The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems

Jan Pawlowski, Mary Kelly-Quinn, Florian Altermatt, Laure Apothéloz-Perret-Gentil, Pedro Beja, Angela Boggero, Angel Borja, Agnès Bouchez, Tristan Cordier, Isabelle Domaizon, Maria Joao Feio, Ana Filipa Filipe, Riccardo Fornaroli, Wolfram Graf, Jelger Herder, Berry van der Hoorn, J. Iwan Jones, Marketa Sagova-Mareckova, Christian Moritz, Jose BarquínJeremy J. Piggott, Maurizio Pinna, Frederic Rimet, Buki Rinkevich, Carla Sousa-Santos, Valeria Specchia, Rosa Trobajo, Valentin Vasselon, Simon Vitecek, Jonas Zimmerman, Alexander Weigand, Florian Leese, Maria Kahlert

Research output: Contribution to journalArticlepeer-review


The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.

Original languageEnglish
Pages (from-to)1295-1310
Number of pages16
JournalScience of the Total Environment
StatePublished - 1 Oct 2018
Externally publishedYes

Bibliographical note

Funding Information:
This paper is a result of the COST Action CA15219 “Developing new genetic tools for bioassessment of aquatic ecosystems in Europe” (DNAqua-Net), funded by the European Union. JP has been supported by the Swiss National Sciences Foundation (grant 313003A_159709). MK has been supported by the Swedish Agency for Marine and Water Management (SwAM). FA has been supported by the Swiss National Science Foundation (grants PP00P3_150698 and 31003A_173074). PB was supported by EDP Biodiversity Chair and the ERA Chair in Environmental Metagenomics (EU Horizon 2020 research and innovation programme Grant agreement No 668981). AFF was supported by the FRESHING Project funded by FCT and COMPETE (PTDC/AAG-MAA/2261/2014—POCI-01-0145-FEDER-356 016824). JZ and FL have been supported by the German Federal Ministry for Education and Research (BMBF) Grant 01LI1501E and 01Li1501K for GBOL-2. MP and VS thank FFABR grants from Italian Ministry of University and Research (MIUR), and ImPrEco project funded by Interreg-ADRION 2014-2020 (CUP C69H18000250007). BR was supported by the Ministry of National Infrastructures, Energy and Water Resources, Israel. AB, FR and VV have been supported by the French Biodiversity Agency (AFB). MS-M has been supported by Ministry of Education, Youth and Sports of the Czech Republic, Grant No. LTC17075.

Publisher Copyright:
© 2018 Elsevier B.V.


  • Bioassessment
  • Biomonitoring
  • Environmental DNA
  • Freshwater
  • Marine
  • Metabarcording

ASJC Scopus subject areas

  • Pollution
  • Waste Management and Disposal
  • Environmental Engineering
  • Environmental Chemistry


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