Bony fish 12S rRNA sequencing data from coastal water samples in gulf of Maine

<p>Ecosystems in coastal waters of Gulf of Maine (GOM) are undergoing environmental challenges in response to climate change and anthropogenic stressors.  eDNA metabarcoding, a powerful tool for assessing fish community structure, was used to identify fish communities in three types of GOM aquatic environments (sand, macroalgae, and eelgrass) in Maine and New Hampshire, USA. The available 12S rRNA fish universal primer analysis system was modified using nested PCR (MiFish and 12S-V5) to improve targeting of fish products and reduce to non-target products.  The nested PCR strategy allowed successful amplification of 12S rRNA genes in fishes without production of non-target products and identified 28 fish groups at the genus level. Presence/Absence data and Relative Abundance showed significant differences among locales but not among habitats.  <em>Myoxocephalus sp</em>. were found at all sampling sites.  Relative Abundance data revealed that <em>Menidia menidia</em> and <em>Brevoortia sp.</em> were statistical indicator species in Goosefare, Maine and New castle, New Hampshire, respectively. Although beta diversity indicated that fish communities were not different across habitats, statistical analysis found that <em>Pholis sp</em>. and <em>Ammodytes sp</em>. were dominant species in macroalgae and sand respectively.  To our knowledge, this is the first metabarcoding study to assess fish communities in the Western Atlantic region using the MiFish primer set and the study suggests that metabarcoding is useful for mapping geographic and temporal marine fish diversity.</p>