Cyanobacteria / blue-green-algae

Cyanobacteria, also known as blue-green algae, are among the most ancient bacteria on earth and the oldest oxygen-producing life forms on Earth. Naturally present in aquatic ecosystems, they occur worldwide in nearly all water bodies and many moist environments, including in Switzerland.  While generally natural components of these systems, some species release harmful toxins (cyanotoxins) that can pose threats to humans and animals. Eawag researchers are therefore studying the ecology of toxic cyanobacteria to better predict their occurrence and improve risk assessments.


Cyanobacteria are often called blue-green algae because of their colour, which comes from the pigments chlorophyll (green) and phycocyanin (blue) used for photosynthesis. However, depending on the species, they can also be coloured green, yellow, brown or red. For a long time, people thought they were algae, but scientists later discovered that they are actually bacteria — which is why their correct name is cyanobacteria. Specialists often use microscopes to detect cyanobacteria.

Cyanobacteria are one of the first organisms capable of obtaining energy through photosynthesis, thereby releasing the first oxygen into the atmosphere. There are several thousand species of cyanobacteria on Earth, and they are common photosynthetic microorganisms in the oceans and in freshwaters. 

To date, around 40 species of cyanobacteria are known to produce toxic metabolites (cyanotoxins). Climate change is increasingly promoting mass proliferation of cyanobacteria – a threat to ecosystems and public health.

Where To Find Cyanobacteria In Surface Waters

Cyanobacteria are classified as pelagic or benthic depending on where they grow in surface waters.

Pelagic Blooms In The Water Column

In open water, the pelagic zone, cyanobacteria can multiply on a massive scale in strong sunlight, with sufficiently warm temperature and nutrients (nitrogen and phosphorus), leading to a «bloom». These blooms float at different depths in lakes and are therefore not always immediately visible. In some cases, cyanobacteria can actively rise to the surface. However, seasonal mixing of the water or strong winds can also passively bring cyanobacteria to the surface. When the biomass floats to the surface, the cyanobacteria are easily recognisable. It is then advisable for humans and animals to avoid contact with them.

Appearance: Cloudiness or blue, green, yellow or red discolouration of the water indicates a high concentration of cyanobacteria. Streaks, foam carpets, flakes or clumps may form.

Occurrence: Cyanobacterial blooms in the water column occur mainly in late summer and autumn, but depending on the species, they can also be visible in winter/spring.

Toxins: The best known and most thoroughly researched class of substances are microcystins, which act as liver toxins (hepatotoxins). These microcystins are produced by many pelagic cyanobacteria.

Danger: There is a particular danger for small children and dogs if they ingest biomass or have prolonged contact with water containing high concentrations of cyanotoxins. This can lead to skin irritation, vomiting, or breathing difficulties.

Benthic Mats growing On The Bottom and Floating To The Surface

Cyanobacteria grow not only in calm, open waters, but also at the bottom – the benthic zone of rivers, ponds or lakes. There, cyanobacteria form a biofilm on stones, pieces of wood or aquatic plants – benthic mats (also known as «toad skins»). 

Unlike blooms in open water, benthic mats can also form when the overlying water is nutrient-poor, clear or only slightly turbid so that sunlight can penetrate to the bottom.

Appearance: These benthic mats can be several millimetres to centimetres thick and often form unnoticed at first on the bottom. Benthic mats appear brown, black or dark green, and air bubbles can sometimes be seen on the surface, which are produced by photosynthesis and contribute to the detachment of mats or fragments from the bottom.  The fragments then float to the surface of the water body where they become more apparent. When they dry out on the shore, they often take on a grey or brown colour.

Occurrence: Unlike pelagic blooms, benthic mats also occur in streams and rivers and can cause problems from spring to late autumn.

Toxins: Some benthic cyanobacteria can produce potent neurotoxins, which belong to the class of anatoxins. Anatoxins are believed to be responsible for acute deaths of dogs in Switzerland and worldwide.

Danger: Dogs are attracted by the foul smell of the mats and can ingest toxins when drinking water, gnawing on pieces of wood or licking biomass out of their fur. The concentration of neurotoxins can be very variable and reach toxic levels in benthic mats, even when the concentration in the open water around them is at times barely detectable. Even swallowing small amounts can then be fatal to dogs. Small children may also play with the debris on the shore and accidentally swallow it.

Video: Underwater Drone for Detection of Benthic Cyanobacteria

Our researchers used the BlueROV (Remotely Operated Vehicle) to detect cyanobacterial mats and observe their growth throughout the year. After a successful search, the samples were taken to the laboratory to analyse their potential toxicity.

Aquascope – Live Images From the Underwater Microscope


The underwater microscope adapted for freshwater at Eawag provides images of plankton in near real time (currently from Greifensee and Lake Zug). Immerse yourself in the otherwise hidden miniature world of algae (including cyanobacteria), water fleas, small crustaceans and other creatures: www.aquascope.ch  

For real-time classification from Greifensee

Picture galleries

Experts

Dr. Francesco Pomati
  • algae
  • biodiversity
  • ecology
  • plankton
  • ecotoxicology
PD Dr. Elisabeth Janssen
  • photochemistry
  • organic pollutants
  • algae
  • biological degradation

Scientific publications

Jones, M. R.; Pinto, E.; Torres, M. A.; Dörr, F.; Mazur-Marzec, H.; Szubert, K.; Tartaglione, L.; Dell'Aversano, C.; Miles, C. O.; Beach, D. G.; McCarron, P.; Sivonen, K.; Fewer, D. P.; Jokela, J.; Janssen, E. M. -L. (2021) CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria, Water Research, 196, 117017 (12 pp.), doi:10.1016/j.watres.2021.117017, Institutional Repository
Pittino, F.; Fink, S.; Oliveira, J.; Janssen, E. M. L.; Scheidegger, C. (2024) Lithic bacterial communities: ecological aspects focusing on Tintenstrich communities, Frontiers in Microbiology, 15, 1430059 (12 pp.), doi:10.3389/fmicb.2024.1430059, Institutional Repository
Rougé, V.; von Gunten, U.; Janssen, E. M. L. (2024) Reactivity of cyanobacteria metabolites with ozone: multicompound competition kinetics, Environmental Science and Technology, 58(26), 11802-11811, doi:10.1021/acs.est.4c02242, Institutional Repository
Torres, M. de A.; Dax, A.; Grand, I.; vom Berg, C.; Pinto, E.; Janssen, E. M..L. (2024) Lethal and behavioral effects of semi-purified microcystins, Micropeptin and apolar compounds from cyanobacteria on freshwater microcrustacean Thamnocephalus platyurus, Aquatic Toxicology, 273, 106983 (9 pp.), doi:10.1016/j.aquatox.2024.106983, Institutional Repository
de Almeida Torres, M.; Jones, M. R.; vom Berg, C.; Pinto, E.; Janssen, E. M. -L. (2023) Lethal and sublethal effects towards zebrafish larvae of microcystins and other cyanopeptides produced by cyanobacteria, Aquatic Toxicology, 263, 106689 (11 pp.), doi:10.1016/j.aquatox.2023.106689, Institutional Repository
Wang, X.; Wullschleger, S.; Jones, M.; Reyes, M.; Bossart, R.; Pomati, F.; Janssen, E. M. -L. (2024) Tracking extensive portfolio of cyanotoxins in five-year lake survey and identifying indicator metabolites of cyanobacterial taxa, Environmental Science and Technology, 58(37), 16560-16569, doi:10.1021/acs.est.4c04813, Institutional Repository
Eyring, S.; Reyes, M.; Merz, E.; Baity-Jesi, M.; Ntetsika, P.; Ebi, C.; Dennis, S.; Pomati, F. (2025) Five years of high-frequency data of phytoplankton zooplankton and limnology from a temperate eutrophic lake, Scientific Data, 12(1), 653 (13 pp.), doi:10.1038/s41597-025-04988-9, Institutional Repository
Janssen, E. M. -L. (2019) Cyanobacterial peptides beyond microcystins – a review on co-occurrence, toxicity, and challenges for risk assessment, Water Research, 151, 488-499, doi:10.1016/j.watres.2018.12.048, Institutional Repository
Kakouei, K.; Kraemer, B. M.; Anneville, O.; Carvalho, L.; Feuchtmayr, H.; Graham, J. L.; Higgins, S.; Pomati, F.; Rudstam, L. G.; Stockwell, J. D.; Thackeray, S. J.; Vanni, M. J.; Adrian, R. (2021) Phytoplankton and cyanobacteria abundances in mid-21st century lakes depend strongly on future land use and climate projections, Global Change Biology, 27(24), 6409-6422, doi:10.1111/gcb.15866, Institutional Repository

Cover picture: Bloom of Microcystis sp., Lake Constance (Amt für Wasser und Energie, St. Gallen, Lukas Taxböck) aegeliana, Greifensee (Eawag, Francesco Pomati).