Root endophytes of coffee (Coffea arabica): Variation across climatic gradients and relationships with functional traits

Abstract

The root microbiome of Central American coffee trees was studied from four different sites experiencing different annual temperatures and precipitation levels, sampling from plots grown conventionally and under agroforestry management (with shade trees). Total community DNA was separately extracted from roots from four trees sampled from each site/management pair and analyzed using terminal restriction fragment polymorphism analysis and also next generation sequencing (Illumina) of fungal and bacterial ribosomal amplicons. Community profiles were analyzed for site and management effects and correlations to environmental parameters and tree leaf and root economic traits. Communities of both bacteria and fungi varied with site locations, but were not impacted by management system type. They also both varied strongly with environmental parameters. Fungal communities also showed significant variation that could be attributed to plant leaf and root traits. Pooled DNA samples from each site/management regime were used to generate amplicons for next generation sequencing to determine the dominant members of the coffee root microbiome at these locations. Core bacterial genera included Pantoea, Enterobacter, and Burkholderia, while fungal core communities were dominated by members of Cladosporium, Penicillium, Exidiopsis, Trechispora, and Mycena. The potential ecological function of these microbial associates is discussed.