Evaluation of marine zooplankton community structure through environmental DNA metabarcoding

Anni Djurhuus, Kathleen Pitz, Natalie A. Sawaya, Jamie Rojas-Márquez, Brianna Michaud, Enrique Montes, Frank Muller-Karger, Mya Breitbart

Research output: Contribution to journalArticlepeer-review

105 Citations (Scopus)


Zooplankton dominate the abundance and biomass of multicellular animals in pelagic marine environments; however, traditional methods to characterize zooplankton communities are invasive and laborious. This study compares zooplankton taxonomic composition revealed through metabarcoding of the cytochrome oxidase I (COI) and 18S rRNA genes to traditional morphological identification by microscopy. Triplicates of three different sample types were collected from three coral reef sites in the Florida Keys National Marine Sanctuary: (1) 1 L surface seawater samples prefiltered through 3 μm filters and subsequently collected on 0.22 μm filters for eDNA (PF-eDNA); (2) 1 L surface seawater samples filtered on 0.22 μm pore-size filters (environmental DNA; eDNA), and (3) zooplankton tissue samples from 64 μm, 200 μm, and 500 μm mesh size net tows. The zooplankton tissue samples were split, with half identified morphologically and tissue DNA (T-DNA) extracted from the other half. The COI and 18S rRNA gene metabarcoding of PF-eDNA, eDNA, and T-DNA samples was performed using Illumina MiSeq. Of the families detected with COI and 18S rRNA gene metabarcoding, 40% and 32%, respectively, were also identified through morphological assessments. Significant differences in taxonomic composition were observed between PF-DNA, eDNA, and T-DNA with both genetic markers. PF-eDNA resulted in detection of fewer taxa than the other two sample types; thus, prefiltering is not recommended. All dominant copepod taxa (> 5% of total abundance) were detected with eDNA, T-DNA, and morphological assessments, demonstrating that eDNA metabarcoding is a promising technique for future biodiversity assessments of pelagic zooplankton in marine systems.
Original languageEnglish
Pages (from-to)209-221
Number of pages13
JournalLimnology and Oceanography: Methods
Issue number4
Publication statusPublished - 17 Jan 2018


  • pelagic marine environments
  • zooplankton


Dive into the research topics of 'Evaluation of marine zooplankton community structure through environmental DNA metabarcoding'. Together they form a unique fingerprint.

Cite this