High diversity of crustose coralline algae microbiomes across species and islands, and implications for coral recruits

Crustose Coralline Algae (CCA) play a crucial role in coral reef ecosystems, contributing significantly to reef formation and serving as substrates for coral recruitment. The microbiome associated with CCAs may promote coral recruitment, yet these microbial communities remain largely understudied. This study investigates the microbial communities associated with a large number of different CCA species across six different islands of French Polynesia, and assess their potential influence on the microbiome of coral recruits. Our findings reveal that CCA harbor a large diversity of bacteria that had not been reported until now. The composition of these microbial communities was influenced by geographic location, and was also closely linked to the host species, identified at a fine taxonomic unit using the 16S rRNA gene of the CCA chloroplast. We demonstrate the usefulness of these ecologically meaningful units that we call CCA chlorotypes. Additionally, we observed a correlation between host phylogeny and microbiome composition (phylosymbiosis) in two CCA species. Contrary to expectations, the CCA microbiome did not act as a microbial reservoir for coral recruits. However, the microbial community of coral recruits varied according to the substrate on which they grew. The study significantly expands the number of characterized CCA microbiomes, and provides new insight into the extensive diversity of these microbial communities. We show distinct microbiomes between and within CCA species, characterized by specific chloroplast 16S rRNA gene sequences. We term these distinct groups "chlorotypes", and demonstrate their utility to differentiate CCA. We also show that only few bacterial taxa were shared between CCA and coral recruits growing in contact with them. Nevertheless, we observed that the microbial community of coral recruits varied depending on the substrate they grew on. We conclude that CCA and their associated bacteria influence the microbiome composition of the coral recruits.