@mastersthesis {83154,
	title = {Ecosystem Functions of Pacific Northwest Estuaries: The Role of Ocean and Watershed Drivers in Eelgrass and Coho Salmon Dynamics},
	year = {2020},
	note = {This wide-ranging doctoral dissertation aims to {\textquotedblleft}investigate ocean and watershed dynamics to better understand the key drivers and consequences of ecosystem change in Pacific Northwest (PNW) estuaries{\textquotedblright} (from the Abstract). Topics explored include eelgrass and macroalgae, coho salmon and the Dungeness crab catch. },
	pages = {274 p.},
	school = {Oregon State University},
	type = {Doctoral Dissertation},
	edition = {Ph. D.},
	chapter = {Dept. of Integrative Biology},
	address = {Corvallis, Or.},
	keywords = {Alsea Bay, Beaver Creek, carbon dioxide, climate, Coho salmon = Oncorhynchus kisutch, Coos Bay, dissolved oxygen, Dungeness crab =   Metacarcinus magister (Cancer magister), eelgrass = Zostera marina, El Nino, Oregon Coast, Pacific Decadal Oscillation, pH, phosphate, precipitation, salinity, sea lettuce = Ulva spp., Siletz Bay, Siuslaw River estuary, Umpqua River, upwelling, water temperature, Yaquina Bay},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/gt54kv37z },
	author = {Magel, Caitlin L.}
}
@article {83113,
	title = {Temporal and habitat differences in the juvenile demersal fish community at a marine-dominated northeast Pacific estuary},
	journal = {Fisheries Research},
	volume = {227},
	number = {105557},
	year = {2020},
	note = {Estuaries provide habitat for many juvenile marine fishes.  A lack of systematic studies of fish communities in estuaries has hampered our understanding of estuaries{\textquoteright} roles in the early life histories of many marine fish. In this article, the authors compare the community structure of juvenile fishes in the Yaquina Estuary for 2008-2009, 2012-2013 and 2016-2017.  Sampling took place around docks and eelgrass beds. {\textquotedblleft}Greater abundances and reduced change in communities over time at eelgrass sites suggests that maintaining these habitats is potentially critical for many estuary-rearing species and temporal changes in these communities highlights the importance of long-term monitoring.{\textquotedblright} (from the Abstract)},
	month = {2020, Jul.},
	pages = {11 p.},
	keywords = {community ecology, eelgrass = Zostera marina, habitats, juvenile fishes, Pacific Decadal Oscillation, Pacific staghorn sculpin = Leptocottus armatus, Rockfish = Sebastes spp., Saddleback gunnel  = Pholis ornata, salinity, temporal distribution, upwelling, water temperature, Yaquina Bay},
	doi = {https://doi.org/10.1016/j.fishres.2020.105557 },
	author = {Schwartzkopf, Brittany D. and Whitman, Alison D. and Lindsley, Amy J. and Heppell, Scott A.}
}
@article {82911,
	title = {Evidence for regional-scale controls on eelgrass (<i>Zostera marina</i>) and mesograzer community structure in upwelling-influenced estuaries},
	journal = {Limnology and Oceanography},
	volume = {64},
	number = {3},
	year = {2019},
	note = {{\textquotedblleft}In estuaries of the U.S. Pacific Northwest coast, eelgrass (Zostera marina ) ecosystems are exposed to latitudinally varying oceanographic inputs in the form of ocean upwelling. Previous research suggests that ocean upwelling is critical to eelgrass and ulvoid macroalgae abundance, but the degree to which secondary producers are controlled by processes at regional vs. local scales is unknown. Here, we consider the relationships among primary producers (eelgrass, ulvoid macroalgae, and epiphytic microalgae), epifaunal mesograzers, and mesopredator fish within and across three Oregon, U.S.A., estuaries during a spring{\textendash}summer season to examine the role of multiple scales in structuring these communities.{\textquotedblright} (from the Abstract)  Suppplementary material in a separate file accompanies this article.},
	month = {2019, May},
	pages = {p.1120-1134},
	keywords = {algae, community ecology, Coos Bay, eelgrass = Zostera marina, eutrophication, fish, Grazing, Netarts Bay, primary production, Ulva spp., upwelling, Yaquina Bay},
	doi = {https://doi.org/10.1002/lno.11102 },
	author = {Hayduk, Jennifer L. and Hacker, Sally D. and Henderson, Jeremy S. and Tomas, Fiona}
}
@article {76596,
	title = {A method to identify estuarine water quality exceedances associated with ocean conditions},
	journal = {Environmental Monitoring and Assessment},
	volume = {187},
	year = {2015},
	note = {Major coastal upwelling events bring water that is low in oxygen and high in nutrients closer to the surface, at times killing marine animals.  Upwelled waters can and do enter estuaries.  Is there a way to distinguish poor water quality in estuaries that results from upwelling events from poor water quality derived from other causes?  The authors introduce an example of logistic regression models {\textquotedblleft}to predict the probability of exceedance of a water quality threshold{\textellipsis}{\textquotedblright}  Yaquina Bay is used as the example, and remaining issues are discussed.},
	month = {2015, Mar.},
	pages = {14 p.},
	keywords = {chlorophyll, climate, dissolved oxygen, mathematical modeling, salinity, upwelling, water quality, water temperature, Yaquina Bay},
	doi = {10.1007/s10661-015-4347-3},
	author = {Brown, Cheryl A. and Nelson, Walter G.}
}
@article {36566,
	title = {Upwelling-influence, macroalgal blooms, and seagrass production; temporal trends from latitudinal and local scales in northeast Pacific estuaries},
	journal = {Limnology and oceanography},
	volume = {58},
	number = {3},
	year = {2013},
	note = {{\textquotedblleft}In coastal marine systems worldwide, land-based nutrient inputs are often correlated with blooms of macroalgae, which can negatively affect seagrass habitats. We used spatiotemporal trends in production to identify the role of marine-derived nutrients in mediating these interactions. Among ocean upwelling-influenced estuaries along the northeastern Pacific, we documented a negative correlation between annual production of ulvoid macroalgae and the seagrass, Zostera marina L., at a regional scale that included four estuaries along a 400 km distance. While macroalgal biomass was , 30 times greater in southern (Yaquina Bay and Coos Bay, Oregon) compared to northern (Willapa Bay, Washington, and Netarts Bay, Oregon) estuaries, no temporal patterns of eelgrass decline were observed within the estuaries over a 5 yr period{\textellipsis}{\textquotedblright} (from the Abstract)},
	month = {2013, May},
	pages = {p,1103-1112},
	keywords = {algae, Coos Bay, eelgrass = Zostera marina, Netarts Bay, nitrogen, phosphorus, primary production, Ulva spp., upwelling, Willapa Bay, Yaquina Bay},
	doi = {doi:10.4319/lo.2013.58.3.1103},
	author = {Hessing-Lewis, Margot L. and Hacker, Sally D.}
}
@mastersthesis {34456,
	title = {Eelgrass-Macroalgae Interactions:  Context-Dependency in Upwelling-Influenced Estuaries},
	year = {2011},
	note = {"Throughout these studies I demonstrated that the mechanisms determining context-dependency in upwelling-influenced estuaries are informed by physical and biogeochemical conditions, coupled with high ambient marine-derived nutrient concentrations. These findings are important to coastal management because they suggest that the strength, direction and mechanisms of interactions are shaped by local abiotic conditions and long-term nutrient regimes, rather than high nutrient concentrations per se." (p.iii)  Co-major professors were Sally D. Hacker and Bruce A. Menge.},
	pages = {136 p.},
	school = {Oregon State University},
	type = {Doctoral Dissertation},
	edition = {Ph. D.},
	chapter = {Dept. of Zoology},
	address = {Corvallis, Or.},
	keywords = {algae, Coos Bay, eelgrass = Zostera marina, Netarts Bay, nutrient cycles, South Slough (Coos Bay), spatial distribution, species composition, temporal distribution, theses, Ulva species, upwelling, Willapa Bay, Yaquina Bay},
	url = {https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/mp48sg67r},
	author = {Hessing-Lewis, Margot}
}
@article {34441,
	title = {Historic and recent patterns of dissolved oxygen in the Yaquina Estuary (Oregon, USA): Importance of anthropogenic activities and oceanic conditions},
	journal = {Estuarine, Coastal and Shelf Science},
	volume = {92},
	number = {3},
	year = {2011},
	note = {Dissolved oxygen (DO) levels in estuaries can drop due to human activities.  They can also fall due to upwelling events offshore."This paper assesses whether there have been long-term changes in DO levels in the Yaquina Estuary, Oregon (USA) and the effect of ocean conditions on DO levels within that estuary. In addition, it compares  recent DO levels in the Yaquina Estuary to historical data from other estuaries in the region and the inner Oregon shelf to evaluate whether the hypoxia recently observed on the inner shelf has previously occurred." (from the Introduction)},
	month = {2011, May 1},
	pages = {p.446-455},
	keywords = {anoxia, dissolved oxygen, historical, upwelling, Yaquina Bay},
	doi = {10.1016/j.ecss.2011.01.018},
	author = {Brown, Cheryl A. and Power, James H.}
}
@article {80271,
	title = {Nutrient fluxes in the microalgal-dominated intertidal regions of the lower Yaquina estuary, Oregon (USA)},
	journal = {Northwest Science},
	volume = {81},
	year = {2007},
	note = {This study was launched to learn how important microalgae were to the productivity of Yaquina Bay, and to determine {\textquotedblleft}sediment nutrient fluxes in the microalgal dominated sediments{\textquotedblright} (p.51).  Microalgae on sediment are an important food source for benthic dwellers, and contribute nutrients to the water column when they decompose. The study examined seasonal nutrient fluxes, compared Yaquina Bay to other estuaries, and characterized the relationship between silica and nitrate in the Bay.  The study suggests that {\textquotedblleft}benthic microalgae control the nutrient fluxes to the water column" (p.59).},
	pages = {p.50-61},
	keywords = {algae, ammonium, chemistry, estuarine dynamics, Hatfield Marine Science Center, Idaho Flats, nitrate, nitrogen dioxide, nutrient cycles, phosphate, precipitation, primary productivity, Sally{\textquoteright}s Bend, sediments, silicon, upwelling, Yaquina Bay},
	doi = {https://doi.org/10.3955/0029-344X-81.1.50},
	author = {Sin, Yongsik and Sigleo, Anne C. and Song, Eunsook}
}
@article {34056,
	title = {Nitrate variability along the Oregon coast: Estuarine{\textendash}coastal exchange},
	journal = {Estuarine, Coastal and Shelf Science},
	volume = {64},
	number = {2-3},
	year = {2005},
	note = {Summer upwelling in the Eastern North Pacific Ocean brings nutrient-rich waters to the surface and is a major source of nutrients for bays and estuaries. This paper examines the effects of summer upwelling events on the nitrate concentrations in Yaquina Bay and the effects of river flow on nearshore waters.. },
	pages = {p.211-222},
	keywords = {nitrate-nitrite data, nitrogen, nutrient cycles, upwelling, Yaquina Bay},
	doi = {10.1016/j.ecss.2005.02.018},
	author = {Sigleo, Anne C. and Mordy, C. W. and Stabeno, P. and Frick, Walter E.}
}
