Automatic Identification System (AIS) data case study: vessel traffic through the Yaquina Bay breakwater at Newport, Oregon - Kress, Marin M. (ERDC/TN DOTS-, 2023)
Although there are two potential openings in the breakwater on the north of Yaquina Bay, there is no approved Federal channel that passes through the breakwater. There is interest in a possible passage through the breakwater, and the Portland District of the Army Corps of Engineers is interested in exploring this possibility. “[S]taff were interested in historical vessel transits, with a special focus on isolating transits for the largest (i.e., longest) vessels, identified as vessels 80 feet or longer, currently utilizing the area inside the breakwater. The Automatic Identification System Analysis Package (AISAP) software . . . was used to analyze vessel traffic” (p.1). An interesting look at the movement of large vessels in the bay.
Keywords: breakwater; harbors; navigation; ports; Sally’s Bend; Yaquina Bay

Cementation and Groundwater Chemistry in Pleistocene Paleodune Deposits of the Central Oregon Coast - Stephens, Adrienne Lynn (Portland State University, 2023)
Anyone who has driven along the Oregon coast has seen roadside deposits of light-colored rock close to the soil surface that looks like sand. These are actually ancient sand dunes. Pleistocene paleodunes have some cementation, but often display slope instability. “Weakening of cementing agents via changes to groundwater conditions due to altered vegetation, climate change, or contamination, for example, could promote slope instability, threatening lives and infrastructure. This study aims to investigate the variability in the type and degree of cementation and to determine how they are affected by changes in groundwater conditions” (from the Abstract). This interesting study addresses the Newport dune sheet, extending from Johnson Creek in the north to Yachats in the south. PSU Dissertations and Theses. Paper 6309.
Keywords: Agate Beach; Alsea Bay; Beaver Creek; Beverly Beach; chemistry; coastal hazards; Driftwood Beach; erosion; geology; Johnson Creek Landslide; landslides; Ona Beach; paleosciences; Seal Rock; sediments; Yaquina Bay

Estimating juvenile salmon estuarine carrying capacities to support restoration planning and evaluation - Hall, Jason; Roni, Phil; Ross, Kai; Camp, Meghan J.; Nuckols, Jason; Ruffing, Claire (Estuaries and Coasts, 2023)
What is the carrying capacity of salmon habitat in a time of global warming and rising sea levels? To answer this question, the authors of this paper took a hard dive into the literature, involving over 4,500 printed estimates of densities of juvenile salmonids in estuaries and floodplains. This data was then used in a habitat expansion approach to estimate historic, current potential and predicted population densities after sea level rise. “We demonstrate the habitat expansion approach by applying the quantiles of observed juvenile Chinook salmon (Oncorhynchus tshawytscha) and coho salmon (O. kisutch) densities (fish/ha) to spatial data describing current, historical or potential, and predicted (based on seal level rise) habitat extents for 16 coastal Oregon estuaries to estimate carrying capacities” (from the Abstract). This information will be important in the design and evaluation of restoration projects. This is an open-access article.
Keywords: Alsea Bay; Chetco River; Chinook salmon = Oncorhynchus tshawytscha; Coho salmon = Oncorhynchus kisutch; Coos Bay; Coquille River; Elk River; juvenile fish; natural resource management; Necanicum River; Nehalem River; Nestucca Bay; Rogue River; Salmon River; sea levels; Siletz Bay; Siuslaw River; Sixes River; Tillamook Bay; Umpqua River; Yaquina Bay

Oregon shellfish farmers: Perceptions of stressors, adaptive strategies, and policy linkages - Green, Kristen Marie; Spalding, Ana K.; Ward, Melissa; Levine, Arielle; Wolters, Erika Allen; Hamilton, Sara Luanne; Rice, Lauren (Ocean and Coastal Management, 2023)
The demand for oysters in the United States exceeds supply, marking the oyster growing as an industry meriting support. On the west coast, growers must cope with climate change, particularly ocean acidification, as well as regulatory problems and labor shortages. In order to help resource managers help oyster farmers, the authors of this paper went to the growers. In 2022, they conducted detailed interviews with Oregon oyster growers, and their comments abundantly populate this paper. “To expand and enhance United States oyster production, and support domestic food security and livelihoods, a better understanding of the limitations that oyster farmers’ experience, and corresponding pathways forward for adaptation is needed. Through semi-structured interviews conducted with commercial Oregon shellfish farmers, we assess the environmental, economic, social and regulatory stressors impacting oyster growing operations, and the corresponding adaptive strategies employed or envisioned by aquaculture farmers” (from the Abstract). The authors note adaptive strategies oyster growers adopt to cope, and advocate for more targeted outreach to support the oyster growers.
Keywords: aquaculture; aquatic invertebrates; bivalves; climate; commercial fisheries – shellfish; Coos Bay; economics; environmental law and policy; mollusks; Netarts Bay; ocean acidification; oysters; South Slough; Tillamook Bay; Umpqua River estuary; Yaquina Bay

Restoring Sea Otters to the Oregon Coast: A Feasibility Study - Tinker, M. Tim; Estes, James; Bodkin, James; Larson, Shawn; Murray, Mike; Hodder, Jan; Elakha Alliance. (Elakha Alliance, 2023)
When sea otters were exterminated in Oregon, there was no predator to stop the sea urchin population from expanding. Sea urchins eat kelp. More urchins mean less kelp. Less kelp means that many animals lose valuable habitat. Nearshore waters become rougher, because kelp beds cause the seas to lie down. The post-otter environment is less diverse and less hospitable. The Elakha Alliance (named for the Chinook Jargon word for sea otter) has been formed to realize the vision of bringing the sea otter back to Oregon. This book is about their dream. The authors have meticulously examined multiple aspects of the problem, from environmental to legal, and conclude that it is possible to bring otters back. Interestingly, estuaries may provide valuable launching grounds, offering more protection than the open sea. As keystone predators, sea otters would help restore an environment badly out of balance, and would provide many benefits aside from being adorable. As they say, the best dreams happen when we are awake. Colored maps, colored pictures.
Keywords: Coos Bay; economics; ecosystem health; environmental law and policy; genetics; habitats; histology; historical; human impacts; marine mammals; population biology; Reintroductions; Sea otter = Enhydra lutris; sociology; Tillamook Bay; Translocations; Yaquina Bay

Status of the European Green Crab, Carcinus maenas, (aka 5-spine crab) in Oregon Estuaries. Report for 2022 - Yamada, Sylvia Behrens; Royer, Cameron; Schooler, Shon; Flitcroft, Rebecca; Vance, Mitch; Randall, Andrea; Fisher, Jennifer (Pacific States Marine Fisheries Commission. Aquatic Nuisance Species Project, 2023)
The invasive European green crab is a voracious predator of bivalve molluscs, small crustaceans and other organisms. It has been present in Oregon since the late 1990s. The population grows when winter waters are warm, as they are during El Niños. Since 2015, however, “recruitment has been good every year. Since green crabs live for 6 years, these recent strong year classes can produce larvae until 2027. . . Now that populations in Oregon, Washington and British Columbia have built up, we have evidence for local production and for larvae sources from a genetically distinct population on Vancouver Island. . .” (from the Executive Summary)
Keywords: aquatic invertebrates; Coos Bay; crustaceans; El Nino; European green crab = Carcinus maenas; Grays Harbor (Wa.); introduced species; Netarts Bay; Pacific Decadal Oscillation; population count; Salmon River; Siuslaw River; Tillamook Bay; Umpqua River estuary; Willapa Bay (Wa.); Yaquina Bay

Benthic microbial fuel cell systems for marine applications - Reimers, Clare E.; Wolf, Michael; Alleau, Yvan; Li, Cheng (Journal of Power Sources, 2022)
There’s a lot happening on the seafloor these days: aquaculture, trawling, mining, communication cables. This means that there is a need for accurate, self-powered sensors for benthic environments. In this article, the authors report on a benthic microbial fuel cell and a power management platform that can recharge lithium batteries. The authors conclude that the systems described “are now sufficiently mature to be applied within marine observation networks. They represent an alternative power source that may be integrated readily with many kinds of innovative sensors.” (from the Abstract)
Keywords: chemical; Continental slope; energy; microbiology; sediments; Sensors; Yaquina Bay

Differential coastal uplift quantified by luminescence dating of marine terraces, central Cascadia forearc, Oregon - McKenzie, K.A.; Kelsey, H.M.; Kirby, E.; Rittenour, T.M.; Furlong, K.P. (Quaternary Science Reviews, 2022)
At Yaquina Bay, there are marine terraces north and south of the bay. Although these terraces were deposited at the same time, they now have different elevations. This fact implies differential displacement along a fault in Yaquina Bay. The authors report on a study using luminescence dating to help determine what is happening in this area. “Our results confirm that Yaquina Bay has been active during the late Pleistocene, and it also appears that the fault has experienced significant variations in displacement over the last 125 kyrs, and that a significant amount of displacement accrued during a relatively short time period post-106 ka” (p.13, section 6.1, “Faulting at Yaquina Bay”).
Keywords: coastal hazards; earthquakes; Faults; geology; paleosciences; tsunamis; Yaquina Bay

Discovery of a large offshore population of the northeast Pacific burrowing shrimp Neotrypaea sp. (Decapoda: Axiidea) - Henkel, Sarah K.; Revelas, Eugene C.; Wodzicki, Stefan; Chapman, John (Estuarine, Coastal and Shelf Science, 2022)
The ghost shrimp, Neotrypaea spp., has long been known as a burrower in soft estuarine sediments. While scattered numbers of ghost shrimp were found on the continental shelf, they were believed to be strays from estuaries; that is, until 2019, when a large population of ghost shrimp was found on the continental shelf off Newport in waters 58-77 meters deep. The offshore population was thought to be giant ghost shrimp (Neotrypaea gigas), known to be present in Yaquina Bay, but not often written about. This population has multiple years and multiple size classes. “This is the first report of a major burrowing shrimp population on the continental northeast Pacific coastal ocean” (from the Abstract). Is a native species expanding or shifting its habitats in response to climate or other anthropogenic change? Or does this find represent an introduction of a new species? Stay tuned… This is an open-access article.
Keywords: Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Giant ghost shrimp = Neotrypaea gigas; habitats; morphology; sediments; taxonomy; water temperature; Willapa Bay; Yaquina Bay

Morphology, Sediment Microbial Analysis, and Species Distribution Modeling of a New Offshore Population of Ghost Shrimp (Neotrypaea sp.) - Hardisty, Sarah (Oregon State University, 2022)
Ghost shrimp (Neotrypaea spp.) are typically seen as burrowing species in estuaries. In 2019, after years of abnormally warm offshore waters, a population of ghost shrimp was discovered about 7 miles offshore of Newport, Oregon. The author of this Master’s thesis attempts to answer some questions about the newly revealed enclave. Was the new population a new species? Examination revealed that the offshore ghost shrimp closely resembled the giant ghost shrimp, which is found in Yaquina Bay, except for the eyestalk. Could the sediment microbial communities in the new deep-water habitat support the shrimp? Researchers learned that, “Bacteria of the genus Shewanella, which have been shown to induce oyster and mussel settlement and metamorphosis, were found in both the estuary and offshore locations and in five times greater abundance with Neotrypaea than without” (from the Abstract). Finally, the author attempted to predict where other offshore populations of ghost shrimp might be found, and found clusters off Nehalem and Nestucca estuaries. The major professor was Sarah K. Henkel.
Keywords: bacteria; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Giant ghost shrimp = Neotrypaea gigas; habitats; Microbiome; morphology; Nehalem River; Nestucca River; sediments; taxonomy; water temperature; Yaquina Bay

Protocol for using autoclaved intertidal sediment as a medium to enrich marine cable bacteria - Li, Cheng; Reimers, Clare E; Chace, Peter J. (STAR Protocols, 2022)
Cable bacteria come from the family Desulfobulbaceae, but have not yet been identified as to genus and species. The name “cable bacteria” comes from their tendency to form long networks of filaments. The length of the filaments allows cable bacteria to tap into energy harvested from sulfide oxidation. This article gives a protocol for extracting cable bacteria from natural sediment, inoculate cultivated sediment in the laboratory, and evaluate the quantity of cable bacteria in the cultivated sediment. Techniques for collection and extraction are described in detail.
Keywords: chemistry; Desulfobulbaceae; energy; Idaho Flats; microbiology; Sally’s Bend; sediments; Sensors; Yaquina Bay

Relationship between Ascarophis Sp. (Nematoda: Cystidicolidae), Sturgeon Feeding Pit Density and Ghost Shrimp Burrowing Behavior - Brockman, Joseph N. (Oregon State University, 2022)
One of the most challenging problems in biology is to map the life cycle of a parasite. Many parasites often have more than one intermediate host, before the final host, and it can be very difficult to determine the life stages of the parasite. This work is concerned with the use of a parasitic nematode worm as a possible biological control on ghost shrimp. Ghost shrimp burrow in mudflats, and can disturb oyster grounds. They were formerly controlled by pesticides, but this technique is no longer practiced. There is an economic incentive to find a way to limit their population around oyster beds. Sturgeon are bottom-feeders, and burrow in mud, creating feeding pits to find benthic prey. The author of this Master’s thesis sought to determine if sturgeon were the final hosts of the Ascarophis nematode, and if infection with the nematode changed burrowing patterns of ghost shrimp. Major professors were Jessica Miller and Brett Dumbauld.
Keywords: Biocontrol; bioturbation; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Green sturgeon = Acipenser medirostris; Idaho Flats; life history information; mudflats; Pacific oyster = Crassostrea gigas; parasites; Parasitic nematode = Ascarophis spp.; Tongue Island (Yaquina); White sturgeon = Acipenser transmontanus; Willapa Bay; Yaquina Bay

Status of the European Green Crab, Carcinus maenas, in Oregon and Washington Coastal Estuaries. Report for 2020 and 2021 - Yamada, Sylvia Behrens; Royer, Cameron; Schooler, Shon; Fisher, Jennifer; Randall, Andrea; Buffington, Chelsey; Stote, Alex; Akmajian, Adrianne (Pacific States Marine Fisheries Commission. Aquatic Nuisance Species Project, 2022)
The COVID-19 pandemic affected this report, leading to combined years and trapping on a reduced number of estuaries. The invasive European green crab is a voracious predator of bivalve molluscs, small crustaceans and other organisms. It has been present in Oregon since the late 1990s. The population grows when winter waters are warm, as they are during El Niños. Since 2015, however, “recruitment has been good every year. Since green crabs live for 6 years, these recent strong year classes can produce larvae until 2027. . . Now that populations in Oregon, Washington and British Columbia have built up, we have evidence for local production and for larvae sources from a genetically distinct population on Vancouver Island. . .” (from the Executive Summary) This report is accompanied by a dataset, available at: https://ir.library.oregonstate.edu/concern/datasets/b8515w17z
Keywords: aquatic invertebrates; Coos Bay; crustaceans; El Nino; European green crab = Carcinus maenas; Grays Harbor (Wa.); introduced species; Netarts Bay; Pacific Decadal Oscillation; population count; Tillamook Bay; Willapa Bay (Wa.); Yaquina Bay

A doubled down invasion of the northeast Pacific by the Asian mud shrimp, Upogebia major, and its coevolved bopyrid isopod parasite, Orthione griffenis - Chapman, John W.; Li, Jingchun; McGowan, Michael F.; Breitenstein, Ralph A.; Appy, Ralph; Hieb, Kathryn A.; Piotrowski, Christina N.; Elder, Leanne E. (Aquatic Invasions, 2021)
The blue mud shrimp, Upogebia pugettensis, is known to be an ecosystem engineer, turning over and re-suspending, and aerating sediments (bioturbation), burrowing, and deposit feeding. The mud shrimp affects organic structure, nutrients, and the grain size of sediments in mudflats. Some of this activity creates difficulties for oyster growers, causing the application of pesticides in oyster growing areas in the 1950s. It may be that the changes in the ecosystem caused by introduced oysters and pesticides opened the doors for subsequent invasions. In 1999, a parasitic isopod was discovered to be infecting the native mud shrimp, and effectively sterilizing the shrimp. A related species, the Asian mud shrimp. Upogebia major, is less susceptible to the parasite, and has begun to fill in spaces formerly occupied by the blue mud shrimp. While this article is concerned with mud shrimp populations in California, the dynamics discussed are relevant to Oregon estuaries. If the ways our estuaries are engineered changes thanks to the double invasion, the way we manage our estuaries will also have to change. This is an open-access article, and it has also been re-printed as no.21-021 in the ORESU-R series.
Keywords: Alsea Bay; Asian mud shrimp Upogebia major; bioturbation; community ecology; Coos Bay; depleted populations; Griffen’s isopod = Orthione griffensis; introduced species; Mud shrimp = Upogebia pugettensis; natural resource management; Nestucca Bay; Netarts Bay; Upogebia macginitieorum; Yaquina Bay

A maximum rupture model for the central and southern Cascadia subduction zone—reassessing ages for coastal evidence of megathrust earthquakes and tsunamis - Nelson, Alan R.; DuRoss. Christopher B.; Witter, Robert C.; Kelsey, Harvey M.; Engelhart, Simon E.; Mahan, Shannon A.; Gray, Harrison J.; Hawkes, Andrea D.; Horton, Benjamin P.; Padgett, Jason S. (Quaternary Science Reviews, 2021)
“A new history of great earthquakes (and their tsunamis) for the central and southern Cascadia subduction zone shows more frequent (17 in the past 6700 yr) megathrust ruptures than previous coastal chronologies.” (from the Abstract) The article contains a link to supplementary data, also accessible through U.S. Geological Survey data releases.
Keywords: Alsea Bay; coastal hazards; Columbia River; Coos Bay; Coquille River; earthquakes; geology; mathematical modeling; Nehalem River; Nestucca Bay; Netarts Bay; paleosciences; Siletz Bay; Siuslaw River; tsunamis; Yaquina Bay

Relationship between ocean ecosystem indicators and year class strength of the invasive European green crab (Carcinus maenas) - Yamada, Sylvia Behrens; Fisher, Jennifer L.; Kosro, P. Michael (Progress in Oceanography, 2021)
The link between invasive European green crab populations on the American west coast and warm oceanic conditions is well established. This article closely examines the link between ocean climate and these crab populations and probes aspects of this population’s increase.
Keywords: California Current; Coos Bay; Davidson current; El Nino; European green crab = Carcinus maenas; Grays Harbor; introduced species; mathematical modeling; Netarts Bay; Pacific Decadal Oscillation; population biology; Tillamook Bay; water temperature; Willapa Bay; Yaquina Bay

Shell Boring Polychaetes and the Oregon Oyster Aquaculture Industry: Spatial Distribution, Regulatory Actions, and Stakeholder Engagement - Considine, Megan E. (Oregon State University, 2021)
In 2020, an infestation of invasive shell-boring polychaete worms (mud-blister worms) was discovered in Puget Sound, providing the impetus for this study. While the boring done by the worms does not damage the quality of the oyster, it does affect its aesthetic appeal, and to some extent lowers productivity. In this Master’s thesis, the author endeavors to ascertain the distribution of mud blister worms in Oregon commercial oyster farms. The author also hoped to understand whether culture methods, seasonal changes and “oyster shell metrics” affect the prevalence of the worms. Finally, the author attempted to show if their findings and outreach could improve the management of oyster farms and resource management decisions. (p.10) Netarts Bay was found to be the most affected by the infestation.
Keywords: Annelid worms; aquaculture; aquatic invertebrates; bivalves; Coos Bay; invasive species; mollusks; Mud blister worm = Polydora spp.; Netarts Bay; oysters; Pacific oyster = Crassostrea gigas; Polychaetes; Tillamook Bay; Yaquina Bay

Analysis of earthquake and tsunami impacts for people and structures inside the tsunami zone for five Oregon coastal communities: Gearhart, Rockaway Beach, Lincoln City, Newport, and Port Orford - Bauer, John M.; Allan, Jonathan C.; Gabel, Laura L. S.; O’Brien, Fletcher E.; Roberts, Jed T. (Open-File Report (Oregon. Department of Geology and Mineral Industries), 2020)
“This report evaluates the effects of a great (M w 9.0) earthquake and tsunami on the Cascadia Subduction Zone for five Oregon coast communities, in order to understand the degree of potential destruction, including: potential building losses, debris generated, fatalities and injuries, and estimated numbers of the displaced populations. The goal is to help coastal communities prepare” (p.ii). Very interesting community profiles, colored maps. The report is accompanied by an Excel file, a casualty model spreadsheet.
Keywords: Agate Beach; coastal hazards; Cutler City; demographics; earthquakes; erosion; floods; Gearhart (Or.); landslides; Lincoln City (Or.); Necanicum River estuary; Newport (Or.); Newport bayfront; Nye Beach; Port Orford (Or.); Rockaway Beach (Or.); Siletz Bay; South Beach; tsunamis; Yaquina Bay

Are They What They Eat? A Stable GIT Microbiome Characterized in P. resecata - Gustafson, Tarah N. (Oregon State University, 2020)
“Intertidal herbivores, such as isopods, help regulate and contribute to nutrient cycling and organic carbon flow through the trophic levels in estuaries and coastal ecosystems. Though much is known about the microbiomes of macrophyte leaves that serve as the primary food source for isopods, and (to a lesser extent) the microbiomes of herbivores themselves, little has been studied about the community assembly dynamics of herbivore microbial communities” (from the Abstract). This Honors Bachelor of Science thesis describes a project to better understand the microbiomes associated with these isopods. Isopods were gathered from Netarts Bay, while the intertidal vegetation they fed on was gathered at Yaquina Bay. The isopods were fed diets limited to one plant species and then their gastrointestinal microbes were genetically sequenced to determine if the microbiomes changed due to diet. They did not, which supports work indicating that marine isopods have stable gastrointestinal tract microbiomes
Keywords: diet; eelgrass = Zostera marina; Eelgrass isopod = Pentidotea resecata; Gastrointestinal; genetics; Microbes; Netarts Bay; Sea lettuce = Ulva lactuca; Sugar kelp = Laminaria saccharina; Yaquina Bay

Ecosystem Functions of Pacific Northwest Estuaries: The Role of Ocean and Watershed Drivers in Eelgrass and Coho Salmon Dynamics - Magel, Caitlin L. (Oregon State University, 2020)
This wide-ranging doctoral dissertation aims to “investigate ocean and watershed dynamics to better understand the key drivers and consequences of ecosystem change in Pacific Northwest (PNW) estuaries” (from the Abstract). Topics explored include eelgrass and macroalgae, coho salmon and the Dungeness crab catch.
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

Effect of sulfide and the role of root mass on metabolic fluxes in the seagrass Zostera marina - Peyer, Suzanne M.; Maricle, Brian R.; Young, David R. (Environmental and Experimental Botany, 2020)
Eelgrass offer vital habitats for many species. Yet eelgrass populations around the world are declining. In this article, the authors examine the potential role of hydrogen sulfide in inhibiting eelgrass growth. This study showed that the size of eelgrass root mass was an important variable in understanding the plants’ interactions with sulfides.
Keywords: carbon dioxide; eelgrass = Zostera marina; growth; hydrogen sulfide; Idaho Point; nitrogen; oxygen; Yaquina Bay

Effects of Anthropogenic Stressors on Seagrass and Coral Microbiomes - Wang, Lu (Oregon State university, 2020)
Coral reefs and seagrass beds provide important habitats and perform vital ecosystem services to a variety of ocean life. Unfortunately, corals and seagrasses are both suffering population declines due to human-derived stressors. In this wide-ranging doctoral dissertation, the author examines how anthropogenic changes stress the microbiomes surrounding seagrasses and corals. “This body of work utilized 16S rRNA amplicon and metagenome sequencing to characterize changes in the taxonomic composition and functional potential of seagrass and coral microbiomes under varying environmental stressors. This work was done to gain fuller understanding of seagrass and coral holobiont responses to the changing oceans” (from the Abstract). Ryan S. Mueller was the major professor.
Keywords: carbon; climate; eelgrass = Zostera marina; eutrophication; Florida Keys; genetics; human impacts; Ischia; Italy; Massive starlet coral = Siderastrea sidereal; Microbes; nitrogen; ocean acidification; water temperature; Yaquina Bay

Fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits in the California Current Ecosystem - Lee, Elizabeth M. J.; O'Malley, Kathleen G. (Marine Ecology Progress Series, 2020)
“Dynamic marine environments can shape complex spatial and temporal patterns in the population connectivity of marine species, and this is often exemplified in species with long larval phases. Here, we used a genotyping-by-sequencing (GBS) approach to examine fine-scale spatial and temporal genomic variation among Dungeness crab Cancer magister larval recruits sampled in the California Current Ecosystem. . . Overall, our findings provide evidence for high connectivity within Dungeness crab, but suggest that selective pressures and ocean conditions influence the genetic composition of larval recruits both intra- and inter-annually” (from the Abstract). This publication was re-printed online in the Sea Grant reprint series as ORESU-R-20-010.
Keywords: aquatic invertebrates; California Current Ecosystem; Coos Bay; crustaceans; Dungeness crab = Metacarcinus magister (Cancer magister); genetics; larvae; Pacific Decadal Oscillation; population biology; Yaquina Bay

Influence of Soil Texture on Carbon Storage of PNW Coastal Blue Carbon Ecosystems - Fox, Conner S. (Oregon State University, 2020)
Interest in carbon sequestration has risen as concern about climate change has increased. “Blue carbon” refers to carbon captured by the oceans and intertidal areas adjoining the oceans. It is necessary to understand the dynamics of blue carbon storage in order to understand the world’s carbon budget. In this Honors Bachelor of Science thesis, the author examines the relationship between soil texture and carbon storage at multiple West Coast sites. The advisor was J. Boone Kauffman.
Keywords: carbon; Carbon sequestration; Columbia River; Coos Bay; Grays Harbor (Wash.); Humboldt Bay (Calif.); Nehalem Bay; Padilla Bay (Wash.); salt marsh; sediments; Skagit River (Wash.); Snohomish Estuary (Wash.); wetland vegetation; Yaquina Bay

Life history and population dynamics of green crabs (Carcinus maenas) - Young, Alan M.; Elliott, James A. (Fishes, 2020)
The European green crab has been present in the Pacific Northwest for the past thirty years. The International Union for the Conservation of Nature considers it one of the top 100 worst invasive species in the world. This article reviews current knowledge about this species around the world. “This review provides an up-to-date account of the current published information on the life history and population dynamics of this very important species, including genetic differentiation, habitat preferences, physical parameter tolerances, reproduction and larval development, sizes of crabs, densities of populations, sex ratios, ecosystem dynamics and ecological impacts in the various established global populations of green crabs." This is an Open Access article.
Keywords: Coos Bay; European green crab = Carcinus maenas; habitats; introduced species; life history information; Netarts Bay; physiology; population biology; Tillamook Bay; Yaquina Bay

Lost in plain sight: the evolution of Oregon's nearshore groundfish trawl fleet - Sjostrom, Anja; Conway, Flaxen D. L.; Ciannelli, Lorenzo; Wakefield, Waldo (ORESU-S, 2020)
In 2000, thanks to double troubles of strong El Niños and overfishing, the nearshore west coast groundfish fishery collapsed. This report documents how the fishery has come back from that disaster, and where it is headed now. Groundfish are longer-lived fish, slow to grow, and their populations do not replenish at the rapid rate characteristic of shorter-lived species. In this glossy, beautifully photographed report, we meet the members of the “beach fleet” and learn how they have coped with increased regulation and the necessity of adapting to change.
Keywords: commercial fisheries – groundfish; depleted populations; economics; El Nino; natural resource management; Newport (Or.); population biology; ports; Trawling; Yaquina Bay

A simple, dynamic, hydrological model for mesotidal salt marshes - Marois, Darryl E.; Stecher, Hilmar A. (Estuarine, Coastal and Shelf Science, 2020)
Marshes provide essential ecological services by cleaning water, preventing flooding, sequestering carbon and offering valuable habitats. In order to understand the physical parameters of marshes, natural resource managers need to understand their hydrology. In this article, the authors offer a simple model that has proven to be accurate that allows for a rapid picture of a complex environment. In addition to facilitating predictions of marsh water levels, the model can help with understanding soil chemistry, vegetation zonation and implications of sea level rise.
Keywords: Bayocean Peninsula Park (Tillamook); Kilchis Point Reserve (Tillamook); mathematical modeling; salt marsh; sea level; sediments; tidal data; tidelands; Tillamook Bay; wetland delineation; wetland vegetation; Winant Slough (Yaquina); Yaquina Bay

Temporal and habitat differences in the juvenile demersal fish community at a marine-dominated northeast Pacific estuary - Schwartzkopf, Brittany D.; Whitman, Alison D.; Lindsley, Amy J.; Heppell, Scott A. (Fisheries Research, 2020)
Estuaries provide habitat for many juvenile marine fishes. A lack of systematic studies of fish communities in estuaries has hampered our understanding of estuaries’ 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. “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.” (from the Abstract)
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

Application of the extractable lipofuscin aging method to estimate mortality and population dynamics of the burrowing shrimp, Neotrypaea californiensis - Bosley, Katelyn M.; Wainwright, Thomas; Dumbauld, Brett R. (Estuarine, Coastal and Shelf Science, 2019)
Burrowing shrimp play important roles in estuaries by moving sediment (bioturbation). They also create problems for oyster farmers by burying oyster seed, and have been widely regarded as pests. In the past, the pesticide carbaryl was used on mudflats to exterminate burrowing shrimp. While less toxic methods are currently used, it is important for the oyster industry to understand the population and age of burrowing shrimp in the ecosystem. This article reports on a new method of aging the shrimp population and estimating its mortality using the cellular waste product lipofuscin and reports on implications of varying levels of burrowing shrimp populations.
Keywords: age composition; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Idaho Flats; mathematical modeling; mortality; population biology; Yaquina Bay

Big Fishery, Big Data, and Little Crabs: Using a Genomic Approach to Examine Larval Recruitment Patterns of Dungeness Crab (Cancer magister) in the California Current Ecosystem - Lee, Elizabeth M. J. (Oregon State University, 2019)
The California Current Ecosystem is a highly productive area of offshore waters extending from southern California to southern British Columbia. Its most valuable commodity is the Dungeness crab. The Dungeness crab fishery is by far the most valuable fishery on the North American west coast. Intensive study of Dungeness crabs in Coos Bay indicates that ocean conditions affect the number of surviving larval crabs (megalopae) and their distribution. In this Master’s thesis, the author reports on studies of larval crabs in 2014, 1017 and 2018 in Coos Bay and Yaquina Bay. The author’s aim was “was to better understand how ocean conditions influence larval transport and the ultimate population connectivity of the Dungeness crab within and between the marine ecosystems along the west coast of North America: the California Current Ecosystem (CCE), the Salish Sea Ecosystem (SSE), and the Gulf of Alaska Ecosystem (GOA)” (from the Abstract). By better understanding genetics, researchers will better understand population connectivity, an important part of species’ resilience in a time of climate change. The major professor was Kathleen G. O'Malley.
Keywords: aquatic invertebrates; California Current; Coos Bay; crustaceans; Dungeness crab = Metacarcinus magister (Cancer magister); genetics; larvae; population biology; Yaquina Bay

Environmental and morphologic controls on wave-induced dune response - Cohn, Nicholas; Ruggiero, Peter; García-Medina, Gabriel; Anderson, Dylan; Serafina, Katherine A.; Reuben Biel, Reuben (Geomorphology, 2019)
“Coastal erosion poses a major threat to coastal communities by limiting beach access, endangering backshore infrastructure, and impacting ecologically important environments. The preservation of coastal foredunes, features which provide the first line of defense for liiting backshore flooding is of particular interest as a valuable form of green infrastructure…” (p.108) In this paper, the authors examine factors affecting dune growth and erosion. They compare three different sites on the Northwest Coast: Oysterville, the Netarts Littoral Cell and South Beach. Field observations were supplemented with a modeling program, and the combination of the two has led to new insights.
Keywords: Cape Lookout; climate; coastal dunes; coastal hazards; erosion; mathematical modeling; Netarts Littoral Cell; Oysterville (Wa.); sea level; South Beach; wave height; Yaquina Bay

Evaluation of a Habitat Suitability Model to predict the geospatial distribution of Olympia oyster presence in Yaquina Bay, Oregon - Bohlen, Victoria L. (Oregon State University, 2019)
This intriguing Capstone Project report takes the place of a Masters thesis. In this work, the author explores Habitat Suitability Modeling, a way to predict how wild Yaquina oysters are distributed through understanding their environmental requirements. “This project evaluates the use of an HSM, developed using geospatial raster layers of salinity, substrate, and elevation, in Yaquina Bay, Oregon to predict locations of Olympia oyster presence. This study was unable to make a conclusive determination regarding the predictive capacity of the HSM due to a small number of field samples. Recommendations are provided for expanding the HSM and supporting several other management applications, including characterizing the abiotic and biotic attributes of the habitat occupied by Olympia oysters and identifying biological monitoring sites” (from the Abstract). Colored maps. The major professor was Steven S. Rumrill.
Keywords: aquatic invertebrates; bivalves; Craigie Point; depleted populations; geographical distribution; habitats; mathematical modeling; McClean Point; mollusks; Olympia oyster=Ostrea lurida (Ostrea conchaphila); oysters; The Bend; Yaquina Bay

Evidence for regional‐scale controls on eelgrass (Zostera marina) and mesograzer community structure in upwelling‐influenced estuaries - Hayduk, Jennifer L.; Hacker, Sally D.; Henderson, Jeremy S.; Tomas, Fiona (Limnology and Oceanography, 2019)
“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–summer season to examine the role of multiple scales in structuring these communities.” (from the Abstract) Suppplementary material in a separate file accompanies this article.
Keywords: algae; community ecology; Coos Bay; eelgrass = Zostera marina; eutrophication; fish; Grazing; Netarts Bay; primary production; Ulva spp.; upwelling; Yaquina Bay

The Influence of Microbial Communities on Spatiotemporal Elemental Cycling in Coastal Margins Revealed by Community- and Population-level Genomics and Proteomics - Kieft, Brandon P. (Oregon State University, 2019)
If we want to understand carbon and nutrient cycling in our rivers and on our coastal margins, then we need to understand what is happening at the smallest levels, i.e., with microbes. This masterful doctoral dissertation examines the roles microbes play in carbon and nutrient cycling in Yaquina Bay, the Yaquina River plume, and nearby coastal margins. The author generated and interpreted several datasets for this work. The major professor was Ryan S. Mueller.
Keywords: bacteria; carbon; Microbes; nitrogen; nutrient cycles; Phages; Yaquina Bay; Yaquina River

PSU researchers find suspected microplastics in Oregon oysters - Woods, Tiffany (Confluence, 2019)
In April and July, 2017, Britta Baechler, a Portland State University doctoral student, purchased Pacific oysters each from six different oyster growers on Oregon’s Pacific coast. Out of the 120 oysters, she found on average 11 suspected microplastics, mostly tiny fibers, per oyster. The data is preliminary, pending analysis of the microparticles, but the implications of a world awash in plastic, are disturbing.
Keywords: aquatic invertebrates; bivalves; Coos Bay; human impacts; molluscs; Netarts Bay; North Bend (Or.); Pacific oyster = Crassostrea gigas; Plastic; pollution; Tillamook Bay; Umpqua River estuary; Winchester Bay; Yaquina Bay

The Yaquina estuary and Its inhabitants - Gleason, Barbara (ORESU-H, 2019)
This field guide covers the flora and fauna you may see along the one-mile Yaquina Estuary nature trail. The trailhead is on the east side of the Visitor Center at the Hatfield Marine Science Center in Newport, Oregon. It was originally published 1999; revised 2019.
Keywords: aquatic invertebrates; birds; crustaceans; eelgrass = Zostera marina; Field guide; fish; habitats; Hatfield Marine Science Center; mollusks; salt marsh; terrestrial plants; tidelands; Yaquina Bay

Characterizing the adherence profiles of virulent Vibrio parahaemolyticus isolates - Aagesen, Alisha M.; Phuvaste, Sureerat; Su, Yi-Cheng; Hase, Claudia C. (Microbial Ecology, 2018)
Vibrio parahaemolyticus is a pathogen associated with shellfish poisoning caused by eating raw or undercooked oysters. Depuration is a standard method for making shellfish safe by placing live animals in clean seawater in order to reduce bacterial contaminants. Unfortunately, it is not very effective at removing this organism. Thus, it is important to understand how V. parahaemolyticus is associated with oysters. This article examines how Vibrios colonize surfaces. Eight different strains were examined to see how they adhered to surfaces, to see if motility could predict persistence in oyster tissues, and to see if examining genetic differences could provide insights. The authors observed “that the motility phenotype of a strain appeared to be a better indicator for persistence in the oyster.”
Keywords: bivalves; molluscs; motility; Oregon Oyster Farms; shellfish poisoning; Vibrio = Vibrio parahaemolyticus; Willapa Bay; Yaquina Bay

Comparison of Habitat Restoration and Enhancement Methods for Olympia Oysters (Ostrea lurida) in Yaquina Bay, Oregon - Law, Karen H. (Oregon State University, 2018)
The native Olympia oyster played an important role in the history and pre-history of Yaquina Bay, from sustaining Native Americans to providing an economic incentive for the development of the town of Newport. Due to pollution and over-fishing, the Olympia oyster came close to disappearing from Yaquina Bay. Now, thanks to restoration efforts, the delicious mollusk is back. This Master’s thesis explores three methods of encouraging juvenile Olympia oyster settlement. “To determine the efficacy of different methods of oyster habitat restoration methods in enhancing juvenile life history traits, this study compared the settlement, growth, and mortality of wild juvenile Olympia oysters among three shell treatments: (1) bagged shells and (2) loose shells, which are commonly used methods of oyster habitat restoration, and (3) rafted-line shells . . . “ (from the Abstract) William C. Hanshumaker was the major professor.
Keywords: aquaculture; aquatic invertebrates; bivalves; habitat restoration; mollusks; natural resource management; Olympia oyster=Ostrea lurida (Ostrea conchaphila); Oregon Oyster Farm; oysters; Oysterville; population biology; Yaquina Bay

Ecological Effects of Tide Gate Upgrade or Removal: A Literature Review and Knowledge Synthesis - Souder, Jon A.; Tomaro, Londi M.; Giannico, Guillermo R.; Behan, Jeff R. (Institute for Natural Resources, Oregon State University, 2018)
“This document reports on findings, conclusions and recommendations derived from scientific literature and knowledge regarding the effectiveness of tide gate removal or upgrade in improving conditions for Oregon’s native migratory fish species, particularly salmonids, and other plant and animal species that utilize estuarine ecosystems. The project was commissioned by the Oregon Watershed Enhancement Board (OWEB) to foster better understanding of the effectiveness of their past investments in estuary habitat restoration involving tide gates, and to aid in targeting future investments. This will be especially important because many less-complicated projects (e.g. those on public land, smaller, single-action projects, those with consensus on land use) have already been completed, and restoration efforts are becoming increasingly complex and resource intensive” (from the Executive Summary).
Keywords: Bandon Marsh; Coho salmon = Oncorhynchus kisutch; Columbia River estuary; Coos Bay; depleted populations; dike removal; environmental law and policy; fish passage; flooding; human impacts; Little Nestucca River; Nehalem River; Pacific salmonids = Oncorhynchus spp.; salinity; Salmon River Estuary; Siletz Bay; Siuslaw River; Tidal channels; Tide gates; Tillamook Bay; water temperature; wetland restoration; Yaquina Bay

Effects of microtopographic variation and macroalgal cover on morphometrics and survival of the annual form of eelgrass (Zostera marina) - Nelson, Walter G.; Sullivan, Gary (Aquatic Botany, 2018)
The native eelgrass, Zostera marina, plays a vital role in estuaries, sheltering and providing food for many estuarine inhabitants. The species has both annual and perennial life cycles. This paper reports on a population of the annual form of the seagrass. Minor differences in topography, amounting to only a few centimeters in elevation, had large effects on this population: lower plants were more abundant, had more shoots per plant and more general biomass than the plants on higher elevations. Desiccation effects in higher elevations were suggested to be less significant than competition from macroalgae.This article is available from the authors via ResearchGate.
Keywords: aquatic vegetation; community ecology; decomposition; eelgrass = Zostera marina; green algae; Hatfield Marine Science Center; Idaho Flats; life history information; species composition; sulfides; Ulva species = Ulva spp.; Yaquina Bay; zonal distribution

Environmental controls of oyster-pathogenic Vibrio spp. In Oregon estuaries and a shellfish hatchery - Gradoville, Mary R.; Crump, Byron C.; Hase, Claudia C.; White, Angelicque E. (Applied and Environmental Microbiology, 2018)
Vibrio species present huge problems for oyster hatcheries. They can cause foodborne illnesses, and some species kill shellfish. This article gives the result of a study of the presence of Vibrios in Netarts Bay, Yaquina Bay and the Whiskey Creek Shellfish Hatchery in Netarts Bay. Efforts to reduce Vibrio species at the hatchery are described. These efforts met with success with many species, but not with regard to Vibrio coralliilyticus, a pathogen that kills larval oysters. Conditions in Netarts Bay that may favor this particular species are described. This is an open-access article.
Keywords: aquaculture; bacteria; genetics; Hatfield Marine Science Center; molecular biology; Netarts Bay; Vibrio = Vibrio coralliilyticus; Vibrio spp.; Whiskey Creek Shellfish Hatchery; Yaquina Bay

An evaluation of factors controlling the abundance of epiphytes on Zostera marina along an estuarine gradient in Yaquina Bay, Oregon, USA - Nelson, Walter G. (Aquatic Botany, 2018)
In layperson’s terms, epiphytes are plants that grow on other plants. Epiphytes growing on seagrass leaves increase productivity and add food for grazers to the ecosystem. Too many epiphytes, however, shade the host seagrass and interfere with its ability to absorb sunlight. This article reports on a 4-year study of seagrass epiphytes in the lower intertidal of Yaquina Bay, contrasting marine and riverine environments and dry and wet seasons.
Keywords: Epiphytes; molluscs; nitrogen; nutrients; phosphorus; seagrass = Zostera marina; Yaquina Bay

Genetic by environment interactions for harvest traits of the Pacific oyster Crassostrea gigas (Thunberg) across different environments on the West Coast, USA - RodriguesDeMelo, Claudio Manoel; Morvezen, Romain; Durland, Evan; Langdon, Christopher J. (Journal of Shellfish Research, 2018)
Oyster growers in the Pacific Northwest operate under a wide range of environmental conditions, from the sedate waters of Puget Sound to the dynamic coastal seas. How can Pacific oysters be bred to increase yields in such different conditions? This article describes a study of oysters grown in nine different test localities, describes the test results and outlines a strategy for increasing yield while maintaining genetic diversity.
Keywords: aquaculture; aquatic invertebrates; bivalves; Dabob Bay (Wa.); genetics; hypoxia; Molluscan Broodstock Program; molluscs; Netarts Bay; ocean acidification; Oyster Bay (Wa.); Pacific oyster = Crassostrea gigas; salinity; Sequim Bay (Wa.); Thorndyke Bay (Wa.); Totten Inlet (Wa.); Westcott Bay (Wa.); Willapa Bay (Wa.); Yaquina Bay

HMSC high tide lesson plan: Salinity in the estuary - Carroll, Lindsa (ORESU-E, 2018)
This lesson plan introduces students to the concepts of salinity and density. In this lesson students create and test a hypothesis about how the distance from the mouth of an estuary influences salinity levels.
Keywords: estuarine dynamics; geography; Hatfield Marine Science Center; Lesson plan; salinity; tidal data; tides; Yaquina Bay

Recovery Plan for the Southern Distinct Population Segment of North American Green Sturgeon (Acipenser medirostris) - U.S. National Marine Fisheries Service. (National Marine Fisheries Service, 2018)
The Umpqua and Yaquina River estuaries are among those coastal bays and estuaries that host seasonal populations of green sturgeon, with the population peaking in summer and autumn. While the Umpqua and Yaquina River sturgeon are not the main focus of this publication, this document does make a number of points about problems these populations face, and the need for more information. Issues include: competition from invasive species such as smallmouth bass, climate change, ocean acidification, increased stream temperatures, dredging and sedimentation.
Keywords: climate; Columbia River; Coos Bay; dredging; environmental law and policy; Green sturgeon = Acipenser medirostris; habitats; introduced species; Nehalem Bay; reproductive behavior; sediments; Umpqua River estuary; water quality; water temperature; Winchester Bay; Yaquina Bay

Recruitment ecology of burrowing shrimps in US Pacific Coast estuaries - Dumbauld, Brett R.; Bosley, Katelyn M. (Estuaries and Coasts, 2018)
“A series of surveys were undertaken to characterize recruitment and post-settlement processes for two species of burrowing shrimps, Neotrypaea californiensis and Upogebia pugettensis in order to determine how they influenced broader adult populations in US west coast estuaries. . . Patterns in strong recruitment years amongst estuaries, particularly for U. pugettensis, suggest the presence of multi-estuary metapopulations linked via larval dispersal. These results have important implications for shrimp population management including control for shellfish aquaculture, but also conservation of estuarine habitats due to the strong influence of these ecosystem engineers on the benthic community.” (from the Abstract)
Keywords: ecosystem engineer; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); larvae; Mud shrimp = Upogebia pugettensis; population biology; settlement; Willapa Bay; Yaquina Bay

Status of the European Green Crab, Carcinus maenas, in Oregon and Washington coastal Estuaries in 2017 - Yamada, Sylvia Behrens; Yednock, Bree; Indivero, Julia; Geierman, Christina; Prickett, Joel A.; Randall, Andrea; Akmajian, Adrianne (Pacific States Marine Fisheries Commission. Aquatic Nuisance Species Project, 2018)
The invasive European green crab is a voracious predator of bivalve molluscs, small crustaceans and other organisms. It has been present in Oregon since the late 1990s. The population grows when winter waters are warm, as they are during El Niños. “Prior to 2015, green crabs were too rare to exert measurable effects on the native benthic community and on shellfish culture in Oregon and Washington. Following the recent strong El Niño, however, we documented the arrival of three strong year classes in 2015, 2016 and 2017. Average catch rates in over the last three years steadily increased from 0.5 to 0.8 and to 1.9 crabs per trap. These catches are much higher than in any of the previous years, including 1998. Since green crabs live for 6 years, these three consecutive year classes will provide larvae until 2023. A switch to cooler ocean conditions in the coming years will result in poor recruitment, but a return to high PDO and strong El Niño patterns would signal good recruitment and higher green crab densities.” (from the Executive Summary) Coos Bay, in particular, has experienced shocking growth of this population, going from 9 crabs captured in 2002 to 1,653 crabs captured in 2017. This report is accompanied by a dataset, available at: https://ir.library.oregonstate.edu/concern/datasets/rn3016632
Keywords: Alsea Bay; aquatic invertebrates; Boat ramp (Netarts); Coos Bay; Coquille River estuary; crustaceans; El Nino; European green crab = Carcinus maenas; Grays Harbor (Wa.); Hatfield Marine Science Center; introduced species; Johnson’s Slough (Yaquina); Makah Bay (Wa.); Nehalem Bay; Netarts Bay; North of Nevor Shellfish (Netarts); Oregon Coast Aquarium mudflat; Pacific Decadal Oscillation; population count; Sally’s Bend; Tillamook Bay; Whiskey Creek Salmon Hatchery; Willapa Bay (Wa.); Yaquina Bay

Demographic and genetic connectivity: the role and consequences of reproduction, dispersal and recruitment in seagrasses - Kendrick, Gary A.; Orth, Robert J.; Statton, John; Hovey, Renae; Ruiz Montoya, Leonardo; Lowe, Ryan J.; Krauss, Siegfried L.; Sinclair, Elizabeth A. (Biological Reviews, 2017)
The valuable ecological roles provided by seagrasses are well known. Population connectivity in seagrasses, however, is less well understood. “Accurate estimation of connectivity among populations is fundamental for determining the drivers of population resilience, genetic diversity, adaptation and speciation” (from the Abstract). This article provides a review about what is known about this aspect of seagrass ecology around the world, and includes a study of eelgrass in Yaquina Bay. The authors point out what is known, gaps in knowledge, and potential directions for future research.
Keywords: aquatic vegetation; eelgrass = Zostera marina; genetics; recruitment; reproductive biology; Yaquina Bay

Effect of green macroalgal blooms on the behavior, growth, and survival of cockles (Clinocardium nuttallii) in Pacific NW estuaries - Lewis, Nathaniel S.; DeWitt, Theodore H. (Marine Ecology Progress Series, 2017)
This paper examines the effects of algal blooms in Yaquina Bay on a population of cockle clams. Sediment under algal mats lacks dissolved oxygen, and decomposing algae release chemical compounds that affect the clams. The authors found that macroalgal mats caused cockles to emerge from sediment, and to move away from the algae. Clams atop the sediment were stressed, vulnerable to predation and particularly vulnerable to temperature stress. “Regardless of nutrient source, our research demonstrates that macroalgal mats pose a threat to the growth and survival of these intertidal bivalves” (p.118). The online link includes access to supplemental videos illustration aspects of the cockle's biology.
Keywords: aquatic invertebrates; behavior; bivalves; Cockle clam = Clinocardium nuttallii; green algae; Hatfield Marine Science Center; Idaho Flats; Idaho Point (Hinton Point); molluscs; predation; seagulls = Larus spp.; Yaquina Bay

Human Dimensions of Climate Change in Coastal Oregon - Hoelting, Kristin; Burkardt, Nina (OCS Study BOEM, 2017)
An attractive climate relative to the rest of the state and nation draws more people to the Oregon Coast. Longer, drier summers bring more tourists, more forest fires and less available freshwater. Heavier winter rains bring more flooding and erosion events. Higher water temperatures cause the ranges of animals (terrestrial and aquatic) to change, increase toxic algae blooms, kill salmon and stress Dungeness crabs. Increasing ocean acidity stresses shellfish. More intense winter storms and higher sea levels threaten infrastructure. These are some of the consequences of climate change outlined in this excellent report. One of the more valuable aspects of this comprehensive look at climate change in our area is extensive quotations from local residents. Good information on the Coos Bay and Newport areas. This report is highly recommended.
Keywords: climate; coastal hazards; commercial fisheries; Coos Bay; demographics; ecosystem modeling; general; general ecosystem health; human impacts; ocean acidification; precipitation; sea levels; water temperature; Yaquina Bay

Investigation of Crangon species assemblage and spawning patterns in Yaquina Bay, OR [PowerPoint Presentation] - Danilchik, Nikolai M.; Loewenherz, Larkin (Oregon State University, 2017)
This PowerPoint presentation was part of a final project for the undergraduate class Biology 450, Marine Biology. The authors examined the distribution of four species of shrimp in different environments: in the main channel of Yaquina Bay, on a nearby beach, and offshore. The bay shrimp was the most prevalent species in the bay, while the Alaskan bay shrimp dominated offshore. The authors endeavored to learn where the most gravid Alaskan bay shrimp females were to be found, but found no difference in the percentage of gravid females between channel and offshore habitats, which raises the questions, where do they spawn? and is salinity a predictor of gravidity in Crangon females? More research is needed.
Keywords: Alaskan bay shrimp = Crangon alaskensis; Bay shrimp = Crangon franciscorum; fecundity; geographical distribution; Main channel; Smooth bay shrimp = Crangon stylirostris; species composition; Stout shrimp = Crangon alba; Yaquina Bay

The limitation of spread of non-native marine invertebrates from artificial structures to natural habitats [poster] - McClees, Whitney; de Rivera, Catherine (ESM Colloquium, 2017)
Human activities can cause invasive species to be introduced into estuaries, and anthropogenic structures can give them niches where they can establish themselves in new environments. In this poster, the authors explore the invasion risk inside and outside a marina that has been colonized with non-native species. 84 settling tiles were placed inside and outside a marina, and given different treatments. There was much higher species diversity inside the marina than outside. The authors suggest that a combination of predation outside the marina, along with dispersal, is responsible for this difference.
Keywords: benthos; community ecology; Embarcadero Marina; geographic distribution; human impacts; introduced species; predation; species composition; Yaquina Bay

Modeling Sea Level Rise Impacts to Oregon's Tidal Wetlands: Maps and Prioritization Tools to Help Plan for Habitat Conservation into the Future - Brophy, Laura S.; Ewald, Michael J. (Institute for Applied Ecology. Estuary Technical Group, 2017)
This study tracks possible conditions for Oregon coastal wetlands under six possible sea level rise scenarios between 2017 and 2160. “If tidal wetland plant communities are unable to survive the increased inundation associated with sea level rise, they will have to move to higher ground through dispersal of seeds, roots, or rhizomes. This process is called "landward migration," and the areas that could become future tidal wetlands are called “landward migration zones” (LMZs) in this study.” (p.5) Potential landward migration zones are mapped. Maps, charts, color photographs. This document is accompanied by maps, a PowerPoint presentation, a file of geospatial data, and a poster. “Prepared for: MidCoast Watersheds Council, Newport, Oregon.” “With assistance from: Fran Recht, Pacific States Marine Fisheries Commission.”
Keywords: Alsea Bay; Beaver Creek; climate; habitats; human impacts; Netarts Bay; salinity; Salmon River Estuary; sea level; Siletz Bay; Siuslaw River estuary; Umpqua River estuary; wetland vegetation; wetlands; Yachats River estuary; Yaquina Bay

Response of primary producer communities to short-term nutrient additions in a Pacific Northwest estuarine tidal wetland - Weilhoefer, C. L.; Jakstis, K.; Fischer, C. (Wetlands, 2017)
As populations in the Pacific Northwest continue to increase, our wetlands are likely to have to absorb more nutrients from increased human activity. This article explains a study of a wetland in the lower Yaquina Bay that was subjected to three different treatments of increased nitrogen, increased phosphorus, and increased nitrogen and phosphorus. Nutrient levels were selected to mimic projected nutrient loads impacted by human activity. This study is unique in that it addresses both changes in terrestrial vegetation as well as changes in algae in wetland sediments. This is important because, “Benthic macroalgae, particularly diatoms, are the preferred food source of invertebrates and fish in these ecosystems” (p.694). This is a most interesting exploration of complex ecological relationships. A copy of the article may be obtained by writing the authors on ResearchGate.
Keywords: diatoms; human impacts; nitrogen; nutrient cycles; phosphorus; Saltgrass = Distichlis spicate; Seaside arrowgrass = Triglochin maritima; sediments; wetland vegetation; Yaquina Bay

Trends in the Pacific herring (Clupea pallasii) metapopulation in the California Current Ecosystem - Thompson, Sarah Ann; Sydeman, William J.; Thayer, Julie A.; Weinstein, Anna; Krieger, Katherine L.; Hay, Doug (California Cooperative Oceanic Fisheries Investigations, Progress Report, 2017)
This paper examines population trends for Pacific herring on the West Coast. The authors find that overall populations have been declining since the 1980s, although there are areas such as Yaquina Bay that have not seen large declines. The data hints at cyclic fluctuations in population, but more study is needed. “We do not understand the drivers of changes occurring in the herring metapopulation, nor have the consequences to upper trophic levels in this marine ecosystem been investigated comprehensively. Expansion of current monitoring and new directed research on relationships between herring and the environment and higher level consumers is therefore warranted and essential.” (p.11)
Keywords: abundance; climate; depleted populations; geographic distribution; Pacific Decadal Oscillation; Pacific herring = Clupea pallasii; population biology; statistical analysis; Yaquina Bay

Were they all giants? Perspectives on late Holocene plate-boundary earthquakes at the northern end of the Cascadia subduction zone - Hutchinson, Ian; Clague, John J. (Quaternary Science Reviews, 2017)
While this article is focused on the northern end of the Cascadia Subduction Zone, it offers an up-to-date look at research on prehistoric tsunamis on the West Coast. The authors attempt to match buried soils in southwest Washington that show seven different tsunamis with evidence on Vancouver Island. They also note what can be correlated with earthquake evidence from the entire subduction zone. The authors found that three earthquakes were definitely caused by a rupture of the entire plate margin. Three other earthquakes left tsunami evidence in the north, but the deposited soils have not yet been accurately dated. One earthquake seems to have taken place in the north, but is not well correlated in the south, indicating a possible partial plate rupture.
Keywords: coastal hazards; Coos Bay; earthquakes; Ecola Creek; geology; Lagoon Creek; Nestucca Bay; Netarts Bay; paleosciences; Talbot Creek (Coos Bay); tsunamis; turbedites; Vancouver Island; Washington (State); Yaquina Bay

Characterization of ecosystem structure within transplanted and natural eelgrass (Zostera marina) beds - Lewis, Nathaniel S.; Henkel, Sarah K. (Northwest Science, 2016)
The native seagrass Zostera marina plays a vital role in Oregon estuaries, producing oxygen and providing valuable habitat for many species. In 2010, NOAA moved its Marine Operations Center – Pacific to Newport, Oregon. It was necessary to dredge the bay to put in new docks for NOAA research vessels, and in the process a .68 acre eelgrass bed was destroyed. In order to mitigate this damage, the original eelgrass was replanted in a new site. In this paper, the authors report on the results of the transplantation, noting ecological diversity, sediment characteristic and species abundance throughout the year.
Keywords: ecosystem health; eelgrass = Zostera marina; geographical distribution; habitat restoration; habitats; Hatfield Marine Science Center; Port of Newport; sediments; species composition; species list; temporal distribution; tides; Yaquina Bay

The demographic consequences of growing older and bigger in oyster populations - Moore, Jacob L.; Lipcius, Romuald N.; Puckett, Brandon; Schreiber, Sebastian J. (Ecological Applications, 2016)
Modeling populations of marine animals, particularly animals that reproduce through broadcast spawning, is . . . complicated. In the case of oysters, there is great variation between size and age. For example, larger female oysters can hold more eggs and produce many more young than smaller females, but despite their difference in size, they can be the same age. Older oysters are more susceptible to disease, while younger oysters are more vulnerable to predation. Thus, a good population model must take both age and size into account. “To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age-and size structured IPM, using a population of Crassostrea gigas oysters in the northeastern Pacific Ocean” (from the Abstract).
Keywords: age composition; aquaculture; bivalves; demographics; fecundity; growth; Hatfield Marine Science Center; mathematical modeling; Molluscan Broodstock Program; molluscs; oysters; Pacific oyster = Crassostrea gigas; population biology; recruitment; Yaquina Bay

Ecophysiology of Marine Bivalves: Physiological Rate Processes in Dynamic Environments - Gray, Matthew W. (Oregon State University, 2016)
The five chapters of this doctoral dissertation address a wide range of issues related to the cultivation of bivalves. Much of the work is concerned with bivalve feeding and ecosystem services in adult and larval bivalves. There are interesting comparisons between the feeding behavior of the native Olympic oyster and the introduced Pacific oyster. The effects of ocean acidification on feeding physiology are also explored. Major professor was Christopher J. Langdon.
Keywords: aquaculture; aquatic invertebrates; bivalves; calcium carbonate; digestion; ecosystem modeling; estuarine dynamics; filtration; Hatfield Marine Science Center; larvae; Mediterranean mussel = Mytilus galloprovincialis; molluscs; ocean acidification; Olympia oyster=Ostrea lurida (Ostrea conchaphila); Oregon Oyster Farms; Pacific oyster = Crassostrea gigas; physiology; theses; Yaquina Bay

Effect of climate change on water temperature and attainment of water temperature criteria in the Yaquina Estuary, Oregon (USA) - Brown, Cheryl A.; Sharp, Darrin; Mochon Collura, T. Chris (Estuarine, Coastal and Shelf Science, 2016)
This paper examines the effects of climate change, which is predicted to cause warmer air temperatures and higher sea levels on the Yaquina Estuary. “Temperature is the most common cause of water quality impairments in Oregon coastal streams and estuaries (US EPA, 2006) and climate change is likely to increase the frequency and duration of these water quality impairments.” (p.137) Data for this study was gathered from 2000-2004 and supplemented by historical data from 1970-2010. The data was used to model changes in the estuary based on projected sea level rises of 0-90 cm and projected air temperature increases of 0-4° C to show potential changes from the present to the year 2100. The upper estuary was shown to be the most vulnerable to climate change. Rising sea level, a factor not considered in previous studies, may moderate the effect of climate change on the lower estuary.
Keywords: Blodgett (Or.); Chitwood (Or.); climate; Elk City (Or.); Elk Creek; Hatfield Marine Science Center; mathematical modeling; Newport (Or.); sea level; Toledo (Or.); water quality; water temperature; Yaquina Bay; Yaquina River

The Effects of Artificial Structures on Estuarine Infaunal Communities and Offshore Biofouling Communities - Mendoza, Maritza (Oregon State University, 2016)
One promising source of renewable energy now being studied on the Oregon Coast is wave energy. The artificial structures used to generate wave energy will necessarily affect the marine environment and the plants and animals that live near them. In this thesis, the author investigates “the spatial effect of artificial structures on the surrounding infaunal communities in an estuarine environment after the artificial structures have been in the water for 8 years.” The artificial structures were deployed in soft sediments in Yaquina Bay. The author also sought “[t]o identify and quantify the biofouling communities present on offshore surface and bottom artificial structures after a period of two years.” Good discussion of issues, possible applications of this research and areas where more research is needed. The major professor was Sarah K. Henkel.
Keywords: algae; aquatic invertebrates; biofouling; breakwater; habitats; human impacts; Idaho Flats; industrial development; sediments; Yaquina Bay

Genomic and phylogenetic analysis of Ceramium cimbricum (Ceramiales, Rhodophyta) from the Atlantic and Pacific Oceans supports the naming of a new invasive Pacific entity Ceramium sungminbooi sp. Nov. - Hughey, Jeffery R.; Boo, Ga Hun (Botanica Marina, 2016)
The flow of introduced species across the Pacific Ocean is from East to West. That is, most introduced species on the U.S. West Coast come from Asia. This is true in the case of Ceramium sungminbooi, a red alga from Korea. This article describes the distinction between the Asian type of Ceramium as opposed to the European species, Ceramium cimbricum and calls for the Asian species now on the American West Coast to be recognized as a new species. “It is unknown whether C. sungminbooi was introduced to Oregon as a result of oyster mariculture or if it was hull-borne.” (p.219) Free access to an ahead-of-print version of this article is available.
Keywords: aquatic vegetation; Coos Bay; genetics; Hatfield Marine Science Center; introduced species; new species description; red algae; taxonomy; Yaquina Bay

Hatfield Marine Science Center Dynamic Revetment Project DSL permit # 45455-FP: Final Monitoring Report February, 2016 - Cowen, Robert; Nelson, Walt; Arbuckle, Scarlett; Folger, Christina; Allan, Jonathan; Heppell Laboratory, (Oregon State University. Hatfield Marine Science Center,, 2016)
This is the fifth and final document in a series of five annual reports concerning control of severe erosion along Yaquina Bay next to the Hatfield Marine Science Center. Parts of the shoreline were stabilized in 2007 and 2011. Severe erosion in the unmodified Reference area led to extension of the dynamic revetment into the Reference area in 2015. The 2015 work “has largely stabilized shoreline erosion within the project area” (p.32). Concerns remain about the need for more gravel and high-water events, including king tides. Aerial photograph, color photographs.
Keywords: amphipods; aquatic invertebrates; beaches; benthos; coastal hazards; erosion; fish; Hatfield Marine Science Center; Pacific staghorn sculpin = Leptocottus armatus; physical; Shiner perch = Cymatogaster aggregate; species list; terrestrial vegetation; wave height data; Whitebait smelt = Allosmerus elongates; Yaquina Bay

An Integrated Approach to the Investigation of Age, Growth and Population Dynamics of Burrowing Thalassinidean Shrimps in a U.S. West Coast Estuary - Bosley, Katelyn Marie (Oregon State University, 2016)
“Two indigenous species of burrowing shrimp inhabit and often dominate the intertidal zone of estuaries along the US West Coast, the ghost shrimp, Neotrypaea californiensis, and the blue mud shrimp, Upogebia pugettensis. Both species are considered ecosystem engineers and play a role in maintaining estuarine health and ecosystem function. They also have a negative interaction with oyster production in Pacific Northwest (PNW) estuaries, which has necessitated a better understanding of their ecology and population dynamics in order to try to manage their impacts” (from the Abstract). Laboratory and field experiments explored growth and aging in the two species, and population simulations explored shrimp density. Co-major professors were Christopher J. Langdon and Brett R. Dumbauld.
Keywords: age composition; crustaceans; decapods; geographic distribution; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Hatfield Marine Science Center; Idaho Flats; mathematical modeling; Mud shrimp = Upogebia pugettensis; Oysterville; population biology; Raccoon Flat; Sally’s Bend; Seawall Island; Tongue Island; Yaquina Bay

Juvenile Rockfish (Sebastes spp.) Community Composition and Habitat use of Yaquina Bay, Oregon - Lindsley, Amy J (Oregon State University, 2016)
Estuaries offer important habitats for many species of fish. Rockfish are among the fishes that use estuaries as nurseries for their young. In recent years, most West Coast estuaries have undergone extensive development. How has human-caused environmental change affected fish habitats? In this thesis, the author explored Yaquina Bay to determine what species of rockfish were in Yaquina Bay, studied how rockfish abundance changed with the seasons, and contrasted the use of natural habitat (eelgrass beds) with anthropogenic habitat (piers). Several previously undocumented species of rockfish were found to use the bay, and patterns of juvenile rockfish use of the estuary are shown. Valuable new information on important species is presented. Major professor was Scott Heppell.
Keywords: Black rockfish = Sebastes melanops; Bocaccio rockfish = Sebastes paucispinis; Brown rockfish = Sebastes auriculatus; Canary rockfish = Sebastes pinniger; China rockfish = Sebastes nebulosus; community ecology; Copper rockfish = Sebastes caurinus; eelgrass = Zostera marina; fishes; geographic distribution; habitats; human impacts; juvenile fish; life history information; Quillback rockfish = Sebastes maliger; temporal abundance; temporal distribution; Yaquina Bay; yellowtail rockfish = Sebastes flavidus

A new species of Halolaelapidae (Acari: Mesostigmata: Rhodacaroidea) from beach wrack in Yaquina Bay, Oregon, USA, with comments on opisthonotal plasticity and cribral development in the family - Krantz, G. W. (Journal of Natural History, 2016)
This article describes a new species of mite, Halolaelaps hatfieldi, found in the summer of 2013 on decomposing sea lettuce ()Ulva)) and eelgrass in a backwater of Yaquina Bay near the Hatfield Marine Science Center. The species is described through different life phases and diagnostic characteristics are given. The author discusses certain anatomical features and hypotheses about their possible functions. The species is named after the Hatfield Marine Science Center.
Keywords: arthropods; eelgrass = Zostera marina; Halolaelaps hatfieldi; Hatfield Marine Science Center; morphology; taxonomy; Ulva species; Yaquina Bay

Buried alive: an invasive seagrass (Zostera japonica) changes its reproductive allocation in response to sediment disturbance - Henderson, Jeremy; Hacker, Sally D. (Marine Ecology Progress Series, 2015)
This paper examines how Japanese eelgrass responds to disturbances in its environment that result in increased sedimentation. The more sediment disturbance, the more likely the plants were to reproduce sexually, and produce seeds. “If disturbance increases sexual reproduction, it may facilitate the invasion by increasing propagule pressure and genetic diversity. This could create an increased likelihood that Z. japonica reaches new sites, and, as has been shown in other invasive grasses, could allow this species to successfully proliferate across a wider range of environmental conditions…” (p.135) Full-text of this article is available from the authors via ResearchGate.
Keywords: fecundity; germination. Introduced species; ghost shrimp = Neotrypaea californiensis; human impacts; Japanese eelgrass = Zostera japonica; King Slough; Oregon Oyster Farms; reproduction; Sally’s Bend; sediments; Yaquina Bay

Coastal flood hazard study, Lincoln County, Oregon - Allan, Jonathan C.; Ruggiero, Peter; Cohn, Nick; Garcia, Gabriel; O’Brien, Fletcher E.; Stimely, Laura L.; Roberts, Jed T. (Open-File Report (Oregon. Department of Geology and Mineral Industries), 2015)
This is a technical document giving the factors and assumptions behind the flood hazard study. There are some colored maps and discussions of some sites, but it does not give the final maps. “The objective of the Lincoln County coastal flood hazard project is to develop a digital flood insurance rate map (DFIRM) and flood insurance study (FIS) report for Lincoln County, Oregon. . . DOGAMI has been contracted to perform detailed coastal flood hazard studies for the entire length of the Lincoln County shoreline of the Pacific Ocean.…” (p.1)
Keywords: Alsea Bay; Alsea Spit; climate; coastal hazards; Depoe Bay; erosion; flooding; Fogarty Creek; geography; geology; Lincoln County (Or.); paleosciences; precipitation; Rocky Creek; Salmon River Estuary; Siletz Bay; Siletz Spit; Waldport (Or.); Whale Cove; Yachats (Or.); Yachats River; Yaquina Bay; Yaquina Head

Comparison of non-native dwarf eelgrass (Zostera japonica) and native eelgrass (Zostera marina) distributions in a northeast Pacific estuary: 1997-2014 - Young, David; Patrick J Clinton; Specht, David; Collura, T. Chris Mochon (Botanica Marina, 2015)
“In this study, we investigated the rate and pattern of expansion of a non-native eelgrass, Zostera japonica, in relation to the distribution of the native eelgrass Zostera marina in a coastal estuary of the northeastern Pacific Ocean. The distributions of the Zostera congeners were monitored between 1997 and 2014 in Yaquina Estuary on the central Oregon coast, USA, using digital classification of color infrared aerial photographs and ground surveys.” (from the Abstract) This is an open-access article.
Keywords: aquatic vegetation; eelgrass = Zostera marina; fecundity; introduced species; Japanese eelgrass = Zostera japonica; Yaquina Bay; Yaquina River Estuary; zonal distribution

Duration of temperature exposure controls growth of Zostera japonica: Implications for zonation and colonization - Kaldy, James E.; Shafer, Deborah J.; Magoun, A. Dale (Journal of Experimental Marine Biology and Ecology, 2015)
This study looks at the distinct zonation of the native eelgrass (Z. marina) and the introduced Japanese eelgrass (Z. japonica). None of the “usual suspects” (dessication tolerance, light limitation, interspecific competition) adequately explain the different estuarine zones occupied by the two species. The authors “hypothesize that differences in thermal optima may be responsible for the observed zonation patterns.” (p.68) This interesting paper has important implications for the possible future spread of Japanese eelgrass.
Keywords: eelgrass = Zostera marina; Idaho Point; introduced species; Japanese eelgrass = Zostera japonica; Sally’s Bend; temperature; Yaquina Bay; zonal distribution

Effects of temperature, salinity and seed age on induction of Zostera japonica germination in North America, USA - Kaldy, James E.; Shafer, Deborah J.; Ailstock, M. Stephen; Magoun, A. Dale (Aquatic Botany, 2015)
This paper examines seed germination in the invasive Japanese eelgrass. “Our results suggest that seasonal pulses of cold temperatures coupled with low salinity may stimulate Z. japonica seed germination. . . However, prolonged exposure to freshwater is likely to result in increased incidence of rotten seeds and poor subsequent seedling survival. Consequently, it would appear that optimum conditions for Z.japonica seed germination consist of cold temperature stratification with brief pulses of low salinity (<10) conditions followed by a gradual return to higher salinity conditions that favor the development of seedlings and adult plants. This is similar to estuarine salinity dynamics following significant storm events during the wet season in Oregon coastal systems.” (p.77-78)
Keywords: fecundity; germination. Introduced species; Japanese eelgrass = Zostera japonica; reproduction; salinity; water temperature; Yaquina Bay

An Experimental Investigation of the Effects of Temperature and Dissolved Oxygen on the Growth of Juvenile English Sole and Juvenile Dungeness Crab - Bancroft, Morgan P. (Oregon State University, 2015)
This M.S. thesis describes laboratory simulations of typical summer oceanographic conditions at Yaquina Bay and Moolack Beach, two nursery habitats used by juvenile English sole and Dungeness crab. Simulations explored effects of temperature and dissolved oxygen levels on the two species, particularly as related to upwelling-driven hypoxia. Young English sole were more resilient and were able to handle lower oxygen levels than Dungeness crabs. The author also describes an exhibit explaining hypoxia to the general public at the Hatfield Marine Science Center in Newport, Oregon. Major professor was Lorenzo Ciannelli.
Keywords: crustaceans; decapods; dissolved oxygen; Dungeness crab = Metacarcinus magister (Cancer magister); English sole = Parophrys vetulus; hypoxia; juvenile fish; Moolack Beach; theses; water temperature; Yaquina Bay

Hatfield Marine Science Center Dynamic Revetment Project DSL permit # 45455-FP: Monitoring Report, February 2015 - Cowen, Robert; Nelson, Walt; Arbuckle, Scarlett; Folger, Christina; Allan, Jonathan; Heppell Laboratory, (Oregon State University. Hatfield Marine Science Center,, 2015)
This is the fourth in a series of five annual reports concerning control of erosion along Yaquina Bay next to the Hatfield Marine Science Center. Parts of the shoreline were stabilized in 2007 and 2011. Before more dynamic revetments will be permitted, a five-year study of nearby unmodified shorelines is required. “Monitoring of beach profiles indicated that as of January 2015, the 2011 Dynamic Revetment Project (DRP) has generally successfully stabilized the shoreline in the project area. Beach profile data also indicated that the 2007 DRP continued to be successful in stabilizing further retreat of the shoreline. . . Rapid erosion has continued in the adjacent Reference beach area and over the period 2009-2015 has been as great as 11 m (36 ft).”(p.2) Aerial photograph, color photographs.
Keywords: amphipods; aquatic invertebrates; beaches; benthos; chum salmon = Oncorhynchus keta; coastal hazards; erosion; fish; Hatfield Marine Science Center; Pacific staghorn sculpin = Leptocottus armatus; physical; Shiner perch = Cymatogaster aggregate; species list; terrestrial vegetation; wave height data; Whitebait smelt = Allosmerus elongates; Yaquina Bay

A method to identify estuarine water quality exceedances associated with ocean conditions - Brown, Cheryl A.; Nelson, Walter G. (Environmental Monitoring and Assessment, 2015)
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 “to predict the probability of exceedance of a water quality threshold…” Yaquina Bay is used as the example, and remaining issues are discussed.
Keywords: chlorophyll; climate; dissolved oxygen; mathematical modeling; salinity; upwelling; water quality; water temperature; Yaquina Bay

Modeling lugworm irrigation behavior effects on sediment nitrogen cycling - Dornhoffer, T. M.; Waldbusser, G. G.; Meile, C. (Marine Ecology Progress Series, 2015)
“Benthic infauna in marine sediments have well-documented effects on biogeochemical cycling, from individual to ecosystem scales, including stimulation of nitrification and nitrogen removal via denitrification. However, the effects of burrowing depth and irrigation patterns on nitrogen cycling have not been as well described. Here we examined the effects of lugworm behavior on sediment nitrogen cycling…” (from the Abstract)
Keywords: annelids; aquatic invertebrates; bioturbation; denitrification; nitrogen; nutrient cycling; Pacific lugworm = Abarenicola pacifica; polychaete worms; sediments; Yaquina Bay

The Olympia oyster Ostrea lurida: recent advances in natural history, ecology, and restoration - Pritchard, Catharine; Shanks, Alan; Rimler, Rose; Oates, Mark; Rumrill, Steven S. (Journal of Shellfish Research, 2015)
This is an excellent review of the present state of knowledge about the Olympia oyster. Biology and restoration attempts are described.
Keywords: aquaculture; aquatic invertebrates; bivalves; Coos Bay; depleted populations; life history information; mollusks; Olympia oyster=Ostrea lurida (Ostrea conchaphila); San Francisco Bay; Tomales Bay; Willapa Bay; Yaquina Bay

P.I.B. Ping: A Kansan in 1880s Oregon - Summers, Lynn (Oregon Historical Quarterly, 2015)
This article describes the experiences of a Kansan working for the General Land Office in Oregon from 1882-1885. It contains a description of early work on the jetty at Yaquina Bay, and includes a photograph of the tramway by which rocks were hauled to form a jetty. “[We] were shown around, walked out on the tramway where the main work was going on, that of driving piling, the waves underneath dashing and throwing spray in every direction, and fairly shaking the very foundations of the earth as a swell comes in and breaks on striking the cause-way.” (p.121)
Keywords: bathymetry; harbors; historical; industrial development; jetties; navigation; ports; Yaquina Bay

Ports of Newport and Toledo, Lincoln County, Oregon - Oregon Department of Geology and Mineral Industries,; Oregon Emergency Management,,; Virginia Institute of Marine Science,; National Tsunami Hazard Mitigation Program (U.S.), (Oregon Maritime Tsunami Response Guidance, 2015)
Unless a boat is at sea, if there is a nearshore earthquake triggering a tsunami, there is no time for the owner to get the boat to safer waters. If the earthquake is distant, however, there will be a minimum of about 4 hours to move the boat offshore. This publication offers a thorough discussion of issues boat owners face, and what they should do. Colored maps, colored pictures.
Keywords: coastal hazards; earthquakes; harbors; Maritime transportation; Newport (Or.); Port of Newport; Port of Toledo; ports; Toledo (Or.); tsunamis; Yaquina Bay

A sea-level database for the Pacific coast of central North America - Engelhart, Simon E.; Vacchi, Matteo; Horton, Benjamin P.; Nelson, Alan R.; Kopp, Robert E. (Quaternary Science Reviews, 2015)
When the glaciers melted at the end of the last ice age, sea levels along the Pacific Coast of North America did not rise uniformly. Areas where the earth had been pressed down by the weight of glaciers saw relatively little sea level rise, as the land rebounded when the weight was removed. Sites further away from the great glaciers saw higher sea levels. In this paper, the authors describe a database of sea levels and reference points for the last 16,000 years in our area. Appendices give reference points, descriptions, and referenced publications. Interestingly, Alsea Bay in Appendix 1 is spelled “Alsey Bay.”
Keywords: Alsea Bay; Coos Bay; Coquille River; geology; Glaciation; Nehalem River; Nestucca Bay; Netarts Bay; paleosciences; Salmon River; sea level; Siletz Bay; Siuslaw River estuary; Yaquina Bay

Stratigraphic and microfossil evidence for a 4500-year history of Cascadia subduction zone earthquakes and tsunamis at Yaquina River estuary, Oregon, USA - Graehl, Nicholas A.; Kelsey, Harvey M.; Witter, Robert C.; Hemphill-Haley, Eileen; Engelhart, Simon E. (Geological Society of America Bulletin,, 2015)
There’s a freshwater spruce swamp buried near the northeastern shore of Sally’s Bend in Yaquina Bay. Sediment cores show 8-10 different soil sequences buried there, going back about 4500 years before the present. Each sequence terminates abruptly with a sandy deposit and then over 10 centimeters of mud. The authors of this paper infer that “each buried soil represents a Cascadia subduction zone earthquake…” (from the Abstract) The article includes maps of the bay, and show locations of previous research by other scientists. The Yaquina Bay sequence is compared with sequences from other Oregon estuaries.
Keywords: Alsea Bay; Cannon Beach; coastal hazards; Coos Bay; Coquille River; earthquakes; geology; Netarts Bay; paleosciences; Sally’s Bend; Salmon River; sediments; Sixes River; South Slough; tsunamis; Yaquina Bay; Yaquina River Estuary

Thermogeographic variation in body size of Carcinus maenas, the European green crab - Kelley, Amanda L.; de Rivera, Catherine E.; Grosholz, Edwin D.; Ruiz, Gregory M.; Yamada, Sylvia Behrens; Gillespie, Graham (Marine Biology, 2015)
For many ectotherms, or “cold-blooded” animals, a warmer environment leads to a smaller body size, and these animals grow larger in cooler temperatures. “Here, we test whether biogeographic differences in size (carapace width) exist for a recent invasion of the non-native European green crab, Carcinus maenas, along the west coast of North America. . . Forces that shape the phenotypic trajectory of species may play an important role in both invasion dynamics and subsequent ecological impacts.” (from the Abstract)
Keywords: aquatic invertebrates; Bodega Bay; Coos Bay; crustaceans; decapods; Elkhorn Slough; European green crab = Carcinus maenas; Gales Passage; introduced species; Netarts Bay; phenology; Pipestem Inlet; San Francisco Bay; Seadrift Lagoon; temperature; Tillamook Bay; Tomales Bay; Yaquina Bay

Tidal channel diatom assemblages reflect within wetland environmental conditions and land use at multiple scales - Weilhoefer, Christine L.; Nelson, Walter G.; Patrick J Clinton (Estuaries and Coasts, 2015)
The authors examined diatom assemblages collected from surface sediment in tidal channels of 47 tidal wetlands on the Oregon coast during the summer of 2007. They found some interesting and enlightening differences between the different groups of diatom species collected. “The tidal channel benthic diatom community was most strongly correlated with variables related to human disturbance at all scales surrounding the wetland and not with any tidal channel water quality parameter, including salinity. . . The sensitivity of the tidal creek benthic diatom assemblage to both wetland and landscape level factors indicates that it might be a useful bioindicator of human disturbance to tidal wetland ecosystems.” (from the Abstract)
Keywords: Alsea Bay; Amphora coffeaeformis; Coos Bay; Coquille River; diatoms; Ecola Creek; ecosystem health; environmental disturbance; marshes; Navicula gregaria; Necanicum River; Nehalem Bay; Nestucca River; Netarts Bay; nitrogen; Planothidium delicatulum; salinity; Salmon River; Sand Lake; Siletz Bay; Siuslaw River; species list; Tillamook Bay; Umpqua River; wetlands; Yaquina Bay

Utilization of the Non-Native Seagrass, Zostera japonica, by Crab and Fish in Pacific Northwest Estuaries - Sund, Daniel M. (Oregon State University, 2015)
This M.S. thesis describes a study of the invasive Japanese eelgrass beds in Willapa Bay and Yaquina Bay. “The goals of this project were to 1) examine the community composition of a variety of available estuarine habitats in Willapa Bay, Washington, and Yaquina Bay, Oregon, via paired deployment of cameras and small fish traps; and 2) to explore the different management strategies used in the PNW and identify strengths and weaknesses associated with invasive species management, as indicated by short interviews with professionals working on Z. japonica.” (from the Abstract) Co-major professors were Brett R. Dumbauld and Flaxen Conway.
Keywords: community composition; Dungeness crab = Metacarcinus magister (Cancer magister); geographical distribution; habitats; introduced species; Japanese eelgrass = Zostera japonica; Sally’s Bend; species list; staghorn sculpin = Leptocottus armatus; surfperch = Embiotocidae; theses; three-spine stickleback = Gasterosteus aculeatus; Willapa Bay; Yaquina Bay

Yaquina Bay and River Maintenance Dredging Environmental Assessment (US Army Corps of Engineers. Portland District, 2015)
This document is an environmental assessment of ongoing dredging performed by the Army Corps of Engineers. The Bay has been dredged annually since 1919. Although the Corps is authorized to dredge from the harbor entrance to 14 river miles upstream, currently dredging is only performed at the harbor entrance, at an access channel to South Beach Marina, and every five to eight years at Depot Slough in Toledo. A good historical account of Federal activities in Yaquina Bay is given.
Keywords: Depot Slough; dredging; historical; Main channel; sediments; South Beach Marina; species list; Yaquina Bay

Autonomous in situ Measurements of Estuarine Surface PCO2: Instrument Development and Initial Estuarine Observations - Wall, Colleen McKay (Oregon State University, 2014)
Understanding the carbon cycle is increasingly important in a world feeling the effects of anthropogenic climate change. While oceans absorb carbon dioxide, estuaries release CO2 into the atmosphere, so understanding estuarine processes is particularly important. The carbon cycle in estuaries, however, is complex. In this thesis, the author describes a new instrument that can be used to measure the partial pressure of carbon dioxide and details how it was used in the Yaquina Bay estuary, and in the Pacific Ocean. Measurements of CO2 in Alsea Bay and Netarts Bay are also discussed. The thesis gives a good overview of carbon chemistry and dynamics in the estuarine environment. Major professor was Burke R. Hales.
Keywords: Alkalinity; Alsea Bay; Canyon Quarry Park; carbon dioxide; estuarine dynamics; Netarts Bay; salinity; theses; Toledo; Toledo Boat Launch; Yaquina Bay

A comparison of bulk estuarine turnover timescales to particle tracking timescales using a model of the Yaquina Bay Estuary - Lemagie, Emily P.; Lerczak, James A. (Estuaries and Coasts, 2014)
Water flows in and out of Oregon estuaries with the tides. The Oreon coast enjoys two high tides and two low tides daily. With new water coming in twice a day, and old water flowing out, how long does it take for the water in an estuary to be replaced by new seawater and freshwater inflow? In this technical paper, the authors compare different theoretical models of estuarine turnover with particle tracking methods.
Keywords: hydrology; mathematical modeling; tides; Yaquina Bay; Yaquina River Estuary

Comparison of photosynthetic characteristics of the seagrass congeners Zostera marina L. and Zostera japonica Ascher. & Graeb. - Shafer, Deborah J.; Kaldy, James E. (Aquatic Botany, 2014)
“On the Pacific coast of North America two seagrass species in the genus Zostera co-exist; the native species, Zostera marina, and an introduced species, Zostera japonica. These two species typically occupy separate tidal elevations, with Z. marina occupying the lower intertidal and shallow subtidal zones, and Z. japonica occupying the mid- to upper intertidal zone. This study was designed to compare the photosynthetic characteristics of Z. japonica and Z. marina after exposure to high and low light. . . . “
Keywords: aquatic plants; carbon; eelgrass = Zostera marina; habitats; Idaho Flats; introduced species; Japanese eelgrass = Zostera japonica; natural resource management; oxygen; Yaquina Bay; zonal distribution

Ecological effect of a nonnative seagrass spreading in the Northeast Pacific: A review of Zostera japonica - Mach, Megan E.; Wyllie-Echeverria, Sandy; Chan, Kai M. A. (Ocean & Coastal Management, 2014)
This review article examines studies of Japanese eelgrass to see if this invasive species harms native species or damages habitats. While the literature is not extensive enough to permit solid conclusions, the data suggest that Z. japonica harms large invertebrate species and the native eelgrass, Z. marina, while providing advantageous habitat for smaller marine invertebrates. The authors urge that “rigorous scientific investigation is needed” in order to develop the best policies for managing the species.
Keywords: community ecology; Coos Bay; eelgrass = Zostera marina; Grays Harbor; habitats; introduced species; Japanese eelgrass = Zostera japonica; Netarts Bay; Padilla Bay; Roberts Bank; Tillamook Bay; Willapa Bay; Yaquina Bay

Effect of temperature and nutrient manipulations on eelgrass Zostera marina L. from the Pacific Northwest, USA - Kaldy, James E. (Journal of Experimental Marine Biology and Ecology, 2014)
"Global climate change will impact the three dominate drivers of estuarine seagrass productivity, temperature, light and nutrients. The response of Pacific Northwest (PNW) Z. marina to interactive effects of temperature and nitrogen conditions was experimentally evaluated. . . . Temperature played a dominant role controlling Z. marina response to nutrients; nitrogen toxicity was not observed, and in general the effects of temperature and nutrients were not synergistic. This work highlights the complex nature of Z. marina response to environmental conditions; additional multifactor experiments will be required to tease apart these interactions." (from the Abstract)
Keywords: climate change; eelgrass = Zostera marina; nitrate-nitrite; nitrogen; nitrous oxide; nutrients; primary production; temperature; Yaquina Bay

EPA’s Benthic Habitat Data for Yaquina Estuary [PowerPoint Presentation] - DeWitt, Ted (2014)
This is a .pdf of a PowerPoint presentation highlighting various datasets on Yaquina Bay that are maintained by the scientists at EPA’s National Health and Environmental Effects Research Laboratory, Western Ecology Division (WED). A number of maps of Yaquina Bay featuring this data are shown.
Keywords: amphipods; aquatic vegetation; bathymetry; benthos; Craigie Point; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); habitats; Hatfield Marine Science Center; Idaho Flat; Japanese seagrass = Zostera japonica; maps; Mud shrimp = Upogebia pugettensis; North Jetty; Poole Slough; Riverend; Sally’s Bend; seagrass = Zostera marina; South Beach Marina; South Jetty; Toledo Airport; ultraviolet radiation; wave data; wind data; Yaquina Bay

Hatfield Marine Science Center Dynamic Revetment Report DSL Permit #45455-FP Monitoring Report February, 2014 Report - Cowan, Robert; Nelson, Walt; Allan, Jonathan; Arbuckle, Scarlett; Heppell Laboratory,; Folger, Christina L. (Oregon State University. Hatfield Marine Science Center, 2014)
This is the third in a series of five annual reports concerning control of erosion along Yaquina Bay next to the Hatfield Marine Science Center. Parts of the shoreline were stabilized in 2007 and 2011. Before more dynamic revetments will be permitted, a five-year study of nearby unmodified shorelines is required. “Monitoring of beach profiles indicated that as of December 2013, the 2011 Dynamic Revetment Project (DRP) has successfully stabilized the shoreline in the project area, while rapid erosion has continued in the adjacent Reference beach area. Erosion in the unprotected Reference area in the period 2009-2013 has been as great as 9.6 m (31.5 ft).” (from the Abstract) Aerial photograph, color photographs.
Keywords: amphipods; aquatic invertebrates; beaches; benthos; coastal hazards; Dungeness crab = Metacarcinus magister; erosion; fish; Hatfield Marine Science Center; Pacific staghorn sculpin = Leptocottus armatus; physical; Shiner perch = Cymatogaster aggregate; species list; terrestrial vegetation; wave height data; Whitebait smelt = Allosmerus elongates; Yaquina Bay

Intertidal habitat utilization patterns of birds in a Northeast Pacific estuary - Frazier, Melanie R..; Lamberson, Janet O.; Nelson, Walter G. (Wetlands Ecology and Management, 2014)
The authors conducted bird censuses for five major habitats in the Yaquina River Estuary, “ Zostera marina (eelgrass), Upogebia (mud shrimp)/ mudflat, Neotrypaea (ghost shrimp)/ sandflat, Zostera japonica (Japanese eelgrass), and low marsh.” They studied spatial and temporal variation within habitats and found that the native eelgrass, Zostera marina, was “an important habitat based on nearly all metrics of bird use…” (from the Abstract)
Keywords: birds; eelgrass = Zostera marina; geographical distribution; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Idaho Flat; Japanese eelgrass = Zostera japonica; Mud shrimp = Upogebia pugettensis; population count; Raccoon Flat; Sally’s Bend; temporal distribution; Yaquina Bay

Isolation and characterization of novel microsatellite loci in two species of burrowing shrimp, Neotrypaea californiensis and Upogebia pugettensis - Dumbauld, Brett R.; Mercer, Dacey M.; Camara, Mark (Conservation Genetics Resources, 2014)
The authors characterized 31 microsatellite loci for the two West Coast shrimp species. “These are the first microsatellites characterized for these species and provide a useful tool for further characterization of population structure and diversity.” (from the Abstract)
Keywords: Bodega Bay; genetics; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Humboldt Bay; Mud shrimp = Upogebia pugettensis; Yaquina Bay

Records of trace metals in sediments from the Oregon shelf and slope: Investigating the occurrence of hypoxia over the past several thousand years - Erhardt, Andrea M.; Reimers, Clare E.; Kadko, David; Paytan, Adina (Chemical Geology, 2014)
In recent years, strong coastal winds have caused strong upwelling events, so strong that a layer of low-oxygen seawater has been brought closer to the surface, leading to mass die-offs of marine life, and affecting estuarine waters as well. A current question about these hypoxic events has to do with whether or not they are related to climate change. A look at the history of the region is therefore called for. “A record of past hypoxia occurrence frequency would help distinguish human-induced causes from those related to natural climate changes. . . . Determining trends in trace metal abundances can serve as an indicator for changes in oxygenation conditions over time.” (p.33) The authors look at trace metals in sediments from the Yaquina, Alsea and Siuslaw Rivers and consider other factors possibly influencing their data. “Supplementary data to this article can be found online at http://dx.doi.org/10.1016/j.chemgeo.2014.05.029 .” (p.42)
Keywords: Alsea Bay; chemistry; climate change; dissolved oxygen; hypoxia; paleosciences; sediments; Siuslaw Bay; Trace metals; winds; Yaquina Bay

Science and management of the introduced seagrass Zostera japonica in North America - Shafer, Deborah J.; Kaldy, James E.; Gaeckle, Jeffrey L. (Environmental Management, 2014)
The Pacific Coast of North America is home to two species of eelgrass: the native Zostera marina, and the introduced Zostera japonica. This review looks at the two species, which are managed very differently in different parts of the West Coast. Should the invader be driven out and destroyed? Should it be ignored? The authors identify gaps in knowledge that limit resource managers’ ability to decide, and make recommendations for management and future research.
Keywords: Coos Bay; Coquille River estuary; eelgrass = Zostera marina; geographic distribution; habitats; introduced species; Japanese eelgrass = Zostera japonica; natural resource management; Netarts Bay; Tillamook Bay; Yaquina Bay

Sea Level Affecting Marshes Model (SLAMM) - Lee II, Henry; Reusser, Deborah A.; Frazier, Melanie R..; McCoy, Lee M.; Patrick J Clinton; Clough, Jonathan S.; U.S. Environmental Protection Agency. National Health and Environmental Effects Research Laboratory. Office of Research and Development. Western Ecology Division, (2014)
This is a technical document discussing how to use a computer program to model the effects of sea-level rise on native seagrass. “Because of the ecological importance of SAV [submerged aquatic vegetation] habitats, U.S. EPA, USGS, and USDA partnered with Warren Pinnacle Consulting to enhance the SLAMM modeling software to include new functionality in order to predict changes in Zostera marina distribution within Pacific Northwest estuaries in response to sea level rise.” (from the Introduction) The Yaquina River estuary and Willapa Bay are used as examples. While the emphasis of the document is on GIS, there are some good maps of Yaquina Bay. Clearly, a sea-level rise would have an impact on native seagrass distribution, with Zostera present in fewer areas. The latest version of the tool can be found at: https://coast.noaa.gov/digitalcoast/tools/slamm.html .
Keywords: aquatic vegetation; bathymetry; climate change; eelgrass = Zostera marina; geographic information system; salt marsh; sea level; topography; Willapa Bay; Yaquina Bay

SEACOR Findings – Yaquina Bay [web page] - Oregon Department of Fish and Wildlife. Shellfish and Estuarine Assessment of Coastal Oregon (SEACOR),, (Oregon Department of Fish and Wildlife, 2014)
This excellent guide to what clams are where in Yaquina Bay is based on a 2012 survey. Maps show the number of clams by species and by volume. Includes links to printable clamming maps and driving directions to clamming spots.
Keywords: Breakwater Flat; Bridge Flat; Butter clam = Saxidomus giganteus; Cockle clam = Clinocardium nuttallii; Gaper clam = Tresus capax; Idaho Flats; Littleneck clam = Leukoma staminea; maps; population count; Racoon Flat; recreational fisheries – shellfish; Sally’s Bend; Yaquina Bay

Temporal trends and spatial distribution of DDT in bivalves from the coastal marine environments of the continental United States, 1986–2009 - Sericano, José L.; Wade, Terry L.; Sweet, Stephen T.; Ramirez, Juan; Lauenstein, Gunnar G. (Marine Pollution Bulletin, 2014)
“While the use of DDT in the United States was banned or rigorously restricted forty years ago, this compound and breakdown products continue to be available to bivalves at virtually every location in the continental U.S. coastal areas sampled during the NOAA’s NS&T “Mussel Watch” Program. The concentration in the coastal areas, as a whole, is decreasing with a half-life of about 10–14 years; faster in the south, slower in the north. Under these dissipation rates, average concentrations along the East, Gulf, and West coasts will decrease below 10% of today’s concentrations by approximately 2050.” (p.315) The Oregon sites showed relatively low levels of ΣDDT (below the national 15th percentile) (p.315).
Keywords: aquatic invertebrates; bivalves; Coos Bay; DDE; DDT; Fogarty Creek; molluscs; pesticides; pollution; Russell Point; Yaquina Bay

Variation in tidal wetland plant diversity and composition within and among coastal estuaries: assessing the relative importance of environmental gradients - Janousek, Christopher N.; Folger, Christina L. (Journal of Vegetation Science : Offical Organ of the International Association for Vegetation Science, 2014)
The authors ask, “What is the relative importance of topographic (elevation), edaphic (soil salinity, nitrogen and particle size) and hydrologic (estuarine river flow) gradients for variation in tidal wetland plant composition and diversity?”(from the Abstract) To answer this question, they analyzed wetland vegetation in four Oregon estuaries. They conclude that elevation and salinity are the most important factors affecting species distribution, and note that sea level rise should change distributions and reduce wetland plant diversity. Supporting documentation in four appendices is available online.
Keywords: Alsea Bay; Baltic rush = Juncus balticus ssp. ater; Chickenclaws = Sarcocornia perennis; Coquille River estuary; elevation; geographic distribution; habitats; hydrology; Marsh jaumea = Jaumea carnosa; Netarts Bay; nitrogen; nutrients; salinity; Saltgrass = Distichlis spicata; sediments; species composition; species list; Tufted hairgrass = Deschampsia cespitosa; wetland vegetation; Yaquina Bay

Characterization of Ecosystem Structure and Function Recovery within the NOAA MOC-P Mitigation Basin, Newport, Oregon - Lewis, Nate S. (Oregon State University, 2013)
The native seagrass Zostera marina plays a vital role in Oregon estuaries, producing oxygen and organic matter, trapping sediment, offering forage to waterfowl and giving shelter and habitat to many species. When the NOAA Marine Operations Center – Pacific (MOC-P) was moved to Newport, it was necessary to dredge the bay to put in new docks for NOAA research vessels. In the process, a .68 acre eelgrass bed was destroyed. To mitigate this damage, the original eelgrass was replanted in a new site, in an attempt to re-establish the bed nearby. In this thesis, the author compares the new site to two nearby reference sites, noting ecological diversity, sediments and species abundance through the year. “The re-planted eelgrass bed within the NOAA MOC-P mitigation area was not observed to be a failed ecosystem during this study, but rather an expanding eelgrass bed that was adequately performing the functions associated with eelgrass ecosystems in the Pacific Northwest.” (from the Abstract). Nicely written. The major professor was Sarah K. Henkel.
Keywords: ecosystem health; eelgrass = Zostera marina; general ecosystem description; geographic distribution; Hatfield Marine Science Center; mitigation; Port of Newport; sediments; species composition; species list; temporal distribution; theses; Yaquina Bay

Comparing Metacarcinus magister Settlement Preferences among the Seagrasses Zostera marina and Zostera japonica - Heidmann, Sarah; Jaco, Erin (Oregon State University, 2013)
This is an undergraduate student project report. Juvenile crabs need both protection from predators and easily available prey. These needs are met in complex habitats, such as eelgrass beds. This raises a question about the effects of the invasive Japanese eelgrass on the crabs, as contrasted with the native eelgrass. In this undergraduate research paper, a study of settlement patterns of Dungeness crabs is described. Bags of oyster shells were placed in beds of native and Japanese eelgrass and on mud. The number of juvenile crabs were counted after two weeks. “Overall, M. magister abundance varies widely over the habitats we studied, and was highest in seagrass habitats, especially seagrass with a large biomass, as well as at a low tidal height.” Results indicated that Japanese eelgrass might be beneficial for crab larvae.
Keywords: crustaceans; decapods; Dungeness crab = Metacarcinus magister (Cancer magister); eelgrass = Zostera marina; geographic distribution; habitats; Japanese eelgrass = Zostera japonica; Oregon shore crab = Hemigrapsus oregonensis; Yaquina Bay

Direct Effects and Tradeoffs Affect Vegetative Growth and Sexual Reproduction in an Invasive Seagrass Experiencing Different Disturbance Regimes - Henderson, Jeremy Scott (Oregon State University, 2013)
“In this thesis, I have addressed three broad questions related to the role of disturbance in the invasion dynamics of dwarf eelgrass, Zostera japonica. My questions were: (1) Is there a relationship between disturbance severity at a site and seasonal trends in the allocation of resources to vegetative growth and sexual reproduction (flowering)? (2) Does increasing disturbance severity result in a tradeoff between the allocation of resources to sexual reproduction versus vegetative growth? (3) If so, what are the implications of these tradeoffs to the proliferation of this invasive species?” (p.50) A most interesting look at the relationship between anthropogenic disturbances in a watershed, resulting sedimentation and the spread of an invasive species. Major professor was Sally Hacker.
Keywords: aquatic vegetation; Coquille Point; Green Point; human impacts; Idaho Point; introduced species; Japanese eelgrass = Zostera japonica; Oregon Oyster Farms; Sally’s Bend; sediments; theses; Yaquina Bay

Geographic range and structure of cryptic genetic diversity among Pacific North American populations of the non-native amphipod Grandidierella japonica - Pilgrim, Erik M.; Blum, Michael J.; Reusser, Deborah A.; Lee II, Henry; Darling, John A. (Biological Invasions, 2013)
In this article, the authors attempt to reconstruct the invasion history of the introduced amphipod Gradidierella japonica. DNA analysis shows two distinct groups – one from San Francisco south, and the other north of San Francisco. There are significant genetic differences between the two groups, which, coupled with low genetic diversity within each group, suggests that there were two separate introductions of this species to the West Coast.
Keywords: amphipods; Columbia River estuary; Coos Bay; crustaceans; genetics; Grandidierella japonica; introduced species; Puget Sound; San Francisco Bay; Umpqua River estuary; Winchester Bay; Yaquina Bay

Hatfield Marine Science Center Dynamic Revetment Report DSL Permit #45455-FP Monitoring Report February, 2013 - Janet G Webster; Nelson, Walt; Allan, Jonathan; Stephensen, Shawn; Politano, Vincent; Folger, Christina L. (Oregon State University. Hatfield Marine Science Center, 2013)
This is the second in a series of five annual reports concerning control of erosion along Yaquina Bay next to the Hatfield Marine Science Center. Parts of the shoreline were stabilized in 2007 and 2011. Before more dynamic revetments will be permitted, a five-year study of nearby unmodified shorelines is required. “Monitoring of beach profiles indicated that as of December 2012, the 2011 Dynamic Revetment Project (DRP) has successfully stabilized the shoreline in the project area, while rapid erosion has continued in the adjacent Reference beach area. Erosion in the unprotected Reference area in the period 2009-2012 has been as great as 9 m (29.5 ft).” (from the Abstract) Aerial photograph, color photographs.
Keywords: American Coot = Fulica Americana; amphipods; aquatic invertebrates; beaches; benthos; birds; coastal hazards; erosion; fish; Hatfield Marine Science Center; Pacific staghorn sculpin = Leptocottus armatus; physical; Shiner perch = Cymatogaster aggregate; species list; terrestrial vegetation; wave height data; Western gull = Larus occidentalis; Yaquina Bay

In situ13C tracer experiments elucidate carbon translocation rates and allocation patterns in eelgrass Zostera marina - Kaldy, James E.; Brown, Cheryl A.; Andersen, Christian P. (Marine Ecology Progress Series, 2013)
In this project, native seagrass was studied in summer and in winter using carbon-13 as a tracer to monitor changes in carbon uptake. “The results provide important estimates of carbon uptake and translocation that can be used to better understand whole plant carbon budgets as well as the transfer of seagrass-derived carbon to other trophic communities.” (from the Abstract)
Keywords: carbon; eelgrass = Zostera marina; isotopes; Yaquina Bay

Inter-specific variation in salinity effects on germination in Pacific Northwest tidal wetland plants - Janousek, Christopher N.; Folger, Christina L. (Aquatic Botany, 2013)
The authors used 162 reference plots in Yaquina, Coquille, Netarts and Alsea Bays to look at the distribution of marsh plants and establish the salinity ranges for their distribution. “The effects of future climate change on coastal estuaries are yet unknown, but changes such as sea-level rise and reduced precipitation in coastal watersheds are likely to increase salinity in high intertidal marshes and swamps. . . . Our data show that elevated salinity may lower germination rates in a number of common Pacific Northwest wetland species, suggesting potential changes in plant composition through impacts on seed germination and establishment.”
Keywords: Alsea Bay; Bearberry honeysuckle = Lonicera involucrate; Chickenclaws = Sarcocornia perennis; climate change; Common yarrow = Achillea millefolium; Coquille River estuary; Creeping bentgrass = Agrostis stolonifera; Criter’s Moorage; Douglas aster = Symphyotrichum subspicatum; ecosystem modeling; germination; Hatfield Marine Science Center; Juncus balticus ssp. ater; Meadow barley = Hordeum brachyantherum; Netarts Bay; Oregon gumplant = Grindelia stricta; Poole Slough; salinity; salt marsh; Salt sandspurry = Spergularia salina; sea level; Sea plantain = Plantago maritime; Seaside arrowgrass = Triglochin maritime; Tufted hairgrass = Deschampsia cespitosa; wetland vegetation; Yaquina Bay

Newport dock remediation and geotechnical risk mitigation in variably weathered rock conditions - Schlechter, S. M.; Greenfield, M. W.; Reed, M. W. (Ports 2013: Success through Diversification, 2013)
"Proceedings of the thirteenth triennial international conference, April 25-28, 2013, Seattle, Washington." Discusses the removal of the WWII-era concrete ship Pasley and the stabilization of the Port of Newport’s International Terminal. “In 1948, the Port of Newport sank two reinforced-concrete cargo ships on the north shore of Yaquina Bay to serve as wharves for cargo handling. Over time, the ships cracked and moved up to 3 ft toward the bay, resulting in ground settlement, damage to structures near the ships, and an increased risk of releasing petroleum contaminants stored inside the ships into the bay. Through an extensive analysis of alternatives to make the best use of available funds, the selected alternative was to construct a temporary cofferdam and remove the western ship, stabilize the eastern ship with anchors and ballast, and construct a new 800-ft-long, 40-ft-wide dock with an anchored bulkhead wall.” (from the Abstract) Engineering challenges and solutions are discussed. Color photographs, schematic drawings.
Keywords: engineering; harbors; human impacts; Port of Newport; ports; urban development; Yaquina Bay

Plant responses to increased inundation and salt exposure: interactive effects on tidal marsh productivity - Janousek, Christopher N.; Mayo, Cara (Plant Ecology, 2013)
Climate change is projected to bring heavier seasonal rainfall and higher sea levels. These would mean more inundation events and potential exposure to higher salinities, respectively. What might the effect of these changes be on salt marsh vegetation? This is the question this article seeks to answer. The authors tested transplanted plants in three marshes in the Yaquina estuary with different degrees of brackishness. “Our results suggest that inundation and salinity stress individually and (often) interactively reduce productivity across a suite of common marsh species.” (from the Abstract)
Keywords: Bearberry honeysuckle = Lonicera involucrate; climate change; Common yarrow = Achillea millefolium; Creeping bentgrass = Agrostis stolonifera; flooding; Idaho Flats; Juncus balticus ssp. ater; Oregon gumplant = Grindelia stricta; River mile 11; River Mile 14; salinity; salt marsh; Sea plantain = Plantago maritima; Seaside arrowgrass = Triglochin maritima; terrestrial vegetation; Tufted hairgrass = Deschampsia cespitosa; Tufted harigrass = Deschampsia cespitosa; Yaquina Bay; Yaquina River

Tidal wetlands of the Yaquina and Alsea River estuaries, Oregon: Geographic Information Systems layer development and recommendations for National Wetlands Inventory revisions - Brophy, Laura S.; Reusser, Deborah A.; Janousek, Christopher N.; Green Point Consulting,; U.S. Geological Survey,; U.S.Environmental Protection Agency, (Open-File Report (Geological Survey (U.S.)), 2013)
“Geographic Information Systems (GIS) layers of current, and likely former, tidal wetlands in two Oregon estuaries were generated by enhancing the 2010 National Wetlands Inventory (NWI) data with expert local field knowledge, Light Detection and Ranging-derived elevations, and 2009 aerial orthophotographs. Data were generated for two purposes: First, to enhance the NWI by recommending revised Cowardin et al. (1979) classifications for certain NWI wetlands within the study area; and second, to generate GIS data for the 1999 Yaquina and Alsea River Basins Estuarine Wetland Site Prioritization study…. The GIS products of this project improve the accuracy and utility of the NWI data, and provide useful tools for estuarine resource management.” (from the Abstract) Color maps. Appendix A includes excellent color photographs of wetland sites and plants.
Keywords: Alsea Bay; Alsea River; Bain Slough; Boone Slough; Depot Slough; Drift Creek; Eckman Slough; geographic information system; hydrography; Idaho Flats; Lint Slough; maps; McCaffery Slough; Nute Slough; Olalla Slough; Pooles Slough; Risley Creek; salinity; salt marsh; wetland delineation; wetland vegetation; wetlands; Yaquina Bay; Yaquina River

Tsunami inundation maps for Newport North, Lincoln County, Oregon - Oregon. Dept. of Geology and Mineral Industries,; National Tsunami Hazard Mitigation Program (U.S.), (Tsunami Inundation Map, 2013)
2 maps : col. ; 84 x 133 cm., on sheet 86 x 135 cm. Plate 1. Local source (Cascadia Subduction Zone) tsunami inundation map Newport North, Oregon -- Plate 2. Distance source (Alaska-Aleutian Subduction Zone) tsunami inundation map Newport North, Oregon. May be viewed online at the NANOOS website (click on DOGAMI to access).
Keywords: coastal hazards; earthquakes; maps; McLean Point; Newport (Or.); Sally’s Bend; tsunamis; Yaquina Bay; Yaquina River

Tsunami inundation maps for Newport South, Lincoln County, Oregon - Oregon. Dept. of Geology and Mineral Industries,; National Tsunami Hazard Mitigation Program (U.S.), (Tsunami Inundation Map, 2013)
2 maps : col. ; 84 x 133 cm., on sheet 86 x 135 cm. Plate 1. Local source (Cascadia Subduction Zone) tsunami inundation map Newport South, Oregon -- Plate 2. Distance source (Alaska-Aleutian Subduction Zone) tsunami inundation map Newport South, Oregon. May be viewed online at the NANOOS website (click on DOGAMI to access).
Keywords: coastal hazards; Coquille Point; earthquakes; Hatfield Marine Science Center; Hinton Point; Idaho Point; maps; McCaffery Slough; McLean Point; Newport (Or.); Oneatta Point; Poole’s Slouth; Sally’s Bend; South Beach (Or.); tsunamis; Yaquina (Or.); Yaquina Bay; Yaquina River

Upwelling-influence, macroalgal blooms, and seagrass production; temporal trends from latitudinal and local scales in northeast Pacific estuaries - Hessing-Lewis, Margot L.; Hacker, Sally D. (Limnology and oceanography, 2013)
“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…” (from the Abstract)
Keywords: algae; Coos Bay; eelgrass = Zostera marina; Netarts Bay; nitrogen; phosphorus; primary production; Ulva spp.; upwelling; Willapa Bay; Yaquina Bay

Boring crustaceans damage polystyrene floats under docks polluting marine waters with microplastic - Davidson, Timothy M. (Marine Pollution Bulletin, 2012)
A nonindegenous boring isopod, S. quoianum, bores into Styrofoam floats commonly used in docks, espeically at aquaculture facilities. The process of boring out burrows in the plastic caused microplastic pollution, which can harm species that eat it, and release persistent pollutants. Floats at an oyster farm in Yaquina Bay and a similar facility at Tainan, Taiwan were severely damaged by the borers. A survey of the shoreline around Yaquina Bay was made looking for microparticles from damaged floats. Includes photographs of damaged floats from Yaquina Bay. The type of plastic influenced the boring: while the softer Styrofoam floats were ideal habitat, the isopods avoided harder XPS foam in the laboratory. Coos Bay was also surveyed
Keywords: aquaculture; Coos Bay; crustaceans; invasive species; isopods; pollution; salinity; Sphaeroma quoianum; Yaquina Bay; Yaquina Bay Oyster Farm

Determining bathymetric distributions of the eelgrass Zostera marina L. in three turbid estuaries on the eastern North Pacific coast - Young, David R.; Clinton, Patrick J.; Specht, David T.; Collura, Chris Mochon; Lee II, Henry (Botanica Marina, 2012)
This paper describes a method for mapping estuarine eelgrass beds that can be applied to other subsurface aquatic vegetation, and to give a method for estimating the part of the eelgrass that is too deep to be detected by this method. Bathymetric models of three estuaries were made and then compared with eelgrass distribution.
Keywords: Alsea Bay; aquatic vegetation; eelgrass = Zostera marina; map; spatial distribution; temporal abundance; Tillamook Bay; Yaquina Bay

Ecosystem services of coastal habitats and fisheries: multiscale ecological and economic models in support of ecosystem-based management - Jordan, Stephen J.; O'Higgins, Timothy; Dittmar, John A. (Marine and Coastal Fisheries: Dynamics, Management and Ecosystem Science, 2012)
This work addresses problems of scale in ecosystem-based management -- balancing small critical habitats within larger ecosystems and economic systems.The economic valuation of the Yaquina Bay recreational salmon fishery is one of the examples given. The fishery was valued using two methods -- travel cost of anglers and willingness to pay to preserve salmon. Total value of the fishery was estimated at $540,817.
Keywords: ecology; economics; Pacific salmonids = Oncorhynchus species; recreational fisheries - salmon; Yaquina Bay

Ecosystem Services Provided by Olympia Oyster (Ostrea lurida) Habitat and Pacific Oyster (Crassostrea gigas) Habitat; Dungeness Crab (Metacarcinus magister) Production in Willapa Bay, WA - Ramsay, Jessica (Oregon State University, 2012)
"A final report submitted to Oregon State University in partial fulfillment of the requirements for the degree of Professional Science Master’s." "Oyster reefs provide an array of ecosystem services. Specifically, they provide structurally complex habitat for fish and invertebrate species such as the commercially important Dungeness crab, Metacarcinus magister. This ecosystem service, once provided by the native oyster Ostrea lurida, is now provided by the commercially cultured oyster Crassostrea gigas in many estuaries on the U.S west coast. An economic investigation was conducted examining the ecosystem services provided by oyster habitat, common economic valuation theories and techniques, and tradeoffs between oyster restoration and aquaculture expansion. A scientific investigation, comprised of three studies, was also conducted to examine Dungeness crab production as an ecosystem service provided by oyster habitat." (from the Abstract) Major professor was Flaxen Conway.
Keywords: aquaculture; Coos Bay; Dungeness crab = Metacarcinus magister (Cancer magister). eelgrass = Zostera marina; economics; habitats; natural resources management; Netarts Bay; nutrient cycles; Olympia oyster=Ostrea lurida (Ostrea conchaphila); Pacific oyster = Crassostrea gigas; sediments; Willapa Bay; Yaquina Bay

Estuary Inhabitants Species List for Yaquina and Coos Bays, Oregon - Chapman, John W.; Breitenstein, Ralph Arthur; Marine Bioinvasions Lab, (2012)
The Marine Bioinvasions Lab is located at Oregon State University's Hatfield Marine Science Center. A major focus is identification of native, introduced and invasive species found in Oregon's estuaries. This spreadsheet is the most up to date list of the marine algae and invertebrates in the Yaquina and Coos Bays. This list is not complete and will never be done. It is a combination of prior inventories of estuary species and observations by active taxonomists. The date at the top of the spreadsheet is the most recent version. References are included. A valuable resource in tracking introduced species in Yaquina and Coos Bay. Includes charts.
Keywords: algae; annelids; bryozoans; cnidarians; Coos Bay; crustaceans; introduced species; molluscs; nemerteans; species composition; species list; sponges; tunicates; Yaquina Bay

Genetic Population Structure and Cryptic Speciation of Ghost Shrimp (Neotrypaea californiensis) in North American West Coast Estuaries - Gille, Daphne Anne (San Jose State University, 2012)
Surveyed the West Coast from Puget Sound to San Diego to study the genetics of the ghost shrimp population and thereby infer the potential for larval dispersal in ghost shrimp. “Multiple haplotypes were shared among 346 adult ghost shrimp specimens collected from estuaries in Washington, Oregon, and California indicated that larvae of this species are transported across great distances during the pelagic dispersal phase of development.” The author also found the population structure was influenced by “the presence of three putative cryptic species that were deeply divergent from N. californiensis.” (from the Abstract) Paper 4232.
Keywords: Alsea Bay; Columbia River; Coos Bay; genetics; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Heceta Head; life history information; Nestucca Bay; population biology; theses; Tillamook Bay; Umpqua River estuary; Winchester Bay; Yaquina Bay; Yaquina Head

Hatfield Marine Science Center Dynamic Revetment Report DSL Permit #45455-FP Monitoring Report February, 2012 - Boehlert, George; Nelson, Walt; Allan, Jonathan; Harris, Erica; Stephensen, Shawn; Politano, Vincent; Folger, Christina L. (Oregon State University. Hatfield Marine Science Center, 2012)
This is the first of a series of five annual reports concerning control of erosion along Yaquina Bay next to the Hatfield Marine Science Center. Parts of the shoreline were stabilized in 2007 and 2011. Before more dynamic revetments will be permitted, a five-year study of nearby unmodified shorelines is required. “A Dynamic Revetment (gravel beach) was installed in November, 2011 on the shoreline along the northeastern edge of the HMSC to mitigate erosion that threatened HMSC critical infrastructure. Shoreline topographic and biological monitoring was initiated before and continued after the project completion. Monitoring of beach profiles along the project area showed that a Dynamic Revetment installed in 2007 had been successful in stabilizing further retreat of the beach. As of January 2012, the2011 project also appears to have stabilized the shoreline, while rapid erosion has continued in the adjacent Reference beach area. “ (from the Abstract) The report includes aerial photographs, charts and color photographs.
Keywords: American Coot = Fulica Americana; amphipods; aquatic invertebrates; beach wrack; beaches; benthos; birds; coastal hazards; erosion; fish; Hatfield Marine Science Center; Pacific staghorn sculpin = Leptocottus armatus; physical; Shiner perch = Cymatogaster aggregate; species list; terrestrial vegetation; wave height data; Yaquina Bay

Hydrographic Surveys [website] - U.S. Department of the Army. Portland District, (2012)
Most recent surveys only
Keywords: Coos Bay; Depoe Bay; Depot Slough; map; physical; Siuslaw River; South Beach Marina; Umpqua River; Yaquina Bay; Yaquina Bay Bar

An introduced Asian parasite threatens northeastern Pacific estuarine ecosystems - Chapman, John W.; Dumbauld, Brett R.; Itani, Gyo; Markham, John C. (Biological Invasions, 2012)
The non-indigenous isopod Orthione griffenis effectively castrates the mud shrimp Upogebia. The spread of the invasive parasite has dramatically depleted mud shrimp populations along the northwestern coast of North America. "All previously known abundant Upogebia populations were either absent or at greatly reduced abundances in all California, Oregon and Washington estuaries examined." (p.1225) "[U]rgent, immediate responses, including captive breeding programs for the most impacted Upogebia populations and species are warranted." (p.1234)
Keywords: Alsea Bay; bioturbation; Coos Bay; depleted populations; invasive species; Mud shrimp = Upogebia pugettensis; Netarts Bay; Orthione griffenis; parasites; Sand Lake; Siletz Bay; Tillamook Bay; Yaquina Bay

LOBO: Land Ocean Biogeochemical Observatory - Satlantic [Corporation], (2012)
Environmental monitoring station. The station was removed from the water in 2013. Data from Nov. 1, 2007-Sept. 25, 2013 is available.
Keywords: conductivity; dissolved oxygen; phosphorus; salinity; turbidity; water temperature; Yaquina Bay

Microsatellite and Mitochondrial DNA Analysis of Dungeness Crab (Cancer magister) from California to Northern British Columbia - Barney, Bryan Thomas (Dept. of Biological Sciences, 2012)
In the summer of 2009, the author did genetic sampling on 20-25 crabs at each of 14 locations along the U.S. West Coast, from Iceberg Bay, British Columbia to San Luis Obispo, California. Both mitochondrial DNA and microsatellite nuclear markers were sampled. “The objective of this study was to investigate the genetic connectivity of Dungeness crab between central California and northern British Columbia using both mitochondrial DNA and nuclear markers (microsatellites). We sampled adult Dungeness crab across ~2500 km of the Pacific coastline to test for signals of population substructure and limitations to gene flow across the ecological range.” (p.3)
Keywords: Alsea Bay; biology; crustaceans; decapods; Dungeness crab = Metacarcinus magister (Cancer magister); genetics; life history information; population biology; Yaquina Bay

Sediment diatom species and community response to nitrogen addition in Oregon (USA) estuarine tidal wetlands - Hankin, Shanon L.; Weilhoefer, Christine L.; Kaldy, James E.; DeWitt, Theodore H. (Wetlands, 2012)
Tested responses of sediment diatom communities in tidal wetlands of Yaquina Bay to nitrogen addition in the summers of 2009 and 2010. Identified 88 diatom taxa in the area. The four individual plots showed high species richness, of about 32-42 different species per plot. A strong response to nitrogen addition was found. Suggests that “the sediment diatom community is a strong candidate for use as an aquatic bioassessment tool in tidal wetlands…” (p.1029)
Keywords: algae; Amphora spp.; aquatic vegetation; Cocconeis placentula; diatoms; fertilizers; Hatfield Marine Science Center; Idaho Point; nitrogen; Planothidium delicatulum; Sally’s Bend; salt marsh; Saltgrass = Distichlis spicata; Saltwort = Sarcocornia virginica; wetlands; Yaquina Bay

Settlement patterns of young-of-the-year rockfish among six Oregon estuaries experiencing different levels of human development - Dauble, Alison D.; Heppell, Scott A.; Johansson, Mattias L. (Marine Ecology Progress Series, 2012)
"The goal of this study was to investigate natural and anthropogenic influences on the estuarine settlement process of rockfishes, with a focus on black rockfish, S. melanops. Trap surveys conducted in 6 Oregon estuaries indicate that young-of-the-year (YOY; age 0) rockfish utilize ..multiple Oregon estuaries from spring through late fall... Catches were higher in the more developed estuaries, suggesting that the continued development of Oregon estuaries may not adversely affect the rockfish settlement process." (from the Abstract) This study is the first documentation of juvenile rockfish in the Nehalem, Siletz, Alsea and Coquille estuaries.
Keywords: Alsea Bay; Black rockfish = Sebastes melanops; Coos Bay; Coquille River estuary; habitats; human impacts; industrial development; juvenile fish; Nehalem River estuary; Rockfish = Sebastes spp.; Siletz Bay; Yaquina Bay

Site Selection by Migratory Shorebirds in Oregon Estuaries Over Broad and Fine Spatial Scales - Miller, Aileen Kilpatrick (Portland State University, 2012)
“My goal in this research was to identify environmental features or habitat characteristics that predict shorebird abundance in Oregon estuaries“ (p.72). The author found differences in preferred habitat between spring and fall migrations. In the spring, shorebirds have a relatively narrow window in which to make it to their Arctic breeding grounds. In this intensely social time, the birds preferred larger estuaries. On the other hand, in the fall, shorebird preference was more strongly influenced by habitats. Marsh habitats and grasslands for roosting sites were good fall density predictors. Estuarine channels were preferred feeding sites. In Oregon, the Coquille River estuary, Coos Bay and Siletz Bay were the preferred fall sites. This most interesting and enlightening work can help wildlife managers better understand the relative importance of various habitats.
Keywords: Alsea Bay; birds; Columbia River estuary; Coos Bay; Coquille River estuary; Dowitcher = Limnodromus spp.; Dunlin = Calidris alpine; feeding behavior; food availability; habitats; Humboldt Bay; Least sandpiper = Calidris minutilla; Necanicum River; Necanicum River estuary; Nehalem Bay; Nestucca Bay; Netarts Bay; San Francisco Bay; Sand Lake; Sanderling = Calidris alba; Siletz Bay; Siuslaw River estuary; spatial distribution; temporal distribution; theses; Tillamook Bay; western sandpiper = Calidris mauri; Willapa Bay; Yaquina Bay

Steamboats of Yaquina Bay and Yaquina River [web page] - Anonymous (2012)
A rewarding account of the history of steamships and ferries in Yaquina Bay. Lots of data and links to historic photographs. See also the related Steamboats of the Oregon Coast ( https://en.wikipedia.org/wiki/Steamboats_of_the_Oregon_Coast )
Keywords: historical; Newport (Or.); Olssonville; Oneatta Point; Oysterville; Toledo (Or.); transportation; Winant; Yaquina Bay; Yaquina City; Yaquina River

U.S. Pacific Northwest coastal hazards: tectonic and climate controls - Komar, Paul D.; Allan, Jonathan C.; Ruggiero, Peter (Coastal Hazards, 2012)
This is a comprehensive, up-to-date and important discussion of coastal hazards. There’s an excellent discussion of historic problems, a good look at current issues, and a chilling discussion of the implications of rising sea levels and climate change. Charts, b+w and color photographs. Anyone considering purchasing property at the coast should read this first.
Keywords: Alsea Bay; Alsea Spit; Bayocean Spit; Cape Lookout State Park; climate change; coastal hazards; Columbia River; dunes; earthquakes; El Nino; erosion; flooding; geology; Gleneden Beach; historical; jetties; Lincoln City (Or.); Lincoln City Littoral Cell; minerals; Neskowin (Or.); Nestucca River; Nestucca Spit; Netarts Bay; Netarts Spit; Newport (Or.); Pacific City (Or.); Rockaway (Or.); sea level; sediments; Siletz Bay; Siletz Spit; tidal data; Tillamook Bay; tsunamis; wave heights; Willapa Bay; Yaquina Bay

Yaquina Bay, Oregon: Ocean Dredged Material Disposal Sites Evaluation Study and Environmental Assessment - U.S. Army Corps of Engineers. Portland District,; U.S. Environmental Protection Agency. Region 10, (U.S. Army Corps of Engineers, Portland District, 2012)
This document outlines potential disposal sites for dredging tailings close inshore off Newport and makes recommendations. Includes maps of alternatives.
Keywords: dredging; geography; harbors; navigation; ports; sediments; Yaquina Bay

Is the collapse of mud shrimp (Upogebia pugettensis) populations along the Pacific Coast of North America caused by outbreaks of a previously unknown bopyrid isopod parasite (Orthione griffenis)? - Dumbauld, Brett R.; Chapman, John W.; Torchin, Mark E.; Kuris, Armand M. (Estuaries and Coasts, 2011)
“A dramatic increase in prevalence of the recently discovered bopyrid isopod parasite, Orthione griffenis, likely introduced in the 1980s from Asia to the Pacific coast of North America, coincided with the 2002 collapse of a population of its burrowing mud shrimp host, Upogebia pugettensis, in Willapa Bay, Washington that had been stable since monitoring began in 1988. An examination of whether O. griffenis infections were sufficient to cause this decline and other recently noted U. pugettensis population collapses in Pacific Coast estuaries was conducted.” (from the Abstract)
Keywords: aquatic invertebrates; crustaceans; depleted populations; Idaho Flats; Mud shrimp = Upogebia pugettensis; Orthione griffenis; parasites; Tillamook Bay; Willapa Bay; Yaquina Bay

Eelgrass-Macroalgae Interactions: Context-Dependency in Upwelling-Influenced Estuaries - Hessing-Lewis, Margot (Oregon State University, 2011)
"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.
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

Effects of climate change on water quality in the Yaquina Estuary, Oregon [PowerPoint presentation] - Brown, Cheryl A.; Sharp, Darrin; Chang, Heejun; Steele, Madeline (The Oregon Water Conference 2011: Evaluating and Managing Water Resources in a Climate of Uncertainty, 2011)
PowerPoint presentation discussing the effects climate change will have on the Yaquina Estuary. Maps, aerial photographs, charts.
Keywords: air temperature; climate change; Criteser’s Moorage; Elk City; Oneatta Point; precipitation; salinity; water temperature; Yaquina Bay; Yaquina River Estuary

Historic and recent patterns of dissolved oxygen in the Yaquina Estuary (Oregon, USA): Importance of anthropogenic activities and oceanic conditions - Brown, Cheryl A.; Power, James H. (Estuarine, Coastal and Shelf Science, 2011)
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)
Keywords: anoxia; dissolved oxygen; historical; upwelling; Yaquina Bay

Identification of Optimal Broodstock for Pacific Northwest Oysters - Stick, David A. (Oregon State University, 2011)
With the goal of identifying optimal broodstock, the author mapped microsatellites on genes of Olympia oysters and identified the genetic structure of surviving remnant populations of the native oyster. He used microsatellite and AFLP markers to develop an integrated linkage map for the Pacific oyster, and attempted to identify and map genetic sites that influence growth in the Pacific oyster. Co-major professors were Mark D. Camara and Christopher J. Langdon.
Keywords: aquaculture; bivalves; Coos Bay; genetics; growth; Hatfield Marine Science Center; molluscs; Olympia oyster=Ostrea lurida (Ostrea conchaphila); Oregon Oyster Farms; population biology; spatial distribution; statistical analyses; theses; Yaquina Bay

Important Bird Areas in the United States. Site report: Yaquina Bay (2011)
Yaquina Bay is recognized as an Important Bird Area by the National Audubon Society. This is the summary page of data about the Yaquina estuary in the National Audubon Society database. "Yaquina Bay regularly hosts thousands of waterfowl and shorebirds."
Keywords: birds; Black Brant = Branta bernicla nigricans; Brown pelican = Pelecanus occidentalis californicus; habitat conservation; habitat restoration; Heermann's gull = Larus heermanni; Marbled murrelet = Brachyramphus marmoratus; population count; Sooty shearwater = Puffinus griseus; Yaquina Bay

Joint Permit Application to Stabilize Portion of Yaquina Bay Shoreline at Hatfield Marine Science Center (area of erosion along eastern edge of HMSC property) - Hatfield Marine Science Center,; Oregon State University (Hatfield Marine Science Center, 2011)
These four items document the 2010-2011 permitting process to stabilize the eastern edge of the Hatfield Marine Science Center property. During late 2006, erosion forced the closure of the HMSC public estuary trail. In March 2007, an erosion control project using a gravel beach or "dynamic revetment" resulted in the stabilization of approximately 200 linear feet of shoreline. This remains stable since that time. Erosion continued at a slower rate south the original project. In the winter of 2009-2010, weather conditions resulted in rapid erosion of up to 13 feet along approximately 500 feet of the shoreline. This erosion moved the shoreline to the edge of the HMSC nature trail in one location and with 25 feet of the 800,00 gallon seawater storage facility. To address the erosion, the HMSC applied for a permit to extend the 'dynamic revetment'. The permit was granted with limitations. The permit application, public comments and final approval are included. Includes documents from the U.S. Army Corps of Engineers and comments from the Oregon Dept. of Fish and Wildlife.
Keywords: coastal hazards; erosion; ghost shrimp = Neotrypaea californiensis; habitats; Hatfield Marine Science Center; juvenile fish; mitigation; natural resource management; sediments; Yaquina Bay

Oregon’s Non-Consumptive Recreational Ocean User Community : Understanding an Ocean Stakeholder - Eardley, Christopher S.; Conway, Flaxen D. L.; Oregon State University. Sea Grant College Program; National Sea Grant College Program (U.S.), (ORESU-S, 2011)
This is a study of "the non-consumptive recreational ocean user (NROU) community. The NROU group includes surfers, kayakers, boaters, divers, and many others..." (p.3) Who are marine recreationists who are not hunters or fishers? Where do they go? What factors motivate their recreational choices? How do they contribute to local economies? How do they relate to marine renewable energy such as wind or tidal power generation? This publication offers insights on these questions.
Keywords: Agate Beach; Alsea Bay; Bayview County Park; boating; Cannon Beach; Cape Kiwanda; Cape Lookout; Coos Bay; Depoe Bay; economics; energy; environmental tourism; Nehalem Bay; Nehalem Bay State Park; Netarts Bay; Newport Pinnacles; North Jetty; Oregon Dunes National Recreational Area; Orford Reef; Port Orford; recreation; Redfish Rocks; scuba diving; Siletz Bay; Siuslaw River; South Jetty; surfing; Tillamook Bay; tourism; Whales Head Rock; Winchester Bay; Yaquina Bay

Sea level variations along the U.S. Pacific Northwest Coast: tectonic and climate controls - Komar, Paul D.; Allan, Jonathan; Ruggiero, Peter (Journal of Coastal Research, 2011)
"Analyses of the progressive multidecadal trends and climate-controlled annual variations in mean sea levels are presented for nine tide-gauge stations along the coast of the U.S. Pacific Northwest: Washington, Oregon, and Northern California. The trends in relative sea levels are strongly affected by the tectonics of this region..." The two Oregon sites are Yaquina and Coos bays. Tectonic processes such as subsidence and uplift can affect trends in relative sea levels. In the Yaquina Bay area, the land is slowly sinking, and the area has seen more sea level rise than an area such as Neah Bay, where the land is rising. Significant climate events such as El Nino are noted. This work has shown a trend for progressively higher wave heights in large storms, and the size of the largest waves is increasing at the highest rate, which has significant implications for coastal erosion.
Keywords: coastal hazards; Coos Bay; El Nino; erosion; sea level; Yaquina Bay

Utilization Patterns of Intertidal Habitats by Birds in Yaquina Estuary, Oregon - Lamberson, Janet O.; Frazier, Melanie R..; Nelson, Walter G.; Patrick J Clinton; U.S. Environmental Protection Agency. Western Ecology Division, (2011)
"An assessment of bird utilization patterns of the intertidal soft sediment and low marsh habitats of the Yaquina estuary, Oregon was conducted from December 2007-November 2008. . . Gulls and terns comprised 42% of the total birds and, together with ducks, shorebirds, corvids and geese, accounted for about 92% of the total abundance. The addition of herons/egrets, rails (i.e. coots), and pelicans/cormorants comprised just over 98% of all birds observed. The remaining birds consisted of songbirds, loons/grebes, raptors and alcids." (p.3)
Keywords: American crow = Corvus brachyrhynchos; American wigeon = Anas Americana; birds; Boone Slough; Bufflehead = Bucephala albeola; Coquille Point; Criteser's Marina; eelgrass = Zostera marina; ghost shrimp = Neotrypaea californiensis; Grassy Point; Great blue heron = Ardea herodias; gulls = Larus species; habitats; Idaho Flats; Japanese eelgrass = Zostera japonica; Johnson Slough; King Slough; Mud shrimp = Upogebia pugettensis; Northern pintail = Anas acuta; Nute Slough; Oneatta Point; River Mile 7; River Mile 8; Sally's Bend; scaup = Aythya species; The Bend; tidal marsh; western sandpiper = Calidris mauri; Winant; Yaquina; Yaquina Bay; Yaquina River

Biological Assessment and Essential Fish Habitat Assessment for the Construction of NOAA's Marine Operations Center-Pacific in Newport, Oregon (Township 11 South, Range 11 West, and Section 17 6th field HUC 171002040303) - van Staveren, John; Hawkins, Amy; Tumer, Craig; Groff, Dale; Lomnicky, Gregg; Pacific Habitat Services Inc., (Pacific Habitat Services, Inc., 2010)
"This is a Biological Assessment (BA) addressing the potential effects on aquatic species currently listed or proposed for listing under the Federal Endangered Species Act (ESA) from the construction of the National Oceanic and Atmospheric Administration’s (NOAA) Marine Operations Center – Pacific (MOC-P) in Newport, Oregon." (from the Introduction) Includes maps, charts, aerial photographs, colored illustrations, architectural drawings and construction schematics.
Keywords: Coho salmon = Oncorhynchus kisutch; depleted populations; dredging; eelgrass = Zostera marina; Green sturgeon = Acipenser medirostris; habitats; Hatfield Marine Science Center; human impacts; introduced species; killer whale = Orca orcinus; life history information; mitigation; NOAA Marine Opeations Center - Pacific; Pacific smelt = Thaleichthys pacificus; salinity; sediments; Steller sea lion=Eumetopias jubatus; water quality; Yaquina Bay

Ecological periodic tables for nekton usage of four US Pacific Northwest estuarine habitats - Ferraro, Steven P.; Cole, Faith A. (Canadian Journal of Fisheries and Aquatic Sciences, 2010)
The authors take the interesting approach of using the periodic table of elements as a model for summarizing species richness and biomass in an estuary, as related to habitat. Eelgrass and 2 kinds of burrowing shrimp holes were used as habitat types. Yaquina Bay was the study site, and is used as an example of this approach.
Keywords: abundance; eelgrass = Zostera marina; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); habitats; Mud shrimp = Upogebia pugettensis; salinity; sediments; species composition; water temperature; Yaquina Bay

Endangered Species Act Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Conservation Recommendations for the NOAA Marine Operations Center-Pacific Relocation Yaquina Bay (6th field HUC 171002040303)... - U.S. Army. Corps of Engineers,; National Marine Fisheries Services. Northwest Region, (2010)
This document is the final biological opinion on the environmental suitability of construction of the NOAA Marine Operations Center - Pacific facility on Yaquina Bay. "The Corps determined the proposed action is likely to adversely affect Oregon Coast (OC) coho salmon (Oncorhynchus kisutch), Southern green sturgeon (Acipenser medirostris), and Southern Eulachon (Thaleichthys pacificus). The Corps also determined the proposed action is likely to adversely affect designated critical habitat forOC coho salmon and Southern green sturgeon.." In light of these determinations, the Corps consulted with NMFS to learn if the construction would be permissible, and what measures must be taken to mitigate the impact of the construction. This document outlines possible hazards and mandates mitigation activities. Full title: Endangered Species Act Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Conservation Recommendations for the NOAA Marine Operations Center-Pacific Relocation Yaquina Bay (6th field HUC 171002040303) Lincoln County, Oregon.
Keywords: Coho salmon = Oncorhynchus kisutch; depleted populations; dredging; eelgrass = Zostera marina; Green sturgeon = Acipenser medirostris; habitats; Hatfield Marine Science Center; human impacts; introduced species; life history information; mitigation; NOAA Marine Opeations Center - Pacific; Pacific smelt = Thaleichthys pacificus; salinity; sediments; water quality; Yaquina Bay

Geographic variation in lower pharyngeal jaw morphology in the Shiner Perch Cymatogaster aggregata (Embiotocidae, Teleostei) - Woods, Pamela J. (Environmental Biology of Fishes, 2010)
Shows that variations in jaw and body shape have more to do with habitat and prey than geographic location in the subject species. Studied shiner perch from Friday Harbor, Washington to Humboldt Bay, California. The biggest contrast in jaw morphology seemed to be between Coos Bay, Oregon and Friday Harbor specimens, and these differences are frequently referenced in the article. "Recognizing ecological patterns via morphology is an important first step in understanding how and when ecological mechanisms influence the functional role of an organism within its environment."
Keywords: Coos Bay; diet; habitats; shiner perch=Cymatogaster aggregata; Yaquina Bay

Habitat scale mapping of fisheries ecosystem service values in estuaries - O'Higgins, Timothy G.; Ferraro, Steven P.; Dantin, Darrin D.; Jordan, Steve J.; Chintala, Marnita M. (Ecology and Society, 2010)
Attempts to quantify economic values of recreational and commercial fisheries in three different estuaries and thereby assign economic values to habitats. Economic values for the subtidal, intertidal and eelgrass areas of Yaquina Bay are given. .pdf is accessible from online file and has more readable maps and charts.
Keywords: Alabama; commercial fisheries - salmon; commercial fisheries - shellfish; Dungeness crab = Metacarcinus magister (Cancer magister); economics; habitats; Lagoon Pond; Massachusetts; Pacific oyster = Crassostrea gigas; recreational fisheries - salmon; recreational fisheries - shellfish; salmonid species; Weeks Bay; Yaquina Bay

Impacts of climate change on Oregon’s coasts and estuaries - Ruggiero, Peter; Brown, Cheryl A.; Komar, Paul D.; Allan, Jonathan C.; Reusser, Deborah A.; Lee II, Henry (Oregon Climate Assessment Report, 2010)
This is Chapter 6 of the Oregon Climate Assessment Report. Predicts “Increased winter–early spring flow of coastal rivers and creeks and reduced flow during summer” for the Umpqua River (p.242)
Keywords: Alsea Bay; Alsea Spit; bacteria; Bayocean Spit; climate change; climate precipitation; coastal hazards; Columbia River estuary; Coos Bay; dissolved oxygen; El Nino; erosion; estuaries; geology; landslides; Nehalem Bay; Nehalem Spit; Neskowin (Or.); Netarts Bay; ocean acidification; Rockaway Beach; salinity; Salmon River Estuary; sea level; Siletz Bay; Tillamook Bay; water temperature; wave heights; Yachats River; Yaquina Bay

Interannual Differences in the Estuarine Ghost Shrimp, Neotrypaea californiensis. - Buncic, Michael (San Jose State University, 2010)
This thesis studies the genetics of ghost shrimp collected off the Oregon and Washington coasts. Ghost shrimp at Yaquina Bay are included "to compare differences with the ocean-bound larvae and possibly infer a relationship to any resulting recruitment." (from the Abstract) The study did find that Yaquina Bay ghost shrimp formed "a genetically distinct group" from the oceanic population. (p.32)
Keywords: Cape Meares; Cascade Head; genetics; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Heceta Head; spatial distribution; theses; Yaquina Bay

Joint Permit Application [NOAA Marine Operations Center - Pacific Relocation] - Port of Newport,; Pacific Habitat Services, (2010)
This is the application filed by the Port of Newport with the Army Corps of Engineers for permission to alter Yaquina Bay in order to allow the NOAA Marine Operations Center for the Pacific fleet to relocate from the Seattle area to Newport. "The construction of the MOC-P includes the demolition of existing structures (in-water as wellas upland structures), pile installation, wharf and access pier construction, as well as the construction of the upland facilities, including an administrative building and warehouse. The use of steel piles will require the installation of a cathodic protection system. Dredging and excavation to provide appropriate depths for NOAA ships to berth, as well as the placement of riprap for slope stabilization is also necessary." (p.4) Includes timeline, maps, tables, architectural drawings and construction schematics.
Keywords: Bentnose clam = Macoma nasuta; Butter clam = Saxidomus giganteus; dredging; Dungeness crab = Metacarcinus magister (Cancer magister); eelgrass = Zostera marina; English sole = Parophrys vetulus; green algae; harbors; Hatfield Marine Science Center; human impacts; mitigation; mysids; NOAA Marine Opeations Center - Pacific; Pacific sea blenny = Lumpenus sagitta; Port of Newport; ports; salinity; sediments; shiner perch = Cymatogaster aggregata; Ulva species. Enteromorpha species; water quality; Yaquina Bay

Linking ocean conditions to year class strength of the invasive European green crab, Carcinus maenas - Yamada, Sylvia Behrens; Kosro, P. Michael (Biological Invasions, 2010)
The authors correlate recruitment strength in the introduced European green crab in the Pacific Northwest with certain prevailing ocean conditions. "Once a non-native species arrives and survives in an area, its long-term persistence depends on its recruitment success. If conditions are not favorable for recruitment it will ultimately disappear. . . . Right now, green crabs are still too rare to exert a measurable effect on the native benthic community and on shellfish culture in Oregon and Washington. However, if their numbers were to increase, we would be able to predict the arrival of strong year classes from ocean conditions and alert managers and shellfish growers of possible increases in predation pressure from this invader. " [from the article abstract]
Keywords: Coos Bay; European green crab = Carcinus maenas; introduced species; Netarts Bay; Tillamook Bay; Yaquina Bay

Mapping intertidal eelgrass (Zostera marina L.) in three coastal estuaries of the Pacific Northwest USA using false colour near-infrared aerial photography - Young, David R.; Patrick J Clinton; Specht, David T. (International Journal of Remote Sensing., 2010)
Describes a technique for mapping seagrass beds from aerial photography. Includes maps showing Zostera marina beds in Yaquina, Umpqua and Coos estuaries. Yaquina Bay beds were photographed April 9, 2004.
Keywords: biological; Coos Bay; eelgrass=Zostera marina; geographic information system; Idaho Flats; Lower Yaquina River; map; Umpqua River estuary; Upper Yaquina River; Yaquina Bay; Yaquina River

Nuclear rDNA sequences of Wittrockiella amphibia (Collins) comb. nov. (Cladophorales, Chlorophyta) and morphological characterization of the mat-like growth form - Boedeker, Christian; Hansen, Gayle I. (Botanica Marina, 2010)
"Cladophora amphibia was found in Yaquina Bay (Oregon, USA) for the first time since the type collection from California in 1903. Vegetative plants were buried in the top centimeter of intertidal mud, partially covered by mats of Rhizoclonium and Chaetomorpha."
Keywords: algal species; Cladophora amphibia; genetics; taxonomy; Wittrockiella amphibia (Collins) comb. nov.; Wittrockiella paradoxa; Yaquina Bay

Recommended NWI Revisions and GIS Layer Development for Tidal Wetlands of the Yaquina and Alsea River Estuaries - Brophy, Laura S.; Green Point Consulting, (Green Point Consulting, 2010)
"Prepared for U.S. Geological Survey, Western Fisheries Research Center" Summarizes work done to generate a GIS dataset on tidal wetlands in the Yaquina and Alsea estuaries, updates a 1999 report prioritizing sites for conservation in the two estuaries, and recommends revisions to the National Wetlands Inventory of wetlands in the study area.
Keywords: Alsea Bay; Alsea River; aquatic vegetation; Bayview Oxbow; Boone Slough; Depot Slough; Drift Creek; Eckman Lake; geographic information system; habitat restoration; Lint Slough; McCaffery Slough; Nute Slough; Olalla Slough; Poole Slough; salt marsh; Starr Creek; terrestrial vegetation; wetlands; Yaquina Bay

Red alder (Alnus rubra) distribution influences nitrate discharge to coastal estuaries: comparison of two Oregon watersheds - Sigleo, Anne C.; Frick, Walter E.; Prieto, Lourdes (Northwest Science, 2010)
The Yaquina River typically carries almost twice as high a rate of dissolved nitrogen into its bay as does the Alsea River, although the total volumes are similar, because the Alsea River Basin is about twice as large as the Yaquina Basin. The difference in nitrogen load seems to be derived from the heavy alder stands in the upper Yaquina basin. Gives a model for rapid estimate of nitrogen export based on hardwood cover and water discharge data.
Keywords: Alsea Bay; nitrate-nitrite; nitrogen; red alder = Alnus rubra; terrestrial vegetation; Yaquina Bay

Rupture area and displacement of past Cascadia great earthquakes from coastal coseismic subsidence - Leonard, Lucinda J.; Currie, Claire A.; Mazzotti, Stephane; Hyndman, Roy D. (Geological Society of America Bulletin., 2010)
Keywords: Alsea Bay; Coos Bay; Coquille River; earthquakes; geology; Necanicum River; Nehalem River; Nestucca Bay; Netarts Bay; Salmon River; sediments; Siletz Bay; Siuslaw River; Sixes River; Tillamook Bay; tsunamis; Umpqua River; Yaquina Bay

A tsunami forecast model for Newport, Oregon - Righi, Dylan; Arrcas, Diego; Pacific Marine Environmental Laboratory, (PMEL Tsunami Forecast Series, 2010)
This document reports on the development of a tsunami forecast model for Yaquina Bay. The authors used 11 past Pacific basin earthquakes, from the 1946 Unimak to the 2007 Chile events, to generate a model that would explain the wave heights experienced at Yaquina Bay and to predict future wave heights. Although this publication does not make any predictions about "The Big One," it does report on past wave heights. Extensive color illustrations show how the waves affected the Bay. "NOAA OAR Special Report." This publication is also numbered as Contribution No. 3344 from NOAA/Pacific Marine Environmental Laboratory and Contribution No. 1771 from Joint Institute for the Study of the Atmosphere and Ocean (JISAO).
Keywords: coastal hazards; earthquakes; tsunamis; wave data; wave height; Yaquina Bay

Classification of Regional Patterns of Environmental Drivers and Benthic Habitats in Pacific Northwest Estuaries - National Health and Environmental Effects Research Laboratory (U.S.). Western Ecology Division, (2009)
"This report describes a pilot effort at classifying PNW estuaries with regards to landscape attributes and their susceptibility to nutrient enrichment." Much data is presented. Although the report focuses on seven estuaries (Alsea, Coos Bay, Nestucca, Salmon River, Tillamook Bay, Umpqua and Yaquina), many other estuaries are mentioned, and basic statistical data is given for all PNW estuaries.
Keywords: Alsea Bay; climate; Coos Bay; demographics; eelgrass = Zostera marina; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); hydrography; hydrology; Japanese eelgrass = Zostera japonica; Mud shrimp = Upogebia pugettensis; Nestucca River estuary; nitrate-nitrite; nitrogen; phosphorus; phytoplankton; precipitation; salinity; Salmon River Estuary; sediment data; tidal currents; Tillamook Bay; turbidity; Umpqua River estuary; Yaquina Bay

Conserved Lands of Yaquina Bay [cartographic material] - Lincoln Soil & Water Conservation District, (Lincoln Soil & Water Conservation District, 2009)
Overlay on aerial photograph. “The Lincoln County Soil and Water Conservation District produced this map to illustrate existing conservation easements as of 2009. The largest ownerships on the map are 8000 acres owned by Pacific Forest Trust and being managed for older forest conditions with revenue generation from thinning and selective logging, the Van Eck Trust Lands, and land owned by The Wetlands Conservancy. The Central Coast Land Conservancy owns two parcels and 2 conservation easements.” (Abstract)
Keywords: land ownership; maps; Yaquina Bay

Coupling between the coastal ocean and Yaquina Bay, Oregon: importance of oceanic inputs relative to other nitrogen sources - Brown, Cheryl A.; Ozretich, Robert J. (Estuaries and Coasts, 2009)
Shows that the ocean (through seasonal upwelling) is the dominant source of nitrogen in Yaquina Bay during the dry (May-October) season, while the river is the dominant source of nitrogen for the rest of the year. Modeled nitrates, phosphates and chlorophyll a in the bay.
Keywords: nitrate-nitrite; nutrient cycles; phosphate; Yaquina Bay; Yaquina River

The ecological role of bivalve shellfish aquaculture in the estuarine environment: A review with application to oyster and clam culture in West Coast (USA) estuaries - Dumbauld, Brett R.; Ruesink, Jennifer l.; Rumrill, Steven S. (Aquaculture, 2009)
Excellent review of the ecological impact of bivalve aquaculture on the West Coast.
Keywords: aquaculture; aquatic invertebrates; Baynes Sound (B.C.); bivalves; carbaryl; Coos Bay; Drakes Estero; Dungeness crab = Metacarcinus magister (Cancer magister); eastern oyster = Crassostrea virginica; economics; ecosystem health; eelgrass = Zostera marina; Geoduck clam = Panopea generosa; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Grays Harbor; Humboldt Bay; Manila clam = Venerupis japonica; molluscs; Netarts Bay; Olympia oyster=Ostrea lurida (Ostrea conchaphila); Pacific oyster = Crassostrea gigas; sediments; Softshell clam = Mya arenaria; Tillamook Bay; Tomales Bay; Totten Inlet (Puget Sound); water quality; Willapa Bay; Yaquina Bay

Estuarine Crab Resource Monitoring and Assessment Project: Yaquina Bay and Alsea Bay, Oregon - Vance, Mitch; Ainsworth, Justin; Oregon. Dept. of Fish and Wildlife. Marine Resources Program, (Oregon Dept. of Fish and Wildlife, 2009)
This is a poster-style presentation. Describes the beginning of a crab sampling program in 2008 and 2009. Sampling was done at 3 sites in Alsea Bay and 4 sites in Yaquina Bay. "Yaquina and Alsea bays are distinctly different estuarine ecosystems due to the differences in their size and drainage, their level of marine dominance, and anthropogenic alterations. Differences between the crab populations in these two estuaries may be related to the differences in the bays themselves. For example, the fact that we do not catch any red rock crab in Alsea Bay is probably due to the lack of rocky habitat that they prefer." (from the Discussion section)
Keywords: Alsea Bay; catch statistics; crustaceans; Dungeness crab = Metacarcinus magister (Cancer magister); growth; life history information; population biology; Red rock crab=Cancer productus; spatial distribution; Yaquina Bay

Geoarchaeological themes in a dynamic coastal environment, Lincoln and Lane Counties, Oregon - Davis, Loren G.; Jenevein, Steven A.; Punke, Michele L.; Noller, Jay S.; Jones, Julia A.; Willis, Samuel C. (Volcanoes to Vineyards: Geologic Field Trips through the Dynamic Landscape of the Pacific Northwest, 2009)
"In many ways, the modern Oregon coastline bears little resemblance to that associated with prehistoric coastal peoples prior to 3000 years ago..." (from the abstract). Examines how geological forces (earthquakes, sea level rise) have changed the landscape and obscured early peoples' occupations of the area. First stop on the tour is at the main HMSC parking lot, and the second stop is at Yaquina Head. Mentions Siletz, Yaquina, Alsea, Yachats and Siuslaw paleorivers. Includes maps showing paleorivers and what was above water before all the ice melted.
Keywords: archeology; Florence dune sheet; geology; Neptune State Park; Oregon State University Hatfield Marine Science Center; paleosciences; subsidence; tsunamis; Yaquina Bay; Yaquina Head

History of Olympia oysters (Ostrea lurida Carpenter 1864) in Oregon estuaries, and a description of recovering populations in Coos Bay - Groth, Scott; Rumrill, Steve (Journal of Shellfish Research, 2009)
"Historical evidence indicates that Olympia oysters (Ostrea lurida) are indigenous to at least three of Oregon's estuaries. Populations of O. lurida occur in Yaquina Bay, Netarts Bay, and Coos Bay, although only the population in Yaquina Bay seems likely to have been continuous since prewestern settlement."
Keywords: Coos Bay; historical; Netarts Bay; Olympia oyster = Ostrea lurida; population biology; Yaquina Bay

Utilization of Natural and Supplemental Biofuels for Harvesting Energy from Marine Sediments - Nielsen, Mark E (Oregon State University, 2009)
A benthic microbial fuel cell (BMFC) is an electrochemical device that generates current from the redox gradient at the sediment-water interface. Early prototypes had anodes buried in anoxic sediments and cathodes in overlying water. The BMFCs described in this dissertation are based on a chamber design that enables the use of high surface-area fiber electrodes and facilitates enhanced mass transport to the anode. Results from Yaquina Bay, OR, show that mass transport resistance accounted for at least 93% of the total internal resistance for a particular BMFC configuration. Power output was increased 18-fold by mechanically induced fluid transport through the anode chamber. At a cold seep in Monterey Canyon, CA, naturally driven advection resulted in a five-fold increase in power from a BMFC with low-pressure check valves relative to an identical BMFC with high-pressure check valves. Enhanced transport coincided with a change in the microbial community on the anode from one dominated by epsilonproteobacteria to one with relatively even representation from deltaproteobacteria, epsilonproteobacteria, firmicutes and flavobacterium/cytophaga/bacterioides. Laboratory experiments investigated the effect of adding supplemental carbon sources to anode chambers. Repeated lactate injections appeared to stimulate sulfate reduction resulting in short term power gains but did not apparently shift the process responsible for baseline current. When a specific inhibitor of sulfate reduction was added, lactate-supplemented and unsupplemented BMFCs performed similarly. BMFCs have been proposed as power sources for monitoring systems in remote locations. Practical implementation of this technology is governed by three conditions: 1) low-voltage current must be stepped up to meet the requirements of off-the-shelf electronic devices, 2) modest power production and variable power demands require integrated energy storage, and 3) BMFCs should be operated at the most efficient potential for energy production. A combination power converter/potentiostat/rechargeable battery system was described based on these considerations and tested with a chambered BMFC in Yaquina Bay, OR. The BMFC provided intermittent power to an acoustic receiver, and results highlight the need to increase power, make design improvements to better seal the chamber to the sediment and increase the capacity for energy storage.
Major professor was Clare Reimers.
Keywords: chemical; Embarcadero Marina; energy; Hatfield Marine Science Center; microbiology; theses; Yaquina Bay

The Coastal Connection: Assessing Oregon Estuaries for Conservation Planning - Aldous, Allison; Brown, Jenny; Elseroad, Adrien; The Nature Conservancy in Oregon (The Nature Conservancy in Oregon, 2008)
A good overview of the concepts used for evaluating the health of estuaries in Oregon. Identifies data sources, standards. Good bibliography.
Keywords: Alsea Bay; Beaver Creek; Chetco River; coastal hazards; Coos Bay; Coquille River; Depoe Bay; eelgrass = Zostera marina; erosion; general ecosystem description; habitats; hydrology; introduced species; landslides; marshes; Necanicum River; Nehalem River; Nestucca Bay; Netarts Bay; Rogue River; salinity; Salmon River Estuary; Sand Lake; sediments; Siletz Bay; Siltcoos Creek; Siuslaw River; Sixes River; Tahkenitch Creek; Tenmile Creek; Tillamook Bay; water quality; Yachats River; Yaquina Bay

Colonial power and indigenous justice: fur trade violence and its aftermath in Yaquina narrative - Byram, Robert Scott (Oregon Historical Quarterly, 2008)
Why were there so few Native Americans in Yaquina Bay when white settlers arrived? One possible answer is that many of them were murdered in 1832 by staff of the Hudson’s Bay Company. The attack was in retaliation for the killing by Alsea Indians of two Hudson’s Bay trappers. Many inhabitants of a large village near Oysterville were killed. “Diminished as a nation and displaced from their homelands, Yaquina survivors memorialized their losses in oral narrative that reveals the depth of impacts throughout the colonization process, and the injustice of colonial power relations.” (p.382)
Keywords: Alsea Bay; Alsea Indians; Beaver Creek; Coastal Indian Reservation; historical; Hudson’s Bay Company; Native Americans; Oysterville; Siletz Indian Reservation; Yaquina (Or.); Yaquina Bay; Yaquina Indians

Dispersal and Population Structure of Neotrypaea californiensis - Kozuka, Kenji (San Jose State University, 2008)
Keywords: genetics; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); spatial distribution; theses; Yaquina Bay; zooplankton

A dynamic model of an estuarine invasion by a non-native seagrass - Almasi, Kama N.; Eldridge, Peter M. (Estuaries and Coasts, 2008)
The authors model an invasion of an introduced seagrass in Yaquina Bay. They predict it will grow rapidly for the first 20 years following its introduction. "This rapid expansion is followed by apparent cycles around an equilibrium point, and is unaffected by spatial scale differences." The authors believed that the Japanese eelgrass in Yaquina Bay was, at the time the article was written, in a cycle of "high population growth." (p.173)
Keywords: eelgrass=Zostera marina; introduced species; Japanese eelgrass = Zostera japonica; Yaquina Bay

Economic Benefits of Conservation Natural Lands: Case Study: Yaquina Bay Conservation Opportunity Area, Oregon - Kroeger, Timm; McMurray, Anna (Defenders of Wildlife, 2008)
If you have ever wondered what undeveloped land in estuaries is worth, this publication might be of interest. This study, based on 2004 data, wasn’t able to quantify the value of every service performed by undeveloped land and open spaces, but does a good job of detailing what is possible to quantify. “Recreational fishing is the activity that generates the single largest value, followed by commercial crabbing and oyster harvests. Carbon sequestration, the only ecosystem service included in our analysis, generates substantial economic value as well, although the current uncertainties surrounding access and credit prices on emerging carbon markets make this estimate somewhat less reliable than those for the other uses we examine.” (p.1-2)
Keywords: agriculture; carbon; commercial fisheries - groundfish; economics; education; forestry; Hatfield Marine Science Center; human impacts; recreation; recreational fisheries – groundfish; salmon; shellfish; Yaquina Bay

Effects of erosion and macroalgae on intertidal eelgrass (Zostera marina) in a northeastern Pacifid estuary (USA) - Boese, Bruce L.; Robbins, Bradley D. (Botanica Marina, 2008)
This study is concerned with the natural factors that limit the distribution and growth of inter-tidal eelgrass. The authors suggest that dessication from exposure to the air, along with macroalgae and erosion all limit eelgrass, "and that these factors operate in an acute rather than a chronic manner." (from the Abstract)
Keywords: algae; Coquille Point; eelgrass = Zostera marina; erosion; Hatfield Marine Science Center; Idaho Flats; Oneatta Point; sediments; Ulva species; Yaquina Bay

A fishermen's agreement and co-op in Yaquina Bay roe herring - Leal, D. R. (Case Studies in Fisheries Self-Governance, 2008)
This paper describes a private agreement between fishermen participating in a limited-entry commercial fishery for herring roe in Yaquina Bay. The co-operative formed by this agreement gives the fishermen greater flexibility, allowing them to fish when roe is likely to likely to be more abundnat, and the agreement "has proven resilient to widely fluctuating resource and market conditions..." (p.422) Map, tables. Gives statistics for herring landings in Yaquina Bay from 1978-2006.
Keywords: abundance; commercial fisheries; depleted populations; economics; fecundity; Pacific herring = Clupea pallasi; Yaquina Bay

Measuring the contribution of benthic ecosystem engineering species to the ecosystem services of an estuary: a case study of burrowing shrimps in Yaquina Estuary, Oregon [abstract only] - DeWitt, Theodore H.; D’Andrea, Anthony F.; Griffen, Blaine D.; Eldridge, Peter; O’Higgins, Timothy G. (ACES: A Conference on Ecosystem Services, 2008)
This is a brief summary of EPA’s studies on burrowing shrimp in the Yaquina River estuary.
Keywords: bioturbation; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Mud shrimp = Upogebia pugettensis; sediments; Yaquina Bay

The potential for mitten crab Eriocheir sinensis H. Milne Edwards, 1853 (Crustacea: Brachyura) invasion of Pacific Northwest and Alaskan Estuaries - Hanson, Erik; Sytsma, Mark (Biological Invasions, 2008)
The estuaries of the Pacific Northwest are generally too small, too cold, and have too short flushing times to permit mitten crabs to thrive in them. Coos Bay and Yaquina Bay were studied in Oregon.
Keywords: Coos Bay; introduced species; Mitten crab = Eriocheir sinensis; Yaquina Bay

Re-emergence of Vibrio tubiashii in bivalve shellfish aquaculture: severity, environmental drivers, geographic extent and management - Elston, Ralph A.; Hasegawa, Hiroaki; Humphrey, Karen L.; Polyak, Ildiko K.; Hase, Claudia C. (Diseases of Aquatic Organisms, 2008)
An outbreak of vibriosis that appeared on the West Coast in the summer of 2006 and peaked in 2007 is described, along with methods of reducing contamination. Relationships between oyster die-offs and severe upwellings and El Nino are suggested. "We first recorded a severe outbreak of vibriosis, for which the etiological agent was later confirmed to be toxigenic Vibrio tubiashii, in 1998 from a hatchery on Netarts Bay. The SST [sea surface temperature] during this period was unusually elevated and remarkably similar to the elevated temperature regime observed in 2007, when severe vibriosis re-emerged."
Keywords: aquaculture; molluscs; Netarts Bay; shellfish disease; Vibrio tubiashii; Yaquina Bay

Regional Surveys and Outreach for the Non-Indigenous Burrowing Isopod, Sphaeroma quoianum. - Davidson, Timothy M.; de Rivera, Catherine E. (2008)
"Report Submitted to the Western Regional Panel on Aquatic Nuisance Species, U.S. Fish and Wildlife Service." "While S. quoianum has not spread to these new areas, ... the populations in Yaquina Bay appear to have expanded since 2005. S. quoianum was found in 42% (21/50) of surveyed sites in Yaquina Bay and some sites hosted very high densities of the isopod... In addition, S. quoianum is now potentially impacting the local economy of Yaquina Bay: Oregon Oyster replaced their dock floats recently and nearly every one of the 60 one-meter long newly removed Styrofoam billets were riddled with S. quoianum burrows..." (p.10) Includes photographs of damaged floats at Oregon Oyster Farms on Yaquina Bay.
Keywords: Coos Bay; erosion; invasive species; isopods; Oregon Oyster Farms; Sphaeroma quoianum; Yaquina Bay

Use of Extractable Lipofuscin As an Age Biomarker to Determine Age Structure of Ghost Shrimp (Neotrypaea californiensis) Populations in West Coast Estuaries - Cassidy, Katelyn M. (Oregon State University, 2008)
"The data presented here show that biochemical-based aging can now be widely used to assess age in N. californiensis, facilitating more in-depth investigations of basic biological and ecological processes for this species." (from the Abstract) Major professors were Brett R. Dumbauld and Christopher J. Langdon.
Keywords: age composition; genetics; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); life history information; population biology; statistics; theses; Tillamook Bay; Willapa Bay; Yaquina Bay

Will the European green crab (Carcinus maenas) persist in the Pacific Northwest? - Yamada, Sylvia Behrens; Gillespie, Graham E. (ICES Journal of Marine Science: Journal du Conseil, 2008)
After the strong 1997/1998 El Nino, young green crabs appeared in several West Coast estuaries. The question is: would European green crabs maintain viable populations in their new environments once ocean conditions became less favorable to their survival? This paper reports on a study of European green crabs during their first ten years in the Pacific Northwest. Their populations declined as the 1997/1998 El Nino ebbed and less favorable conditions resumed. The downward trend was reversed in 2005 and 2006, however, and it now seems likely that "if winters remain mild and green crabs continue to recruit well, it is highly likely that they will spread to northern British Columbia and Alaska."
Keywords: Coos Bay; El Nino; European green crab = Carcinus maenas; Grays Harbor; invasive species; Netarts Bay; Tillamook Bay; Willapa Bay; Yaquina Bay

An Approach to Developing Nutrient Criteria for Pacific Northwest Estuaries : a Case Study of Yaquina Estuary, Oregon - Brown, Cheryl A.; National Health and Environmental Effects Research Laboratory (U.S.). Western Ecology Division., (U.S. Environmental Protection Agency, Office of Research and Development, 2007)
Color illustrations, maps. "June 2007.""EPA 600/R-07/046." Good summary of physical and biotic characteristics of the estuary, as well as the history of land use.
Keywords: nutrient cycles; water pollution; water quality; Yaquina Bay

Contaminant exposure in outmigrant juvenile salmon from Pacific Northwest estuaries of the United States - Johnson, Lyndal L.; Ylitalo, Gina M.; Arkoosh, Mary R.; Kagley, Anna N.; Stafford, Coral; Bolton, Jennie L.; Buzitis, Jon; Anulacion, Bernadita F.; Collier, Tracy K. (Environmental Monitoring and Assessment, 2007)
When juvenile salmonids migrate downstream towards the ocean, they can encounter and absorb harmful chemicals such as DDT, polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and pesticides. The authors of this paper measured harmful chemicals in tissues of juvenile salmonids, and in their prey. They also measured stomach contents of salmon from estuaries and hatcheries. Results were not surprising: industrial estuaries such as the Columbia River, Coos Bay and Yaquina Bay showed high contaminant exporsure (Yaquina Bay was high in PCBs in Chinook salmon), while natural estuaries like the Salmon and Elk River estuaries, had low exposures to harmful chemicals. Some of the conservation estuaries, including Alsea Bay, had relatively high exposures to contaminants. . Juvenile Chinook were more vulnerable than coho salmon.
Keywords: Alsea Bay; Chinook salmon = Oncorhynchus tshawytscha; Coho salmon = Oncorhynchus kisutch; Columbia River; Coos Bay; Coquille River estuary; DDT; Elk River; juvenile fish; migration; pesticides; Salmon River; Salmon River Hatchery; Tillamook Bay; water pollution; Yaquina Bay

An examination of the spatial and temporal generality of the influence of ecosystem engineers on the composition of associated assemblages - Berry, Richard L.; Rowden, Ashley A. (Aquatic Ecology, 2007)
Examined the manner and mechanisms by which ghost shrimp and eelgrass influenced associated benthic assemblages. Compared temperate estuaries in New Zealand and the U.S. Studied Otago Harbour, Blueskin Bay and Papanui Inlet in New Zealand and Tillamook Bay, Yaquina Bay and Netarts Bay in Oregon. Transplanted shrimp into low- and high-density plots of eelgrass and eelgrass into low- and high-density plots of ghost shrimp. Noted which associated benthic species were sensitive to the differences in density. Also noted seasonal factors: seagrass has a competitive advantage in spring, while ghost shrimp are most active and have a greater advantage in summer. "Most discriminating taxa generally showed a strong prevalence for treatment sites that contained seagrass, implying that seagrass is the dominant ecosystem engineer in the systems studied."
Keywords: bioturbation; ecosystem modeling; Ghost shrimp = Neotrypaea californiensis (Callianassa californiensis); Japanese eelgrass = Zostera japonica; Netarts Bay; Tillamook Bay; Yaquina Bay

Nutrient fluxes in the microalgal-dominated intertidal regions of the lower Yaquina estuary, Oregon (USA) - Sin, Yongsik; Sigleo, Anne C.; Song, Eunsook (Northwest Science, 2007)
This study was launched to learn how important microalgae were to the productivity of Yaquina Bay, and to determine “sediment nutrient fluxes in the microalgal dominated sediments” (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 “benthic microalgae control the nutrient fluxes to the water column" (p.59).
Keywords: algae; ammonium; chemistry; estuarine dynamics; Hatfield Marine Science Center; Idaho Flats; nitrate; nitrogen dioxide; nutrient cycles; phosphate; precipitation; primary productivity; Sally’s Bend; sediments; silicon; upwelling; Yaquina Bay

Small-scale heterogeneity in the geochemistry of seagrass vegetated and non-vegetated estuarine sediments: causes and consequences - Hebert, Andrew B.; Morse, John W.; Eldridge, Peter M. (Aquatic Geochemistry, 2007)
Study of seagrass growth in Yaquina illustrates the complexity of the environment and the biological and geochemical processes taking place.
Keywords: carbon cycle; eelgrass=Zostera marina; geochemistry; Idaho Point; sediments; sulfur cycle; Yaquina Bay

The Collaborative Study of Juvenile Rockfish, Cabezon, and Kelp Greenling Habitat Associations between Morro Bay, California and Newport, Oregon: Final report to: Pacific States Marine Fisheries Commission Summarizing Data for 2003, 2004 and 2005 - Schlosser, Susan; Bloeser, Jennifer (2006)
"California Sea Grant and Pacific Marine Conservation Council Cooperative Research Project." Various juvenile rockfish, kelp greenling and cabezon were trapped both offshore and in various bays and ports in Oregon and California. Port Orford, Coos Bay and Newport were the Oregon sites. Trapping took place between June, 2003 and December, 2005. The goal was to identify the habitat associated with each species. The most abundant trapped juvenile species in Yaquina Bay was the black rockfish (181), followed by kelp greenling (69), copper rockfish (58) and cabezon (27). Yaquina Bay rockfish and cabezon preferred pilings and mud sites in deeper water in channels near eelgrass. Yaquina Bay kelp greenling preferred mud and sand sites, with over 90% found near piling.
Keywords: Black rockfish = Sebastes melanops; cabezon = Scorpaenichthys marmoratus; Coos Bay; Copper rockfish = Sebastes caurinus; geographic distribution; habitats; juvenile fish; kelp greenling=Hexagrammos decagrammus; Rockfish = Sebastes spp.; Yaquina Bay

Development of an autonomous in-situ analyzer for dissolved copper in the marine environment - Holm, C.E.; Chase, Z.; Johnson, K.S.; Jannasch, H.W. (EOS, Transactions of the American Geophysical Union, 2006)
Keywords: chemical; Yaquina Bay

Evidence for resource partitioning and competition in nursery estuaries by juvenile flatfish in Oregon and Washington - Rooper, Christopher N.; Gunderson, Donald R.; Armstrong, David A. (Fishery Bulletin, 2006)
Estuaries can provide important nursery areas for juvenile fish. Juvenile flatfish often congregate in areas that are distinct from adult populations. In this study, juvenile fish from four flatfish species were found to use different parts of Pacific Northwest estuaries during the summer. Temperature, salinity, and sediment type may affect distribution. The authors did find evidence of competition for food between English sole and Pacific sanddab.
Keywords: Coos Bay; English sole = Pleuronectes vetulus; feeding behavior; geogrphical distribution; Grays Harbor; Pacific sanddab = Citharichthys sordidus; sand sole = Psettichthys melanostictus; Starry flounder = Platichthys stellatus; territoriality; Willapa Bay; Yaquina Bay

The Invasion of the Australasian Burrowing Isopod (Sphaeroma quoianum) in Coos Bay, Oregon - Davidson, Timothy Mathias (University of Oregon, 2006)
"During an intertidal survey of Yaquina Bay, Oregon, a single adult Sphaeroma specimen was discovered burrowed into a piece of decayed wood in Boone Slough on March 2, 2005... In a subsequent survey (August 29, 2005), numerous burrows were found in a marsh bank in the same location. Several adult and juvenile Sphaeroma were found within the burrows, suggesting the establishment of a reproducing population ..." (p.127)
Keywords: Boone Slough; Coos Bay; erosion; introduced species; isopods; life history information; population biology; theses; Yaquina Bay

Laboratory and field evidence for structural habitat affinity of young-of-the-year lingcod - Petrie, M. E.; Ryer, C. H. (Transactions of the American Fisheries Society, 2006)
Juvenile lingcod were captured in Yaquina Bay. Their habitat preferences were studied in the laboratory, then fish were radio-tagged and released in the bay, and those habitat preferences were studied. Juvenile lingcod seem to prefer relatively deep water and structurally complex sites that provide refuge from predators.
Keywords: behavior; habitats; life history information; Lingcod = Ophiodon elongatus; Yaquina Bay

Range expansion in the northeast Pacific by an estuary mud crab -- a molecular study - Petersen, Christine (Biological Invasions, 2006)
Authors checked for signs of presence of the introduced Harris mud crab. Adults closely resemble the Oregon shore crab, Hemigrapsus oregonensis. First found in Yaquina Bay in 1978. "R. harrisii was discovered in ... Yaquina River 12 km from the ocean near the town of Toledo, approximately where the 10 ppt salinity isocline occurs. In Oregon, R. harrisii always occurred at salinities below 15 ppt, and rarely could be found to co-occur with H. oregonensis."
Keywords: Coos Bay; Harris mud crab = Rhithropanopeus harrisii; introduced species; Netarts Bay; Oregon shore crab = Hemigrapsus oregonensis; Tillamook Bay; Umpqua River; Yaquina Bay

Salmon Recovery in the Pacific Northwest: Defining What Constitutes a Wild Salmon - Courter, Ian I. (Oregon State University, 2006)
Attempts to define the concept of "wild" salmon as a continuum including hatchery fish. Asserts that criticism of the effects of hatcheries on wild salmonids is influenced by values, not science. Includes statistics on hatcheries, wetland loss and runs. Major professor was Robert T. Lackey.
Keywords: Alsea Bay; Beaver Creek; Coos Bay; Coquille Bay; depleted populations; habitats; hatcheries; hatchery salmonids; human impacts; Lower Umpqua River; Necanicum Bay; Nehalem Bay; Nestucca Bay; Oncorhynchus species; Salmon River Estuary; Siletz Bay; Siltcoos Creek; Siuslaw estuary; Sixes River estuary; Tahkenitch Creek; Tenmile Creek; theses; Tillamook Bay; Upper Umpqua River; wild salmonids; Yaquina Bay

Bay Clam Dive Fishery - MdCrae, Jean; Oregon. Dept. of Fish and Wildlife. Developmental Fisheries, (2005)
This is an exhibit prepared by the Oregon Dept. of Fish and Wildlife for the Oregon Fish and Wildlife Commission. Prior to November, 2005, ODFW managed a developmental fishery program for commercial harvest of bay clams by scuba divers. This document recommends removing bay clams from the developmental fisheries species list and setting up a limited entry system for the commercial bay clam divers.
Keywords: Alsea Bay; Butter clam = Saxidomus giganteus; Cockle clam = Clinocardium nuttallii (Cardium corbis); commercial fisheries - shellfish; Coos Bay; natural resource management; Nehalem Bay; Netarts Bay; Tillamook Bay; Umpqua River estuary; Winchester Bay; Yaquina Bay

Dessication is a limiting factor for ellgrass (Zostera marina L.) distribution in the intertidal zone of a northeastern Pacific (USA) estuary. - Boese, Bruce L.; Robbins, Bradley D.; Thursby, G. B. (Botanica Marina., 2005)
Keywords: biological; eelgrass = Zostera marina; growth; Idaho Flats; Idaho Point; King Slough; life history information; The Bend; Yaquina Bay; Yaquina City

Hatfield Marine Science Center Trail Erosion Study: Technical Report - Parametrix, Inc. (2005)
"Erosion is impacting a portion of the Estuary Nature Trail located adjacent to Oregon State University's Hatfield Marine Science Center (HMSC) facility, located on the south side of the Yaquina Bay estuary approximately one mile from the open waters of the Pacific Ocean. The HMSC Estuary Nature Trail is important to many trail users, as it is the only trail in the Yaquina Bay estuary running along side the bay." (From the Background section, p.1-1) Includes color photographs and color infrared aerial photographs.
Keywords: coastal hazards; erosion; Hatfield Marine Science Center; Yaquina Bay

Nitrate variability along the Oregon coast: Estuarine–coastal exchange - Sigleo, Anne C.; Mordy, C. W.; Stabeno, P.; Frick, Walter E. (Estuarine, Coastal and Shelf Science, 2005)
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..
Keywords: nitrate-nitrite data; nitrogen; nutrient cycles; upwelling; Yaquina Bay

The Size of the Oregon Coastal Salmon Runs in the Mid-1800s - Meengs, Chad C. (Oregon State University, 2005)
"Presented July 12, 2004. Commencement June 2005." Attempts to reconstruct data regarding salmon populations circa 1850 and contrast that data with contemporary statistics. Tables give estimated run sizes and loss of lands in estuaries. Suggests that ocean conditions are the most significant factor affecting salmon runs, and that improving habitats in estuaries and lowlands would be a way to improve salmon runs. Includes historical photographs. Major professor was Robert T. Lackey.
Keywords: Alsea; Chetco; chinook salmon=Oncorhynchus tshawytscha; coho salmon=Oncorhynchus kisutch; Coos; Coquille; depleted populations; habitats; historical; logging; mining; Necanicum; Nehalem; Nestucca; Netarts; Rogue; Salmon River; Sand Lake; Siletz; Siuslaw; theses; Tillamook Bay; Umpqua; Yaquina Bay

A telemetry study of downstream coho smolt movement in the Yaquina River and estuary [abstract only] - Power, James H.; Johnson, Steven L.; Wilson, Derek (American Fisheries Society. Oregon Chapter. Meeting & Symposium. Annual meeting & symposium, 2005)
Presented at Oregon Chapter of the American Fisheries Society, Corvallis, OR, February 16 - 18, 2005.
Keywords: biological; coho salmon=Oncorhynchus kisutch; Yaquina Bay; Yaquina River

Tide gates in the Pacific Northwest: operation, types, and environmental effects - Giannico, Guillermo R.; Souder, Jon A. (ORESU-T, 2005)
Like all Sea Grant publications, this is a very helpful document, guiding landowners and interested parties in understanding how tide gates work, how to upgrade them, and whether to remove them. This well illustrated report includes information about environmental effects of tide gates, design types, manufacturers and relevant legislation.
Keywords: Coho salmon = Oncorhynchus kisutch; depleted populations; dike removal; environmental law and policy; fish passage; flooding; human impacts; Pacific salmonids = Oncorhynchus spp.; salinity; Salmon River Estuary; sediments; Siletz Bay; Tidal channels; Tide gates; water temperature; wetland restoration; Yaquina Bay

Yaquina Bay and South Beach Marine Sediment Quality Evaluation Report - Sherman, Tim; U.S. Army. Corps of Engineers. Portland District, (U.S. Army Corps of Engineers. Portland District, 2005)
Keywords: chemical; dredging; physical; sediment data; sediments; South Beach Marina; Yaquina Bay

Yaquina Bay, Oregon Geographic Response Plan (GRP) - Northwest Area Committees, (2005)
"1 September 2005." This is an emergency response plan for an oil spill in or near Yaquina Bay. "This plan prioritizes resources to be protected and allows for immediate and proper action. By using this plan, the first responders to a spill can avoid the initial confusion that generally accompanies any spill." (p.iv)
Keywords: Arnold Creek; Blind Slough; Boone Slough; breakwater; Butler Bridge; Coquille Point; Depot Slough; Embarcadero Marina; Flesher Slough; Hatfield Marine Science Center; hazardous waste; Johnson Slough; McCaffery Slough; McLean Point; Mill Creek; Nute Slough; oil spills; Olalla Slough; Oregon Oyster Farm; Parker Slough; Poole Slough; South Beach Marina; Toledo; Weiser Point; Yaquina Bay; Yaquina Bay Bridge

The Application of Geographic Information Systems for Delineation and Classification of Tidal Wetlands for Resource Management of Oregon’s Coastal Watersheds - Scranton, Russell W. (Oregon State University, 2004)
This report is the product of a Capstone Project and is submitted in place of a thesis. "Research paper submitted to Marine Resource Management Program, College of Oceanic & Atmospheric Sciences, Oregon State University, Corvallis, Oregon, in partial fulfillment of the requirements for the degree of Master of Science." Not just a technical report, this is a reader-friendly look at GIS in conservation. Good summary of historical regulation. Gives acreages potentially available as wetlands for streams covered. Major professor was Robert Frenkel.
Keywords: Alsea River; Beaver Creek; Coos Bay; Coquille River; Depoe Bay; geographic information systems; Necanicum River; Nehalem River; Nestucca Bay; Netarts Bay; Salmon River Estuary; salt marsh vegetation; Sand Lake; Siletz Bay; Siltcoos River; Siuslaw River; Sixes River; Ten Mile Creek; tidal data; Tillamook Bay; Umpqua River; wetland vegetation; wetlands; Yaquina Bay

The effects of tide gates on estuarine habitats and migratory fish - Giannico, Guillermo R.; Souder, Jon A. (ORESU-G, 2004)
“Tide gates tend to be effective at maintaining low water levels on the upland side of dikes. Unfortunately, by altering water flow they have some undesirable side effects that can be classified into three main—but interrelated—categories: physical, chemical, and biological” (p.1). This report summarizes these effects. Richly illustrated with line drawings and photographs.
Keywords: Coho salmon = Oncorhynchus kisutch; depleted populations; dike removal; environmental law and policy; fish passage; human impacts; Pacific salmonids = Oncorhynchus spp.; salinity; Salmon River Estuary; sediments; Siletz Bay; Tidal channels; Tide gates; water temperature; wetland restoration; Yaquina Bay

Improving Pacific Oyster (Crassostrea gigas) Production through Selective Breeding - Evans III, Sanford (Oregon State University, 2004)
This dissertation describes efforts to assess the importance of nursery conditions and genetics on Pacific oyster production. Environmental conditions in Yaquina Bay and Yaquina River, including water temperature and salinity, are discussed. Major professor was Christopher J. Langdon.
Keywords: aquaculture; aquatic invertebrates; bivalves; Dabob Bay (Washington); genetics; growth; Hatfield Marine Science Center; Molluscan Broodstock Program; molluscs; Oregon Oyster Farm; Pacific oyster = Crassostrea gigas; salinity; water temperature; Yaquina Bay; Yaquina River

Yaquina Bay - Query, Charles Floyd (Oregon Ferries: a History of the Ferries on Oregon's Major Waterways Since 1826, 2004)
Lists 16 ferries that worked on the Yaquina River from 1869 to 1936. In some cases, only the name of the boat is given. Sources given and locations of photographs, when available.Index, bibliography.
Keywords: ferries; Yaquina Bay