Genetic Information Reveals Species: 1,072 Species in a Bucket of Water

Till-Hendrik Macher and Robin Schütz, both doctoral students in biology at the University of Duisburg-Essen at the time, traveled to the renaturalized mouth of the Lippe River near Wesel every two weeks for a year and filtered two water samples on each visit—26 visits, 52 samples. In total, they identified 1,072 species: 40 species of fish and lampreys, 41 species of birds and 26 species of mammals, 425 aquatic and 350 terrestrial invertebrates, and 190 species of diatoms. By comparison: For the same location, a total of 1,029 species are registered in the global biodiversity database GBIF, compiled over more than 130 years.

With the traditional method, organisms are identified individually using a dip net, tweezers, a magnifying glass, and a microscope. With DNA metabarcoding, however, species can be identified based on their genetic information, which can be detected in the samples.

“Using just two liters of water per sampling session, we detected 1,072 species spanning the entire tree of life—from diatoms to mayflies to beavers,” says Till-Hendrik Macher, the study’s lead author, who is now conducting research at the University of Trier. “And we were able to demonstrate that our data actually reflect the biology of the Lippe River and are not just DNA washed into the river by chance,” adds Robin Schütz, now a researcher at the Federal Agency for Nature Conservation. “For example, winter spawners like burbot and pike showed their DNA peaks in winter, while the white-fronted goose showed its peak precisely during its wintering period.”

The approach is also interesting from an economic perspective, as the demand for such data is growing: Both the Kunming-Montreal Global Biodiversity Framework (GBF) and national and European reporting requirements demand a spatial and temporal density of data that is virtually impossible to achieve with traditional methods.

Effective and Cost-Effective

Using the method developed by Macher and Schütz, the analysis of all 52 samples cost approximately 12,000 euros; a comparable traditional survey of the same groups of organisms over the course of a year would cost about 70,000 euros—roughly six times as much. For the EU Water Framework Directive, an average of 1.71 of the four biological quality components (fish, invertebrates, microalgae, aquatic plants) are currently surveyed per river, with very few water bodies being assessed for all four. A combination of traditional monitoring with three surveys based on environmental DNA would cover all four—at about 115 percent of the current budget.

“The calculation shows the potential inherent in combining these methods,” says Florian Leese, head of the Aquatic Ecosystem Research Group at UDE. “Environmental DNA does not provide data on biomass or individual counts, so we still need other methods to get a complete picture.”