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• 1. [Article] Interpretation and design of ocean acidification experiments in upwelling systems in the context of carbonate chemistry co-variation with temperature and oxygen

  This is the publisher’s final pdf. The article is Published by Oxford University Press on behalf of International Council for the Exploration of the Sea 2015. This work is written by (a) US Government ...

  Citation × Citation Citation Abstract Copy Title: Interpretation and design of ocean acidification experiments in upwelling systems in the context of carbonate chemistry co-variation with temperature and oxygen Author: Lucey, Noelle, Evans, Wiley, Mathis, Jeremy T., Hales, Burke, Harvey, Chris J., Newton, Jan, Alin, Simone R., Sabine, Christopher L., Bednaršek, Nina, McElhany, Paul, Feely, Richard A., Reum, Jonathan C. P. This is the publisher’s final pdf. The article is Published by Oxford University Press on behalf of International Council for the Exploration of the Sea 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US. It can be found at: http://icesjms.oxfordjournals.org/ Title: Interpretation and design of ocean acidification experiments in upwelling systems in the context of carbonate chemistry co-variation with temperature and oxygen Author: Lucey, Noelle, Evans, Wiley, Mathis, Jeremy T., Hales, Burke, Harvey, Chris J., Newton, Jan, Alin, Simone R., Sabine, Christopher L., Bednaršek, Nina, McElhany, Paul, Feely, Richard A., Reum, Jonathan C. P. This is the publisher’s final pdf. The article is Published by Oxford University Press on behalf of International Council for the Exploration of the Sea 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US. It can be found at: http://icesjms.oxfordjournals.org/ Close

• 2. [Article] Trophically transmitted parasites as ecosystem indicators : relationships among parasite community structure, juvenile salmon diet composition, and ocean conditions

  Recent research conducted throughout the Northern California Current (NCC) on the ecology of Pacific salmon (Oncorhynchus spp.) indicates that variable ocean conditions affect the community composition ...

  Citation × Citation Citation Abstract Copy Title: Trophically transmitted parasites as ecosystem indicators : relationships among parasite community structure, juvenile salmon diet composition, and ocean conditions Author: Losee, James P. Recent research conducted throughout the Northern California Current (NCC) on the ecology of Pacific salmon (Oncorhynchus spp.) indicates that variable ocean conditions affect the community composition of zooplankton in the nearshore environment which, in turn, can affect the quality of prey for fish, sea birds and mammals. Interannual variability in the quality and composition of the copepod community in the NCC during early marine residency of some Pacific salmon populations is related to survival to adulthood. However, copepods make up a small portion of the diet of coho and Chinook salmon, and the mechanistic linkages between ocean climate, zooplankton composition and salmon prey remain unclear. Parasite analysis provides a supplement to traditional diet analysis that can describe the foraging history of a host species. Coho salmon (O. kisutch) and Chinook salmon (O. tshawytscha) serve as hosts to an array of marine parasites acquired through consumption of infected intermediate hosts such as copepods, euphausiids, and planktivorous fishes. Causing little or no harm to their salmon host, the presence of trophically transmitted parasites provides information on the dietary history of their salmonid host beyond the 24 hours associated with traditional diet analysis. This study (1) examined differences in feeding behavior of coho and Chinook salmon during their early marine residency using both stomach and parasite community analyses and (2) tested the hypothesis that variability in ocean circulation patterns (measured through the Pacific Decadal Oscillation, sea surface temperature (SST) and Bakun's upwelling index) and copepod species composition are related to variability in the community structure of trophically transmitted marine parasites found in juvenile salmon. I compared the abundance and species composition of parasites recovered from juvenile Columbia River coho and upper Columbia River summer and fall Chinook salmon captured off the coast of Washington from 2002 to 2009. I also compared interannual variability in parasite assemblages to physical and biological indices of ocean conditions. Coho and Chinook salmon consumed similar prey taxa; however, the species richness and abundance of trophically transmitted parasites indicated that Chinook salmon consumed a greater diversity and abundance of infected prey. In addition, differences in the abundance of fish in the diet and Anisakis simplex, a parasitic nematode known to infect salmon through fish consumption, suggest that Chinook salmon consistently consumed more fish prey than coho. In contrast, coho appeared to consume more euphausiids as indicated by stomach content analysis and increased abundance of the euphausiid parasite, Rhadinorhynchus trachuri. Shifts in the parasite community composition of both coho and Chinook salmon were related to interannual variability in SST and the biomass of southern-origin copepods (r > 0.7, P < 0.05). The acanthocephalan R. trachuri and a tetraphyllid cestode were associated with "warm" SSTs and greater biomass of lipid-poor, subtropical copepods while the nematode A. simplex was more abundant in years of "cold" SST and a relatively low biomass of subtropical copepods. These results provide novel insight into differences in the diet of Columbia River coho and Chinook salmon and illustrate linkages between ocean climate, zooplankton community composition and salmon diet during early marine residency. Title: Trophically transmitted parasites as ecosystem indicators : relationships among parasite community structure, juvenile salmon diet composition, and ocean conditions Author: Losee, James P. Recent research conducted throughout the Northern California Current (NCC) on the ecology of Pacific salmon (Oncorhynchus spp.) indicates that variable ocean conditions affect the community composition of zooplankton in the nearshore environment which, in turn, can affect the quality of prey for fish, sea birds and mammals. Interannual variability in the quality and composition of the copepod community in the NCC during early marine residency of some Pacific salmon populations is related to survival to adulthood. However, copepods make up a small portion of the diet of coho and Chinook salmon, and the mechanistic linkages between ocean climate, zooplankton composition and salmon prey remain unclear. Parasite analysis provides a supplement to traditional diet analysis that can describe the foraging history of a host species. Coho salmon (O. kisutch) and Chinook salmon (O. tshawytscha) serve as hosts to an array of marine parasites acquired through consumption of infected intermediate hosts such as copepods, euphausiids, and planktivorous fishes. Causing little or no harm to their salmon host, the presence of trophically transmitted parasites provides information on the dietary history of their salmonid host beyond the 24 hours associated with traditional diet analysis. This study (1) examined differences in feeding behavior of coho and Chinook salmon during their early marine residency using both stomach and parasite community analyses and (2) tested the hypothesis that variability in ocean circulation patterns (measured through the Pacific Decadal Oscillation, sea surface temperature (SST) and Bakun's upwelling index) and copepod species composition are related to variability in the community structure of trophically transmitted marine parasites found in juvenile salmon. I compared the abundance and species composition of parasites recovered from juvenile Columbia River coho and upper Columbia River summer and fall Chinook salmon captured off the coast of Washington from 2002 to 2009. I also compared interannual variability in parasite assemblages to physical and biological indices of ocean conditions. Coho and Chinook salmon consumed similar prey taxa; however, the species richness and abundance of trophically transmitted parasites indicated that Chinook salmon consumed a greater diversity and abundance of infected prey. In addition, differences in the abundance of fish in the diet and Anisakis simplex, a parasitic nematode known to infect salmon through fish consumption, suggest that Chinook salmon consistently consumed more fish prey than coho. In contrast, coho appeared to consume more euphausiids as indicated by stomach content analysis and increased abundance of the euphausiid parasite, Rhadinorhynchus trachuri. Shifts in the parasite community composition of both coho and Chinook salmon were related to interannual variability in SST and the biomass of southern-origin copepods (r > 0.7, P < 0.05). The acanthocephalan R. trachuri and a tetraphyllid cestode were associated with "warm" SSTs and greater biomass of lipid-poor, subtropical copepods while the nematode A. simplex was more abundant in years of "cold" SST and a relatively low biomass of subtropical copepods. These results provide novel insight into differences in the diet of Columbia River coho and Chinook salmon and illustrate linkages between ocean climate, zooplankton community composition and salmon diet during early marine residency. Close

• 3. [Article] Analysis of particulate organic matter distribution along surface waters of the California Current

  Water samples along the Washington, Oregon and California coastline were collected using high resolution sampling and analyzed to determine particulate organic carbon and nitrogen concentrations. Over ...

  Citation × Citation Citation Abstract Copy Title: Analysis of particulate organic matter distribution along surface waters of the California Current Author: Welch, Kylie Water samples along the Washington, Oregon and California coastline were collected using high resolution sampling and analyzed to determine particulate organic carbon and nitrogen concentrations. Over 28 days during August 2011, nearly 1500 samples were collected aboard the R/V Wecoma (W1108C) using a semi-automated filtration system. Additional subsurface samples were collected from CTD casts. In-situ measurements of temperature, salinity, chlorophyll fluorescence, and beam attenuation were combined with the data from individual samples to provide a near-synoptic, spatial distribution of particulate organic matter along the California Current. Marked contrasts in the concentrations and compositions of particulate organic matter were observed among different water masses along the margin, including those directly affected by Columbia River discharge, recently upwelled near-shore waters, and filaments associated with mesoscales eddies. My results demonstrate the utility of high-resolution sampling techniques can be integrated with remote sensing approaches to better understand physical-biological interactions in the coastal ocean. Title: Analysis of particulate organic matter distribution along surface waters of the California Current Author: Welch, Kylie Water samples along the Washington, Oregon and California coastline were collected using high resolution sampling and analyzed to determine particulate organic carbon and nitrogen concentrations. Over 28 days during August 2011, nearly 1500 samples were collected aboard the R/V Wecoma (W1108C) using a semi-automated filtration system. Additional subsurface samples were collected from CTD casts. In-situ measurements of temperature, salinity, chlorophyll fluorescence, and beam attenuation were combined with the data from individual samples to provide a near-synoptic, spatial distribution of particulate organic matter along the California Current. Marked contrasts in the concentrations and compositions of particulate organic matter were observed among different water masses along the margin, including those directly affected by Columbia River discharge, recently upwelled near-shore waters, and filaments associated with mesoscales eddies. My results demonstrate the utility of high-resolution sampling techniques can be integrated with remote sensing approaches to better understand physical-biological interactions in the coastal ocean. Close

• 4. [Article] Coastal ocean response to alongshore variations in topography and wind forcing

  The effects of alongshore variability in topography (banks and capes) and spatial variability in the wind forcing, including the wind-stress curl, on coastal ocean circulation are studied using a combination ...

  Citation × Citation Citation Abstract Copy Title: Coastal ocean response to alongshore variations in topography and wind forcing Author: Castelao, Renato Menezes The effects of alongshore variability in topography (banks and capes) and spatial variability in the wind forcing, including the wind-stress curl, on coastal ocean circulation are studied using a combination of observations and model simulations. Satellite sea surface temperature observations are used to describe the seasonal evolution of temperature fronts in the California Current System. The evolution is consistent with the seasonal cycle of wind forcing, but also reveals the profound influence of major capes in creating convoluted and offshore-diverted fronts. Although the greatest offshore excursion of fronts is found south of Cape Blanco, observations suggest that late in the upwelling season, the upwelling front (and jet) leaves the shelf to the north of the Cape, around Heceta Bank. This is supported by in situ observations obtained during the Coastal Ocean Advances in Shelf Transport (COAST) project, which depicted jet separation at Heceta Bank's downstream asymmetry with an average off-shelf transport around 0.7 Sv. Simulations exploring a large range in parameter space show that jet separation is expected to occur when the flow is strong (high Rossby number) and when the Burger number (the ratio of the squares of the internal Rossby radius of deformation and curvature of the topography) is close to one. Observations reveal that conditions at Heceta Bank during spring and summer are often nearly ideal for separation. The importance of the wind-stress curl to coastal circulation is also investigated. A region of upwelling-favorable wind-stress curl close to the coast downstream of a cape is shown to create a strong offshore intensification of the alongshore velocities, which helps jet separation via continuity and by creating potential vorticity contours that track far offshore of the cape. Stronger upwelling-favorable curl leads to earlier separation, while increasing the offshore extend of the region of strong curl leads to more separation. Finally, satellite scatterometer observations are used to show that the wind-stress curl is strongly enhanced around Cabo Frio, Brazil, during summer. At that time, curl-driven upwelling is as strong as coastal upwelling, which helps explain the observation that the coldest water along the coast is found near Cabo Frio. Title: Coastal ocean response to alongshore variations in topography and wind forcing Author: Castelao, Renato Menezes The effects of alongshore variability in topography (banks and capes) and spatial variability in the wind forcing, including the wind-stress curl, on coastal ocean circulation are studied using a combination of observations and model simulations. Satellite sea surface temperature observations are used to describe the seasonal evolution of temperature fronts in the California Current System. The evolution is consistent with the seasonal cycle of wind forcing, but also reveals the profound influence of major capes in creating convoluted and offshore-diverted fronts. Although the greatest offshore excursion of fronts is found south of Cape Blanco, observations suggest that late in the upwelling season, the upwelling front (and jet) leaves the shelf to the north of the Cape, around Heceta Bank. This is supported by in situ observations obtained during the Coastal Ocean Advances in Shelf Transport (COAST) project, which depicted jet separation at Heceta Bank's downstream asymmetry with an average off-shelf transport around 0.7 Sv. Simulations exploring a large range in parameter space show that jet separation is expected to occur when the flow is strong (high Rossby number) and when the Burger number (the ratio of the squares of the internal Rossby radius of deformation and curvature of the topography) is close to one. Observations reveal that conditions at Heceta Bank during spring and summer are often nearly ideal for separation. The importance of the wind-stress curl to coastal circulation is also investigated. A region of upwelling-favorable wind-stress curl close to the coast downstream of a cape is shown to create a strong offshore intensification of the alongshore velocities, which helps jet separation via continuity and by creating potential vorticity contours that track far offshore of the cape. Stronger upwelling-favorable curl leads to earlier separation, while increasing the offshore extend of the region of strong curl leads to more separation. Finally, satellite scatterometer observations are used to show that the wind-stress curl is strongly enhanced around Cabo Frio, Brazil, during summer. At that time, curl-driven upwelling is as strong as coastal upwelling, which helps explain the observation that the coldest water along the coast is found near Cabo Frio. Close

• 5. [Article] Climate shifts the interaction web of a marine plankton community

  This is the publisher’s final pdf. The published article is copyrighted by John Wiley & Sons, Inc. and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2486. This article ...

  Citation × Citation Citation Abstract Copy Title: Climate shifts the interaction web of a marine plankton community Author: Tolimieri, Nick, Francis, Tessa B., Peterson, William T., Scheuerell, Mark D., Ruzicka, James J., Brodeur, Richard D., Levin, Phillip S. This is the publisher’s final pdf. The published article is copyrighted by John Wiley & Sons, Inc. and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2486. This article is a U.S. Government work and is in the public domain in the U.S.A. Title: Climate shifts the interaction web of a marine plankton community Author: Tolimieri, Nick, Francis, Tessa B., Peterson, William T., Scheuerell, Mark D., Ruzicka, James J., Brodeur, Richard D., Levin, Phillip S. This is the publisher’s final pdf. The published article is copyrighted by John Wiley & Sons, Inc. and can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2486. This article is a U.S. Government work and is in the public domain in the U.S.A. Close

• 6. [Article] Large medusae in surface waters of the Northern California Current: variability in relation to environmental conditions

  This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springerlink.com/content/0018-8158/. To the best of our knowledge, one or more authors ...

  Citation × Citation Citation Abstract Copy Title: Large medusae in surface waters of the Northern California Current: variability in relation to environmental conditions Author: Emmett, Robert L., Suchman, Cynthia L., Daly, Elizabeth A., Brodeur, Richard D. This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springerlink.com/content/0018-8158/. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Title: Large medusae in surface waters of the Northern California Current: variability in relation to environmental conditions Author: Emmett, Robert L., Suchman, Cynthia L., Daly, Elizabeth A., Brodeur, Richard D. This is the publisher’s final pdf. The published article is copyrighted by Springer and can be found at: http://www.springerlink.com/content/0018-8158/. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. Close

• 7. [Article] Environmental drivers and reproductive consequences of variation in the diet of a marine predator

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier ...

  Citation × Citation Citation Abstract Copy Title: Environmental drivers and reproductive consequences of variation in the diet of a marine predator Author: Horton, Cheryl A., Parrish, Julia K., Gladics, Amanda J., Peterson, William T., Daly, Elizabeth A., Suryan, Robert M. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/journal-of-marine-systems/. Title: Environmental drivers and reproductive consequences of variation in the diet of a marine predator Author: Horton, Cheryl A., Parrish, Julia K., Gladics, Amanda J., Peterson, William T., Daly, Elizabeth A., Suryan, Robert M. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by Elsevier and can be found at: http://www.journals.elsevier.com/journal-of-marine-systems/. Close

• 8. [Article] Variability in mesoscale circulation and its effects on zooplankton distribution in the Northern California Current

  In eastern boundary current upwelling ecosystems, mesoscale circulation features such as eddies and upwelling filaments play a prominent role in the transfer of water and the associated plankton from the ...

  Citation × Citation Citation Abstract Copy Title: Variability in mesoscale circulation and its effects on zooplankton distribution in the Northern California Current Author: Keister, Julie Eileen In eastern boundary current upwelling ecosystems, mesoscale circulation features such as eddies and upwelling filaments play a prominent role in the transfer of water and the associated plankton from the productive nearshore to the oligotrophic deep sea. The relationship between mesoscale circulation, zooplankton distributions, and the across-shelf transport of coastal taxa and biomass in the California Current System was studied using data collected as part of the U.S. Global Ocean Ecosystems Dynamics (GLOBEC) Northeast Pacific Program. Sea surface height from >13 years of satellite altimeter data was used to characterize the spatial and temporal variability in mesoscale circulation in the northern California Current (35°N-49°N) and explore mechanisms of variability. High spatial and temporal variation in mesoscale energy occurred. Energy was not strongly linked to upwelling winds, but did correspond to climate indices, indicating that basin-scale processes play a role in controlling the circulation. CTD casts, zooplankton net tows, and Acoustic Doppler Current Profiler (ADCP) velocities collected during a research cruise conducted in summer 2000 off Oregon and northern California were used to describe the effects of mesoscale circulation on distributions of zooplankton. During the cruise, a filament of the coastal upwelling jet extended seaward of Cape Blanco (42.8°N) resulting in the displacement of coastal zooplankton to >100 km off the continental shelf. Velocities and standing stocks of zooplankton were used to estimate seaward transport of 0.5 Sv in the upper 100 m of the filament, in which zooplankton biomass averaged ~20 mg carbon/m³. That offshore transport equated to >900 metric tons of carbon each day, and 4-5x10⁴ tons over the 6-8 week lifetime of the circulation feature. Although the flux represented a small portion (<2%) of the shelf zooplankton biomass, the transport resulted in an offshore "hot-spot" in which biomass was 3-4X higher than in the surrounding ocean. Distributions of early life history stages of euphausiids indicated that retention of coastal populations may be strongly affected by the offshore advection. Finally, satellite sea surface temperature (SST) and sampling conducted during five summers were used to explore variability in the relationship between mesoscale circulation features and distributions of zooplankton. Circulation patterns differed among cruises and were reflected in zooplankton distributions. Circulation features resulted in the occurrence of cold surface water and coastal taxa offshore, but species abundances and presence/absence of taxa at specific locations were not predictable from satellite SSTs. These results are relevant to studies of ecosystem dynamics and the global carbon cycle because mesoscale circulation plays an important role in the seaward transport of carbon, retention and loss of taxa from the continental shelf, and creation of offshore structure which may be exploited by upper trophic level organisms. Title: Variability in mesoscale circulation and its effects on zooplankton distribution in the Northern California Current Author: Keister, Julie Eileen In eastern boundary current upwelling ecosystems, mesoscale circulation features such as eddies and upwelling filaments play a prominent role in the transfer of water and the associated plankton from the productive nearshore to the oligotrophic deep sea. The relationship between mesoscale circulation, zooplankton distributions, and the across-shelf transport of coastal taxa and biomass in the California Current System was studied using data collected as part of the U.S. Global Ocean Ecosystems Dynamics (GLOBEC) Northeast Pacific Program. Sea surface height from >13 years of satellite altimeter data was used to characterize the spatial and temporal variability in mesoscale circulation in the northern California Current (35°N-49°N) and explore mechanisms of variability. High spatial and temporal variation in mesoscale energy occurred. Energy was not strongly linked to upwelling winds, but did correspond to climate indices, indicating that basin-scale processes play a role in controlling the circulation. CTD casts, zooplankton net tows, and Acoustic Doppler Current Profiler (ADCP) velocities collected during a research cruise conducted in summer 2000 off Oregon and northern California were used to describe the effects of mesoscale circulation on distributions of zooplankton. During the cruise, a filament of the coastal upwelling jet extended seaward of Cape Blanco (42.8°N) resulting in the displacement of coastal zooplankton to >100 km off the continental shelf. Velocities and standing stocks of zooplankton were used to estimate seaward transport of 0.5 Sv in the upper 100 m of the filament, in which zooplankton biomass averaged ~20 mg carbon/m³. That offshore transport equated to >900 metric tons of carbon each day, and 4-5x10⁴ tons over the 6-8 week lifetime of the circulation feature. Although the flux represented a small portion (<2%) of the shelf zooplankton biomass, the transport resulted in an offshore "hot-spot" in which biomass was 3-4X higher than in the surrounding ocean. Distributions of early life history stages of euphausiids indicated that retention of coastal populations may be strongly affected by the offshore advection. Finally, satellite sea surface temperature (SST) and sampling conducted during five summers were used to explore variability in the relationship between mesoscale circulation features and distributions of zooplankton. Circulation patterns differed among cruises and were reflected in zooplankton distributions. Circulation features resulted in the occurrence of cold surface water and coastal taxa offshore, but species abundances and presence/absence of taxa at specific locations were not predictable from satellite SSTs. These results are relevant to studies of ecosystem dynamics and the global carbon cycle because mesoscale circulation plays an important role in the seaward transport of carbon, retention and loss of taxa from the continental shelf, and creation of offshore structure which may be exploited by upper trophic level organisms. Close