The resilience of coral reefs is dependent on the ability of corals to settle after disturbances. While crustose coralline algae (CCA) are considered important substrates for coral settlement, it remains unclear whether coral larvae respond to CCA metabolites and microbial cues when selecting sites for attachment and metamorphosis. This study tested the settlement preferences of an abundant coral species (Acropora cytherea) against six different CCA species from three habitats (exposed, subcryptic and cryptic), and compared these preferences with the metabolome and microbiome characterizing the CCA. While all CCA species induced settlement, only one species (Titanoderma prototypum) significantly promoted settlement on the CCA surface, rather than on nearby dead coral or plastic surfaces. This species had a very distinct bacterial community and metabolomic fingerprint. Furthermore, coral settlement rates and the CCA microbiome and metabolome were specific to the CCA preferred habitat, suggesting that microbes and/or chemicals serve as environmental indicators for coral larvae. Several amplicon sequence variants and two lipid classes—glycoglycerolipids and betaine lipids—present in T. prototypum were identified as potential omic cues influencing coral settlement. These results support that the distinct microbiome and metabolome of T. prototypum may promote the settlement and attachment of coral larvae.

Although many coral reefs have shifted from coral-to-algal dominance, the consequence of such a transition for coral -algal interactions and their underlying mechanisms remain poorly understood. At the microscale, it is unclear how diffusive boundary layers (DBLs) and surface oxygen concentrations at the coral -algal interface vary with algal competitors and competitiveness. Using field observations and microsensor measurements in a flow chamber, we show that coral (massive Porites) interfaces with thick turf algae, macroalgae, and cyanobacteria, which are successful competitors against coral in the field, are characterized by a thick DBL and hypoxia at night. In contrast, coral interfaces with crustose coralline algae, conspecifics, and thin turf algae, which are poorer competitors, have a thin DBL and low hypoxia at night. Furthermore, DBL thickness and hypoxia at the interface with turf decreased with increasing flow speed, but not when thick turf was upstream. Our results support the importance of water-mediated transport mechanisms in coral-algal interactions. Shifts towards algal dominance, particularly dense assemblages, may lead to thicker DBLs, higher hypoxia, and higher concentrations of harmful metabolites and pathogens along coral borders, which in turn may facilitate algal overgrowth of live corals. These effects may be mediated by flow speed and orientation.