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4971. [Article] The role of near-stream zones on flow, chemistry and isotopic composition at the headwater scale
Stream discharge is a key water balance component and important factor in global change evaluations. Nevertheless, the mechanisms for streamflow generation are poorly understood. Near- stream surface saturation ...Citation Citation
- Title:
- The role of near-stream zones on flow, chemistry and isotopic composition at the headwater scale
- Author:
- Frentress, Jay
Stream discharge is a key water balance component and important factor in global change evaluations. Nevertheless, the mechanisms for streamflow generation are poorly understood. Near- stream surface saturation during precipitation events is one of the most iconic, visible indicators of rapid runoff production in upland humid catchments around the world. Despite years of study, we lack understanding of what occurs within the near-stream saturated area, its mixing dynamics and how this affects catchment geochemical- and flow-response dynamics during events. This thesis explores the mechanisms that control near-stream saturated area behavior in a headwater catchment. First, I explore the relation between catchment geochemical response and the flow duration curve (FDC) for the 46-ha Weierbach catchment in Luxembourg across 10 years of runoff monitoring. The shape of the Weierbach FDC suggested a two-phase system, a high-flow, precipitation-driven period and a dry, evapotranspiration-driven, low-flow period. I hypothesized that the two phases were correlated with activation of shallow hillslope and subsurface streamflow sources and that the activation of these sources would be reflected in stream chemistry and surface saturation dynamics. During high-flow periods of the FDC, stream geochemistry was largely unchanging, lacking a dilution effect and appeared a mix of the highly variable soil and groundwater. Thermal infrared (TIR) imagery suggested large surface saturation dynamics at high flows. The geochemical signature of streamflow and soil riparian water during low-flow periods most closely resembled groundwater chemistry and led to increasing base cation concentrations and electrical conductivity. Secondly, to better understand the effect of rain falling on saturated areas and the contribution of rainfall to saturation excess overland flow, I quantified surface saturation dynamics in a near- stream area during rainfall events using high-frequency TIR imagery. During 10 rainfall events across a 34-day period starting December 2013, a total of 161 mm of rainfall elicited 133 mm of runoff at the 6-ha outlet. Surface saturation within a 25-m² thermal infrared imaged area increased from 2 to 20% but was highly variable and weakly correlated to discharge and precipitation. Rainfall onto mapped, near-stream saturated areas accounted for little of the flow generated within a headwater reach. Streamflow isotopic composition at the 6-ha, headwater outlet deflected little throughout the 30-day rainfall period, 0.7 and 1.2 ‰ for δ¹⁸O and δ²H, respectively. Groundwater exfiltration within the saturated area generated nearly all of the streamflow as well the persistent saturation throughout the event. Thirdly, I examined the underlying controls on streamwater chemostasis in a forested, headwater catchment. Thermal infrared imagery was simultaneously used to quantify saturation expansion and groundwater exfiltration hotspots within the headwater reach. Streamflow during a series of rainfall events responded chemostatically, most measured geochemical species (Ca²⁺, Mg²⁺, Na⁺, SiO₂, Cl⁻, SO₄²⁻ and NO₃⁻) varied little (< 0.5 mg/L), despite discharge increases from 0.2 to 4 L/s. Groundwater levels within the saturated zone increased after an initial 24 mm of event rainfall and remained within 0.05 m of the soil surface throughout the runoff period. TIR imagery identified consistent groundwater exfiltration zones from temperature differences across the event-period in the saturated zone. This suggested that unlike many headwater systems, the alluvial aquifer was well connected to groundwater outside the riparian zone and the mapped seepage area was a focused discharge point for the catchment-scale groundwater flow system. Overall this work suggests that for this catchment, groundwater exfiltration in the near-stream zone strongly controls stream geochemical response as well as the timing, duration and quantity of streamflow generation.
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4972. [Article] Sediment Transport Modeling and Implications for Benthic Primary Producers in Oak Creek, OR
The spatial and temporal variability of sediment transport processes in Oak Creek, OR was investigated and used to explore two study questions: 1) How do sediment transport processes influence benthic ...Citation Citation
- Title:
- Sediment Transport Modeling and Implications for Benthic Primary Producers in Oak Creek, OR
- Author:
- Katz, Scott B.
The spatial and temporal variability of sediment transport processes in Oak Creek, OR was investigated and used to explore two study questions: 1) How do sediment transport processes influence benthic algal communities?, and 2) Can fluvial-hydraulic models make accurate predictions of bed load transport rates? Our study was conducted in a 96 m reach of Oak Creek, OR – a small gravel bed stream in the Oregon Coast range. The study site is located in the same reach that was used to collect the historic Oak Creek bed load dataset of Milhous [1973]. To answer study question 1 we characterized the variability in sediment transport for a series of eight high flow events ranging from 0.64-3.4 m³/s using modeled shear stress (τ) from a field calibrated, high resolution (<0.1 m²) 2- dimensional hydrodynamic model (FaSTMECH) coupled with detailed measurements of the channel substrate. The stream bed was then categorized into regions of high and low disturbance based on potential mobility of the median grain size using a Shield’s stress approach. High resolution (<0.25m²), in-situ measurements benthic Chlorophyll-a (used as a metric of benthic algal production) were taken before and after high flow events in regions of contrasting disturbance to understand how benthic algal communities respond to sediment transport disturbance through both space and time. Growth factors including temperature, light, and nutrients were also measured. There was high spatial and temporal variability in both sediment transport and benthic Chl-a throughout the study period. We found significant differences (p<0.05) in benthic Chl-a concentrations between regions of high and low disturbance in half of the sampling events. The influence of sediment transport on benthic Chl-a was dependent on both the bed mobility and pre-disturbance Chl-a concentrations. There were also differences in benthic algal recovery rates in regions of contrasting disturbance following high flow events. The relationship between τ and Chl-a was highly variable, however the 95th percentile quantile regression of Chl-a was consistent with the bell-curve shape of the intermediate disturbance hypothesis for 10/18 sampling events. This study shows that sediment transport processes do influence benthic algal growth dynamics however the magnitude of that influence is also dependent on pre-disturbance productivity. To answer study question 2 we made contemporary bed load measurements during 5 flow events ranging from 0.24 bankfull (Q[subscript bf]) to 0.52 Q[subscript bf] using a Helly-Smith bed load sampler in order to confirm the stability of sediment transport dynamics in Oak Creek. The contemporary measurements were consistent with the historical dataset for total load however, they had a finer grain size distribution (GSD). A 2- dimensional (2-D) hydrodynamic model (FaSTMECH) was used to calculate spatial distributions of τ for 5 flow levels ranging from 0.2 Qbf to Qbf (0.64-3.4 m³/s). Results indicate that τ is highly variable within the study reach and that mean normalized τ distributions are remarkably similar between flow levels. The τ distributions were then discretized and used to calculate bed load using surface and subsurface transport equations, and compared against the historical dataset for accuracy. Modeled bed load was consistently larger and coarser than the historical samples. Areas of τ greater than 2 times the mean comprised <2.5% of the bed and were responsible for transporting >32% of the bed load. We hypothesize that the inconsistency in our estimates may be due to combining 2-D τ with a reach averaged reference shields stress (τr*) value which may have caused such high transport rates from a small portion of the bed. Scaling τr* with τ throughout a reach may provide the basis for future work to incorporate spatially variable τ into commonly used bed load transport functions.
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4973. [Article] Polylcaprolactone-Based Microfluidic Devices : Fabrication Methods and Applications in Low-Cost Analytical Devices
The overall concept of reducing laboratory operations to a scale that fits on a single microfluidic chip has been an attractive area of research over the last several decades. Despite a surge in research, ...Citation Citation
- Title:
- Polylcaprolactone-Based Microfluidic Devices : Fabrication Methods and Applications in Low-Cost Analytical Devices
- Author:
- Heist, Christopher Adam
The overall concept of reducing laboratory operations to a scale that fits on a single microfluidic chip has been an attractive area of research over the last several decades. Despite a surge in research, few commercial success stories have been written. Lab-on-a-chip technologies have the capability to be cost effective due to reduced reagent consumption, offer shorter analysis times due to their small scale, i.e. path lengths, and have the ability to work with decreased sample sizes. Due to these benefits, microfluidic devices show great promise as point-of-care devices for the analysis of biologically relevant analytes as they are inherently compact, have the potential to be produced at low-cost, and can be manufactured out of materials that allow for single-use followed by responsible disposal. In this work, a series of new fabrication techniques for low-cost microfluidic platforms in both capillary-driven (wicking) and pressure-driven platforms as well as their potential applications in low-cost clinical chemistry analysis are explored. In the first component of this research effort a new method of fabricating microfluidic paper-based analytical devices (µPADs) using aerosolized deposition of polycaprolactone (PCL) was developed. PCL is a biodegradable, semicrystalline polyester with excellent thermal properties including a glass transition temperature (T[subscript g]) of -60 ˚C and a melting point of 60 ˚C. Hydrophilic substrates were masked with low-adhesive painter’s tape and PCL was applied using an airbrush to create capillary-driven microfluidic devices. With this approach, the traditional fabrication processes used for manufacturing µPADs have been simplified allowing rapid, low-cost fabrication of µPADs with hydrophilic features as small as 480 µm, and hydrophobic barriers as small as 260 µm. Point-of-care applications involving enzymatic determination of glucose and chemical determination of protein concentration were successfully demonstrated. The second portion of this research involved the development of a smartphone (iOS) application for conducting colorimetric analysis of µPADs. The application, OccuChrome, was created as a capstone project with the School of Electrical Engineering and Computer Science at Oregon State University. OccuChrome was designed to allow all aspects of colorimetric analysis including model development, calibration curve development, unknown analysis, and results sharing on a single platform. Results obtained from OccuChrome compared favorably with those obtained using traditional colorimetric image analysis via ImageJ. The next stage of work explored the application of PCL saturated paper as a low-cost material for the fabrication of open channel microfluidic devices in both pressure-driven and capillary-driven formats. The favorable thermal properties of PCL, namely the low T[subscript g] and low T[subscript m] allow for easy fabrication using a simple method of cut and stack lamination to assemble both 2D and 3D microfluidic devices. A variety of bonding techniques including microwave adhesion and laser welding were explored as alternatives to thermal lamination. The classic diffusion limited laminar flow of two miscible solutions observed in traditional open-channel microfluidic devices was able to be replicated. Other pressure-driven microfluidic applications including passive mixing, droplet generators, and serial dilution generators were also demonstrated in this low-cost platform. Despite being composed primarily of high porosity material; these devices were able to operate under normal conditions for hours without leaking so long as a maximum operating pressure of ~1.2 psi is maintained. The final stage of work involved the development of PCL saturated paper hybrid microfluidic devices, that is devices consisting of both open channel and paper wicking regions. Creatinine and urea assays were developed using creatinine deiminase and urease for the in-situ generation of NH₃ as a product. Using one of the unique properties of PCL saturated paper, gas permeability, the enzymatic reaction is able to be separated from the detection reaction allowing simple pH indicators to be used for the detection of gaseous NH₃. Reaction conditions were optimized to increase the percentage of volatile NH₃ generated via the enzymatic processes in an effort to decrease the overall assay time. It was experimentally determined that a pH of ~10 was ideal to increase the relative NH3 concentration without impairing the enzyme activity.
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4974. [Article] Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality
Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native ...Citation Citation
- Title:
- Responses of Aquatic Non-Native Species to Novel Predator Cues and Increased Mortality
- Author:
- Turner, Brian Christopher
- Year:
- 2017
Lethal biotic interactions strongly influence the potential for aquatic non-native species to establish and endure in habitats to which they are introduced. Predators in the recipient area, including native and previously established non-native predators, can prevent establishment, limit habitat use, and reduce abundance of non-native species. Management efforts by humans using methods designed to cause mass mortality (e.g., trapping, biocide applications) can reduce or eradicate non-native populations. However, the impacts of predator and human induced mortality may be mitigated by the behavior or population-level responses of a given non-native species. My dissertation examined the responses of non-native aquatic species to the risk of predation by novel (i.e., no previous exposure) predators in the recipient community and indicators of potential compensatory responses by non-native populations to increased mortality resulting from removal efforts. My dissertation addresses four primary questions. 1) Can first generation, naïve invaders recognize and defend against predators found within the region of invasion through the expression of inducible defenses? 2) Can the overcompensatory potential of a population be predicted though examinations of intraspecific interactions of individuals from the population? 3) What is the relationship between removal effort outcome (i.e., successful or unsuccessful reduction of the target population) and compensatory population responses? 4) Is there a relationship between characteristics of removal efforts that are typically available to managers (e.g., target area size, target area connectivity, removal methodology) and compensatory population responses that could indicate the relative likelihood of compensation resulting from removal efforts? An invading species should be more likely to establish if it can successfully identify and defend against predators in the recipient range, such as through the expression of inducible defenses. Inducible defenses are behavioral or physiological changes that reduce an organism's susceptibility to predation. Through a series of laboratory experiments, I tested whether inducible defenses, in the form of increased burrowing depth, may have benefited the early stage of invasion of Nuttallia obscurata (purple varnish clam), an established Northeast Pacific invader. Specimens of N. obscurata were collected from introduced populations in the Northeast Pacific and from a native population in Japan. The clams were exposed to chemical and physical cues from Northeast Pacific crab predators, including the native Metacarcinus magister (Dungeness crab), an abundant and frequent predator of N. obscurata. While introduced N. obscurata increased their burrowing depth in the physical presence of M. magister, clams collected from their native range showed no such response. This lack of increased burrowing depth by naïve clams in response to a predator native to the newly invaded range, but a significant increase in depth for clams from populations established in the range suggests that while inducible defenses likely did not contribute to the initial establishment of N. obscurata in the Northeast Pacific, they may contribute to their continued persistence and expansion in their introduced range. Some efforts to reduce invasive populations have paradoxically led to population increases. This phenomenon, referred to as overcompensation, occurs when strong negative density-dependent interactions are reduced through increased mortality within a population, resulting in an increase in the population's recruitment rate sufficient to increase the population's overall abundance. Increases in a population's recruitment rate can result from reduced cannibalism of juveniles resulting in lower mortality of new recruits, from increased adult reproductive output, which increases the number of potential recruits, or from reductions in size and/or age at maturity of the unharvested population, which increases the number of reproductive individuals. I predicted the overcompensatory potential of a population of Carcinus maenas (European green crab) in Bodega Harbor, California, using a series of laboratory and field experiments examining intraspecific pressures of adults on juveniles in the population. This measure of intraspecific pressure was used to predict the overcompensatory potential of the population in response to increased mortality from ongoing removal efforts. This prediction was then assessed using pre- and post-removal surveys of juvenile recruitment in Bodega Harbor compared to nearby populations, testing for evidence of overcompensation. While adult C. maenas in Bodega Harbor had limited negative impacts on juveniles, I concluded it was unlikely to result in overcompensation. Relative juvenile abundance did not statistically increase in removal compared to reference populations, consistent with my conclusion from the experiments. Increases in recruitment rates can occur as a result of efforts to remove non-native species. This increase in recruitment can result in overcompensation, but more commonly results in compensation, where recruitment rates increase relative to pre-removal recruitment but does not result in in the population's abundance exceeding pre-removal levels. However, a detailed and accurate prediction of the response of a population to harvest is time consuming and data intensive. This is not feasible for most efforts to eradicate non-native species, which have the greatest chance of success when enacted rapidly after detection. For my final chapter, I performed a literature review and accompanying statistical analysis to determine if typically available information related to the removal effort (site size, site connectivity, and removal technique) could be used to determine increased risk of compensation for a given effort to remove aquatic invasive species. Compensation was closely linked to unsuccessful removal efforts and was observed only among efforts utilizing physical removal methods. However, the frequency with which compensation occurred varied with the exact technique employed, occurring most frequently in removal utilizing electrofishing. Additionally, evidence of compensation was more frequent among larger removal areas with variable connectivity. While other predictors (temperature, effort, etc) might add to the predicative power, the findings of the review provide criteria for managers to determine the relative risk of compensation prior to the start of removal. Further understanding of how invasive species respond to lethal biotic interactions, including anthropogenically mediated control measures, can aid in assessing the risk of invasion for a given species and inform managers of the risk of complications resulting from removal efforts. While inducible defenses may contribute to the long-term success of an introduced species in their recipient range, my findings did not support the idea that inducible defenses triggered by predator cues contributed to their initial introduction in this case. However, research on other non-native species and offspring of previously naïve prey would allow for a clearer picture of the role of inducible defenses in the invasion process. Compensation resulting from removal efforts does not guarantee failure, and certain characteristics of removal efforts seem to indicate increased risk of compensation. Together these components help identify how biotic interactions surrounding mortality risk of an invading species help shape the trajectory of invasion.
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4975. [Article] Juvenile survival and birth-site selection of Rocky Mountain elk in northeastern Oregon
With declining populations and low calf recruitment in northeastern Oregon, much interest has been generated to study the survival rates and causes of mortality of Rocky Mountain elk (Cervus elaphus nelsoni). ...Citation Citation
- Title:
- Juvenile survival and birth-site selection of Rocky Mountain elk in northeastern Oregon
- Author:
- Rearden, Spencer N.
With declining populations and low calf recruitment in northeastern Oregon, much interest has been generated to study the survival rates and causes of mortality of Rocky Mountain elk (Cervus elaphus nelsoni). I investigated the causes of elk calf mortality and the effects of predation risk on birth-site selection by cow elk. Cow elk were captured in March of 2002-2004 to determine their pregnancy status and condition (percent fat, mass, and age). Pregnant cows had temperature-sensitive vaginal implant transmitters inserted that were expelled at parturition in order to locate newborn calves and birth sites later during the calving season. Elk calves were captured in two adjacent study areas, the Wenaha and Sled Springs, with the use of vaginal implant transmitters, a helicopter and net gun, and ground searching. A total of 222 calves were captured during the spring and summer of 2002-2004. Calves were sexed, aged, weighed, and fitted with radio-transmitting collars that had mortality sensors integrated into the circuitry. Monitoring of the radio-collared calves was done from fixed-wing aircraft. Calf collars in mortality mode were located on foot to investigate and determine cause of death. Predator-related mortalities were marked with a global positioning unit and the most likely spot where the calf was killed was flagged. I took microhabitat measurements that described horizontal and vertical cover at each birth and predation site and 2 paired random sites. During the summers of 2003-2004, I measured 49 birth sites and 62 predation sites along with 2 paired random sites for each. Using a geographic information system (GIS) I obtained slope and aspect for each site. I also used GIS to obtain macrohabitat data on birth, predation, and 80 random sites (for comparison). For each site, I measured the percent canopy cover and the amount of forest edge within a 250, 500, and 1,000 m radius circle. In addition, I also obtained the distance from each site to the nearest edge. I found differences in annual survival rates between the two adjacent study areas, with calves in Wenaha having lower survival (0.26; 95% CI = 0.15 to 0.42) rates than calves in Sled Springs (0.52; 95% CI = 0.37 to 0.56). Overall, predation was the main proximate cause of death. In 2003-2004, cougars (Felis concolor) killed 54% and 35% of radio-collared calves in Wenaha and Sled Springs, respectively. Annual calf survival was influenced by birth date (13 -0.35; 95% CI = -0.64 to -0.06). Both birth date (13 = -0.25 3; 95% CI = -0.502 to -.0003) and birth weight (13 = 0.13; 95% CI = -0.14 to 0.39) influenced summer calf survival, with earlier and heavier-born calves having higher survival rates than late and light-born calves. I found no differences in annual survival rates between the sexes in this study. However, I did find differences in summer survival rates between the sexes depending on the area. In Wenaha, females (0.57; 95% CI = 0.42 to 0.72) had higher survival than males (0.42; 95% CI 0.27 to 0.59), and in Sled Springs, males (0.82; 95% CI = 0.66 to 0.91) had higher survival than females (0.46; 95% CI = 0.31 to 0.61). Preliminary analyses suggested that cow condition did not influence calf survival, nor was cow condition correlated with the estimated birth date and birth weight of calves. However, the analyses that examined the effects of cow condition on calf survival were preliminary and inconclusive due to small sample sizes. I found that birth-site selection of cow elk was influenced by predation risk at the microhabitat scale. Cow elk selected birth sites that had less horizontal cover (0.97 times the odds; 95% CI = 0.94 to 0.99) and more overhead density of vegetation (1.022 times the odds; 95% CI = 1.005 to 1.040) than paired-random sites. Although predation sites also had less horizontal cover (0.985 times the odds; 95% CI = 0.973 to 0.998) than random sites, birth sites had less horizontal cover (0.983 times the odds; 95% CI = 0.967 to 1.001) and more overhead density of vegetation (1.02 times the odds, 95% CI = 1.01 to 1.04) than predation sites. I found no evidence that cow elk were influenced by predation risk at the macrohabitat scale. Cow elk chose birth sites with less canopy cover than random sites within a 500 m-radius circle. Cow elk were likely more influenced by forage availability rather than predation risk when selecting a birth site at the macrohabitat scale. When birth sites were compared to predation sites at this scale, I found no differences, further suggesting that birth-site selection was not influenced by predation risk. Cow elk were likely selecting broad areas for parturition that had sufficient forage to meet high nutritional demands due to lactation. Within these areas, cow elk selected birth sites that had high visibility at the microhabitat scale, presumably to detect predators visually and to avoid predation on calves.
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First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations ...
Citation Citation
- Title:
- Potential for dispersal of the non-native parasite Myxobolus cerebralis : qualitative risk assessments for the state of Alaska and the Willamette River Basin, Oregon
- Author:
- Arsan, E. Leyla
First introduced to the USA in 1958, Myxobolus cerebralis, the parasite responsible for whirling disease in salmonids, has since spread across the country causing severe declines in wild trout populations in the intermountain west. Recent development of risk assessment models used to assess the likelihood and consequences of exotic parasite introduction, have strengthened the process of science-based decision-making in aquatic animal health. In the case of M. cerebralis, it is necessary to use a risk assessment model with two unique segments that clearly address the distinct life stages and respective hosts of the parasite separately. The studies described examine the probability of M. cerebralis introduction and establishment for two regions: the state of Alaska, and the Willamette River basin, Oregon. The Alaska risk assessment was based on the assumption that the parasite did not already occur in the state. However, in the process of validating this assumption, we documented the first polymerase chain reaction (PCR) detection of the parasite in the state. The pathogen was identified in hatchery rainbow trout (Oncorhynchus mykiss) from the Anchorage area. Although this is the first detection of the parasite in Alaska, clinical whirling disease has never been documented in the state. To qualitatively assess the risk of further spread of M. cerebralis in Alaska, four potential routes of dissemination were examined: movement of fish by humans, natural dispersal (via migratory birds and stray anadromous salmon), recreational activities, and commercial seafood processing. This research indicates the most likely pathway for M. cerebralis transport in Alaska is human movement of fish. In the Willamette River basin, Oregon, introduction of M. cerebralis has already occurred, though establishment appears limited to a single private hatchery. Introduction in this region was considered the most likely to occur as a result of human movements of fish. Straying anadromous salmonids were also assessed and were present in higher numbers than predicted. However, they were not infected with the parasite, and thus the probability for introduction by this route is low. The probability of introduction of the parasite varies throughout the Willamette River basin. Areas with the highest probability for M. cerebralis introduction were identified as the Clackamas and Santiam River subbasins. The Clackamas River has already experienced an introduction of the parasite, has the largest concentration of hatcheries (state, federal, and private), has a popular sport fishery, and is the closest major tributary to the enormous piscivorous bird-populations in the Columbia River estuary. The Santiam subbasin has a popular sport fishery, received the highest number of stray fish in the Willamette River basin, and has the second largest concentration of hatcheries in the Willamette River basin. Unique from introduction, establishment of the parasite is dependent upon several environmental and biological factors including: water temperatures, spatial/temporal overlap of hosts, and the distribution and genetic composition of the parasite’s invertebrate host, Tubifex tubifex. The distribution, genetic composition and susceptibility of T. tubifex, were considered the most important factor in the ability of M. cerebralis to establish in both systems. Surveys of oligochaete populations were conducted in both study regions. In Alaska, T. tubifex was not detected from the southeast region and the apparent lack of appropriate tubificid hosts may prevent establishment in that part of the state. However, 4 lineages (I, III, IV, and VI) of the species were identified from southcentral Alaska. Lineage IV has not been previously been described in North America and its susceptibility to M. cerebralis was unknown. When lineage IV T. tubifex and 3 mixed-lineage (I, III, IV and VI) groups were exposed to M. cerebralis, only lineage III became infected under our experimental conditions. Thus, if the parasite were dispersed, conditions are appropriate for establishment and propagation of the parasite life cycle in southcentral Alaska, although detrimental effects on fish populations may be reduced as a result of the presence of non-susceptible lineages of T. tubifex. The probability of further establishment in this area is greatest in Ship Creek, where the abundance of susceptible T. tubifex, the presence of susceptible rainbow trout (Oncorhynchus mykiss), and the proximity to the known area of infection make conditions particularly appropriate. Similar to findings in Alaska, the Willamette River basin, Oregon also supports populations of susceptible T. tubifex. If the pathogen were introduced, probability of establishment is high in certain areas of the basin as all conditions are appropriate for propagation of the parasite life cycle. Tributaries to the mainstem Willamette River have the highest probability of establishment as these areas have the greatest numbers of susceptible T. tubifex. However, the abundance of resistant strains of T. tubifex could mitigate the effects of M. cerebralis if introduced. Management recommendations to reduce the likelihood of parasite dissemination are similar for Oregon and Alaska since human movement of fish and angler activities were considered the most likely routes of introduction for both regions. Based on this research, steps should also be taken to limit human movement of fish, whether by restricting carcass planting for stream enrichment in Oregon, or by prohibiting use of fish heads as bait in southcentral Alaska. The states should also allot resources to angler education and awareness of the effects of angler activity and recreation on dispersal of M. cerebralis. This could be done using a combination of brochures and signage at boat ramps describing how to prevent spread of aquatic nuisance species.
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Novel synthetic strategies are developed to prepare new intercalation compounds and nanocomposites with several layered hosts (NiPS₃, Na-montmorillonite, MoS₂ and MoO₃). In these products, alkali metals ...
Citation Citation
- Title:
- Synthesis of Intercalation Compounds and Nanocomposites of Inorganic Layered Hosts
- Author:
- Liyanage, Medagama Liyanage Amila Udayanga
Novel synthetic strategies are developed to prepare new intercalation compounds and nanocomposites with several layered hosts (NiPS₃, Na-montmorillonite, MoS₂ and MoO₃). In these products, alkali metals are ionic intercalates and linear polymers, dendrimers or amines act as co-intercalates. In addition to new synthetic approaches, new structures are identified and characterized. A template synthesis method to prepare NiPS₃/polymer nanocomposites is reported for the first time. Polymers studied were polyethylene oxide (PEO), polyethylenimine (PEI), polyvinyl alcohol (PVA) and polyvinylpyrrolidone (PVP). NiPS₃/PEO nanocomposites prepared by this template method contain polymer monolayers (delta d = 0.42 nm) between host layers, in contrast to the polymer bilayers reported in previous reports using a topotactic method. Packing fraction calculations reveals that the interlayer space is denser for template synthesized NiPS₃/PEO than for the topotactically-derived MPS₃/PEO nanocomposites (M = Ni, Fe, Cd, and Mn). NiPS₃/PEI, NiPS₃/PVA and NiPS₃/PVP nanocomposites were prepared for the first time and also have polymer monolayers between host layers (delta d = 0.41, 0.42 and 1.56 nm, respectively). The monomer unit / NiPS₃ formula ratio is ~ 1 for PEO, PEI and PVA nanocomposites and ~ 0.5 for PVP nanocomposites. More dilute conditions, more polar solvents, and longer aging times increase the crystallite size of the obtained products. Reaction progress studies indicate that the P₂S₆⁴⁻ and Ni²⁺ concentrations in the reaction mixture govern nanocomposite nucleation and growth. Intercalated nanocomposites with lower generation (G0.0-2.0) polyamidoamine (PAMAM) dendrimers and Na-montmorillonite (Na-MMT) are synthesized using an exfoliation–adsorption method. This is the first report of the G0.0 and G1.0 PAMAM/Na-MMT nanocomposites and of a structurally-ordered G2.0 PAMAM/Na-MMT nanocomposite. The structures obtained depend on the PAMAM generation and the starting reactant ratio. The spherical PAMAM in aqueous medium transforms to a highly flattened conformation after incorporation between the host layers. G0.0 PAMAM forms only monolayer galleries (delta d = 0.42 nm), while G2.0 PAMAM forms monolayers, bilayers, (delta d = 0.84 nm) and mixed phase structures at lower, higher, and intermediate, organic content, respectively, and exhibits an interesting monolayer to bilayer transition. G1.0 PAMAM shows intermediate behavior, with a monolayer to mixed-phase transition observed at the reactant ratios studied. This is the first report of a monolayer arrangement for PAMAM/clay nanocomposites. The maximum organic contents of G0.0 PAMAM monolayer and G2.0 PAMAM bilayer nanocomposites are ∼7% and ∼14% respectively, and these materials have ~2 times lower packing fractions (0.31-0.32) than for linear polymer intercalate nanocomposites of Na-MMT. Under acidic conditions all these nanocomposites form only monolayer galleries, which is ascribed to the stronger electrostatic attraction between negatively charged MMT layers and protonated PAMAM. Acidic conditions also slow the rate of formation of the nanocomposites and generate more ordered products. The Na⁺ ions in the Na-MMT structure play a significant role in PAMAM/Na-MMT nanocomposite formation. Both Na-MMT and PAMAM structural units are preserved in the nanocomposites obtained. Electride solutions obtained by dissolution of Na(m) in ethylenediamine (en) are used for the first time to generate MoS₂ intercalation compounds with Na and en as intercalate and cointercalate, respectively. Two new phases, labeled α and β, have delta d = 0.35 and 0.57 nm, respectively; the different gallery dimensions are ascribed to parallel vs. perpendicular orientations of en in the galleries. The B phase structure has not been reported previously in any MS₂ intercalation compounds. The intercalation reaction proceeds via the formation of a metastable kinetic product, the β phase, and the subsequent generation of the thermodynamically stable α phase. Lower electride concentrations, lower reaction temperatures and shorter reaction times favor production of the β phase. The products obtained have compositions of Na₀.₂-₀.₃MoS₂·0.3-0.4en with a larger packing fraction than the structurally analogous A-en-GICs (A = alkali metal, GIC = Graphite intercalation compound). The electrochemical reduction of MoS₂ in en/NaPF₆ does not result in these intercalation reactions. The incorporation of dendrimers into MoO₃ is reported for the first time. PAMAM/MoO₃ nanocomposites are synthesized using an exfoliation - adsorption method. G0.0 PAMAM only forms monolayers (delta d = ~ 0.5 nm) between MoO₃ layers and G2.0 PAMAM forms both monolayer and bilayers (delta d = ~ 0.7-0.8 nm). In addition to these two structures, a third unknown phase is observed with a much larger gallery expansion (delta d = ~ 1.4 nm). These nanocomposites have a comparable structures, compositions (12-14% organic component for G0.0 monolayer and 22-25% for G2.0 bilayer) and packing fractions (0.5-0.7 for monolayer and 0.7-0.9 for bilayer) to those in the previously reported linear polymer/MoO₃ nanocomposites. In the above studies, analyses by powder X-ray diffraction (PXRD) are supported by compositional data from thermogravimetric analyses (TGA) and structural optimization (Gaussian). Additionally, the product morphologies, surface properties and constituents are evaluated using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and Fourier transform infrared (FTIR) and Raman spectroscopies. UV-visible spectroscopy (UV-vis) is used to monitor reaction progress. Capillary zone electrophoresis (CZE) is used to study compositions and reaction progress.
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4978. [Article] Restoring the Columbia River Estuary : Chinook Salmon Recovery and Invasive Species Management
As highlighted in this study, shallow-water habitats and the prey they provide are important for juvenile salmon in the Columbia River estuary, but the spread of invasive species and large-scale changes ...Citation Citation
- Title:
- Restoring the Columbia River Estuary : Chinook Salmon Recovery and Invasive Species Management
- Author:
- Klopfenstein, Rachael
As highlighted in this study, shallow-water habitats and the prey they provide are important for juvenile salmon in the Columbia River estuary, but the spread of invasive species and large-scale changes to the estuary influence how these habitats are utilized. Reed canarygrass (Phalaris arundinacea) (“PHAR” hereafter) is a highly invasive aquatic plant species that affects a number of emergent wetland habitats in the upper Columbia River estuary, and is of concern to those trying to restore important shallow-water habitats for juvenile salmon. The presence of PHAR undoubtedly reduces plant diversity, but this study seeked to elucidate how PHAR affects juvenile Chinook Salmon rearing success relative to natural emergent vegetation. The study further evaluated the importance of wetland-deriver prey to juveniles found in shallow-water habitats along a habitat gradient (i.e., back-water channel, confluence, and main stem). We conducted research at a floodplain wetland restoration site in the tidal-fluvial portion of the estuary, where a water control structure is used to manage water levels and the spread of PHAR. The goal of the research was to compare two microhabitats within the floodplain: areas dominated by PHAR and areas dominated by natural emergent vegetation. Using hatchery-raised juvenile Chinook salmon, we designed a series of feeding experiments in artificial enclosures to determine whether invasive PHAR and natural emergent vegetation provide similar foraging and growth opportunities for juvenile salmon. We further identified differences in physical and biological parameters of each habitat (e.g., temperature, dissolved oxygen, and invertebrate community) and examined feeding characteristics (e.g., diet composition and modeled growth rates) for juveniles through a stomach content analysis. Additionally, we conducted beach seining and diet analysis for fish collected along a habitat gradient and compared the diet composition and modeled growth rates between the sample areas. In the floodplain wetland, invertebrate prey compositions from the 2015-2016 (March- June) fallout and emergence traps were similar, but prey abundances and diversity varied seasonally. Across both years, for emergence traps, the average total density (per m²) of invertebrates in the natural vegetation and in PHAR was 154±18 m² and 225±34 m², respectively, and for the fallout traps was 664±95 m² and 662±64 m², respectively. Salmon diets were mostly similar, and a large proportion of diets in both habitats were made up of Copepoda/Cladocera (60-98% composition by biomass). Growth during the net pen experiment differed significantly between the two vegetation types (Kruskal-Wallis: p<0.001), with fish growing more in the natural emergent vegetation. In 2015, juveniles grew an average 6.4 mm FL in the natural emergent vegetation, compared to 4.7 mm FL in PHAR, and consumed fewer Copepoda/Cladocera and more Diptera over the 10 days. In 2016, juveniles grew an average 9.2 mm FL in the natural emergent vegetation compared to 7.6 mm FL in PHAR. In 2016, fish from both habitats consumed a higher abundance of Copepoda/Cladocera and grew more, despite poor water quality conditions at the site. Of the subyearlings (n=170) and yearlings (n=14) collected in habitats adjacent to the floodplain wetland, 48% were of known hatchery origin. Modeled potential growth rates for subyearlings were similar on average between February and May in the back channel, confluence, and main stem, ranging from 0.067–0.07 g/g/d, but the rates varied seasonally. Growth potential was higher in the back channel habitat earlier in the sampling season (February-March), as the modeled daily growth rates were 0.08 g/g/d compared to 0.06 g/g/d in the main stem. All fish collected prior to May were relatively small and unclipped, highlighting the seasonal benefits of shallow-water habitats to support a variety of life-history traits. When comparing modeled growth rates of the juveniles reared at the floodplain wetland compared to the in adjacent habitats, estimates from the floodplain wetland were higher across all months. Restoration of shallow-water habitats is important for the overall health of the estuary, but the effects of large-scale ecosystem changes (e.g., flow regulation and spread invasive species) on salmon recovery and estuary-management decisions are uncertain. For example, water control structures to limit the spread of PHAR also reduce fish access to floodplain habitats, and fewer high-flow events further limit fish access and may facilitate the spread of invasive species. PHAR has been shown to reduce overall plant diversity and, as observed in this study, may provide habitat that is less suitable to juvenile Chinook Salmon. The high density of important prey for salmon found at the site, regardless of the presence of PHAR, and high potential growth measured at the site, emphasize the importance of restoring shallow-water habitats that are accessible to juvenile Chinook Salmon in the upper estuary.
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Strawberry is economically the most important berry crop grown worldwide and breeders are continuously striving to develop improved cultivars. So far, marker assisted breeding (MAB) in strawberry has been ...
Citation Citation
- Title:
- Validation of Molecular Markers Associated with Perpetual Flowering (PF) and Soluble Solids Content (SSC) in Strawberry (Fragaria xananassa Duch. ex Rozier)
- Author:
- Salinas, Natalia R.
Strawberry is economically the most important berry crop grown worldwide and breeders are continuously striving to develop improved cultivars. So far, marker assisted breeding (MAB) in strawberry has been limited to the private sector. However, loci controlling some traits of economic importance such as perpetual flowering (PF) and soluble solids content (SSC) associated with fruit sweetness were recently mapped in the cultivated strawberry, a prerequisite to enabling MAB. The first objective of this research was to investigate usefulness of markers linked to the FaPFRU locus controlling PF in 'Capitola' and strawberry germplasm containing the same F. virginiana subsp. glauca source collected by Bringhurst in Utah’s Wasatch Mountains through 'Tribute' and 'Seascape', and from other sources such as 'Pan American' through 'Fort-Laramie', and an unknown source through 'Sarian'. The second objective was to assess the ability of an SSC-associated simple sequence repeat (SSR) marker for predicting high soluble solids content in different environments in strawberry. Five SSR markers (EMFvi136, Bx89, Bx215, Bx56 and Bx63) that are linked to PF on linkage group IVb were used to genotype 893 strawberry individuals. Based on Mendel's Law of Inheritance, parentage was confirmed for most seedlings. Those that had unlikely genotypes or alleles were identified in each of the mapping and breeding populations from Michigan State University (MSU) and those of the USDA-ARS in Corvallis (ORUS). Off type frequencies in breeding populations were 17.1%, on average. Furthermore, multiple genotypes of parents were identified and included: 'Fort Laramie' and FRA 1701 in the MSU breeding programs and 'Tillamook' and 'Puget Reliance' in the ORUS program. Genotype of the FRA 1701 used as parent was different between both programs. Six alleles were associated with PF in the entire dataset: EMFvi136_167, Bx89_251, Bx89_262, Bx215_129 and Bx56_209. However, none of these alleles were present in the FRA 1701-derived progeny and could not be used to predict PF. Since Bx215 mapped closest to the FaPFRU locus, we used repeated rounds of ANOVA to identify combinations of alleles at this SSR that best explained the PF trait in the breeding populations. The presence of 129 and absence of 160 increased predictivity of PF from 63% to ~80% while the absence of 129, 123, 127 and 134 predicted OF in 100% of the germplasm where the original source of PF was that obtained from the F. virginiana subsp. glauca from the Wasatch Mountains through 'Capitola', 'Seascape' and 'Tribute'. In 'Sarian'-derived germplasm, other alleles, 123 and 134 or 127, were predictive of PF. Establishing allele composition at each subgenome using microsatellite allele dose and configuration establishment MADCE for Bx215, Bx56 and Bx63 identified the associated alleles as shared among three or four of the subgenomes, thus unable to predict PF based on allele presence in all PF individuals. Absence of these alleles was more predictive of once flowering and could be used to eliminate those individuals and therefore increase the proportion of PF progeny to evaluate. Determining haplotypes in this region and evaluating haplotype association with PF could be much more accurate in predicting PF than allele presence or absence and should be investigated. Soluble solid content-associated EMFv006 was used to genotype 602 individuals. Alleles and genotypes associated with low (209, 215), medium (207, 213, 217) and high SSC (219, 221) were obtained. Plants with the 213:219 EMFvi006 genotype always had higher SSC than those with the 213:209 or 213:215 genotypes in all states except for California. When converted to functional alleles and analyzed by ANOVA in each of the states, a consistent increase in SSC mean was observed between genotypes with the lower SSC types and the higher SSC genotypes in each of the states and years. Heritability (H²) was low (0.02-0.09) in all states but NH_12 indicating that this trait is highly influenced by environmental conditions. The proportion of phenotypic variance (PVE) was high in comparison with those of H² in all states except for CA_12 and ranged from 0.65 in MI_11 to 0.86 in NH_12, indicating that most of the genotypic variance observed can be explained by this locus that can strongly predict differences in SSC content. Much of the variability seen in the SSC trait in this study could be explained by differences in environments and fruit ripening at the time of harvest and their effects on SSC as SSC is very sensitive to environmental factors such as temperature and harvest date. It may be necessary to develop a more standardized protocol of measuring SSC across states and years to obtain more reliable SSC data for each individual. Most importantly, this study illustrates the usefulness of introgressing novel alleles from wild accessions into the cultivated gene pool. Both alleles consistently associated with high SSC, 219 and 221, originated from wild F. virginiana parents (FRA 1701-I1, and FRA 1701, respectively) from the "supercore" and were not present in any of the F. ×ananassa cultivars genotyped in this study except for an old European selection, 'Jucunda', of unknown pedigree. Based on the results obtained in this study, breeders may be able to select progeny with desired flowering type and increased soluble solid content after evaluating the alleles present in their parental material.
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4980. [Article] The Factors Affecting the Diets of Groundfish in the Gulf of Alaska : Ecological and Modeling Considerations
Marine systems undergo changes in community composition over time as a result of a variety of environmental and anthropogenic factors. Understanding these community changes and the factors that drive them ...Citation Citation
- Title:
- The Factors Affecting the Diets of Groundfish in the Gulf of Alaska : Ecological and Modeling Considerations
- Author:
- Thompson, Kevin A.
Marine systems undergo changes in community composition over time as a result of a variety of environmental and anthropogenic factors. Understanding these community changes and the factors that drive them is critical for ecosystem management of marine resources. The Gulf of Alaska (GOA) is a large marine ecosystem that includes a variety of species that support large scale fisheries. This is also a system in which large scale community shifts, or regime shifts, have occurred due to the Pacific Decadal Oscillation (PDO) and fishing pressure. Given the economic and conservation importance of this marine system, the GOA has been modeled using a variety of multispecies, or ecosystem, models. While this work has been critical in understanding the ecosystem dynamics of the GOA and helped generate management recommendations for commercial species, these models often make assumptions regarding trophic-dynamics, particularly that predator-prey relationships follow a standard functional response and do not change through time in response to environmental variables. However, empirical evidence suggests that a predator's diet can be influenced by a variety of factors, abiotic and biotic, at large and small spatial scales. Our overall objective was to investigate the potential impact environmental variables may have in structuring this ecosystem by using statistical analyses of diets and an ecosystem modeling framework. We focused on three commercially and ecologically important groundfish predators: Pacific Cod (Gadus macrocephalus), Pacific Halibut (Hippoglossus stenolepis), and Sablefish (Anoplopoma fimbria). We also focused on a key prey species, Walleye Pollock (Gadus chalcogrammus), and used environmental data collected during trawl surveys and PDO data generated for the entire North Pacific region. The first study completed was focused solely on the consumption of Walleye Pollock, a critical fishery species and ecosystem link. We used data from trawl surveys to determine the potential influence of local environmental variables on the predation rate of Walleye Pollock in the system by these groundfish. Using an information-theoretic approach, we found that predator length was positively related to Walleye Pollock presence and proportion of total diet weight in all predators. Increased temperatures positively affected consumption of Walleye Pollock by Pacific Halibut, but not the other predators. We found evidence for a number of inter-predator effects of co-occurring predators, both positive (facultative) and negative (competitive). Observed prey density was not statistically significant with respect to consumption for these predators, suggesting that trawls sample the environment differently than Walleye Pollock predators or species interactions are more complex than those used in previous multispecies models. In our second study, we considered the entire diet of these predators, rather than one key prey. Furthermore, because PDO had been described as leading to community changes in the system previously, we hypothesized that it could also be driving shifts in diets in the three groundfish predators we studied. We used a multivariate statistical approach to compare the diets of these predators by PDO state (warm or cold years) and also included local environmental covariates. Overall, we found that diets observed in PDO cold years were significantly different than diets in fish in warm years. In general, predators were found to be consuming more Walleye Pollock and euphausiids in warm years, and more benthic invertebrates and other forage fish in cold years. Local environmental covariates contributed to the diets observed in these predators, however no general pattern was observed. Our results also show the benefit of using diet data from large scale monitoring efforts as indicators of community shifts in a large marine ecosystem through time. Ultimately, we used our statistical analyses regarding diet and PDO state to drive a modeling exercise using alternate representations of the diets of the predators in the GOA. We investigated the potential impact of shifting diets in groundfish in an ecosystem-modeling framework, using Ecopath trophic-mass balance models. We changed the diets of key groundfish predators in the model based on our previous results for three alternative model parametrizations; 1) average conditions over the time period, 2) cold PDO state, and 3) warm PDO state. We noted a number of differences in model estimated ecosystem indices. Biomass accumulation estimates indicated that some ecologically and commercially important species groups would be expected to greatly diverge in population size if models were based on data from warm vs. cold PDO years compared to the averaged climatic state. In general, predator overlap was at its lowest in the cold year model, as predators had more diverse diets and therefore predation was more diffuse in the system in general. These results indicate the potential importance of environmental context when collecting diet data to be used in ecosystem models designed to provide fishery management recommendations. As ecosystem models are used more commonly, taking the time to investigate the factors that structure diets and how predation changes due to environment can yield more representative, and potentially more accurate biomass projections and recommendations for the GOA and likely many other managed marine ecosystems.