Investigating the hyperdiversity of fungal endophytes in wild Rubiaceae tropical plants and coffee plantations.

Abstract

Fungal endophytes are an essential component of a plant’s microbiome, their effect spreads to fitness, disease dynamics, stress tolerance, water acquisition and nutrient uptake. Plant ecosystems, from natural forest to plantations bear the indelible signature of its presence. The current investigation was designed to understand the diversity of endophytes in the Rubiaceae family, in plants associated to natural and managed ecosystems. The effect of location, leaf developmental stage, tissue type, host genotype, and anthropogenic interference was evaluated through amplicon sequencing. Costa Rica served as base for the sample collection. Leaves and sapwood from a variety of tropical plant species were collected in old-growth natural forests and foliar tissue from domesticated coffee plants were sampled in two plantations under different management. Fungal diversity was assessed by metabarcoding using the ITS2 nrDNA region fITS7 – ITS4, and library sequencing was completed by Ion Torrent. We identified a hyperdiversity of endophytes inhabiting these plants and were able to isolate a total of 659 fungi from coffee leaves. This investigation provides relevant information about overall community composition, the ecological drivers of community assemblage and the characteristics of the fungal endophytic communities, including potential interactions among the identified taxa. Endophytes may harness the potential to transform agriculture and conservation science, however we currently lack the knowledge to engineer microbial communities through breeding or management. It is essential to continue the efforts on understanding community functions and dynamics, and how host, endophyte interactions, and other ecological and human- related mechanisms influence their diversity in both forest species and agronomically important crops.