Scientists at NOAA's Northeast Fisheries Science Center (NEFSC) are using environmental DNA (eDNA) to identify fish communities and monitor ecosystems by collecting a water sample and analyzing the DNA found in it, identifying the species that left it behind without capturing a single animal. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. A water sample is first collected from the ocean and filtered to concentrate DNA in it. NOAA scientists then make millions of copies of a target DNA region through polymerase chain reaction (PCR) to make enough genetic material for high throughput sequencing. The metabarcoding process described above for eDNA analysis allows scientists to look for many species in the same sample. The final step is like a matching game, in which the DNA sequences are compared with a reference library of known species to find a match. The eDNA method is particularly useful for detecting species that are not easily captured, including rare or migratory species. It can also help in areas that are difficult to sample because of challenging ocean conditions, sensitive habitats, or a rugged seafloor. An eDNA analysis provides a snapshot of the community of species at the time of sampling and over time. This can help us detect shifts in marine ecosystems. eDNA samples have been collected on NOAA Ecosystem Monitoring (EcoMon) surveys since 2019. These samples will help develop best eDNA practices using metabarcoding, an innovative way to determine what fish species live in what parts of the ocean without actually seeing any fish.

Under the National Fish Habitat Partnership, scientists at the NEFSC, NWFSC, and Silver Spring Headquarters are compiling information on the nation's estuarine and coastal habitats and the species they support in order to assess their current potential for restoration and protection. National project headed up by F/ST. Jihong Dai documents InPort metadata. Geographic data on the nation's coasts and estuaries.

EcoMon is the NOAA Northeast Fisheries Science Center Ecosystem Monitoring program for the Northeast U.S. continental shelf. EcoMon main objective is hydrography and zooplankton sampling along the Mid-Atlantic and New England coasts . Funding for the project was provided by the NOAA JPSS PGRR program (https://www.nesdis.noaa.gov/current-satellite-missions/currently-flying/joint-polar-satellite-system/proving-grounds). Additional information for this project can be found in Turner et al., 2021 (https://www.sciencedirect.com/science/article/abs/pii/S0034425721004491).

The Marine Mammal and Sea Turtle Survey, conducted by the Conservation Ecology Branch at the Northeast Fisheries Science Center, develops abundance and distribution models that incorporate environmental factors to better understand how protected species such as whales, dolphins, and sea turtles use our waters. The program coordinates the data collection and analysis efforts of NOAA Fisheries Northeast and Southeast Science Centers and the U.S. Fish and Wildlife Service Division of Migratory Birds. Through these efforts, we are providing enhanced data to managers and supporting conservation initiatives.

The Commonwealth of the Northern Mariana Islands (CNMI), Division of Fish and Wildlife (DFW) staff conducted shore-based creel surveys which have 2 major sub-surveys; one to estimate participation (fishing effort), and one to provide catch-rate (CPUE), species composition data, and size of fishes. As is the case for all of these shore-based surveys, shore-based means fishing without a powered boat and can include effort such as spearfishing. DFW made early attempts at shore-based creel surveying back in the early years, but many problems existed and there were limited resources available. It is not likely that the older data was converted from the Apple to the PC environment, but this needs to be checked. A new survey design was created and implemented in about 2005 and is continuing. It has mostly focused on the west coast lagoon side of Saipan but recently has been extended to the south and part of the west coast where some shoreline areas are accessible as well. These data are considered confidential.

NOAA's NEFSC collects fisheries data from the Penobscot Estuary using several types of fishing gear. The data is used to determine species presence, relative numbers, and migration timing for diadromous and resident fish species.

The Southeast Fisheries Science Center Mississippi Laboratories conducts standardized fisheries independent resource surveys in the Gulf of Mexico, South Atlantic, and U.S. Caribbean to provide abundance and distribution information to support regional and international stock assessments. The reef fish survey is conducted primarily on the outer continental shelf of the Gulf of Mexico along topographic features (e.g. reefs, banks and ledges) between Brownsville, TX to the Dry Tortugas, FL. A two-stage sampling design is used with the first stage or primary sampling units being blocks 10 minutes of latitude by 10 minutes of longitude and the second stage being randomly selected sites within the blocks. The first-stage units are selected by stratified random sampling, with stratum boundaries defined by geographic region (4 regions: South Florida, Northeast Gulf, Louisiana-Texas Shelf, and South Texas), and by reef habitat area (Blocks < 20 km² reef, Blocks > 20 km² reef). Sampling is conducted using a video camera array, vertical line gear and chevron traps with approximately 400 video cameras, 400 vertical line and 100 traps conducted. The camera array consists of four housings positioned orthogonally and center mounted at a height of 51 cm above the bottom of the array. Each housing contains a pair of black-and-white Videre stereo cameras along with a color mpeg camera. Sampling of reef sites with video cameras occurs only during daylight hours, with the first gear deployment one hour after sunrise and the last gear retrieval one hour prior to sunset. Video arrays soak for 35 minutes. At sites selected for fish sampling, a chevron (or arrow) fish trap or vertical line is used to capture fish for biological samples. The chevron fish trap is constructed with 1.5-inch vinyl-clad mesh. In its greatest dimensions, the trap is 1.76 m in length, 1.52 m in width and 0.61 m in depth. A 0.4 m by 0.29 m blow out panel is placed on one side and kept closed using 7-day magnesium releases. The fish trap soaks for one hour and is baited with squid. The vertical line consists of a mainline with 10 gangions. One 8/0, 11/0 or 15/0 circle hook is attached to each gangion and baited with mackerel (Scomber scombrus). The mainline is soaked for five minutes. Most of the animals captured are measured, weighed, tagged and then released. Those individuals which are moribund or have expired are retained to collect biological data pertaining to the life history of these fishes. Habitat mapping is conducted using the SIMRAD ME70 multibeam echosounder. At each site hydrological data is collected using Conductivity Temperature Depth sensor (CTD).

Small otter trawl and epibenthic sled catches of fishes/invertebrates: concentration on YOY fishes inside and outside NY Habor

Spatial information on the arrangement of geological features, habitats and living marine resources on the seabed are often the foundation for decision-making in ecosystem management and ocean planning. Collecting information on the seabed depths and geomorphology is an expensive operation requiring airborne platforms like satellites, planes or drones, or small vessels to large research ships. Coordinating these data needs and data collection efforts will better leverage collective resources and meet shared goals. To help enable this coordination, in 2020 the National Oceanic and Atmospheric Administration (NOAA) National Centers for Coastal Ocean Science (NCCOS) developed a spatial framework, process, and online application to identify common data collection priorities for seafloor mapping, sampling, and visual surveys along shore and offshore of the Southeast United States (North Carolina, South Carolina, and Georgia). Twenty-five representatives from federal and state agencies, academic institutions, and non-governmental conservation groups, designated seafloor mapping priorities using an online prioritization tool. Participants allocated virtual coins across 5 km x 5 km grid cells to denote their organization’s regions of seafloor mapping needs. Grid cells with more coins were higher priorities than cells with fewer coins. Participants also reported why these locations were important and what data types were needed. Results were analyzed and mapped using statistical techniques to identify significant relationships between priorities, reasons for those priorities and data needs. These data are the summarized results from this project and can also be viewed in an online web map (https://noaa.maps.arcgis.com/apps/webappviewer/index.html?id=04cdd2a68c4f427f893f2042f326dc80). Several common areas of interest were identified in the spatially explicit analysis of the responses. Nearshore surfzone along Georgia, South Carolina, and North Carolina were highlighted by several agencies and organizations interested in sediment and sand resources as well as potential for rocky reef habitats. Inshore estuarine areas were highlighted by state agencies and conservation groups interested in monitoring change in managed areas like National Estuarine Reserves. On the outer continental shelf, areas near Blake Plateau off South Carolina and the continental shelf break off North Carolina were identified by federal agencies and conservation organizations as areas of sensitive habitats or historically significantly shipwrecks and maritime resources. The seafloor mapping prioritization approach described in the Buckel et al. (2021) report associated with these data provides recommendations to organizations charged with mapping the seabed for navigation and commerce as well as resource assessments and management. Already, the priority areas identified in this exercise are being used by NOAA to focus planned seafloor mapping missions. Furthermore, the outcomes from this regional exercise contribute into a National Mapping Prioritization under the lead of NOAA to coordinate mapping activities across the entire US EEZ. Together, these quantitative seafloor mapping prioritization approaches will enable improved coordination and more efficient allocation of resources needed to conduct seafloor mapping providing data to support environmental stewardship, safe navigation and commerce.

Coastal researchers, fishermen, fishery managers and educators teamed up to understand changes in shrimp populations in response to shifting environmental conditions in estuaries. The Project Shrimping has deep cultural and economic ties to the South Carolina and Georgia coasts, and the southeast US Atlantic coast region as a whole. However, over the past two decades, commercial shrimp landings have been highly variable. Fishery management agencies, extension offices, and several southeastern Reserves have identified the need to better understand how shrimp populations are responding to changing environmental conditions, including warmer winters and altered salinity regimes. To do this work, a diverse team with members from universities, fishery management agencies, fisheries extension offices, and Reserves came together to form the Lowcountry Shrimp Collaborative. The Lowcountry Shrimp Collaborative used a comprehensive approach to examine how environmental conditions in estuaries are affecting abundance and timing of shrimp populations throughout the region through examination of each stage of the shrimp life cycle. Together, the Collaborative: Analyzed and synthesized numerous ongoing, long-term (30+ years) datasets on multiple shrimp life history stages (postlarval, juvenile, sub-adult, adult, commercially harvested) and environmental conditions (water quality, including System-Wide Monitoring Program data); Conducted field sampling targeting shrimp and their prey in salt marsh creeks during spring and summer seasons, over two years, at three southeast Reserves; Ran controlled seawater laboratory experiments to understand the impacts of competition for limited resources between shrimp species during their overlapping periods of estuarine residency; and, Interviewed commercial shrimpers based in Georgia and South Carolina, to better understand historical changes in, and perceptions of environmental impacts on, the shrimp industry in the southeast US. The project found that estuarine water temperature is rising across the region, mainly driven by increases during winter months. Warming temperatures can alter the life histories of shrimp, including shifting body size, altering the timing of migratory cues, and modifying habitat use. These warmer temperatures are also resulting in longer shrimping seasons with shrimpers often able to continue harvesting well into January. These results were confirmed by observations shared by shrimpers, who joined for a project wrap-up event where the team presented results and engaged in lively discussions about research needs and opportunities for collaboration between researchers, managers, and the industry.