AndreaBozzo/ceres-open-data-index huggingface dataset:
Dissolved Oxygen - Live Hauling of Fish

In certain markets, live fish can be sold for substantially higher prices than fresh dressed fish. A significant live-haul industry has developed in the U.S. and fish are commonly hauled 1,500-2,000 miles (25-30 hours) to market. The most common species hauled are tilapia, channel catfish, and rainbow trout; a smaller amount of marine rockfish, hybrid striped bass, and carp are also hauled. The most significant advancement in hauling technology in the last 20 years has been the use of bottled oxygen gas or liquid oxygen to maintain adequate dissolved oxygen levels. These types of systems can maintain significantly higher DO levels than systems using air. Some common stressors include harvest and loading procedures (pumping or out of water transfer), shaking as the transport vehicle is moving, low frequency sound from the vehicle and water treatment systems, crowding, and poor water quality (high ammonia and carbon dioxide levels, low dissolved oxygen), high light levels, or extreme water temperature. The physical shape and construction of the hauling unit may have an important impact on localized low DOs, physical damage to the fish, and survivability. Very little information has been published on the chemical and physical conditions in transport systems during long-distance transport and this limited data may not be representative of current commercial systems. 

This research will be conducted with NWFSC staff in cooperation with private fish farmers in the Pacific Northwest. Specific sub-objectives will include the following:

(1) Documentation of water quality during transport and impact on mortality and product quality

(2) Design of efficient aeration systems for oxygen transfer and carbon dioxide stripping

(3) Determination of the impact of transport tank design and aerator type on the thermal balance during hauling.

The impact of this project will be increased survival and product quality of transported fish as a result of adopting the recommended protocols and utilization of the models. Project outputs will include peer-reviewed publications, popular publications, and conference presentations.
Dissolved oxygen will be measured with a YSI ProODO or a YSI 556 MPS unit and results expressed in mg/Liter. Units will be air calibrated daily.

Tags: aquaculture, doc/noaa/nmfs/nwfsc, gas transfer, hagerman valley, heat transfer, idaho, in-situ instrument - automated dissolved oxygen sensor, migrated from resource enhancement and utilization technologies division, montlake, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, water quality
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Model outputs - Developing end-to-end models of the Gulf of California

The purpose of this project is to develop spatially discrete end-to-end models of the northern Gulf of California, 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 a consortium of Mexican federal, state, NGO and academic scientists. The specific work entails model development, scoping issues with stakeholders and policy makers, running scenarios, and analyzing and writing up the results. Products include peer-reviewed papers, presentations, and workshops with modelers and/or stakeholders. Management audiences include Mexican governmental bodies and conservation organizations. The project is an on-going, stand-alone project with no firm deadline for completion.
Outputs of Atlantis model scenarios.

Tags: artisanal fisheries, atlantis, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, ecosystem modeling, gulf of california, instrument not applicable, international collaboration, management strategy evaluation, mexico, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, vaquita
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Production data - Snake River sockeye salmon captive propagation

Gene rescue captive broodstock program was established for ESA-listed endangered Snake River sockeye salmon from Redfish Lake, Idaho.  The program has 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.  Fish are being released to native habitats as part of recovery efforts.
Information on the number of eyed eggs, juveniles, and adults received into the program is maintained and summarized by year.  The production of adults spawned, adults transferred to Idaho for release, green eggs taken, and eyed eggs shipped to Idaho and Oregon facilities for restoration activities is also annually summarized.

Tags: artificial propagation, doc/noaa/nmfs/nwfsc, 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 manchester, salmon, snake river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Mirror Lake contaminanats - Lower Columbia River Restoration Action Effectiveness Monitoring

1) The purpose of this project is to measure changes in juvenile salmon habitat occurrence and health following restoration activities at the Mirror Lake Complex and Horsetail Falls in the Lower Columbia River and estuary. 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 (NWFSC 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 (e.g., the Lower Columbia River Estuary Partnership).

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 to be produced 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 action effectiveness monitoring program overseen by the Estuary Partnership.

7) This is an ongoing project with a soft completion deadline; however, there are specific tasks to be completed on a yearly basis.

Chemical contaminants in chinook salmon bodies.

Tags: chinook salmon, coho salmon, doc/noaa/nmfs/nwfsc, fish community composition, 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, portland harbor, sand island, sandy island, toxicology, wallace island
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Chemical tracers in Northwest Atlantic dogfish

Each year, a number of seafood samples are exported from the US to Europe, including edible tissues collected from high trophic level marine fish species such as dogfish.  Obtaining information on concentrations of potentially toxic environmental contaminants [e.g., polychlorinated biphenyls, mercury] in these samples is important to ensure that these export products are safe for human consumption.  As part of a pilot study, edible tissues (back and belly muscle) of spiny and smooth dogfish collected during fleet study and dockside surveillance operations in the Northeast Region of the US were analyzed at the Northwest Fisheries Science Center for a suite of persistent organic pollutants including PCBs, DDTs and other chlorinated pesticides to determine the influence of biological factors (e.g., length, sex) and geographical collection region on contaminant levels.
Persistent organic pollutants, stable isotopes, and lipids in smooth and spiny dogfish from the northwestern Atlantic.

Tags: doc/noaa/nmfs/nwfsc, dogfish, efs (environmental and fisheries sciences) division, instrument not applicable, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, persistent organic pollutants
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Egg to Fry - Chinook Egg-to-Fry Survival

Few estimates of Chinook egg-to-fry survival exist despite the fact that this is thought to be one of the life stages limiting production of many listed Chinook populations. The objective of this project is to estimate egg-to-fry survival for Chinook salmon at a variety of habitat conditions throughout the Yakima & Wenatchee basins. Egg-to-fry survival is estimated in more than 100 artificial redds in nine reaches in the Yakima and three in the Wenatchee River.
Egg to fry survival estimates.

Tags: chinook salmon, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, gps, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, sediment trap, survival, washington, wenatchee river, yakima river
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Temperature - Impact of chiller failure on the short-term temperature variation in the incubation of salmonids

In salmon recovery programs it is commonly necessary to chill incubation and early rearing temperatures to match wild development times. The most common failure mode for a chiller system is failure of the chiller or circulating pumps. Following chiller failure, the water temperature can rise from 5-7 C to 10-13 C depending on the well temperatures and ambient air temperatures.

The speed and magnitude of the temperature increases depends on how the chillers are designed. The simplest design is a direct-coupled chiller with chilled gas/process water heat exchanger. Other chiller designs include both chilled glycol and water reservoirs. The addition of these reservoirs serves to reduce the maximum rate of temperature change following chiller failure. Increased deformities have been observed in direct-coupled chiller systems for sockeye salmon following chiller failures.
Variation of temperature in incubation system following chiller failure.

Tags: doc/noaa/nmfs/nwfsc, efs (environmental and fisheries sciences) division, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Juvenile Salmonid Trophic Data - Juvenile Salmon & Ocean Ecosystem Survey

FY20 will mark the 23nd year of sampling, making the Juvenile Salmon and Ocean Ecosystem Survey (JSOES) the longest running salmon survey on the west coast. JSOES has clearly demonstrated correlations between ocean conditions and the distribution, abundance, and survival of juvenile Columbia River (CR) salmon in the Northern California Current (NCC) nearshore ecosystem. For example, our ocean indicators provide managers from the federal and state governments, tribes, and other agencies/groups the ability to forecast adult returns one to two years in advance for coho and spring/summer Chinook salmon. We continue to show the importance of evaluating ocean conditions to support management decisions and to provide context for efforts by the Northwest Power and Conservation Council (NWPCC) and BPA to restore and enhance salmon production. 

The primary goal of our work is to develop a mechanistic understanding of how trophic dynamics and conditions in the ocean and CR plume affect survival of juvenile salmonids. This knowledge will allow us to improve forecasts in a quantitative rather than qualitative manner, and decouple the effects of mitigation efforts in the freshwater environment from the effects of a changing ocean environment. These improved forecasts will lead to well-informed recommendations for an ecosystem approach to management strategies based on the full suite of river, plume, and ocean environments.
Stomach Contents from juvenile salmonids, primarily Chinook and Coho.

Tags: animal and plant collection device, climate change, columbia river, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, instrument not applicable, marine ecosystems, marine survival, national marine fisheries service, newport, noaa. u.s. department of commerce, northern california current, northwest fisheries science center, oceanography, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Chemical 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.
Whole fish proximate composition.

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
LGR adult trap data - Operation of the adult trap at Lower Granite Dam

This Bonneville Power Administration (BPA) - funded project pays for NOAA staff to operate the adult salmon trap located in the fish ladder at Lower Granite Dam. The trap is operated to provide access to fish for sampling for several NOAA projects as well as other researchers from many agencies. The trap is used for random sampling of adults used in run reconstructions, determining age classes of returning adults, assess injuries from marine mammals, brood stock collection for hatcheries, scale sampling to determine age of ocean entry for fall Chinook, radio tagging of adults, and various other uses. NOAA has operated this trap since it was built in the mid-1970s, with BPA funding beginning in 2006. An annual report is provided to BPA summarizing trap activities.
Lower Granite Dam adult trap data.

Tags: animal and plant collection device, animal mounted instrument - animal mounted instrument (not specified), artificial propagation, chinook salmon, doc/noaa/nmfs/nwfsc, fe legacy data sets, length board, lower granite dam adult trap, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, obsolete, salmonids, snake river, steelhead, temperature sensor
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Chinook Bycatch - Contemporary Salmon Genetic Stock Composition Estimates

1. The purpose of this project is to measure and monitor impacts on ESA-listed populations and to estimate overall Chinook salmon stock composition in bycatch associated with the hake fisheries (including tribal and non-tribal, shoreside, and at-sea). The work is carried out by NOAA staff.

2. Fin clips collected by NOAA observers are characterized genetically allowing allocation of the mixture to source populations.

3. Written reports are produced regularly and forwarded to the NWR and interested parties.

4. The NWR is the primary management audience in facilitation of NOAA's MSA obligations to measure and monitor ESA impacts.

5. This is an ongoing project (see also Historical Salmon Genetic Stock Composition Estimates). 

6. This is a stand-alone project in one sense, but is closely coordinated with stock composition studies in directed harvest as well as similar studies of historical bycatch using archival scale material. 

7. There are no specific hard deadlines associated with this project.
Chinook genetics bycatch in hake.

Tags: animal and plant collection device, cb (conservation biology) division, chinook salmon, dna sequencer, doc/noaa/nmfs/nwfsc, fishery-dependent, genetics, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, pacific hake
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Physical - Elwha River Dam Removal Study

This project monitors ecosystem response to dam removals on the Elwha River, Washington State. The Elwha Dam removal project is the largest project of its kind in the world and is the largest restorative action that has taken place in any Western U.S. Evolutionarily Significant Unit (ESU). Ecosystem response includes changes to aquatic habitat, the food web, and all aspects of the viable salmon parameters of listed and non-listed salmonid species. The project is based on the development and implementation of the Elwha Monitoring and Adaptive Management Guidelines (EMAM), which was developed as a collaborative effort between the Watershed Program at the NWFSC, the Lower Elwha Klallam Tribe (LEKT), the United States Department of Fish and Wildlife Service (USFWS), the United States Geologic Survey (USGS), the Washington Department of Fish and Wildlife (WDFW), and the National Park Service (NPS). We employ a variety of metrics to efficiently monitor ecosystem condition over space and time. This project will provide data to assess changes for the listed Elwha River populations (Chinook salmon and steelhead), and help determine whether those populations are improving, static, or declining. Such analyses are crucial to help inform future large-scale dam removals for multiple ESUs across the Western U.S.
All relevant physical data.

Tags: dam removal, doc/noaa/nmfs/nwfsc, effectiveness monitoring, elwha river, fe (fish ecology) division, floodplain, gps, instrument not applicable - instrument not applicable, juvenile salmonid, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, nwfsc montlake, restoration, salmon
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fall transport - A study to compare smolt-to-adult return rates (SARs) of Snake River fall Chinook salmon under alternative transport and dam operational strategies

This U.S. Army Corps of Engineers (USACE)-funded study that began in 2005 compares the SARs of PIT tagged juvenile hatchery Snake River fall Chinook that are split into two groups, released above Lower Granite Dam, and when detected at downstream dams, one group is transported (if detected) and the other group bypassed if detected. When adult returns are complete, their SARs will be compared to determine the efficacy of smolt transport of this stock. Scales are collected on returning adults to determine age at ocean entry. The study is a collaborative effort with the U.S. Fish and Wildlife Service (USFWS), Washington Dept. of Fish and Wildlife (WDFW), and the Nez Perce Tribe (NPT). Juvenile releases began in 2005, and will be completed in 2012. Adult returns will be completed in 2016, with a final report provided to the USACE and region summarizing study results.

Fall Chinook transport study data.

Tags: barging, biological, chinook salmon, doc/noaa/nmfs/nwfsc, fe legacy data sets, lower granite, national marine fisheries service, noaa. u.s. department of commerce, non-noaa funded, northwest fisheries science center, pit tag
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
EPA2011 Microbial & nutrient database - Evaluating the ecological health of Puget Sound's pelagic foodweb

To evaluate effects of human influence on the health of Puget Sound's pelagic ecosystems, we propose a sampling program across multiple oceanographic basins measuring key attributes of the pelagic foodweb. We will quantify seasonal abundance and composition of pelagic biota from lower trophic levels (e.g., bacteria and phytoplankton) to middle trophic levels (e.g., zooplankton, small pelagic fishes, and jellyfish), as well as assess the individual condition of forage fish and juvenile salmon. 

The goals of this program:

1) Determine how foodweb endpoints vary across natural and anthropogenic gradients.

2) Determine how these characteristics vary across Puget Sound.

3) Evaluate a number of biological metrics for monitoring ecosystem health.

These outputs will improve our basic understanding of pelagic ecology in Puget Sound, better define what comprises a healthy pelagic ecosystem in Puget Sound, determine foodweb-relevant indicators that are sensitive to human influence, and help prioritize regional protection and restoration efforts. Work is conducted by NOAA personnel and contractors in collaboration with tribal partners (Squaxin, Port Gamble/S'Klallam), undergraduate research interns, and citizen volunteers.
Filemaker Pro database containing microbial abundance, heterotrophic production, chlorophyll a, and inorganic nutrients.

Tags: admiralty inlet, bacterial communities, chlorophyll a, dna sequencer, doc/noaa/nmfs/nwfsc, ecosystem, food web, heterotrophic production, hood canal, low dissolved oxygen, marine microbes, microbial abundance, migrated from resource enhancement and utilization technologies division, national marine fisheries service, nearshore pelagic, noaa. u.s. department of commerce, north central ps basin, northwest fisheries science center, nutrients, puget sound, quantitative pcr machine, rosario basin, salmon, sonde and probe, south central ps basin, south ps basin, unknown instrument, water sampler bottle - niskin bottle, whidbey basin north, whidbey basin south
Organization: National Oceanic and Atmospheric Administration, Department of Commerce