Population Differentiation of Rhodobacteraceae Along Coral Compartments

Coral mucus, tissue and skeleton harbor compositionally different microbiota, but how these coral compartments shape the microbial evolution remains unexplored. Here, we focused on the Rhodobacteraceae, which represents a significant but variable proportion (5-50%) of the coral microbiota. We sequenced 234 genomes constituting two divergent populations inhabiting a prevalent coral species Platygyra acuta. One population diverged into two clades colonizing the mucus and skeleton respectively. We reconstructed the ancestral gene changing events that potentially drove the split, and found that the affected genes matched well with the distinct physicochemical features of the mucus and skeleton. Specifically, the mucus clade acquired functions involved in the utilization of coral osmolytes abundant in the mucus (e.g., methylamines, DMSP, taurine and L-proline), whereas the skeleton clade uniquely harbored traits that may promote adaptation to the low-energy and diurnally anoxic skeleton (e.g., sulfur oxidation and swimming motility). These between-clade genetic differences were largely supported by physiological assays. Expanded analyses by including relatives isolated from various marine environments suggest that the mucus and skeleton clades may have diversified in non-coral habitats, but they also consolidated a key role of distinct coral compartments in diversifying many of the above-mentioned traits. The second population varied only at a few dozen nucleotide sites across the whole genomes, and the Slatkin-Maddison test supported that dispersal limitation between coral compartments is another key mechanism driving microbial population differentiation. Collectively, our results suggest that different coral compartments represent ecologically distinct and microgeographically separate habitats that drive the evolution of the coral microbiota.