The ecological distribution of soil arbuscular mycorrhizal fungi in coffee agroforestry systems of Uganda

Arbuscular mycorrhizal (AM) fungi are key allies in agroecosystems, enhancing nutrient and water uptake, stress tolerance, and plant hormone balance, while contributing to global soil carbon cycling. They associate with nearly 80% of land plants, including coffee, one of Uganda's most important cash crops, contributing 3% to GDP and 12.4% of formal exports. Ugandan coffee is primarily grown by smallholder farmers, predominantly as Robusta (Coffea canephora) and, to a lesser extent, Arabica (Coffea arabica), in a 4:1 ratio. AM fungi are known to improve coffee performance under low-nutrient conditions, yet their ecological distribution in coffee agroforestry systems (CAFs) remains poorly understood. The study was conducted across Uganda's dry, semi-arid, and wet climate zones in Robusta coffee systems spanning a diversification gradient (coffee monoculture, banana–coffee, banana–coffee– crops, and coffee–shade trees and banana–coffee–crops–shade trees). To characterize AM fungal diversity, 120 soil samples were collected from smallholder farms and analyzed using an AM-specific metabarcoding approach, including DNA extraction, PCR amplification, and paired-end Illumina MiSeq sequencing (2 × 250 bp) on the MGX Genotyping platform (CIRAD, UMR AGAP, Montpellier, France). Spatial distribution of AM fungal richness and abundance was modeled with a joint species distribution framework (Hierarchical Modelling of Species Communities, R package), integrating ecological variables such as vigorous vegetation density, precipitation, temperature (maximum and variation), and wind. The effects of diversification on AM fungal communities were further assessed using PERMANOVA and HOMOVA implemented in the vegan R package. The distribution of AM fungi across Uganda's coffee-growing regions was primarily influenced by climatic factors, such as precipitation and maximum annual temperature, rather than by vigorous vegetation density. No significant differences were observed in terms of diversification levels. A hotspot of AM fungal richness was predicted in southern Uganda, whereas northern regions were characterized by lower richness (Figure 1). The families Glomeraceae and Acaulosporaceae were the most abundant, with distributions predicted throughout the country. In contrast, distinct biogeographical patterns were predicted for other families, particularly Diversisporaceae and Gigasporaceae. Diversisporaceae were mainly associated with the eastern side of a geographical diagonal extending from the southwest to the northeast, whereas Gigasporaceae were predicted to occur at the southwestern and northeastern extremities of Uganda. Robusta coffee systems in southern Uganda were characterized by higher AM fungal richness compared to those in the north. Predicted biogeographical patterns also differed among AM fungal families: families associated with stress tolerance and disturbed ecosystems were widespread across the country, while families specialized in nutrient foraging exhibited more localized occurrences. The higher AM fungal richness observed in southern Uganda suggests that Robusta coffee systems in this region may benefit from enhanced soil health, nutrient cycling, and overall plant productivity. Interestingly, no effects of coffee diversification were detected at the national scale, whereas climate parameters were strong predictors of AM fungal richness. The distinct biogeographical patterns of AM fungal families indicate that different functional groups provide complementary ecosystem services: widespread families associated with stress tolerance may confer resilience across all coffee-growing regions, regionally distributed resilient families could inform site-specific management strategies, and localized nutrient- foraging families highlight the importance of preserving soil biodiversity to optimize nutrient acquisition. Together, these patterns emphasize the need to consider multiple environmental and management levers beyond diversification to maintain AM fungal diversity, enhance ecosystem functioning, and support sustainable coffee production across Uganda.

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