Impacts of Host Genotype and Grafting on Root, Rhizosphere, and Core Microbiomes in Theobroma cacao Seedlings

Recent advances in understanding microbial contributions to plant growth and soil health have sparked interest in breeding plants that cultivate a beneficial microbiome. Yet optimizing phytobiomes requires knowledge of the genetic architecture of host influence on the associated microbiome, and this knowledge is particularly lacking in perennial crops such as Theobroma cacao. Grafting adds an additional layer of complexity: What are the relative impacts of rootstock and scion on the root and rhizosphere microbiomes? Plant-microbe interactions have rarely been investigated in Theobroma cacao despite the global significance of this crop. We sought to 1) characterize the effect of host genotype on the cacao root endophyte and rhizosphere microbiomes, 2) identify a core microbiome across six open-pollinated rootstock groups, and 3) investigate whether members of the core microbiome were linked to plant growth traits in greenhouse-grown trees. Rootstock and scion identity did not affect within-sample diversity of the root or rhizosphere microbiomes, but rootstock explained 7-13% of variation in prokaryotic communities and 9-12% of variation in fungal communities. However, rootstock genetic distance was not related to taxonomic or phylogenetic dissimilarity of the root or rhizosphere microbiomes. We identified a conserved core microbiome that contained numerous taxa found in both root and rhizosphere microbiomes. Structural topic model and multivariate regression approaches identified both co-varying groups and individual taxa within the core microbiome that were associated with metrics of plant growth and development. These preliminary results could be used to inform breeding programs and potentially soil bio-amendment strategies for cacao seedlings.