Genomic prediction of symbiotic interactions between two Endozoicomonas clades and their coral host, Acropora loripes.

Background: The bacterial genus Endozoicomonas is a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience.

Results: Using long- and short-read whole-genome sequencing of 11 Endozoicomonas strains from Acropora loripes, genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), the latter of which suggests involvement of Endozoicomonas in host 'sex-type' steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicating Endozoicomonas in holobiont phosphorus cycling and stress responses.

Conclusions: This study reveals clade-specific genomic signatures of Endozoicomonas supporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning.