Microbiome environmental shifts differ between two co-occurring octocoral hosts

Abstract

Corals harbor a complex suite of beneficial microbial symbionts. Shuffling the composition of these symbionts could, in theory, help the host withstand rapidly emerging or geographically varying stressors without requiring genetic change to the coral itself. The relative impact of host qualities on microbiome (bacteria) composition should provide insight into the extent that shifting microbial symbionts can play in resilience to environmental disturbance on reefs. We sought to assess the differences in microbiome composition across a large spatial scale (between Puerto Rico and Bonaire; >700 km apart) and in response to localized anthropogenic impacts in 2 co-occurring Caribbean soft corals (Eunicea flexuosa and Gorgonia ventalina) with well-documented differing degrees of population genetic differentiation. Host species was the strongest determinant of microbiome composition, with between-hosts distinction due largely to differences in the abundant genera Endozoicomonas and Mycoplasma. Interestingly, the microbiome of the more genetically subdivided G. ventalina showed stronger differentiation between islands and in response to local anthropogenic impacts than the less subdivided E. flexuosa. For both hosts, anthropogenic impacts on microbiome composition were stronger in Bonaire. Again, Endozoicomonas was responsible for much of the differentiation between and within islands and included host- and island-specific sequence variants. The level of intra-species microbiome variation mirrored the known geographic differentiation of their hosts, a trend that is consistent in the literature for 8 other coral species. Thus, while potentially adaptive bacteria may shuffle in response to environmental changes, our findings suggest that most changes to microbiomes are likely constrained by host genetics.