Portland Harbor Phase 3 Subyearling Chinook 2018 Samples

The Upper Willamette River (UWR) Chinook salmon Ecologically Significant Unit (ESU) includes naturally spawned Chinook salmon originating from the Clackamas River and from the Willamette River and its tributaries above Willamette Falls, as well as Chinook salmon from six artificial propagation programs. UWR Chinook salmon migrate through highly industrialized Portland Harbor (an active Superfund site) in the lower Willamette River, despite historical contamination. Juvenile salmon may be especially vulnerable to toxicant exposures.

The purpose of this study is to evaluate the growth of naturally spawned UWR juvenile Chinook salmon within the area of Portland Harbor compared to upstream reference sites, and to evaluate relationships between fish growth and tissue concentrations of legacy persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and dichlorodiphenyltrichloroethanes (DDTs), and tributyltin (TBT). Previous research has demonstrated a distinctive DDT signature in the UWR juvenile Chinook salmon out-migrating through an area of known historical DDT contamination (~ river mile 7). Sampling for this study will include a broader geographic representation within the contaminated area of the river than previous efforts, which will provide a more comprehensive understanding of the tissue contaminant levels in Willamette River salmonids, including DDTs, PCBs, PAHs, and TBT. Evaluating the association of tissue contaminant levels with indicators of skeletal growth will provide a metric of associated injury to this salmon population. UWR juvenile Chinook salmon will be collected by beach seine from select sites within Portland Harbor during the spring outmigration. Individual fish will have genetic confirmation of stock. Whole body and stomach content composites for UWR juvenile Chinook salmon will be analyzed for persistent organic pollutant (POP) concentrations including PCBs and DDTs, among others. Additionally, otolith analysis will be conducted to measure and quantify recent growth. The samples and related data from this study will support restoration and recovery efforts including projects specifically aimed at addressing and compensating the public for injuries to juvenile salmon from contaminant exposures.

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The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Laboratory quality assurance:

Representativeness is the degree to which data represent a characteristic of an environmental condition. In the field, this is addressed in the sampling design by the selection of sampling sites and the sample collection procedures. In the laboratory this is ensured by the proper handling and storage of samples and initiation of analysis within holding times. The sample collection procedures for this study will collect fish at a given site by beach seine, with selection of target species only restricted by size [target fork length: 50-80 mm]. This will ensure representativeness of the distribution of fish stocks at a given site.

Chemical analysis, fish tissue and stomach contents:

Representativeness is the degree to which data represent a characteristic of an environmental condition. In the field, this is addressed in the sampling design by the selection of sampling sites and the sample collection procedures. In the laboratory this is ensured by the proper handling and storage of samples and initiation of analysis within holding times. The sample collection procedures for this study will collect fish at a given site by beach seine, with selection of target species only restricted by size. This will ensure representativeness of the contamination across target species collected at a given site.

Otolith analysis:

Representativeness is the degree to which data represent a characteristic of an environmental condition. In the field, this is addressed in the sampling design by the selection of sampling sites and the sample collection procedures. In the laboratory this is ensured by the proper

handling and storage of samples and initiation of analysis within holding times. The sample collection procedures for this study will collect fish at a given site by beach seine, with selection of target species only restricted by size. This will ensure representativeness of the growth across target species collected at a given site.

The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Laboratory quality assurance:

Power analyses indicate that the 185 locus SNP database can be used to estimate the proportions of Columbia River Basin stock groups in estuary mixtures of 200 fish. From this the assignments have >99% accuracy for Upper Willamette River spring lineage. Individuals with an assignment probability of 0.80 or greater to a reporting group will be allocated to their genetic reporting group (Moran et al. 2014). This assignment probability criterion has been demonstrated to result in 98% accuracy in individual assignment. A second check is the ‘leave one out’ test, which evaluates how well fish within the baseline can be assigned to their population and reporting group of origin. Each fish with a complete genotype is sequentially removed from the baseline and its origin is assigned using the rest of the baseline. The summary output estimates the within and without reporting groups assignments to each baseline and reporting group. This method is described in Anderson et al. (2008) and Kalinowski et al. (2007) (Anderson et al. 2008; Kalinowski et al. 2007). The ‘leave one out’ self-assignment results for the Willamette River Spring lineage was > 99.9%.

The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Chemical analysis, fish tissue and stomach contents:

Quality assurance criteria for persistent organic pollutants (POPs; i.e., PCBs and DDTs) and PAHs analyzed in salmon whole body and stomach contents samples for this study are summarized (Table 6; taken from Sloan et al., 2006, Table 8). Details on the quality assurance criteria for TBT analysis in salmon whole body composite samples will be reported with findings if tissue mass is sufficient for analysis.

The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Laboratory quality assurance:

Bias demonstrates the degree to which the measured value represents the true value. Bias or accuracy of samples is evaluated by comparing measured SRM values with NIST certified values. Concentrations of ≥70% of individual analytes are to be within 30% of either end of the 95% confidence interval of the reference values. Results of QA analysis will be reviewed by the Laboratory QA Officer.

Chemical analysis, fish tissue and stomach contents:

Bias demonstrates the degree to which the measured value represents the true value. Bias or accuracy of samples is evaluated by comparing measured SRM values with NIST certified values. Concentrations of ≥70% of individual analytes are to be within 30% of either end of the 95% confidence interval of the reference values. Results of QA analysis will be reviewed by the Laboratory QA Officer.

Otolith analysis:

Bias demonstrates the degree to which the measured value represents the true value. Each otolith will be read without any knowledge of fish sample site. Bias of samples will be minimized through consistency in the measurement protocols, ensuring the increment being measured is in optimum focus, and ensuring the otolith is mounted so that the incremental plane is as close to horizontal as possible.

The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Laboratory quality assurance:

Comparability is the similarity among different datasets for use in combining or comparing data. The methods used in this analysis follow similar protocols with previous studies, including use of similar juvenile Chinook salmon baseline and reporting groups (Teel et al. 2009). As such, the genetic data and stock identification will be comparable to other datasets derived from juvenile Chinook salmon in this region.

Chemical analysis, fish tissue and stomach contents:

Comparability is the similarity among different datasets for use in combining or comparing data. The methods used in this analysis follow similar protocols with previous studies, with comparable or lower limits of detection. One distinction in the protocol described in this study will be chemistry measures on whole bodies minus stomach contents, otoliths, a fin clip, and 35 livers, whereas previous studies have retained the liver and otoliths in the whole body analyses. This may bias study samples to underrepresent the contamination profiles of the fish sampled. The extent to which removing the livers may modify the contaminant concentration of the whole body fish composites is not known at this time.

Otolith analysis:

Comparability is the similarity among different datasets for use in combining or comparing data. The methods used in this analysis follow similar protocols with previous studies. The average daily growth will be comparable to similar data derived from juvenile Chinook salmon otoliths.

The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Laboratory quality assurance:

The circumstances of incomplete data for genotyping analysis are most often related to a low quality sample collected in the field (degraded, or too small), rather than instrumentation or genetic laboratory protocols. Great care will be taken to collect fin clips of adequate size, and to follow the protocol for sample handling and storage. Within the laboratory, samples are tracked through all steps including extraction, concentration, amplification, the addition of primers for the loci of interest, and addition of the index library.

Otolith analysis:

Completeness is the ratio of usable data from the otolith analyses. It is fully expected that allotoliths will be processed and read, producing a reliable data point from each fish.

The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Laboratory quality assurance:

Fin clip genomic DNA extracts will be sequenced for individuals with a known stock identification (positive controls) along with negative controls and replicate samples. Error rates in the genotyping will be derived from positive controls (n=59) to estimate accuracy, and replicate genotyping of 20% of the fish collected for this study to estimate precision. For both measures, a percent error of <0.1% is considered acceptable. Any sample with a high percent error will be investigated to determine the cause of the mis-match. All genotype error rates will be reported.

Chemical analysis, fish tissue and stomach contents:

Precision represents the reproducibility of the individual measurements from the same sample. Precision is monitored and controlled within batches using laboratory replicates of field samples and across batches by analyzing SRM of applicable matrix i.e., tissue. For this study, a National Institute of Standards and Technology (NIST) mussel SRM 1974c will be used as the reference material for PAH analyses, and a NIST fish tissue SRM 1947 will be used for POPs analyses [Note, SRM 1974b was previously used, but is no longer available from NIST]. Crossbatch precision is expressed as the relative standard deviation (RSD) for repeated measurements. The RSD of analyte responses relative to the internal standard must be ≤ 15% for the repetitions.

Otolith analysis:

Precision represents the reproducibility of the individual measurements from the same sample. Precision is monitored and controlled by having the same person read each otolith, and a minimum of 10% of the otoliths two times, with each reading occurring on a different day. If the distance from the otolith core to the edge of the otolith (i.e., otolith radius at the time of capture) and distance from otoliths core to seven daily increments in from the otolith edge (i.e., otolith radius measured at 7 days before capture) match then the associated data is assigned to that otolith. A match is considered a RSD ≤ 15% for the measurements from the same otolith. If the readings do not match then all otoliths will be read twice, and a third reading will be performed for any otolith where the repeated measurement RSD is > 15%. If none of the three readings match then the otolith will be excluded from the statistical analyses.

The following text references figures, tables, and citations that can be located in the Quality Assurance Project Plan (QAPP) and Field Sampling Plan (FSP), which can be accessed with through DIVER:

https://pub-data.diver.orr.noaa.gov/portland-harbor/20181109_PH_JuvenileChinook_QAPP-FSP_FINAL_4264.pdf

Chemical analysis, fish tissue and stomach contents:

The lower limit of quantitation (LOQ) for all organic chemicals in this study is “the concentration that would be calculated if that analyte had a GC/MS response area equal to its area in the lowest level calibration standard used in that calibration. When an analyte is not detected in a sample or it has a response area that is smaller than its area in the lowest level calibration standard used, the concentration of the analyte in that sample is reported to be less than the value of its lower LOQ.” (Sloan et al. 2006). Typically LOQ values in 2 g fish whole-body composites range from 0.65 to 1.5 ng/g wet weight for PAHs and 0.15 to 0.50 ng/g wet weight for POPs, while LOQs for 0.7 g fish stomach content composites range from 1.0 to 2.5 ng/g wet weight for PAHs and 0.20 to 1.0 ng/g wet weight for POPs.

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