Cracking nature’s code: African researchers reveal hidden ecosystems

Young scientists in the final running for one of Africa’s richest research funding grants couldn’t have picked more different areas of study. But their proposed projects do share a few common ingredients: a savvy mix of technology and networking, an eye on climate change, and a view that policymaking must rest on robust, accessible data.

Levy Otwoma remembers the frustration clearly. Samples of seawater he had gathered off Kenya’s coast were ready to be analysed, but they sat waiting for a permit that took more than a year to come through.

“We collected samples and needed to sequence them… But we had a very lengthy period for applying for a permit … It took more than one year,” he says. What should have been discovery turned into delay, a pointer of how rules and dependence on overseas labs can hold African science back. For Otwoma, it was like reading a book but needing permission to turn the pages.

That frustration became his turning point. His current project, Emancipate, which means setting somebody free, will use cutting-edge third-generation DNA sequencing to study environmental DNA (eDNA) collected from seawater and sediment, providing insights into the genetic code floating in seawater. The freedom he seeks is scientific; the ability to study Africa’s own oceans without waiting for foreign permissions.

That urgency echoes across the continent. In Nairobi, Beatrice Nganso, a scientist at the International Centre of Insect Physiology and Ecology (ICIPE) looks at a global map of bee forage plants and sees absence. Apart from South Africa, the continent is blank. “We are flying blind in Africa,” she says. “Without robust data on plant pollinator networks, we wouldn’t be able to design concrete policy at the continental level that supports our biodiversity, food security, and livelihood.”

And in South Africa’s Eastern Cape, Nompumelelo Baso remembers childhood days by the riverbank while her parents did laundry. Those rivers now sit at the centre of her research. “My proposal is looking at… how to future-proof Africa’s freshwater ecosystems against climate change and invasive species.”

Together, the three scientists, finalists for the 2025 Jennifer Ward Oppenheimer Research Grant, are working in different ecosystems, but their message is the same: Africa is nearing ecological tipping points. Pollinators, fish, and rivers are under pressure. If the thresholds are crossed, collapse will be sudden, livelihoods will be lost, and recovery may be impossible.

Seeing what is hidden

That’s 650 million farmers betting their harvests on pollinators. Another 200 million coastal Africans depending on fish. Rivers that keep entire communities alive. Yet much of this life goes unseen.

“Plant-insect pollinator network matters. Because they are the engine of Africa’s food production system,” says Nganso. “They put food on our table.” But she warns: “We know very little about their identity, their distribution, and even the forage plants that support their health and productivity.”

Otwoma’s says a blind spot in traditional marine surveys lies beneath the waves where cryptobenthic reef fish often go undetected. And if you are diving, recording fish population and species with the naked eye, you might only see one species, but in that picture, there are more than one, he says. Cryptobenthic reef fish, small but essential, slip beneath traditional surveys. Some methods are worse. “Some of these methods involve catching the organism and actually killing it which becomes counterproductive in terms of biodiversity conservation.”

Baso sees the same blindness in freshwater systems, where invasive species and warming water alter entire food webs. “Let’s say there’s a native plant species that is directly correlated with a specific fish. If that native plant is out-competed, then you also lose that associated fish… and that leads to direct effects on human livelihoods.”

Building tools for foresight

Each of the three are designing a tool to characterise and analyse the changes taking place.

Nganso is building a continent-wide platform hosting more than 300,000 records of plant–pollinator interactions. “We would develop the graphical user interface… that will clearly showcase the digitised images of all the plant and insect pollinators present in our established network.” It will feature nutritional maps of forage plants and resilience metrics. The aim is to help the public document plant–insect interactions.

Otwoma’s answer is environmental DNA, or eDNA, which reveals species present in a water sample. “This method is very sensitive, and non-invasive, and provides a very powerful alternative in terms of detecting the tiny cryptobenthic fish species which are tiny, secretive, and well-camouflaged. He wants to create a continental mitochondrial DNA database, drawn from fish specimens already stored in national museums. Portable sequencers costing less than $5,000 can make the work accessible. “You can actually use it in basic condition in the field,” he says.

Baso is modelling trophic cascades to identify thresholds. “The ultimate output… is building a model that can be used to predict those tipping points. We want to identify where things start to change. Is it 50% cover? Is it 25%?” She is also building an Ecosystem Stability Dashboard, where managers can test interventions. “You can select how far into the future you want to project… and see what happens when you do some type of intervention. Do we see a recovery of those ecosystems and of those food webs?”

Beyond science

It’s the same story in policy. None of the three is content to keep their findings within academia. People are central.

Nganso warns that without pollinator data, “we wouldn’t be able to design concrete policy” for food security. Her team spans local institutions, international modellers and regional biodiversity experts. She plans to train students, youth and community data stewards.

Otwoma has built policy dialogue into his project, with workshops, focus groups and surveys involving ministers, regulators and fishers. He also wants training hubs in five countries. “It’s not just a training and you get a certificate . . . You continue working with experienced scientists in these sequencing centres.”

Baso says her models and dashboards will be modular, able to be picked up by other researchers.

The thresholds

Pollinators vanish, and agriculture falters. Fish diversity slides, and coastal food systems weaken. Invasive plants gain ground, and rivers lose resilience.

Collapse is sudden. “When the primary producers are simplified, and you only have one producer, which is the invasive species, you’d assume that in the food web, the associated species, the primary consumers, will be simplified as well,” says Baso. This reduction in diversity weakens the ecosystem, making it far more vulnerable to disturbances like disease, climate change, or further invasions.”

Otwoma stresses that oceans defy borders. “Fish resources and fish species are transboundary in nature. They don’t occur in one nation… they go across borders, so we need solutions that are transboundary.”

And Nganso insists on seeing the full picture. “The available databases do not report on species interaction. Meanwhile, species… they don’t live alone, okay? They don’t live in isolation. They interact with each other.”

The Jennifer Ward Oppenheimer grant will go to one winner, but together the three projects show the same truth that Africa cannot afford to remain blind.

“I’d love Africans to be the first ones to come to the table with solutions instead of always being the ones who are left behind,” Baso says.

The winner of the Jennifer Ward Oppenheimer Research Grant will be announced at the annual Oppenheimer Research Conference, which takes place from October 15-17 in Johannesburg.

• Kemunto Ogutu is a freelance correspondent for Roving Reporters. This story was produced with assistance from Jive Media Africa, science communication partner to Oppenheimer Generations Research and Conservation (OGRC).