The Deep SEARCH Project (Deep sea exploration to advance research on cold corals/canyon/cold seep habitats) included a cruise in April 2019 aboard the NOAA ship Ron Brown to various sites along the Mid-Atlantic North American coast. An ROV was used to collect samples of bottom water at these sites, which were then subjected to eDNA extraction and analyses. This data release describes what samples were collected for eDNA analyses, and how eDNA was extracted, sequenced, and bioinformatically analyzed.

We sampled seawater from nine mesophotic reef sites in the Pinnacles Trend and DeSoto Rim areas in the northern Gulf of America in October 2022 to complement and inform restoration investments for coral communities. Four primer sets were used to amplify environmental DNA (eDNA) from seawater, targeting metazoans, eukaryotic plankton and protists, corals, and fishes. Across all markers, four Kingdoms were detected including Animalia, Chromista, Plantae, and Protista based on 11,793 amplicon sequence variants (ASVs). Within Kingdom Animalia, 11 Phyla containing 33 Classes were detected from the surface to the seafloor. Corals and fishes, which are of particular interest, were detected at all sites and in congruence with previous video sightings for the area.In some cases eDNA analyses were able to identify fish and coral to a lower taxonomic identification than was possible through video analyses. This study provides evidence that the addition of an eDNA component to habitat characterization and biodiversity assessments can provide essential information about ecosystem dynamics from the surface, through the water column, to the benthic community.

Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the NOAA Ship Pisces from June 30-July 11, 2022. Samples were collected at depths throughout the water column using Niskins mounted to rosettes on Connectivity-Temperature-Depth instruments (CTDs). Each eDNA sample was amplified using four primer sets: MiFish 12S rRNA marker targeting ray-finned fishes; 28S rRNA marker targeting corals and other cnidarians; and 18S rRNA and CO1 mtDNA general markers for eukaryotic plankton, protists, and other invertebrates. Sequences were then processed bioinformatically to infer amplicon sequence variants (ASVs) and assign taxonomic identifications from the WoRMs database. This data was collected as part of the Mesophotic and Deep Benthic Communities (MDBC) restoration project launched after the Deepwater Horizon oil spill. The data is formatted as per guidelines for upload to the Ocean Biodiversity Information System (OBIS, https://obis.org/).

Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the R/V Point Sur in September 2022. Samples were collected at depths throughout the water column. Each eDNA sample was amplified using four primer sets: MiFish 12S rRNA marker targeting ray-finned fishes; 28S rRNA marker targeting corals and other cnidarians; and 18S rRNA and CO1 mtDNA general markers for eukaryotic plankton, protists, and other invertebrates. Sequences were then processed bioinformatically to infer amplicon sequence variants (ASVs) and assign taxonomic identifications from the WoRMs database. This data was collected as part of the Mesophotic and Deep Benthic Communities (MDBC) restoration project launched after the Deepwater Horizon oil spill. The data is formatted as per guidelines for upload to the Ocean Biodiversity Information System (OBIS, https://obis.org/).

Data from environmental DNA (eDNA) samples filtered from seawater collected in the Gulf of America during a research expedition on the R/V Nancy Foster in August 2022. Samples were collected at depths throughout the water column using Niskins mounted to rosettes on Connectivity-Temperature-Depth instruments (CTDs) or Niskins mounted to remote operated vehicles (ROVs). Each eDNA sample was amplified using four primer sets: MiFish 12S rRNA marker targeting ray-finned fishes; 28S rRNA marker targeting corals and other cnidarians; and 18S rRNA and CO1 mtDNA general markers for eukaryotic plankton, protists, and other invertebrates. Sequences were then processed bioinformatically to infer amplicon sequence variants (ASVs) and assign taxonomic identifications from the WoRMs database. This data was collected as part of the Mesophotic and Deep Benthic Communities (MDBC) restoration project launched after the Deepwater Horizon oil spill. The data is formatted as per guidelines for upload to the Ocean Biodiversity Information System (OBIS, https://obis.org/).

The Expanding Pacific Research and Exploration of Submerged Systems, or EXPRESS initiative is a multi-year, multi-agency project to survey and map undersea habitat throughout the California Current Large Marine Ecosystem. Scientists and engineers from NOAA, the Global Foundation for Ocean Exploration, the U.S. Geological Survey (USGS), and Bureau of Ocean Energy Management (BOEM) conducted a 29-day expedition aboard NOAA Ship Reuben Lasker along the California, Oregon, and Washington coasts, including sites within four National Marine Sanctuaries. GFOE’s ROVs and satellite system were used for this telepresence-enabled cruise, in partnership with OER. This EXPRESS expedition represented an unprecedented level of government cooperation. Eight different NOAA offices along with USGS and BOEM contributed financial or scientific expertise. During this expedition, researchers surveyed deep-sea coral and sponge environments off the U.S. West Coast. This cruise was part of a four-year West Coast Deep Sea Coral Initiative, supported by the Deep Sea Coral Research and Technology Program, to better understand the basic biology, abundance, and diversity of deep-sea coral throughout the California Current Large Marine Ecosystem as well as their ecological role with invertebrates and fish. The researchers collected samples to help identify West Coast corals and sponges, and revisit previously surveyed sites to document changes that have occurred over time. One was to collect essential fish habitat baseline information at 12 sites along the West Coast. The Pacific Fishery Management Council proposed modifications to these habitats to better support commercially important groundfish. Another important goal of characterizing this undersea habitat was to inform possible locations offshore northern and central California for wind energy development. Characterization identified sensitive habitats to avoid when establishing future offshore wind energy sites.

The Expanding Pacific Research and Exploration of Submerged Systems, or EXPRESS initiative is a multi-year, multi-agency project to survey and map undersea habitat throughout the California Current Large Marine Ecosystem. Scientists and engineers from NOAA, the Global Foundation for Ocean Exploration, the U.S. Geological Survey (USGS), and Bureau of Ocean Energy Management (BOEM) conducted a 29-day expedition aboard NOAA Ship Reuben Lasker along the California, Oregon, and Washington coasts, including sites within four National Marine Sanctuaries. GFOE’s ROVs and satellite system were used for this telepresence-enabled cruise, in partnership with OER. This EXPRESS expedition represented an unprecedented level of government cooperation. Eight different NOAA offices along with USGS and BOEM contributed financial or scientific expertise. During this expedition, researchers surveyed deep-sea coral and sponge environments off the U.S. West Coast. This cruise was part of a four-year West Coast Deep Sea Coral Initiative, supported by the Deep Sea Coral Research and Technology Program, to better understand the basic biology, abundance, and diversity of deep-sea coral throughout the California Current Large Marine Ecosystem as well as their ecological role with invertebrates and fish. The researchers collected samples to help identify West Coast corals and sponges, and revisit previously surveyed sites to document changes that have occurred over time. One was to collect essential fish habitat baseline information at 12 sites along the West Coast. The Pacific Fishery Management Council proposed modifications to these habitats to better support commercially important groundfish. Another important goal of characterizing this undersea habitat was to inform possible locations offshore northern and central California for wind energy development. Characterization identified sensitive habitats to avoid when establishing future offshore wind energy sites.