Symbiotic State Affects Microbiome Recovery in a Facultatively Symbiotic Cnidarian

The cnidarian holobiont consists of host cells, algal symbionts, and a complex microbiome that resides in and on the host tissue and the algal symbionts. To investigate the interactions between a host cnidarian, its algal symbionts, and its bacterial microbiome, we used antibiotics to deplete the microbiome of the facultatively symbiotic sea anemone Exaiptasia pallida (Aiptasia) in both symbiotic and aposymbiotic states. To understand the dynamics of microbiome reestablishment following disruption, we used 16S gene sequencing of the bacterial microbiome to characterize communities during recovery following antibiotic treatment. We assessed the host molecular response to microbiome depletion and recovery using RNA-seq and Western blotting of the immune transcription factor NF-κB. 16S results demonstrate that, following depletion, symbiotic Aiptasia can reestablish bacterial communities (based on diversity metrics and community composition) alike to those of controls before microbiome depletion. However, the microbiomes of aposymbiotic Aiptasia fail to reestablish to control conditions even after seven days of recovery. Bacteria in the Family Endozoicomonadaceae reestablish to control levels in symbiotic, but not aposymbiotic, Aiptasia, suggesting an association between Endozoicomonadaceae and algal symbionts. Our molecular analyses show that host immune system gene expression is downregulated during recovery from antibiotic treatment, but that NF-κB protein levels increase during recovery, suggesting mechanisms for microbiome reestablishment following disruption. This study shows the dynamics of microbiome recovery following depletion and the influence of microbiome community members on host gene expression in a cnidarian model, providing a foundation for future research involving pairwise interactions between microorganisms and cnidarian hosts.