetic and morphological analyses. At the 99% similarity threshold, MOTUs with high proportions of sequence reads were identified as biomass-dominant species in each field-collected sample. The metagenetic approach reported here can be an effective tool for rapid and comprehensive assessment of copepod community structure.

Method steps

  1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1

Taxonomic Coverages

Geographic Coverages

Bibliographic Citations

  1. Hirai J, Kuriyama M, Ichikawa T, Hidaka K, Tsuda A. 2015. A metagenetic approach for revealing community structure of marine planktonic copepods. Mol Ecol Resour vol. 15 - DOI:10.1111/1755-0998.12294

Contacts

originator
Plankton laboratory
metadata author
Plankton laboratory
administrative point of contact
Plankton laboratory
What is GBIF? API FAQ Newsletter Privacy Terms and agreements Citation Code of Conduct Acknowledgements
Contact GBIF Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø Denmark
GBIF is a Global Core Biodata Resource