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The hidden drivers of cyanobacterial blooms

July 20, 2026 | Simon Koechlin

Toxic blue-green algae blooms are a threat to lake ecosystems and can be toxic for humans and animals. At present, it is only possible to predict roughly when and where such blooms will form – based on water temperature and nutrient levels. Now, a long-term study by Eawag researchers shows that the accumulation of blue-green algae in a lake depends crucially on other plankton species: some organisms promote blue-green algae blooms, whilst others can prevent them even under favourable environmental conditions.

When cyanobacteria multiply explosively, caution is advised. This is because some of these bacteria, also known as ‘blue-green algae’, produce toxins. Such toxic algal blooms occur time and again in Swiss lakes. The authorities then strongly advise against swimming or close off sections of the lake, as swallowing water can lead to diarrhoea, vomiting and even liver damage. For dogs, a swim in the algal mat can even be fatal.

Determining in good time when and where blue-green algae blooms will occur is a challenge. When conditions are right, blue-green algae blooms form within a few days. The prerequisites for this are warm water temperatures and high nutrient levels. “Today, such abiotic environmental factors are used almost exclusively for forecasts, but this is not enough for accurate predictions,” says Francesco Pomati, head of the ‘Plankton Ecology’ research group at the Eawag water research institute.

This is because the growth of toxic cyanobacteria depends to a large extent on which other organisms are present in their vicinity and how they interact with them. This is demonstrated by a long-term study led by the Plankton Ecology team, recently published in the journal *Nature Ecology & Evolution*. The lead author of the study is Eawag PhD student Pinelopi Ntetsika. She analysed vast amounts of data collected by the research group over a five-year period in Lake Greifensee, Canton Zurich, as part of the long-term ‘Aquascope’ project.
 

Underwater microscope in the lake

The aim of ‘Aquascope’ is to study plankton communities in their natural environment without disrupting the interactions and dynamics of the species. An automated underwater microscope photographs every hour, 24/7, all organisms in the water ranging in size from five micrometres to one centimetre and classifies them using artificial intelligence. “The camera allows us to immerse ourselves in a completely new world and, for the first time, photograph plankton directly in a lake,” says Francesco Pomati. “We have, so to speak, an eye in the water and are observing these tiny, beautiful creatures – just like with a wildlife camera in the savannah.”

In total, the researchers recorded 83 different groups of planktonic organisms during the study period. Together with all key physical and chemical parameters, this amounted to more than 1,700 measurement points per day. This made it possible to paint an unprecedentedly accurate picture of how cyanobacterial populations increased or decreased from day to day.

The study focused on two globally significant groups of toxic cyanobacteria: Microcystis and Dolichospermum. Both can produce dangerous toxins, but differ in their ecological strategy. Microcystis frequently forms dense surface blooms in warm, nutrient-rich water. Dolichospermum prefers more moderate nutrient conditions.

The underwater microscope in Lake Greifensee captures images of even the tiniest plankton species. The Aquascope captures them on camera every hour. (Photos: Eawag)

Predators and promoters

To understand why cyanobacterial populations change, the researchers calculated the daily increase or decrease in biomass – the so-called net growth rates. Using a recently developed analytical method, they quantified the extent to which a particular factor altered the temperature and nutrient conditions necessary for cyanobacterial growth. The results reveal a highly complex system. While classic environmental factors such as temperature or phosphate do have a significant influence on cyanobacteria, “But on a daily timescale, biological factors proved to be even more important,” says Pinelopi Ntetsika.

Certain groups of zooplankton and other algae had a particularly significant impact. For example, so-called rotifers – microscopic aquatic animals that take their name from a ring of cilia on their head that moves like rotating wheels – have an inhibitory effect on cyanobacteria. High rotifer densities increased the water temperature required for accumulation of Dolichospermum biomass by around 13 degrees Celsius. “Rotifers clearly feed on the cyanobacteria and act as regulators,” says Pinelopi Ntetsika. “That was surprising. Until now, it was assumed that water fleas, known as Daphnia, were the cyanobacteria’s main predators.”

Other organisms had the opposite effect. In particular, chrysophytes, a group of mostly golden-brown single-celled organisms, appear to promote the growth of cyanobacteria. In their presence, Dolichospermum populations grew even at water temperatures nearly nine degrees lower and under extremely low phosphorus concentrations.

New predictive possibilities

How such synergistic interactions arise has hardly been investigated to date. It could be, for example, that one species excretes certain metabolic products that another species requires as a nutrient source, says Pinelopi Ntetsika. “Or: a plankton-feeding organism prefers a green alga because it is easier to digest than a blue-green alga. If both occur side by side, the blue-green algae benefit because the grazing pressure on them decreases.”

According to the study, favourable conditions for an algal bloom therefore arise in dynamic processes through the interaction of numerous species within the ecosystem. A temperature that does not trigger a bloom in one year can suddenly become highly problematic under changed biological conditions. Conversely, not every warm summer in a nutrient-rich lake necessarily leads to a massive proliferation of blue-green algae.

The findings also have practical implications for water management. Rather than focusing solely on temperature, phosphorus or nitrogen, the researchers suggest that in future, greater attention should be paid to monitoring specific plankton groups. The abundance of rotifers, water fleas or chrysophytes could provide indications of whether a cyanobacterial bloom is developing in a lake.

However, the interactions between species are extremely complex and site-dependent. “Our results apply to Lake Greifensee – in other lakes, different species and interactions may be important for cyanobacterial growth,” says Pinelopi Ntetsika. To investigate such differences, more research is needed – and more automated underwater microscopes, such as those used by the team in Lake Greifensee. Francesco Pomati and Pinelopi Ntetsika are convinced that this is how the secrets of cyanobacterial blooms can be unravelled step by step.
 

Cover picture: What looks like streaks of dirt is actually toxic cyanobacteria. (Foto: F. Pomati, Eawag)

Original publication

Ntetsika P.; Eyring S.; Merz E.; Reyes M.; Käch B.; Munch S.; Dennis S.; Baity-Jesi M.; Pomati F. (2026) Biotic interactions shape the realised niche of toxic cyanobacteria, Nature Ecology & Evolution, https://www.nature.com/articles/s41559-026-03131-0