Marine Biology

, 163:149 | Cite as

Is metabarcoding suitable for estuarine plankton monitoring? A comparative study with microscopy

  • David Abad
  • Aitor Albaina
  • Mikel Aguirre
  • Aitor Laza-Martínez
  • Ibon Uriarte
  • Arantza Iriarte
  • Fernando Villate
  • Andone Estonba
Original paper


Metabarcoding is becoming an increasingly valuable alternative approach to biodiversity assessment, due to the combination of extreme sensitivity and potential for the highest taxonomic resolution in a cost- and time-effective methodology. To evaluate the capacity of metabarcoding for estuarine plankton monitoring, a comparison between the results obtained with this approach were compared with those based on traditional taxonomic analysis (microscopy). Database incompleteness, one of the main limitations of metabarcoding, was somewhat overcome by the addition of DNA sequences for local species, which increased the taxonomic assignment success from 23.7 to 50.5 %. When the communities were studied along with environmental variables, similar spatial and temporal trends of taxonomic diversity were observed for metabarcoding and microscopic studies of zooplankton, but not for phytoplankton. This is most likely attributable to the lack of representative sequences for phytoplankton species in current databases. In addition, there was high correspondence in community composition when comparing abundances estimated from metabarcoding and microscopy, suggesting semiquantitative potential for metabarcoding. Furthermore, metabarcoding allowed the detection and identification of two non-indigenous species (NIS) found in the study area at abundances hardly detectable by microscopy. Overall, our results indicate that metabarcoding is a powerful approach with excellent possibilities for use in plankton monitoring, early detection of NIS and plankton biodiversity shifts.


Phytoplankton Copy Number Variation Plankton Community Representative Sequence Taxonomic Resolution 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The authors thank Ann Bucklin (University of Connecticut) for her comments on the manuscript. The authors also thank the SGIker (UPV/EHU) for the technical and human support provided and the Hydrometeorology Service of the Regional Council of Bizkaia for the precipitation data.


AA and DA work was supported by a contract with the Euskampus Foundation (Euskampus Fundazioa) and a Basque Government doctoral fellowship (UPV/EHU “ZabaldUz” program), respectively. This study was funded by a Basque Government Grant “Grupo de Investigación Consolidado del Sistema Universitario Vasco” to support activities of the Genomic Resources Research Group (IT-558-10), the Phytoplankton (IT-699-13) and Zooplankton (IT-778-13) Ecology Groups. Sampling was also partly financed by the Euskampus Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with animals performed by any of the authors.

Archiving of data

Metabarcoding data (quality-filtered, chimera-free merged reads) are available at Qiita repository (; ID 10518).

Supplementary material

227_2016_2920_MOESM1_ESM.pdf (571 kb)
Supplementary material 1 (PDF 571 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Genomic Resources Group, Department of Genetics, Physical Anthropology and Animal PhysiologyUniversity of the Basque Country, UPV/EHULeioaSpain
  2. 2.Environmental Studies Centre (CEA)Vitoria-Gasteiz City CouncilVitoria-GasteizSpain
  3. 3.Phytoplankton Group, Department of Plant Biology and EcologyUniversity of the Basque Country, UPV/EHULeioaSpain
  4. 4.Zooplankton Group, Laboratory of Ecology of Zooplankton, Department of Plant Biology and EcologyUniversity of the Basque Country, UPV/EHUGasteizSpain
  5. 5.Zooplankton Group, Laboratory of Ecology of Zooplankton, Department of Plant Biology and EcologyUniversity of the Basque Country, UPV/EHULeioaSpain

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