Assessing the threat of toxic contaminants to early marine survival of Chinook salmon in the Salish Sea

Human development of the Salish Sea has resulted in loss and modification of salmonid habitats, including reduced habitat quality due to contaminant inputs, particularly in the lower reaches of rivers and estuaries of the central Puget Sound. Chemical contaminants released into the Salish Sea from anthropogenic sources can reduce the health and productivity of salmon. Juvenile salmon are exposed to contaminants in freshwater, estuarine, and marine habitats but they are particularly vulnernable as they transition from fresh to saltwater because this life history stage is especially sensitive to stressors that may reduce their early marine survival. Reduced growth and disease resistance have been demonstrated for juvenile Chinook salmon exposed to environmentally relevant contaminant levels; however, synoptic, Puget Sound-wide surveys to assess the extent and magnitude of contaminant exposure are lacking. In this study we measured exposure of juvenile Chinook salmon to chemicals of concern that enter Puget Sound via stormwater, wastewater treatment facilities, atmospheric deposition to marine waters, and groundwater. During the spring and summer of 2013, outmigrating fish were sampled from the river mouthes and two adjacent marine shorelines at each of five Puget Sound river-estuary systems: Skagit, Snohomish, Green/Duwamish, Puyallup/Hylebos, and Nisqually. We (1) report the extent and magnitude of exposure, (2) compare exposure in outmigrants across five major river-estuary systems, and (3) evaluate potential effects on marine survival. Results will be used to establish a time series of contaminant conditions in juvenile Chinook salmon to measure the effectiveness of current toxics reductions strategies and actions, inform future pollution reduction efforts, and enhanced recovery of Chinook salmon

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Persistent Pollutants in Puget Sound Juvenile Chinook Salmon: Changes after 25 years

Puget Sound Chinook salmon (Oncorhynchus tshawytscha) have been listed as a threatened species under the Endangered Species Act since 1999. Factors contributing to their decline include overharvest, hatchery impacts, and loss and modification of salmon habitats, including reduced habitat quality due to contaminant inputs. Since the late 1980s, NOAA Fisheries has been measuring concentrations of persistent organic pollutants (POPs) in juvenile salmon from Puget Sound, WA. Initial studies in 1986 and 1989 revealed unexpectedly high concentrations of polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethanes (DDTs), and polycyclic aromatic hydrocarbons (PAHs) in juvenile Chinook salmon or their prey from urban areas in the Sound. Over the following 25 years, there have been numerous efforts to reduce contamination in Puget Sound, includ­ing remediation and restoration of superfund sites in Elliott Bay, Seattle, WA and Commencement Bay, Tacoma WA, with associated assessment of contaminant exposure in juvenile salmon and other trust resources. In 2013, NOAA Fisheries and Washington Department of Fish and Wildlife conducted a joint study to measure concentrations of contaminants, including POPs, in juvenile salmon from five Puget Sound river-estuary systems: Skagit, Snohomish, Green/ Duwamish, Puyallup/Hylebos, and Nisqually. We compare the extent and magnitude of current exposure to concentrations measured in salmon in previous studies conducted from the late 1980s to 2006. Results indicate declines in exposure to DDTs, PCBs, and PAHs in juvenile Chinook salmon from several estuary systems, suggesting that efforts to reduce inputs of these chemicals to the Sound have had some success. However, in a significant proportion of salmon, exposure to PCBs and PAHs is still above estimated toxicity thresholds. These data establish a time series of contaminant conditions in juvenile Chinook salmon to measure the effectiveness of past and current toxics reductions strategies and actions, inform future pollution reduction efforts, and enhanced recovery of Chinook salmon

Chemicals of emerging concern in marine biota: presence of estrogenic chemicals in bile of English sole from Puget Sound

Priority lists of Chemicals of Emerging Concern typically include estrogenic chemicals (ECs) such as natural and synthetic estrogens; 17β-estradiol (E2), estrone (E1), estriol (E3), and 17α-ethynylestradiol (EE2), as well as phenolic compounds [e.g., bisphenol A (BPA), octylphenol (OP) and nonylphenol (NP)]. A recent pilot study in Puget Sound reported a range of biliary E2 and BPA concentrations in male English sole, which were also correlated with abnormal reproduction and elevated plasma vitellogenin in this benthic species. The current study expands the geographic scope and analyzes a larger suite of biliary ECs in both sexes. English sole were sampled in 2011 and 2013 from 10 long-term monitoring sites representing a wide range of upland development intensity and type. The 2011/13 effort initiates long term monitoring of these CECs in English sole to support the Puget Sound Ecosystem Monitoring Program and the Toxics in Fish Vital Sign. The natural hormones E1 and E3 were highest in male and female sole from Elliott Bay, which is adjacent to Puget Sound’s most highly developed watershed, and were 7 to 13 times greater than sole from Nisqually Reach, a low-development site with the second highest concentrations. Similarly, the highest E2 concentrations were measured in sole from Elliott Bay, but E2 was higher in females than males at that site. BPA and OP were detected less frequently, but concentrations in sole from developed sites were generally higher than moderate- and low-development sites. EE2 and NP were never detected. Overall, ECs in both sexes from the same site were highly correlated, indicating a common environmental source for these chemicals. In addition to fulfilling monitoring needs, measuring the levels of these CECs in sole will help determine environmentally-relevant concentrations for follow-up laboratory exposure studies, a critical first-step in defining thresholds of concern for these CECs in marine fish

Assessing the threat of toxic contamination to early marine survival of Chinook salmon from Puget Sound

Juvenile salmon migrating from freshwater into Puget Sound en route to the Pacific Ocean encounter a wide range of water quality conditions that may impair their health, depending on their migration route and the duration of time spent in contaminated habitats. In 2013, we measured contaminant exposure in juvenile Chinook salmon from estuary, nearshore, and offshore habitats, including persistent organic pollutants (POPs) in whole-body fish samples, polycyclic aromatic hydrocarbons (PAHs) in stomach contents, and trace metals in gill tissues. Approximately one third of the Chinook salmon sampled from Puget Sound had elevated concentrations of toxic contaminants, high enough to affect their early marine survival. Levels of polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) in whole body samples of salmon from the Snohomish, Green/Duwamish and Hylebos/Puyallup estuary and nearshore habitats, and PCBs in fish from the offshore habitat of the Whidbey and Central Basins were high enough to potentially cause adverse effects, including reduction in growth, disease resistance, and altered hormone and protein levels. Additionally, levels of PAHs in stomach contents of salmon from the Snohomish and Green/Duwamish nearshore habitats were high enough to potentially affect growth and alter plasma chemistry and lipid class profiles. Elevated concentrations of copper and lead were measured in gills tissue of salmon from developed nearshore habitats, however, the potential effects on salmon health are unknown. Results from this study and future monitoring will identify areas where salmon may be at risk of contaminant exposure so appropriate toxics reduction activities can be implemented and will track the effectiveness of recovery actions to improve the health of Puget Sound Chinook salmon

Chemicals of emerging concern in marine biota: presence of estrogenic chemicals in bile of English sole from Puget Sound, WA

Marine waters near urban centers receive frequent inputs of chemicals that are emerging as threats to ecological and human health referred to as chemicals of emerging concern (CECs). Priority lists of CECs include some endocrine disrupting chemicals (EDCs) such as natural and synthetic estrogens; 17β-estradiol (E2), estrone (E1), estriol (E3), and 17α-ethynylestradiol (EE2), as well as the industrial phenolic compounds [e.g., bisphenol A (BPA), octylphenol (OP) and nonyphenol (NP)]. Recent information on the levels of these EDCs in water indicates that they may pose a risk due to their widespread occurrence and their potential estrogenicity, affecting growth, development and reproduction of marine fish. Although limited data are available on exposure concentrations of EDCs in biota of marine ecosystems, recent studies in Puget Sound have reported measurable levels of selected EDCs in bile of male English sole that are correlated with abnormal reproductive cycles and elevation in plasma vitellogenin levels in this benthic species. To determine the baseline levels of these chemicals in marine fish and increase our knowledge of EDC exposure in Puget Sound, we applied a recently developed method for quantitative analysis of a larger suite of EDCs (i.e., E1, E2, E3, EE2, BPA, OP, NP) in bile of male and female English sole collected at 10 different sites, including urban, near-urban and non-urban sites. Concentrations of EE2, OP and NP were below the limit of quantitation (1.5, 15 and 15ng/mL of bile, respectively) in fish bile whereas BPA was detected in most samples collected throughout Puget Sound. Higher mean levels of the natural hormones E1, E2, E3 were found in bile from both male and female sole collected in the urban and near-urban sites. Determining the ranges of biliary concentrations of these EDCs in marine fish from Puget Sound will provide information on environmentally-relevant concentrations for follow-up laboratory exposure studies and is a critical first-step in defining thresholds of concerns for these CECs in marine fish

Legacy habitat contamination as a limiting factor for Chinook salmon recovery in the Willamette Basin, Oregon, USA.

In the western United States, the long-term recovery of many Pacific salmon populations is inextricably linked to freshwater habitat quality. Industrial activities from the past century have left a legacy of pollutants that persist, particularly near working waterfronts. The adverse impacts of these contaminants on salmon health have been studied for decades, but the population-scale consequences of chemical exposure for salmonids are still poorly understood. We estimated acute and delayed mortality rates for seaward migrating juvenile Chinook salmon that feed and grow in a Superfund-designated area in the Lower Willamette River in Portland, Oregon. We combined previous, field-collected exposure data for juvenile Chinook salmon together with reduced growth and disease resistance data from earlier field and laboratory studies. Estimates of mortality were then incorporated into a life cycle model to explore chemical habitat-related fish loss. We found that 54% improved juvenile survival-potentially as a result of future remediation activities-could increase adult Chinook salmon population abundance by more than 20%. This study provides a framework for evaluating pollution remediation as a positive driver for species recovery