High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral <i>Stylophora pistillata</i>

Abstract

Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with <i>Stylophora pistillata</i> and quantify their cell abundance. Our analysis reveals that multiple <i>Endozoicomonas</i> phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the <i>Endozoicomonas</i> cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant <i>Endozoicomonas</i> phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into <i>Endozoicomonas</i>-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.