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An investigation of the fishes of the Willamette River and three of its larger tributaries was made during July, August, September, and November of 1951, to ascertain the possibility of using them as bio-indices ...
Citation Citation
- Title:
- The Willamette River fishes as biological indicators of pollution
- Author:
- Noble, Richard Earl
An investigation of the fishes of the Willamette River and three of its larger tributaries was made during July, August, September, and November of 1951, to ascertain the possibility of using them as bio-indices of pollution. Thirteen stations were established on the Willamette River and tributaries. These stations were selected in respect to the major tributaries, cities, and sources of pollution. Two stations were located on the McKenzie river; two on the North Fork of the Santiam River; eight on the main stem of the Willamette River from above Eugene to Oregon City; and one on the Clackamas River. Fishes were collected at each station by means of a seine. The fishes were preserved in a 10 percent formalin solution and returned to Corvallis where they were classified as to species and the numbers of each recorded. Stomach analysis were performed on a portion of the fishes collected from each of the stations. In an attempt to determine the affect of pollution on the fishes of an area, the samples from a clean-water station were compared with those taken from a polluted station. From this survey a tentative list of fishes which were sensitive, intermediate and tolerant to pollution was formed. In general, the trout, salmon, whitefishes and sculpins were found to be sensitive; falcate dace, white crappie, smallmouth black bass, mountain suckers, and longnosed dace were intermediate; and redsided shiner, blacksided dace, coarse-scaled sucker, three-spined stickle back, squawfish, bullhead catfish, chiselmouth, largemouth black bass, Columbia River chub, and larvae of the Pacific lamprey were tolerant. It was found that even the most tolerant fishes disappeared when pollution was excessive. In addition to the biological data collected at each station, certain chemical and physical tests were also determined. Air and water temperatures were taken, along with hydrogen-ion concentration (pH), and dissolved oxygen content of the water. Bio-chemical oxygen demand (B.O.D.) readings were taken at some of the stations by the Oregon State Sanitary Authority. River flow measurements were obtained from U.S.G.S. records for the gage at Salem, Oregon. The physical and chemical tests were used in conjunction with the biological findings to determine the condition of each station. Water flow data was used to determine low water periods. Chemical, physical and water flow data are shown in table form as well as graphically. The numbers of each species of fish and the food organisms found by stomach analysis are listed for each monthly sample and these data are also shown in table form. According to observations from this survey there was a definite indication that pollution can be detected by using the species, numbers and stomach contents of fishes from a waterway.
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582. [Article] Assessing disease impacts of hatcheries on downstream salmonids in the Willamette River Basin, Oregon
Hatcheries are often perceived as a source of pathogen amplification, potentially increasing disease risk to free-ranging populations; at the same time, free-ranging fishes may introduce pathogens into ...Citation Citation
- Title:
- Assessing disease impacts of hatcheries on downstream salmonids in the Willamette River Basin, Oregon
- Author:
- Jakaitis, Michelle
Hatcheries are often perceived as a source of pathogen amplification, potentially increasing disease risk to free-ranging populations; at the same time, free-ranging fishes may introduce pathogens into hatcheries through untreated water sources. Many pathogens exist naturally within the environment (with the exception of introduced pathogens) and the presence of a pathogen does not guarantee infection or disease (Naish, Taylor III, Levin, Quinn, Winton, Huppert & Hilborn 2007). Infections can be acute, chronic, or asymptomatic, fish may die, recover, or become carriers (Naish et al. 2007), and pathogens may be shed from any of these stages (Scottish Executive 2002). Most salmon and trout hatcheries along the Willamette River Basin, Oregon, USA, utilize an untreated river water supply for their rearing ponds and release this water, untreated, back into the river. This creates a potential for waterborne pathogens present in free-ranging hosts to be transmitted through the water supply to hatchery populations. Moreover, any hatchery epizootic can amplify pathogens and release these into the water, which could have a direct impact on free-ranging populations exposed to those pathogens in hatchery effluent. The goal of this thesis was to assess transmission of the pathogens Flavobacterium columnare, F. psychrophilum, Aeromonas salmonicida, Renibacterium salmonicida, and Infectious Hematopoietic Necrosis Virus (IHNV), at selected hatcheries in the Willamette River Basin. To accomplish this, I considered historical data and hatchery-specific and pathogen-specific factors involved in transmission and disease. Additionally, I conducted sentinel fishes exposures (Oncorhynchus mykiss and O. tshawytscha) at hatcheries during both epizootics and non-epizootic periods. Naïve sentinel fish were placed in hatchery influents and effluents to determine transmission direction and pathogen prevalence associated with hatcheries. I found that sentinel fishes developed infections downstream of hatcheries that were undergoing specific bacterial epizootics, or had low levels of pathogen prevalence within the hatchery, but not at any other time. Infections and mortality were due to the same pathogens responsible for hatchery epizootics, indicating the hatchery as a potential source. This may be a limited effect dependent on distance, dilution, and pathogen. The presence of large numbers of returning, congregating adult fishes may also contribute pathogens to the river in hatchery areas. Sentinel fishes held in hatchery influents did not, at any point, become infected with target pathogens, even during hatchery epizootics. Although I was unable to identify the pathogen entry point leading to hatchery epizootics, I determined that pathogen transmission appeared to be dependent on the pathogen, species, and location where sentinel fish were held. This thesis identifies routes and risks of pathogen transmission at selected Oregon hatcheries, with applications to inform state-wide fish health management.
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583. [Article] Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing
Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental ...Citation Citation
- Title:
- Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing
- Author:
- Bellinger, M. Renee
Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental gaps in our knowledge remain. In my dissertation, I applied emerging genetic technologies to conduct a top-down and bottom-up investigation of animal movement and cue perception. First, in partnership with Project CROOS and the California Salmon Genetic Stock Identification project, stock-specific, marine migratory distributions of Chinook salmon (Oncorhynchus tshawytscha) were characterized for five consecutive months (2010) over 1000 km of coastline. A statistical model was developed to provide measures of relative stockspecific abundance, insights into broad factors that influence migratory distribution, and for fisheries management applications. For the second component of my dissertation, I studied specialized olfactory cells of salmonids that are proposed to contain nanometer-sized magnetite crystals that interact with earth strength magnetic fields to transduce them into neural signals. The transcriptome profiles of candidate magnetoreceptor and non-magnetic cells isolated from olfactory rosette tissue, whole olfactory rosettes, and blood and muscle tissue were characterized from ~661 million Illumina RNA-seq reads. A total of 1,006 differentially expressed genes were identified in the magnetic cell sample type. Results, consistent with having identified genes involved in magnetite crystal formation in fish, were used to develop a genetic model of magnetic sensory perception. Finally, to provide insights into olfaction-based homing that takes place in freshwater, the olfactory repertoire of salmonids was inferred from the Rainbow trout (O. mykiss) genome and compared to that of 15 other teleosts and the jawless fish, sea lamprey (Petromyzon marinus), an ancient species. The abundance and diversity of trace amine-associated and V2R-like genes suggests that these classes of chemoreceptors have biological importance. These findings have relevance for resolving if salmon and other marine organisms imprint on magnetic fields, and contribute to our understanding of how magnetic sense, olfaction, and genetic programming are involved in migratory distributions.
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Interest in the distribution of Clostridium botulinum type E was heightened by the sudden outbreak of human botulism from smoked whitefish chubs and canned tuna fish in 1963. The question arose as to how ...
Citation Citation
- Title:
- Distribution of Clostridium botulinum type E in fish, shellfish and the marine environment of the Pacific Northwest, and protein patterns of the toxigenic and non-toxigenic stains
- Author:
- Craig, James Morrison
Interest in the distribution of Clostridium botulinum type E was heightened by the sudden outbreak of human botulism from smoked whitefish chubs and canned tuna fish in 1963. The question arose as to how widely the organism is distributed among fish and shellfish in the Northwest and what potential hazard exists for the consumer of fish products. This sporeforming anaerobic orgnism is heat sensitive and had eluded detection in other surveys where heat shock had been used to eliminate non sporeforming contaminants. More recent study using other techniques than heat to facilitate recovery has shown this organism to be widespread, especially in the marine environment. This study was undertaken to find the incidence and distribution of C. botulinum in the marine organisms and environment of the Pacific Northwest and the food products derived therefrom. All species of fish were examined by incubating the gills and viscera individually in tryptone-peptone-glucose medium anaerobically at 28 C for four days and testing the culture filtrate for mouse toxicity by intraperitoneal injection. Toxic filtrates were typed by retesting them in mice protected by specific botulinal antitoxin of type A, B, E, or F. Among salmonid fish the proportions of specimens of each species yielding toxic filtrates were as follows. Sockeye salmon from the Columbia River, 14 of 59 (23.7%); Chinook salmon from the Columbia River, 19 of 106 (18.0%); Chinook salmon from the Pacific Ocean, 1 of 18 (5,6%); Coho salmon from the Columbia River, 10 of 19 (34.4%); Coho salmon from the Pacific Ocean, 13 of 186 (7.0%); Steelhead trout from the Alsea River, 7 of 37 (19.0%). About one-third of the toxic cultural filtrates were successfully typed and proven to contain botulinal toxin. Most of them proved to be type E toxin but 3 were type A, 3 were type B and one, a comparatively new type, type F, was isolated from a Sockeye salmon in the Columbia River. Pure cultures of Clostridium botulinum type E were isolated from 18 specimens and one specimen yielded a pure culture of type F from a sockeye salmon. This was the second time this type had been isolated. In all of the experimental groups the proportion of fish producing toxigenic cultures was significantly higher in those taken in the two rivers than those of the same species taken from the ocean waters. "Bottom fish" represented by Cod, Sole, Grouper and members of the Sebastodes group were also tested in the manner described above. The number of specimens yielding toxic filtrates were 28 of 157 (17.8%). When grouped according to location at which the fish were caught, those near the mouth of the Columbia River produced a greater percentage of toxic filtrates than did those caught off the open shore line. The results were as follows: Bottom fish from Astoria, 23 of 70 (32.8%), Botton fish from Coos Bay, 5 of 87 (5.6%). Sturgeon specimens produced 3 of 24 (12.5%) toxic filtrates. Most of the species contained type E; however, one type A and one type B were found on typing, with about one-third of the toxic filtrates being successfully typed. Environmental swab samples from the "deep sea" fillet processing plants produced 3 of 39 (7.7%) toxic filtrates. None of the 53 samples taken in the salmon processing plants produced toxic filtrates. Shellfish were collected along the ocean beach and in the estuaries. Three to five shellfish were combined into a single specimen and treated as described. All shellfish obtained from the estuaries demonstrated a higher percentage of toxic filtrates than those obtained from the ocean beach. The results were as follows: Razor clams, 11 of 75 (14.6%), Cockle clams, 12 of 15 (80.0%); Softshell clams, 8 of 12 (66.4%); Littleneck clams, 4 of 11(36.2%); Horseneck clams, 1 of 3 (33.3%); Oysters, 6 of 19 (31.6%); Dungeness crabs, 17 of 24 (71%). Only the razor clams were collected exclusively from the ocean beach. Loss of toxicity on holding mixed cultures at -15 C while awaiting typing was a continual problem. This accounts for only one-third of toxic filtrates being successfully typed. Electrophoretic analysis of the total bacterial proteins was carried out on cell sonicates and cell free culture filtrates by first growing cells for four days at 28 C anaerobically. The cells were separated, washed and disrupted with ultrasonic energy. The cell free culture filtrate was concentrated 10 fold by dialysis against polyethylene glycol 4000. Both the toxigenic organisms and the toxic filtrate demonstrated an extra common protein band in the upper third of the electrophoretic pattern not present in the nontoxic spectra. This band might represent the type E toxin. Differences could also be noted in the number of protein bands in the lower third of the patterns in different nontoxigenic strains and also when the toxigenic and nontoxigenic strains were compared. This could suggest an association with a phage in the toxigenic cultures.
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The growing demand for water in the arid regions of the West increases the need for optimal allocation of water among competing uses. An efficient allocation of water between instream and out-of-stream uses ...
Citation Citation
- Title:
- A bioeconomic analysis of altering instream flows anadromous fish production and competing demands for water in the John Day River basin, Oregon
- Author:
- Johnson, Neal S.
The growing demand for water in the arid regions of the West increases the need for optimal allocation of water among competing uses. An efficient allocation of water between instream and out-of-stream uses has been impeded by institutional constraints and the scarcity of information regarding instream flow benefits. The objectives of this thesis were to provide preliminary economic data on the value of instream water in "producing" recreational fishing and to examine the effect of forestry, agriculture, and livestock practices on temporal streamflow patterns and anadromous fish production. The steelhead trout (Salmo gairdneri) sport fishery within the John Day River basin in north-central Oregon provided the setting for this research. The interdisciplinary methodology employed in estimating the marginal value of water with respect to steelhead production consisted of two tasks. The first task involved valuing a marginal change in the quality of the steelhead recreational fishery. The contingent valuation method (CVM) was selected for this purpose. Both open- and closed-ended willingness-to-pay (WTP) questions were included in a questionnaire administered to John Day River steelhead anglers during the 1986/87 steelhead fishing season. Survey data were analyzed to arrive at individual and aggregate bid functions relating WTP to expected angling success rates. Results indicate that, under current conditions, the average angler is willing to pay approximately $7.20 to catch an additional steelhead. The second task of the instream water valuation methodology was directed at deriving a streamflow/steelhead production relationship. By including variables influencing steelhead production in a Ricker stock-recruitment model, it was possible to develop a model which could be estimated using linear regression techniques. Some difficulty arose, however, with interpretation of the model due to the unavailability of cohort escapement data and the subsequent use of standing crop data. While possibly masking the true magnitude of streamflow's effect on fish production, this drawback was not deemed limiting within the general context of the interdisciplinary methodology. Results of the biological model conformed to a priori expectations. Increases in summer and winter streamflows led to increased steelhead survival, whereas higher spring flows increased mortality levels. Other results indicate that the John Day Dam was responsible for a 31.5 percent decline in the population index for the 1969-1983 period. Combining the economic and biological results into one equation yielded an estimate of the marginal value of summer instream water in "producing" recreational steelhead angling. Similar equations were developed for winter and spring flows. The marginal value of water in producing recreational steelhead fishing within the John Day basin was estimated at $0.56 per acre-foot for summer flows, $0.046 for winter flows, and -$0.075 for spring flows. By including out-of-basin benefits, these values increased to $2.26, $0.19, and -$0.30, respectively. In comparison, water's value in irrigation within the John Day basin has been estimated at between $10 to $24 per acre-foot. However, nonuse values of steelhead, as well as the increased production of other fish species (such as spring chinook salmon) were not included in the instream water values. In addition, no attempt was made at valuing instream water's contribution to boating, camping, or other benefit-producing activities. A secondary objective of this thesis was to briefly examine the possible benefits accruing to other instream and out-of-stream users due to an alteration in streamflow patterns. In addition, the impact of activities by other resource users -- namely forestry, agriculture, and livestock production --on anadromous fish production was reviewed. Improper management practices by these activities can negatively impact the aquatic and riparian ecosystems. While no firm conclusions were drawn, it appears the quality of these ecosystems, as opposed to the amount of streamflow, has the largest marginal impact on anadromous fish populations.
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The research presented in this thesis is concerned with the characterization of two salmonid cell lines, CSE 119 derived from embryos of coho salmon (Oncorhynchus kisutch) and STE 137 derived from embryos ...
Citation Citation
- Title:
- Characteristics of two salmonid fish cell lines : glycolytic rates, CO₂ requirements and susceptibility to Reovirus and Reovirus-like agents
- Author:
- Kleeman, Karl Terrence
The research presented in this thesis is concerned with the characterization of two salmonid cell lines, CSE 119 derived from embryos of coho salmon (Oncorhynchus kisutch) and STE 137 derived from embryos of steelhead trout (Salmo gairdneri). The rates of glucose utilization and lactic acid production during the most active growth phase of each cell line were determined and the results were compared to data from parallel experiments using a human embryonic cell line. The salmonid cells were grown at 23° C and the human cells at 35° C. All cells were grown in Eagle's minimal essential medium supplemented with 20% dialyzed newborn agamma calf The Q[superscript]O₂[subscript]CO₂ serum. values (equivalent microliters CO₂ produced per mg dry weight of cells per hour) were calculated for each cell type, and values of 7.97 and 4.50 were obtained for CSE 119 and STE 137, respectively. These values were somewhat lower than the value of 13.19 calculated for the human cells. In all three cell lines studied, the rates of glucose utilized and lactic acid produced per cell decreased over the growth periods observed. The decreases in the salmonid cells were most likely related to a concomitant increase in population density. In addition, it was shown that the very gradual fall in pH observed during the growth of the salmonid cells is apparently due in part, at least, to the smaller amount of lactic acid produced by these cells. During the course of the studies with the salmonid cell lines, an investigation of the CO₂ requirements of these cells was undertaken. For these experiments, Tris buffer was used to replace the bicarbonate in the medium and 20% dialyzed serum was again used. Results from the salmonid cells grown at 18° C were compared to parallel experiments using He La cells grown at 35° C. It was shown that growth under 2% (salmonid) and 3% (He La) atmospheric CO₂ was comparable to growth in stoppered cultures for CSE 119, STE 137 and the He La cells. The salmonid cells showed good growth in cul- tures that were open to the air (0.03% CO₂), but little or no growth occurred in the He La cells under the same conditions. To determine if CO₂ was actually required for growth of the salmonid cells, CO₂ free cultures were prepared using Conway microdiffusion dishes in which the cells were grown in the center well and a 10% solution of KOH was added to the outer well. The cultures were sealed with high vacuum grease. Under these conditions, both salmonid cell lines demonstrated a growth requirement for CO₂ comparable to that shown by the He La cells. Attempts were made to use oxalacetate to substitute for CO₂ in these cultures. Oxalacetate partially substituted for CO₂ in the He La cell cultures, but little or no growth occurred in the salmonid cell cultures under the same conditions. As part of a continuing effort to determine the viral susceptibility of salmonid cell lines, the coho cells (CSE 119) and the steelhead cells (STE 137) were tested for their susceptibility to Reovirus types 1 and 3, Infectious Pancreatic Necrosis (IPN) virus and Wound Tumor virus (WTV). Neither salmonid cell line nor He La cells were shown to produce infectious virus when inoculated with either reovirus type at 26° C. The salmonid cells would not tolerate 30° C for even short periods of time. Good replication of both reovirus types occurred in He La cells at 35° C. IPN virus replicated well in both salmonid cell lines at 18° C. Phase contrast studies of IPN infected salmonid cells showed an early webbing of the cytoplasm, followed by a rounding up of the cells, shrinkage of the nuclei and a heavy margination of nuclear chromatin. Because of its similarity to the reoviruses and its ability to replicate in an insect cell line, attempts were made to infect the salmonid cells with WTV at 23° C. No indications of WTV inclusion bodies or of a cytopathic effect were found in either salmonid cell line.
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587. [Article] The physiology ecology and run diversity of adult Pacific lamprey, Entosphenus tridentatus, during the freshwater spawning migration
Pacific lamprey, Entosphenus tridentatus, have shown recent and rapid declines in abundance. These anadromous fish return to streams where they mature, spawn and die. It has been inferred that Pacific ...Citation Citation
- Title:
- The physiology ecology and run diversity of adult Pacific lamprey, Entosphenus tridentatus, during the freshwater spawning migration
- Author:
- Clemens, Benjamin Jacob, 1976-
Pacific lamprey, Entosphenus tridentatus, have shown recent and rapid declines in abundance. These anadromous fish return to streams where they mature, spawn and die. It has been inferred that Pacific lamprey enter freshwater and reside for ~ 1 year before spawning. This long exposure to the freshwater environment may affect the plasticity of the maturation process and the migration timing of Pacific lamprey. Diversity in run times and body size has been observed for Pacific lamprey, yet it is unknown if this diversity is induced by the freshwater environment or if it is genetic. My first goal was to describe the maturation and migration characteristics of adult Pacific lamprey during their freshwater migration. My second goal was to use these data to make an estimation of the run diversity in Pacific lamprey. I conducted three complementary studies, in the laboratory and the field, to achieve these goals. I held immature adult lamprey (non-ripe fish that had ceased parasitic feeding in the ocean and had returned to freshwater) in the laboratory at temperatures that mimicked what these fish would experience in the wild, during the summer (mean: 21.8 °C), and another group of lamprey at cooler temperature (mean: 13.6 °C) to compare maturation timing and characteristics. The warm water group of lamprey showed significantly greater proportional decreases in body mass following temperature exposure than fish in the cooler water. All fish exposed to the warm water matured the following spring (8-10 months later) whereas only about half of the fish from the cool water exposure matured. To understand the migration distances and timing of adult Pacific lamprey, I tracked radio-tagged fish throughout the Willamette Basin above Willamette Falls, Oregon, by airplane and recorded their location. Fish migrated primarily during the spring to early summer period before stopping during the remainder of summer, when peak river temperatures (≥ 20°C) occurred. These fish tended to remain stationary through the fall and winter. However, at least a few fish continued to migrate upstream after September. I monitored maturation characteristics of adult Pacific lamprey, over time at Willamette Falls, Oregon and compared these fish with recent migrants collected from the Pacific Ocean as they entered freshwater. The results suggest a unimodal spawn timing between April and June, at water temperatures < 20 °C. Between July and mid-September, as water temperatures peaked at ~ 25 °C, relatively immature fish for both sexes prevailed. Warm summer temperatures coincided with an increase and prevalence of testicular atrophy in males, and I also observed a large die-off of lamprey during this time. The immature fish had maturation stages and phenotypic characteristics similar to recent migrants collected at the mouth of the Klamath River, suggesting that the immature fish at Willamette Falls would spawn the following year, and spawners in any given year may have been recent migrants during the previous year. However there is a temporal overlap in the spring of immature and mature fish, and I found evidence from gonad histology of maturing fish as they entered the river from the ocean, suggesting that a cohort is comprised of recent migrants that spawn within several weeks of entering freshwater, and another cohort is comprised of recent migrants that mature and spawn at least 1 year later. I hypothesize that the recent migrants that would likely spawn shortly after entering freshwater are akin to a winter or "ocean maturing" steelhead, Oncorhynchus mykiss, that optimizes feeding and growth in the open ocean for a few years before entering freshwater to spawn low in the river system shortly afterwards. Alternatively, these lamprey may be similar to coastal cutthroat trout, O. clarki clarki, that feed and grow in the coastal areas of the ocean for a few months before entering freshwater to spawn. There could be other less apparent explanations as well. I also hypothesize that the lamprey that would likely spawn within ~ 1 year of entering freshwater are akin to a "stream maturing" steelhead that foregoes feeding and growth opportunities, enters freshwater during the summer – fall, and accesses spawning grounds to spawn at temperatures that promote evolutionary fitness via successful spawning the following spring. Based on the results of my research, I hypothesize that warm summer temperatures (> 20 °C) can act as a strong selection factor against stream maturing Pacific lamprey in two ways. First, these temperatures may expedite their maturation, while at the same time slowing their migration. If these hypotheses are true, then I predict an uncoupling of spawn timing with optimal habitat characteristics, that would promote fitness, in the upper watershed. Second, summer temperatures may cause gonad atrophy and death prior to spawning. This scenario may select for ocean maturing Pacific lamprey.
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588. [Article] Surface Water and Groundwater Interactions in the Walla Walla River, Northeast Oregon, USA : A Multi-Method Field-Based Approach
Surface water and groundwater interactions are a key component in the functioning of stream ecosystems. Exchange of water between the stream and the hyporheic zone creates habitat for aquatic organisms ...Citation Citation
- Title:
- Surface Water and Groundwater Interactions in the Walla Walla River, Northeast Oregon, USA : A Multi-Method Field-Based Approach
- Author:
- Gryczkowski, Landon
Surface water and groundwater interactions are a key component in the functioning of stream ecosystems. Exchange of water between the stream and the hyporheic zone creates habitat for aquatic organisms and serves as a control for stream biogeochemical, thermal, and flow processes. This study takes a multi-method field-based approach to gain a better understanding of exchange processes in the Walla Walla River, Northeast Oregon, USA, with focus on advancing methodologies, spatial and temporal exchange dynamics, fish ecology and habitat, and geomorphic controls on hyporheic exchange. Fiber-optic distributed temperature sensing (DTS) was used to identify, quantify, and map cold-water inflows at the meter scale. Analysis of the maximum and minimum daily temperature traces separated each cold-water inflow into either hyporheic or groundwater-derived. DTS identified a very active hyporheic zone in this system, with a near-equal importance of hyporheic and groundwater inflows. Approximately one-third of the 2-km study reach was influence by cold-water inflows, providing significant cooling in certain areas. Using piezometers in conjunction with DTS provided validation and supplementation of DTS results, increased the reliability of conclusions, and helped to identify and understand specific exchange processes. Piezometer data showed downwelling conditions (negative head differential) except immediately downstream of riffles, with head differentials becoming increasingly negative farther downstream from a riffle. Furthermore, head differentials increased in the negative direction from left bank to right bank, indicating lateral movement of groundwater and more loss of river water from the right bank. Nearest to riffles and river bends, head differentials remained more stable over time, which may indicate that geomorphic structures influence head variations locally, while aquifer levels and dynamics have an increasing influence farther from these structures. Seasonally, head differentials became increasingly negative through the summer into fall as aquifer levels decreased, and areas of the river that lost the most water to the subsurface tended to lose more water at a faster rate as the summer progressed. However, the seasonal trend of head differentials may be counteracted by decreasing bed permeability, yielding little or no temporal change in vertical flux of water through the streambed. During high-flow events, river losses to the subsurface decreased overall; in particular, areas with the greatest water loss at low flows showed reduced losses during high flows. High variability and lack of patterns in the response to high flow events suggests complexity in this process. Temperature-related variables from DTS data were combined with habitat-related variables to determine which variables best explain pool-scale salmonid abundance. Two snorkel surveys of 23 pools within the study reach were performed. The change in temperature across the pool showed the strongest overall relationship to salmonid abundance, particularly Chinook salmon. Chinook salmon showed a stronger preference for specific pools compared to steelhead/rainbow trout. The magnitude of cold-water inflows appears more important than the presence or proportion of the pool receiving cold-water inflows, and salmonid abundance was more strongly explained by hyporheic inflows compared to groundwater. Temperature variables increased in importance relative to habitat variables in the second snorkel sample compared to sample one. The highest river temperatures of the summer occurred between the two sample dates, and this may suggest that salmonids’ affinity for cold-water refuge was enhanced through behavioral adaptation following periods of high temperature approaching the lethal threshold. The combined use of DTS, continuous electrical resistivity/induced polarization profiling, LiDAR, aerial imagery analysis, and field surveys allowed for the quantification of many geomorphic and hydraulic variables known or hypothesized to contribute to surface water and groundwater exchange processes. Regression analysis was used to determine which of these variables best explain the presence and magnitude of both groundwater and hyporheic inflows. For the first time, the cross-sectional area of the hyporheic zone was estimated at high resolution at the reach scale, and decreasing hyporheic cross-sectional area best explained both the presence and magnitude of cold-water inflows of either type. Higher water surface slope and sinuosity/curvature were next in order of importance. The presence of hyporheic inflows was also explained by higher water surface slope, sinuosity, and Reynolds number, while the magnitude of hyporheic inflows was best explained by higher sinuosity. Groundwater inflows were also explained by higher width-to-depth ratio, higher water surface slope, decreasing distance from a stream bank to the bankfull or floodplain extent, and decreasing flow velocity. Lateral processes (e.g. sinuosity) and vertical processes (e.g. water surface slope) were found to be of comparable importance, but lateral processes better explained larger decreases in stream temperature, possibly because lateral subsurface flow paths are longer in distance and duration. Hydraulic conductivity variables did not show up among the most important variables likely because of the difficulty in estimating hydraulic conductivity at the meter scale using electrical geophysical tools.