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Item Understanding the effects of floodplain shade on hyporheic and stream channel temperature cycles(Montana State University - Bozeman, College of Agriculture, 2024) Fogg, Sarah Kathleen; Chairperson, Graduate Committee: Geoffrey C. Poole; This is a manuscript style paper that includes co-authored chapters.River reaches with coarse-grained alluvial floodplains have a breadth of lateral interaction between the channel and surrounding landscape, yielding extensive riparian zones and high rates of gross water exchange between the channel and substrate (i.e., hyporheic exchange). The lateral hyporheic zone on floodplain rivers is often near the ground surface, allowing for heat exchange between the atmosphere, unsaturated sediments, and hyporheic zone. We hypothesized that floodplain shade overlying lateral hyporheic water influences the conductive heat flux through unsaturated sediments, thus influencing hyporheic temperatures and temperatures in associated stream channels. We conducted simulation modeling experiments to test the potential effects of floodplain shade on hyporheic and stream channel temperatures. We found that scenarios with floodplain shade led to cooler hyporheic and stream temperatures than scenarios lacking floodplain shade under a variety of realistic floodplain conditions. We conclude that floodplain forest shade is a novel consideration for riparian management on floodplain river reaches and may be crucial in managing and maintaining cold-water habitat into the future.Item Macroinvertebrate diversity, community structure, and dispersal are affected by tributary identity and confluence conditions in a regulated river(Montana State University - Bozeman, College of Letters & Science, 2023) Maguire, Zachary John; Chairperson, Graduate Committee: Lindsey Albertson; This is a manuscript style paper that includes co-authored chapters.Tributaries are essential components of freshwater ecosystems, playing a crucial role in maintaining connectivity and providing habitat for a diverse array of aquatic organisms. The role of tributaries in creating heterogeneity in physical conditions and food resources for fishes could be critical, yet little is known about how variable conditions in different tributaries in regulated river systems influence the mainstem. Using field observations in five tributaries on the Madison River, Montana, we found that tributaries in the same network and within relatively short distances of 60km varied greatly in their environmental conditions, macroinvertebrate densities, and macroinvertebrate community structure. Downstream of confluences macroinvertebrate richness increased overall, and per capita weight of drifting macroinvertebrates decreased overall. These findings suggest that confluences may act as hotspots for biodiversity in regulated rivers and introduce smaller bodied macroinvertebrates to the drift. The amount that a tributary influenced benthic richness and mean per capita weight in the drift downstream of its confluence was related to land use and abiotic factors within that tributary; both macroinvertebrate metrics significantly increased in magnitude downstream of confluences with higher percentage of US Forest Service land, cooler temperatures, decreased discharge, and increased elevation loss (i.e. steeper watershed slope). In contrast, tributaries that had a larger proportion of agricultural land, warmer temperatures, and higher discharge more strongly influenced benthic macroinvertebrate metrics. These tributaries supported higher benthic density and biomass downstream of confluences. Our results offer insight into the ways that tributaries can create heterogeneous habitats that in turn structure macroinvertebrate communities in mainstem rivers and suggest that conservation and restoration of these essential components of freshwater ecosystems is a well-spent endeavor in rivers with regulated mainstems. Future research will need to test the ubiquity of the patterns we observed in other river networks and under other global changes such as pollution, invasive species, and drought. Continued understanding of the importance of heterogeneity imparted by tributaries and their confluences on diversity, availability, and quality of food for threaten fishes is needed to guide restoration efforts aimed at improving river condition and resilience.Item Geomorphology, biodiversity and ecosystem function, and food web dynamics in large riverscapes(Montana State University - Bozeman, College of Letters & Science, 2021) Scholl, Eric Arthur; Chairperson, Graduate Committee: Wyatt F. Cross; This is a manuscript style paper that includes co-authored chapters.Humans have transformed the Earth's surface so extensively that we now play a dominant role in regulating geomorphological processes around the world. These effects are particularly prevalent in large rivers, which despite their high biophysical complexity, face widespread habitat alteration and simplification. The way species respond to such changes will unquestionably impact the structure and function of ecosystems, with cascading effects on numerous goods and services they provide. Consequently, efforts to understand how the physical habitat template shapes the structure and function of larger river ecosystems are critically needed to predict how future perturbations will impact these imperiled and iconic environments. My dissertation blends approaches from the physical and ecological sciences to uncover connections between the geophysical habitat template, biodiversity and ecosystem function, and the dynamics of food webs in large riverscapes. My questions were: 1) what are the spatial patterns and potential drivers of riverbed habitat, and how do they relate to process domain structures in large rivers? 2) how does the geophysical habitat template influence connections between invertebrate diversity and secondary production? and 3) how are trophic interactions supporting the federally endangered Pallid Sturgeon (Scaphirhynchus albus) shaped by the geophysical habitat template? I found consistent patterns of nested patchiness in riverbed substrate, indicating that multiple factors operating at different scales influence spatial patterns of substrate in the Missouri and Yellowstone Rivers. Invertebrate assemblages were tied to attributes of the geophysical habitat template, with strong relationships between large sediments and diversity. Invertebrate diversity, in turn, was positively related to secondary production, with the most diverse assemblages found in secondary production 'hotspots'. Finally, I found a general relationship between habitat diversity and trophic interaction strengths supporting Pallid Sturgeon, with geophysically diverse areas containing much weaker, and thus potentially stabilizing, interactions than homogenous areas. Additionally, habitat characteristics, such as sediment size, intensified these effects. Together, the chapters of my dissertation broadly highlight the role of nature's stage in governing patterns in biodiversity, secondary production, and trophic interactions across large and dynamic riverscapes, and provide empirical insights for guiding future management and conservation of large rivers in an increasingly simplified world.Item Small scale denil development for use in headwater streams in southwest Montana(Montana State University - Bozeman, College of Engineering, 2021) Conley, Megan Elizabeth; Chairperson, Graduate Committee: Kathryn Plymesser; Katey Plymesser, Kevin Kappenman, Matt Blank and Joel Cahoon were co-authors of the article, 'Arctic grayling (Thymallus arcticus) passage through a scaled denil fishway' submitted to the journal 'Journal of fish and wildlife management' which is contained within this thesis.The Big Hole River is located in an agricultural valley in Southwest Montana and is home to the last fluvial (river dwelling) population of Arctic grayling (Thymallus arcticus) in the contiguous United States. Grayling mostly populate the tributary streams in the upper portion of the watershed, where there are many irrigation diversions, which greatly fragments grayling's natural habitat. While many of these irrigation diversions have fish ladders installed at them to assist with habitat reconnection, these ladder become impassable when the water levels get too low in the system or irrigators chose to block the fish ladders in order to divert more water. This study investigated and characterized a smaller scale Denil fish ladder that would use less water while providing adequate fish passage. Three different flow rate calculations were applied to a series of scaled Denils to compare to the expected flow rates of the full scale Denil to determine the scaled sizes to construct. A 0.6 scale and a 0.75 scale Denil were selected and hydraulic lab testing confirmed that 25.4 cm baffle spacing was the best for both scaled models. The fish swimming study, conducted at the outdoor flume at the Bozeman Fish Technology Center, used eight hatchery-raised grayling in each of the eight treatments. Each treatment was repeated 3 times using the 0.6-scale model for a total of 24 trials with 192 fish. Each treatment used a different combination of headwater depth (between 30.5 cm and 61.0 cm) and tailwater depth (between 15.2 cm and 61.0 cm). The grayling passed with near perfect success at all headwater and tailwater combinations except when the head difference between the headwater and tailwater was at its greatest (61.0 cm headwater and 15.2 cm tailwater). This preliminary study showed that grayling are willing to pass smaller-scale structures at a variety of flow rates but did not test a wide range of slopes, age classes or fish sizes. These results should be useful to water managers when looking to modify or install new Denil fishways in the Big Hole River Basin and around the western United States.Item Hydraulics, hydrology, and resulting fish passage at the Huntley Diversion Nature-like Bypass(Montana State University - Bozeman, College of Engineering, 2020) Tupen, Haley Noel; Chairperson, Graduate Committee: Kathryn PlymesserDams and other instream structures have been constructed for hundreds of years in the United States for various purposes; these dams have the potential to 'disconnect' rivers and negatively impact fish upstream and downstream movement. Nature-like bypasses were created to facilitate movement around these structures and provide passage to a wide variety of morphologically different fish species. The Huntley Diversion Dam nature-like bypass was constructed in 2015 on the Yellowstone River, but its effectiveness has not yet been evaluated. This project aimed to evaluate its efficacy through monitoring and determining water stage, flow rates, channel roughness, and a detailed channel bathymetry. These data were then used in the creation of multiple two-dimensional hydraulic models encompassing the nature-like bypass channel and surrounding Yellowstone River area. Velocity results from these models were compared to species-specific swimming capabilities from literature for four Yellowstone River species. Additionally, hydraulics at the downstream bypass entrance were evaluated for disorienting hydraulic formations that might prevent fish from locating the bypass entrance. Velocity results indicate Sauger (Sander canadensis) may successfully ascend the bypass on all but five days of the modeled hydrograph and may face occasional difficulty in returning to their pre-spawning upstream habitat. Burbot (Lota lota), Channel Catfish (Ictalurus punctatus), and Smallmouth Bass (Micropterus dolomieu) are unlikely to successfully ascend the bypass for much of May, June, and July. This holds significant implications for Channel Catfish and Smallmouth Bass, both of which move upstream to spawn in the months of May and June. Hydraulics at the downstream end of the bypass indicate high attraction at high flows, but that lower flows are likely to create disorienting hydraulic characteristics at this bypass entrance and lead to low fish attraction.Item The effect of permafrost thaw and geologic substrate on dissolved organic carbon mobilization and transformation in northern streams(Montana State University - Bozeman, College of Agriculture, 2019) Wologo, Ethan Andrew; Chairperson, Graduate Committee: Stephanie A. Ewing; Sarah Shakil, Scott Zolkos, Sadie Textor, Stephanie Ewing, Jane Klassen, Robert G.M. Spencer, David C. Podgorski, Suzanne E. Tank, Michelle A. Baker, Jonathan A. O'Donnell, Kimberly P. Wickland, Sydney S.W. Foks, Jay P. Zarnetske, Joseph Lee-Cullin, Futing Liu, Yuanhe Yang, Pirkko Kortelainen, Jaana Kolehmainen, Joshua F. Dean, Jorien E. Vonk, Robert M. Holmes, Gilles Pinay, Michaela M. Powell, Jansen Howe, Rebecca Frei and Benjamin W. Abbott were co-authors of the article, 'No evience of dissolved organic matter priming in permafrost stream networks: a circumpolar assessment' submitted to the journal 'Global biogeochemical cycles' which is contained within this thesis.; Stephanie Ewing, Jonathan A. O'Donnell, Jim Paces, Rob Striegl, Duane Froese and Joshua Koch were co-authors of the article, 'Groundwater connection and doc transport in the Yukon River Basin: uranium and strontium isotopes in permafrost catchments' submitted to the journal 'Global biogeochemical cycles' which is contained within this thesis.Permafrost landscapes exhibit unique hydrology that is linked both chemically and physically to nutrient cycling and geochemical processes. Permafrost thaw is expected to result in a positive feedback to Earth's climate system through carbon release to the atmosphere; this potential demands better understanding of hydrologic pathways in permafrost landscapes in the face of global change. The work that follows is divided into two main bodies of research that explore both carbon dynamics and isotope geochemistry of river waters draining permafrost catchments in the Yukon River Basin (YRB). The first study uses in-vitro incubations of stream water from seven permafrost regions to investigate how biolabile carbon additions (acetate) and inorganic nutrients (nitrogen and phosphorus) 'prime' water-column dissolved organic carbon (DOC) decomposition. No priming effect from biolabile carbon addition was evident through changes in DOC concentrations or compositional transformations, but consumption of added acetate was correlated with ambient nutrient concentrations. Sites with fine-textured, ice-rich substrate and proximal thermokarst features had higher ambient DOC and nutrient concentrations, and consequently the fastest rates of acetate consumption. We conclude that the fate of biolabile DOC released from degrading permafrost will depend largely on inorganic nutrient availability in receiving waterbodies. The second part of this thesis focuses on hydrology of intermediate-sized catchments in the YRB. We evaluate uranium isotope activity ratios ([234U/238U]) as tracers of groundwater-surface water connection in thawing permafrost landscapes. Streams draining loess-mantled areas had [234U/238U] values moderately increased relative to meteoric values. Streams draining low-order catchments with rocky substrate and surface disturbance exhibit dramatically increased [234U/238U] values, consistent with groundwater connection. In addition, we observed higher DOC concentrations both in areas influenced by recent thaw and where flow is restricted by ice-rich silt. The transformation of northern stream chemistry will likely continue as northern permafrost environents warm, with greatest resilience of ground ice in loess-blanketed areas not subject to thermal erosion by groundwater. As subsurface storage expands and groundwater exchange intensifies, ecosystems within and connected to northern streams will also be transformed, with implications for resource managers concerned with fish and wildlife management in these systems.Item Glacial effects on stream water nitrate: an examination of paired catchments in southern Montana(Montana State University - Bozeman, College of Letters & Science, 2019) Allen, Jordan Jon; Chairperson, Graduate Committee: Mark L. Skidmore and Jean Dixon (co-chair)Nitrogen is frequently a limiting nutrient in biologic systems. Previous research on alpine streams and lakes in the Beartooth Mountains, Montana/Wyoming has demonstrated nitrate concentrations in waters draining glaciated catchments that are up to ten times greater than comparable adjacent non-glaciated catchments. The enhanced nitrate concentrations in the glacial fed lakes have been associated with increased diatom abundance relative to the snow fed-lakes. However, the source of the enhanced nitrate input remained undetermined, as well as how nitrate concentrations vary temporally during summer melt. This study measured concentrations of nitrate and ammonium and the isotopic composition of nitrate over the 2016 melt-season in a paired catchment system, in the Beartooth Mountains, Montana. The two catchments have similar elevations, atmospheric inputs, bedrock geology, area, and contain lakes, however, one catchment contains a glacier, the other does not. The stream waters in the glaciated catchment showed significantly elevated nitrate concentrations relative to those in the non-glaciated catchment and to catchment atmospheric input, as determined by snowpack nitrate concentrations. Nitrate concentrations in the glacial stream were observed to increase both temporally as the melt-season progressed, and spatially, with distance downstream from the glacier terminus. Ammonium concentrations in the glacial stream were highest close to the glacier terminus, declining with distance downstream, but also increasing during the melt season. Nitrate isotopic values distinguish the stream waters from atmospheric inputs indicating additional nitrate sources in the catchment. Potential additional sources include inorganic nitrogen released from bedrock sources and microbially fixed nitrogen. Abiotic laboratory weathering experiments simulating subglacial conditions reacted deionized water with finely milled bedrock at 4°C, and a modest quantity of ammonium was released. Potassium is often replaced by ammonium in minerals. Rocks from the study area contained ~3% potassium by weight. Ammonium could then be converted to nitrate through microbial processes within the proglacial environment adding to the atmospheric nitrate input to the stream nitrate budget. However, estimated rates of sediment production, and by inference ammonium production, cannot account for the observed nitrate concentrations and flux, indicating an additional nitrate source, which is most likely ultimately derived from microbial nitrogen fixation.Item The response of parafluvial soils to beaver mimicry restoration in a Montane stream(Montana State University - Bozeman, College of Agriculture, 2020) Whitehead, Briana Katherine; Chairperson, Graduate Committee: Tracy M. Sterling and William Kleindl (co-chair); Paul Stoy, William Kleindl, Martin Rabenhorst, Rob Payn, David Wood and Anthony Hartshorn were co-authors of the article, 'Parafluvial soil response to beaver mimicry restoration in a montane stream' submitted to the journal 'Restoration ecology' which is contained within this thesis.Beaver Mimicry Restoration (BMR) is a relatively new aquatic restoration practice that seeks to improve deteriorated stream ecological functions. BMR is designed to rejoin hydrologically disconnected streams with their adjacent floodplains via the installation of small-scale, stream-spanning structures derived from natural materials and inspired by the influence of natural beaver (Castor spp.) dams. These structures capture sediment, elevate stream stage and groundwater tables, create thermal refugia, and re-establish riparian vegetation. Most research on BMR has focused on the hydrological or botanical results, but little is known about the response of parafluvial soils. I report measurements of soil water content, soil temperature, soil biogeochemical reduction, and vegetation responses at paired BMR-influenced treatment and non-BMR-influenced control locations from June through September of 2018 and 2019 in a montane stream in southwestern Montana (USA). In comparison to soils at control sites, soils adjacent to BMR activity experienced an extended period of higher water contents (0.23 m 3/m 3 higher), increased anoxic conditions (on average 27% more during the field season), a less variable and cooler soil temperature range (on average 5 °C cooler), and supported longer durations of vegetation greenness (additional 20 days) during the dry months. Results demonstrate how BMR produces conducive conditions for the development of new and/or the reestablish of historic hydric soils.Item An economic analysis of the Smith River float lottery(Montana State University - Bozeman, College of Agriculture, 2020) Walker, Chase Nelson; Chairperson, Graduate Committee: Randal R. RuckerOutdoor recreation is a popular pastime for many and provides an opportunity to unwind and take a break in nature and on public resources. In recent years, overcrowding and commercial use have been highlighted in the media for taking away from the recreational experience and stressing some of the resources. To explore this issue, I collect data on float permit application numbers over 15 years for the Smith River, which is a popular lottery accessed recreational river in Montana that receives over 10,000 float applications per year and also allows private commercial guiding. To attempt to gain insights into whether commercial use is viewed negatively, I use variation in the number of outfitted trips that are permitted to launch each day within the float season to identify how outfitter use impacts application rates. I find that application rates during the peak season decrease by an average of 11 percent on days in which two outfitters launch compared to days when only one outfitter can launch. Because outfitter launch allocations effect the supply of permits available in the lottery, this result could be attributed to either an outfitter effect or supply effect. Further analyses that test the differences between the early season when outfitter use is low, and the peak season when outfitter use is high, indicates that there is a combination of both effects, but that the impact of outfitter use is large and significant.Item SR and U isotopes reveal interactions of surface water and groundwater along the mountain headwaters to intermountain basin transition (Hyalite Canyon and Gallatin Valley, MT)(Montana State University - Bozeman, College of Agriculture, 2018) Miller, Florence Rita; Chairperson, Graduate Committee: Stephanie A. Ewing; Stephanie A. Ewing, Robert A. Payn, James B. Paces, Sam Leuthold and Stephan Custer were co-authors of the article, 'SR and U isotopes reveal the influence of lithologic structure on stream-groundwater interaction along a mountain headwater catchment (Hyalite Canyon, MT)' submitted to the journal 'Water resources research' which is contained within this thesis.; Stephanie A. Ewing, Robert Payn, Sam Leuthold, Stephan Custer, Tom Michalek and James B. Paces were co-authors of the article, 'SR and U isotopes reveal mixing patterns of groundwater and surface water influenced by human management in an intermountain basin (Gallatin Valley, MT)' submitted to the journal 'Journal of hydrology' which is contained within this thesis.Mountainous regions of the western United States are characterized by steep, rapidly eroding mountain headwater streams transitioning to more depositional intermountain basins. The character and flux of water across these process domains is subject to projected changes in mountain headwater snowpack and agricultural and urban land use in rapidly developing intermountain basins. Here we evaluate controls on water/rock, water/substrate, and surface/groundwater interactions within Hyalite Creek and the Gallatin Valley of southwest Montana. We use solute loads and geochemical tracers (87 Sr/86 Sr, Ca/Sr, and [234U/238U]) as indicators of such interactions. Surface water, groundwater, and soil samples were collected between 2016 and 2018. Stream water in upper Hyalite Creek had low 87 Sr/86 Sr values typical of volcanic and sedimentary host rock units, and low [234 U/238 U] values consistent with shorter flow path soil, shallow aquifer or runoff water. Middle Hyalite Creek had increased [234 U/238 U] values, reflecting groundwater inflows from the Madison Group limestones. Lower Hyalite Creek had an increase in 87 Sr/86 Sr values and decrease in [234 U/238 U] values, indicated contributions from Archean gneiss fracture flow. Using mixing models, we estimate inflows from the Madison contribute ~4% during summer baseflow conditions and inflows from the Archean contribute ~2% to ~8% of streamflow during summer and winter baseflow conditions. At the mountain front, diverse Ca/Sr, 87Sr/86Sr, and [234U/238U] ratios were observed as a result of convergent flow in mountain headwaters catchments. In the intermountain basin, divergent flow at the mountain front recharges valley aquifers and combines with infiltration through soils. With distance down-valley, we observe intermediate values of Ca/Sr, 87 Sr/86 Sr, and [234 U/238 U], suggesting mixing of diverse source waters. Higher concentrations of Sr, alkalinity, and Ca/Sr and 87 Sr/86 Sr ratios consistent with soil carbonates suggest water infiltration through soil facilitated the influence of soil secondary carbonates on groundwater geochemistry. Additionally, increased water movement through soil facilitates the increase in anthropogenic loading of NO3- and Cl- in surface and groundwaters. Our results provide novel quantification of groundwater contribution to streamflow in mountain headwaters, and elucidate water quality and quantity controls from the mountain front across the intermountain basin, including valley aquifer recharge, infiltration through soils, and anthropogenic solute influxes to groundwater.
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