In an initial research proposal of December 1969, the scientists of the Coniferous Forest Biome (CFB), an ecosystem study centered in the Pacific Northwest and part of the larger International Biological Programme (IBP), expressed optimism that computer simulations and systems modeling could transform empirical knowledge of the carbon, water, and nutrient flows turned into viable forest management practice. The CFB's strategy aimed to use projections of the computer simulations and data from field study to constantly check and direct each other, resulting in a flexible, refined, and accurate understanding of forest ecosystems, as well as a reliable guide to forest management. To what extent did the CFB's research program, centered on a total system model, complete its cycle of field study, modeling, and validation? Despite the innovative strategies of the CFB modelers, ecosystem modeling lost its preeminent status among the goals of the CFB, due to different interpretations of the purpose and philosophy of ecosystem modeling and the practical limitations of administering a large research program. Instead, small field-based studies during the CFB yielded a number of ground-breaking discoveries. Although they diverged from the modeling objectives, these areas of fieldwork emerged from questions the forest's functions and cycling processes that the modeling efforts of the CFB required. Focusing on the work of CFB participants from Oregon State University and the USDA Forest Service in the H. J. Andrews Experimental Forest, this thesis addresses the relationship between the marginalization of the modeling objectives and the rising centrality of field-based forest studies in the CFB from 1969 to 1980. Given the ongoing legacy of CFB research at the Andrews Long-Term Ecological Research (LTER) site and the later implications of CFB findings in debates over forest policy and management, this thesis also seeks to evaluate the Coniferous Forest Biome as a whole and discuss the role of modeling and field work within large ecological research endeavors more generally. / Graduation date: 2006

Klamath Marsh is a wetland complex that lies in the rain shadow of the Cascade Range in the Williamson River sub-basin of the Klamath Basin. The marsh lies directly east of Crater Lake in an area inundated by pyroclastic-flow and -fall deposits from the Holocene eruptions of Mount Mazama. The physical characteristics of rocks of Pleistocene versus Pliocene age combined with NNW -striking fault systems divide the Williamson River basin into two distinct hydrogeologic regimes. The northwestern regime includes the east slope of the Cascades and consists of at least 150 m of interbedded sand, gravel, and stacks (15 to 45 m) of thin (3-5 m) and vesiculated basalt lava flows. Mean annual precipitation ranges from 150 cm near the crest of the Cascades to 50 cm near Klamath Marsh. Moderate to high yield (100 to 4000 gpm) water wells, springs and flowing wells suggest high permeability and ground water potential. The southeastern regime is underlain by Pliocene pyroclastic flows (∼ 40 m) and lava flows (>30 m). Mean annual precipitation ranges from 70 cm in the highlands to 50 cm in the lowlands. Low-yield (20-100 gpm) water wells and perched unconfined aquifers in Holocene pumice deposits suggest low permeability and low ground water potential in areas underlain by the pyroclastic flows. Volumetric analysis of inflows and outflows in Klamath Marsh for 2000 indicates approximately 86% of inflow is from groundwater and 14% from surface water, with nearly 200 x 10⁶ m³ of water removed by evapotranspiration

The effect of contiguous forested habitat area on local avian diversity and species richness in the Tualatin Mountain area of northwestern Oregon was investigated. Observations of eight forested stands representing seven area values (1, 2, 7, 14, 18, 24 and 40 hectares) were made during the spring and summer of 1991 and 1992. The variables measured were chosen in an attempt to show possible relationships between vegetation factors, spatial patterns and bird communities. Kendall's rank correlation coefficients were used to analyze the data. Avian species richness and diversity were significantly correlated with forest stand (patch) size. The only significant correlation between avian species richness and diversity and vegetation measures was with percent shrub layer cover. It seems likely that avian diversity and richness are increased due to the presence of species that can utilize the interior and edges of forest stands along with species which depend upon true forested interior. When forested patch size drops below a critical area, the patch becomes all edge. Interior species are absent due to increased predation and the inability to compete with interior-edge species. Edge effect may be a contributing factor to variation in diversity of birds. The correlation of percent shrub layer cover with avian measures is accompanied by a correlation of percent shrub layer cover with distance from edge. This suggests further investigation is required to assess this relationship. Studies conducted in the northeastern and north central United States have shown a similar relationship between bird communities and forest patch size.

In this study, biological and chemical characteristics were determined for two high-elevation meadow-to-forest transitions located in the Central Oregon Cascades. The chloroform fumigation incubation method (CFIM) was used to determine microbial biomass C(MBC) and the N flush due to fumigation (NF), and meadow values were compared to forest values for each. Meadow and forest MBC values were also compared for estimates of MBC determined with microscopy and these values were compared to CFIM estimates. Net N mineralization and C mineralization were determined for an 85-d incubation period and used as a measure of labile C and N. Microbial biomass C and NF were then compared to these labile pools in order to investigate the relationship between the amount of each nutrient stored in biomass and the magnitude of the respective labile nutrient pool for each. Long-term and short-term net N mineralization rates and C/N ratios were also compared for meadow and forest soils, and the relationship between these two characteristics was examined. In general, microbial biomass estimates made with the CFIM method did not show any significant differences between meadow and forest soils. Mean MBC for both sites as determined by CFIM was estimated to be 369 and 406 μg C g⁻¹ soil in meadow and forest soils, respectively. Mean NF was estimated to be 37 and 56 μg N g⁻¹ soil in meadow and forest soils, respectively. MBC estimates made using microscopy showed biomass C to be greater in the forest than in the meadow. Mean MBC as determined by microscopy was estimated to be 529 and 1846 μg C g⁻¹ soil in meadow and forest soils, respectively. The NF measured as a percentage of the net N mineralized over 85 d was significantly greater in the forest than in the meadow soils, but was a substantial percentage in both. The means of these values were 30 and 166% in meadow and forest soils, respectively. This led to the conclusion that biomass N may be a very important pool of stored labile N in this ecosystem. Net N mineralization rates were almost always greater in the meadow than in the forest soils. Net N mineralization for the 10-d incubations averaged 21 μg N g⁻¹ soil in the meadow and 8 μg N g⁻¹ soil in the forest Rates for long-term N mineralization averaged 126 μg N g⁻¹ soil in the meadow and 52 μg N g⁻¹ soil in the forest. Net N mineralization rates were correlated with C/N ratios for both short-term and long-term incubations. / Graduation date: 2002

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

Marine ecosystems can be exposed to natural and anthropogenic disturbances that can lead to ecological failures. Marine reserves have been lately suggested to protect marine populations and communities that have been affected by habitat destruction and harvest. This research evaluates the potential role of two marine reserves established in Oregon in 1967 (Whale Cove) and 1993 (Gregory Point). The red sea urchin (Strongylocentrotus franciscanus) was selected as indicator of population recovery since it is the only species that is commercially harvested. Changes in density, biomass, average size, size structure, growth and mortality rates were evaluated through time to assess population recovery. These parameters were also compared between reserves and adjacent exploited areas to evaluate the effect of exploitation. Results from Whale Cove (old reserve) indicate that the population in this area is fully recovered. On the contrary, the population in Gregory Point (new reserve) showed signs of recovery after six years of being protected. The importance of red urchins as source populations to provide larvae to adjacent areas was explored by the analysis of drifter's trajectories. Both reserves might be connected in a network where larvae produced in Whale Cove will provide recruits to Gregory Point and adjacent exploited areas, as well as populations in northern California. Gregory Point releases larvae that become recruits for Whale Cove only when spawning takes place in winter, otherwise larvae travel to central California. No clear trends were found in growth and mortality rates between reserves and non-reserves; differences were more related with food availability, competitors, and age specific mortality. We applied qualitative simulations to characterize and differentiate the community network inside reserves and exploited areas. Results suggest that communities from a particular site can be represented by a set of alternative models with consistent species interactions. Differences in predator-prey interactions as well as non-predatory relationships (interference competition, mutualism, amensalism) were found among sites. Each set of models represents a hypothesis of community organization that agreed with natural history information. Alternative models suggest that kelp forest communities are dynamic and can shift from one network configuration to another providing a buffer against a variable environment. / Graduation date: 2002

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

Because riparian canopy controls most energy inputs to stream ecosystems, it directly affects the structure of aquatic food webs and the ecological processes that govern interactions among trophic levels. This study addresses the interdependence among riparian canopy, benthic community structure, and the carrying capacity of high desert streams for salmonid fishes. In streams in the lower John Day River Basin in eastern Oregon, algal, invertebrate, and fish communities were compared in reaches with varying densities of riparian canopy. Water temperatures varied with the density and upstream extent of canopy. Densely canopied sites were cool, while sites with high irradiances had temperatures exceeding the upper lethal limit for salmonids. Periphyton and grazer biomasses were greater in well-lighted sites, but 90% of grazer biomass consisted of Dicosmoecus gilvipes, a large caddisfly inedible by juvenile trout. Warmer water increased metabolic demands for salmonids, while the overwhelming dominance of Dicosmoecus in open sites shifted energy flow away from trout and shrunk their food base. High water temperatures, however, provided suitable habitat for many warmwater fishes which would otherwise not enter tributaries of this size. At higher elevation study sites in Camp Creek, light levels were higher and less variable than at the lower sites. Periphyton and invertebrate abundances were not correlated with irradiance. Rather, periphyton was maintained at low levels by grazers, particularly Dicosmoecus and snails. Manipulations of fish densities in enclosures showed that trout and dace had no negative impacts on numbers of invertebrate prey, and that grazers played a larger role in regulating lower trophic levels than did fish. Dicosmoecus acted as a keystone species in the benthic food web of Camp Creek by simultaneously influencing the trophic level both below and above its own. When irradiance was experimentally reduced under artificial canopies, periphyton standing crops were not different from those in open control pools after 4 wks. However, grazers were more abundant in open pools. The cropping of periphyton to uniform levels in both sunlight and shade indicated that mobile grazers targeted sites of varying productivities. Comparisons between benthic communities in Camp Creek and in a densely canopied reference stream suggested that benthic community structure shifted to accommodate changes in energy resources that occur when canopy density is altered. / Graduation date: 1998

Graduation date: 2006 / This study investigated whether a device commonly used to measure settlement of mussel larvae for ecological studies, the Tuffy™, functions uniformly whether placed in a bed of filamentous algae or on bare rock. During the summers of 2004 and 2005, the number of mussel larvae settling on Tuffys in patches of the filamentous algae Endocladia muricata and Neorhodomela larix, known to be natural substrata for settlement of mussels, was shown to be the same as on Tuffys on adjacent patches of bare rock. The data provide no evidence that adjacent filamentous algae affects settlement to Tuffys and support the utility of this technique for measuring the intensity of larval settlement.