Continental shelves located along eastern boundary currents occupy relatively small volumes of the world’s oceans, yet are responsible for a large proportion of global primary production. The Oregon coast is among these ecosystems. Recent analyses of dissolved oxygen at shallow depths in the water column has suggested increasing episodes of hypoxia and anoxia, events that are detrimental to larger macro-faunal species. Microbial communities, however, are metabolically diverse, capable of utilizing alternative electron donors and acceptors, and can withstand transient periods of low dissolved oxygen. Understanding the phylogenetic and metabolic diversity of microorganisms in these environments is important for assessing the impact hypoxic events have on local and global biogeochemistry. Several molecular ecology tools were used to answer questions about the distribution patterns and activities of microorganisms residing along the coast of Oregon in this dissertation. Ribosomal rRNA fingerprinting and sequence analyses of samples collected during 2007-2008 suggested that bacterial community structure was not substantially influenced by changes in dissolved oxygen. However, substantial depth dependent changes were observed, with samples collected in the bottom boundary layer (BBL) displaying significant differences from those collected in the surface layer. Phylogenetic analyses of bacterial rRNA genes revealed novel phylotypes associated with this area of the water column, including groups with close evolutionary relationships to putative or characterized sulfur oxidizing bacteria (SOB). Analysis of metagenomes and metatranscriptomes collected during 2009 suggested increasing abundances of chemolithoautrophic organisms and their activities in the BBL. Thaumarchaea displayed significant depth dependent increases during the summer, and were detected at maximal frequencies during periods of hypoxia, suggesting that nitrification maybe influenced by local changes in dissolved oxygen. Metagenomic analysis of samples collected from 2010 revealed substantial variability in the metabolic potential of the microbial communities from different water masses. Samples collected during the spring, prior to upwelling clustered independently of those collected during the summer, during a period of upwelling, and did not display any clear stratification. Samples collected during the summer did cluster based on depth, consistent with previous observations, and increases in the relative abundances of chemolithotrophic gene suites were observed in the BBL during stratified conditions, suggesting that the metabolic potential for these processes is a repeatable feature along the Oregon coast. Overall, these observations suggest that depth impacts microbial community diversity, metabolic potential, and transcriptional activity in shallow areas of the Northeast Pacific Ocean. The increase in lithotrophic genes and transcripts in the BBL suggests that this microbial community includes many organisms that are able to use inorganic electron donors for respiration. We speculate that the dissolved organic material in the BBL is semi-labile and not available for immediate oxidation, favoring the growth for microorganisms that are able to use alternative electron donors. / Graduation date: 2012

Recent emphasis on linkages between essential fish habitat and fish stock productivity has raised concerns about the management of fishing activities such as trawling, which have the potential to impact fish habitat. Knowing specifically where and how intensively trawl effort has occurred over time provides ecologists with the necessary background for habitat impact and recovery studies, and provides fishery managers with an assessment of how habitat conservation objectives are being met. The objectives of this study were to (1) examine the extent to which the 2000 Pacific Fishery Management Council footrope restriction has shifted and reduced trawl fishing effort on Oregon fishing grounds, (2) to relate these changes in distribution to the benthic habitat type over which they occur, and (3) to develop methods for enhancing fine-scale spatial review of targeted fishing effort. Density analysis of available trawl start locations provided a spatial and temporal understanding of how fishing efforts increased and decreased in relation to habitat distribution and fishery management actions between 1995 and 2002. Trawl effort patterns exhibit significant inter-annual variability and patchy distribution. Areas of increased fishing effort were still evident between years, despite an overall decline in trawl tows across the time scale of this study. Tow end point locations for the years 1998-2001 were retrieved from manual logbooks for five reference sites located in the proximity of rock habitat features. Trawl towlines were mapped from start to end point and demonstrated a marked enhancement of fine-scale fishing effort resolution, with increased ability to identify effort shifts over benthic habitat. Distinct spatial shifts in fishing intensity (measured as km towed) away from rock habitat were evident at all reference sites, with an average reduction of 86%. Some slight shifts into surrounding unconsolidated sediments also occurred, indicating effort displacement as well as reduction. Fishing intensity was calculated from commercial trawl and research trawl survey towlines to achieve the most accurate assessment of fishing impacts and potential habitat recovery areas. Research trawling intensity was less than 1% of commercial trawl effort originating from the same sites. A brief comparison of Oregon vessel towlines and California vessel towlines demonstrated similar targeted fishing patterns by both fleets, except at one site. Results indicate that the footrope restriction, in conjunction with associated landing limits, was effective in protecting rocky habitats from trawl fishing impacts. Reference areas were identified where essential fish habitat (EFH) recovery is likely occurring off the coast of Oregon. Substantial regulatory changes continue in this fishery, with trip limits and gear restrictions continuously adjusted. Continued monitoring and review of spatial trawl data would assist in fishery management decision-making and assess conservation objectives for depleted groundfish and associated habitats. Future research should incorporate analysis of catch data and expand the review of trawl towlines for the entire US West coast groundfish fishery. The trawl towline spatial analysis developed in this work is a credible method for reviewing fishing effort at the scale of the fishery and in relation to detailed habitat data. The research presented here provides an example of how an interdisciplinary approach and critical assessment of data can work to resolve marine management challenges. / Graduation date: 2004

The Pacific Coastal ecoregion contains large tracts of economically important forest lands that also serve as critical stream habitat for endangered Salmonids. Excessive fine sediment deposition in streams of this region is a major environmental concern in the region but difficult to measure directly. The use of stream invertebrates to monitor fine sediment conditions in streams requires careful consideration of several important factors that complicate their use as bioindicators including high spatial and temporal variability and covariance with other environmental variables. To evaluate the use of stream invertebrates as bioindicators of excessive fine sediment, three hypotheses were tested. The first hypothesis was that invertebrates would be related to broad-scale climate variables (Chapter 2). The second hypothesis was that functional aspects of the invertebrate community would serve as useful indicators of excessive fine sediment condition (Chapter 3). The third hypothesis was that invertebrates in streams with naturally high levels of sediment would be tolerant to fine sediment (<2 mm, Chapter 4). Hypotheses were tested using a temporal data set at two streams in western Oregon, spatial data from 214 sites across the Oregon Coast Range, and in-situ experiment conducted in streams with erosive or resistant geologies. In the temporal study, both invertebrate density and functional traits were positively related to El Nino strength (R2 range = 0.22-0.36, ρ range = 0.008-0.04) and air temperature (R2 range = 0.32-0.49, ρ range = 0.002-0.01). The spatial study identified several environmental and hydrological factors that exhibited strong negative controls on both fine sediment (Mantel r range 0.14-0.25, ρ range = 0.001-0.01) and invertebrate Scrapers (R2 range = 0.11-0.14, ρ range = 0.001-0.04). The result of the experimental study provide evidence that invertebrates in streams with erosive geologies exhibit tolerance to sediment addition when compared to invertebrates in resistant geologies (mean loss=15%, ρ <0.01) and that invertebrate grazing traits were most strongly associated with fine sediment dosing frequency (ρ <0.05). The findings of this research demonstrate the role of geology in shaping invertebrate communities and their functional response to fine sediment addition and identify functional indicators that may be useful in different geologic settings. For environmental managers in the Pacific Coastal ecoregion, these findings are of potential value in assisting with the identification of biologically-relevant changes in stream fine sediment conditions and support efforts to balance economic needs in the region while protecting critical Salmonid habitat.

Oregon's ocean waters are a potential source of wind, wave, and tidal energy; of interest to renewable energy entrepreneurs and to the U.S. government as it seeks to bolster energy security. In order to install technology to capture this energy, however, it may be necessary to mitigate conflict with existing ocean space users. The objective of this research was to construct a conflict analysis model in a GIS to answer the following research questions: (1) Within the study area off the coast of Oregon, where are stakeholders currently using ocean space and how many uses overlap? (2) To what extent might existing ocean space use present potential for conflict with renewable energy development? (3) How do various types of uncertainty affect analysis results? (4) What are the implications of these findings for ecosystem based management of the ocean? All available spatial information on ocean space usage by commercial fishing, commercial non-fishing, recreational, Native American, and scientific communities was gathered. Stakeholder outreach with these communities was used to vet the collected data and allow each to contribute knowledge not previously available through GIS data clearinghouses maintained by government or interest groups. The resulting data were used as inputs to a conflict visualization model written in Python and imported to an ArcGIS tool. Results showed extensive coverage and overlap of existing ocean space uses; specifically that 99.7% of the 1-nm² grid cells of the study area are occupied by at least 6 different categories of ocean space use. The six uses with the greatest coverage were: Fishing – Trolling, Habitat, Military, Fishing - Closure Areas, Protected, and Marine Transportation - Low Intensity. An uncertainty analysis was also completed to illustrate the margin for error and therefore the necessity of appropriate stakeholder outreach during the renewable energy siting process, as opposed to relying only on a GIS. Ranking of each category by its potential for conflict with renewable energy development demonstrated which areas of the ocean may be particularly contentious. Because rankings are subjective, a tool was created to allow users to input their own rankings. For the purpose of this report, default rankings were assigned to each as justified by the literature. Results under these assumptions showed that space use and potential for conflict were highest between the coast and approximately 30 nm at sea. This is likely because certain space use is limited by depth (e.g., recreational use); there is increased shipping density as vessels approach and depart major ports; and increased fuel costs associated with traveling further from shore. Two potential applications of model results were demonstrated. First, comparison with existing wave energy permit sites highlighted relative potential for conflict among the sites and the input data detailed the specific uses present. Second, comparison with areas determined most suitable for development by the wave energy industry illustrated that areas of high suitability often also had high rankings for potential for conflict. It appeared that the factors that determined development suitability were often the same factors that drew current ocean space users to those locations. Current support at the state, regional and federal level under the National Ocean Policy for the use of marine spatial planning as a tool to implement ecosystem based management of the oceans requires that tools such as the one developed in this research are used, to ensure that all components of the marine ecosystem are considered prior to implementation of a management plan. The addition of renewable energy to the current social landscape of the ocean will reduce the resource base for many categories of ocean space use. Model results demonstrated that mitigation of conflict between development and existing space use is not merely a best practice supported by current policy, but a necessity. Results presented a visualization of the social landscape of the ocean that could help managers determine which stakeholders to engage during the initial stage of choosing a site for development. / Graduation date: 2012

Expanding groundfish production on the West Coast and in the United States in total, over the past decade, has increased competition in the groundfish market. During the same period, regulations have evolved to control production in the groundfish industry for the purpose of conserving the resource. Other regulations exist to control certain aspects of the market for groundfish. Such regulations are generally expected to have local impacts. However, little consideration is usually given to the impact regulations may have outside a local area. Indeed, since market competition has increased so significantly in this industry, the geographical distribution area has expanded considerably in recent years. Inter-regional impacts should be considered when regulations are established. The purpose of this research was to examine the impact selected regulations may have on markets for groundfish. The hypothesis tested by this research is stated as the following: regulations intended to impact local regions have no more than a local affect. Stated another way, regulatory authorities at state or regional levels generally intend to impose regulations that do not impact regions other than those under their jurisdiction. The test, then, is to determine if other regions are affected by "localized" regulations. The regulations to be examined include restriction or alteration of production in a limited region and established intra-state transportation rates (for seafood) that limit competition in the state transportation market. Specifically, alternative distribution patterns were generated in response to postulated changes in: (1) the availability of groundfish in the Oregon region and (2) California intra-state transportation rates to reflect more competition in the seafood transportation market (lower rates). The hypothesis was tested by estimating demand equations for groundfish, employing these in a spatial equilibrium model, and subjecting the results to a sensitivity analysis. The hypothesis testing consists of four parts, each independently insufficient to reject the hypothesis. As a whole, however, the four parts should provide enough evidence (although not a statistical test) to reject the hypothesis. The results of the research indicate rejection of the hypothesis was acceptable. Indeed, several of the regions where no affect was expected in response to the postulated changes showed significant impacts. This research was a pioneering attempt. The results are not conclusive, in part because of the absence of appropriate data. However, the results were significant enough to indicate promising possibilities for future research. In fact, a major contribution of the work was to point out how this research technique can be improved by refining inputs to the model and increasing its complexity to reflect more of the available routes associated with different product forms, product transport techniques and different species. The major result of the research was to indicate the need to consider impacts which extend beyond the local market in establishing regulations. / Graduation date: 1986

Graduation date: 2004

Graduation date: 2004

Interannual variability of Humboldt squid (Dosidicus gigas) occurrence in the northern California Current System is largely unknown. In Oregon, the distribution of this versatile predator and what is influencing their range expansion from Mexico is poorly understood due to the recent nature of their "invasion" and a lack of monitoring. Humboldt squid are large predators that have the potential to affect ecosystem structure and fisheries because of their high-energy demands and ability to exploit a variety of oceanographic conditions and prey sources. Developing baseline distribution information is a critical first step to assess their potential ecological, social, and economic impacts, and to develop models to predict future range expansion. This study has two main objectives: (1) to document where and when Humboldt squid have been present in Oregon through cooperative fisheries research, and (2) to correlate the sightings with oceanographic conditions using a geographic information system (GIS) and species distribution modeling (SDM). I conducted 54 interviews with local fishermen and aggregated their squid sightings with available fishery-independent survey and fishery-dependent observer data from the National Marine Fisheries Service. I compiled a total of 339 Humboldt squid sightings, reported for the years 2002-2011 from the Oregon coast to 131�� west longitude. Correlation analyses were performed for Humboldt squid sightings and sea surface temperature (SST), chlorophyll a content (chla), sea surface height anomalies (SSH), dissolved oxygen at 30 m depth (30 m DO), and sea surface salinity (SSS) using a GIS, nonparametric multiplicative regression (NPMR) habitat modeling, and maximum entropy modeling (Maxent). Results indicate that oceanographic conditions have the potential to influence Humboldt squid occurrence, and in Oregon, sightings vary temporally and spatially. Combining the sightings from fishermen and scientific surveys greatly enhanced the spatial extent of the data. Humboldt squid were most frequently observed between 124.4��W and 125��W in proximity to the shelf-break at the 200 m isobath, with peak sightings (116) recorded in 2009 and the fewest (6) reported in 2003 and 2011. The highest occurrence of Humboldt squid were observed at a SST of 10.5-13.0��C, 0.26-3.0 mg m����� chla content, -4.0-1.0 m SSH anomalies, 32.2-32.8 psu SSS, and at 3-4.5 ml L����� and 6-7 ml L����� 30 m depth DO. Maps of estimated likelihood of occurrence generated by NPMR were consistent with overlayed observations from fishermen, which were not used in the model because they were limited to presence-only information. An interdisciplinary approach that incorporates cooperative fisheries research and ecosystem-based management is necessary for monitoring Humboldt squid in Oregon. Traditional methods are insufficient because Humboldt squid are data-poor, highly migratory, and are main predators of many commercially important fisheries in Oregon. Based on my findings, sightings recorded by fishermen covered a much larger area over a longer time frame than the scientific survey and observer data, and excluding their knowledge would have led to a different interpretation of Humboldt squid distribution and environmental tolerances. Although there is uncertainty in the data from potential map bias or misidentification of smaller Humboldt squid, incorporating sightings from fishermen with traditional fisheries research increases the quantity and quality of information. Cooperative monitoring for Humboldt squid could include training in species identification and sea condition reporting in logbooks. Future "invasions" are likely, and more eyes on the water will improve our understanding of the behavior and impacts of Humboldt squid on coastal resources. / Graduation date: 2013

Understanding sandbar dynamics and variability is integral to developing a predictive capacity for nearshore flows, sediment transport, morphological change, and ultimately for determining coastline exposure to damaging storm waves. Along the high-energy U.S. Pacific Northwest (PNW) coast, sandbars typically dominate the bathymetry of the active zone. Here we report on a nearshore bathymetric data set that covers an exceptionally long stretch of coast and crosses several littoral cell boundaries. Our study area stretches from Point Grenville, Washington to Cascade Head, Oregon, including 8 littoral cells and approximately 250 km in the alongshore. We describe and quantify the morphological variability of sandbars in the PNW over large spatial scales as well as attempt to explain the inter-littoral cell variability via trends and variability in environmental parameters. From 560 bathymetric profiles (~1000 km of measurements) we have extracted over 500 distinct subtidal sandbars. The bar zone extends to over 1km from the shoreline in the northern part of the study area, but only to about 600m in the southern part. Maximum bar crest depths are typically 7m below MLLW. Bar heights range from a step in the cross-shore profile to over 3m from crest to trough. The northernmost littoral cells typically have two or more bars per cross-shore profile whereas the littoral cells in the southern part of our study area have only one bar. The mean depths of the bars, however, are much more consistent across littoral cells. The mean depths remain consistent even while the upper shoreface slope significantly increases from north to south, requiring that the maximum bar distance from the shoreline decreases from north to south. This regional gradient in upper shoreface slope is likely a response, at least in part, to a general coarsening trend in the sediment from north to south and hence linked to variations in regional geology. / Graduation date: 2013

No description available.