49 leaves ; 29 cm Typescript Thesis (M.S.)--University of Oregon, 1974 Includes bibliographical references (leaves 45-49) Unif. Title University of Oregon theses, Dept. of Biology, M.S., 1974

The focus of this research was to develop bacterial community indicators of stream sanitary and ecological condition. The first study compared substrate utilization patterns between centrifuged and uncentrifuged split samples. We found a shift in the relative proportion of each group of bacteria following centrifugation, with a marked increased in the fecal coliform group and relatively fewer heterotrophic and total coliform bacteria. Centrifuged samples consistently responded faster and oxidized more substrate than did their uncentrifuged counterparts. Substrate utilization patterns of centrifuged sub-samples from 19 sites showed better separation between Willamette Valley and Cascade ecoregions than did the uncentrifuged sub-samples in ordination space. We recommend developing microtiter plates with substrates specific types of environmental stress. The second study determined the minimum volume of water needed and the maximum time and temperature that bacteriological water samples captured on a membrane filter can be held in guanidine isothiocyanate buffer (GITC) prior to DNA extraction for community fingerprint analysis. We found 100 ml water samples yielded more information than the 50 ml or the 250 ml water samples and observed a marked decrease in information for samples that were held at room temperature for more than 24 hours. We concluded that 100 ml samples were optimal for bacterial community DNA fingerprint analysis. Furthermore, we recommended transporting filtered water samples held in GITC on ice and keeping the samples frozen until DNA is extracted for further analysis. The third study addressed questions of sampling error and response variability of two PCR-based indicators, bacterial community-level Terminal-Restriction Fragment Length Polymorphisms and Bacteroidetes ruminant and human specific fecal source tracking markers. We found the T-RPLP and Bacteroidetes markers to show very little sampling error, and suggested collecting a single 1-liter water sample. A high turbidity scenario resulting in higher fecal pollution and lower bacterial species richness explained why decreased TRF richness was strongly associated with high fecal coliform density, turbidity, and human Bacteroidetes detection. We propose that in times of increased turbidity, a disturbance in the bacterial community occurs, reducing bacterial richness and increasing a few types of stress-resistant fecal bacteria. / Graduation date: 2004

Traditional public health bacterial indicators of water quality and the Biolog�� system were evaluated to compare their response to other indicators of stream condition with the state of Oregon and between ecoregions (Coast Range, Willamette Valley, Cascades, and Eastern Oregon). Forty-three randomly selected Oregon rivers were sampled during the summer low flow period in 1997 and 1998. Testing included heterotrophic plate counts (HPC), total coliforms, fecal coliforms, E. coli, and Biolog�� GN plates. Statewide, HPC correlated strongly with physical habitat and chemistry indicators while fecal coliforms and E. coli were highly correlated only with the river chemistry indicators. Total coliform bacteria did not correlate with either of the above environmental indicators. Dividing the sites by ecoregion, Eastern Oregon was characterized by high HPC, fecal coliforms, E. coli, nutrient loads, and indices of human disturbance, whereas the Cascades ecoregion had correspondingly low counts of these indicators. The Coast Range reflected statewide results and the Willamette Valley presented no consistent indicator pattern. Attempts to separate ecoregions with the Biolog system were not successful nor did a statistical pattern emerge between the first five principle components and the other environmental indicators. Our research has shown that traditional public health microbial indicators may, however, be useful in measuring the effects of anthropogenic stress over large spatial scales. / Graduation date: 2000

The Environmental Monitoring and Assessment Program (EMAP) site selection protocol was used to generate a random sample of streams throughout the state of Oregon. One hundred and forty-six selected streams were sampled during the summer, low-flow period of 1997. Traditional microbial public health indicators, including heterotrophic plate counts (HPC), total coliforms (TC), fecal coliforms (FC) and E. coli, were enumerated using the membrane filtration technique. Nearly 17% (3.4-23.6%, 95% C.I.) of streams exceeded the current state of Oregon standard for water-contact recreation. Levels of bacteria were also shown to differ significantly by ecoregion. The Cascades ecoregion had low levels of all types of bacteria. The Willamette Valley, Columbia Plateau and Snake River Basin had high levels of one or more groups of bacteria measured. Twenty-six sites were resampled and FC and E. coli estimates were not significantly different for the different sampling dates. Biolog GN plates were used to provide a measure of the functional diversity of microbial communities for the same streams as above. Two groups were formed based on inoculum density and Biolog GN plates were analyzed using principal component analysis (PCA). The first few principal components explained nearly half of the variation of the data in both groups. Principal components were correlated with the average carbon source utilization, levels of coliform bacteria, and ecoregions. These results indicate that patterns produced by Biolog GN plates may be useful in the assessment of ecological condition of freshwater streams. Subsequent publications will explore the relationships between the pattern of substrate utilization of Biolog GN plates with other indicators of ecological function. / Graduation date: 1999

Intermittent, headwater streams recently have been recognized as important components of forest ecosystems and have been provided increased protection by the Northwest Forest Plan. However, few studies have examined their distribution, dynamics, and ecological roles, such as habitat for wildlife. My goal was to provide additional information on the ecology of intermittent streams in the Pacific Northwest. I examined and compared hydrologic, water quality, and physical characteristics of 16 intermittent streams in old-growth and young forest stands in the central Cascade Range in western Oregon. I documented amphibian communities and habitat associations in these streams during spring and summer. I used comparisons of current habitat conditions and amphibian communities between stand types to gain insight into potential impacts of timber harvesting on these stream systems. Of the streams surveyed in old-growth and young forest stands, relatively few (23%) were designated as intermittent based on my definition which included presence of a definable channel, evidence of annual scour and deposition, and lack of surface flow along at least 90% of the stream length. Intermittent streams in old-growth stands exhibited the following characteristics: (1) annual flow pattern in which streams started to dry in May and June and were mostly dry by July; (2) lengthy annual flow durations (range 6-11 months); (3) cool and stable daily stream temperatures; (4) primarily coarse substrates, such as cobbles and pebbles; (5) streamside vegetation comprised of predominantly coniferous overstories, and plant species associated with uplands or dry site conditions, such as Oregon-grape and salal, as well as riparian areas or wet site site conditions, such as Oregon-grape and salal, as well as riparian areas or wet site conditions, such as red alder, oxalis, red huckleberry, and vine maple (Steinblums et al. 1984, Bilby 1988); and (6) low to moderate densities of large wood, mostly moderately- and well-decayed. Study streams in young forest appeared to dry about one to two months later than the streams in old growth but had similar annual flow durations. They also were characterized by higher daily stream temperatures, similar diel fluctuations, finer substrates, more deciduous overstory and herbaceous understory cover, and lower densities of moderately-decayed large wood. Differences in habitat conditions between stand types may be attributed to timber harvesting as well as discrepancies in physiographic and geological factors, such as elevationgradient, and soil type. Amphibian communities in spring and summer were comprised primarily of the Cascade torrent salamander (Rhyacotriton cascadae), Dunn's salamander (Plethodon dunni), and Pacific giant salamander (Dicamptodon tenebrosus). Amphibian communities in streams in young forest stands exhibited different species composition and seasonal patterns in total density from those in old growth. Cascade torrent salamanders and Dunn's salamanders maintained similar densities and biomass between spring and summer by potentially adopting drought avoidance strategies. Species differed in their use of habitat types and associations with habitat features. In general, amphibian species were positively correlated with percent surface flow, water depth, intermediate-sized substrates and negatively associated with overstory canopy cover, elevation, and wood cover. Results of my study suggest that intermittent streams may warrant protection for their potential effects on downstream habitat and water quality and for their role as habitat for aquatic species, such as amphibians. Streamside vegetation should be maintained along intermittent channels to provide shade protection for water temperature regulation and sources of large woody debris and other allochthonous energy input, to help stabilize slopes, and to minimize erosion and sedimentation. At a minimum, intermittent stream channels should receive protection from physical disturbance during timber harvesting operations. However, since intermittent stream systems are highly variable, management should address individual site conditions and vary accordingly. / Graduation date: 1997

Seven streams, one of them permanent, were studied in western Oregon, USA. The research was designed to assess the value of summer-dry headwaters for conservation oriented landscape management. Streams were categorized primarily according to exposure (forest versus meadow sites) and secondarily according to flow duration (ephemeral = short-flow versus temporary = long-flow sites). Ephemeral streams have discontinuous flow and last less than three months annually. Temporary streams have continuous flow for more than five months each season. Ephemeral forest streams were highly efficient at filtering road-generated sediment. Uptake lengths for suspended sediment were short (36 m-105 m) at moderately elevated input concentrations. As a result of the filtration mechanism, filtration efficiency is expected to increase as annual flow duration decreases. Injection experiments yielded nitrate uptake rates of almost 1% per m of temporary stream channel. Exchange with subsurface flow was the most important route for nitrate removal from the water column. Biological uptake was insignificant in a light-limited forest stream, whereas a considerable amount of nitrate was retained by the biota a nutrient-limited meadow channel. At least 207 insect species were collected from the summer-dry streams. Species richness recorded from temporary forest streams exceeded that in an adjacent permanent headwater and there was high overlap between the fauna of the permanent and the temporary streams. Species richness in ephemeral channels was only 1/4 to 1/3 of that in long-flow forest streams. Multivariate analysis of community structure revealed flow duration and microhabitat pattern (riffle-pool) as the most important environmental factors determining faunal composition in temporary forest streams. Summer drought conditions at the sample sites also were important. By providing habitat and contributing to water quality in permanent downstream reaches, summer-dry streams have the potential to serve multiple purposes in conservation management. Their value from a conservation perspective is unexpectedly high. Landscape management therefore should be directed toward the preservation and protection of ephemeral and temporary streams. / Graduation date: 1993

Initially, components of an aquatic food web were examined to study impacts of recreational use on the aquatic ecology of Quartzville Creek, Oregon in 1995 and 1996. Measurements of the food web components consisted of observations of harlequin ducks (Histrionicus histrionicus), visual counts of the larval caddisfly Dicosmoecus gilvipes, benthic macroinvertebrate samples, and chlorophyll a biomass of epiphytic algae. In February 1996, a major flood forced closure of the study area to the general public throughout the 1996 season, providing a "natural experiment" situation. The difficulty was how to distinguish between effects of flood damage and effects of the presence/absence of humans. By accounting for various measured abiotic and biotic factors using multiple regression, distinctions between disturbance effects were made with regard to abundances of D. gilvipes and benthic invertebrates. Regression analysis also was used to account for annual site differences in average depth, habitat types and substrates. Generally, recreational impacts were apparent at more localized spatial and temporal scales than were effects from extensive flooding. However, scales at which these disturbances affected components of the food web varied. Impacts of the flood included an 81% reduction in overall D. gilvipes densities, a 37% decrease in benthic abundance, reduced chlorophyll a biomass, fewer numbers of ducks and changes in site substrates and habitats. These impacts occurred across all study sites and throughout the 1996 season, except for the recovery of benthic abundance to 1995 levels by July 1996. Recreational impacts were apparent at the site scale and appeared to be seasonal in duration. In 1995, sites without human use had significantly higher densities of D. gilvipes than those sites impacted by recreation. In 1996, no significant differences in D. gilvipes densities among sites were observed after accounting for flood effects and site differences. There were no direct significant relationships to human use among sites with regard to total benthic invertebrates, chlorophyll a biomass or H. histrionicus. Despite the lack of a direct spatial relationship between H. histrionicus and D. gilvipes at the local scale of this study, there were strong temporal correlations between harlequin brood development and D. gilvipes maturation. / Graduation date: 1997

This study assessed the influence of landscape development on stream-associated amphibians in forested riparian areas within the Portland-Vancouver metropolitan region. Human alteration of landscapes may dramatically affect the ecology of neighboring aquatic systems. It was hypothesized that lotic amphibians would be negatively associated with greater amounts of landscape development and positively associated with forested area within the surrounding watershed. Thirty-seven 1st-3rd order streams were sampled between June 21st and September 21st in 2011. Streams potentially providing adequate habitat for stream-obligate amphibians were randomly selected. Amphibians were surveyed along 30-meter stream transects using an active-cover search (ACS). Environmental variables associated with development in surrounding landscapes were measured in situ. GIS delineation was conducted to define landscape-scale variables at stratified distances from riparian networks up-stream of each site via the utilization of the 2006 NLCD dataset and a finer-scale, regional dataset compiled by the Institute for Natural Resources (INR). Amphibians were detected at seventeen of the thirty-seven sampled streams. The most commonly detected species were Dicamptadon tenebrosus, Plethadon vehiculum and Plethadon dunni. Streams where amphibians were observed had lower average water temperature and conductivity, coarser stream substrate and were located on public property more often than streams where no amphibians were detected. Landscape variables were most significant to amphibians within 100 and 200 meters of the upstream stream network. Occupancy of a site by facultative species was best explained by the proportion of mixed forest in the surrounding watershed (R2=0.343, p<0.001). Occupancy of a stream by obligate species was best predicted by measurements of water quality and in-stream cover (Water Temperature: R2=0.275, p<0.001; Water Conductivity: R2=0.248, p<0.001; Cover: R2=0.323, p<0.001). Occupancy of stream refugia by all observed amphibians was positively influenced by higher percentages of forest cover and lower percentages of urban development and herbaceous vegetation in the surrounding watershed. Results of this study indicate that urban refugia must contain adequate riparian forest area, coarse stream substrate and clean, cool water to sustain stream-amphibian communities. Protection of remnant forested headwater stream networks is essential to the conservation of lotic amphibians in this urbanized region.

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.