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

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.