Estuarine fishes associated with intertidal oyster reefs characterised using environmental DNA and baited remote underwater video

It has been widely shown that oyster reefs enhance local biodiversity and fisheries production. Therefore, in this study fish assemblages from oyster reefs were compared to sandy habitats using environmental DNA (eDNA) metabarcoding and baited remote underwater video. Fish diversity from eDNA was characterised using three metabarcoding assays - two that target the mitochondrial 16S region and one that targets the 12S region. Fish assemblages differed with each assay, as well as to that detected by BRUVs. Overall, 112 fish genera were identified, with 78 more genera detected using eDNA metabarcoding than those observed with BRUVs. Both eDNA and BRUVs resolved a higher number of fish genera associated with oyster reefs than with sand sites, and a different fish composition between habitats was also resolved using each method. Furthermore, eDNA was shown to be useful towards characterising the gamma diversity of the estuary, due to the intertidal nature and hydrodynamics of the system, as well as the alpha diversity associated with oyster reefs and sand sites.

Methods
DNA was extracted from seawater samples collected from Port Stephens, NSW Australia.

The DNA was used in PCR using three independent metabarcoding assays (16SNest, Fish16S and MiFishU) to generate amplicon libraries. 

Sequence data files were generated from the amplicon libraries on an Illumina MiSeq using a 300 cycle kit V2.

At the same sites as for eDNA, baited mini-BRUVs were deployed for 30 minutes.