Hologenomic Insights into the Molecular Adaptation of Deep-sea Coral Bathypathes pseudoalternata

Deep-sea coral ecosystems support biodiversity and nutrient cycling through interactions with symbionts. However, the molecular mechanisms underlying coral–symbiont interactions remain unexplored. Here, we conducted hologenomic analyses of Bathypathes pseudoalternata to explore the molecular adaptations facilitating its interactions with dominant symbionts. Genomic evidence reveals that B. pseudoalternata exhibits adaptations related to nutrient transport, immune response, and lysosomal digestion regulation, reflecting its genomic adjustments for a stable symbiosis. Candidatus Nitrosopumilus bathypathes (78.43% ± 3.65%) is inferred to oxidize host-derived ammonia into amino acids and vitamins, which are then supplied for the host cells. CRISPR/Cas and restriction–modification systems suggest that Ca. Bathyplasma bathypathes and Ca. Thalassoplasma bathypathes (10.68% ± 2.99%) may protect the host from phage infections. Ca. Bathybacter bathypathes (8.39% ± 1.53%) is hypothesized to synthesize heme, lipoic acid, and glutathione, which may serve dual functions as antioxidants and nutrients. These findings collectively provide insights into how hologenome integration contributes to the survival of B. pseudoalternata in the extreme environment.