Citrus Microbiome Shifts Associated with Plant Phenology - Bacterial and Fungal Sequences

In this study, we tested the hypothesis that shifts in host phenology act as a driver of community shifts within the above (foliar) and below (root) ground microbiomes of citrus, a domesticated, evergreen, perennial tree crop. Indeed, we determined that the significant shifts in both diversity and composition of the microbial community structure were primarily driven by host phenological stage and not exogenous environmental factors such as rainfall, hours of irrigation or temperature. Foliar communities were more affected by shifts in host phenology than root microbiomes, which were comparably more stable. Interestingly, major shifts in foliar microbial community composition correlated with the transition from vegetative to reproductive growth of the host, namely during flower initiation to fruit set. More specifically, subsets of these microbial enrichments displayed relative abundance patterns that suggest these taxa were under positive and negative natural selection as trees shifted to reproductive growth. We also observed taxa typically associated with pollinator species that were substantially enriched only during flowering suggesting that these taxa were introduced into the foliar microbiome as microbial immigrants via an insect-mediated dispersal mechanism.