Eukaryotic 18S rRNA Sequences as part of eDNA analyses of Diel Vertical Migration of Mixed Consortia in the Gulf of Mexico from 2016-05-03 to 2017-05-11

Oceanic diel vertical migration (DVM) constitutes the movement of various mesopelagic organisms migrating vertically daily from depth to feed shallow and return to deeper water during the day. Accurate classification of taxa that participate in DVM remains non-trivial, and there can be discrepancies between methods. DEEPEND consortium (www.deependconsortium.org) scientists have been characterizing the diversity and trophic structure of pelagic communities in the northern Gulf of Mexico (GOM). Profiling has included acoustic echo sounders to provide accurate and quantitative estimates of organismal density and timing. In addition, microbial communities (also known as “microbiomes”) can be characterized via environmental DNA (eDNA) remnants they leave from the surface down to 1600 m depth. We demonstrate that high throughput (HT) sequence analyses would complement ongoing characterizations of DVM via acoustic and net sampling. During two DEEPEND cruises in the GOM, we examined the fine-scale acoustic responses of a vertically migrating layer using an autonomous multifrequency echosounder at about 320 m. We then placed CTDs to collect water samples before and during the upward DVM of organisms. Multiple amplicon libraries (n=40) of 16S rRNA (for prokaryotes) and 18S rRNA (for eukaryotes) were derived and sequenced from 19 pre-, 18 during and 3 post DVM samples. Comparisons of acoustic and microbiome data types have tested the limits of microbial forensics, inferring organismal identities and co-occurrences that could elucidate ecological patterns. This dataset contains genetic sequences collected from seawater samples taken at various depths.