Host Evolutionary Lineage Shapes Assembly, Network Topology, and Metabolic Potential of Coral Skeletal Endolithic Microbiomes

Evolutionary history of the host may influence the skeletal morphology of scleractinian corals. However, its effects on the assembly and function of endolithic microbiomes remain unknown. We analyzed bacterial and archaeal microbiomes from the coral skeleton by using 16S rRNA gene sequencing. We collected the samples of seven coral genera distributed among the diverse "Complex" and "Robust" clades. In this study, bacterial α-diversity was significantly higher in the Complex clade relative to the Robust clade. Archaea, on the other hand, remained stable and showed no significant differences between the two host clades, and were most abundantly Nanoarchaeota and Thermoproteota. Analysis of the network topologies showed that network structures were different between the Complex group and the Robust clade. The Robust clade formed a dense and closely knit network among bacteria and archaea. The Com-plex group formed a more modular network structure. Functional predictions further highlighted lineage-specific metabolic strategies. Enrichment was apparent in both nitrification genes (<i>amoB</i>, <i>amoC</i>) and denitrification genes (<i>nirK</i>, <i>nirS</i>) in the Complex clade. This suggests that the coupling of these nitrogen cycles is possible. The opposite was observed for the Robust clade, which had low potential for both types of nitrogen cycling. This reflects the degree of diffusion limitation in the more massive skeleton of this host lineage. Overall, species evolutionary lineage is a pre-eminent driver for the selective filtering of endolithic assembly. It generates discrete skeletal micro-niches on which microbial strategies diverge. In particular, Complex corals favor fast metabolic flux, and Robust corals favor strong network connectivity.