Agroforestry Management Systems Drive the Composition, Diversity, and Function of Fungal and Bacterial Endophyte Communities in Theobroma Cacao Leaves.

Hervé Bertin Bisseleua Daghela,Franziska Wemheuer,Dirk Berkelmann,Stefan Vidal,Rolf Daniel,Bernd Wemheuer

doi:10.3390/microorganisms8030405

Hervé Bertin Bisseleua Daghela, Franziska Wemheuer + Show 4 more

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https://doi.org/10.3390/microorganisms8030405

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Abstract

Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Despite the important role of endophytes for plant growth and health, very little is known about the effect of agroforestry management systems on the endophyte communities of T. cacao. To close this knowledge gap, we investigated the diversity, community composition, and function of bacterial and fungal endophytes in the leaves of T. cacao trees growing in five major cacao-growing regions in the central region of Cameroon using DNA metabarcoding. Fungal but not bacterial alpha diversity measures differed significantly between the agroforestry management systems. Interestingly, less managed home-garden cacao forests harbored the lowest fungal richness and diversity. Our results suggest that the composition of bacterial and fungal endophyte communities is predominantly affected by agroforestry management systems and, to a lesser extent, by environmental properties. The core microbiome detected comprised important fungal phytopathogens, such as Lasiodiplodia species. Several predicted pathways of bacterial endophytes and functional guilds of fungal endophytes differed between the agroforest systems which might be attributed to bacteria and fungi specifically associated with a single agroforest. Our results provide the basis for future studies on foliar fungal and bacterial endophytes of T. cacao and their responsiveness towards agroforestry management systems.

Highlights

Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide
Studies on fungal and bacterial endophytes in T. cacao trees growing in different agroforestry systems are lacking
We applied large-scale metabarcoding to assess compositional and functional responses of fungal and bacterial endophytes in the leaves of T. cacao trees growing in five major cacao-growing regions in the Central Region of Cameroon

Summary

Introduction

Cacao (Theobroma cacao L.) is one of the most economically important crops worldwide. Cacao trees have been traditionally established under thinned canopies of primary or old secondary forests [1]. To enhance their short-term income, farmers in many parts of the world have converted these shaded cacao systems into non-shaded, high intensive monocultures [1,2]. Cacao AMSs include numerous cultivated plants (e.g., cocoa and bananas) and natural forest tree species. They provide a wide range of benefits, including livelihoods for farmers, as well as the conservation of natural resources [1,8]. The relationship among different cacao AMSs and their role in maintaining biodiversity has received more attention during the last years [1,4,9]

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