This data set is comprised of one table with sampling information and NCBI BioProject accession numbers for sequence information of this amplicon-based study targeting Labyrinthula, Phytophthora, and Halophytophthora of known pathogenic and non-pathogenic [to eelgrass (Zostera marina)] strains from eDNA samples. eDNA samples included water, sediment, and eelgrass from Notsuke Wan (Cove) Japan, Safety Sound, Izembek Lagoon, Port Moller, Chignik Lagoon, and Frederick Sound, Alaska and cloacal swabs from waterfowl hunted near Cold Bay Alaska. Replicate samples and multiple sampling dates of the same location were included. Highly conserved primers which could differentiate species of interest were developed for four portions of mtDNA genes (5.8S, 18S, ITS, and COI). The reference list and conserved primer sets to identify species present were developed using publicly available data https://www.ncbi.nlm.nih.gov/genbank/

PURPOSE: Provide early detection of newly arrived Aquatic Invasive Species (AIS) and determine the spread, establishment and spatial distribution of existing AIS within marine waters of the southern Gulf of St. Lawrence (sGSL), DFO Gulf Region boundaries (northern and eastern coastal shores of NB, Gulf shore of NS, and PEI shoreline). DESCRIPTION: DFO Science monitors for AIS in the Gulf Region. The data collected from DFO's biofouling monitoring program provides an overview of the distribution and abundance of Aquatic Invasive Species (AIS) in the Gulf Region. This information can be used by the general public, scientists and DFO managers. Monitoring program targeting aquatic invasive species (AIS). Native biofouling species are not included in this dataset. Botrylloides violaceus: Violet tunicate Botryllus schlosseri: Golden star tunicate Ciona intestinalis: Vase tunicate Styela clava: Clubbed tunicate Caprella mutica*: Japanese skeleton shrimp Membranipora membranacea: Coffin box bryozoan Carcinus maenas*: European green crab Codium fragile*: Oyster thief alga *indicates species that are not included as percent cover as they are not accurately captured by the sampling method, but are included as detections. Included here is a dataset of detection and percent cover data of AIS, as well as a monitoring station dataset. Environmental data collected, including from temperature loggers, are stored but not included here. PARAMETERS COLLECTED: Air and water temperature, salinity, depth, dissolved oxygen, weather conditions, list of biofouling AIS, percent cover of AIS on PVC plates. NOTES ON QUALITY CONTROL: Each sample and species is processed and identified in a standardized fashion using standardized DFO Science AIS protocols and taxonomic references. Data is manually entered into DFO Gulf Region's AIS Science biofouling database and randomly verified for accuracy. SAMPLING METHODS: Biofouling monitoring is conducted using PVC collector plates that are deployed in the water column approximately 1 meter below the sea surface in the spring of each year. Biofouling organisms settle on these plates which are collected in the fall of the same year. Abundances of AIS are given as percent plate cover. Physico-chemical data including temperature, conductivity, and depth as well as weather conditions are noted at each geo-referenced biofouling monitoring site during initial deployment and at time of retrieval. All biofouling organisms settled on the underside of the PVC plates are noted and percent cover of each AIS is estimated. USE LIMITATION: To ensure scientific integrity and appropriate use of the data, we would encourage you to contact the data custodian.

The goal of the tidal-fluvial estuary study is to determine the estuary's contribution to the spatial structure and life history diversity of Columbia River salmon stocks and the implications for estuary restoration. The study targets salmon use of tidal-fresh habitats in the estuary from Rkm 75 to Bonneville Dam, and addresses four primary objectives: 1. Characterize the temporal and spatial distribution of Chinook salmon genetic stock groups throughout the estuary (March 2010 - March 2012). 2. Determine stock-specific habitat use, life histories, and performance of juvenile salmon in key habitat complexes to fill data gaps in the tidal fluvial reaches of the estuary (2012-2016). 3. Monitor juvenile salmon life histories and their contributions to adult returns in selected estuary tributaries, including tributary examples where tidal habitats have been restored (2012-2018). 4. Evaluate estuary restoration needs for recovery of all salmon ESUs and account for projected effects of climate change through application of a salmon life-cycle model (2011-1015). The study, funded by the U.S. Army Corps of Engineers, involves a large team of researchers organized by NOAA Fisheries, including researchers from the Oregon Health and Sciences University, University of Washington, and Washington Department of Fish and Wildlife. The study addresses critical uncertainties identified in the research, monitoring, and evaluation (RME) program for the Federal Columbia River Estuary Program (FCREP). The Estuary Program is intended to conserve and restore the estuary ecosystem to improve the performance of listed salmonid populations. Products from the tidal-fluvial study will include: 1. Descriptions of stock-specific temporal and spatial distributions of Chinook salmon throughout the estuary. 2. Estimates of variations in Chinook salmon stock composition and stock-specific growth, food habits, consumption rates, and bioenergetic efficiencies within selected tidal-fluvial habitats. 3. Estimated contributions of estuarine life histories among returning adult Chinook salmon from selected populations throughout the Columbia River Basin. 4. A hydrological model quantifying the dynamics of rearing habitat opportunities for juvenile salmon at estuary reach and habitat scales. 5. Improved life-cycle models to account for the estuarine life histories of juvenile salmon and estimating the potential effectiveness of estuary restoration actions on the recovery and viability of selected salmon stocks. These results will directly address information needs to support estuary actions specified in the Federal Columbia River Power System (FCRPS) Biological Opinion for the Columbia River. The tidal-fluvial estuary study is part of an ongoing estuary research program initiated in 2002. The current study expands upon earlier research conducted in the lower 100 km of the estuary from 2002 to 2008. Although all objectives will be addressed by 2018 to correspond with a review of progress implementing the FCRPS Biological Opinion, some sampling activities may extend beyond this date to allow brood-year reconstruction of estuary contributions to adult returns in selected streams (Objective 3). PIT detection data (residence time, travel time) in estuary wetland channels from juvenile salmon tagged by this project and other projects.

Scientists at NOAA's Northeast Fisheries Science Center (NEFSC) are using environmental DNA (eDNA) to identify fish communities and monitor ecosystems by collecting a water sample and analyzing the DNA found in it, identifying the species that left it behind without capturing a single animal. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. A water sample is first collected from the ocean and filtered to concentrate DNA in it. NOAA scientists then make millions of copies of a target DNA region through polymerase chain reaction (PCR) to make enough genetic material for high throughput sequencing. The metabarcoding process described above for eDNA analysis allows scientists to look for many species in the same sample. The final step is like a matching game, in which the DNA sequences are compared with a reference library of known species to find a match. The eDNA method is particularly useful for detecting species that are not easily captured, including rare or migratory species. It can also help in areas that are difficult to sample because of challenging ocean conditions, sensitive habitats, or a rugged seafloor. An eDNA analysis provides a snapshot of the community of species at the time of sampling and over time. This can help us detect shifts in marine ecosystems. eDNA samples have been collected on NOAA Ecosystem Monitoring (EcoMon) surveys since 2019. These samples will help develop best eDNA practices using metabarcoding, an innovative way to determine what fish species live in what parts of the ocean without actually seeing any fish.

Scientists at NOAA Northeast Fisheries Science Center (NEFSC) are using environmental DNA (eDNA) to identify fish communities and monitor ecosystems by collecting a water sample and analyzing the DNA found in it, identifying the species that left it behind without capturing a single animal. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. A water sample is first collected from the ocean and filtered to concentrate DNA in it. NOAA scientists then make millions of copies of a target DNA region through polymerase chain reaction (PCR) to make enough genetic material for high throughput sequencing. The metabarcoding process described above for eDNA analysis allows scientists to look for many species in the same sample. The final step is like a matching game, in which the DNA sequences are compared with a reference library of known species to find a match. The eDNA method is particularly useful for detecting species that are not easily captured, including rare or migratory species. It can also help in areas that are difficult to sample because of challenging ocean conditions, sensitive habitats, or a rugged seafloor. An eDNA analysis provides a snapshot of the community of species at the time of sampling and over time. This can help us detect shifts in marine ecosystems. eDNA samples have been collected on NOAA Ecosystem Monitoring (EcoMon) surveys since 2019. These samples will help develop best eDNA practices using metabarcoding, an innovative way to determine what fish species live in what parts of the ocean without actually seeing any fish.

U.S Fish and Wildlife Services (USFWS) Lower Great Lakes Fish and Wildlife Conservation Office (LGLFWCO) Aquatic Invasive Species (AIS) Early Detection and Monitoring (EDM) program began in 2012 following the onset of Great Lakes Restoration Initiative (GLRI) funding. This program is apart of a larger basin-wide Great Lakes AIS EDM effort by the USFWS. The goal of this program is to detect novel AIS species (fish and aquatic invertebrates) by sampling a diversity of habitats with a wide array of gear types. Sampling focuses on harbors, rivers and tributaries of the lower Great Lakes (Erie and Ontario) as determined by a risk-based prioritization framework for AIS in the Great Lakes. The program is composed of three components of AIS surveillance: juvenile/adult fish, ichthyoplankton (larval fish), and aquatic invertebrates (including crayfish). Sampling strategies and protocols are analyzed and designed to capture the maximum species richness at locations with the assumption that capturing an abundance of species, including singletons and doubletons, could lead to detecting rare novel AIS species if present. Protocols vary depending on the component of the program and descriptions can be found within the metadata of each dataset. This program is adaptive in nature and standardization, although important for comparisons, is not the primary intention of this AIS sampling strategy. Any significant AIS detections are reported to partners following an internal communications protocol.

U.S Fish and Wildlife Services (USFWS) Lower Great Lakes Fish and Wildlife Conservation Office (LGLFWCO) Aquatic Invasive Species (AIS) Early Detection and Monitoring (EDM) program began in 2012 following the onset of Great Lakes Restoration Initiative (GLRI) funding. This program is apart of a larger basin-wide Great Lakes AIS EDM effort by the USFWS. The goal of this program is to detect novel AIS species (fish and aquatic invertebrates) by sampling a diversity of habitats with a wide array of gear types. Sampling focuses on harbors, rivers and tributaries of the lower Great Lakes (Erie and Ontario) as determined by a risk-based prioritization framework for AIS in the Great Lakes. The program is composed of three components of AIS surveillance: juvenile/adult fish, ichthyoplankton (larval fish), and aquatic invertebrates (including crayfish). Sampling strategies and protocols are analyzed and designed to capture the maximum species richness at locations with the assumption that capturing an abundance of species, including singletons and doubletons, could lead to detecting rare novel AIS species if present. Protocols vary depending on the component of the program and descriptions can be found within the metadata of each dataset. This program is adaptive in nature and standardization, although important for comparisons, is not the primary intention of this AIS sampling strategy. Any significant AIS detections are reported to partners following an internal communications protocol.

NOAA Fisheries and its partners conduct fisheries-independent surveys in 8 regions in the US (Northeast, Southeast, Gulf of Mexico, West Coast, Gulf of Alaska, Bering Sea, Aleutian Islands, Hawai’i Islands). These surveys are designed to collect information on the seasonal distribution, relative abundance, and biodiversity of fish and invertebrate species found in U.S. waters. Over 900 species of fish and invertebrates have been identified in these surveys.

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. Oblique Bongo Tows for juvenile salmonid prey field index.

Ichthyoplankton (biological) data from cruise 0701 from the Yucatan Peninsula, Mexico, Belize, and South Florida. Data is housed in a spreadsheet database (Excel) format for use of members of the Early Life History (ELH) group.