Microbiome variation in wild versus captive spotted eagle ryas (Aetobatus narinari)

Abstract

The microbial communities (microbiomes) associated with elasmobranchs are currently not well-understood. The spotted eagle ray (Aetobatus narinari) is a slow-maturing ray that is globally distributed in tropical and warm-temperate waters, and is listed as near-threatened by the IUCN Red List. To evaluate how the environment shapes the spotted eagle ray microbiome, we used 16S rRNA Illumina sequencing to compare the microbiomes of the dorsal skin, gill, and cloaca from a ray population sampled in Sarasota Bay, FL to those from a captive population in the Ocean Voyager exhibit at Georgia Aquarium. Cloaca microbiomes of both populations had the lowest alpha diversity and highest beta diversity. The composition of the gill and skin microbiomes differed between captive and wild populations and are similar to, but distinct from, the water column communities while cloaca microbiomes are more divergent from that of the water. This pattern is consistent with that seen in teleost fishes and marine mammals. These results indicate a dual role for body niche and environmental conditions in shaping ray microbiomes and identify key taxa that may be important to the health of the rays.