Shaping the tripartite symbiosis: are termite microbiome functions directed by the environmentally acquired fungal cultivar?

Microbiome assembly critically impacts the ability of hosts to access beneficial symbiont functions. Fungus-farming termites have coevolved with a fungal symbiont for plant biomass degradation and complex gut microbiomes that complement termite and fungal metabolism. A large subset of the bacterial community residing within termite guts are inherited (vertically transmitted) from the parental colony, while the fungal symbiont is, in most termite species, acquired from the environment (horizontally transmitted). It has remained unknown how the gut microbiota sustains incipient colonies prior to the acquisition of the fungal cultivar, and how, if at all, microbial functions are modulated by fungus garden establishment. Here we test this by determining the composition and predicted functions of the gut microbiome using metabarcoding and shotgun metagenomics, respectively. We focus our functional predictions on bacterial carbohydrate-active enzyme and nitrogen cycling genes and verify compositional patterns of the former through enzyme activity assays. Our findings reveal that the vast majority of microbial functions are encoded in the inherited microbiome, and that the establishment of fungal gardens incurs only minor modulations of predicted bacterial capacities for CAZy and N-metabolism. While we cannot rule out that other symbiont functions are obtained post-fungus garden establishment, our findings suggest that farming termite hosts are equipped with a near-complete set of gut microbiome functions at the earliest stages of colony life, likely contributing to the high extent of specificity and coevolution observed between termite hosts, gut microbiomes, and the fungal cultivar.