Assessing deep-sea marine metazoan and bacterial community structure in cold-seep, canyon, and cold-water coral reef habitats using high-throughput sequencing of DNA extracted from water samples

High-throughput sequencing of targeted “barcode” loci in DNA extracted from marine environmental samples such as water and sediments (metabarcoding of environmental DNA, or eDNA) has exploded in popularity over the last few years due to the ability to generate a taxonomic community profile that usually surpasses what is obtainable from using traditional monitoring methods in terms of biodiversity and detection of rare taxa. Indeed, given the poor biodiversity inventory of many marine habitats coupled with their high cost and difficulty of access, eDNA biomonitoring of these remote ecosystems is attractive if it can reliably inventory the taxa present for a modest cost and with little required sample material. Most applications of metabarcoding to deep-sea environments such as canyons to date have utilized sediments, though the use of water sampling is increasing. As part of the DEEP SEARCH (DEEP Sea Exploration to Advance Research on Coral/Canyon/Cold seep Habitats) project, we collected water samples from among ten JASON2 Remotely Operated Vehicle dives using two identical mounted Niskin bottles at sites within canyon, cold-seep, and coral reef habitats along the U.S. Atlantic coast in April 2019. Use of an ROV allowed controlled water sample collection near features of interest. One and ten liter samples of seawater were filtered through separate 0.2 µm Sterivex filters from each Niskin, as well as ten liters of water filtered through 0.8 µm glass fiber pre-filters from each 10L Sterivex. Here, we discuss preliminary results of metazoan and bacterial metabarcoding efforts, providing insight into the impact of filter pore size and volume of water filtered on the community recovered, as well as baseline levels of biodiversity of the habitats sampled. In addition, we describe progress on building a mitogenomic reference database to assist with both taxonomic assignment and new metabarcoding primer design.