AndreaBozzo/ceres-open-data-index huggingface dataset:
Water chemistry - Thornton Creek Restoration Project Effectiveness Monitoring

NOAA has designed and is currently implementing a hyporheic monitoring plan for the Thornton Creek watershed in North Seattle. This work is being conducted for Seattle Public Utilities, who in 2015 completed two large-scale floodplain reconnection projects in the Thornton Creek Watershed.  This study will evaluate restoration effectiveness by comparing control and treatment study reaches to each other and to forested references streams before and after restoration. NOAAs data collection focuses on hyporheic invertebrates, water temperature, and nutrient concentrations.

Hyporheic and surface water concentrations of DOC, TN, TP, and dissolved nutrients.

Tags: doc/noaa/nmfs/nwfsc, fe (fish ecology) 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
Tabular statistical summay of data analysis - Calawah River Riverscape Study

The objective of this study was to identify the patterns of juvenile salmonid distribution and relative abundance in relation to habitat correlates. It is the first dataset of its kind because the entire river was snorkeled by one person in multiple years.

During two consecutive summers, we completed a census of juvenile salmonids and stream habitat across a stream network. We used the data to test the ability of habitat models to explain the distribution of juvenile coho salmon (Oncorhynchus kisutch), young-of-the-year (age 0) steelhead (Oncorhynchus mykiss), and steelhead parr (= age 1) for a network consisting of several different sized streams. Our network-scale models, which included five stream habitat variables, explained 27%, 11%, and 19% of the variation in the density of juvenile coho salmon, age 0 steelhead, and steelhead parr, respectively. 

We found weak to strong levels of spatial auto-correlation in the model residuals (Moran's I values ranging from 0.25 - 0.71). Explanatory power of base habitat models increased substantially and the level of spatial auto-correlation decreased with sequential inclusion of variables accounting for stream size, year, stream, and reach location. The models for specific streams underscored the variability that was implied in the network-scale models. Associations between juvenile salmonids and individual habitat variables were rarely linear and ranged from negative to positive, and the variable accounting for location of the habitat within a stream was often more important than any individual habitat variable. The limited success in predicting the summer distribution and density of juvenile coho salmon and steelhead with our network-scale models was apparently related to variation in the strength and shape of fish-habitat associations across and within streams and years.
Summary of statistical analysis of the Calawah Riverscape data. NOAA was not involved and did not pay for the collection of this data. This data represents the statistical analysis carried out by Martin Liermann as a NOAA employee.

Tags: abundance, calawah river, distribution, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, habitat, instrument not applicable, juvenile salmonid, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Proximate analyses - Utilization of Marine Process Waste for Aquaculture Feeds

Limited amounts of forage fish are available as an ingredient in feeds for the expanding aquaculture industry. Work is being conducted on a variety of underutilized materials to provide new sources of protein, oils, and minerals for fish feeds. These materials include invasive species such as carp and mussels, waste from fish and clam processing, and process waste from fish farms. Successful utilization of these materials adds needed protein and marine oils to the growing aquaculture industry, and eliminates the environmental impact of landfill or dumping at sea of these waste streams.
Proximate analysis and solubility of new materials.

Tags: aquafeeds, 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, utilization
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Qwuloolt hydrology - 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.
Water level, temperature, and salinity at project and reference sites.

Tags: and depth, birds, doc/noaa/nmfs/nwfsc, estuary, fe (fish ecology) division, juvenile salmonid, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, puget sound, qwuloolt - snohomish estuary, restoration, sonde and probe - conductivity, temperature, wetland
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Data logger database - Physical and biological effects of fish-friendly tide gates

The purpose of this one-time stand-alone study is to evaluate how effective "fish-friendly" or self-regulating tide gates (SRTs) are at increasing connectivity for fish rearing in estuaries. The work was carried out in North Puget Sound, Washington Coast, and Columbia River estuaries by Correigh Greene, Jason Hall, and Eric Beamer (Skagit River System Cooperative), and compared SRTs with traditional flap gates and reference sites that were not blocked by any tide gate. Thus far, the study has produced a report for ESRP (Estuary Salmon Restoration Program), the organization that funded it. Up to two peer-reviewed papers are planned. The audience for this work includes federal and state managers, local planners, Watershed Councils, and applied ecologists.
Access database of data loggers.

Tags: animal and plant collection device, chehalis estuary, connectivity, doc/noaa/nmfs/nwfsc, fe (fish ecology) division, habitat use, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, samish bay, skagit estuary, sonde and probe - sonde and probe (not specified), swinomish channel, tide gates, young's bay
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
LCREP chemistry and lipids - 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.

Concentrations of chemical contaminants in bodies and stomach contents of Chinook salmon from Lower Columbia sampling sites.

Tags: 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, toxicology
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Harbor porpoise - Passive acoustic monitoring of harbor porpoises in Puget Sound

Drs. Marla Holt, Brad Hanson, and Candice Emmons of the NWFSC, along with efforts from the NWFSC dive team (coordinated by Nick Tolimieri), are currently conducting passive acoustic monitoring of harbor porpoises in Puget Sound. The occurrence of harbor porpoises are being acoustically documented using porpoise detectors (CPODs, made by  Chelonia, Ltd), which detect and log harbor porpoise echolocation clicks and store the data on flash memory cards. CPODs are deployed on the sea floor by scientific divers, and must be recovered every three months to replace batteries and memory cards. The project is ongoing, and will document occurrence and habitat use of this protected marine species. The project is a well-defined component of a larger study that addresses harbor porpoise occurrence and habitat use in the Salish Sea.
Passive acoustic monitoring.

Tags: cb (conservation biology) division, cpod, doc/noaa/nmfs/nwfsc, harbor porpoise, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, passive acoustic monitoring, puget sound, sonde and probe
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Mirror Lake salmon growth rate - 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.

Growth rates of juvenile chinook salmon as estimated from otoliths.

Tags: biomass sampling, chinook salmon, coho salmon, doc/noaa/nmfs/nwfsc, fish community composition, habitat recovery data, 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, wallace island
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Fish weights - 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 spreadsheet.

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
Oceanographic Trawl 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.
Nekton and juvenile salmon collections from surface trawl.

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
Fish abundance, composition, distribution - 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.
Density and distribution of resident trout and Pacific salmon during summer, spring and fall in main stem and tributary habitat.

Tags: abundance, animal and plant collection device, balance, cedar river watershed, current meter, doc/noaa/nmfs/nwfsc, experiments, fe (fish ecology) division, fish passage, 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, thermistor chain, tributary to cedar r.
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
SRKW occurrence coastal - Occurrence and habitat use of SRKW and other top marine predators

The Southern Resident killer whale (SRKW) population is threatened by a number of identified risk factors including prey availability, contaminants, vessel noise and disturbance, and small population size. In addition, there are several data gaps SRKW regarding their ecology.  Although summer distribution is well documented, their winter distribution is not well known. Satellite tagging, acoustic recorders, and a compilation of public sightings has allowed for a much better assessment of this populationâs winter distribution. Satellite tagging has been suspended in response to the mortality of a tagged SRKW, such that acoustic recorders and public sightings will be the primary approaches used to improve our understanding of the whale populationâs occurrence and habitat use.  Recent data has shown changes in the whalesâ summer distribution patterns.  Consequently, additional data on occurrence and movement patterns will be particularly important to document in the near term as the next couple of years to assess their potential response to the expected to have relatively lower abundance of returning Chinook, their primary prey.
SRKW coastal sightings.

Tags: animal mounted instrument, cb (conservation biology) division, doc/noaa/nmfs/nwfsc, killer whale, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center, occurrence, puget sound
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
Physical oceanography - Developing end-to-end models of the California Current Large Marine Ecosystem

The purpose of this project is to develop spatially discrete end-to-end models of the California Current LME, 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 other NOAA scientists, academics, and NGOs.  The specific work entails model development, scoping issues with stakeholders and policy makers, running scenarios, and analyzing and writing up the results.  Products will include peer-reviewed papers, presentations, and workshops with modelers and/or stakeholders.  Management audiences include NMFS west coast regions and the PFMC.  The project is an on-going, stand-alone project with no firm deadline for completion.
Outputs of the ROMS model.
Metadata and .nc datafile at https://www.nodc.noaa.gov/oceanacidification/data/0131198.xml
Generated from Atlantis ecosystem model, version AtlantisTrunk5425. 
Model code from CSIRO Australia, available via SVN after contacting CSIRO staff at http://atlantis.cmar.csiro.au/.

Tags: atlantis, california current lme, cb (conservation biology) division, climate change, doc/noaa/nmfs/nwfsc, economics, ecosystem modeling, food web, global change, instrument not applicable, management strategy evaluation, national marine fisheries service, noaa. u.s. department of commerce, northwest fisheries science center
Organization: National Oceanic and Atmospheric Administration, Department of Commerce