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• 1. [Article] OSU Marine Team: Long-term sampling of ichthyofauna in Yaquina Bay

  PDF of PowerPoint presentation (16 slides)

  Citation × Citation Citation Abstract Copy Title: OSU Marine Team: Long-term sampling of ichthyofauna in Yaquina Bay Author: Gallagher, Brett, Heppell, Selina, Heppell, Scott PDF of PowerPoint presentation (16 slides) Title: OSU Marine Team: Long-term sampling of ichthyofauna in Yaquina Bay Author: Gallagher, Brett, Heppell, Selina, Heppell, Scott PDF of PowerPoint presentation (16 slides) Close

• 2. [Article] The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats

  Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation ...

  Citation × Citation Citation Abstract Copy Title: The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats Author: McClees, Whitney, de Rivera, Catherine E. Year: 2017 Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation is limiting the spread of non-native species, while other research has indicated that it is dispersal-driven. To determine the effects of dispersal limitation and predation on the risk to surrounding habitats of being invaded by non-native species established on marina docks, we used a three-factor design, deploying seven unglazed ceramic panels per each treatment combination of 1) inside versus outside a marina in Yaquina Bay, Oregon; 2) cage keeping out predators >mesh size, no cage, or partial cage; 3) fixed near the substrata (benthic) versus floating 1m below the surface. We also moved panels of either adults or recruits from floating in the marina to any of the treatment combinations to test if they would have lower survival outside by the substrate. The community on panels suspended in the marina only minimally overlapped with panels outside of the marina near the bottom. However, there was no difference between the cage treatments, which suggests that predators excluded by the cages are not responsible for the observed differences in species richness or composition. Title: The Limitation of Spread of Non-native Marine Invertebrates from Artificial Structures to Natural Habitats Author: McClees, Whitney, de Rivera, Catherine E. Year: 2017 Artificial structures created for aquatic anthropogenic activities are often colonized and fouled by many non-native species, few of which have invaded natural areas. Some research has indicated predation is limiting the spread of non-native species, while other research has indicated that it is dispersal-driven. To determine the effects of dispersal limitation and predation on the risk to surrounding habitats of being invaded by non-native species established on marina docks, we used a three-factor design, deploying seven unglazed ceramic panels per each treatment combination of 1) inside versus outside a marina in Yaquina Bay, Oregon; 2) cage keeping out predators >mesh size, no cage, or partial cage; 3) fixed near the substrata (benthic) versus floating 1m below the surface. We also moved panels of either adults or recruits from floating in the marina to any of the treatment combinations to test if they would have lower survival outside by the substrate. The community on panels suspended in the marina only minimally overlapped with panels outside of the marina near the bottom. However, there was no difference between the cage treatments, which suggests that predators excluded by the cages are not responsible for the observed differences in species richness or composition. Close

• 3. [Article] Effect of riparian areas on the ecological condition of small, perennial streams in agricultural landscapes of the Willamette Valley : research plan, June 1997

  Little research has been directed toward determining the status and ecological role of riparian areas in agricultural landscapes of the Willamette Valley, Oregon. A research project has been designed to ...

  Citation × Citation Citation Abstract Copy Title: Effect of riparian areas on the ecological condition of small, perennial streams in agricultural landscapes of the Willamette Valley : research plan, June 1997 Author: Moser, Thomas J., Schuft, Michael J., Wigington, P.J., Herlihy, Alan T., Van Sickle, John, Kaufmann, Phillip R., McAllister, Lynne S. Little research has been directed toward determining the status and ecological role of riparian areas in agricultural landscapes of the Willamette Valley, Oregon. A research project has been designed to contribute to the development and evaluation of alternative future scenarios and to improve the basic understanding of the role of riparian areas on the ecological condition of small, perennial streams in agricultural landscapes of the Willamette Valley. The objectives of the research are: (1) to quantify relationships between riparian attributes at varying spatial scales and stream ecological condition, and (2) to estimate the influence of selected riparian area-agricultural configurations on the indicators of stream ecological condition. To address these objectives, remotely-sensed imagery (aerial photography and thematic mapper satellite imagery) will be used to quantify land cover at multiple spatial scales (i.e., stream reach, stream network, watershed), from which riparian vegetation function, land use stressor, and stream network structure indicators (i.e., potential explanatory variables) are derived for 41 study watersheds. Title: Effect of riparian areas on the ecological condition of small, perennial streams in agricultural landscapes of the Willamette Valley : research plan, June 1997 Author: Moser, Thomas J., Schuft, Michael J., Wigington, P.J., Herlihy, Alan T., Van Sickle, John, Kaufmann, Phillip R., McAllister, Lynne S. Little research has been directed toward determining the status and ecological role of riparian areas in agricultural landscapes of the Willamette Valley, Oregon. A research project has been designed to contribute to the development and evaluation of alternative future scenarios and to improve the basic understanding of the role of riparian areas on the ecological condition of small, perennial streams in agricultural landscapes of the Willamette Valley. The objectives of the research are: (1) to quantify relationships between riparian attributes at varying spatial scales and stream ecological condition, and (2) to estimate the influence of selected riparian area-agricultural configurations on the indicators of stream ecological condition. To address these objectives, remotely-sensed imagery (aerial photography and thematic mapper satellite imagery) will be used to quantify land cover at multiple spatial scales (i.e., stream reach, stream network, watershed), from which riparian vegetation function, land use stressor, and stream network structure indicators (i.e., potential explanatory variables) are derived for 41 study watersheds. Close

• 4. [Article] Fecal Bacteroidetes host distributions and environmental source tracking

  Contamination of recreational and shellfish waters with fecal pollution is a major water quality issue with associated economic impacts and human health risks. Reliable fecal source identification and ...

  Citation × Citation Citation Abstract Copy Title: Fecal Bacteroidetes host distributions and environmental source tracking Author: Dick, Linda K. Contamination of recreational and shellfish waters with fecal pollution is a major water quality issue with associated economic impacts and human health risks. Reliable fecal source identification and rapid, quantitative analyses are essential components of risk assessment. Enteric bacteria that are endemic to specific hosts have a potential role as public health indicators of fecal pollution. Building on previous work to discriminate ruminant and human fecal contamination, we cloned class Bacteroidetes 16S rRNA genes from pig, elk, dog, cat, and seagull fecal DNAs. Unique restriction patterns were identified among clones from each of the host species using Terminal Restriction Fragment Length Polymorphisms (T-RFLP). Clones exhibiting unique patterns were sequenced and analyzed phylogenetically, along with human, horse, and cattle sequences recovered from previous work. The analysis revealed both endemic and cosmopolitan (global) host distributions. The sequence data were used to identify host-specific genetic markers for pig and horse feces, and to design PCR primers that identify these sources of fecal pollution in water. There was a high degree of sequence overlap among the fecal Bacteroidetes of wild and domestic ruminants, and among human, domestic pet, and seagull Bacteroidetes. We compared fecal Bacteroidetes rRNA genes from these hosts using subtractive hybridization, a method that identifies differences between closely related genomes or gene sequences. A Bacteroidetes rDNA marker that distinguishes elk and cow feces was identified, as well as a host-specific marker for dog fecal Bacteroidetes. The four newly designed PCR primers were tested for specificity and sensitivity, and the dog primer was successfully used, along with the human and ruminant-specific primers, in a collaborative study comparing fecal source tracking methods. We also developed a real time Taq nuclease assay for quantification of fecal Bacteroidetes 16S rDNA, and compared it with an EPA-approved enumeration method for the current standard public health indicator, Escherichia coli, in serial dilutions of sewage primary influent. There was a strong, positive correlation between the methods, and the Taq nuclease assay was sensitive and much more rapid than the E. coli assay. PCR source identification and enumeration of fecal Bacteroidetes 16S rDNA show promise for application in a health risk-based analysis of fecal pollution. Title: Fecal Bacteroidetes host distributions and environmental source tracking Author: Dick, Linda K. Contamination of recreational and shellfish waters with fecal pollution is a major water quality issue with associated economic impacts and human health risks. Reliable fecal source identification and rapid, quantitative analyses are essential components of risk assessment. Enteric bacteria that are endemic to specific hosts have a potential role as public health indicators of fecal pollution. Building on previous work to discriminate ruminant and human fecal contamination, we cloned class Bacteroidetes 16S rRNA genes from pig, elk, dog, cat, and seagull fecal DNAs. Unique restriction patterns were identified among clones from each of the host species using Terminal Restriction Fragment Length Polymorphisms (T-RFLP). Clones exhibiting unique patterns were sequenced and analyzed phylogenetically, along with human, horse, and cattle sequences recovered from previous work. The analysis revealed both endemic and cosmopolitan (global) host distributions. The sequence data were used to identify host-specific genetic markers for pig and horse feces, and to design PCR primers that identify these sources of fecal pollution in water. There was a high degree of sequence overlap among the fecal Bacteroidetes of wild and domestic ruminants, and among human, domestic pet, and seagull Bacteroidetes. We compared fecal Bacteroidetes rRNA genes from these hosts using subtractive hybridization, a method that identifies differences between closely related genomes or gene sequences. A Bacteroidetes rDNA marker that distinguishes elk and cow feces was identified, as well as a host-specific marker for dog fecal Bacteroidetes. The four newly designed PCR primers were tested for specificity and sensitivity, and the dog primer was successfully used, along with the human and ruminant-specific primers, in a collaborative study comparing fecal source tracking methods. We also developed a real time Taq nuclease assay for quantification of fecal Bacteroidetes 16S rDNA, and compared it with an EPA-approved enumeration method for the current standard public health indicator, Escherichia coli, in serial dilutions of sewage primary influent. There was a strong, positive correlation between the methods, and the Taq nuclease assay was sensitive and much more rapid than the E. coli assay. PCR source identification and enumeration of fecal Bacteroidetes 16S rDNA show promise for application in a health risk-based analysis of fecal pollution. Close

• 5. [Article] Hatfield Marine Science Center Dynamic Revetment Report DSL permit #45455-FP Monitoring Report February, 2013

  Stabilization of the Yaquina Bay shoreline along the northeastern edge of the Hatfield Marine Science Center (HMSC) campus became necessary to halt erosion that threatened both HMSC critical infrastructure ...

  Citation × Citation Citation Abstract Copy Title: Hatfield Marine Science Center Dynamic Revetment Report DSL permit #45455-FP Monitoring Report February, 2013 Author: Nelson, Walt, Allan, Jonathan, Stephensen, Shawn, Folger, Christina, Webster, Janet G., Politano, Vincent Stabilization of the Yaquina Bay shoreline along the northeastern edge of the Hatfield Marine Science Center (HMSC) campus became necessary to halt erosion that threatened both HMSC critical infrastructure (seawater storage tank) and public access to the HMSC Nature Trail. A Dynamic Revetment (gravel beach) was installed in November, 2011 on 260 feet of shoreline to mitigate erosion. Shoreline topographic and biological monitoring was initiated before and has continued after the project completion. 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). Beach profile data also indicated that the 2007 DRP continued to be successful in stabilizing further retreat of the shoreline. There were significantly more invertebrates associated with beach wrack in the 2011 DRP area as compared with the Reference or 2007 DRP areas. Beach wrack did not tend to accumulate in the Reference area because of vertical beach scarps generated by erosion. The reason for the difference with the 2007 DRP area is unclear. Fish were significantly more abundant in the Reference area compared to the DRP. However, as with the pre-project sampling, maximum abundance was consistently observed at Reference Site 4, which has a uniquely high degree of physical habitat complexity, resulting from trees that have been eroded onto the shore. There were significantly greater vegetation coverage and significantly lesser presence of non-living substrata in the Reference area as compared to the DRP. These differences are consistent with pre-project site differences, probably resulting from a low area of the shoreline which allows increased flooding and associated disturbance in the DRP back shore area. There were no marine mammals observed in either the DRP or Reference areas over the 43 surveys conducted over the 2012 survey period. As was observed in the 2011 report, variability among observation periods for birds was extremely high, with many zero observations. Although there were about three times more birds observed in the Reference area, there were no statistically significant differences in the number of birds observed based either on tide (high vs. low) or sample area (DRP vs. Reference). The number of bird taxa observed was similar in both areas, and most abundant species were similar between the two areas. Fish, birds and wrack invertebrates, such as beach hoppers), were shown to utilize the DRP project area. Biological differences in fish, birds and vegetation observed in year 1of post-project monitoring tended to reflect differences in habitat that were present before the DRP project. Title: Hatfield Marine Science Center Dynamic Revetment Report DSL permit #45455-FP Monitoring Report February, 2013 Author: Nelson, Walt, Allan, Jonathan, Stephensen, Shawn, Folger, Christina, Webster, Janet G., Politano, Vincent Stabilization of the Yaquina Bay shoreline along the northeastern edge of the Hatfield Marine Science Center (HMSC) campus became necessary to halt erosion that threatened both HMSC critical infrastructure (seawater storage tank) and public access to the HMSC Nature Trail. A Dynamic Revetment (gravel beach) was installed in November, 2011 on 260 feet of shoreline to mitigate erosion. Shoreline topographic and biological monitoring was initiated before and has continued after the project completion. 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). Beach profile data also indicated that the 2007 DRP continued to be successful in stabilizing further retreat of the shoreline. There were significantly more invertebrates associated with beach wrack in the 2011 DRP area as compared with the Reference or 2007 DRP areas. Beach wrack did not tend to accumulate in the Reference area because of vertical beach scarps generated by erosion. The reason for the difference with the 2007 DRP area is unclear. Fish were significantly more abundant in the Reference area compared to the DRP. However, as with the pre-project sampling, maximum abundance was consistently observed at Reference Site 4, which has a uniquely high degree of physical habitat complexity, resulting from trees that have been eroded onto the shore. There were significantly greater vegetation coverage and significantly lesser presence of non-living substrata in the Reference area as compared to the DRP. These differences are consistent with pre-project site differences, probably resulting from a low area of the shoreline which allows increased flooding and associated disturbance in the DRP back shore area. There were no marine mammals observed in either the DRP or Reference areas over the 43 surveys conducted over the 2012 survey period. As was observed in the 2011 report, variability among observation periods for birds was extremely high, with many zero observations. Although there were about three times more birds observed in the Reference area, there were no statistically significant differences in the number of birds observed based either on tide (high vs. low) or sample area (DRP vs. Reference). The number of bird taxa observed was similar in both areas, and most abundant species were similar between the two areas. Fish, birds and wrack invertebrates, such as beach hoppers), were shown to utilize the DRP project area. Biological differences in fish, birds and vegetation observed in year 1of post-project monitoring tended to reflect differences in habitat that were present before the DRP project. Close