Invisible Allies: Harnessing Soil Microbiomes for Biodiversity Recovery and Climate Resilient Agriculture in Degraded Africa Landscapes

Tiny, invisible, and often ignored, soil microbes may hold the key to restoring Africa’s degraded landscapes and securing food for millions. Dr Gaudence Nishimwe, a Rwandan soil ecologist, is leading research that puts these microscopic allies – beneficial bacteria and fungi – at the forefront of land restoration in sub-Saharan Africa.

“Despite all the technological advances in agriculture, we’ve overlooked nature’s original engineers,” she says. “Soil microbes build fertility, restore biodiversity, and make crops more resilient. It’s time to work with them, not around them.”

Nishimwe’s work focuses on identifying and harnessing native microbial communities, specifically plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), to enrich soils naturally. Her aim is to develop bioinoculants: affordable, locally adapted microbial products that help smallholder farmers grow more food on tired, degraded land, without relying on expensive synthetic fertilisers.

Her motivation is clear. “In Africa, land degradation, biodiversity loss, and food insecurity are deeply intertwined,” she says. “This project addresses all three by returning to the roots, literally.”

In practical terms, the microbes she studies form symbiotic relationships with plants, helping them access nutrients and water more efficiently while improving soil structure and stability. Her research promises scalable, nature-based alternatives that don’t just boost yields in the short term, but rebuild soil health over time.

A powerful moment that affirmed her direction came during a study comparing organic and conventional coffee farms in Rwanda. Visiting one smallholder, she was struck by the sheer abundance of earthworms wriggling through the organically managed soil. “You could see and feel the difference,” she recalls. Scientific tests backed it up, earthworm numbers were significantly higher in the organic plots, a biological sign of rich, living soil. “That farmer had barely used external inputs. Nature was doing the work.”

In northern Tanzania, she saw similar results in home gardens nourished with decomposed cow manure: fertility increased thanks to the microbial life it supported, transforming the productivity of fragile mountain soils.

Winning the JWO grant would allow her to expand this work across regions and communities, conduct field trials, co-create bioinoculant solutions with local farmers, and train early-career African scientists, especially women, in soil microbiome science.

For Nishimwe, land degradation, not climate change, is Africa’s most urgent environmental crisis. “It’s happening silently, stripping the land of life. Without healthy soils, there’s no food security, no conservation, no resilience,” she says.

Advances in microbial genomics are making it easier and cheaper to map and engineer soil communities. “We can now design precision restoration strategies, grounded in biology, that are both sustainable and accessible to smallholder farmers.”

What gets her up in the morning? “It’s the quiet inspiration of daily life,” she says. “A walk, a conversation, the rhythm of the day. It reminds me why this work matters. Research isn’t separate from life; it’s a way of giving back.”

When she’s not in the lab or the field, Nishimwe indulges in her lifelong passion: discovering and tasting indigenous fruits. “They’re not just food, they’re culture, memory, history,” she says.