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Comparative identification of phytoplankton taxonomic and functional group approach in karst lakes using classical microscopy and eDNA metabarcoding for ecological status assessment

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Abstract

Phytoplankton is one of the five biological quality elements used to assess the ecological status of lakes within the Water Framework Directive. Classical morphological Utermöhl method and eDNA metabarcoding by Ilumina sequencing the hypervariable V9 region of the eukaryotic SSU rRNA gene were used to analyse the qualitative and quantitative composition of the phytoplankton and compared at the taxonomic and FG level to highlight advantages and disadvantages of eDNA metabarcoding method over classical microscopy. Samples were collected from April to September in seven Croatian natural karst lakes. Cluster analysis based on the Bray–Curtis similarity of taxa biomass (microscopy) and number of sequences (eDNA metabarcoding) clearly separated lakes showing that eDNA metabarcoding is sensitive to species change. Overlap at the species level between methods was found primarily in the taxa of Cryptophyta, Miozoa, and Ochrophyta, while some very common taxa of Bacillariophyta, Charophyta, and Chlorophyta identified by microscopy were not detected by eDNA metabarcoding, possibly due to incompleteness of the reference databases. At a higher organizational level, the results showed poor overlap of taxonomic and functional group composition and poor comparability of relative biomass to relative number of sequences, indicating the need to complete reference databases and standardize quantification to further develop eDNA metabarcoding for ecological status assessment.

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Data availability

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

We would like to thank Andrijana Brozinčević, Nikola Markić and Petar Hodak from Plitvice Lakes National Park, Gordana Goreta from Krka National Park, Maja Ćuže Denona, Maja Bjelić and Dario Rogić from Vransko Lake Nature Park, Vera and Andre Bogunović at Baćina Lakes and all the staff of the pumping station at Lake Vransko on the island of Cres for their technical support in the field. We also thank to two unknown reviewers for making this manuscript better with their detailed comments and suggestions.

Funding

This work was supported by Hrvatske vode within the project “Application of eDNA metabarcoding (eDNA) for ecological status assessment in the Republic of Croatia”. SO and KK were partially supported by the project STIM—REI, Contract Number: KK.01.1.1.01.0003, a project funded by the European Union through the European Regional Development Fund—the Operational Programme Competitiveness and Cohesion 2014–2020 (KK.01.1.1.01) and the DNKVODA project, Contract Number: KK.01.2.1.02.0335.

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Authors and Affiliations

  1. Josip Juraj Strossmayer Water Institute, Ulica Grada Vukovara 220, 10000, Zagreb, Croatia

    Nikola Hanžek & Igor Stanković

  2. Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia

    Marija Gligora Udovič

  3. Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia

    Katarina Kajan & Sandi Orlić

  4. Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), 10000, Zagreb, Croatia

    Katarina Kajan & Sandi Orlić

  5. Department of Tisza Research, Centre for Ecological Research, Institute of Aquatic Ecology, Bem square 1, 4026, Debrecen, Hungary

    Gábor Borics & Gábor Várbíró

  6. University of Kaiserslautern, Ecology Group, Erwin-Schrödinger-Straße, 67663, Kaiserslautern, Germany

    Thorsten Stoeck

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  1. Nikola Hanžek
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Correspondence to Igor Stanković.

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Handling editor: Sidinei M. Thomaz

Guest editors: Viktória B-Béres, Luigi Naselli-Flores, Judit Padisák & Gábor Borics / Trait-Based Approaches in Micro-Algal Ecology

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Hanžek, N., Gligora Udovič, M., Kajan, K. et al. Comparative identification of phytoplankton taxonomic and functional group approach in karst lakes using classical microscopy and eDNA metabarcoding for ecological status assessment. Hydrobiologia 851, 1015–1034 (2024). https://doi.org/10.1007/s10750-023-05344-x

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