Symbiotic state affects microbiome recovery in a facultatively symbiotic cnidarian

Cnidarian holobionts consist of host cells, algal symbionts, and a complex microbiome residing in and on host tissue and algal symbionts. To investigate interactions among these three partners, we used antibiotics to deplete the microbiome of the facultatively symbiotic sea anemone Exaiptasia pallida (Aiptasia) in both symbiotic and aposymbiotic states and profiled 16S bacterial communities throughout recovery. We assessed host molecular response to microbiome depletion and recovery using RNA-seq and Western blotting of immune transcription factor NF-κB. 16S results demonstrate that, following depletion, symbiotic Aiptasia readily reestablished bacterial communities similar to control anemones. However, aposymbiotic Aiptasia microbiomes failed to reestablish control-level microbiomes even after seven days of recovery, highlighting differences between symbiotic states. Specifically, Endozoicomonadaceae reestablished to control levels in symbiotic, but not aposymbiotic, Aiptasia, suggesting a close physical association between Endozoicomonadaceae and algal symbionts. Molecular analyses showed that, during antibiotic recovery, host immune system gene expression was downregulated, but NF-κB protein levels increased, suggesting mechanisms for microbiome reestablishment following disruption. This study demonstrates the dynamics of microbiome recovery and how microbiome community members influence host gene expression in a cnidarian, providing a foundation for future research involving pairwise interactions between microorganisms and hosts.