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).

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.

This dataset includes outputs from an ecosystem model, which is a tool for regional science managers to explore marine spatial planning scenarios in the context of static and dynamic environmental covariates. The dataset includes predicted fish biomass from the Ecopath with Ecosim and Ecospace model set up over the Florida Reef Tract, during eight scenarios and across 36 trophic groups during the time period between 1994 and 2012. Simulations considered all pairwise combinations of changing the size of Marine Protected Areas (‘existing MPAs’, ‘large MPAs’), varying rates of movement via modeled diffusion (‘low diffusion’, ‘high diffusion’), and increasing fishing effort (total effect multiplier; ‘low TEM’, ‘high TEM’).

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.

Meteorological dataset: Meteorological data provide information on atmospheric conditions that can affect water quality and biological and physical processes. Core elements currently measured at each National Estuarine Research Reserve (NERR) include air temperature, relative humidity, barometric pressure, wind speed, wind direction, rainfall, and photosynthetically active radiation (PAR). Optional parameters include total solar radiation. Each site maintains at least one meteorological station. Stations are placed at locations typical of local conditions or in areas where a specific need for weather data has been identified. Data are reported at 15 minute intervals. Prior to 2007, hourly and daily average data were also reported. Water Quality dataset: Water quality observations made over long time periods can provide important feedback to scientists and to local, state, and national resource managers about actions taken to manage, protect, and restore estuaries. They also provide valuable information for evaluating the impacts of environmental change on coastal habitats and species. There are at least four water quality stations at each National Estuarine Research Reserve. Each station is designed to characterize long-term variability and short term changes in environmental conditions. Data are collected with data loggers at fifteen minute intervals and instruments are deployed continuously and year round where possible. Water quality parameters collected include: water temperature, specific conductivity, salinity, percent saturation of dissolved oxygen, dissolved oxygen concentration, pH, depth, and turbidity. Chlorophyll fluorescence is an optional parameter and pressure corrected water depth is a calculated value. Nutrient/pigment dataset: There are at least four water quality stations at each National Estuarine Research Reserve. Each station is designed to characterize long-term variability and short term changes in environmental conditions. Discrete samples for nutrient and chlorophyll a concentrations are collected at each long-term monitoring station at least once monthly. More intensive (24-hours over a complete tidal cycle) sampling is conducted each month at one water quality monitoring station to better understand impacts of tide and irradiance on nutrient cycling. Nutrient parameters collected include: nitrate, nitrite, ammonium, orthophosphate, and chlorophyll a. Numerous optional parameters include dissolved organic carbon, total dissolved nitrogen, and total dissolved phosphorus. All data are provided in yearly .CSV files.

NOAA measurements from 1996 to 1999 along the Eastern US coastal region.

This dataset is a collection of files containing the necessary inputs to, and relevant outputs from, the U.S. Gulf-wide ecosystem model, developed using the Ecopath with Ecosim (EwE) modeling software package. The spatial extent of the model is 25°-30.5° N and -81° to -97.3° W and hindcast simulations were run in Ecosim from 1980 (the Ecopath snapshot year) to 2016 at a monthly timestep. Input parameters for Ecopath include biomass, consumption, mortality, diet, landings, and discards for 78 functional groups included in the model. Each input or output parameter type is included as its own csv file with informative names.

This project tested the use of eDNA methods to identify fish communities, assess biodiversity, and detect invasive crabs in different types of estuaries and connected streams. Samples were collected at Apalachicola, Great Bay, He’eai, Hudson, South Slough and Wells Reserves in 2018 and 2019. The project deployed two methods to analyze DNA in water samples: metabarcoding that identifies a wide range of species, and digital droplet Polymerase Chain Reaction (ddPCR) that identifies a single target organism. The team conducted baseline community assessments for fish at five reserve sites and conducted a survey of anadromous fish in a tributary stream at the sixth reserve. The project found that fish community and biodiversity assessments are well suited to eDNA applications, while invasive crabs are much harder to detect because they do not shed much DNA. The project developed protocols and recommendations for the collection, filtering, and extraction of eDNA samples at estuarine sites, and provided information which will support the design of sampling programs for fish communities.