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.

Beginning in the early 1600s, dam construction in New England obstructed anadromous fish access to spawning grounds during migration. As a result, anadromous forage fish populations have declined, which has impacted freshwater, marine, and terrestrial ecosystems. To determine the impacts of dams on anadromous forage fish and freshwater ecosystems, I used historical and current data to estimate population changes in alewives (Alosa pseudoharengus) from 1600-1900. A significant reduction in spawning habitat occurred in New England as a result of 1,642 dams constructed between 1600 and 1900, resulting in 14.8% and 16.6% lake and stream habitat remaining by 1900, respectively. In eight New England watersheds, this translates to an estimated cumulative annual loss of 30 B juvenile alewives available as freshwater forage and 538 M year 1, 2 and 3 alewives available as marine forage. The cumulative annual lost number of adult return spawners was conservatively 17 M fish, or 3,642 metric tons. Lost marine-derived nutrients from adult return spawners were 11 T phosphorus, 64 T nitrogen, and 410 T carbon. A comparison of predator fish growth and condition in alewife and non-alewife lakes showed that white perch (Morone Americana) and yellow perch (Perca flavescens) have higher condition in early summer in lakes with alewives. Predator growth rates (length-at-age) were significantly higher in early life stages (ages 1 and 2) when alewives were present, but significantly lower in late life stages (ages 3 and older). Results indicate a greater maximum length obtained by mature fish when alewives are absent, and an earlier age and length at maturity when alewives are present. These results indicate significant ecosystem impacts of lost anadromous forage fish, with bottom-up trophic effects across multiple time scales and biological processes. An ecosystem-based management approach should be used by inland and marine aquatic managers, and ecosystem connectivity and trophic interactions should be considered when managing migratory fish and prioritizing restoration goals.

Abstract The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus, Mitchell) is an anadromous species that spawns in tidal freshwater rivers from Canada to Florida. Overfishing, river sedimentation and alteration of the river bottom have decreased Atlantic Sturgeon populations, and NOAA lists the species as endangered. Ecologists sometimes find it difficult to locate individuals of a species that is rare, endangered or invasive. The need for methods less invasive that can create more resolution of cryptic species presence is necessary. Environmental DNA (eDNA) is a non-invasive means of detecting rare, endangered, or invasive species by isolating nuclear or mitochondrial DNA (mtDNA) from the water column. We evaluated the potential of eDNA to document the presence of Atlantic Sturgeon in the James River, Virginia. Genetic primers targeted the mitochondrial Cytochrome Oxydase I gene, and a restriction enzyme assay (DraIII) was developed. Positive control mesocosm and James River samples revealed a nonspecific sequence—mostly bacteria commonly seen in environmental waters. Methods more stringent to a single species was necessary. Novel qPCR primers were derived from a second region of Cytochrome Oxydase II, and subject to quantitative PCR. This technique correctly identified Atlantic Sturgeon DNA and differentiated among other fish taxa commonly occurring in the lower James River, Virginia. Quantitative PCR had a biomass detection limit of 32.3 ug/L and subsequent analysis of catchment of Atlantic Sturgeon from the Lower James River, Virginia from the fall of 2013 provided estimates of 264.2 ug/L Atlantic Sturgeon biomass. Quantitative PCR sensitivity analysis and incorporation of studies of the hydrology of the James River should be done to further define habitat utilization by local Atlantic Sturgeon populations. IACUC: AD20127

The purpose of this study was to evaluate the level of nitrate contamination in the water in Cherry Valley. It examines the theory that human effluent is the source of the nitrate and evaluates the role of politics in the nitrate issue.

Humans make decisions within ecosystems to enhance their well-being, but choices can lead to unintended consequences. The ecosystem services (ES) approach supports decision-making that considers all environmental goods and services. Many challenges remain in the implementation of the ES approach like how specific ES vary through space and time. We address this research problem using the Tualatin and Yamhill river basins in northwestern Oregon as a study area. Freshwater ES are quantified and mapped with the spatially-explicit ES modeling tool, Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST). In chapter II, we develop a simple urban land cover change modeling approach with selected stakeholder input. The products of this analysis are used in part to answer the question of how the freshwater ES of water yield, nutrient retention, and sediment retention will change in the future, and how their distribution potentially will change? In chapter III, these ES are modeled in InVEST using the land cover scenarios and three downscaled global climate models. The base period is 1981 to 2010 and the future period is 2036 to 2065. The models are calibrated to empirical estimates, and display different sensitivities to inputs. Water yield increases with higher rainfall but decreases with the highest temperature scenario. Nutrient export and retention estimates are positively correlated. In the Tualatin basin, more urban lands generally lead to increases in nutrient exports and retention. The effect is reversed in the Yamhill basin from much larger agricultural exports. Sediment exports and retention increase with higher winter rainfall but are negatively spatially correlated due to topographic effects. Simulation of a landscape scale installation of riparian buffers leads to decreases in exports and increases in retention. The distribution of the provision of freshwater ES remains unchanged throughout the scenarios. With few parameters in each InVEST model, all display a high degree of sensitivity. Parameterization is subject to high uncertainty even with calibrated values. We discuss the assumptions and limitations of InVEST's freshwater models. The spatially explicit nature of InVEST is its main advantage. This work coupled with other analyses in the study area can facilitate the identification of tradeoffs amongst ES leading to better ecosystem management.