Microbial genomic signals of ecosystem degradation and biodiversity loss in African multi-use freshwater systems

Along the shores of Lake Victoria in Uganda, Dr John Paul Makumbi remembers a childhood defined by birdlife. Abundant flocks were simply part of the everyday landscape.

Returning years later as a scientist, he found something else entirely.
“I observed that signs of eutrophication were widespread,” Makumbi recalls, “and shoreline bird diversity appeared reduced.” 

Conversations with local fishing communities reinforced his fears. “Many reported declining fish catches and increasing difficulty sustaining their livelihoods from the lake.”

The contrast between the vibrant ecosystem of his childhood and the degraded one he encountered as a scientist pulled Makumbi away from his original training in medical microbiology and towards a much broader ecological question: can the microscopic organisms living in Africa’s waters reveal that an ecosystem is approaching a tipping point long before the warning signs become visible to the
human eye?

Freshwater systems across Africa – including the East African Great Lakes, which hold roughly a quarter of the world’s unfrozen surface water – are under growing pressure from urbanisation, agricultural runoff, industrial pollution and climate stress.

The fundamental flaw in conventional monitoring, Makumbi argues, is that it is largely reactive. 

“Most environmental monitoring systems tell us when ecosystems have already been damaged,” says Makumbi, now a postdoctoral researcher at Stellenbosch University. “By the time water quality deteriorates, fish populations decline and harmful algal blooms become common, opportunities to prevent biodiversity loss may already have been reduced.”

Molecular signals

Makumbi’s research takes a different approach: looking for molecular signals of environmental stress in microbial DNA, potentially revealing that an ecosystem is changing while there is still time to intervene. 

Microorganisms can respond rapidly to changes in their environment. Under stress, the microbial communities responsible for processes such as carbon, nitrogen and phosphorus cycling can change in composition and function.

“They have to choose between survival and continuing with their regular ecosystem services,” Makumbi explains. “In disturbed systems, microorganisms might shift from carbon sequestration towards surviving antibiotic pollution. They stop doing the work that is vital for our climate and ecosystems because they are in survival mode. They are no longer in a healthy status.”

Makumbi’s project will track four families of genomic indicators: genes involved in biogeochemical processes; pathways associated with stress and pollution responses; mobile genetic elements that can help reveal how organisms adapt and exchange genetic material; and networks of interactions within microbial communities.

The aim is to turn these molecular changes into a predictive early warning toolkit, tested across sentinel sites in Uganda’s Lake Victoria, Côte d’Ivoire’s Ébrié Lagoon, Ethiopia’s Blue Nile, South Africa and Eswatini.

The approach could have another practical benefit: helping identify the sources of environmental stress and potentially cutting through the blame that can paralyse efforts to address pollution.

“In places like Hartbeespoort Dam or Lake Victoria, there is always a lot of discussion about who is responsible,” Makumbi says. “The municipalities say their wastewater treatment plants aren’t to blame; the farming communities say it’s not their runoff. Everyone is denying responsibility. By tracking how specific microbial metabolic pathways react to specific stressors, we can move past the blame game and provide law enforcement and policymakers with objective, actionable data.”