Using eDNA to Assess Freshwater Bacterial Diversity Along a Forest–Non‐Forest Gradient in the Afrotropics

• Published in: Environmental DNA (Hoboken, N.J.) Vol. 7; no. 4
• Main Authors: Wang, Zihui, Munguleni, Vincent, Kasekendi, Innocent, Chapman, Lauren J., Couton, Marjorie, Ojoatre, Sadadi, Atkinson, Nick, Altermatt, Florian, Davies, T. Jonathan
• Format: Journal Article
• Language: English
• Published: Hoboken John Wiley & Sons, Inc 01.07.2025; Wiley
• Subjects: Agricultural production; Aquatic ecosystems; Bacteria; Biodiversity; Bioindicators; biological monitoring; Biomonitoring; Deforestation; Drinking water; Ecological monitoring; Ecosystem degradation; Ecosystem services; Ecosystems; environmental biomarkers; Environmental degradation; Environmental DNA; Environmental impact; Environmental monitoring; Forest protection; Forests; Fresh water; Freshwater ecology; freshwater ecosystem; Freshwater ecosystems; Human impact; Indicator species; Industrialized nations; Machine learning; Microorganisms; Monitoring systems; National parks; Rainforests; Rivers; Sampling methods; Streams; sub‐Saharan Africa; Swamps; Taxonomy; Uganda; Urban areas; Water quality; Water security; Uganda; United States > US; East Africa; Sub-Saharan Africa
• ISSN: 2637-4943; 2637-4943
• DOI: 10.1002/edn3.70136

ABSTRACT Healthy ecosystems are critical for maintaining ecosystem services and water security; yet many freshwater ecosystems have been subject to environmental degradation. Impacts are often greatest in water‐scarce and developing regions, including across much of Sub‐Saharan Africa, where many people lack access to basic drinking water. However, environmental monitoring programmes to track ecosystem health are generally lacking across this region due to limited resources and funding. Recent advances in environmental DNA (eDNA) methods offer an increasingly cost‐effective and information‐rich solution. Here, we explore the potential of eDNA as a tool for ecological monitoring of freshwater ecosystems in Uganda, East Africa. We sampled eDNA to quantify the bacterial diversity of rivers, streams, and swamps across a gradient of human disturbance in and around Kibale National Park, using off‐the‐shelf sampling methods that require minimal pre‐existing infrastructure. We found distinct bacterial communities between intact and degraded habitats, but the bacterial community in rivers converged when flowing through intact forest. We identified several taxa with differential abundances that might serve as potential bioindicators of degraded ecosystems, and showed that a machine learning tool trained on eDNA can accurately differentiate between intact and degraded habitats. Our proof‐of‐concept study demonstrates the potential of eDNA as a practical and cost‐effective biomonitoring tool for freshwater ecosystems in resource‐limited regions, including Sub‐Saharan Africa. We also highlight the potential benefits of protected forest in modulating bacterial composition in freshwater ecosystems. This study investigates the utility of eDNA for assessing freshwater ecosystem health in Kibale National Park, Uganda. Our results show that eDNA‐based biomonitoring is an effective tool for identifying bioindicators, which could be used to develop cost‐efficient, scalable methods for monitoring freshwater biodiversity and environmental integrity in resource‐limited regions such as Sub‐Saharan Africa.