The Arizona Nature Conservancy's Hassayampa River Preserve is 50 miles northwest of Phoenix near the town of Wickenburg. Four miles of the largely ephemeral Hassayampa River are perennial within the preserve, supporting one of the finest remaining cottonwood-willow forests in the state. Stream flows are affected by wells pumping ground water directly from the alluvial aquifer and may be influenced by wells which intercept lateral inflow from the regional basin-fill aquifer. Developing effective management strategies to protect base flow conditions (∼4 cfs) depends on a clear understanding of the surface and ground-water systems in the preserve. Provided that ground water developers near Wickenburg recognize and incorporate the interconnected nature of each hydrologic system, perennial flow within the preserve is not believed to be immediately threatened. (Abstract shortened with permission of author.)

This dissertation investigates the spatio-temporal dynamics of intermittent stream fish metacommunities in response drought-induced fragmentation and re-connectivity using both field and experimental approaches. A detailed field study was conducted in two streams and included pre-drought, drought, and post-drought hydrological periods. Fish assemblages and metacommunity structure responded strongly to changes in hydrological conditions with dramatic declines in species richness and abundance during prolonged drought. Return of stream flows resulted in a trend toward recovery but ultimately assemblages failed to fully recover. Differential mortality, dispersal, recruitment among species indicates species specific responses to hydrologic fragmentation, connectivity, and habitat refugia. Two manipulative experiments tested the effects of drought conditions on realistic fish assemblages. Fishes responded strongly to drought conditions in which deeper pools acted as refugia, harboring greater numbers of fish. Variability in assemblage structure and movement patterns among stream pools indicated species specific habitat preferences in response predation, resource competition, and desiccation. Connecting stream flows mediated the impacts of drought conditions and metacommunity dynamics in both experiments. Results from field and experimental studies indicate that stream fish metacommunities are influenced by changes in hydrological conditions and that the timing, duration, and magnitude of drought-induced fragmentation and reconnecting stream flows have important consequences metacommunity dynamics.

abstract: Dissolved organic matter (DOM) is an important part of aquatic foodwebs because it contains carbon, nitrogen, and other elements required by heterotrophic organisms. It has many sources that determine its molecular composition, nutrient content, and biological lability and in turn, influence whether it is retained and processed in the stream reach or exported downstream. I examined the composition of DOM from vascular wetland plants, filamentous algae, and riparian tree leaf litter in Sonoran Desert streams and its decomposition by stream microbes. I used a combination of field observations, in-situ experiments, and a manipulative laboratory incubation to test (1) how dominant primary producers influence DOM chemical composition and ecosystem metabolism at the reach scale and (2) how DOM composition and nitrogen (N) content control microbial decomposition and stream uptake of DOM. I found that differences in streamwater DOM composition between two distinct reaches of Sycamore Creek did not affect in-situ stream respiration and gross primary production rates. Stream sediment microbial respiration rates did not differ significantly when incubated in the laboratory with DOM from wetland plants, algae, and leaf litter, thus all sources were similarly labile. However, whole-stream uptake of DOM increased from leaf to algal to wetland plant leachate. Desert streams have the potential to process DOM from leaf, wetland, and algal sources, though algal and wetland DOM, due to their more labile composition, can be more readily retained and mineralized. / Dissertation/Thesis / Masters Thesis Biology 2018

There has been much interest in the last decade concerning the factors that influence diversity, especially how diversity and ecosystem processes may be linked. This study was based in small, cobble streams in South East Queensland. Its aim was to determine how the diversity and composition of consumers (the grazer guild) is influenced by both the production and composition of benthic algae, at different spatial scales. It also aimed to ascertain whether this response differs among grazer sub guilds with different dispersal capabilities. Ten sites in the Upper Brisbane and Mary catchments were sampled. The sites were selected to provide a range of productivity and composition. Grazers from these sites included snails and elmids, and larval mayflies, moths, and caddisflies. Grazer diversity and composition appeared to be structured by catchment scale influences, but environmental variables also affected which animals colonised patches and microhabitats (cobbles) within catchments. Primary productivity and algal composition could not be separated, with highly productive reaches also having a high cover of filamentous algal taxa. Grazer diversity displayed strongly positive, linear relationships with algal variables at the reach scale. It had a negative relationship with filamentous algae at the cobble scale, and a non-significant hump-shaped relationship with primary productivity. Survey data alone could not separate whether grazers were responding to habitat or food-related drivers, or to variations in productivity. Experimental manipulation of algal variables at the patch scale, using light and nutrients, also could not clearly uncouple the relationship between primary productivity and filamentous algal cover. Once reach scale variation was removed, grazer diversity displayed hump-shaped relationships with algal variables, including algal diversity. Much of this variation was due to patterns in mobile grazers, as sedentary grazers did not respond to algal variation at this scale. The density of the more mobile taxa showed similar patterns to those at the cobble scale (hump-shaped). A second field experiment was carried out in order to further investigate the responses of invertebrates to algal community composition at the cobble scale. Data from all three chapters suggested that as sites shifted to a dominance of filamentous algae, often with an associated increase in GPP, there was also a shift in the grazer community towards more sedentary grazers and away from the more mobile taxa. This also occurred at the cobble scale in the second experiment. The gut analysis and diet studies in the third chapter indicated that while many grazers consumed filamentous algae, it was not assimilated. This suggests that the preferences for sedentary taxa for cobbles and reaches dominated by filamentous algae are likely to be due to some other, possibly habitat-related, factor such as flow or predation refuge. The study provides a rare examination of relationships between primary productivity and consumer diversity in freshwater streams, and finds support for the pattern found in other systems of monotonic relationships of these two variables at large scales and hump-shaped relationships at smaller scales. It emphasises the importance of understanding other, potentially confounding, aspects of communities of producers, and investigates the possible roles of the most important of these (community composition) in structuring consumer communities in the small cobble streams of South-East Queensland.

Inter-Basin-Water Transfers significantly reduce flow and sediment regimes to the downstream ecosystem effecting differential channel adjustment at various locations. It is not known how macroinvertebrates adjust to flow regulation, either spatially or temporally, because research is lacking into how morphological adjustment affects benthic habitat. Feedback mechanisms that initiate the adjustment process must first be identified, then the effect on benthic habitat becomes apparent, thus, providing a link to macroinvertebrate response. Since regulation there has been a 95% reduction in flow volume, a complete downward shift in both the flow duration and flood frequency curves and a 194% increase in flow constancy compared to the pre- dam period. Furthermore, Jindabyne Dam traps 99.9% of the total incoming sediment load. Upstream of the tributary the dominant river response was accommodation adjustment with subsequent contraction of the river channel. Associated feedback mechanisms were ?armouring? and vegetation encroachment. Downstream of the tributary response was more complex, with channel contraction through aggradation and specifically the formation of a tributary mouth bar and fan, mid channel lobate bar, transverse bar and in-channel bench. Associated feedback mechanisms were interactions between vegetation and sediment; channel morphology, flow and sediment distribution; and sediment distribution, flow and channel morphology. These processes have had site specific and reach scale impacts on benthic habitat. Macroinvertebrate response to flow regulation was habitat specific (riffle or edge) and seemed to correspond to either site, or reach scale morphological adjustment, whereas, flow constancy seemed to affect edge macroinvertebrates throughout both reaches. Spatially, macroinvertebrates have not adjusted to the post- dam flow regime and temporally, macroinvertebrates have not recovered 30 years after the closure of Jindabyne Dam. How physical processes change habitats and how these impact on a river?s ecology and at what scale, are important considerations in river management.

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

Thesis (M.S.)--Oregon State University, 1975. / Typescript (photocopy). Includes bibliographical references. Also available on the World Wide Web.