Scientists at NOAA 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.

The NOAA/NEFSC Study fleets are a subset of fishing vessels from which high quality, self-reported data on fishing effort, area fished, gear characteristics, catch, and biological observations are collected. Participating vessels collect data within their permitted fisheries using normal commercial fishing operations, and are selected to address specific research topics. Vessels collect data via electronic logbook (ELB) and submit the data to NMFS (refer to VERS system for details). The data collected by the vessel operators serve as the basis for ancillary data which are collected by Study Fleet staff and are usually associated with one or more targeted research objectives. The data collected from these vessels can be used to supplement the stock assessment process and are especially useful when catch data are limited.

The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web interactions, habitat, fisheries, economics, monitoring, and management into a common model framework. This framework allows for thought experiments, including evaluation of alternate management strategies, identifying robust indicators, and assessing relative importance of different ecosystem drivers in regulating important processes. NMFS personnel are conducting this work in broad collaboration with other NOAA scientists, academics, and NGOs. The specific work entails model development, scoping issues with stakeholders and policy makers, running scenarios, and analyzing and writing up the results. Products will include peer-reviewed papers, presentations, and workshops with modelers and/or stakeholders. Management audiences include NMFS west coast regions and the PFMC. The project is an on-going, stand-alone project with no firm deadline for completion. Outputs of the ROMS model. Metadata and .nc datafile at https://www.nodc.noaa.gov/oceanacidification/data/0131198.xml Generated from Atlantis ecosystem model, version AtlantisTrunk5425. Model code from CSIRO Australia, available via SVN after contacting CSIRO staff at http://atlantis.cmar.csiro.au/.

Goal 1: Improve understanding of salmon ocean ecology by integrating stock-specific distribution patterns over space and time with biological and environmental data. Goal 2: Integrate multiple disciplines to develop and apply new scientific technology to improve fisheries management strategies across geo-political boundaries. Goal 3: Improve economic opportunities for fishermen and coastal communities. The Oregon Salmon Commission, California Salmon Council, and Washington Trollers Association lead the Collaboration. Partners include Oregon Sea Grant, Community Seafood Initiative, Columbia River Inter-Tribal Fish Commission, University of California Santa Cruz, Oregon State University, Oregon and Washington Departments of Fish and Wildlife, California and Idaho Departments of Fish and Game, National Marine Fisheries Service Northwest, and Southwest Fisheries Science Centers. Fishermen sample Chinook salmon at sea. Genetic Stock Identification (GSI) analysis is used to determine stock of origin. Scales are examined to determine age, and other biological and physical data are taken. The purpose is to develop Fishery information system with multiple goals. The target audience is the Pacific Fishery Management Council (PFMC) and Pacific Salmon Commission (PSC) Management, as well as fishermen, scientists, marketers, educators, and the general public. This is a stand-alone project, with one principal point of contact in NMFS. This project is ongoing. Chinook genetics for stock identification.

NOAA Fisheries and its partners conduct fisheries-independent surveys in 8 regions in the US (Northeast, Southeast, Gulf of Mexico, West Coast, Gulf of Alaska, Bering Sea, Aleutian Islands, Hawai’i Islands). These surveys are designed to collect information on the seasonal distribution, relative abundance, and biodiversity of fish and invertebrate species found in U.S. waters. Over 900 species of fish and invertebrates have been identified in these surveys.

Statistical areas for the offshore eastern USA as determined by NOAA's NMFS for use in reporting and scientific research

This project will provide research staff members from the mid-Atlantic reserves with targeted tools, graphical support, and training to facilitate the use of reserve monitoring data. The project team will focus on deciphering trends in water quality parameters, which are related to management issues such as storm surge mitigation. Through workshops and the development of statistical applications, this project will increase capacity to distill monitoring data into a format that resource managers can use. The project team will share their approach and project outputs with the larger reserve system, and collectively, these efforts will demonstrate the value of the reserve monitoring program. This science transfer project was funded by NOAA through the National Estuarine Research Reserve System Science Collaborative to promote the use of science. It did not produce any new data.

The purpose of the Fisheries One-Stop-Shop (FOSS) is to make fisheries dependent information readily available to fisheries managers, scientists and the American public at a national as well as regional level. Collection and management of fisheries dependent data are distributed throughout NOAA Fisheries, State Fisheries, management agencies and regional Fisheries Information Networks (FINs). The distributed nature of NOAA Fisheries information systems, differences in collection authorities and confidentiality requirements increases the importance of this flexible technical architecture that can meet the changing needs for information at national, regional and local levels of resolution. At the same time, the technical architecture is scalable to meet enterprise wide requirements for management of other types of fisheries data and fisheries independent data. Currently available via FOSS are the summarized, non-confidential, annual Commercial Landings by state as provided through the Atlantic Coastal Cooperative Statistics Program (ACCSP), the Gulf of Mexico Fisheries Information Network (GulfFIN). Recreational Landings estimates are available and provided via NMFS Headquarters. In FY2011, FOSS will be expanded to include all commercial landings nationally.

The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, linking oceanography, biogeochemistry, food web interactions, habitat, fisheries, economics, monitoring, and management into a common model framework. This framework allows for thought experiments, including evaluation of alternate management strategies, identifying robust indicators, and assessing relative importance of different ecosystem drivers in regulating important processes. NMFS personnel are conducting this work in broad collaboration with other NOAA scientists, academics, and NGOs. The specific work entails model development, scoping issues with stakeholders and policy makers, running scenarios, and analyzing and writing up the results. Products will include peer-reviewed papers, presentations, and workshops with modelers and/or stakeholders. Management audiences include NMFS west coast regions and the PFMC. The project is an on-going, stand-alone project with no firm deadline for completion. Results of Atlantis ecosystem model simulations Metadata and .nc datafile at https://www.nodc.noaa.gov/oceanacidification/data/0131198.xml Generated from Atlantis ecosystem model, version AtlantisTrunk5425. Model code from CSIRO Australia, available via SVN after contacting CSIRO staff at http://atlantis.cmar.csiro.au/.

This fish and benthic composition database is the result of a multifaceted effort described below. The intent of this work is five fold: 1) To spatially characterize and monitor the distribution, abundance, and size of both reef fishes and macro-invertebrates (conch, lobster, Diadema); 2) To relate this information to in-situ data collected on associated benthic composition parameters; 3) To use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting; 4) To establish the efficacy of those management decisions; and 5) To work with the National Coral Reef Monitoring Program to develop data collection standards and easily implemented methodologies for transference to other agencies and to work toward standardizing data collection throughout the US states and territories. Toward this end, the Center for Coastal Monitoring and Assessment's Biogeography Branch (BB) has been conducting research in Puerto Rico and the US Virgin Islands since 2000 and 2001, respectively. It is critical, with recent changes in management at both locations (e.g. implementation of MPAs) as well as proposed changes (e.g. zoning to manage multiple human uses) that action is taken now to accurately describe and characterize the fish/macro-invertebrate populations in these areas. It is also important that BB work closely with the individuals responsible for recommending and implementing these management strategies. Recognizing this, BB has been collaborating with partners at the University of Puerto Rico, National Park Service, US Geological Survey and the Virgin Islands Department of Planning and Natural Resources. To quantify patterns of spatial distribution and make meaningful interpretations, we must first have knowledge of the underlying variables determining species distribution. The basis for this work therefore, is the nearshore benthic habitats maps (less than 100 ft depth) created by NOAA's Biogeography Program in 2001 and NOS' bathymetry models. Using ArcView GIS software, the digitized habitat maps are stratified to select sampling stations. Sites are randomly selected within these strata to ensure coverage of the entire study region and not just a particular reef or seagrass area. At each site, fish, macro-invertebrates, and benthic composition information is then quantified following standardized protocols. By relating the data collected in the field back to the habitat maps and bathymetric models, BB is able to model and map species level and community level information. These protocols are standardized throughout the US Caribbean to enable quantification and comparison of reef fish abundance and distribution trends between locations. Armed with the knowledge of where "hot spots" of species richness and diversity are likely to occur in the seascape, the BB is in a unique position to answer questions about the efficacy of marine zoning strategies (e.g. placement of no fishing, anchoring, or snorkeling locations), and what locations are most suitable for establishing MPAs. Knowledge of the current status of fish/macro-invertebrate communities coupled with longer term monitoring will enable evaluation of management efficacy, thus it is essential to future management actions.