AndreaBozzo/ceres-open-data-index huggingface dataset:
Skagit IMW - Skagit River Estuary Intensively Monitored Watershed Project

This study evaluates system-level effects of several estuary restoration projects on juvenile Chinook salmon production in the Skagit River estuary. The monitoring encompasses juvenile out-migration from rivers, estuary rearing, and shoreline and subtidal neritic residency. NWFSC is responsible for sampling neritic systems.
Excel spreadsheets and Filemaker Pro databases.

Tags: animal and plant collection device, animal and plant collection device - plankton collection device - plankton net, balance, ctd, doc/noaa/nmfs/nwfsc, estuary, fe (fish ecology) division, habitat use, length board, national marine fisheries service, nearshore, nearshore pelagic, net mensuration, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, restoration, skagit estuary
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Feed formulations - Incorporation of Plant Proteins into Marine Finfish Feeds, a NWFSC-YSFRI Joint Study

This international study is funded through the NOAA Fisheries Office of Science and Technology.  The overall goal of the proposed research is to identify fishery by-product meals that will best facilitate the incorporation of soy and corn protein meals into marine fish feeds.  It is well established that fish proteins are nutritious and valuable feed commodities.  However, in many areas of the world, fish processors currently discard large quantities of fish protein as processing waste due to a lack of appropriate technologies to process these by-products.  NWFSC and the Yellow Sea Fisheries Research Institute (YSFRI) have independently developed unique industrial processes to produce by-product meals from fishery processing waste that are suitable ingredients for aquaculture feeds.  These processes differ in their approach to digestion as the NWFSC process utilizes organic acids to digest tissue homogenates which is contrast to the enzymatic digestion utilized by the YSFRI process.  In the past, NWFSC and YSFRI researchers have utilized processing waste from different fish species in their research. As such, it is uncertain how processing method effects protein functionality and structure, which meals may be best utilized by marine fish, and which meals can overcome the nutritional deficiencies inherent to plant proteins.
MS Excel spreadheet.

Tags: alternative feeds, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, international collaboration, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc, unknown instrument
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
DTAGs SRKW - Using DTAGs to study vessel sound exposure & effects on behavior in southern resident killer whales

Drs. Marla Holt, Brad Hanson, and Candice Emmons of the NWFSC, along with collaborators from Cascadia Research Collective and UC Davis, are currently conducting a study using digital acoustic recording tags (DTAGs) to examine sound exposure, sound use, and behavior of Southern Resident killer whales (SRKWs) in core summer habitat. The DTAG is suction cup attached and consists of a number of different sensors that record sound, pitch, roll, heading, and depth. The tag was developed by Woods Hole Oceanographic Institution specifically to monitor the behavior of marine mammals and their response to sound, continuously throughout the dive cycle. Prey samples and vessel data are also concurrently collected relative to tagged whales in a manner similar to previous work. The project research goals include the following: 

(1) Measure noise levels in biological relevant frequency ranges that are received by individual SRKWs.

(2) Quantify the relationship between vessels and received noise levels. 

(3) Determine acoustic behavior during different activities and matched with fine scale details on movement, especially those indicative of foraging.

(4) Quantify foraging efforts and determine potential effects of vessels and associated noise levels. 

The results of this study will provide pertinent data to address multiple risk factors of SRKWs including vessel disturbance, noise exposure, effects on foraging, and cumulative effects. The specific work that will be done includes experimental design, data collection, data analysis, and writing for submission to peer-reviewed journals.
Southern resident killer whale tag data.

Tags: animal mounted instrument - animal mounted instrument (not specified), bc, behavioral effects of noise, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, dtag, gps, killer whale, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, vessel sound exposure, wa and gulf islands, waters of the san juan islands
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish culture data - Development and optimization of grow out diets for sablefish (Anoplopoma fimbria)

Our experience with juvenile sablefish and long term rearing of broodstock indicate that salmon grower feeds currently used by commercial sablefish farmers for grow out are not optimally formulated to support maximum growth and efficient feed conversion. However, there are no published studies examining the effects of dietary nutrient balance on productive performance and growth at any post larval life-history stage for this species, and there are currently no commercial diets specifically formulated for sablefish in the marketplace. Because of the large impact of feed cost on the economic viability of farming sablefish, we are focusing on grow out diets intended for use during the post larval stages of development when the fish are being reared to harvest size. 
In this research, we use a novel statistical mixture model and response surface analysis method to determine the optimal level of dietary protein, lipid and digestible carbohydrate for testing. This approach permits simultaneous testing of diet formulations encompassing the full range of protein, lipid and digestible carbohydrate that can be produced commercially using todayâs most advanced extrusion feed manufacturing technology.
Raw data on rearing densities, tanks, water temperature, mortalities, ration and feed size may be available.

Tags: aquaculture, aquafeeds, balance, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, length board, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc manchester research station, nwfsc seattle, obsolete, sablefish
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Beaver Evidence - Historical Range of Beaver in the State of California, with an emphasis on areas within the range of coho salmon and steelhead trout

This project examines historical, archaeological, and geological evidence to re-evaluate the existing management paradigm that beaver are non-native to most of California. The purpose of the study is to identify where beaver historically existed or could have existed, with particular emphasis on their likely range within watersheds that are utilized by coho salmon or steelhead trout. Identification of the habitat overlap between beaver and these two salmonids will enable restoration efforts utilizing beaver to be targeted where they will maximize the benefits for these species in terms of rearing and overwintering habitat.
Location of historical locations of beaver in CA.

Tags: beaver, california, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
LCREP growth rates - Lower Columbia River Ecosystem Monitoring Project

1) The purpose of this project is to document juvenile salmon habitat occurrence in the Lower Columbia River and estuary, and examine how habitat conditions influence their distribution, health, and abundance. We also want to monitor habitat conditions and indicators of salmon health in these environments. Parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure.

2) Lyndal Johnson (NFWSC FTE) is the project lead, and other primary staff involved are Sean Sol and Paul Olson (NWFSC FTEs) and Kate Macneale (NWFSC term employee), but the project also involves other NWFSC FTEs, other term employees, contractors, and staff from other programs (Environmental Chemistry) and Divisions (FE, CB), as well as staff from collaborating agencies (i.e, the Lower Columbia River Estuary Partnership, USGS, PNNL, OHSU).

3) The project involves field surveys in which parameters measured include habitat conditions such as vegetation, water temperature, and dissolved oxygen; salmon diet and prey availability; weight, length, growth rate, lipid content, genetic stock, and chemical contaminant exposure.

4) Specific products include annual reports for the Lower Columbia Estuary Partnership, and manuscripts in peer-reviewed journals.

5) Specific audiences include (but are not limited to) the Bonneville Power Administration and other federal, state, and local agencies involved with salmon recovery and environmental management in the Columbia Basin (e.g., EPA, Washington Department of Ecology, Oregon Department of Environmental Quality, the City of Portland); the NMFS regional office, and other agency and academic scientists.

6) This is a stand-alone project, but it is also a component of a larger monitoring program overseen by the Estuary Partnership in which other tasks are conducted by collaborators in USGS, PNNL, and OHSU.

7) This is an ongoing project with a soft completion deadline; however, there are no final deadlines with specific tasks to be completed on a yearly basis.

Growth rates of chinook salmon from Lower Columbia sites estimated from otolith analyses.

Tags: biomass sampling, chemical contaminants, chinook salmon, chinook salmon growth rates, chum salmon, coho salmon, doc/noaa/nmfs/nwfsc, fish community composition, fish diet, lower columbia river, migrated from environmental conservation division, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, salmon lipid content, salmon prey availability
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Lipid composition - Sustainable aquafeeds for marine finfish: Effects of vegetable oil replacement feeds containing novel microalgal and fungal oils on growth performance of juvenile sablefish

The concomitant replacement of fish meal and fish oil in carnivorous marine fish feeds by more sustainable terrestrial alternatives is problematic due to the limited capability of marine fish to synthesize physiological essential long chain n-3 and n-6 highly unsaturated fatty acids (HUFAs) from shorter chain fatty acid precursors present in some vegetable oils. This two-year study will employ sablefish (Anoplopoma fimbria) as a model marine finfish to systematically investigate the potential of fully replacing the added fish oil component of a typical low fishmeal feed suitable for marine aquaculture.

The focus of the proposed study will be on the effects of replacing fish oil in sablefish diets with sustainable lipid sources on diet utilization and growth. In particular, the overall goals of the proposed research are the following: 

1. Determine the ability of sablefish to synthesize essential HUFAs from shorter chain fatty acid precursors.

2. Explore the effects of supplementing alternative vegetable oil feeds with novel sources of essential fatty acids on growth and nutrient utilization.

3. Evaluate the feasibility of using these novel oils in practical feeds. Data obtained in these studies will further our understanding of sablefish nutrition and set the stage for future research on the effects of sustainable feed ingredients on product quality, fish health, and the reproductive potential of cultured broodstock programs. This research specifically addresses a priority of the 2008 National Marine Aquaculture Initiative, which is nutrition research involving alternative protein based diets and the influence of diet on product quality.
Fatty acid profiles.

Tags: alternative feed lipids, aquaculture, doc/noaa/nmfs/nwfsc, instrument not applicable, migrated from reut legacy data sets, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc- montlake laboratory, obsolete, sablefish
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Oil spill related contaminant data for Arctic marine mammals - Obtaining baseline oil spill-related contaminant exposure data for Arctic marine mammals

With increasing oil exploration and ship traffic in the U.S. Arctic, there is concern about the increased potential for an oil spill event in this region of the world.  Baseline exposure levels of oil-spill related contaminants are lacking for marine mammals, particularly endangered or threatened populations (e.g., ice seals, bowhead whales).  Identification of the appropriate tissues/fluids to assess recent exposure of marine mammals to oil components must be determined, as well as the type of oil spill-related contaminant (e.g., parent polycyclic aromatic hydrocarbons (PAHs), metabolites of PAHs).  To help address these data gaps, various matrices of Arctic marine mammals will be collected during subsistence harvests and from fresh dead stranded animals over the next year and these samples will be analyzed for oil-spill related compounds.  These tissues will also be analyzed for additional oil-spill related components after the methods have been developed and validated.  Under the guidance of NOAA Fisheries Office of Protected Resources, we will collaborate with the National Institute of Standards and Technology to develop and test appropriate standard reference materials and control materials for these analyses to ensure that the chemical contaminant data generated for this project are of known and acceptable quality.
Concentrations of PAHs and alkylated PAHs in Arctic marine mammal tissues.

Tags: arctic food web, doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, instrument not applicable, marine mammals, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, obsolete, oil spill-related contaminants
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
SRKW acoustic response - Investigating noise effects on the acoustic signals and behavior of Southern Resident killer whales (Orcinus orca)

In this study, vocal compensation is being investigated in Southern Resident killer whale (SRKW) calls to determine the degree to which whales can adjust to increased background noise levels. In addition, whale and vessel behavior data are also collected to determine what contribution vessel traffic has on noise levels and how noise levels influence whale behavior. The work was part of an NRC-postdoctoral project led by Marla Holt, and includes Dawn Noren (Adams) and Candice Emmons as internal collaborators. The specific work includes experimental design, data collection, data analysis, and writing for submission to peer-reviewed journals. This is a one-time project, and addresses key risk factors (vessel and noise interactions) of SRKW.
Measurements of vocal behavior, whale behavioral states, background noise measurements, vessel counts and other attributes.

Tags: anthropogenic noise, bc, cb legacy data sets, doc/noaa/nmfs/nwfsc, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, sonde and probe, southern resident killer whale, vessels, wa and gulf islands, waters of the san juan islands
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
POPs, Fatty acids, lipid and Stable Isotopes data - The behavioral ecology of deep-diving odontocetes in the Bahamas

This project will use a unique set of individual-based data to quantify and model the behavioral ecology of six Department of Defense priority cetacean species in the Bahamas.
Data collected through individual photo-identification, molecular genetics, chemical markers (i.e., stable isotope ratios, persistent organic pollutants, fatty acids), satellite telemetry and acoustic recordings will be integrated to characterize the social structure, residency patterns, reproductive biology, foraging ecology and population structuring of key deep-diving cetaceans in the region. These data will be collected in collaboration with Bahamas Marine Mammal Research Organization, Southwest Fisheries Science Center, Alaska Fisheries Science Center, and the NWFSC, and will be used to model the response of these species to naval sounds. 

In FY11, the NWFSC analyzed 50 biopsy blubber samples of six priority species of whales from the Bahamas for persistent organic pollutants, fatty acids, lipid classes and percent lipid, as well as the corresponding skin samples for stable isotopes of carbon and nitrogen to help describe the foraging habitats, qualitative prey preferences, and feeding stock structure of these whales. Using these previously collected Bahama whale data as a foundation, we will compare the foraging ecology of sperm, pilot, and melon-headed whales with beaked whales inhabiting the same area. Thus, in like-fashion, using a combination of advanced multivariate statistical methods, the patterns of individual fatty acids (FAs) and persistent organic pollutants (POPs) measured in the blubber of the six priority cetacean species, as well as their skin SI ratios, will be used to do the following:

(1) Identify assemblages of individual whales that may represent stable feeding groups (both short- and long-term).

(2) Test the extent to which each of these species exhibit site fidelity with respect to their foraging habitats

(3) Assess the extent of niche overlap among all these whale species within this ecosystem as indicated by perceived differences in their preferred prey.

Because very little is currently known about the foraging behavior of these whales, this represents a significant advance in our understanding of the trophic dynamics, population structure, and feeding ecology of all of these whales.

Measures concentrations of POPs and fatty acids, total lipid and lipid profiles, and stable isotopes of carbon and nitrogen in tissues of deep-diving cetaceans and their prey.

Tags: biological, biota, doc/noaa/nmfs/nwfsc, environmental, fatty acids, feeding ecology, great bahama canyon, migrated from environmental conservation division, montlake, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, nwfsc montlake, persistent organic pollutants, physical measures: air, protected species and marine mammals, sediments, stable isotopes, water
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Qwuloolt elevation - Monitoring the Qwuloolt Estuarine Levee Breach Restoration

Comprehensive planning and monitoring of abiotic (hydrology, land forms, energy and nutrients, and chemistry) and biotic (plants, fish, invertebrates, birds, mammals) attributes pre- and post-breach at a 150 hectare site in the Snohomish estuary.
RTK GPS point locations at project and reference sites.

Tags: birds, doc/noaa/nmfs/nwfsc, estuary, fe (fish ecology) division, gps, juvenile salmonid, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, puget sound, qwuloolt - snohomish estuary, restoration, wetland
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Bird Distribution and Abundance - Ocean Survival of Salmonids

A study to evaluate the role of changing ocean conditions on growth and survival of juvenile salmon from the Columbia River basin as they enter the Columbia River plume and Pacific Northwest coastal habitats. Adult returns vary dramatically (over 10 fold) as a result of changing (good or bad) ocean conditions juveniles experience. Evaluating the benefit of restoration efforts in the Columbia River to restore endangered salmon populations needs to consider ocean conditions as a contributing factor to recovery. This is a large collaborative project with contributions from NWFSC, Oregon State University, and Oregon Health and Science University.

The work focuses on three objectives:

1) Determining the distribution, growth, and condition of juvenile Columbia River Chinook and coho salmon in the plume and their ocean environments with associated physical and biological features, and effects on salmon survival via regular spring and summer surveys.

2) Using additional focused surveys to obtain critical pieces of information on predator impacts, specific food resources, biological condition, and means by which juvenile salmon exit the Columbia River estuary.

3) Synthesizing the early ocean ecology of juvenile Columbia River Chinook and coho salmon, test mechanisms that control salmonid growth and survival, and produce ecological indices that forecast salmonid survival. 

This project provides critical information on marine survival to the Columbia River salmonid management community (hydrosystem, harvest, hatchery, and habitat management) provides environmental indicators useful for forecasting salmon returns, and provides a greater understanding of ecological controls on salmon populations. This is a long-term monitoring and research project initiated in 1998.
Species, abundance, and distribution of birds during salmon surveys.

Tags: doc/noaa/nmfs/nwfsc, fe (fish ecology) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce