Distinct patterns of microbial association across deep-sea corals from the Western Pacific Magellan Seamounts

Ahermatypic corals are common inhabitants in the Magellan Seamounts of the Western Pacific Ocean, yet their microbiomes are largely unexplored. In the present study, we used 16S rRNA gene amplicon sequencing targeting the V4 variable region to characterize the microbiomes of 30 deep-sea coral samples from 9 coral families collected from this area, including members of the families Schizopathidae, Victorgorgiidae, and Chrysogorgiidae, whose microbiomes had not been previously described. Our analyses revealed distinct patterns of microbial association between the coral families, with most coral samples being dominated by single amplicon sequence variants belonging to 11 prokaryotic genera. Ammonia-oxidizing archaea of the genus Nitrosopumilus were abundant exclusively in schizopathid corals, with relative 16S rRNA gene read abundances ranging from 29.4% to 99.8%. In contrast, Nitrosopumilus was either absent or constituted no more than 5.3% of the reads in the remaining coral families. This may be attributed to the catabolism of the protein-rich zooplankton preferred by schizopathid corals, which could, in turn, facilitate ammonia-driven carbon fixation within the holobiont. Three cladopathid corals hosted abundant sequences of two distantly related bacteria capable of utilizing nitric oxide, which could be used by the symbionts either to generate oxygen for aerobic metabolisms or be reduced as a defense against the host's antibacterial activity. The distinct patterns of microbial association between coral taxa indicate that the microbiomes have differential roles in the adaptation of the hosts to specific ecological niches in the deep-sea environments.IMPORTANCEMicrobiomes play crucial roles in host development, physiology, and health, especially in the deep-sea environments. In this study, we collected 30 deep-sea corals from the Western Pacific Magellan Seamounts at depths ranging from 805 to 5,572 m. These samples spanned nine coral families, including three whose microbiomes have not been previously described. Our analyses revealed distinct patterns of microbial association between coral taxa. A majority of the deep-sea corals were dominated by single microbial species, indicating strong selection for certain microbial symbionts and thus functions, such as chemolithoautotrophy, the production of oxygen or secondary metabolites. Furthermore, we observed an overwhelming dominance of sequences from the ammonia-oxidizing archaeal genus Nitrosopumilus exclusively in black corals from the family Schizopathidae, a phenomenon not previously reported. This may be attributed to the catabolism of the protein-rich zooplankton preferred by the schizopathid corals, which could, in turn, facilitate ammonia-driven carbon fixation within the coral holobiont.