A coupled Delft3D hydrodynamic and Ecopath with Ecosim and Ecospace (EwE) food web modeling approach was used to demonstrate the range of temporal and spatial changes in water temperature, salinity, fisheries species populations and the broader estuarine food web of Apalachicola Bay, FL. The models simulated observed conditions from 2000 to 2019 and future changes in response to scenarios of low and high river flow and sea level rise up until 2049. Model outputs include ASCII grid files of water temperature, salinity, and species biomasses, and csv files of species biodiversity indices at monthly time steps for the years 2000-2019 and the year 2049. Temperature and salinity files are labeled with year and month and species biomass and biodiversity files are labeled by monthly timestep (years 2000-2019 = timesteps 1-240, year 2049 = timesteps 589-600).

These files house the data collected during 2013 in lower Pensacola Bay. The data were used to estimate aquatic primary production and respiration. This dataset is associated with the following publication: Caffrey, J., M. Murrell , K. Amacker, J. Harper, S. Phipps, and M. Woodrey. Seasonal and interannual patterns in primary production, respiration and net ecosystem metabolism in three estuaries in the northeast Gulf of Mexico. Estuaries and Coasts. Estuarine Research Federation, Port Republic, MD, USA, 20, (2013).

This dataset includes the data that was used for the tidal portion of the joint pilot fish habitat assessment. Additional data for non-tidal waters is being archived by USGS in ScienceBase. This data collection contains geospatial data of environmental layers used in the model analysis as well as the outputs of an ensemble fish habitat prediction model. It includes layer inputs at 3 different spatial scales (10x10m, 100x100m, and 1000x1000m) for the following environmental predictive variables: substrate bottom, distance to hardened shoreline, distance to submerged aquatic vegetation beds, distance to protective areas, dissolved oxygen, salinity, water quality, and benthic index of biotic integrity all in the form of TIF files (.tiff). There were 16 total inputs per resolution scale all cropped to a tidal waterbody boundary for the Patuxent watershed. This boundary is also included in the data collection and is represented as a single feature polygon shapefile (.shp). Lastly, there is a csv file containing presence sites for white perch sampled from a variety of different fish survey datasets. These were collected and joined to represent fish presence within the tidal portion of the Patuxent watershed and includes associated spatial and temporal data. For more information see (Nisonson et al., 2024).

Here we archive data collected during a nitrogen addition field experiment in the Sacramento River Deep Water Ship Channel. Calcium nitrate was added on 8 dates to a segment of the ship channel centered at Navigation Light 74. Prior to and following the nutrient additions, we collected water samples and sensor-based measurements at 7 sites between Navigation Light 70 and 76. Water samples for nutrient analyses were collected in 500 mL High Density Poly Ethylene (HDPE) amber containers from 1 m and 8 m depths using a peristaltic pump. Whole water samples for phytoplankton analysis were collected from 1 m depth in 500 mL clear HDPE containers and immediately preserved with 20 mL of Lugol’s iodine solution (Lugol’s, ENG Scientific, Inc.). We collected a vertically integrated zooplankton sample by lowering a 163 µM net to 8 m (~1 m off the bottom) and raised it using an electric winch. We transferred seston contents into new 250 mL HDPE containers and immediately preserved them with 10 mL of Lugol’s. A 1-mL unfiltered water sample from the surface was collected for bacterioplankton abundance. Vertical profiles of temperature, conductivity, dissolved oxygen, pH, turbidity, and algal fluorescence were made using a YSI EXO2 sonde. Measurements were made at 0.5 m and at 1 m resolution to the bottom. The sensor was allowed to stabilize at each depth for at least 10 seconds prior to data acquisition. In total, we sampled on 27 dates between July 8 and August 26, 2019. Lastly, we also report data used in metabolism calculations. Data include 3 methods for estimating metabolism based on continuous DO measurements, laboratory incubations, and an isotope model. Ancillary data include light extinction, stratification strength, wind speed, and gas transfer velocity, Metabolism measurements range from July 2 to September 18, 2019.

Here we archive data collected during a nitrogen addition field experiment in the Sacramento River Deep Water Ship Channel. Calcium nitrate was added on 8 dates to a segment of the ship channel centered at Navigation Light 74. Prior to and following the nutrient additions, we collected water samples and sensor-based measurements at 7 sites between Navigation Light 70 and 76. Water samples for nutrient analyses were collected in 500 mL High Density Poly Ethylene (HDPE) amber containers from 1 m and 8 m depths using a peristaltic pump. Whole water samples for phytoplankton analysis were collected from 1 m depth in 500 mL clear HDPE containers and immediately preserved with 20 mL of Lugol’s iodine solution (Lugol’s, ENG Scientific, Inc.). We collected a vertically integrated zooplankton sample by lowering a 163 µM net to 8 m (~1 m off the bottom) and raised it using an electric winch. We transferred seston contents into new 250 mL HDPE containers and immediately preserved them with 10 mL of Lugol’s. A 1-mL unfiltered water sample from the surface was collected for bacterioplankton abundance. Vertical profiles of temperature, conductivity, dissolved oxygen, pH, turbidity, and algal fluorescence were made using a YSI EXO2 sonde. Measurements were made at 0.5 m and at 1 m resolution to the bottom. The sensor was allowed to stabilize at each depth for at least 10 seconds prior to data acquisition. In total, we sampled on 27 dates between July 8 and August 26, 2019. Lastly, we also report data used in metabolism calculations. Data include 3 methods for estimating metabolism based on continuous DO measurements, laboratory incubations, and an isotope model. Ancillary data include light extinction, stratification strength, wind speed, and gas transfer velocity, Metabolism measurements range from July 2 to September 18, 2019.

Measurements made in the Chesapeake Bay and Mid-Atlantic Bight during 2001 to 2004.

This dataset includes water quality data and phytoplankton community composition data collected from 6 sites along Mullica River-Great Bay and 6 sites along Toms River-Barnegat Bay in New Jersey from April-November 2020-2022. All samples were collected from surface waters. Temperature (℃), salinity (ppt), optical dissolved oxygen (mg/L & percent saturation), pH, and turbidity (FNU), were collected using a YSI multiparameter sonde (EXO2). Two surface grab samples were taken in acid-washed 500 mL amber Nalgene bottles and stored on ice to measure dissolved organic carbon (DOC mg/L), Nitrate/Nitrite (mg/L), Ammonium (mg/L as ion), Ortho-Phosphate (mg/L), Total Phenolic Content (TPC µg/L gallic acid equivalents), and chlorophyll a (mg/L). In 2022, surface water was filtered through a 200 μm mesh and 10 mL transferred to a 15 mL falcon tube with 1% lugols solution to identify phytoplankton community composition using Sedgwick-rafter. The preserved phytoplankton samples were analyzed by identifying plankton in x100 magnification until at least 300 algal cells were counted. Mullica River-Great Bay sites were always collected during ebb tide, while tidal cycle varied for sampling of Toms River-Barnegat Bay.

CTD profile data (128 casts) were collected in the Chukchi and Beaufort Seas from the Fishing Vessel Ocean Starr (OS1701 Legs 1,2,3), August 1 to October 4, 2017). The cruise was part of the Arctic Integrated Ecosystem Survey (Arctic IES) funded as part of the North Pacific Research Board (NPRB) Arctic Integrated Ecosystem Research Program (Arctic IERP). The program and research on this expedition were sponsored by NPRB and the Bureau of Ocean and Energy Management (BOEM), with in-kind support by the National Oceanic and Atmospheric Administration (NOAA). These data contribute to understanding how reductions in Arctic sea ice and associated changes in the physical environment influence the flow of energy through the ecosystems of the two Seas. The physical data are part of a wider range of data collected towards this effort. Notably, there was no sea ice present in the northern regions during the survey area as compared to surveys that occurred during 2012 and 2013 (see cruise report). CTD data and water samples were collected by NOAA, PMEL Ecosystems & Fisheries-Oceanography Coordinated Investigations (EcoFOCI). This data set contains 1-meter-averaged profile data. Profile data from CTD instruments were processed at NOAA/PMEL/EcoFOCI using standard techniques. CTD data contacts: Phyllis Stabeno, Calvin Mordy, Peggy Sullivan, Shaun Bell. Scientist from National Oceanic and Atmospheric Administration (NOAA), Pacific Marine Environmental Laboratory (PMEL), Ecosystems and Fisheries-Oceanography Coordinated Investigations (EcoFOCI), University of Washington, Cooperative Institute for Climate, Ocean, and Ecosystem Studies (CICOES), North Pacific Research Board (NPRB) Arctic Integrated Ecosystem Research Program (IERP), Bureau of Ocean and Energy Management (BOEM) participated. Data are in NetCDF. Longitudes are in degW.

IOOS Sensor Observation Service (SOS) Server for NANOOS, the Northwest Association of Networked Ocean Observing Systems (http://nanoos.org). Provides access to marine in-situ observation data for the US Pacific Northwest and lower British Columbia, from the NANOOS asset data store harvested and integrated by NVS (NANOOS Visualization System, http://nvs.nanoos.org). To avoid data duplication, currently only assets not otherwise available to the IOOS Catalog (http://catalog.ioos.us) are accessible through this SOS server; for example, assets from most federal agencies are not accessible on this server, but they are available on the NVS application. This NANOOS service is run by the 52North IOOS SOS server software, and complies with the IOOS SOS "Milestone 1" service profile (https://code.google.com/p/ioostech/wiki/SOSGuidelines). This station provides the following variables: H1 redoxpot, Fractional saturation of oxygen in sea water, Mass concentration of oxygen in sea water, Sea water ph reported on total scale, Sea water salinity, Sea water temperature, Surface partial pressure of carbon dioxide in sea water, Omega aragonite, Dissolved inorganic carbon, Total alkalinity

This dataset includes water quality data and phytoplankton community composition data collected from 6 sites along Mullica River-Great Bay and 6 sites along Toms River-Barnegat Bay in New Jersey from April-November 2020-2022. All samples were collected from surface waters. Temperature (ºC), salinity (ppt), optical dissolved oxygen (mg/L & percent saturation), pH, and turbidity (FNU), were collected using a YSI multiparameter sonde (EXO2). Two surface grab samples were taken in acid-washed 500 mL amber Nalgene bottles and stored on ice to measure dissolved organic carbon (DOC mg/L), Nitrate/Nitrite (mg/L), Ammonium (mg/L as ion), Ortho-Phosphate (mg/L), Total Phenolic Content (TPC µg/L gallic acid equivalents), and chlorophyll a (mg/L). In 2022, surface water was filtered through a 200 μm mesh and 10 mL transferred to a 15 mL falcon tube with 1% lugols solution to identify phytoplankton community composition using Sedgwick-rafter. The preserved phytoplankton samples were analyzed by identifying plankton in x100 magnification until at least 300 algal cells were counted. Mullica River-Great Bay sites were always collected during ebb tide, while tidal cycle varied for sampling of Toms River-Barnegat Bay.