76914 REL 1: Rev 1: WE E: Work Element Summary

Work Element Summary PDF

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Basics

Contract Number:

76914 REL 1

Contract Title:

1998-014-00 EXP OCEAN SURVIVAL OF SALMONIDS (OSU)

Contract Start Date:

1/1/2018

Contract End Date:

12/31/2018

WE ID:

162. Analyze/Interpret Data

Work Element Usage Report

Title:

E: 162 - Assess the role of the estuary and plume on salmon growth and survival

Description:

Data will be analyzed for the following objectives:

1) Assist NOAA in continuing to identify and refine the suite of estuary, plume and ocean indicators that best predict adult returns and survival and support the use of early warning indicators for listed interior Columbia Basin ESU and DPS.

2) Assist NOAA in examining the extent of coupling among estuarine, plume and early ocean habitats and marine survival of interior Columbia juvenile salmon and steelhead.

OSU collaborators will assist NOAA with the following:

* Analytical assessment of biological features of juvenile salmon in and out of the Columbia River plume and assessing the role of unique features of the Columbia River plume that affect salmon growth and survival.

* Juvenile salmon species will be confirmed from cruise sampling, weighed and measured, and dissected, if warranted.

* Continue to develop and refine indicators of juvenile salmon survival.

* Database will be updated. Data regarding each individual juvenile salmon sampled in 2018 and some information from sampling in 2017, including species, size, location of capture, associated oceanographic conditions of sample site, and growth features will be entered into an MS Access database of all juvenile salmon sampled from this project for the period beginning in 1998 to the present.

* Datasets will be incorporated to the updated Access database including current sample analysis.

WE Agreement Type:

Contracted

Deliverable Specification:

Process fish from 2017 and 2018, including lengths, weights, and collection of genetic tissue samples, and enter all data and QA/QC.

- Continue to assist NOAA with analyses of genetic stock-specific distributions of juvenile Chinook salmon.

- Process oceanographic and chlorophyll samples from 2017 and 2018 and upload into database.

- Assist NOAA with further development and refinement of estuary, plume, and ocean indicators.

- Examine food habits of salmon that may relate to connectivity to Columbia River estuary habitat.

WSE Effective Budget:

$195,185

% of Total WSE Effective Budget:

63.96%

WSE Start:

01/01/2018

WSE End:

12/31/2018

WSE Completion:

12/19/2018

WSE Progress:

Concluded

WSE ID Continued From:

n/a

WSE ID Continued To:

n/a

Finite or Recurring:

Recurring

Budget History

SOWRevision	Planned	Updated	Contractor Comments (optional)	BPA Comments (optional)
Work Element Budget (Current Performance Period)	$195,185	$195,185

Milestones

6 Milestones

Sort	Type	Title	Start	End	Status	Modified By	Modified Date
A	PUBPROTOCOL	Review, revise, and Publish protocol, study design, and methods in monitoringmethods.org	1/1/2018	12/31/2018	Concluded	Anne Creason	9/19/2017 9:32:19 AM
		Description: The Protocol (including temporal and spatial design) and Methods for this work element are stored at monitoringmethods.org and need to be finalized (i.e., "Published" through monitoringmethods.org), preferably prior to data collection. Preparations for contract renewals must include reviewing any previously published Protocols/Methods to ensure that they are consistent with how work will be done in any subsequent contract.
B		Otoliths analysis--OSU--May 2017 and May 2018 surveys	1/1/2018	12/31/2018	Concluded	Anne Creason	9/19/2017 9:32:19 AM
		Description: Otolith analyses on a subsample (up to n= 120) of May 2018 and samples as a measure of ocean-estuarine residence time as it relates to growth. This would cover up to 30 hatchery and 30 wild of both Mid/Upper Columbia River, Spring/Summer Chinook and Snake Spring Chinook. Continue analysis on May 2017 otolith samples. We intend to compare attributes from fish that have just arrived in the plume to those from fish that have been in the ocean for longer periods. This requires analysis of strontium/calcium ratios in their otoliths and structural analysis of daily increments to get an accurate estimate of ocean residence time.
C		Stomach sample analysis--OSU-- subset of May 2017 and May 2018 surveys	1/1/2018	12/31/2018	Concluded	Anne Creason	9/19/2017 9:33:26 AM
		Description: Assist with analysis of a subset of stomach samples for diets from ocean collected juvenile Chinook salmon (Mid/Up CR Chinook, spring/summer Chinook, Snake spring) and steelhead from May 2018. Continue analysis of diets from May 2017.
D		Survey report -- May 2018	5/1/2018	12/31/2018	Concluded	Anne Creason	10/17/2017 9:27:25 AM
		Description: May 2018 survey report OSU Lead: Morgan Survey reports will be submitted electronically and will be submitted to BPA by the end of the year of each survey. Survey reports will be completed and include information on: sampling locations, physical conditions at each station. These reports provide a description of cruise objectives, results of the cruise as well as a summary of data collected on each juvenile salmon sampling cruise and include the following items: • Tables showing: (1) station and station location along with start position of each trawl (lat and long), start and end time and trawl duration and trawl duration; (2) hydrographic data at each station (sea surface temperature, sea surface salinity, fluorometer voltage, % transmission, depth and value of oxygen minimum) (3) a table that lists the catches of taxa in the trawl, by station. (4) Information on Genetic Stock Composition of up to 600 juvenile Chinook salmon • Tables showing number of salmonids caught in each haul along with catch per unit effort in units of number of fish caught per km towed, • Charts showing (in plan view) the spatial distribution of 1m temperature, 1m salinity, 1m % transmission, minimum oxygen values and CPUE of each salmonid taxa.
E		Survey report -- June 2018	7/15/2018	12/31/2018	Concluded	Anne Creason	10/17/2017 9:27:25 AM
		Description: June 2018 cruise report OSU Lead: Morgan Survey reports will be submitted electronically and will be submitted to BPA by the end of the year of each survey. Cruise Reports will be completed and include information on: sampling locations, physical conditions at each station. These reports provide a description of cruise objectives, results of the cruise as well as a summary of data collected on each juvenile salmon sampling cruise and include the following items: • Tables showing: (1) station and station location along with start position of each trawl (lat and long), start and end time and trawl duration and trawl duration; (2) hydrographic data at each station (sea surface temperature, sea surface salinity, fluorometer voltage, % transmission, depth and value of oxygen minimum) (3) a table that lists the catches of taxa in the trawl, by station. • Tables showing number of salmonids caught in each haul along with catch per unit effort in units of number of fish caught per km towed, • Charts showing (in plan view) the spatial distribution of 1m temperature, 1m salinity, 1m % transmission, minimum oxygen values and CPUE of each salmonid taxa.
F	DELIV	Assess the role of the estuary and plume on salmon growth and survival		12/31/2018	Concluded	Anne Creason	10/17/2017 9:25:49 AM
		Description: Process fish from 2017 and 2018, including lengths, weights, and collection of genetic tissue samples, and enter all data and QA/QC. - Continue to assist NOAA with analyses of genetic stock-specific distributions of juvenile Chinook salmon. - Process oceanographic and chlorophyll samples from 2017 and 2018 and upload into database. - Assist NOAA with further development and refinement of estuary, plume, and ocean indicators. - Examine food habits of salmon that may relate to connectivity to Columbia River estuary habitat.

Metrics

Implementation Metrics

Metric	Planned	Actual
1464. Primary R, M, and E Focal Strategy [Population Status, Hydrosystem, Tributary Habitat, Estuary/Ocean, Harvest, Hatchery, Predation, Multiple Strategies]	Estuary/Ocean	Estuary/Ocean
1472. Primary R, M, and E Type [Status and Trend Monitoring, Action Effectiveness Research, Uncertainties Research, Project Implementation/ Compliance Monitoring]	Uncertainty Research	Uncertainty Research
1478. Secondary R, M, and E Type [Status and Trend Monitoring, Action Effectiveness Research, Uncertainties Research, Project Implementation/ Compliance Monitoring]	Status and Trend Monitoring	Status and Trend Monitoring
1495. Secondary R, M, and E Focal Strategy [Population Status, Hydrosystem, Tributary Habitat, Estuary/Ocean, Harvest, Hatchery, Predation, Multiple Strategies]	Multiple Strategies	Multiple Strategies

Location

<a target='blank' href='https://www.monitoringresources.org/Designer/Design/Detail/5208'>Location data for Area of Inference (AOI) should be entered into MonitoringResources.org. Click here to go to that site.</a>

Focal Species

Primary Focal Species:

Chinook (Oncorhynchus tshawytscha) - All Populations; Steelhead (Oncorhynchus mykiss) - All Populations

Secondary Focal Species:

Coho (Oncorhynchus kisutch) - Lower Columbia River ESU (Threatened); Sockeye (Oncorhynchus nerka) - All Populations

Environmental Compliance

This work element does not require Environmental Compliance

RM&E Metadata

Data Repositories:

Title	Link
NOAA Ocean Indicators Tool	http://www.nwfsc.noaa.gov
NOAA Public Access to Research Results (PARR)	https://www.ngdc.noaa.gov/parr.html
StreamNet Data Store	https://app.streamnet.org/datastore_search_classic.cfm

Study Plan:

Study Plan Name	Study Plan Owner	Protocol State	Sample Design Name
Ocean Survey of Juvenile Salmon (1998-014-00) v1.0	Cheryl Morgan	Draft	Assess the role of the estuary and plume on salmon growth and survival - Oregon State University v1.0

Methods:

ID	Name	Type	Optional	Customized Based On	Status
4088	Columbia estuary purse seining v1.0	Data Collection	Yes	N/A	Finalized
4090	Individual-Based Model of Salmon Migration v1.0	Data Analysis/Interpretation	No	N/A	Finalized
650	Modified Assessing growth in juvenile salmon using plasma Insulin-like growth factor-I (IGF-1) v1.0	Data Collection	No	Assessing growth in juvenile salmon using plasma Insulin-like growth factor-I (IGF-1) v1.0	Finalized
1376	Northwest Fisheries Science Center Ocean Salmon Survey DNA extraction for Renibacterium salmoninarum v1.0	Data Collection	Yes	N/A	Finalized
1405	Northwest Fisheries Science Center Ocean Salmon Survey Macroparasite Recovery v1.0	Data Collection	No	N/A	Finalized
1379	Northwest Fisheries Science Center Ocean Salmon Survey Nested Polymerase Chain Reaction (PCR) to detect Renibacterium salmoninarum v1.0	Data Collection	Yes	N/A	Finalized
1380	Northwest Fisheries Science Center Ocean Salmon Survey Renibacterium salmoninarum ABC gene Quantitative PCR (qPCR) v1.0	Data Collection	Yes	N/A	Finalized
1707	Northwest Fishery Science Center Ocean Salmon Survey determination of chlorophyll a concentration v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1361	NWFS_Center_Ocean Salmon Survey Bongo Net Marine Zooplantkon Sampling v1.0	Data Collection	No	N/A	Finalized
4081	NWFS_Center_Ocean Salmon Survey Bongo Net Zooplankton Analysis v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1375	NWFS_Center_Ocean Salmon Survey CTD Data Processing v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1706	NWFS_Center_Ocean Salmon Survey Data Analysis for Vessel-based Marine Bird Counts v1.0	Data Analysis/Interpretation	Yes	N/A	Finalized
1704	NWFS_Center_Ocean Salmon Survey Hydroacoustic Data Processing and Analysis v1.0	Data Analysis/Interpretation	Yes	N/A	Finalized
1382	NWFS_Center_Ocean Salmon Survey juvenile salmon Trophic analysis v1.0	Data Collection	No	N/A	Finalized
1371	NWFS_Center_Ocean Salmon Survey Marine Fish Sampling v1.0	Data Collection	No	N/A	Finalized
1373	NWFS_Center_Ocean Salmon Survey Ocean Water Chemistry and Chlorophyll Sampling v1.0	Data Collection	No	N/A	Finalized
1343	NWFS_Center_Ocean Salmon Survey Salmon Stock Identification v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1372	NWFS_Center_Ocean Salmon Survey Salmonid Marine Survival v1.0	Data Analysis/Interpretation	No	N/A	Finalized
4098	NWFS_Center_Ocean Salmon Survey Vertical Net Marine Zooplanktkon Sampling v1.0	Data Collection	No	N/A	Finalized
1722	NWFS_Center_Ocean Salmon Survey Vertical Net Zooplankton Analysis v1.0	Data Analysis/Interpretation	Yes	N/A	Finalized
4093	NWFSC_Ocean Salmon Survey Analysis of Juvenile Salmon Predation Risk v1.0	Data Analysis/Interpretation	No	N/A	Finalized
4092	NWFSCenter_Ichthyoplankton Ocean salmon prey biomass data analysis v1.0	Data Analysis/Interpretation	No	N/A	Finalized
4134	NWFSCenter_Ichthyoplankton Ocean salmon prey community analysis v1.0	Data Analysis/Interpretation	No	N/A	Finalized
4091	NWFSCenter_Ichthyoplankton Ocean salmon prey sampling v1.0	Data Collection	No	N/A	Finalized
1374	NWFSCenter_Ocean Salmon Survey Catch per Unit Effort v1.0	Data Analysis/Interpretation	No	N/A	Finalized
4089	NWFSCenter_Ocean Salmon Survey juvenile salmon Trophic data analysis v1.0	Data Analysis/Interpretation	No	N/A	Finalized
4094	NWFSCenter_Ocean Salmon Survey Ocean Water Nutrient Analysis v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1359	NWFSCenter_Ocean Salmon Survey Oceanographic Sampling v1.0	Data Collection	No	N/A	Finalized
1404	NWFSCenter_Ocean Salmon Survey Salmon Necropsy v1.0	Data Collection	No	N/A	Finalized
1705	NWFSCenter_Ocean Salmon Survey Vessel-based Marine Bird Counts - Strip Transect Sampling v1.0	Data Collection	Yes	N/A	Finalized
1413	NWFSCSalmon Ocean Survey: Reconstruction of juvenile migratory history and marine growth using otolith structure and chemistry v1.0	Data Analysis/Interpretation	Yes	N/A	Finalized
1703	Ocean Salmon Survey Hydroacoustic Surveys v1.0	Data Collection	Yes	N/A	Finalized
1341	Parentage assignments using SNPPIT software v1.0	Data Analysis/Interpretation	No	N/A	Finalized
5446	SNP genotyping using Genotyping in Thousands (GT-seq) on Illumina Sequencer platform v1.0	Data Collection	No	N/A	Finalized

Metrics:

Title	Category	Subcategory	Subcategory focus 1	Subcategory focus 2
Abundance of juvenile salmonids	Fish	Abundance of Fish (ID: 46)	Fish Life Stage: Juvenile Fish	Fish Origin: Both
Species composition of fish	Fish	Composition: Fish Species Assemblage (ID: 56)	Fish Life Stage: Juvenile Fish	Fish Origin: Both
Condition indices of fish	Fish	Condition of Life Stage: Fish (ID: 57)	Fish Life Stage: Juvenile Fish	NA
Distribution of fish	Fish	Distribution of Fish Species (ID: 62)	Fish Life Stage: Juvenile Fish	NA
Food web interactions	Fish	Food Web Interaction: Fish (ID: 69)	NA	NA
Genetic stock identification	Fish	Stock Identity (ID: 95)	Fish Life Stage: RANGE: Juvenile to Juvenile	NA
Timing of life stage of fish	Fish	Timing of Life Stage: Fish (ID: 101)	Fish Life Stage: Juvenile Fish	NA
Oceanographic sampling	Hydrology/Water Quantity	Ocean Conditions (ID: 106)	NA	NA
Plankton Density	Plankton	Abundance of Plankton (ID: 250)	Species Life Stage: RANGE: Juvenile to Adult Species	NA
Plankton Species Composition	Plankton	Composition: Plankton Assemblage (ID: 127)	Species Life Stage: RANGE: Juvenile to Adult Species	NA

Area of Inference:

Name	Value
Latitude, Longitude	44.719299, -124.175278
Latitude, Longitude	44.723202, -124.804245
Latitude, Longitude	48.30973, -125.456235
Latitude, Longitude	48.317036, -124.819028

Please correct the errors noted below.

Implementation Metrics