Fungal Diversity and Community Composition in Cocoa Agroforestry Farms across Two West African Countries Using DNA Metabarcoding

Soil microorganisms are crucial to ecosystem functions and productivity by mediating biogeochemical cycles. However, different land-use changes and management practices in agriculture cropping systems have tremendously influenced their composition, diversity, and abundance, causing significant implications for soil health, plant productivity, and biodiversity. We investigated soil fungal community and diversity associated with land use changes in cocoa production systems amid climate change in Ghana and Côte d’Ivoire. In this study, we employed DNA metabarcoding using PacBio sequencing to examine fungal community composition and diversity by targeting the ITS region of fungi in soils collected from three cocoa agroforestry farms (5, 15 and 30 years old). The results revealed that the Ascomycota and Basidiomycota phyla dominated the communities. The classes Eurotiomycetes and Dothideomycetes prevailed in the soils of both countries. The 15- and 30-year-old cocoa agroforestry farms recorded the highest number of fungi in both countries, with the most abundant found in soils of Ghana within a depth of 15 - 30 cm. The results of this study reveal that the soils of this cocoa agroecosystem are dominated by the fungal genera Phialophora and Aureobasidium, which can be explored in future studies along with other mycorrhizal fungi regarding sustainable cocoa production under a changing climate in Ghana and Côte d’Ivoire.