dr John Paul Makumbi
Using microbial DNA as an early warning for polluted lakes and rivers
On many of Africa’s lakes and rivers, the first signs of environmental stress are not visible to the eye. The water may still look clear, fish may still be present, and the surface may appear unchanged. Yet beneath that surface, the ecological system can already be shifting.
Freshwater systems across the continent are under growing pressure from pollution, rapid urbanisation and climate change. This is particularly acute in the East African Great Lakes, which hold about 25% of the world’s unfrozen freshwater and 10% of global fish diversity, yet face threats to up to 76% of their endemic species.
The challenge is that most monitoring systems only detect trouble once it is already advanced. By the time water quality declines are visible in fish populations or chemical readings, much of the underlying ecosystem has already been altered. While frameworks such as the African Union Biodiversity Strategy and Action Plan (2023–2030) call for stronger monitoring systems, most current approaches remain reactive.
John Paul Makumbi, a finalist for the 2026 Jennifer Ward Oppenheimer Research Grant, is exploring a different approach, one that looks far earlier in the chain of ecological change, at the level of microbial life.
His research focuses on microbial DNA in freshwater systems across Africa, drawing on sites in the Lake Victoria basin in Uganda, the Ebrié Lagoon system in Côte d’Ivoire, the Blue Nile in Ethiopia and heavily used urban waterways in South Africa and eSwatini.
Microbes respond almost immediately to environmental change. Using machine learning and genomic analysis, Makumbi is looking for stress-related genetic signals, such as genes associated with antibiotic or heavy metal resistance and disruptions in key nutrient-cycling pathways.
By comparing microbial DNA across sites under different levels of human pressure, the project aims to identify consistent genetic indicators of ecosystem decline. These could reveal when freshwater systems are beginning to destabilise, even if surface conditions still appear normal.
The goal is to develop open-access genomic tools and decision-support systems that can help water managers detect early signs of degradation. Instead of waiting for fish die-offs or visible algal blooms, authorities could act before irreversible damage occurs.
The implications are wide-ranging: from protecting freshwater biodiversity and fisheries to improving drinking water safety and supporting safer wastewater reuse in water-scarce regions such as Southern Africa.
To support long-term impact, the project also includes training postgraduate researchers and technical staff across participating countries, helping to build sustained African capacity in environmental genomics.
Ultimately, the research aims to turn microbial DNA into an early warning system for freshwater ecosystems, offering a way to detect decline while there is still time to intervene.
About the researcher
Dr Olivier Jean Leonce Manzi is a 33-year-old plant ecophysiologist and research fellow at the University of Rwanda. Manzi’s work examines how tropical forests respond to climate change, particularly the effects of heat and drought on tree physiology, resilience and carbon storage across African ecosystems.
His motivation for this research is deeply personal, rooted in his childhood spent on the shores of Lake Victoria near Entebbe, Uganda. He vividly recalls an abundance of birdlife forming part of his everyday landscape. However, returning on recent sampling trips, the contrast was striking: widespread eutrophication, invasive water hyacinth and local fishing communities reporting declining catches. Witnessing this rapid degradation firsthand inspired his drive to use microbial and genomic signals to detect environmental stress before biodiversity loss becomes irreversible.
Makumbi’s scientific approach has been shaped by a unique blend of mentors. He credits Dr Matthew Lukwiya, a Ugandan physician who led the response to the 2000 Ebola outbreak, for demonstrating the critical importance of rapid, evidence-informed decision-making under stress. In his academic training, mentors like Prof. Thulani Makhalanyane and Prof. Luis Pedro Coelho taught him how to translate fundamental microbiological findings into practical tools for environmental health.
Fieldwork has also taught him humbling lessons about the realities of cross-border African research. After losing weeks of planning to changing access routes and inaccurate coordinates, he learned that successful science relies entirely on trusted relationships with local communities, who often had to personally guide his team to obscure sites. Today, what gets him out of bed is the desire to build this kind of collaborative scientific capacity across Africa, ensuring that the invisible microbial processes shaping our world can be harnessed for better human and environmental health outcomes.
2026 Jennifer Ward Oppenheimer Research Grant finalist John Paul Makumbi is developing a predictive genomic framework to detect early warning signs of ecosystem degradation across Africa’s freshwater systems.