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Tiny single-celled organisms help keep lakes clear, but some can also contaminate the water. An international research team analyzed DNA data from 362 lakes to create the first global genome atlas of these organisms. The atlas lays the foundation for faster and more precise monitoring of lakes.
A single drop of lake water teems with life too small to see: microscopic algae and tiny single-celled organisms such as amoebae. Like our own cells, theirs contain a nucleus, which is why they are known as eukaryotes. The prefix “micro” simply refers to their small size. These organisms convert sunlight into food, feed on bacteria and, in turn, provide food for the tiny animals eaten by fish. When the ecological balance is disrupted, some can become deadly. In 2022, a bloom of a toxic microalga in the Oder River on the German-Polish border killed around 360 tonnes of fish.
For decades, these organisms have been monitored in the same way: counted one by one under a microscope using a method developed in 1958. The process is slow and relies on expertise that is becoming increasingly scarce. It also has a major blind spot. “Under the microscope, a harmless alga and its toxic relative can look identical,” says Adrian-Stefan Andrei, head of the Microbial Evogenomics group at the Limnological Station of the University of Zurich (UZH). “Their DNA likely holds the key to telling them apart.” Until now, however, the genetic reference data needed to identify these organisms from their DNA has been largely missing.
Most species genetically unknown
To expand the genetic reference library, principal investigator Andrei and his team analyzed 3,400 DNA datasets from 362 lakes and reservoirs in 28 countries across all continents. As part of an international collaboration, the researchers reconstructed nearly 20,000 mitochondrial genomes from around 3,660 species. Mitochondria are the structures within cells that produce most of their energy. The result is the first global genomic atlas of these microscopic organisms found in lakes and reservoirs. It reveals a wealth of previously unknown biodiversity: for several groups of algae and related organisms, the researchers identified between six and more than 20 times as many species as are currently listed in the world’s leading reference genomic database.
However, fewer than one in 20 genomes could be assigned to a known genus, and about 750 species could not be matched to any known group. “This shows just how large the gaps in our knowledge still are,” says lead author Lucas Serra Moncadas. “Much of the biodiversity that keeps our lakes functioning has simply remained hidden from us to this day and has never been documented.”
From a bottle of lake water to a list of species
Conventional DNA tests use a molecular 'bait' that catches only the groups it was designed for, so other organisms can slip through. The method used in this study works differently: it starts with a simple water sample. The water is filtered, and all the DNA caught on the filter is sequenced at once. A machine-learning tool then identifies the DNA of mitochondria. Their genome is small, so it is easier to reconstruct. And it generally changes faster over evolutionary time than the DNA in the cell nucleus, so even closely related microeukaryotic species carry clearly different versions.
The team established a clear threshold so that species can be identified consistently across lakes, seasons and studies: two mitochondrial genomes that are at least 98.1 percent identical are considered to belong to the same species. The more comprehensive the DNA pool of the atlas grows, the easier it becomes to check new samples.
Toward global monitoring
In the future, the Genome Atlas could also make it easier to monitor lakes and reservoirs: DNA-based monitoring of microeukaryotes could enable a faster response to overheated or polluted water bodies. Cases of toxic algae, such as those in the Oder River, could also be detected at an early stage. “For more than 60 years, we have seen only a fraction of the life in the lakes and reservoirs that provide drinking water to more than 180 million Europeans,” says Andrei. “Soon, a single bottle of lake water could reveal who lives in it, what’s new and what’s changing.”
Contact
Dr. Adrian-Stefan Andrei
Limnological Station
Department of Plant and Microbial Biology (IPMB)
University of Zurich
Phone: +41 44 634 92 21
E-mail: stefan.andrei@limnol.uzh.ch
Literature
Lucas Serra Moncadas et al. A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity. Nature Communications. 25. September 2026. DOI: 10.1038/s41467-026-78160-1
https://www.news.uzh.ch/en/articles/media/2026/Wasseratlas.html
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Biology, Environment / ecology, Oceanology / climate, Zoology / agricultural and forest sciences
transregional, national
Research results, Transfer of Science or Research
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