Through the eDNA looking glass: Responses of fjord benthic foraminiferal communities to contrasting environmental conditions

Inda Brinkmann, Magali Schweizer, David Singer, Sophie Quinchard, Christine Barras, Joan M. Bernhard, Helena L. Filipsson

Research output: Contribution to journalArticlepeer-review


The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely on microscopic observations of limited taxonomic range and size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal biodiversity in a fjord system (Sweden) on spatial and temporal scales: Alpha and beta diversity responses to natural and anthropogenic environmental trends were assessed and variability of foraminiferal environmental DNA (eDNA) compared to morphology-based data. The identification of eDNA-obtained taxonomic units was aided by single-cell barcoding. Our study revealed wide diversity, including typical morphospecies recognized in the fjords, and so-far unrecognized taxa. DNA extraction method impacted community composition outputs significantly. DNA extractions of 10 g sediment more reliably represented present diversity than of 0.5-g samples and, thus, are preferred for environmental assessments in this region. Alpha- and beta diversity of 10-g extracts correlated with bottom-water salinity similar to morpho-assemblage diversity changes. Sub-annual environmental variability resolved only partially, indicating damped sensitivity of foraminiferal communities on short timescales using established metabarcoding techniques. Systematically addressing the current limitations of morphology-based and metabarcoding studies may strongly improve future biodiversity and environmental assessments.

Original languageEnglish
JournalJournal of Eukaryotic Microbiology
Issue number4
Publication statusPublished - 2023

Bibliographical note

Funding Information:
We acknowledge funding from the Swedish Research Council VR (grant number 2017‐04190), the Crafoord Foundation, and the Royal Physiographic Society in Lund, Sweden. JMB's participation was supported by the at Woods Hole Oceanographic Institution.

Subject classification (UKÄ)

  • Climate Research
  • Environmental Sciences
  • Oceanography, Hydrology, Water Resources
  • Ecology

Free keywords

  • barcoding
  • biodiversity
  • coastal ecosystems
  • environmental DNA
  • foraminifera
  • hypoxia
  • metabarcoding


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