AndreaBozzo/ceres-open-data-index huggingface dataset:
Master Dataset for Elwha Carcass Addition Experiment - Elwha River salmon carcass addition experiment

Dam removal and other fish-barrier removal projects in western North America are assumed to boost freshwater productivity via the transport of marine-derived nutrients from recolonizing Pacific salmon (Oncorhynchus spp). In anticipation of the removal of two hydroelectric dams on the Elwha River in Washington State, we tested this hypothesis with a salmon carcass addition experiment. Our study was designed to examine how background nutrient dynamics and benthic foodwebs vary seasonally, and how these features respond to salmon subsidies. We conducted our experiment in six side channels of the Elwha River, each with a spatially paired reference and treatment reach. Each reach was sampled on multiple occasions from October 2007 to August 2008, before and after carcass placement. We evaluated nutrient limitation status, measured water chemistry, periphyton, benthic invertebrates, and juvenile rainbow trout (O. mykiss) response, and traced salmon-derived nutrient uptake using stable isotopes. Outside of winter, algal accrual was limited by both nitrogen and phosphorous and remained so even in the presence of salmon carcasses. One month after salmon addition, dissolved inorganic nitrogen levels doubled in treatment reaches. Two months after addition, benthic algal accrual was significantly elevated. We detected no changes in invertebrate or fish metrics, with the exception of 15N enrichment. Natural seasonal variability was greater than salmon effects for the majority of our response metrics. Yet seasonality and synchronicity of nutrient supply and demand are often overlooked in nutrient enhancement studies. Timing and magnitude of salmon-derived nitrogen uptake suggest that uptake of dissolved nutrients were favored over direct consumption of carcasses. The highest proportion of salmon-derived nitrogen was incorporated by herbivores (18â30%) and peaked 1â2 months after carcass addition. Peak nitrogen enrichment in predators (11â16%) occurred 2â3 months after addition. All taxa returned to background d15N levels by 7 months.  Since this study was conducted, both dams on the Elwha River were removed over 2011-2014 to open over 90% of the basin to anadromous fishes. We anticipate that as the full portfolio of salmon species expand through the basin, nutrient supply and demand will become more balanced and positive feedback loops of reciprocal nutrient transfer reinforced.
All datasets related to Elwha River carcass addition experiment. Includes physical habitat, chemical, and biological data.

Tags: animal and plant collection device, aquatic invertebrate, bottom sampler, dam removal, doc/noaa/nmfs/nwfsc, effectiveness monitoring, elwha river, fe legacy data sets, floodplain, food web, habitat, instrument not applicable, marine derived nutrients, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nutrient enrichment, periphyton, salmon, side channel, stable isotopes
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Experimental streams - Recolonization of the Cedar River, WA by Pacific salmon

The objective of this study is to quantify population, community, and ecosystem level changes as a result of salmon recolonization of the Cedar River, WA above Landsburg Dam. The dam was installed in 1901, blocking the upstream migration of adult salmon and steelhead from about 43 km of river habitat. A fish ladder was installed in 2003 to allow adult salmon passage. We collected baseline data on water chemistry, habitat, and fish populations including resident trout and sculpin populations in 2000-2002. These field surveys have been ongoing since 2000. 

A mark-recapture study in Rock Creek, the largest tributary available to salmon, was started in 2004 and ended in 2010 to quantify growth, movement, and survival of juvenile coho and resident trout.

Two experimental stream studies conducted to quantify salmon carcass effects on resident organisms.
Data on nutrients and insects to salmon carcass additions.

Tags: abundance, balance, cedar river watershed, doc/noaa/nmfs/nwfsc, experiments, fe (fish ecology) division, fish passage, invertebrate processing, isotopes, juvenile salmonid, length board, movement, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, pit tag, recolonization, rock creek pit tagging, survival, temperature sensor, tributary to cedar r.
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Vibrio ecology in PNW - The Ecology of Vibrio parahaemolyticus in the Pacific Northwest: Implications for risk assessment and early warning systems

Over the past decade, there has been a significant increase in Vibrio parahaemolyticus-related gastroenteritis from the consumption of raw oysters harvested in Washington state, partly attributed to increases in water temperatures. Such illnesses/outbreaks pose a threat to public health and result in severe economic losses to the shellfish growers. Increases in Vibrio populations due to changes in environmental conditions have been previously reported but the ecology of these bacteria and their interactions with the aquatic environment are not clearly understood. 

We are investigating the influence of environmental variables on concentrations of potentially pathogenic and avirulent strains of V. parahaemolyticus in oysters as well as in water and plankton, focusing on harvest areas with historically higher incidences of the bacteria. In addition, we are examining the association of V. parahaemolyticus with co-isolated phytoplankton species. The goal of these studies is to gain a better understanding of the spatial, temporal, environmental, and bacterial genetic relationships that promote the selection of strains responsible for clinical V. parahaemolyticus infections, which may assist in the improvement of risk assessment strategies and mitigation tools to prevent disease outbreaks.
Time series data on pathogen abundance, temperature, salinity and sampling locations.

Tags: doc/noaa/nmfs/nwfsc, grays harbor, hood canal, instrument not applicable, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, pacific oysters, pathogen, vibrio, willapa bay
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish Culture - North Puget Sound Chinook salmon captive propagation

NOAA Fisheries is a cooperator with the Washington Department of Fish and Wildlife and the Lummi, Nooksack, and Stillaguamish Tribes in a 10-year program to rebuild the South Fork Nooksack River spring Chinook and Stillaguamish River fall Chinook stocks through a captive broodstock program.
Raw data on rearing density, loading density, water temperature, ration, and feed size may be available.  Raw data on administration of therapeutic drugs may be available.

Tags: artificial propagation, chinook salmon, doc/noaa/nmfs/nwfsc, instrument not applicable, manchester research station, migrated from resource enhancement and utilization technologies division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Field and laboratory notes on instream research - Research and Development of New Marking and Monitoring Technologies

This project addresses how to expand the current fish-tracking technologies to enable the fisheries community to successfully carry out the actions, research, and monitoring activities outlined in the 2000, 2004, and 2008 BiOps, 2004 UPA, Fish and Wildlife Program, and 2003 systemwide passage summary. The goal of the project is to satisfy these needs by developing interrogation systems that will collect data on migrating juvenile and adult salmonids through mainstem Columbia River Basin (CRB) dams, including juvenile salmon transiting surface-bypass systems and all life-stages transiting small streams. These fish-tracking technologies are then used to assess the effectiveness of management actions and strategies for recovery of ESA-listed fish populations.

For example, development of PIT-tag systems that will work in large streams or even rivers are essential for determining the effectiveness of all types of restoration programs on stock recovery supported by BPA. In addition, these systems would help delineate the different types of interactions between hatchery and wild stocks in the field. Within this project, we propose to develop technologies that help monitor the stocks at critical (and if possible, all) life stages and critical locations. For example, many juvenile salmonids now use unmodified spillbays, spillbays outfitted with temporary spillway weirs (TSWs) or removable spillway weirs (RSWs), and turbines during their migration, but we are unable to monitor them in these locations because they lack PIT-tag interrogation systems. Consequently, we are collecting fewer data points for the different survival models. Therefore, we are proposing to start or continue development programs for interrogation systems (tags, antennas, receivers, etc) that will enable us to monitor these migrating fish through these pathways. Besides project administration, the proposed work for the performance period (October 2010-January 2012) covers four main research areas or work elements:

1. Finished development of the ogee-based PIT-tag system for Ice Harbor Dam.

2. Install and evaluate the ogee-based system for Ice Harbor Dam.

3. Continue the development of in-stream interrogation systems -- antennas and multiplexing transceiver.

4. Evaluate alternative interrogation technologies - HDX systems and ISO transceivers.

Instream research notes.

Tags: biological, columbia river, dams, dams throughout the columbia river basin, decision-making, doc/noaa/nmfs/nwfsc, effectiveness monitoring, fe (fish ecology) division, habitat, laboratory at sand point, management strategy evaluation, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, pit tag, salmon, stream sites throughout the northwest
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Isotopes - Recolonization of the Cedar River, WA by Pacific salmon

The objective of this study is to quantify population, community, and ecosystem level changes as a result of salmon recolonization of the Cedar River, WA above Landsburg Dam. The dam was installed in 1901, blocking the upstream migration of adult salmon and steelhead from about 43 km of river habitat. A fish ladder was installed in 2003 to allow adult salmon passage. We collected baseline data on water chemistry, habitat, isotopes (periphyton, invertebrates, fish, riparian trees) and resident trout and sculpin populations in 2000-2002. These studies have been ongoing since 2000. A mark-recapture study in Rock Creek, the largest tributary available to salmon, was started in 2004 to quantify growth, movement, and survival of juvenile coho and resident trout.
C and N isotope levels in plants, insects and fish in the Cedar River.

Tags: abundance, cedar river watershed, doc/noaa/nmfs/nwfsc, experiments, fe (fish ecology) division, fish passage, instrument not applicable, invertebrate processing, isotopes, juvenile salmonid, movement, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, pit tag, recolonization, rock creek pit tagging, survival, tributary to cedar r.
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Larval Billfish Data from Plankton Tows Conducted off the Kona Coast in West Hawai'i between 1997 and 2018

This is a 20-year (1997-2018) dataset of neustonic ichthyoplankton collections from West Hawai'i and beyond focusing on four species of billfishes (Blue Marlin /Makaira nigricans/, Striped Marlin /Kajikia audax/, Shortbilled Spearfish /Tetrapturus angustirostris/, and Swordfish /Xiphias gladius/). We compiled observations of 1963 larvae over this 20- year period (from 998 discrete ichthyoplankton tows in West Hawaii), and provide specimen information and species level identifications for 1109 larvae using both existing and new genetic assignments. Additionally, we filtered these data to tows with consistent methodologies revealing 1761 larval billfishes (from 771 discrete surface tows in West Hawaii). We also constructed a thorough dataset of environmental variables (temperature, salinity, chlorophyll) associated with each occurrence of larval billfish and all absences using oceanographic data collected in-situ during cruises and satellite data. We present the first complete multispecies larval billfish dataset with coupled environmental data in the Pacific Islands Region ready for statistical analysis. This dataset will be critical for improving our understanding of how oceanographic features and environmental changes will affect larval growth, survival, and ultimately population replenishment.

Tags: animals/vertebrates, aquatic habitat, aquatic sciences, atmospheric/ocean indicators, biological classification, biosphere, central pacific ocean, chlorophyll, chlorophyll concentration, climate indicators, coastal habitat, coastal waters of hawaii, continent, country/territory, date, discrete sample, distance to shore, doc/noaa/nmfs/pifsc, earth science, ecological characterization, ecosystem sciences division, esd, fish, fish eggs and larvae, fish species, fisheries, gear type, geographic information, gps, habitat- slicks, hawaii, hawaii island, hawaiian islands, integrated ecosystem assessment, istiophoridae, kajikia audax, kona coast (19n155w0002), latitude, longitude, makaira nigricans, mesh size, microbiota, national marine fisheries service, neuston, nmfs, noaa, north america, ocean, ocean basin, ocean optics, ocean temperature, oceans, oscar elton sette, pacific islands fisheries science center, pacific ocean, pifsc, plankton, profile, ray-finned fishes, sample identification, sea surface temperature, species identification- organism length, surface salinity, survey, tetrapturus angustirostris, thermosalinographs, time series, tow depth, tow type, townsend cromwell, u.s. department of commerce, united states of america, us doc, visual observation, water column habitat, water depth- average, xiphias gladius, xiphiidae
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
PAH data in tissues of subsistence harvested marine mammal - Determination of PAH baseline values in tissues from subsistence-harvested marine mammals on the North Slope

Over the past 15 years, high quality marine mammal tissue and fluid samples collected by subsistence hunters in the North Slope region of Alaska have been archived by the North Slope Borough (NSB).  Staff from both the NSBâs Department of Wildlife Management and the NWFSC have selected a subset of the samples for analyses of petroleum-related compounds to establish baseline concentrations in top-level predators in the region.  The Environmental Chemistry Program will analyze tissue and stomach content samples of various species of marine mammals harvested in the North Slope region of Alaska for polycyclic aromatic hydrocarbons (PAHs) including alkylated PAH homologs using gas chromatography / mass spectrometry (GC/MS).  The NWFSC will also analyze bile and urine samples collected from a subset of these animals for PAH metabolites using either high-performance liquid chromatography/fluorescence or liquid chromatography/tandem mass spectrometry (LC-MS/MS).  The findings of this study will be drafted for a peer-reviewed journal publication.
Measurements of parent and alkylated PAHs in various matrices of marine mammals.

Tags: doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Northern California Current  Ecosystem Survey (transect)

This layer is intended to represent the geographic extent of NOAA Fisheriesâ Northern California Current Ecosystem Survey transects. The  Northern California Current Ecosystem Surveys  started in 1996 and is led by NMFS Northwest Fisheries Science Center. These surveys expand the biophysical sampling conducted along the Newport Line out to the edge of the U.S. Exclusive Economic Zone. These surveys help us understand lower trophic level responses to environmental variability across the Pacific Northwest and California Current ecosystem. We also incorporate information on the abundance and distribution of mid-trophic level nekton, marine mammals, and birds. These samples inform broad-scale analyses of hydrography, phytoplankton, zooplankton, larval and juvenile fish, and ocean acidification and hypoxia. This survey is also part of a larger collaboration with Oregon State University researchers studying the marine biodiversity and size structure across broad spatial scales in the northern California Current. The Northern California Current Ecosystem Survey samples seasonally from northern Washington to the Oregon/California border, and offshore to 200 nautical miles off Newport, Oregon and 150 nautical miles off Crescent City, California on the NOAA Ship Bell M. Shimada. Seasonal sampling efforts include CTD, acoustic transects, zooplankton, ichthyoplankton, and macro-plankton sampling via bongo and Methot nets, as well as midwater and beam trawls.

Tags: doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, oregon, story map: noaa fisheries west coast offshore scientific surveys, united states, washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Central Puget Sound Ecopath/Ecosim model biological parameters - Developing food web models for ecosystem-based management applications in Puget Sound

This project is developing food web models for ecosystem-based management applications in Puget Sound. It is primarily being done by NMFS FTEs and contractors, in collaboration with scientists from the State of Washington and University of Washington. Ecosystem-scale models will be built in the Ecopath/Ecosim and Atlantis software frameworks. Working models and scientific manuscripts will be the main products. The target audience is the Puget Sound Partnership, resource management agencies and stakeholders in the Puget Sound area. This is an on-going, stand-alone project without a firm deadline.
Spreadsheets.

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, food web, instrument not applicable, management strategy evaluation, marine ecosystems, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
2013 Early Life History Experiment Data - Snake River sockeye salmon captive propagation

In the early 1990s, Redfish Lake sockeye salmon from the Sawtooth Basin in Idaho were on the brink of extinction, and they were listed as endangered under the US Endangered Species Act in 1991. To prevent extinction, a gene rescue captive broodstock program was established for the stock that consisted of taking most of the remaining gene pool into captive culture at specialized conservation hatcheries at the Manchester Research Station and the Idaho Department of Fish and Game Eagle Hatchery. 

Efforts through the decade of the 1990s consisted of developing techniques for successful culture of sockeye salmon to adulthood, establishing rearing and spawning protocols to ensure preservation of stock diversity, and habitat enhancement at the rearing lakes. In the early 2000s, the program began to include a demographic focus to boost the population through rearing and release of enough juveniles to produce some adult returns. For the last few years, NWFSC eyed egg production has resulted in over 150,000 smolts being released into the Stanley basin annually for recovery, with plans to increase NWFSC eyed egg production to support release of half a million smolts in the Stanley Basin by 2017.  In 2011, and for the fourth year in a row, record numbers of sockeye adults have returned to their native home in Idaho.
This work is collecting data on the length, weight, and survival of sockeye salmon ponded under two different incubation temperature profiles.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, obsolete, salmon, snake river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Puget Sound porpoise population - Estimates of harbor porpoise population size in the main basin of Puget Sound

Estimates of harbor porpoise population size in the main basin of Puget Sound. This abundance will be derived from established methodology for marine mammal abundance estimation. Updates to abundance will provide current population levels as well as population trend information for harbor porpoise population size in Puget Sound.
Porpoise population data.

Tags: cb (conservation biology) division, doc/noaa/nmfs/nwfsc, gps, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, population trends, porpoise, puget sound washington
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Social Behavior - Snake River sockeye salmon captive propagation

In the early 1990s, Redfish Lake sockeye salmon from the Sawtooth Basin in Idaho were on the brink of extinction, and they were listed as endangered under the US Endangered Species Act in 1991. To prevent extinction, a gene rescue captive broodstock program was established for the stock that consisted of taking most of the remaining gene pool into captive culture at specialized conservation hatcheries at the Manchester Research Station and the Idaho Department of Fish and Game Eagle Hatchery. 

Efforts through the decade of the 1990s consisted of developing techniques for successful culture of sockeye salmon to adulthood, establishing rearing and spawning protocols to ensure preservation of stock diversity, and habitat enhancement at the rearing lakes. In the early 2000s, the program began to include a demographic focus to boost the population through rearing and release of enough juveniles to produce some adult returns. For the last few years, NWFSC eyed egg production has resulted in over 150,000 smolts being released into the Stanley basin annually for recovery, with plans to increase NWFSC eyed egg production to support release of half a million smolts in the Stanley Basin by 2017.  In 2011, and for the fourth year in a row, record numbers of sockeye adults have returned to their native home in Idaho.
Interfish distance, interfish orientation.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester, salmon, snake river, unknown instrument
Organization: National Oceanic and Atmospheric Administration, Department of Commerce