The waters of Kenya’s Winam Gulf have taken on an alarming green hue. This phenomenon, which is much more than a simple colour change, reveals a major ecological and health crisis. Toxic cyanobacteria are invading freshwater sources and endangering millions of people. A recent study reveals the scale and complexity of this proliferation, as well as its local and global implications.
by Laurie Henry
Cover photo: The Winam Gulf of Lake Victoria. © George Bullerjahn/Bowling Green State University
The proliferation of toxic cyanobacteria in freshwater is a major global health and environmental issue. These microorganisms, which thrive in warmer temperatures and nutrient-rich environments, contaminate lakes that are vital for fishing, irrigation and human consumption.
In Kenya, the Gulf of Winam, the eastern arm of Lake Victoria, is affected year-round by these blooms, known as cyanoHABs. A large-scale study conducted between 2022 and 2023 by an international team (University of Michigan and Bowling Green State University, in collaboration with Kenyan institutions) mapped the phenomenon at 31 sites in the gulf. Published in January 2025 in Applied and Environmental Microbiology, the results of this metagenomic study detail the composition and toxic potential of these blooms. This specific case, rarely documented on this scale on the African continent, also sheds light on the future dynamics expected in other lakes under pressure, such as Lake Erie in North America.
A silent but toxic proliferation
Cyanobacteria, microorganisms invisible to the naked eye, are proliferating massively in the Gulf of Winam, with health consequences that are poorly understood. The phenomenon, visible in the form of green patches in some areas, is also accompanied by invisible contamination. In the absence of appropriate treatment systems, millions of people are potentially exposed to dangerous toxins without being aware of it. Domestic water use – bathing, laundry, dishwashing – increases the number of points of contact with these pathogens. Added to this is the risk of inhaling volatile toxins, particularly during activities near the shore.
Cyanotoxins can cause serious health problems, particularly for immunocompromised individuals such as those living with HIV, who are very numerous in Kisumu and the surrounding area. The situation is all the more critical as blooms are continuous and non-seasonal, making it difficult to anticipate. Drinking boiled water offers no protection, as the heat releases more toxins by bursting the bacterial cells.
True-colour images of Winam Gulf (Lake Victoria, Kenya), captured by Sentinel-2 on 30 June 2022 (top) and 26 May 2023 (bottom). The sampling sites are indicated by symbols. © Lauren N. Hart et al., 2025
Faced with this subtle but constant threat, preventive measures remain limited. Warnings are rare, detection methods are inadequate, and awareness is virtually non-existent. ‘There is no clear signal to avoid exposure, especially in areas where the water is not green,’ explains Lauren Hart. As a result, people continue to use contaminated water without knowing it, even though some of the concentrations measured far exceed established health thresholds.
Dolichospermum, new dominant invader
Metagenomic analysis conducted between May 2022 and June 2023 on the waters of the Gulf of Winam revealed a major shift in the composition of cyanobacteria responsible for toxic blooms. Dolichospermum, a filamentous genus capable of fixing atmospheric nitrogen, is now the dominant species, clearly surpassing Microcystis, which had previously been the most abundant. At some heavily affected sites, such as Homa Bay and areas near the mouth of the Yala River, Dolichospermum accounts for between 56% and 91% of the cyanobacterial community.
Microbial and archaeal composition in the Winam Gulf. Relative abundance of bacterial and archaeal phyla (grey) and cyanobacterial genera (green) at sites sampled in 2022 and 2023. Groups <1% are grouped under “Others”. © Lauren N. Hart et al., 2025
This shift can be explained by a nitrogen deficiency in the water. Researchers measured a nitrogen/phosphorus ratio (TN:TP) of less than 10 at almost all sites, reflecting this deficiency. However, Dolichospermum possesses the nifH, nifDand nifK genes necessary to draw nitrogen directly from the atmosphere. This is a valuable ability in a nutrient-poor environment, where this species, which coexists with Microcystis, appears to be more resistant to turbidity, heat and shallow depths.
A genetic complexity that is still poorly understood
The metagenomic study conducted in the Gulf of Winam revealed unexpected genetic diversity among cyanobacteria, far beyond what could be observed using traditional methods such as microscopy.
By analysing the complete genomes of organisms sampled from 31 sites, the researchers identified more than 300 Biosynthetic Gene Clusters (BGCs), clusters of genes involved in the production of chemical compounds called secondary metabolites. These metabolites are not necessary for the immediate survival of the organism, but can play a crucial role in interactions with the environment: toxins, antibiotics, defence agents, etc.
Some could be highly toxic, others could have pharmacological properties, but the majority remain of unknown origin, function and impact. This uncertainty makes it difficult to assess the real risks associated with the presence of cyanobacteria, especially since these genes are sometimes detected in areas where no visible blooms are observed.
However, the study did clarify one key point: microcystin, the main toxin identified in the region, is produced exclusively by Microcystis, and not by Dolichospermum. But this is not enough to rule out other threats: other toxins that have not yet been characterised could be synthesised from BGCs and prove dangerous to human health or ecosystems. This genetic complexity and uncertainty, combined with marked spatial variability, highlights the urgent need to develop more sophisticated molecular surveillance tools to anticipate and manage emerging health threats.
The Winam Gulf: an open-air climate lab
The Winam Gulf offers valuable insight into the potential upheavals facing some temperate lakes, particularly those in North America and Europe. Its morphology – shallow waters, high biological productivity, massive nutrient inputs from agriculture and urban areas – makes it comparable to systems such as Lake Erie in North America. But in Kenya, the Winam Gulf experiences permanent rather than seasonal cyanobacterial blooms, making it an open-air laboratory.
Current conditions in this part of Lake Victoria could foreshadow what lakes further north may experience as temperatures rise and extreme rainfall events become more frequent, promoting nutrient runoff. The cyanobacterial species observed in Winam Gulf, such as Microcystis, Dolichospermum and Planktothrix, are already present in Lake Erie. Their responses to the environmental stresses and nutritional imbalances observed in Kenya provide useful insights into how water quality may change elsewhere in the world.
Beyond ecological considerations, the case of Lake Victoria also serves as a reminder that lake management must be viewed as a social challenge. The lack of treatment infrastructure, heavy dependence on raw water and the fragile health of the inhabitants exacerbate the effects of toxic blooms. While these extreme conditions cannot be directly transposed, they do make it possible to identify critical thresholds of resilience. While the Winam Gulf illustrates the combined effects of global changes on complex ecosystems, it also shows how sustainable freshwater management is a global issue.
Source : Lauren N. Hart et al, “Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya” . Applied and Environmental Microbiology (2025)