, Volume 818, Issue 1, pp 71–86 | Cite as

Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding

  • A. Banerji
  • M. Bagley
  • M. Elk
  • E. Pilgrim
  • J. Martinson
  • J. Santo Domingo
Primary Research Paper


DNA metabarcoding is a sophisticated molecular tool that can enhance biological surveys of freshwater plankton communities by providing broader taxonomic coverage and, for certain groups, higher taxonomic resolution compared to morphological methods. We conducted 18S rRNA gene metabarcoding analyses on 214 water samples collected over a four-month period from multiple sites within a freshwater reservoir. We detected 1,314 unique operational taxonomic units that included various metazoans, protists, chlorophytes, and fungi. Alpha diversity differed among sites, suggesting local habitat variation linked to differing species responses. Strong temporal variation was detected at both daily and monthly scales. Diversity and relative abundance patterns for several protist groups (including dinoflagellates, ciliates, and cryptophytes) differed from arthropods (e.g., cladocerans and copepods), a traditional focus of plankton surveys. This suggests that the protists respond to different environmental dimensions and may therefore provide additional information regarding ecosystem status. Comparison of the sequence-based population survey data to conventional-based data revealed similar trends for taxa that were ranked among the most abundant in both approaches, although some groups were missing in each data set. These results highlight the potential benefit of supplementing conventional biological survey approaches with metabarcoding to obtain a more comprehensive understanding of freshwater plankton community structure and dynamics.


Aquatic arthropods Biological survey Community dynamics Protists 



We gratefully acknowledge Joel Allen, Mia Varner, Dana Macke, Kit Daniels, and Armah de la Cruz for their role in collecting, transporting and processing the lake water samples used in this study and Chris Nietch and Jade Young for their roles in providing the USACE zooplankton data. The U.S. Environmental Protection Agency, through its Office of Research and Development, partially funded and participated in the research described herein. Any opinions expressed in this paper are those of the authors and do not necessarily reflect the views of the agency; therefore, no official endorsement should be inferred. Any mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Supplementary material

10750_2018_3593_MOESM1_ESM.tif (306 kb)
Supplementary material 1 (TIFF 306 kb) Fig. S1. Rarefaction curve.


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Copyright information

© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply  2018

Authors and Affiliations

  • A. Banerji
    • 1
  • M. Bagley
    • 1
  • M. Elk
    • 1
  • E. Pilgrim
    • 1
  • J. Martinson
    • 1
  • J. Santo Domingo
    • 1
  1. 1.US Environmental Protection AgencyCincinnatiUSA

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