Fish diversity across an inverse salinity gradient

Hypersaline coastal embayments are rare, with research into the effects of high salinity on fish fauna scarce. Significant salinity fluctuations can create a natural ecological barrier, with few fish tolerating salinity above 50 practical salinity units (PSU). We investigated how variation in salinity affected fish and elasmobranch diversity and composition in Shark Bay, a remote hypersaline coastal embayment in Western Australia. We used a 16S eDNA metabarcoding assay that detected ray-finned fish and elasmobranchs to analyse genetic sequences collected from 220 surface water samples and 216 benthic roller samples. Samples were taken across four habitats (sand, seagrass, low relief stromatolites and high relief stromatolites), and from 44 sites across three locations (the Eastern Gulf, Faure Sill and Hamelin Pool). 10,450,337 eDNA sequencing reads were detected and allocated to 39 Families, 15 identified to Genus and 52 to Species. Salinity increased from 40.1 PSU in the Eastern Gulf, to 76.0 PSU in Hamelin Pool. As salinity increased, the number of operational taxonomic units (OTUs) detected per site decreased. Salinity and habitat were the main drivers in fish assemblage composition variation. Seagrass habitats in the Eastern Gulf consistently detected the highest mean number of OTUs per site, as did benthic roller sampling, compared to surface water sampling. Thirty-two species were detected by eDNA that had not previously been identified using baited remote underwater stereo-videos, 11 of which are on the IUCN Red List. eDNA is a useful tool in examining broad level marine diversity however, reconciling DNA-based identifications with conventional species definitions is challenging.