Lake Moomaw, a 1,024-ha flood control reservoir in Bath and Allegheny counties, Virginia contains a migratory population of smallmouth bass that congregate in the headwaters of the reservoir during the spring spawning period, where they are vulnerable to a shore-based, harvest-oriented fishery. The extent of this fishery and resulting effects on the small mouth bass population were analyzed by means of a creel survey in the headwaters area during the spring spawning seasons of 1995 and 1996. Effort, catch, and harvest, as well as user characteristics and motivations data were obtained from direct interviews with anglers using this area. Estimates for 1995 indicated extensive fishing pressure per ha, with 1,167 angler hours per ha spent fishing for smallmouth bass in the headwaters, while in 1996 almost 1,400 angler hours per ha were spent in this area. Catch and harvest rates were relatively low and sustainable during both years, with 124 small mouth bass caught and 82 harvested in 1995, while 318 small mouth bass were caught and 222 harvested in 1996. An extensive capture-recapture study yielded estimates of exploitation rates for small mouth bass in the reservoir of 12- 15% annually. Exploitation of the whole-lake population occurring in the spring headwaters fishery was estimated at 4-6%, while the exploitation rate on the subset of the population using the headwaters during the spring was 11-14%. Analysis of movements of snlallmouth bass in the reservoir using ultrasonic telemetry and dart tag recaptures indicated that the subset of the population using the headwaters was mainly drawn from the upper and middle portions of the reservoir, and that significant amounts of spawning occurred in the lower section of the reservoir as well. Areas used by smallmouth bass for reproduction were documented with summer and fall electrofishing to determine relative abundance of young-of-the-year smallmouth bass in the reservoir, and showed spawning to take place throughout the reservoir. Densities of young-of-the-year shifted as fall progressed, with highest densities in the middle portion of the reservoir in early fall, indicating that reproductive inputs from the headwaters were realized in the lake as fall progressed. The headwaters fishery is a high-profile activity which, during 1995-96, had a low and sustainable impact on the Lake Moomaw smallmouth bass population. / Master of Science

Thesis advisor: Noah P. Snyder / Nitrogen is an important component in the biogeochemical processes of freshwater systems. Likewise, it is unknown if, and to what magnitude, changes in land use in the watersheds of New England lakes have affected nitrogen availability. This study examines the effects of land-use change on the present and historic isotopic signatures of nitrogen in three New England lakes of varied histories, Lower South Branch Pond, Little Kennebago Lake, and Sennebec Pond. The histories of all three sites indicate minimal discernible disturbance before the onset of Euro-American-induced land use change. For two sites, the dominant mechanism of change was timber harvest, which began in the latter half of the 19th century. Sediment cores for each site were examined and variations in geochemical and sedimentological indicators were evaluated in the context of changes within respective basins. Statistical analysis indicates significant shifts in the means and variance of the geochemistry within the Little Kennebago Lake and Sennebec Pond watersheds after the incursion of Euro-American settlers, while the Lower South Branch Pond watershed displays similarities to a more widespread signal of anthropogenic nitrogen that has been deposited remotely. The record of magnetic susceptibility in Little Kennebago Lake displays the largest variation compared to the other two lakes, which may indicate that the magnitude of land-use change within the basin was more impactful relative to Lower South Branch Pond and Sennebec Pond. This is significant in that all three sites experienced some level of land-clearance. / Thesis (MS) — Boston College, 2023. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Earth and Environmental Sciences.

In malting barley, rapid germination is desirable and linked to end use quality. Modern malting varieties have been bred for low seed dormancy leading to issues with pre-harvest sprouting in wetter growing regions. To maintain malting capacity while minimizing germination on the maternal plant requires in-depth understanding of the genetic regulation of dormancy in malting barley. Currently, the major effect QTLs SD1 and SD2 have been shown to influence dormancy across multiple populations of barley, though the physiological mechanisms involved remain unclear. To search for novel genetic regions that influence primary dormancy, three mapping populations were assessed including two Canadian biparental populations (Synch and Legci) as well as a diversity panel sourced from multiple locations worldwide (ICARDA AM-14). The SD2 locus had a major effect in the Synch population while the SD1 locus had a major effect in the Legci population and neither SD1 nor SD2 were linked to dormancy in the diversity panel. Instead, 14 additional marker trait associations were identified in AM-14 suggesting that investigating a broader range of genetic regulation of dormancy outside of North American varieties may provide solutions to regulate this trait. Additional testing on SD1 revealed that variation at this locus did not affect ABA sensitivity during germination or GA or ABA-regulated gene expression during grain fill. Indeed, lines containing the non-dormant SD1 allele germinate at a similar rate as the dormant SD1 seeds when the glumella was removed from the embryo. This indicated that the effect of the alanine aminotransferase gene underlying the SD1 allele is dependent on physical restriction on the embryo or the hypoxic effects produced by the glumella. Imposing a hypoxic (5% oxygen) environment on exposed embryos revealed an association between non-dormancy at SD1 and reduced sensitivity to the suppressive effects of hypoxia on germination. This suggests that alanine aminotransferase regulates dormancy release during barley germination at least in part through regulation of the seed’s response to hypoxia.

Understanding forest carbon uptake and associated growth response is important for carbon sequestration and water management practices given the large quantities of carbon stored in forest ecosystems. Climate variability and forest management practices influence the magnitude and rate of soil CO2 efflux; however, their combined effects are complex and not well understood. This study investigated the response of soil CO2 efflux to the combined effects of climate variability, including those caused by climate oscillations, and shelterwood harvesting in a mature temperate white pine (Pinus strobes L.) forest, located near Lake Erie in southern Ontario, Canada. Analyses indicated that local winter temperatures and precipitation were influenced by climate oscillations, which affected forest carbon dynamics. After the shelterwood harvest removed approximately a third of the overstory canopy, no significant differences were found for soil temperature and soil moisture between the pre-harvesting (2008 to 2011) and post-harvesting (2012 to 2014) periods. Despite similar climate conditions pre- and post-harvesting, soil CO2 effluxes post-harvesting were lower. A Gaussian-Gamma specification model determined that heterotrophic (autotrophic) respiration decreased (increased) between pre- and post-harvesting, respectively. Mineral-soil respiration were similar pre- and post-harvesting. Soil CO2 efflux accounted for 78±9% of the annual ecosystem respiration (RE), derived using eddy-covariance fluxes. However, the overall net ecosystem productivity showed no significant difference between pre- and post-harvesting. This was attributed to an increase in the gross ecosystem productivity post-harvesting, compensating for the increased losses (i.e. increased RE). This study highlights the complexities of measuring various components of ecosystem respiration after a disturbance, such as a harvest. The knowledge gained from this study provides a better understanding of climate variability and shelterwood harvesting influences on ecosystem respiration and can be useful for forest managers focused on carbon sequestration and forest conservation. / Dissertation / Doctor of Science (PhD) / Coniferous forest plantations in eastern North America are undergoing silvicultural management to enhance their carbon sequestration capabilities and native-tree species diversity. This study investigated the combined influence of climate oscillations and shelterwood harvesting on soil carbon dynamics of a planted pine forest in southern Ontario, Canada. Between pre- and post-harvesting, soil temperature and soil moisture did not show any significant differences. However, soil CO2 effluxes in post-harvesting years were lower than pre-harvesting years. A Gaussian-Gamma specification model determined that heterotrophic (autotrophic) respiration decreased (increased) post-harvesting and mineral-soil respiration was similar between pre- and post-harvesting. An increase in ecosystem respiration post-harvesting, despite soil CO2 efflux decreasing and being the largest component, was primarily caused by the increase in autotrophic respiration due to enhancement in forest growth. This study improved the understanding of forest carbon dynamics by highlighting the importance of accounting for all components, which may contribute to ecosystem respiration. Results can be useful for forest management practitioners, specifically those focused on carbon sequestration and forest conservation.

The overall goal of this project was to provide baseline data on amphibian species richness, relative abundance, and habitat use for a long-term landscape ecology study on MeadWestvaco industrial forest in the Allegheny Highlands of West Virginia. From results of area-constrained daytime searches (10 m x 10 m plots) across the landscape, I developed 9 regression models to predict amphibian relative abundance. I constructed models for each year for all plots on all habitat types, plots that were in a Stream Management Zone (SMZ), and plots that were in upland, or non-SMZ, habitat. Distance to perennial or ephemeral streams or perennial ponds (SMZ classification), the amount of available rocks along transects, and site index were the 3 most important habitat variables in models for all plots combined and were responsible for 24-32% of the inherent variation in population relative abundance. Other habitat variables that were significant in models were year, % canopy cover, the amount of available woody debris of decomposition classes 3-5 along transects, % woody stems (<7.5 cm DBH), soil pH, and % herbaceous vegetation. R2PRESS values for all 9 models ranged from 0.08 to 0.35. Amphibian relative abundance showed positive relationships with all significant habitat variables with the exception of year and % woody stems. In natural cover object use/availability analyses, I discovered salamanders preferred rocks over woody debris, relative to the amount available of each. Salamanders preferred flat rocks to any other shape, flagstones to any other type of rock, and rock lengths in the 31-40 cm class. Preferred wood widths were in class 5-10 cm, while preferred wood lengths were in class <50 cm; salamanders exhibited strong preferences for wood in higher states of decomposition (class 3-5). I provided baseline, preharvest data for 28-acre reference areas on 9 forest compartments scheduled for clearcuts. I sampled all 9 reference areas preharvest and sampled 3 during year 1 postharvest using coverboard and night plot surveys. On these 3 areas, species richness declined from preharvest to postharvest, but species diversity showed little change. Overall relative abundance declined significantly preharvest to postharvest with coverboard sampling (p=0.0172) and night plot sampling (p=0.0113). At coverboard stations, relative abundance declined significantly from preharvest to postharvest at a distance of 5-10 m (p=0.0163) and 40-50 m (p=0.0193) away from adjacent mature forest. Finally, using Pianka's index, I compared the night plot and coverboard sampling techniques in terms of proportions of the 4 most common species captured. These sampling techniques on average were >80% similar for all reference areas. / Master of Science

Two lipid-based edible coatings, Apex B (AC Humko, Memphis, TN) and Durafresh (Pacrite, Ecoscience Produce Systems, Orlando, Fl) were evaluated for their ability to preserve post harvest quality changes in green bell peppers (Capsicum annum L. cv. King Arthur). Post harvest storage quality conditions tested included respiration rates, weight, color and texture changes, and stability of ascorbic acid (AA) and dehydroascorbic acid (DHA) content. Results indicated that no appreciable changes between days or treatment groups occurred in three of the parameters tested: weight, texture, and hue angle (p>0.05 for all parameters). Significant weekly changes were seen in respiration rates, dehydroascorbic acid content, and chromaticity values. Respiration rates and DHA were significantly higher during the last two weeks of the study (p=0.0001, p=0.0001 respectively). Chromaticity values were significantly lower, indicating a more faded color on the 14th day of the study alone (p=0.0097). Initial AA levels were much lower than expected (average initial content=78.72mg/100g). Significant differences between coated and uncoated pepper groups were seen in AA and DHA levels. AA content was found to be significantly lower in coated peppers (p=0.0279), while DHA levels were significantly higher in coated groups (p=0.0126). Overall, coated groups differed little from uncoated counterparts, except in the area of vitamin content in which the coated peppers showed an increase in vitamin breakdown. Despite the results, modifications of lipid coatings are needed, such as creating bilayer and composite coatings that contain either polysaccharide or protein constituents to enhance coating effectiveness. / Master of Science

A floating treatment wetland (FTW) is an ecological approach which seeks to reduce point and nonpoint source pollution by installing substrate rooted plants grown on floating mats in open waters. While relatively novel, FTW use is increasing. A review of literature identified several research gaps, including: (1) assessments of the treatment performance of FTWs; (2) evaluations of FTWs in the U.S., particularly within wet ponds that receive urban runoff; and (3) plant temporal nutrient distribution, plant growth rate, and the long-term persistence of the FTWs in temperate regions with periodic ice encasement. An assessment model, i-FTW model, was developed, and its parameter s fitted based on data from 14 published FTW studies in the first research topic. The estimated median FTW apparent uptake velocity with 95% confidence interval were 0.048 (0.018 - 0.059) and 0.027 (0.016 - 0.040) m/day for total phosphorus (TP) and total nitrogen (TN), respectively. The i-FTW model provided a more accurate prediction in nutrient removal than two common performance metrics: removal rate (mg/m2/day) and removal efficiency (%). In the second research topic, the results of a mesocosm experiment indicated that FTWs with 61% coverage, planted with pickerelweed (Pontederia cordata L.) or softstem bulrush (Schoenoplectus tabernaemontani), significantly improved TP and TN removal efficiency of the control treatment by 8.2% and 18.2%, respectively. The pickerelweed exhibited significantly higher phosphorus and nitrogen removal than the softstem bulrush when water temperatures were greater than 25 deg C. Field observations in the third research topic found that pickerelweed demonstrated higher phosphorus removal performance (7.58 mg/plant) than softstem bulrush (1.62 mg/plant). Based on the observed seasonal changes in phosphorus distribution, harvest of above-ground vegetation is recommended to be conducted twice a year in June and September. Planted perennial macrophytes successfully adapted to stresses of the low dissolved oxygen (DO) concentrations (minimum: 1.2 mg/L), ice encasement, and relatively low nutrient concentrations in the water (median: 0.15 mg/L TP and 1.15 mg/L TN). Systematic observation of wildlife activities indicated eight classes of organisms inhabiting, foraging, breeding, nursing, or resting in the FTWs. Recommendations for FTW design and suggestions for further research are made based upon these findings. / Ph. D.

In the United States, the Energy Independence and Security Act of 2007 mandates the annual production of 136 billion liters of renewable fuel in the US by 2022 (US Congress, 2007). As the nation moves towards energy independence, it is critical to address the current challenges associated with large-scale biofuel production. The biomass logistics network considered consists of three core operations: farmgate operations, highway-hauling operations, and receiving facility operations. To date, decision-making has been limited in post-production management (harvesting, in-field hauling, and storage) in farmgate operations. In this thesis, we study the impacts in the logistics network resulting from the selection of one of four harvest scenarios. A simulation model was developed, which simulated the harvest and filling of a Satellite Storage Location (SSL), using conventional hay harvest equipment, specifically, a round baler. The model evaluated the impacts of four harvest scenarios (ranging from short, October-December, to extended, July-March), on baler equipment requirements, baler utilization, and the storage capacity requirements of round bales, across a harvest production region. The production region selected for this study encompassed a 32-km radius surrounding a hypothetical bio-crude plant in Gretna, VA, and considered 141 optimally selected SSLs. The production region was divided into 6 sub-regions (i.e. tours). The total production region consisted of 15,438 ha and 682 fields. The fields ranged in size from 6 to 156 ha. Of the four scenarios examined in the analysis, each displayed similar trends across the six tours. Variations in the baler requirements that were observed among the tours resulted from variability in field size distribution, field to baler allocations, and total production area. The available work hours were found to have a significant impact on the resource requirements to fulfill harvest operations and resource requirements were greatly reduced when harvest operations were extended throughout the 9-month harvest season. Beginning harvest in July and extending harvest through March resulted in reductions in round balers ranging from 50-63%, as compared to the short harvest scenario, on a sub-regional basis. On a regional basis, beginning harvest in July and extending harvest through March resulted in baler reductions up to 58.2%, as compared to the short harvest scenario. For a 9-month harvest, harvesting approximately 50% of total switchgrass harvest in July-September, as compared to harvesting approximately 50% in October-December, resulted in reductions in round balers ranging from 33.3- 43.5%. An extended (9-month) harvest resulted in the lowest annual baler requirements, and on average lower baler utilization rates. The reduced harvest scenarios, when compared to the extended harvest scenarios, resulted in a significant increase in the number of annual balers required for harvest operations. However, among the reduced harvest scenarios (i.e. Scenario 3 and 4), the number of annual balers required for harvest operations showed significantly less variation than between the extended harvest scenarios (i.e. Scenarios 1 and 2). As a result, an increased utilization of the balers in the system, short harvest scenarios resulted in the highest average baler utilization rates. Storage capacity requirements were however found to be greater for short harvest scenarios. For the reduced harvest scenario, employing an October-December harvest window, approximately 50% of harvest was completed by the end of October, and 100% of total harvest was completed by the third month of harvest (i.e. December). / Master of Science

Traditional sparkling wine (SW) production is a flourishing market that has experienced significant growth over the last few decades. SWs are regarded as premium products characterised by their high economic value. This prestige is attributed to the lengthy and costly manufacturing process involving a double fermentation step and a period of aging sur lie. In this regard, maintaining a consistently high-quality profile is crucial for consumer satisfaction and brand reputation. Any compromise in quality due to sensory faults can jeopardise the marketability of these products and erode their premium image. The appearance of sensorial faults is one of the main threats undermining the quality of SWs. Indeed, once the tirage has been done, the operational capacity of the winemaker to adjust the final result is very limited. Atypical ageing (ATA) is a wine aroma fault characterised by the vanishing of varietal aromas and the advent of unpleasant notes reminiscent of wet mop, dirty rag and naphthalene. These sensory faults can significantly impact the aromatic profile of SWs, diminishing their appeal to customers. Addressing ATA adds complexity to the production process. Winemakers must navigate potential issues during the second fermentation and ageing stages, making it essential to understand the factors contributing to the onset of this defect. Research has revealed that stress reactions in the vineyard, inadequate grape handling and unfavourable fermentation conditions are among the causes that lead to the appearance of this taint. Understanding these factors is crucial, especially considering the competitive nature of the sparkling wine market, where maintaining consistent quality is paramount. This doctoral research aimed to expand the knowledge of the root causes and potential remedies associated with ATA and SW production. The approach involved evaluating the agronomic and technological factors contributing to this defect. This encompassed field experiments, fermentation trials, and chemical analyses utilising an ultra-high-pressure liquid chromatographer coupled to a high-resolution mass spectrometer (UHPLC-HRMS). In addition to investigating the genesis of ATA, a crucial aspect of this research involved the development and validation of an analytical method to quickly and effectively quantify the amino acid (AA) content of oenological products. Since yeast biochemistry is involved in ATA formation, measuring the AA taking part in its formation is crucial. In this regard, specific attention was paid to tryptophan, a known ATA precursor. The method, employing a UHPLC-HRMS, was successfully applied to the compositional studies conducted during the experiments. The first field trial demonstrated that different production management systems (organic versus conventional) did not affect the development of ATA in wine. Conversely, the vintage year emerged as a more influential factor in the onset of this defect. Based on this finding, the second field trial aimed to evaluate the impact of soil water holding capacity (AWC) on ATA development. Interestingly, in a vintage characterised by reduced summer rainfall, grapevines planted on shallow soils (AWC &lt; 70 mm) generated wines more prone to be ATA-tainted. With regard to technological factors, the influence of second fermentation and bottle ageing was investigated and found to increase the likelihood of developing the sensorial fault. The research demonstrated that a simple accelerated ageing test carried out on the base wine is an adequate predictive tool to aid in forecasting the fate of the finished SWs. Furthermore, it was demonstrated how the oxygen radical absorbance capacity (ORAC) assay might help foresee the ATA taint during the commercialisation phase. Finally, considering that yeast derivatives (YDs) are often used during vinification to improve fermentation performance, their involvement in the occurrence of ATA was explored. It was discovered that these commercial formulations contain ATA-related compounds in variable amounts. Depending on their physicochemical composition resulting from the manufacturing process, their addition to grape must before fermentation might enhance or reduce the tendency of ATA appearance. In essence, this research contributes to the understanding of the intricacies of ATA and SW production AND provides valuable insights for winemakers to make informed decisions, ensuring the continued excellence of SWs in a competitive market.

Salvia miltiorrhiza is a traditional Chinese herbal medicine widely used to prevent and treat cardiovascular and other diseases. With the increasing awareness and use of herbal medicines worldwide, there has been a rapid increase in the use of medicinal plants in the United States. Currently, the majority of medicinal plants used in the US are imported from foreign countries. However, increasing concerns over safety such as heavy metal and chemical contaminations pose significant challenges to US pharmaceutical and related industries in sourcing quality plant materials. It is critical for US industries to have access to high-quality medicinal plants, which provides an opportunity for US farmers to incorporate medicinal plants as an alternative crop. The purpose of this study is to evaluate and identify adaptive cultivars and develop best management practices for Salvia miltiorrhiza production in Mississippi. Salvia miltiorrhiza seeds from different sources were sown and grown in a greenhouse at Mississippi State University (MSU) in 2019, 2020, and 2021. Plants were transplanted into a container or field located at MSU North Farm to evaluate cultivar performance and production practices including different seed sources, fertilization (0, 2, 4, 6, or 8 g N per plant from NH4NO3), planting density (20×30, 20×45, 30×30, 30×45, 40×30, 40×45 cm), and timing of harvest (60, 120, 180 days after transplanting). The data were processed by ANOVA using the PROC GLM procedure. The three seed sources tested in this study (V1, V2, and V3) differed in germination rates, maximum root lengths, and maximum root diameters in both years (2019, 2020). V1 and V2 had higher germination rates than V3. In general, plants treated with 6 or 8 g N per plant and plants planted in 30×45 or 40×45 cm had better performance in shoot growth, root growth, and content of bioactive compounds, including tanshinone I, tanshinone IIA, cryptotanshinone, and salvianolic acid B. Shoot growth, root growth, and content of bioactive compounds increased with increasing days to harvest after transplanting.