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• 421. [Article] Sediment accumulation and human impacts in Tillamook Bay, Oregon

  Tillamook Bay is the second largest estuary on the Oregon coast, and concerns have been raised whether human induced impacts have been responsible for the perceived increase in sedimentation rates during ...

  Citation × Citation Citation Abstract Copy Title: Sediment accumulation and human impacts in Tillamook Bay, Oregon Author: Styllas, Michael N. Tillamook Bay is the second largest estuary on the Oregon coast, and concerns have been raised whether human induced impacts have been responsible for the perceived increase in sedimentation rates during the past century. Major land-use practices within the five watersheds of the Bay include logging, forest fires, the construction of forest roads, the placement of dikes along the channels of the main rivers and in the estuary, the removal of riparian vegetation, and the construction of jetties at the tidal inlet. Each of these practices has led to impacts on the entire ecosystem of the watersheds and the Bay, but this study focuses on the effects of human disturbances on the Bay's sediment accumulation. This study examines in detail the land-use practices that have occurred in the watersheds, on the beaches, and in the estuary, focusing on those that have had a direct impact on the sedimentation regime of the Bay. One goal of the study is to assess the relative roles of natural processes versus human impacts on the sedimentation. A general description of the physical characteristics of Tillamook Bay and its surroundings is included, and a brief discussion is provided about the tectonic setting of the Northwest Coast, including its history of subduction earthquakes and the associate sea-level changes. Also provided is a summary of the existing information concerning the arrival of Indians and their environmental impacts, followed by a more detailed account of the major impacts that have resulted from the settlement of the Euro-Americans in the Tillamook area, in the 1850's. The study then focuses on the description of the watersheds from a geomorphologic point of view, and the important land-use practices that may have affected sediment yields during the past century. Analyses of the hydrology of the Tillamook Bay watersheds are included, and the relations between annual water yields and total precipitation are examined in distinct time intervals, each corresponding to a different period with different amounts of land uses. The results of these hydrology analyses suggest that the Tillamook watershed gradually recovered from a period of major disturbances (from 1933 to 1955) to more normal conditions (from 1977 to 1998). In addition, this part of the study attempts to quantify the sediment transport regime of the rivers draining the watershed by using a hydraulic model that is based on the principle of stream power, and on considerations of availability of transported material. Application of this model during the 1933-1955 period for the major rivers suggests an average sediment yield on the order of 410,540 tons/year, but most important are the relative changes of the delivered sediment through time. The results of the model suggest a 1.6-factor decrease of the amount of river sediments from the Heavily Impacted Period (1933-1955) of major disturbances to the Normal Period (1977- 1998). The spatial variations of beach and river derived sediments throughout the Bay are determined from textural and mineralogical analyses of surface sediment samples, with the beach sands dominating the area close to the inlet and the river derived sands being mainly deposited at the southeast and northeast parts of the Bay. The relative contributions of these two major sources of sediment were found to be 60% for the marine beach and 40% for the river sands. Further attempt is made to distinguish between the sand transported into the Bay from the individual rivers, and to determine the main processes that are responsible for the dispersion of sediments within the Bay. The attempts to distinguish sands contributed by the individual rivers involved modal analyses of the frequency curves of the surface sediment samples, and the results mainly suggest a grain-size increase away from the mouth of the rivers as a result of sediment reworking by estuarine processes following its initial deposition during episodic river flooding. The main processes that control the dispersion of sediments and their deposition within the Bay were identified by using factor analysis, the results of which suggest that various estuarine processes are responsible for the observed dispersal patterns. A brief review is provided of the study undertaken by Dr. James McManus for the collection and analyses of core samples from Tillamook Bay. Down-core geochemical analyses of major and minor elements indicate that there have been times of episodic input of marine sediment in the central and western portions of the Bay, which is a result of either periodic breaching or washover of Bayocean Spit, so that the beach sand source was more important in the past. This episodic input of marine sand as inferred from the down-core geochemical variations was related to the most recent subduction earthquake, which occurred on January 26th, 1700. Finally, a summary of the results and conclusions of different aspects of this study is presented, so that sedimentation in Tillamook Bay can be viewed as an integrated process involving the watersheds, the estuary, and the ocean beaches. Title: Sediment accumulation and human impacts in Tillamook Bay, Oregon Author: Styllas, Michael N. Tillamook Bay is the second largest estuary on the Oregon coast, and concerns have been raised whether human induced impacts have been responsible for the perceived increase in sedimentation rates during the past century. Major land-use practices within the five watersheds of the Bay include logging, forest fires, the construction of forest roads, the placement of dikes along the channels of the main rivers and in the estuary, the removal of riparian vegetation, and the construction of jetties at the tidal inlet. Each of these practices has led to impacts on the entire ecosystem of the watersheds and the Bay, but this study focuses on the effects of human disturbances on the Bay's sediment accumulation. This study examines in detail the land-use practices that have occurred in the watersheds, on the beaches, and in the estuary, focusing on those that have had a direct impact on the sedimentation regime of the Bay. One goal of the study is to assess the relative roles of natural processes versus human impacts on the sedimentation. A general description of the physical characteristics of Tillamook Bay and its surroundings is included, and a brief discussion is provided about the tectonic setting of the Northwest Coast, including its history of subduction earthquakes and the associate sea-level changes. Also provided is a summary of the existing information concerning the arrival of Indians and their environmental impacts, followed by a more detailed account of the major impacts that have resulted from the settlement of the Euro-Americans in the Tillamook area, in the 1850's. The study then focuses on the description of the watersheds from a geomorphologic point of view, and the important land-use practices that may have affected sediment yields during the past century. Analyses of the hydrology of the Tillamook Bay watersheds are included, and the relations between annual water yields and total precipitation are examined in distinct time intervals, each corresponding to a different period with different amounts of land uses. The results of these hydrology analyses suggest that the Tillamook watershed gradually recovered from a period of major disturbances (from 1933 to 1955) to more normal conditions (from 1977 to 1998). In addition, this part of the study attempts to quantify the sediment transport regime of the rivers draining the watershed by using a hydraulic model that is based on the principle of stream power, and on considerations of availability of transported material. Application of this model during the 1933-1955 period for the major rivers suggests an average sediment yield on the order of 410,540 tons/year, but most important are the relative changes of the delivered sediment through time. The results of the model suggest a 1.6-factor decrease of the amount of river sediments from the Heavily Impacted Period (1933-1955) of major disturbances to the Normal Period (1977- 1998). The spatial variations of beach and river derived sediments throughout the Bay are determined from textural and mineralogical analyses of surface sediment samples, with the beach sands dominating the area close to the inlet and the river derived sands being mainly deposited at the southeast and northeast parts of the Bay. The relative contributions of these two major sources of sediment were found to be 60% for the marine beach and 40% for the river sands. Further attempt is made to distinguish between the sand transported into the Bay from the individual rivers, and to determine the main processes that are responsible for the dispersion of sediments within the Bay. The attempts to distinguish sands contributed by the individual rivers involved modal analyses of the frequency curves of the surface sediment samples, and the results mainly suggest a grain-size increase away from the mouth of the rivers as a result of sediment reworking by estuarine processes following its initial deposition during episodic river flooding. The main processes that control the dispersion of sediments and their deposition within the Bay were identified by using factor analysis, the results of which suggest that various estuarine processes are responsible for the observed dispersal patterns. A brief review is provided of the study undertaken by Dr. James McManus for the collection and analyses of core samples from Tillamook Bay. Down-core geochemical analyses of major and minor elements indicate that there have been times of episodic input of marine sediment in the central and western portions of the Bay, which is a result of either periodic breaching or washover of Bayocean Spit, so that the beach sand source was more important in the past. This episodic input of marine sand as inferred from the down-core geochemical variations was related to the most recent subduction earthquake, which occurred on January 26th, 1700. Finally, a summary of the results and conclusions of different aspects of this study is presented, so that sedimentation in Tillamook Bay can be viewed as an integrated process involving the watersheds, the estuary, and the ocean beaches. Close

• 422. [Article] An experimental investigation of the effects of temperature and dissolved oxygen on the growth of juvenile English sole and juvenile Dungeness crab

  In the past two decades, occurrences of summertime upwelling-driven low dissolved oxygen (DO) events, or hypoxia, have increased along the northeast Pacific coast. If hypoxic events are severe enough to ...

  Citation × Citation Citation Abstract Copy Title: An experimental investigation of the effects of temperature and dissolved oxygen on the growth of juvenile English sole and juvenile Dungeness crab Author: Bancroft, Morgan P. In the past two decades, occurrences of summertime upwelling-driven low dissolved oxygen (DO) events, or hypoxia, have increased along the northeast Pacific coast. If hypoxic events are severe enough to cause marine species mortality, the areas affected are often called "dead zones." In 2002 and again in 2006, the events were lethal, resulting in mass invertebrate and fish kills. Many organisms are impacted by these events, but less mobile juvenile fishes and crabs are potentially more vulnerable to the long-term effects of these stressful conditions than adults. Little is known about how low DO impacts coastal fishes and invertebrates, especially during the juvenile phase. Nursery habitats in the nearshore open-coast and enclosed estuaries may be differentially affected by hypoxia by prevailing summertime oceanographic conditions. Both ecosystems are critical for the early development of many ecologically and commercially important species. While one habitat may be compromised by stressful environmental conditions, the other may provide refuge. In upwelling driven areas, low dissolved oxygen is typically coupled with colder water, while in estuarine or semi-enclosed systems, dissolved oxygen diminishes with increasing temperatures. Temperature and dissolved oxygen are known to have interactive effects on fish behavior and physiology, which underscores the importance of studying hypoxia within different systems and in relation to other co-occurring environmental variables. In order to isolate the effects of these parameters on growth, I conducted three experiments over the course of two years on juvenile Dungeness crab (Cancer magister) and English sole (Parophrys vetulus). During each experiment, I held English sole in the lab in fixed oxygen and temperature conditions for at least thirty days, and Dungeness crab for approximately fifty. I tested a total of 15 oxygen and temperature treatment combinations, with at least two replicates of each treatment. These treatments simulated summertime oceanographic conditions that are typically found in two nursery habitats used by these species: the Yaquina Bay estuary and Moolack Beach, Oregon USA. English sole specific growth (g d⁻¹) increased with higher temperatures (13 and 15°C) and oxygen concentrations (2.0 and 6.0 mL L⁻¹) and was up to four times lower in all low temperature and oxygen treatments (5 and 7°C; < 1.4 mL L⁻¹). Dungeness crab intermolt period decreased with temperature from 48 days at 5°C to 12 days at 15°C. Crab specific growth (mm d⁻¹) increased with temperature, with crabs in the highest temperatures growing nearly five times as much as crabs in the coldest temperatures. Finally, if people have heard of hypoxia, it is commonly in relation to the condition found in the Gulf of Mexico, which is nutrient driven and can be traced to anthropogenic input. Instead, Oregon hypoxia is more difficult to trace directly to human-related activity, making West Coast hypoxia a relatively lesser understood occurrence. In order to share the results of my research and improve general public understanding of hypoxia, I designed a ~3:00 minute video exhibit that was displayed at the Hatfield Marine Science Center Visitor Center. Our intent was to create a video that could be distributed to different Visitor Centers and museums that are interested in educating their visitors about the occurrence, causes and frequency of hypoxia on the Oregon Coast. Title: An experimental investigation of the effects of temperature and dissolved oxygen on the growth of juvenile English sole and juvenile Dungeness crab Author: Bancroft, Morgan P. In the past two decades, occurrences of summertime upwelling-driven low dissolved oxygen (DO) events, or hypoxia, have increased along the northeast Pacific coast. If hypoxic events are severe enough to cause marine species mortality, the areas affected are often called "dead zones." In 2002 and again in 2006, the events were lethal, resulting in mass invertebrate and fish kills. Many organisms are impacted by these events, but less mobile juvenile fishes and crabs are potentially more vulnerable to the long-term effects of these stressful conditions than adults. Little is known about how low DO impacts coastal fishes and invertebrates, especially during the juvenile phase. Nursery habitats in the nearshore open-coast and enclosed estuaries may be differentially affected by hypoxia by prevailing summertime oceanographic conditions. Both ecosystems are critical for the early development of many ecologically and commercially important species. While one habitat may be compromised by stressful environmental conditions, the other may provide refuge. In upwelling driven areas, low dissolved oxygen is typically coupled with colder water, while in estuarine or semi-enclosed systems, dissolved oxygen diminishes with increasing temperatures. Temperature and dissolved oxygen are known to have interactive effects on fish behavior and physiology, which underscores the importance of studying hypoxia within different systems and in relation to other co-occurring environmental variables. In order to isolate the effects of these parameters on growth, I conducted three experiments over the course of two years on juvenile Dungeness crab (Cancer magister) and English sole (Parophrys vetulus). During each experiment, I held English sole in the lab in fixed oxygen and temperature conditions for at least thirty days, and Dungeness crab for approximately fifty. I tested a total of 15 oxygen and temperature treatment combinations, with at least two replicates of each treatment. These treatments simulated summertime oceanographic conditions that are typically found in two nursery habitats used by these species: the Yaquina Bay estuary and Moolack Beach, Oregon USA. English sole specific growth (g d⁻¹) increased with higher temperatures (13 and 15°C) and oxygen concentrations (2.0 and 6.0 mL L⁻¹) and was up to four times lower in all low temperature and oxygen treatments (5 and 7°C; < 1.4 mL L⁻¹). Dungeness crab intermolt period decreased with temperature from 48 days at 5°C to 12 days at 15°C. Crab specific growth (mm d⁻¹) increased with temperature, with crabs in the highest temperatures growing nearly five times as much as crabs in the coldest temperatures. Finally, if people have heard of hypoxia, it is commonly in relation to the condition found in the Gulf of Mexico, which is nutrient driven and can be traced to anthropogenic input. Instead, Oregon hypoxia is more difficult to trace directly to human-related activity, making West Coast hypoxia a relatively lesser understood occurrence. In order to share the results of my research and improve general public understanding of hypoxia, I designed a ~3:00 minute video exhibit that was displayed at the Hatfield Marine Science Center Visitor Center. Our intent was to create a video that could be distributed to different Visitor Centers and museums that are interested in educating their visitors about the occurrence, causes and frequency of hypoxia on the Oregon Coast. Close

• 423. [Article] A cooperative effort to track Humboldt squid invasions in Oregon

  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 ...

  Citation × Citation Citation Abstract Copy Title: A cooperative effort to track Humboldt squid invasions in Oregon Author: Chesney, Tanya A. 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⁻³ chla content, -4.0-1.0 m SSH anomalies, 32.2-32.8 psu SSS, and at 3-4.5 ml L⁻¹ and 6-7 ml L⁻¹ 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. Title: A cooperative effort to track Humboldt squid invasions in Oregon Author: Chesney, Tanya A. 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⁻³ chla content, -4.0-1.0 m SSH anomalies, 32.2-32.8 psu SSS, and at 3-4.5 ml L⁻¹ and 6-7 ml L⁻¹ 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. Close

• 424. [Article] Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development

  While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of ...

  Citation × Citation Citation Abstract Copy Title: Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development Author: Henkel, Sarah K., Goldfinger, Chris While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of these devices and their complex mooring systems. Here I focus on characterizing benthic habitats and biological communities in offshore sedimentary and reef habitats where wind and wave energy facilities could be located. While little is known about species-habitat relationships and community processes in the depths and substrate types targeted for offshore renewable energy installation, an understanding of the natural dynamics of these systems is of utmost importance if we hope to forecast changes that might be brought about by wind and wave development. Since May 2010 we have conducted surveys of benthic habitats from northern California to Washington using a variety of techniques, providing baseline data on habitats and species potentially affected by wind and wave development, identifying species-habitat relationships, and quantifying spatial and temporal trends in species abundances and distributions. The first step in identifying and evaluating benthic communities is sonar mapping to determine depth and substrate types. In summer 2010 and 2011 six new offshore sites were mapped by the Seafloor Mapping and Plate Tectonics Lab at OSU using high-resolution multi-beam sonar and acoustic backscatter. In addition to the backscatter, Shipek grabs were taken in soft-bottom areas to collect sediment samples, which were run through a laser particle size analyzer (LDPSA) to determine actual grain size. Mapping began at the federal jurisdiction line and extended 9 – 12 miles offshore. Oregon and California have undertaken extensive mapping of state waters, so many areas have been mapped inshore of these sites as well. In summer 2011 and 2012, we visited 8 sites (6 newly mapped sites, one previously mapped, and one unmapped site) to collect a total of 153 cores using a 0.1 m2 box-corer. A sub-sample of sediment was collected from the corer and analyzed using the LDPSA; the rest was sieved through 1 mm mesh and all infaunal organisms were counted and identified. At each box core sampling station, CTD casts were conducted to obtain physical data describing the overlying water column for further habitat characterization. Unique infaunal invertebrate assemblages were found in sedimentary habitats at each of the Pacific Northwest shelf sites. Thus for renewable energy siting, it does not appear that baseline surveys conducted at one site can necessarily serve as a proxy for distant sites. However, some general trends were detected. Significantly different invertebrate assemblages were found in different depth ranges with a break at approximately 80 to 90 m depth; deeper sites exhibited greater diversity. Shallower sites had greater spatial heterogeneity in infaunal invertebrate assemblages than deeper sites; thus as monitoring protocols are developed we recommend that shallower sites be sampled more extensively in order to adequately characterize those communities. Molluscs seemed to be the most responsive to substrate type, with different assemblages found in pure sand, slightly muddy sand, and mostly silt/clay. In addition to sampling of sedimentary habitat, we conducted limited surveys of offshore reef habitats. Although it is unlikely that devices would be installed in these areas, reefs may be crossed by electrical cables, and changes in sediment transport due to ocean energy extraction or alterations of flow around large device arrays could lead to community impacts. The aim of this study was to describe baseline relationships between macroinvertebrate communities and habitat features against which to measure potential future impacts and to develop tools to predict community compositions of unsampled areas in the region based on substrate features. To date we have analyzed submersible dive video from three sites conducted in the mid-1990s. In the summers of 2011 and 2012, we visited these previously surveyed sites with an ROV. Analysis of submersible and ROV surveys indicated that two major substratum groups held different macroinvertebrate assemblages: moderate to high-relief rocky habitats and low-relief fine sediment habitats. The majority of macroinvertebrate taxa were associated with high-relief rocks; these taxa were further differentiated between flat and ridge rock habitats. Low-relief fine sediment habitat was most often associated with motile invertebrates. Within this habitat it appeared that fine-sediment substrata mixed with mud, boulders, or gravel each yield unique macro-invertebrate associations versus those found on uniformly mud or sand substrata. Latitude also was correlated with variation in macroinvertebrate assemblages. A major challenge will be detecting effects of wind and wave energy installations above the inherent natural variability in these systems. Decadal scale shifts in the California Current affect this ecosystem, with warm regimes and associated declines in planktonic production resulting in degradation of benthic community. On shorter timescales El Niño events can cause major, short-term disturbances. Off the Oregon coast, summer hypoxia events can have dramatic effects on benthic communities, and ocean acidification is an increasing concern. Thus, evaluation of this ecosystem must be made in the context of seasonal and climatic trends. Prior to installation of device arrays, baseline sampling is usually required as part of the permitting process. However, one-time sampling will not capture the variability of the system in a given area, and developers and regulators typically are not able to make the investment (in time or money) to repeatedly survey an area before development. Funding agencies rarely support long-term monitoring studies. Thus, finding support for repeated field sampling across time and space is especially challenging. The biggest issue facing wind and wave energy developers in the environmental arena is the high level of uncertainty regarding environmental effects. Without a substantial understanding of the natural dynamics of a system, it will be difficult to reduce that uncertainty. Title: Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development Author: Henkel, Sarah K., Goldfinger, Chris While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of these devices and their complex mooring systems. Here I focus on characterizing benthic habitats and biological communities in offshore sedimentary and reef habitats where wind and wave energy facilities could be located. While little is known about species-habitat relationships and community processes in the depths and substrate types targeted for offshore renewable energy installation, an understanding of the natural dynamics of these systems is of utmost importance if we hope to forecast changes that might be brought about by wind and wave development. Since May 2010 we have conducted surveys of benthic habitats from northern California to Washington using a variety of techniques, providing baseline data on habitats and species potentially affected by wind and wave development, identifying species-habitat relationships, and quantifying spatial and temporal trends in species abundances and distributions. The first step in identifying and evaluating benthic communities is sonar mapping to determine depth and substrate types. In summer 2010 and 2011 six new offshore sites were mapped by the Seafloor Mapping and Plate Tectonics Lab at OSU using high-resolution multi-beam sonar and acoustic backscatter. In addition to the backscatter, Shipek grabs were taken in soft-bottom areas to collect sediment samples, which were run through a laser particle size analyzer (LDPSA) to determine actual grain size. Mapping began at the federal jurisdiction line and extended 9 – 12 miles offshore. Oregon and California have undertaken extensive mapping of state waters, so many areas have been mapped inshore of these sites as well. In summer 2011 and 2012, we visited 8 sites (6 newly mapped sites, one previously mapped, and one unmapped site) to collect a total of 153 cores using a 0.1 m2 box-corer. A sub-sample of sediment was collected from the corer and analyzed using the LDPSA; the rest was sieved through 1 mm mesh and all infaunal organisms were counted and identified. At each box core sampling station, CTD casts were conducted to obtain physical data describing the overlying water column for further habitat characterization. Unique infaunal invertebrate assemblages were found in sedimentary habitats at each of the Pacific Northwest shelf sites. Thus for renewable energy siting, it does not appear that baseline surveys conducted at one site can necessarily serve as a proxy for distant sites. However, some general trends were detected. Significantly different invertebrate assemblages were found in different depth ranges with a break at approximately 80 to 90 m depth; deeper sites exhibited greater diversity. Shallower sites had greater spatial heterogeneity in infaunal invertebrate assemblages than deeper sites; thus as monitoring protocols are developed we recommend that shallower sites be sampled more extensively in order to adequately characterize those communities. Molluscs seemed to be the most responsive to substrate type, with different assemblages found in pure sand, slightly muddy sand, and mostly silt/clay. In addition to sampling of sedimentary habitat, we conducted limited surveys of offshore reef habitats. Although it is unlikely that devices would be installed in these areas, reefs may be crossed by electrical cables, and changes in sediment transport due to ocean energy extraction or alterations of flow around large device arrays could lead to community impacts. The aim of this study was to describe baseline relationships between macroinvertebrate communities and habitat features against which to measure potential future impacts and to develop tools to predict community compositions of unsampled areas in the region based on substrate features. To date we have analyzed submersible dive video from three sites conducted in the mid-1990s. In the summers of 2011 and 2012, we visited these previously surveyed sites with an ROV. Analysis of submersible and ROV surveys indicated that two major substratum groups held different macroinvertebrate assemblages: moderate to high-relief rocky habitats and low-relief fine sediment habitats. The majority of macroinvertebrate taxa were associated with high-relief rocks; these taxa were further differentiated between flat and ridge rock habitats. Low-relief fine sediment habitat was most often associated with motile invertebrates. Within this habitat it appeared that fine-sediment substrata mixed with mud, boulders, or gravel each yield unique macro-invertebrate associations versus those found on uniformly mud or sand substrata. Latitude also was correlated with variation in macroinvertebrate assemblages. A major challenge will be detecting effects of wind and wave energy installations above the inherent natural variability in these systems. Decadal scale shifts in the California Current affect this ecosystem, with warm regimes and associated declines in planktonic production resulting in degradation of benthic community. On shorter timescales El Niño events can cause major, short-term disturbances. Off the Oregon coast, summer hypoxia events can have dramatic effects on benthic communities, and ocean acidification is an increasing concern. Thus, evaluation of this ecosystem must be made in the context of seasonal and climatic trends. Prior to installation of device arrays, baseline sampling is usually required as part of the permitting process. However, one-time sampling will not capture the variability of the system in a given area, and developers and regulators typically are not able to make the investment (in time or money) to repeatedly survey an area before development. Funding agencies rarely support long-term monitoring studies. Thus, finding support for repeated field sampling across time and space is especially challenging. The biggest issue facing wind and wave energy developers in the environmental arena is the high level of uncertainty regarding environmental effects. Without a substantial understanding of the natural dynamics of a system, it will be difficult to reduce that uncertainty. Close

• 425. [Article] Where's the ground surface? Elevation bias in LIDAR-derived digital elevation models due to dense vegetation in Oregon tidal marshes

  Light Detection and Ranging (LIDAR) is a powerful resource for coastal and wetland managers and its use is increasing. Vegetation density and other land cover characteristics influence the accuracy of ...

  Citation × Citation Citation Abstract Copy Title: Where's the ground surface? Elevation bias in LIDAR-derived digital elevation models due to dense vegetation in Oregon tidal marshes Author: Ewald, Michael J. Light Detection and Ranging (LIDAR) is a powerful resource for coastal and wetland managers and its use is increasing. Vegetation density and other land cover characteristics influence the accuracy of LIDAR-derived ground surface digital elevation models; however, the degree to which wetland land cover biases LIDAR estimates of the ground surface is largely unknown. The minimum-bin LIDAR gridding technique has been proposed as a way to mitigate dense vegetation interference to generate LIDAR-derived digital elevation models (DEM). Past research has focused on the ability to resolve the marsh plain elevation and only limited research has investigated the overall DEM accuracy across the landscape using a wide range of cell sizes and land cover classes. I compared LIDAR-derived DEM accuracy across a 174 ha tidal wetland restoration site with a mix of native wetland and non-native agricultural pasture species. I found an optimum cell size of 1.4 m (1.96 m²) with a mean positive bias of 4.5 cm and a mean absolute error of 24.3 cm. At cell sizes smaller than the optimum, vegetation interferes with the LIDAR sensor and positively biases DEM models. At cell sizes larger than 1.4 m, the DEM captures and favors low features within the landscape, such as channels and ditches, which thereby degrade overall DEM performance. In addition, I investigated LIDAR interference by twelve common tidal wetland vegetation associations across six Oregon estuaries, using survey-grade Global Positioning System (GPS) measurements of the wetland surface and quantitative vegetation data (percent cover by species) for each measurement location. The fundamental vertical accuracy (FVA) of the LIDAR datasets was 4.5 cm root mean square error (RMSE) and had no consistent positive or negative bias in open landcover. Within wetland vegetation communities, my results suggest that LIDAR estimates of the ground surface in tidal wetlands are typically 10 cm to 30 cm above GPS measurements. Plant associations dominated by Carex obnupta and Carex lyngbyei exhibited the largest discrepancy between LIDAR and GPS measurements (mean discrepancies 36.6 cm and 48.8 cm respectively). The smallest errors observed in the study were about 10 cm to 11 cm and occurred in several different plant associations, including two low tidal marsh associations dominated by a mixture of Deschampsia cespitosa, Distichlis spicata, Sarcocornia perennis and Jaumea carnosa. These results suggest that the minimum-bin gridding technique for LIDAR may mitigate vegetation interference by densely vegetated land covers within LIDAR-derived DEM. However, care should be taken to select an appropriate cell size and validate the results before relying on the DEM for analysis. My research yields new information for coastal LIDAR users and increases our understanding of uncertainty in LIDAR-derived datasets to improve the ability to accurately evaluate and manage coastal environments. Title: Where's the ground surface? Elevation bias in LIDAR-derived digital elevation models due to dense vegetation in Oregon tidal marshes Author: Ewald, Michael J. Light Detection and Ranging (LIDAR) is a powerful resource for coastal and wetland managers and its use is increasing. Vegetation density and other land cover characteristics influence the accuracy of LIDAR-derived ground surface digital elevation models; however, the degree to which wetland land cover biases LIDAR estimates of the ground surface is largely unknown. The minimum-bin LIDAR gridding technique has been proposed as a way to mitigate dense vegetation interference to generate LIDAR-derived digital elevation models (DEM). Past research has focused on the ability to resolve the marsh plain elevation and only limited research has investigated the overall DEM accuracy across the landscape using a wide range of cell sizes and land cover classes. I compared LIDAR-derived DEM accuracy across a 174 ha tidal wetland restoration site with a mix of native wetland and non-native agricultural pasture species. I found an optimum cell size of 1.4 m (1.96 m²) with a mean positive bias of 4.5 cm and a mean absolute error of 24.3 cm. At cell sizes smaller than the optimum, vegetation interferes with the LIDAR sensor and positively biases DEM models. At cell sizes larger than 1.4 m, the DEM captures and favors low features within the landscape, such as channels and ditches, which thereby degrade overall DEM performance. In addition, I investigated LIDAR interference by twelve common tidal wetland vegetation associations across six Oregon estuaries, using survey-grade Global Positioning System (GPS) measurements of the wetland surface and quantitative vegetation data (percent cover by species) for each measurement location. The fundamental vertical accuracy (FVA) of the LIDAR datasets was 4.5 cm root mean square error (RMSE) and had no consistent positive or negative bias in open landcover. Within wetland vegetation communities, my results suggest that LIDAR estimates of the ground surface in tidal wetlands are typically 10 cm to 30 cm above GPS measurements. Plant associations dominated by Carex obnupta and Carex lyngbyei exhibited the largest discrepancy between LIDAR and GPS measurements (mean discrepancies 36.6 cm and 48.8 cm respectively). The smallest errors observed in the study were about 10 cm to 11 cm and occurred in several different plant associations, including two low tidal marsh associations dominated by a mixture of Deschampsia cespitosa, Distichlis spicata, Sarcocornia perennis and Jaumea carnosa. These results suggest that the minimum-bin gridding technique for LIDAR may mitigate vegetation interference by densely vegetated land covers within LIDAR-derived DEM. However, care should be taken to select an appropriate cell size and validate the results before relying on the DEM for analysis. My research yields new information for coastal LIDAR users and increases our understanding of uncertainty in LIDAR-derived datasets to improve the ability to accurately evaluate and manage coastal environments. Close

• 426. [Article] Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents

  Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal ...

  Citation × Citation Citation Abstract Copy Title: Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents Author: Rutherford, Alexander Fenner Year: 2014 Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal vents is based primarily on the reduction-oxidation (redox) of inorganic chemicals by Bacteria and Archaea. However, the distributional patterns of the microorganisms that colonize deep-sea hydrothermal vent deposits and their link to the geologic setting are still not deeply understood. The goal of the studies presented in this thesis was to quantify the abundance, and distribution of major and understudied vent colonizing archaeal groups from globally distributed and geochemically distinct hydrothermal vent fields. The archaeal community composition was analyzed using quantitative PCR with lineage specific functional gene primers that target methanogens, and 16S rRNA gene primers designed or optimized from this study for the Thermococcales, Archaeoglobus, Ignicoccus and marine Nanoarchaeota. Overall, a general relationship was demonstrated between the geochemical differences of the hydrothermal vent fields and the archaeal community structure. The archaeal community assemblage varied dramatically from hydrothermal vents with different vent host rocks along the Mid-Atlantic Ridge and Eastern Lau Spreading Center. In contrast, two vent fields in the East Pacific, 9°N on the EPR and Guaymas Basin that are basalt and basalt-sediment hosted were found to have similar community composition. These observed differences may be driven in part by the metabolically available chemical energy as hydrogen oxidizing lineages of the methanogens and Archaeoglobus were found in higher abundance in the samples from vent field that had a high concentration of end-member hydrogen and the heterotrophic Thermococcales constituted a higher proportion of the archaeal community at the less enriched vent fields. Interestingly, the Nanoarchaeota and the genus of its only confirmed symbiont, Ignicoccus, were found to have an inconsistent proportional relationship, with the Nanoarchaeota comprising a larger proportion of the archaeal community at the ultramafic and fast spreading basalt vent fields and Ignicoccus at the ultra-slow spreading basalt and andesite hosted vent fields. There was also a more localized pattern identified within the hydrothermal vent deposit. The chemosynthetic lineages of the methanogens and Archaeoglobus constituted a higher proportion of the archaeal community in chimney samples compared to Thermococcales that was found in a higher proportion at horizontal flange samples. This archaeal proportional shift could be driven by energetic micro-niches within the vent deposit, as the chemolithotrophic lineages colonize the area closest to the venting source, and the heterotrophic Thermococcales dominate in more mature structures further from the venting source. Quantitative assessments of the archaeal community composition from this study provided added insight into the dynamic geologic influence on the archaeal lineages that colonize deep-sea hydrothermal vents, on a global and local scale. Title: Abundance and Distribution of Major and Understudied Archaeal Lineages at Globally Distributed Deep-Sea Hydrothermal Vents Author: Rutherford, Alexander Fenner Year: 2014 Deep-sea hydrothermal vents are some of the most biologically productive ecosystems on Earth, yet receive little to no input of photosynthetically derived organic matter. The trophic system at hydrothermal vents is based primarily on the reduction-oxidation (redox) of inorganic chemicals by Bacteria and Archaea. However, the distributional patterns of the microorganisms that colonize deep-sea hydrothermal vent deposits and their link to the geologic setting are still not deeply understood. The goal of the studies presented in this thesis was to quantify the abundance, and distribution of major and understudied vent colonizing archaeal groups from globally distributed and geochemically distinct hydrothermal vent fields. The archaeal community composition was analyzed using quantitative PCR with lineage specific functional gene primers that target methanogens, and 16S rRNA gene primers designed or optimized from this study for the Thermococcales, Archaeoglobus, Ignicoccus and marine Nanoarchaeota. Overall, a general relationship was demonstrated between the geochemical differences of the hydrothermal vent fields and the archaeal community structure. The archaeal community assemblage varied dramatically from hydrothermal vents with different vent host rocks along the Mid-Atlantic Ridge and Eastern Lau Spreading Center. In contrast, two vent fields in the East Pacific, 9°N on the EPR and Guaymas Basin that are basalt and basalt-sediment hosted were found to have similar community composition. These observed differences may be driven in part by the metabolically available chemical energy as hydrogen oxidizing lineages of the methanogens and Archaeoglobus were found in higher abundance in the samples from vent field that had a high concentration of end-member hydrogen and the heterotrophic Thermococcales constituted a higher proportion of the archaeal community at the less enriched vent fields. Interestingly, the Nanoarchaeota and the genus of its only confirmed symbiont, Ignicoccus, were found to have an inconsistent proportional relationship, with the Nanoarchaeota comprising a larger proportion of the archaeal community at the ultramafic and fast spreading basalt vent fields and Ignicoccus at the ultra-slow spreading basalt and andesite hosted vent fields. There was also a more localized pattern identified within the hydrothermal vent deposit. The chemosynthetic lineages of the methanogens and Archaeoglobus constituted a higher proportion of the archaeal community in chimney samples compared to Thermococcales that was found in a higher proportion at horizontal flange samples. This archaeal proportional shift could be driven by energetic micro-niches within the vent deposit, as the chemolithotrophic lineages colonize the area closest to the venting source, and the heterotrophic Thermococcales dominate in more mature structures further from the venting source. Quantitative assessments of the archaeal community composition from this study provided added insight into the dynamic geologic influence on the archaeal lineages that colonize deep-sea hydrothermal vents, on a global and local scale. Close

• 427. [Article] Prey density and distribution drive the three-dimensional foraging strategies of the largest filter feeder

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

  Citation × Citation Citation Abstract Copy Title: Prey density and distribution drive the three-dimensional foraging strategies of the largest filter feeder Author: Friedlaender, Ari S., et al., Hazen, Elliott L., Goldbogen, Jeremy A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and British Ecological Society and published by John Wiley & Sons Ltd. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2435/ Title: Prey density and distribution drive the three-dimensional foraging strategies of the largest filter feeder Author: Friedlaender, Ari S., et al., Hazen, Elliott L., Goldbogen, Jeremy A. To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and British Ecological Society and published by John Wiley & Sons Ltd. It can be found at: http://onlinelibrary.wiley.com/journal/10.1111/%28ISSN%291365-2435/ Close

• 428. [Article] Wintertime grazing rates of Antarctic krill, Euphausia superba, along the Northern Antarctic Peninsula

  Poster

  Citation × Citation Citation Abstract Copy Title: Wintertime grazing rates of Antarctic krill, Euphausia superba, along the Northern Antarctic Peninsula Author: Gunther, Lacey Poster Title: Wintertime grazing rates of Antarctic krill, Euphausia superba, along the Northern Antarctic Peninsula Author: Gunther, Lacey Poster Close

• 429. [Article] Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://www.plosone.org/.

  Citation × Citation Citation Abstract Copy Title: Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient Author: Crump, Byron C., Fortunato, Caroline S. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://www.plosone.org/. Title: Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient Author: Crump, Byron C., Fortunato, Caroline S. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://www.plosone.org/. Close

• 430. [Article] Poor Transferability of Species Distribution Models for a Pelagic Predator, the Grey Petrel, Indicates Contrasting Habitat Preferences across Ocean Basins

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://www.plosone.org/.

  Citation × Citation Citation Abstract Copy Title: Poor Transferability of Species Distribution Models for a Pelagic Predator, the Grey Petrel, Indicates Contrasting Habitat Preferences across Ocean Basins Author: Thompson, David R., Torres, Leigh G., et al., Sutton, Philip J. H. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://www.plosone.org/. Title: Poor Transferability of Species Distribution Models for a Pelagic Predator, the Grey Petrel, Indicates Contrasting Habitat Preferences across Ocean Basins Author: Thompson, David R., Torres, Leigh G., et al., Sutton, Philip J. H. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://www.plosone.org/. Close