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Background  Understanding the associations among corals, their photosynthetic zooxanthella symbionts ( Symbiodinium ), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral  Astrangia poculata  at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state ( Symbiodinium  density in the coral) on microbiome community composition.    Results  Change in season had a strong effect on  A. poculata  microbiome composition. The seasonal shift was greatest upon the winter to spring transition, during which time  A. poculata  microbiome composition became more similar among host individuals. Within each of the four seasons, microbiome composition differed significantly from that of surrounding seawater but was surprisingly uniform between symbiotic and aposymbiotic corals, even in summer, when differences in  Symbiodinium  density between brown and white colonies are the highest, indicating that the observed seasonal shifts are not likely due to fluctuations in  Symbiodinium  density.    Conclusions  Our results suggest that symbiotic state may not be a primary driver of coral microbial community organization in  A. poculata , which is a surprise given the long-held assumption that excess photosynthate is of importance to coral-associated microbes. Rather, other environmental or host factors, in this case, seasonal changes in host physiology associated with winter quiescence, may drive microbiome diversity. Additional studies of  A. poculata  and other facultatively symbiotic corals will provide important comparisons to studies of reef-building tropical corals and therefore help to identify basic principles of coral microbiome assembly, as well as functional relationships among holobiont members.    Electronic supplementary material  The online version of this article (10.1186/s40168-017-0329-8) contains supplementary material, which is available to authorized users.

Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata