Do we have sufficient reference data and the appropriate methods and techniques to identify the biodiversity of marine fauna in the dynamic waters of the North Sea using genetic traces from seawater? The aim of a study by the HIFMB Focus Group Marine Molecular Ecology was to evaluate these uncertainties and to bring the method of environmental DNA (eDNA) metabarcoding into application for monitoring and questions on marine conservation in the North Sea. Equipped with canisters, pumps, sieves and lots of filters, we sampled and analyzed both the animals and eDNA over a period of nine days.
Understanding marine biodiversity and its changes due to cumulative effects is a high priority in marine science. Molecular genetic methods are increasingly applied to analyze the taxonomic diversity of marine fauna and complement the classical methods of species identification based on species-specific morphological characteristics. Ideally, we no longer inspect the animals, but identify the biodiversity non-invasively by analyzing their genetic traces in the water – the eDNA – in a standardized way to draw conclusions about the biodiversity.
The aim of this study was to examine the extent to which the prerequisites for such molecular monitoring already exist for the North Sea. We checked this with an integrative study that identified the model group zooplankton morphologically and with metabarcoding. We validated the marine metazoan multi-species identification by comparing the results and then, based on this validated methodology, analyzed the eDNA from seawater for the entire fauna.
We chose Helgoland Roads to evaluate this method because its fauna is very well described and there is a solid base of reference sequence data for this fauna in public sequence databases.
On nine consecutive days, we analyzed the zooplankton from in total more than 120,000 liters of seawater and the eDNA from 288 liters from the Helgoland Roads to generate more than 10 Mio sequences for the marine fauna. We successfully identified the marine fauna in its whole complexity, in total 354 species from the zooplankton, benthos and nekton from 16 phyla. Of these, 96% are typical representatives for the North Sea, some of them have not been documented for 70-120 years. The remaining 4% are already described neozoans, species that are not expected and yet not described for the North Sea, such as the copepod species Acartia (Acartiura) hudsonica or species that were misidentified due to errors in sequence database entries.
“I am still amazed and relieved each time we finally end up with a solid species list after sampling some liters of water, continuing in the lab with dirty filters at first and then pipetting tiny amounts of colorless fluids for days.”
Alica Ohnesorge
Molecular ecologist and main author of the study
Using high-frequent eDNA sampling alone, we recorded 260 species. Of these, we detected 22 species continuously, suggesting their occurrence in large numbers and a constant shedding of genetic material into the water column. In contrast to this, we identified a third of the 260 species on only one out of the in total 129 filters analyzed. This demonstrates the high patchiness and different concentrations/dilutions of the species-specific genetic material in dynamic waters and highlights the importance of water sampling replicating to assess regional biodiversity. The increasing cumulative species numbers over the entire sampling period not reaching saturation support this theory.
A CTD helps to sample water from different depths to identify the marine fauna based on the eDNA, as here on board of the RV Heincke near an offshore wind farm in the German Bight.
Based on our integrative approach and the comparative examination of different filter pore sizes, replicates, genetic markers, taxonomic assignment and sequence reference databases, we verified eDNA and zooplankton metabarcoding as reliable and sensitive tools to identify the marine fauna in the German Bight.The findings of this study are now the basic element for our application of molecular monitoring of marine fauna with a clear conscience. In the North Sea, we apply these protocols to assess and to monitor the biodiversity of the marine fauna in marine protected areas (MPAs) as well as between MPAs to identify MPA connectivity. The latter is part of the CREATE project in the sustainMare research mission of the German Marine Research Alliance, funded by the Federal Ministry of Education and Research (BMBF) and the Federate States of Bremen, Hamburg, Lower Saxony, Schleswig-Holstein and Mecklenburg-Western Pomerania. Next year, these connectivity studies will be supplemented by biodiversity analyses in offshore wind parks to contribute to our understanding of the impact of offshore wind parks on biodiversity and MPA connectivity.
“I am fascinated with each new data set that the eDNA approach is working and that we are detecting the species that we find from standard sampling with nets, grabs and trawls.”
Silke Laakmann
Head of the Focus Group on Marine Molecular Ecology
Beyond the boundaries of the North Sea, our protocols find application in the Beagle Channel observatory in Patagonia (DynAMo project, BMBF) as well as in collaborations with our colleagues from the Nelson Mandela University in Gquberha, the partner university of the University of Oldenburg. Here, we apply eDNA metabarcoding to identify communities in and across stromatolite pools along the South African coast (German Research Foundation-funded project) and to identify marine mammals and cartilaginous fish in MPAs off South Africa.From copepods, comb jellyfish, Iceland clams, brittle stars, plaice, penguins to the great white sharks, every sample holds new surprises.
Silke Laakmann, Alica Ohnesorge
Ohnesorge A, John U, Taudien S, Neuhaus S, Kuczynski L & Laakmann S. (2023). Capturing drifting species and molecules—Lessons learned from integrated approaches to assess marine metazoan diversity in highly dynamic waters. Environmental DNA.
doi:10.1002/edn3.478