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• 3671. [Article] A UK perspective on marine renewable energy environmental research: Keeping up with a ‘Deploy & Monitor’ philosophy

  There are many drivers for the pursuit of renewable energy extraction from coastal seas. In the United Kingdom these include moving away from fossil fuels to mitigate the impacts of climate change, improving ...

  Citation × Citation Citation Abstract Copy Title: A UK perspective on marine renewable energy environmental research: Keeping up with a ‘Deploy & Monitor’ philosophy Author: Wilson, Ben There are many drivers for the pursuit of renewable energy extraction from coastal seas. In the United Kingdom these include moving away from fossil fuels to mitigate the impacts of climate change, improving energy security by diversifying supply options, increasing wealth generation in outlying coastal communities, and seeking alternative sources of power as existing infrastructure (power stations) near the end of their useful lives. In Scotland these drivers are particularly strong because of the additional factors of decline of North Sea oil reserves; the political pressure not to re-develop nuclear power plants; and the abundant offshore wind, wave and tidal-stream resources. While these drivers are strong, and backed up by ambitious political targets, a variety of constraints currently limit development of a vibrant marine renewables sector in UK coastal waters. In addition to financial, technological and logistical issues, a diversity of environmental restrictions limitprogress of the renewables sector. Many of these environmental issues actually stem from a lack of basic knowledge of how marine renewable energy devices are likely to interact with the receiving environment and vulnerable species (particularly those protected by European legislation such as the Habitats and Species as well as the Birds Directives). Furthermore where negative interactions are known, there may be limited knowledge about, or options for, mitigating these impacts. Strictly applying precautionary principals to these new and diverse technologies with respect to their potential local negative environmental impacts threatens to halt development of these technologies despite their potential benefits for global climate and other environmental issues. This problem applies particularly to wave and tidal-stream technologies which are diverse, new, and without track-record. To overcome this issue, the Scottish government is implementing a staged introduction of these technologies under what has been termed a “Survey-Deploy-&-Monitor” policy. That is, commercial scale devices are being placed singly or in small arrays (< 10 MW) into areas of pre-determined and acceptable environmental sensitivity and then impacts are being quantified through a monitoring program. In parallel to this approach, The Crown Estate (the seabed owner) has performed a series of licensing rounds to lease preferred sites to specific wind, wave and tidal-stream developers. If consented, these sites will represent commercial-scale developments of all three technologies in Scottish and wider UK waters. Part of that consenting progress requires that developers provide evidence (through Environmental Impact Studies and the production of Environmental Statements) that their developments will not harm the surrounding environment. It is these consenting exercises and related fundamental questions about impacts that are currently driving most of the environmental research related to offshore wind and marine renewable technologies in the UK. Research tends to fall into three divisions based on the source of funding and the geographic scope of the issues. At the smallest scale are studies of individual sites of interest to individual developers seeking consents for a specific technology. More generic studies funded by government or industry consortia may be performed to understand environmental issues surrounding a particular group of technologies, installation methods, or operational parameters. In this case, the actual site may be less important. Finally, fundamental research (funded by Research Councils) may be carried out to understand how and why animals use renewable energy relevant sites. Because there are a large number of research studies currently underway at a wide range of scales, sites, and taxa in Scotland and the wider UK, it is not possible to summarize them all in this short talk. Instead, I will outline examples of the three broad areas of environmental research (site/device specific, technology generic and more basic ecology). These examples have also been chosen because they represent an ongoing project, a recently established group of research studies, and a potential new research program. Some of the perhaps less intuitive lessons that have arisen from some of such projects include : 1. The responses of organisms may not be tied to particular brands of device or energy extraction, whether wind, wave, tidal-stream or even oil platform. For fouling organisms the particulars of the substrate might be the important factor rather than the device’s method of energy extraction. Likewise for fish it may be the device complexity and position in the water column that is key to their interactions. 2. Conversely, particular, seemingly unimportant features of devices may have relevance to marine organisms. For example, the color of a turbine may be extremely important for animals maneuvering around the rotors, a duct or the pile. 3. Test centers used to assess full-scale devices may seem like excellent places to also perform environmental research; however care must be taken as the devices in test centers are typically early generation prototypes and may be swapped out frequently. Furthermore activities by other companies at neighboring berths may invalidate site or device specific experiments. 4. Inter-annual variability does not suit the current pace of marine renewables development and careful consideration of the use of control sites and BACI designs should be made. 5. Cumulative impacts of multiple renewable and other developments offer a massive challenge to determining environmental impact. This difficulty represents a significant area of uncertainty for developers seeking consent and may encourage a development race with companies not wanting to have to consider their development relative to all of the others that preceded them. 6. Finally, while much effort is currently being devoted to gathering sufficient data to permit consent and early stage deployments, the significant investments only come when developers set up arrays capable of producing commercially relevant power. At this point there may be a step change in the degree of monitoring required of any potential environmental interactions. Should intolerable impacts be found, then mitigation will be urgently required or an exit strategy implemented. Title: A UK perspective on marine renewable energy environmental research: Keeping up with a ‘Deploy & Monitor’ philosophy Author: Wilson, Ben There are many drivers for the pursuit of renewable energy extraction from coastal seas. In the United Kingdom these include moving away from fossil fuels to mitigate the impacts of climate change, improving energy security by diversifying supply options, increasing wealth generation in outlying coastal communities, and seeking alternative sources of power as existing infrastructure (power stations) near the end of their useful lives. In Scotland these drivers are particularly strong because of the additional factors of decline of North Sea oil reserves; the political pressure not to re-develop nuclear power plants; and the abundant offshore wind, wave and tidal-stream resources. While these drivers are strong, and backed up by ambitious political targets, a variety of constraints currently limit development of a vibrant marine renewables sector in UK coastal waters. In addition to financial, technological and logistical issues, a diversity of environmental restrictions limitprogress of the renewables sector. Many of these environmental issues actually stem from a lack of basic knowledge of how marine renewable energy devices are likely to interact with the receiving environment and vulnerable species (particularly those protected by European legislation such as the Habitats and Species as well as the Birds Directives). Furthermore where negative interactions are known, there may be limited knowledge about, or options for, mitigating these impacts. Strictly applying precautionary principals to these new and diverse technologies with respect to their potential local negative environmental impacts threatens to halt development of these technologies despite their potential benefits for global climate and other environmental issues. This problem applies particularly to wave and tidal-stream technologies which are diverse, new, and without track-record. To overcome this issue, the Scottish government is implementing a staged introduction of these technologies under what has been termed a “Survey-Deploy-&-Monitor” policy. That is, commercial scale devices are being placed singly or in small arrays (< 10 MW) into areas of pre-determined and acceptable environmental sensitivity and then impacts are being quantified through a monitoring program. In parallel to this approach, The Crown Estate (the seabed owner) has performed a series of licensing rounds to lease preferred sites to specific wind, wave and tidal-stream developers. If consented, these sites will represent commercial-scale developments of all three technologies in Scottish and wider UK waters. Part of that consenting progress requires that developers provide evidence (through Environmental Impact Studies and the production of Environmental Statements) that their developments will not harm the surrounding environment. It is these consenting exercises and related fundamental questions about impacts that are currently driving most of the environmental research related to offshore wind and marine renewable technologies in the UK. Research tends to fall into three divisions based on the source of funding and the geographic scope of the issues. At the smallest scale are studies of individual sites of interest to individual developers seeking consents for a specific technology. More generic studies funded by government or industry consortia may be performed to understand environmental issues surrounding a particular group of technologies, installation methods, or operational parameters. In this case, the actual site may be less important. Finally, fundamental research (funded by Research Councils) may be carried out to understand how and why animals use renewable energy relevant sites. Because there are a large number of research studies currently underway at a wide range of scales, sites, and taxa in Scotland and the wider UK, it is not possible to summarize them all in this short talk. Instead, I will outline examples of the three broad areas of environmental research (site/device specific, technology generic and more basic ecology). These examples have also been chosen because they represent an ongoing project, a recently established group of research studies, and a potential new research program. Some of the perhaps less intuitive lessons that have arisen from some of such projects include : 1. The responses of organisms may not be tied to particular brands of device or energy extraction, whether wind, wave, tidal-stream or even oil platform. For fouling organisms the particulars of the substrate might be the important factor rather than the device’s method of energy extraction. Likewise for fish it may be the device complexity and position in the water column that is key to their interactions. 2. Conversely, particular, seemingly unimportant features of devices may have relevance to marine organisms. For example, the color of a turbine may be extremely important for animals maneuvering around the rotors, a duct or the pile. 3. Test centers used to assess full-scale devices may seem like excellent places to also perform environmental research; however care must be taken as the devices in test centers are typically early generation prototypes and may be swapped out frequently. Furthermore activities by other companies at neighboring berths may invalidate site or device specific experiments. 4. Inter-annual variability does not suit the current pace of marine renewables development and careful consideration of the use of control sites and BACI designs should be made. 5. Cumulative impacts of multiple renewable and other developments offer a massive challenge to determining environmental impact. This difficulty represents a significant area of uncertainty for developers seeking consent and may encourage a development race with companies not wanting to have to consider their development relative to all of the others that preceded them. 6. Finally, while much effort is currently being devoted to gathering sufficient data to permit consent and early stage deployments, the significant investments only come when developers set up arrays capable of producing commercially relevant power. At this point there may be a step change in the degree of monitoring required of any potential environmental interactions. Should intolerable impacts be found, then mitigation will be urgently required or an exit strategy implemented. Close

• 3672. [Article] Effects of Altered Habitats and Fishing Practices in Wind and Wave Farms

  Offshore renewable energy development (ORED) could induce local ecological changes, negatively affecting species of conservation interest. If well planned and coordinated, on the other hand, ORED could ...

  Citation × Citation Citation Abstract Copy Title: Effects of Altered Habitats and Fishing Practices in Wind and Wave Farms Author: Wilhelmsson, Dan Offshore renewable energy development (ORED) could induce local ecological changes, negatively affecting species of conservation interest. If well planned and coordinated, on the other hand, ORED could be beneficial to the marine environment in the region of device deployment in several respects. Because of the current scale and pace of offshore renewable energy development, interest is growing in the opportunities offered by the changes in fishing patterns that could result. Trawling, one of the most severe threats to the marine environment, particularly to fish and benthic invertebrate assemblages, will be prohibited or limited inside wind and wave farms. Areas of several square kilometres may therefore, in some important respects, resemble Marine Protected Areas; for areas that were previously trawled this exclusion could lead to average increases in biomass of motile organisms. Primary data from wind and wave farms are still scarce, but results to date from surveys targeting fish assemblages within offshore wind farms in Denmark, the Netherlands, and Sweden basically indicate either increased abundance of some fish species (e.g., sand eels (Ammodytidae), cod (Gadus morhua), whiting (Merlangius merlangus), sole (Solea solea)) or no effect compared to conditions before construction of the wind farm. Effects are likely to be most prominent for species that had been heavily exploited in the area prior to the wind or wave farm establishment. It is believed that a relatively large area of exclusion is required to enhance biodiversity and generate spill-over effects. Construction and deployment of artificial reefs (AR) in coastal waters is practiced worldwide to manage fisheries, mitigate damage to the environment, protect (i.e., from trawling) and facilitate the rehabilitation of certain habitats (e.g., spawning sites) or water bodies, or to increase the recreational value of an area (e.g., by providing opportunities for recreational diving and fishing). Unless animals are deterred by potential disturbances, such as noise, maintenance work, and electromagnetic fields from turbines, it is reasonable to expect offshore wind energy structures, and also foundations of some types of wave energy devices, to function as artificial reef modules and enhance local abundance of marine organisms, including commercially important fish and crustaceans. However, taxon- and age-specific responses of fishes to ARs vary greatly with AR design and position as well as by region and latitude. It can therefore be difficult to predict the structure of fish and crustacean assemblages associated with the submerged parts of wind and wave energy devices, as well as the radius of influence. Nevertheless, relatively recent studies targeting the potential for wind turbines and wave energy foundations to aggregate fish and motile invertebrates in Sweden, the Netherlands, Belgium, and Denmark suggest that densities of a number of fish and decapod species increase with proximity to these structures. Another category of artificial habitat is a Fish Aggregation Device (FAD), a floating structure deliberately placed on the surface or suspended in the water column to attract fish and enhance fishing efficiency. FADs are widely used in Asia and the western Indian Ocean. It has been suggested that floating offshore energy devices may function as FADs for pelagic fish, which could provide additional opportunities for fisheries management. Both ARs and FADs can have negative environmental and social effects if not properly planned and/or used. If ARs only aggregate fish from surrounding areas and do not contribute to added production, enhanced fishing efficiency in the AR area may aggravate overfishing if the new circumstances are not managed with caution. Similarly, increasing catchability, the main purpose of an FAD, may exacerbate the problem of overfishing on commercial species that are already at risk. ARs can also give rise to conflicts over user rights among fisher groups, and between recreational divers and fishers. Further, densities of benthic prey items have been shown to decrease with proximity to ARs due to predation by fish residing on the structures. FADs have been suggested as potential “ecological traps,” meaning that their presence could lure fish into remaining near the structures under non-optimal local feeding conditions, affecting physical condition and growth. Artificial structures may also provide habitats suitable for establishment of non-indigenous species; deployment of clusters of artificial structures may facilitate the establishment of new taxa in the recipient region by providing “beach heads” and stepping-stones. Non-indigenous sessile invertebrates have already been recorded at wind farms in the North Sea and the Baltic Sea. A range of design and location factors may influence the fish community structure on artificial reefs, such as height, size, inclination, protuberance, surface structure, void space and number of interior hollows, shade effects, distance between modules, isolation, and composition of the surrounding seabed. Research is underway to evaluate species-specific habitat preferences in the design of offshore energy foundations to optimize biomass of desired species, or alternatively, minimize artificial reef effects where desired. For example, in an experiment with wave energy foundations on the west coast of Sweden the potential for enhancing the abundance of associated fish and crustaceans through low-cost manipulations of the structural complexity of foundations was examined. Additional experiments will provide further guidance on the influence of different designs of foundations on commercially important fish and shellfish. This presentation will focus on the potential influence of offshore wind and wave farms on fish and commercially important crustaceans. The uncertainties with regard to positive and negative effects of on benthic and pelagic assemblages and specific species will also be discussed. The presentation will draw on results from a number of field studies and experiments conducted in offshore wind and wave farms, as well as on secondary literature on the influence of differently designed artificial habitats on benthic fauna. Title: Effects of Altered Habitats and Fishing Practices in Wind and Wave Farms Author: Wilhelmsson, Dan Offshore renewable energy development (ORED) could induce local ecological changes, negatively affecting species of conservation interest. If well planned and coordinated, on the other hand, ORED could be beneficial to the marine environment in the region of device deployment in several respects. Because of the current scale and pace of offshore renewable energy development, interest is growing in the opportunities offered by the changes in fishing patterns that could result. Trawling, one of the most severe threats to the marine environment, particularly to fish and benthic invertebrate assemblages, will be prohibited or limited inside wind and wave farms. Areas of several square kilometres may therefore, in some important respects, resemble Marine Protected Areas; for areas that were previously trawled this exclusion could lead to average increases in biomass of motile organisms. Primary data from wind and wave farms are still scarce, but results to date from surveys targeting fish assemblages within offshore wind farms in Denmark, the Netherlands, and Sweden basically indicate either increased abundance of some fish species (e.g., sand eels (Ammodytidae), cod (Gadus morhua), whiting (Merlangius merlangus), sole (Solea solea)) or no effect compared to conditions before construction of the wind farm. Effects are likely to be most prominent for species that had been heavily exploited in the area prior to the wind or wave farm establishment. It is believed that a relatively large area of exclusion is required to enhance biodiversity and generate spill-over effects. Construction and deployment of artificial reefs (AR) in coastal waters is practiced worldwide to manage fisheries, mitigate damage to the environment, protect (i.e., from trawling) and facilitate the rehabilitation of certain habitats (e.g., spawning sites) or water bodies, or to increase the recreational value of an area (e.g., by providing opportunities for recreational diving and fishing). Unless animals are deterred by potential disturbances, such as noise, maintenance work, and electromagnetic fields from turbines, it is reasonable to expect offshore wind energy structures, and also foundations of some types of wave energy devices, to function as artificial reef modules and enhance local abundance of marine organisms, including commercially important fish and crustaceans. However, taxon- and age-specific responses of fishes to ARs vary greatly with AR design and position as well as by region and latitude. It can therefore be difficult to predict the structure of fish and crustacean assemblages associated with the submerged parts of wind and wave energy devices, as well as the radius of influence. Nevertheless, relatively recent studies targeting the potential for wind turbines and wave energy foundations to aggregate fish and motile invertebrates in Sweden, the Netherlands, Belgium, and Denmark suggest that densities of a number of fish and decapod species increase with proximity to these structures. Another category of artificial habitat is a Fish Aggregation Device (FAD), a floating structure deliberately placed on the surface or suspended in the water column to attract fish and enhance fishing efficiency. FADs are widely used in Asia and the western Indian Ocean. It has been suggested that floating offshore energy devices may function as FADs for pelagic fish, which could provide additional opportunities for fisheries management. Both ARs and FADs can have negative environmental and social effects if not properly planned and/or used. If ARs only aggregate fish from surrounding areas and do not contribute to added production, enhanced fishing efficiency in the AR area may aggravate overfishing if the new circumstances are not managed with caution. Similarly, increasing catchability, the main purpose of an FAD, may exacerbate the problem of overfishing on commercial species that are already at risk. ARs can also give rise to conflicts over user rights among fisher groups, and between recreational divers and fishers. Further, densities of benthic prey items have been shown to decrease with proximity to ARs due to predation by fish residing on the structures. FADs have been suggested as potential “ecological traps,” meaning that their presence could lure fish into remaining near the structures under non-optimal local feeding conditions, affecting physical condition and growth. Artificial structures may also provide habitats suitable for establishment of non-indigenous species; deployment of clusters of artificial structures may facilitate the establishment of new taxa in the recipient region by providing “beach heads” and stepping-stones. Non-indigenous sessile invertebrates have already been recorded at wind farms in the North Sea and the Baltic Sea. A range of design and location factors may influence the fish community structure on artificial reefs, such as height, size, inclination, protuberance, surface structure, void space and number of interior hollows, shade effects, distance between modules, isolation, and composition of the surrounding seabed. Research is underway to evaluate species-specific habitat preferences in the design of offshore energy foundations to optimize biomass of desired species, or alternatively, minimize artificial reef effects where desired. For example, in an experiment with wave energy foundations on the west coast of Sweden the potential for enhancing the abundance of associated fish and crustaceans through low-cost manipulations of the structural complexity of foundations was examined. Additional experiments will provide further guidance on the influence of different designs of foundations on commercially important fish and shellfish. This presentation will focus on the potential influence of offshore wind and wave farms on fish and commercially important crustaceans. The uncertainties with regard to positive and negative effects of on benthic and pelagic assemblages and specific species will also be discussed. The presentation will draw on results from a number of field studies and experiments conducted in offshore wind and wave farms, as well as on secondary literature on the influence of differently designed artificial habitats on benthic fauna. Close

• 3673. [Article] Potential effects of climate change and fire management on fire behavior and vegetation patterns on an east Cascades landscape

  Climate exerts considerable control on wildfire regimes, and climate and wildfire are both major drivers of forest growth and succession in interior Northwest forests. Estimating potential response of ...

  Citation × Citation Citation Abstract Copy Title: Potential effects of climate change and fire management on fire behavior and vegetation patterns on an east Cascades landscape Author: Greaves, Heather E. Climate exerts considerable control on wildfire regimes, and climate and wildfire are both major drivers of forest growth and succession in interior Northwest forests. Estimating potential response of these landscapes to anticipated changes in climate helps researchers and land managers understand and mitigate impacts of climate change on important ecological and economic resources. Spatially explicit, mechanistic computer simulation models are powerful tools that permit researchers to incorporate climate and disturbance events along with vegetation physiology and phenology to explore complex potential effects of climate change over wide spatial and temporal scales. In this thesis, I used the simulation model FireBGCv2 to characterize potential response of fire, vegetation, and landscape dynamics to a range of possible future climate and fire management scenarios. The simulation landscape (~43,000 hectares) is part of Deschutes National Forest, which is located at the interface of maritime and continental climates and is known for its beauty and ecological diversity. Simulation scenarios included all combinations of +0°C, +3°C, and +6°C of warming; +10%, ±0%, and -10% historical precipitation; and 10% and 90% fire suppression, and were run for 500 years. To characterize fire dynamics, I investigated how mean fire frequency, intensity, and fuel loadings changed over time in all scenarios, and how fire and tree mortality interacted over time. To explore vegetation and landscape dynamics, I described the distribution and spatial arrangement of vegetation types and forest successional stages on the landscape, and used a nonmetric multidimensional scaling (NMS) ordination to holistically evaluate overall similarity of composition, structure, and landscape pattern among all simulation scenarios over time. Changes in precipitation had little effect on fire characteristics or vegetation and landscape characteristics, indicating that simulated precipitation changes were not sufficient to significantly affect vegetation moisture stress or fire behavior on this landscape. Current heavy fuel loads controlled early fire dynamics, with high mean fire intensities occurring early in all simulations. Increases in fire frequency accompanied all temperature increases, leading to decreasing fuel loads and fire intensities over time in warming scenarios. With no increase in temperature or in fire frequency, high fire intensities and heavier fuel loads were sustained. Over time, more fire associated with warming or less fire suppression increased the percentage of the landscape occupied by non-forest and fire-sensitive early seral forest successional stages, which tended to increase the percentage of fire area burning at high severity (in terms of tree mortality). This fire-vegetation relationship may reflect a return to a more historical range of conditions on this landscape. Higher temperatures and fire frequency led to significant spatial migration of forest types across the landscape, with communities at the highest and lowest elevations particularly affected. Warming led to an upslope shift of warm mixed conifer and ponderosa pine (Pinus ponderosa) forests, severely contracting (under 3° of warming) or eliminating (under 6° of warming) area dominated by mountain hemlock (Tsuga mertensiana) and cool, wet conifer forest in the high western portion of the landscape. In lower elevations, warming and fire together contributed to significant expansion of open (<10% tree canopy cover) forest and grass- and shrubland. The compositional changes and spatial shifts simulated in the warming scenarios suggest that climate change is likely to significantly affect forests on this landscape. Warming and associated fire also tended to increase heterogeneity of forest structural stages and landscape pattern, resulting in a more diverse distribution of structural stages, especially in lower elevations, and a more divided landscape of smaller forest stands. The NMS ordination emphasized the dissimilarity between the severe +6° scenarios and the other two temperature scenarios. The +0° and +3° scenarios differed from each other in composition (mainly because cool forest was lost in the +3° scenarios), but within a given level of fire suppression they remained remarkably similar in terms of overall composition, structure, and landscape pattern, while the +6° scenarios separated noticeably from them. Such decisive differences suggest that under the simulated ranges of precipitation and fire suppression, the interval between 3 and 6 degrees of warming on this landscape may capture an ecological threshold, or tipping point. Additional simulation research that incorporates (for example) management actions, insects and pathogens, and a wider array of precipitation scenarios could help illuminate more clearly the possible range of future landscape conditions. Still, these results provide a glimpse of potential divergent outcomes on this important landscape under possible future climates, and suggest that these forests will undergo considerable changes from both historical and current conditions in response to higher temperatures expected in this area. Some changes may be inevitable with warming, such as the upslope shift of warm forest types, but careful planning for fire and fuels management might allow land managers to modulate fire behavior and steer vegetation dynamics toward the most desirable outcome possible. Title: Potential effects of climate change and fire management on fire behavior and vegetation patterns on an east Cascades landscape Author: Greaves, Heather E. Climate exerts considerable control on wildfire regimes, and climate and wildfire are both major drivers of forest growth and succession in interior Northwest forests. Estimating potential response of these landscapes to anticipated changes in climate helps researchers and land managers understand and mitigate impacts of climate change on important ecological and economic resources. Spatially explicit, mechanistic computer simulation models are powerful tools that permit researchers to incorporate climate and disturbance events along with vegetation physiology and phenology to explore complex potential effects of climate change over wide spatial and temporal scales. In this thesis, I used the simulation model FireBGCv2 to characterize potential response of fire, vegetation, and landscape dynamics to a range of possible future climate and fire management scenarios. The simulation landscape (~43,000 hectares) is part of Deschutes National Forest, which is located at the interface of maritime and continental climates and is known for its beauty and ecological diversity. Simulation scenarios included all combinations of +0°C, +3°C, and +6°C of warming; +10%, ±0%, and -10% historical precipitation; and 10% and 90% fire suppression, and were run for 500 years. To characterize fire dynamics, I investigated how mean fire frequency, intensity, and fuel loadings changed over time in all scenarios, and how fire and tree mortality interacted over time. To explore vegetation and landscape dynamics, I described the distribution and spatial arrangement of vegetation types and forest successional stages on the landscape, and used a nonmetric multidimensional scaling (NMS) ordination to holistically evaluate overall similarity of composition, structure, and landscape pattern among all simulation scenarios over time. Changes in precipitation had little effect on fire characteristics or vegetation and landscape characteristics, indicating that simulated precipitation changes were not sufficient to significantly affect vegetation moisture stress or fire behavior on this landscape. Current heavy fuel loads controlled early fire dynamics, with high mean fire intensities occurring early in all simulations. Increases in fire frequency accompanied all temperature increases, leading to decreasing fuel loads and fire intensities over time in warming scenarios. With no increase in temperature or in fire frequency, high fire intensities and heavier fuel loads were sustained. Over time, more fire associated with warming or less fire suppression increased the percentage of the landscape occupied by non-forest and fire-sensitive early seral forest successional stages, which tended to increase the percentage of fire area burning at high severity (in terms of tree mortality). This fire-vegetation relationship may reflect a return to a more historical range of conditions on this landscape. Higher temperatures and fire frequency led to significant spatial migration of forest types across the landscape, with communities at the highest and lowest elevations particularly affected. Warming led to an upslope shift of warm mixed conifer and ponderosa pine (Pinus ponderosa) forests, severely contracting (under 3° of warming) or eliminating (under 6° of warming) area dominated by mountain hemlock (Tsuga mertensiana) and cool, wet conifer forest in the high western portion of the landscape. In lower elevations, warming and fire together contributed to significant expansion of open (<10% tree canopy cover) forest and grass- and shrubland. The compositional changes and spatial shifts simulated in the warming scenarios suggest that climate change is likely to significantly affect forests on this landscape. Warming and associated fire also tended to increase heterogeneity of forest structural stages and landscape pattern, resulting in a more diverse distribution of structural stages, especially in lower elevations, and a more divided landscape of smaller forest stands. The NMS ordination emphasized the dissimilarity between the severe +6° scenarios and the other two temperature scenarios. The +0° and +3° scenarios differed from each other in composition (mainly because cool forest was lost in the +3° scenarios), but within a given level of fire suppression they remained remarkably similar in terms of overall composition, structure, and landscape pattern, while the +6° scenarios separated noticeably from them. Such decisive differences suggest that under the simulated ranges of precipitation and fire suppression, the interval between 3 and 6 degrees of warming on this landscape may capture an ecological threshold, or tipping point. Additional simulation research that incorporates (for example) management actions, insects and pathogens, and a wider array of precipitation scenarios could help illuminate more clearly the possible range of future landscape conditions. Still, these results provide a glimpse of potential divergent outcomes on this important landscape under possible future climates, and suggest that these forests will undergo considerable changes from both historical and current conditions in response to higher temperatures expected in this area. Some changes may be inevitable with warming, such as the upslope shift of warm forest types, but careful planning for fire and fuels management might allow land managers to modulate fire behavior and steer vegetation dynamics toward the most desirable outcome possible. Close

• 3674. [Article] Breeding an open pollinated broccoli for organic production systems using participatory methods

  Organic agriculture is an important and growing sector of U.S. and world food production. Consumers are increasingly aware of and interested in the production practices and impacts associated with agriculture ...

  Citation × Citation Citation Abstract Copy Title: Breeding an open pollinated broccoli for organic production systems using participatory methods Author: McKenzie, Laurie R. Organic agriculture is an important and growing sector of U.S. and world food production. Consumers are increasingly aware of and interested in the production practices and impacts associated with agriculture and as such, are showing a preference for sustainably produced, raised, and harvested foods. In order to continue to meet the growing demand for organic produce, organic growers need cultivars that are optimally adapted to organic and low input conditions. Quality seed is the foundation of any functional and stable farming system. Unfortunately the lack of organically bred and produced seed is hindering the continued growth and success of organic farming. Meeting the needs of the organic sector has been a challenge for the seed industry; it is an industry that often doesn't understand the specific and unique requirements associated with the diversity of environmental and market demands of organic systems. However, organic farmers and the organic food systems they supply, require a robust organic seed system that is appropriately adapted to regional agronomic challenges and market needs, meets standards and regulations, and encompasses the social and ecological values of organic agriculture. One plausible approach to meeting the cultivar and seed needs of organic and low input production systems is through the use of participatory plant breeding (PPB). PPB is a collaborative approach for identifying and developing genetically diverse plant material and varieties involving partnerships among formal sector breeders and researchers, farmers, extension agents, educators, and end users. Participatory plant breeding fundamentally changes the way that formal breeding programs and farmers manage germplasm and plant genetic resources. Typically, formal breeding programs restrict access to germplasm and breeding materials and only supply farmers with finished varieties. In PPB, farmers are involved in the early stages of creation and evaluation of germplasm and breeding material, and stay engaged with the breeding process until new varieties are created. PPB is an excellent model for breeding specifically for organic systems because organic systems in developed countries have many similarities to low-input agricultural systems in the developing world. Some of these parallels include heterogeneous growing environments, a wide range of end uses and marketing strategies, lack of suitably adapted and/or derived varieties, lack of attention from the formal seed sector, and a reduced reliance on synthetic inputs (compared to conventional systems). Breeding for organic systems is a relatively young field and breeders in the formal sector do not have a good handle on what traits are important for robust production under organic conditions. Thus the opportunity to meld farmers' experience and knowledge with breeders' expertise is an effective way to breed for organic production systems. The purpose of this project was to investigate and explore the opportunities and challenges of organic plant breeding using participatory research methods. This research had three goals: 1) to develop an open pollinated broccoli with contemporary quality traits for organic production systems using participatory strategies; 2) to compare broccoli selections made by formally trained plant breeders and farmer breeders; and 3) to capture the stories and experiences of the formal breeders and farmer breeders involved with this broccoli material in order to contribute to the growing wealth of knowledge on collaborative and organic breeding work. The Oregon State University Vegetable Breeding Program made significant progress towards decreasing the variability of the broccoli project material through three successive years of modified half-sibling selections. Evaluations and selections were based more strongly on quality traits rather than soley on production traits such as yield. Although progress was incremental and statistically verified in only three out of the fifteen quality traits, we observed trends in the data indicating progress towards an increasingly uniform, stable, and reliable open pollinated broccoli with specific adaptation for organic production systems. There were very few differences between broccoli materials developed by formally trained plant breeders and farmer breeders. This was especially true for the three cultivars developed in the Pacific Northwest (PNW) (one in Washington and two in Oregon). The 'East Coast' population, which had been collaboratively selected by formal and farmer breeders in New York, expressed significantly distinct differences from the PNW materials. When the farmer breeder and formal breeder materials were pooled together and compared to pooled check cultivars they expressed significant differences for nearly all traits across all years. This demonstrated that all of the collaboratively developed open pollinated materials are distinctly different from the F1 hybrids currently available. Our work has demonstrated a few of the myriad of positive outcomes achievable with the use of participatory plant breeding for organic production systems. The participatory nature of this project resulted in increased confidence and feelings of empowerment for all involved. Both farmers and breeders felt their involvement was socially beneficial and widened their networking and seed community circles. The farmer-bred cultivar 'Solstice' is now available as a result of Jonathan Spero's work, and a cultivar tentatively named 'Benton' is about to be released for sale through Oregon State University. Our results agree with previous study findings that formal and farmer breeder selections are often not distinctly different; thus providing evidence for continuing to support the involvement and education of farmers in plant breeding, especially in reference to organic production systems. This study demonstrates the potential of collaboratively developed and farmer-bred cultivars to become viable and vibrant open pollinated alternatives to the current open pollinated cultivars on the market today. Title: Breeding an open pollinated broccoli for organic production systems using participatory methods Author: McKenzie, Laurie R. Organic agriculture is an important and growing sector of U.S. and world food production. Consumers are increasingly aware of and interested in the production practices and impacts associated with agriculture and as such, are showing a preference for sustainably produced, raised, and harvested foods. In order to continue to meet the growing demand for organic produce, organic growers need cultivars that are optimally adapted to organic and low input conditions. Quality seed is the foundation of any functional and stable farming system. Unfortunately the lack of organically bred and produced seed is hindering the continued growth and success of organic farming. Meeting the needs of the organic sector has been a challenge for the seed industry; it is an industry that often doesn't understand the specific and unique requirements associated with the diversity of environmental and market demands of organic systems. However, organic farmers and the organic food systems they supply, require a robust organic seed system that is appropriately adapted to regional agronomic challenges and market needs, meets standards and regulations, and encompasses the social and ecological values of organic agriculture. One plausible approach to meeting the cultivar and seed needs of organic and low input production systems is through the use of participatory plant breeding (PPB). PPB is a collaborative approach for identifying and developing genetically diverse plant material and varieties involving partnerships among formal sector breeders and researchers, farmers, extension agents, educators, and end users. Participatory plant breeding fundamentally changes the way that formal breeding programs and farmers manage germplasm and plant genetic resources. Typically, formal breeding programs restrict access to germplasm and breeding materials and only supply farmers with finished varieties. In PPB, farmers are involved in the early stages of creation and evaluation of germplasm and breeding material, and stay engaged with the breeding process until new varieties are created. PPB is an excellent model for breeding specifically for organic systems because organic systems in developed countries have many similarities to low-input agricultural systems in the developing world. Some of these parallels include heterogeneous growing environments, a wide range of end uses and marketing strategies, lack of suitably adapted and/or derived varieties, lack of attention from the formal seed sector, and a reduced reliance on synthetic inputs (compared to conventional systems). Breeding for organic systems is a relatively young field and breeders in the formal sector do not have a good handle on what traits are important for robust production under organic conditions. Thus the opportunity to meld farmers' experience and knowledge with breeders' expertise is an effective way to breed for organic production systems. The purpose of this project was to investigate and explore the opportunities and challenges of organic plant breeding using participatory research methods. This research had three goals: 1) to develop an open pollinated broccoli with contemporary quality traits for organic production systems using participatory strategies; 2) to compare broccoli selections made by formally trained plant breeders and farmer breeders; and 3) to capture the stories and experiences of the formal breeders and farmer breeders involved with this broccoli material in order to contribute to the growing wealth of knowledge on collaborative and organic breeding work. The Oregon State University Vegetable Breeding Program made significant progress towards decreasing the variability of the broccoli project material through three successive years of modified half-sibling selections. Evaluations and selections were based more strongly on quality traits rather than soley on production traits such as yield. Although progress was incremental and statistically verified in only three out of the fifteen quality traits, we observed trends in the data indicating progress towards an increasingly uniform, stable, and reliable open pollinated broccoli with specific adaptation for organic production systems. There were very few differences between broccoli materials developed by formally trained plant breeders and farmer breeders. This was especially true for the three cultivars developed in the Pacific Northwest (PNW) (one in Washington and two in Oregon). The 'East Coast' population, which had been collaboratively selected by formal and farmer breeders in New York, expressed significantly distinct differences from the PNW materials. When the farmer breeder and formal breeder materials were pooled together and compared to pooled check cultivars they expressed significant differences for nearly all traits across all years. This demonstrated that all of the collaboratively developed open pollinated materials are distinctly different from the F1 hybrids currently available. Our work has demonstrated a few of the myriad of positive outcomes achievable with the use of participatory plant breeding for organic production systems. The participatory nature of this project resulted in increased confidence and feelings of empowerment for all involved. Both farmers and breeders felt their involvement was socially beneficial and widened their networking and seed community circles. The farmer-bred cultivar 'Solstice' is now available as a result of Jonathan Spero's work, and a cultivar tentatively named 'Benton' is about to be released for sale through Oregon State University. Our results agree with previous study findings that formal and farmer breeder selections are often not distinctly different; thus providing evidence for continuing to support the involvement and education of farmers in plant breeding, especially in reference to organic production systems. This study demonstrates the potential of collaboratively developed and farmer-bred cultivars to become viable and vibrant open pollinated alternatives to the current open pollinated cultivars on the market today. Close

• 3675. [Article] Identifying habitat factors for canary rockfish (Sebastes pinniger) off Washington and Oregon using environmental data and trawl logbooks

  If fisheries managers are to effectively manage commercially exploited fish populations, a basic understanding of the factors that influence fish distribution and abundance is required. In 2005, efforts ...

  Citation × Citation Citation Abstract Copy Title: Identifying habitat factors for canary rockfish (Sebastes pinniger) off Washington and Oregon using environmental data and trawl logbooks Author: Vestfals, Cathleen D. If fisheries managers are to effectively manage commercially exploited fish populations, a basic understanding of the factors that influence fish distribution and abundance is required. In 2005, efforts to identify Essential Fish Habitat (EFH) for the 82 groundfish species managed by the Pacific Fishery Management Council along the West Coast resulted in the entire continental margin being designated as EFH. Clearly, our knowledge of EFH needs to be refined, which can be accomplished by gaining insight into how environmental variables shape the distribution of managed species. Habitat is commonly used to describe a set of environmental variables that are thought to influence occupancy. The aim of this thesis research is to detect and analyze the quantitative relationships between canary rockfish (Sebastes pinniger) presence/absence data, their spatial distribution, and various biotic and abiotic factors. The presence of canary rockfish at various locations was correlated against co-located environmental variables including bottom depths, temperatures, locations (latitude and longitude), seafloor substrate types, canary rockfish hotspots, and the presence/absence of other groundfish and invertebrate species. The statistical analysis was conducted using the generalized additive model (GAM), which is a nonparametric regression technique very well suited to model nonlinear speciesenvironment interactions. The GAM analysis was conducted using information collected from four different data sources. Data collected by the Alaska Fisheries Science Center (AFSC) from 1986 to 2001 provided information at distinct locations and times on the presence/absence of canary rockfish and other groundfish and invertebrate species, and associated depths and temperatures. Seafloor lithology maps for Oregon and Washington and 100-meter gridded bathymetric data, obtained from the Active Tectonics and Seafloor Mapping Lab at Oregon State University, provided information on the physical characteristics of the seafloor. These data were used in conjunction with the AFSC bottom trawl survey data to investigate the relationships between substrate type, slope and rugosity, and the presence of canary rockfish. Finally, locations of canary rockfish hotspots, or areas with high canary rockfish catch, were identified from Oregon commercial trawl logbook data (1995-2001) and provided information on distinct areas where the trawl fishing fleet had successfully caught canary rockfish in the past. Canary rockfish presence in trawl survey tows was associated with specific locations and ranges of bathymetry, temperatures, and substrate types, as well as proximity to canary rockfish hotspots, and particular fish and invertebrate communities. Survey year had a strong effect on the presence of canary rockfish, as did location (latitude and longitude) and depth. The geographic location of a survey tow had a negative effect on the presence of canary rockfish in the nearshore region, and a positive effect the further the location was from the coastline, with canary rockfish presence being highest off the Washington coast between 47.5°N and 48.5°N. While canary rockfish were found at depths between 57 m and 307 m in the survey, the majority of the tows with canary rockfish catch, over 90%, occurred between the depths of 57 m and 199 m. Though temperature did not have a significant effect on canary rockfish presence in the GAM, canary rockfish were associated with specific temperature ranges, only being caught at temperatures between 6.2°C and 9.0°C in the survey. Over 89% of the tows with canary rockfish catch occurred between 6.2°C and 7.9°C. Since temperature and bottom depth of the trawl survey tows were highly correlated, it was difficult to determine which variable was the causative factor in determining the probability of a canary rockfish being present. Canary rockfish presence was higher in survey tows made closer to canary rockfish hotspots, as well as hard bottom types. Finally, the presence of lingcod, yellowtail, silvergray, or redstripe rockfish in a survey tow increased the likelihood of canary rockfish being present, as did the presence of basketstars and corals. By studying the relationships between species and their environment, we can begin to understand the relative importance of how environmental variables shape the distribution of managed species. For ecosystem-based management strategies to be successful, the functional relationships between organisms and their habitat must be understood. The predictive model developed in this study can be used to identify areas off Oregon and Washington where canary rockfish are likely to be found in relation to various habitat factors, and can potentially be used to delineate areas that should be sampled in future surveys of canary rockfish. Additionally, this research will help to improve our understanding of the factors that influence canary rockfish distribution, which may produce a more realistic definition of canary rockfish habitat, and improve assessment. This study specifically focuses on canary rockfish, because this species currently constrains many West Coast fisheries for groundfish, however, the methods outlined here could be applied more generally to other species of interest. Title: Identifying habitat factors for canary rockfish (Sebastes pinniger) off Washington and Oregon using environmental data and trawl logbooks Author: Vestfals, Cathleen D. If fisheries managers are to effectively manage commercially exploited fish populations, a basic understanding of the factors that influence fish distribution and abundance is required. In 2005, efforts to identify Essential Fish Habitat (EFH) for the 82 groundfish species managed by the Pacific Fishery Management Council along the West Coast resulted in the entire continental margin being designated as EFH. Clearly, our knowledge of EFH needs to be refined, which can be accomplished by gaining insight into how environmental variables shape the distribution of managed species. Habitat is commonly used to describe a set of environmental variables that are thought to influence occupancy. The aim of this thesis research is to detect and analyze the quantitative relationships between canary rockfish (Sebastes pinniger) presence/absence data, their spatial distribution, and various biotic and abiotic factors. The presence of canary rockfish at various locations was correlated against co-located environmental variables including bottom depths, temperatures, locations (latitude and longitude), seafloor substrate types, canary rockfish hotspots, and the presence/absence of other groundfish and invertebrate species. The statistical analysis was conducted using the generalized additive model (GAM), which is a nonparametric regression technique very well suited to model nonlinear speciesenvironment interactions. The GAM analysis was conducted using information collected from four different data sources. Data collected by the Alaska Fisheries Science Center (AFSC) from 1986 to 2001 provided information at distinct locations and times on the presence/absence of canary rockfish and other groundfish and invertebrate species, and associated depths and temperatures. Seafloor lithology maps for Oregon and Washington and 100-meter gridded bathymetric data, obtained from the Active Tectonics and Seafloor Mapping Lab at Oregon State University, provided information on the physical characteristics of the seafloor. These data were used in conjunction with the AFSC bottom trawl survey data to investigate the relationships between substrate type, slope and rugosity, and the presence of canary rockfish. Finally, locations of canary rockfish hotspots, or areas with high canary rockfish catch, were identified from Oregon commercial trawl logbook data (1995-2001) and provided information on distinct areas where the trawl fishing fleet had successfully caught canary rockfish in the past. Canary rockfish presence in trawl survey tows was associated with specific locations and ranges of bathymetry, temperatures, and substrate types, as well as proximity to canary rockfish hotspots, and particular fish and invertebrate communities. Survey year had a strong effect on the presence of canary rockfish, as did location (latitude and longitude) and depth. The geographic location of a survey tow had a negative effect on the presence of canary rockfish in the nearshore region, and a positive effect the further the location was from the coastline, with canary rockfish presence being highest off the Washington coast between 47.5°N and 48.5°N. While canary rockfish were found at depths between 57 m and 307 m in the survey, the majority of the tows with canary rockfish catch, over 90%, occurred between the depths of 57 m and 199 m. Though temperature did not have a significant effect on canary rockfish presence in the GAM, canary rockfish were associated with specific temperature ranges, only being caught at temperatures between 6.2°C and 9.0°C in the survey. Over 89% of the tows with canary rockfish catch occurred between 6.2°C and 7.9°C. Since temperature and bottom depth of the trawl survey tows were highly correlated, it was difficult to determine which variable was the causative factor in determining the probability of a canary rockfish being present. Canary rockfish presence was higher in survey tows made closer to canary rockfish hotspots, as well as hard bottom types. Finally, the presence of lingcod, yellowtail, silvergray, or redstripe rockfish in a survey tow increased the likelihood of canary rockfish being present, as did the presence of basketstars and corals. By studying the relationships between species and their environment, we can begin to understand the relative importance of how environmental variables shape the distribution of managed species. For ecosystem-based management strategies to be successful, the functional relationships between organisms and their habitat must be understood. The predictive model developed in this study can be used to identify areas off Oregon and Washington where canary rockfish are likely to be found in relation to various habitat factors, and can potentially be used to delineate areas that should be sampled in future surveys of canary rockfish. Additionally, this research will help to improve our understanding of the factors that influence canary rockfish distribution, which may produce a more realistic definition of canary rockfish habitat, and improve assessment. This study specifically focuses on canary rockfish, because this species currently constrains many West Coast fisheries for groundfish, however, the methods outlined here could be applied more generally to other species of interest. Close

• 3676. [Article] Survival Assessment, Inactivation Kinetics Models, and Farm-to-Table Quantitative Risk Analysis of Food Pathogens

  About 48 million cases of Foodborne illnesses (FBIs) are estimated to occur every year in the US. These are diseases caused by contamination of foods with bacteria, viruses, protozoa, parasites and toxic ...

  Citation × Citation Citation Abstract Copy Title: Survival Assessment, Inactivation Kinetics Models, and Farm-to-Table Quantitative Risk Analysis of Food Pathogens Author: Deng, Kai About 48 million cases of Foodborne illnesses (FBIs) are estimated to occur every year in the US. These are diseases caused by contamination of foods with bacteria, viruses, protozoa, parasites and toxic chemicals. Clostridium difficile infections (CDIs) are an important health-care and community associated problem. Since C. difficile spores have been frequently isolates from meat product, this pathogen should be considered an emerging food pathogen. Low temperature and reduced water activity (a[subscript w]) are commonly used methods to preserve meats and meat products. Chapter 3 covers studies on the viability of C. difficile spores during 4 months at -80°C, -20°C, refrigeration (4°C) and room temperature (20°C), and after ten freeze-thaw cycles (10 cycles). Two epidemic strains, R20291 (PCR ribotype 027, human isolate) and M120 (PCR ribotype 078, animal isolate), were used in this published study. At 20°C and -80°C, the spore viability of both strains declined with storage time. The viability of M120 spores also declined during storage at 4°C and 20°C. Although no significant changes were observed in the viability of R20291 spores stored at 4°C, their significant viability increase when stored at 20°C is most remarkable and raises food safety concerns. Finally, the viability of both strains decreased when subjected to ten freeze-thaw cycles. In summary, this study provides evidence that C. difficile spores can survive the room and low temperature conditions found in food processing, storage and distribution. Chapter 4 covers studies on the aw effect on the viability of C. difficile spores stored at room temperature. In addition to the spores of the strains previously described, spores of a food isolate strain, C. difficile DK1 (unidentified ribotype), were included in this study. The viability of their spores during 3 months at room temperature in phosphate buffer saline (PBS) at a[subscript w] of ~1.00, 0.82 and 0.72, and in commercial samples of beef jerky with a[subscript w] 0.82 and 0.72 was investigated. Spores of the strains M120 and DK1 showed a ~1 decimal reduction after 3 months in PBS kept at room temperature, while no significant changes in spore viability were observed in the reduced a[subscript w] beef jerky. The steady and significant 2 decimal increase in the viability of R20291 spores in PBS and ~1 decimal increase in the beef jerky during the 3-month storage raises again food safety concerns. This study provides evidence that beef jerky enhanced spore survival and viability during room temperature storage. Furthermore, it suggests that R20291 spores lost superdormancy but the mechanism involved remains to be determined. Changes in the surface hydrophobicity of C. difficile spores have been reported to be associated with the loss of the exosporium and an increase in their viability. In this study, the R20291 spore viability increase during room temperature storage was not associated with a change in surface hydrophobicity. Chapter 5 covers the determination and modeling of the thermal resistance of spores of the C. difficile strains M120 and DK1. They were treated at 70, 75, 80 and 85°C in PBS buffer and at 80°C in sterile ground beef. Linear 1.5 and 0.8 decimal reductions for strains M120 and DK1, respectively, were observed in PBS after 60 min at 70°C. At higher temperatures, non-linear inactivation reached 3.2 and 1.6 decimal reductions in 32 min at 75°C, and 3.1 and 2.9 decimal reductions in 24 min at 80°C, respectively. During come-up time to 85°C, a 1.1 decimal reduction was observed for M120 but none for DK1. Spores of M120 and DK1 strains in ground beef showed a 1.6 and 1.4 decimal ¬reductions, respectively, after 24 min at 80°C, i.e., a much lower value than in PBS. The modified Gompertz model for nonlinear microbial activation fitted the spore inactivation in PBS data better than the Weibull model yielding smaller maximum inactivation levels (A), faster maximum inactivation rates (μ[subscript max]), and shorter lag times (λ) for strain M120 than DK1. This study confirmed the high resistance of C. difficile spores suggesting the need to lower their presence in animal meat products. Chapter 6 focuses on the development of a model for the microbial inactivation achieved by a novel food processing technology, high pressure carbon dioxide (HPCD). The non-linear survival curves for the microbial inactivation by HPCD depend on the processing temperature and CO₂ pressure. In this study, the nonlinear inactivation of Escherichia coli CGMCC1.90 in apple juice by HPCD treatments was best described using a modified Gompertz primary model and the secondary models for its parameters b(T,P)=14.21+0.011P-0.67T+0.0085T² and c(T,P)= -0.10 +0.0023P+0.0037T (T and P in °C and MPa). Monte Carlo simulations were used to incorporate the variability and uncertainty of the parameter b and c estimates, which were then used to predict microbial inactivation values for a given time, temperature and CO₂ pressure combination and desired confidence boundary. The model predicts that HPCD processes can meet 5 decimal reduction at 95% confidence but at relative long apple juice processing times, i.e., 35-124 min treatments in the experimental temperature and pressure range of 32-42°C and 10-30 MPa, respectively. Risk assessments of food microbial safety have become a valuable tool to understand, analyze and control microbial risks. They address the pathogen source, load reduction by processing, and pathogen survival during storage and distribution in a quantitative manner. Chapter 7 describes a Monte Carlo based quantitative microbial risk assessment tool developed for the consumption of raw oysters potentially contaminated with the pathogen Vibrio vulnificus. It predicted that depuration at 15°C for 47 and 16 h would reduce the risk of oysters harvested during the warm (Jun-Aug) and transition seasons (Apr-May, Oct-Nov), respectively, to an acceptable level. Furthermore, the model predicted that the consumption of untreated raw oysters harvested during the cold season (Dec-Mar) can be considered an acceptable and very low risk. Moreover, the model can be adjusted by an individual processor to reflect the conditions at their specific location. This study demonstrated that Monte Carlo based models are an effective approach to use in quantitative risk management when considering the variability of multiple farm-to-table factors. Title: Survival Assessment, Inactivation Kinetics Models, and Farm-to-Table Quantitative Risk Analysis of Food Pathogens Author: Deng, Kai About 48 million cases of Foodborne illnesses (FBIs) are estimated to occur every year in the US. These are diseases caused by contamination of foods with bacteria, viruses, protozoa, parasites and toxic chemicals. Clostridium difficile infections (CDIs) are an important health-care and community associated problem. Since C. difficile spores have been frequently isolates from meat product, this pathogen should be considered an emerging food pathogen. Low temperature and reduced water activity (a[subscript w]) are commonly used methods to preserve meats and meat products. Chapter 3 covers studies on the viability of C. difficile spores during 4 months at -80°C, -20°C, refrigeration (4°C) and room temperature (20°C), and after ten freeze-thaw cycles (10 cycles). Two epidemic strains, R20291 (PCR ribotype 027, human isolate) and M120 (PCR ribotype 078, animal isolate), were used in this published study. At 20°C and -80°C, the spore viability of both strains declined with storage time. The viability of M120 spores also declined during storage at 4°C and 20°C. Although no significant changes were observed in the viability of R20291 spores stored at 4°C, their significant viability increase when stored at 20°C is most remarkable and raises food safety concerns. Finally, the viability of both strains decreased when subjected to ten freeze-thaw cycles. In summary, this study provides evidence that C. difficile spores can survive the room and low temperature conditions found in food processing, storage and distribution. Chapter 4 covers studies on the aw effect on the viability of C. difficile spores stored at room temperature. In addition to the spores of the strains previously described, spores of a food isolate strain, C. difficile DK1 (unidentified ribotype), were included in this study. The viability of their spores during 3 months at room temperature in phosphate buffer saline (PBS) at a[subscript w] of ~1.00, 0.82 and 0.72, and in commercial samples of beef jerky with a[subscript w] 0.82 and 0.72 was investigated. Spores of the strains M120 and DK1 showed a ~1 decimal reduction after 3 months in PBS kept at room temperature, while no significant changes in spore viability were observed in the reduced a[subscript w] beef jerky. The steady and significant 2 decimal increase in the viability of R20291 spores in PBS and ~1 decimal increase in the beef jerky during the 3-month storage raises again food safety concerns. This study provides evidence that beef jerky enhanced spore survival and viability during room temperature storage. Furthermore, it suggests that R20291 spores lost superdormancy but the mechanism involved remains to be determined. Changes in the surface hydrophobicity of C. difficile spores have been reported to be associated with the loss of the exosporium and an increase in their viability. In this study, the R20291 spore viability increase during room temperature storage was not associated with a change in surface hydrophobicity. Chapter 5 covers the determination and modeling of the thermal resistance of spores of the C. difficile strains M120 and DK1. They were treated at 70, 75, 80 and 85°C in PBS buffer and at 80°C in sterile ground beef. Linear 1.5 and 0.8 decimal reductions for strains M120 and DK1, respectively, were observed in PBS after 60 min at 70°C. At higher temperatures, non-linear inactivation reached 3.2 and 1.6 decimal reductions in 32 min at 75°C, and 3.1 and 2.9 decimal reductions in 24 min at 80°C, respectively. During come-up time to 85°C, a 1.1 decimal reduction was observed for M120 but none for DK1. Spores of M120 and DK1 strains in ground beef showed a 1.6 and 1.4 decimal ¬reductions, respectively, after 24 min at 80°C, i.e., a much lower value than in PBS. The modified Gompertz model for nonlinear microbial activation fitted the spore inactivation in PBS data better than the Weibull model yielding smaller maximum inactivation levels (A), faster maximum inactivation rates (μ[subscript max]), and shorter lag times (λ) for strain M120 than DK1. This study confirmed the high resistance of C. difficile spores suggesting the need to lower their presence in animal meat products. Chapter 6 focuses on the development of a model for the microbial inactivation achieved by a novel food processing technology, high pressure carbon dioxide (HPCD). The non-linear survival curves for the microbial inactivation by HPCD depend on the processing temperature and CO₂ pressure. In this study, the nonlinear inactivation of Escherichia coli CGMCC1.90 in apple juice by HPCD treatments was best described using a modified Gompertz primary model and the secondary models for its parameters b(T,P)=14.21+0.011P-0.67T+0.0085T² and c(T,P)= -0.10 +0.0023P+0.0037T (T and P in °C and MPa). Monte Carlo simulations were used to incorporate the variability and uncertainty of the parameter b and c estimates, which were then used to predict microbial inactivation values for a given time, temperature and CO₂ pressure combination and desired confidence boundary. The model predicts that HPCD processes can meet 5 decimal reduction at 95% confidence but at relative long apple juice processing times, i.e., 35-124 min treatments in the experimental temperature and pressure range of 32-42°C and 10-30 MPa, respectively. Risk assessments of food microbial safety have become a valuable tool to understand, analyze and control microbial risks. They address the pathogen source, load reduction by processing, and pathogen survival during storage and distribution in a quantitative manner. Chapter 7 describes a Monte Carlo based quantitative microbial risk assessment tool developed for the consumption of raw oysters potentially contaminated with the pathogen Vibrio vulnificus. It predicted that depuration at 15°C for 47 and 16 h would reduce the risk of oysters harvested during the warm (Jun-Aug) and transition seasons (Apr-May, Oct-Nov), respectively, to an acceptable level. Furthermore, the model predicted that the consumption of untreated raw oysters harvested during the cold season (Dec-Mar) can be considered an acceptable and very low risk. Moreover, the model can be adjusted by an individual processor to reflect the conditions at their specific location. This study demonstrated that Monte Carlo based models are an effective approach to use in quantitative risk management when considering the variability of multiple farm-to-table factors. Close

• 3677. [Article] Effective Bonding Parameters for Hybrid Cross-Laminated Timber (CLT)

  Cross-laminated timber (CLT) is a massive engineered wood product made of orthogonally bonded layers of solid-sawn lumber, and is intended for roof, floor, or wall applications. Although it was developed ...

  Citation × Citation Citation Abstract Copy Title: Effective Bonding Parameters for Hybrid Cross-Laminated Timber (CLT) Author: Larkin, Blake Cross-laminated timber (CLT) is a massive engineered wood product made of orthogonally bonded layers of solid-sawn lumber, and is intended for roof, floor, or wall applications. Although it was developed in Europe in the early 90s, CLT is relatively new to North America. CLT products must be certified for structural use. First North American product standard stipulating test methods and qualification criteria for benchmark structural properties and adhesive bond integrity in structural CLT is ANSI/APA PRG320-2012. These methods and criteria have been adapted from existing laminated timber products (glulam), sometimes disregarding substantial differences between parallel laminates and CLT, in which layers are perpendicular to each other. From the point of view of long term sustainability of the CLT industry in North America, the critical questions are: 1. Is it possible to use low-grade timber harvested in the Pacific Northwest region in CLT products without compromising critical engineering parameters? Utilization of low- grade lumber, which is typically under-valued, in value-added engineered products should reduce the pressure on the high end structural lumber supply and may also provide a substantial outlet for lower-grade lumber timber species, including beetle-killed pine (BKP) harvested in the affected areas. 2. Can alternative adhesive systems, currently used in related engineered wood products and manufactured by domestic industry, be successfully used in CLT production? This is an important question, and is related to the fact that polyurethane (PUR) is the primary adhesive currently used by CLT manufacturing industry, and is supplied worldwide by a single Europe-based company. This adhesive is optimized for the species commonly used in CLT products to-date. ANSI/APA PRG320-2012 standard allows alternative adhesive types (PRF and EPI are specifically named), but to-date, only one alternative (MUF) has been used in commercial products. The objective of this project is to determine effective adhesive systems and bonding pressures for the hybrid cross-laminated timber (CLT) combinations. A secondary objective is to evaluate the testing methods prescribed in PRG 320-2012 for cross-laminated bond integrity. Integrity of hybrid CLT layups was evaluated on small specimens derived from CLT billets fabricated in-house using test procedures and qualification criteria specified in ANSI/APA PRG 320-2012 section 8.2.3. Test results were compared to prescribed qualification criteria. The Hybrid CLT combinations for this study include both structural grade lumber and low-grade lumber. For a reference species, lodgepole pine was selected, since it is a member of the US-SPF group closely related to the European species commonly used for CLT construction. The structural-grade, local species will be represented by Douglas-fir, while the low-grade species will be represented by low-grade lodgepole Pine, Douglas-fir, and Western Hemlock. The two adhesive systems investigated were 1) polyurethane-based PUR (currently the most common adhesive used by the CLT industry), which will serve as a reference system, and 2) phenol-resorcinol formaldehyde (PRF), which will represent a potential domestic alternative. PRF was chosen because it is a cold setting adhesive commonly used by the engineered wood products industry in North America; however, no CLT manufacturers utilize this adhesive system. The variables included species combinations (6), adhesive types (2), and clamping pressures (3), with repetition of 9 specimens per combination coming from at least three different CLT billets. The specimen’s bond integrity was assessed by the qualification panel requirements in PRG 320-2012 section 8.2. The qualification tests are block shear and cyclic delamination. A combination must pass both of the test requirements to qualify. The results of the study show that, of the 36 combinations, six failed the block shear test requirements and twenty-five failed the delamination test requirements. The 10 variable combinations that passed both requirements were DDL10F, DDL40F, DPL40F, PPH10F, PPH69F, PPH10U, PPH40U, PPL10U, PPL69U, and PHL69U. Initial inspection of test results show that no single variable that seems to make a significant impact on the bond integrity. It did reveal that no combinations with the use of Douglas-fir as a face material and PUR as an adhesive met the requirement, and only one combination with western hemlock as a core material met the requirements. It is evident that the delamination test was the major restriction on whether or not a combination passes the bond qualification. We believe that the adaption of a delamination test standard designed for layers with parallel grains makes the passing requirement too strict for an orthogonally bonded product. In conclusion, there were 10 combinations that passed both bond integrity test requirements. It was unclear whether the species and/or grade combination, adhesive system, or clamping pressure made the biggest impact on the bond integrity. Relative to the reference adhesive (PUR), and species combination (lodgepole pine), the hybrid panels performed similarly and showed that certain species and/or grade combinations could pass the qualification requirements for specific requirements. The knowledge gained by this screening study will allow further qualification testing of the passing combinations per PRG320-2012. This also has the potential to supply the CLT manufacturing community with greater flexibility of manufacturing techniques and materials, as well as offer value to underutilized lumber. Title: Effective Bonding Parameters for Hybrid Cross-Laminated Timber (CLT) Author: Larkin, Blake Cross-laminated timber (CLT) is a massive engineered wood product made of orthogonally bonded layers of solid-sawn lumber, and is intended for roof, floor, or wall applications. Although it was developed in Europe in the early 90s, CLT is relatively new to North America. CLT products must be certified for structural use. First North American product standard stipulating test methods and qualification criteria for benchmark structural properties and adhesive bond integrity in structural CLT is ANSI/APA PRG320-2012. These methods and criteria have been adapted from existing laminated timber products (glulam), sometimes disregarding substantial differences between parallel laminates and CLT, in which layers are perpendicular to each other. From the point of view of long term sustainability of the CLT industry in North America, the critical questions are: 1. Is it possible to use low-grade timber harvested in the Pacific Northwest region in CLT products without compromising critical engineering parameters? Utilization of low- grade lumber, which is typically under-valued, in value-added engineered products should reduce the pressure on the high end structural lumber supply and may also provide a substantial outlet for lower-grade lumber timber species, including beetle-killed pine (BKP) harvested in the affected areas. 2. Can alternative adhesive systems, currently used in related engineered wood products and manufactured by domestic industry, be successfully used in CLT production? This is an important question, and is related to the fact that polyurethane (PUR) is the primary adhesive currently used by CLT manufacturing industry, and is supplied worldwide by a single Europe-based company. This adhesive is optimized for the species commonly used in CLT products to-date. ANSI/APA PRG320-2012 standard allows alternative adhesive types (PRF and EPI are specifically named), but to-date, only one alternative (MUF) has been used in commercial products. The objective of this project is to determine effective adhesive systems and bonding pressures for the hybrid cross-laminated timber (CLT) combinations. A secondary objective is to evaluate the testing methods prescribed in PRG 320-2012 for cross-laminated bond integrity. Integrity of hybrid CLT layups was evaluated on small specimens derived from CLT billets fabricated in-house using test procedures and qualification criteria specified in ANSI/APA PRG 320-2012 section 8.2.3. Test results were compared to prescribed qualification criteria. The Hybrid CLT combinations for this study include both structural grade lumber and low-grade lumber. For a reference species, lodgepole pine was selected, since it is a member of the US-SPF group closely related to the European species commonly used for CLT construction. The structural-grade, local species will be represented by Douglas-fir, while the low-grade species will be represented by low-grade lodgepole Pine, Douglas-fir, and Western Hemlock. The two adhesive systems investigated were 1) polyurethane-based PUR (currently the most common adhesive used by the CLT industry), which will serve as a reference system, and 2) phenol-resorcinol formaldehyde (PRF), which will represent a potential domestic alternative. PRF was chosen because it is a cold setting adhesive commonly used by the engineered wood products industry in North America; however, no CLT manufacturers utilize this adhesive system. The variables included species combinations (6), adhesive types (2), and clamping pressures (3), with repetition of 9 specimens per combination coming from at least three different CLT billets. The specimen’s bond integrity was assessed by the qualification panel requirements in PRG 320-2012 section 8.2. The qualification tests are block shear and cyclic delamination. A combination must pass both of the test requirements to qualify. The results of the study show that, of the 36 combinations, six failed the block shear test requirements and twenty-five failed the delamination test requirements. The 10 variable combinations that passed both requirements were DDL10F, DDL40F, DPL40F, PPH10F, PPH69F, PPH10U, PPH40U, PPL10U, PPL69U, and PHL69U. Initial inspection of test results show that no single variable that seems to make a significant impact on the bond integrity. It did reveal that no combinations with the use of Douglas-fir as a face material and PUR as an adhesive met the requirement, and only one combination with western hemlock as a core material met the requirements. It is evident that the delamination test was the major restriction on whether or not a combination passes the bond qualification. We believe that the adaption of a delamination test standard designed for layers with parallel grains makes the passing requirement too strict for an orthogonally bonded product. In conclusion, there were 10 combinations that passed both bond integrity test requirements. It was unclear whether the species and/or grade combination, adhesive system, or clamping pressure made the biggest impact on the bond integrity. Relative to the reference adhesive (PUR), and species combination (lodgepole pine), the hybrid panels performed similarly and showed that certain species and/or grade combinations could pass the qualification requirements for specific requirements. The knowledge gained by this screening study will allow further qualification testing of the passing combinations per PRG320-2012. This also has the potential to supply the CLT manufacturing community with greater flexibility of manufacturing techniques and materials, as well as offer value to underutilized lumber. Close

• 3678. [Article] Mixed-conifer forests of central Oregon : structure, composition, history of establishment, and growth

  The structure and composition of mixed-conifer forest (MCF) in central Oregon has been altered by fire exclusion and logging. The resulting increased density, spatial contagion, and loss of fire resistant ...

  Citation × Citation Citation Abstract Copy Title: Mixed-conifer forests of central Oregon : structure, composition, history of establishment, and growth Author: Merschel, Andrew G. The structure and composition of mixed-conifer forest (MCF) in central Oregon has been altered by fire exclusion and logging. The resulting increased density, spatial contagion, and loss of fire resistant trees decrease the resiliency of this ecosystem to fire, drought, and insects. The historical and current composition and structure of MCF are characterized by steep environmental gradients and a complex mixed-severity fire regime. This inherent variation makes it difficult to determine the magnitude of anthropogenic effects and set objectives for restoration and management. As a result, there is a lack of consensus regarding how MCF should be managed and restored across the landscape. My primary research objectives were to: (1) Characterize the current structure and composition of MCF and how these vary with environmental setting; and (2) Characterize establishment and tree growth patterns in MCF in different environmental settings. To address these objectives, I collected field data on structure and composition and increment cores across a range of environmental conditions in MCF of the eastern Cascades and Ochoco Mountains. I used cluster analysis to identify four stand types based on structure and composition in the eastern Cascades study area and four analogous types in the Ochoco Mountains study area. Variation in understory composition and the presence of large diameter shade tolerant species distinguish each type. Stand types occupied distinct environmental settings along a climatic gradient of increasing precipitation and elevation. At relatively dry PIPO sites understories were dominated by ponderosa pine. At wetter PIPO/PSME and PIPO ABGC sites understories were dominated by shade tolerant species, but ponderosa pine was dominant in the overstory. At the coolest and wettest PIPO/PSME/ABGC sites understories were dominated by grand fir and shade tolerant species were common in the overstory. In the eastern Cascades current density of all live trees and snags was 432, 461, 570, 372 trees per hectare (TPH) for the four stand types identified. Stand types in the drier Ochoco Mountains were currently less dense at 279, 304, 212, and 307 TPH. Current MCF densities in both areas are 2-3 times higher than densities estimated for the late 19th and early 20th centuries from other studies in those two areas. Reconstruction of cuts in each stand type indicates that the density of large diameter ponderosa pine has been reduced by approximately 50% in all stand types in both study regions. Age histograms demonstrate that current density and composition of MCF stand types is a product of abrupt increases in tree establishment following fire exclusion in the late 19th century. The number of trees established increased after 1900 in all stand types, but the timing and composition of changes in establishment varied with climate. At dry PIPO sites increases in establishment were delayed until the 1920s and 1930s and were composed of ponderosa pine. At PIPO/PSME and PIPO/ABGC sites with intermediate precipitation, establishment was dominated by ponderosa pine prior to 1900, but after 1900 establishment was dominated by a large pulse of Douglas-fir and grand fir. At the wettest PIPO/PSME/ABGC there was less evidence of changes in structure and composition over time. My results indicate that compared to dry pine and dry-mixed conifer sites, relatively productive moist mixed-conifer sites were characterized by large changes in structure and composition. Such sites could be considered more ecologically altered by lack of fire than drier forest types that had high fire frequencies but slower rates of stand development and less plant community change. Radial growth patterns of cored ponderosa pines differed between the eastern Cascades and Ochoco Mountains. In the eastern Cascades mean growth rates and variance decreased during favorable climatic periods after 1900. This is likely related to increased competition, and provides evidence that current stand density lacks a temporal analog in the 18th and 19th centuries. Sensitivity of growth to climate and harvest suggest competition for water in the denser forest of the eastern Cascades, and indicates thinning will increase the diameter growth rate of large old pines. In the Ochoco Mountains, ponderosa pine tree growth was less responsive to climate prior to fire exclusion in the late 1800s, and growth did not respond to fire events. This suggests competition among trees was historically low in this region. After fire exclusion growth became more responsive to wet and dry climatic cycles, which may indicate that increased density and competition made trees more responsive to climate variability. Patterns of slow and fast growth appeared to differ between study regions and likely differ at the sub-regional scale. Further analysis of the relationship between growth and climate in different environmental settings is needed to distinguish where stand development has been modified by disruption of fire regimes. Title: Mixed-conifer forests of central Oregon : structure, composition, history of establishment, and growth Author: Merschel, Andrew G. The structure and composition of mixed-conifer forest (MCF) in central Oregon has been altered by fire exclusion and logging. The resulting increased density, spatial contagion, and loss of fire resistant trees decrease the resiliency of this ecosystem to fire, drought, and insects. The historical and current composition and structure of MCF are characterized by steep environmental gradients and a complex mixed-severity fire regime. This inherent variation makes it difficult to determine the magnitude of anthropogenic effects and set objectives for restoration and management. As a result, there is a lack of consensus regarding how MCF should be managed and restored across the landscape. My primary research objectives were to: (1) Characterize the current structure and composition of MCF and how these vary with environmental setting; and (2) Characterize establishment and tree growth patterns in MCF in different environmental settings. To address these objectives, I collected field data on structure and composition and increment cores across a range of environmental conditions in MCF of the eastern Cascades and Ochoco Mountains. I used cluster analysis to identify four stand types based on structure and composition in the eastern Cascades study area and four analogous types in the Ochoco Mountains study area. Variation in understory composition and the presence of large diameter shade tolerant species distinguish each type. Stand types occupied distinct environmental settings along a climatic gradient of increasing precipitation and elevation. At relatively dry PIPO sites understories were dominated by ponderosa pine. At wetter PIPO/PSME and PIPO ABGC sites understories were dominated by shade tolerant species, but ponderosa pine was dominant in the overstory. At the coolest and wettest PIPO/PSME/ABGC sites understories were dominated by grand fir and shade tolerant species were common in the overstory. In the eastern Cascades current density of all live trees and snags was 432, 461, 570, 372 trees per hectare (TPH) for the four stand types identified. Stand types in the drier Ochoco Mountains were currently less dense at 279, 304, 212, and 307 TPH. Current MCF densities in both areas are 2-3 times higher than densities estimated for the late 19th and early 20th centuries from other studies in those two areas. Reconstruction of cuts in each stand type indicates that the density of large diameter ponderosa pine has been reduced by approximately 50% in all stand types in both study regions. Age histograms demonstrate that current density and composition of MCF stand types is a product of abrupt increases in tree establishment following fire exclusion in the late 19th century. The number of trees established increased after 1900 in all stand types, but the timing and composition of changes in establishment varied with climate. At dry PIPO sites increases in establishment were delayed until the 1920s and 1930s and were composed of ponderosa pine. At PIPO/PSME and PIPO/ABGC sites with intermediate precipitation, establishment was dominated by ponderosa pine prior to 1900, but after 1900 establishment was dominated by a large pulse of Douglas-fir and grand fir. At the wettest PIPO/PSME/ABGC there was less evidence of changes in structure and composition over time. My results indicate that compared to dry pine and dry-mixed conifer sites, relatively productive moist mixed-conifer sites were characterized by large changes in structure and composition. Such sites could be considered more ecologically altered by lack of fire than drier forest types that had high fire frequencies but slower rates of stand development and less plant community change. Radial growth patterns of cored ponderosa pines differed between the eastern Cascades and Ochoco Mountains. In the eastern Cascades mean growth rates and variance decreased during favorable climatic periods after 1900. This is likely related to increased competition, and provides evidence that current stand density lacks a temporal analog in the 18th and 19th centuries. Sensitivity of growth to climate and harvest suggest competition for water in the denser forest of the eastern Cascades, and indicates thinning will increase the diameter growth rate of large old pines. In the Ochoco Mountains, ponderosa pine tree growth was less responsive to climate prior to fire exclusion in the late 1800s, and growth did not respond to fire events. This suggests competition among trees was historically low in this region. After fire exclusion growth became more responsive to wet and dry climatic cycles, which may indicate that increased density and competition made trees more responsive to climate variability. Patterns of slow and fast growth appeared to differ between study regions and likely differ at the sub-regional scale. Further analysis of the relationship between growth and climate in different environmental settings is needed to distinguish where stand development has been modified by disruption of fire regimes. Close

• 3679. [Article] Kinetic and molecular effects of sulfate reduction on a dechlorinating culture under chemostat growth conditions

  Chlorinated ethenes are common groundwater contaminants that may be treated through in-situ bioremediation. Relationships between the reducing environment, available electron donors and acceptors, reaction ...

  Citation × Citation Citation Abstract Copy Title: Kinetic and molecular effects of sulfate reduction on a dechlorinating culture under chemostat growth conditions Author: Berggren, Dusty Rose V. Chlorinated ethenes are common groundwater contaminants that may be treated through in-situ bioremediation. Relationships between the reducing environment, available electron donors and acceptors, reaction kinetics, and microbial community composition must be further understood to successfully engineer remediation schemes in the complex subsurface environment. This thesis work investigated the effect of sulfate reduction on a dehalogenating culture grown under very controlled conditions. Two chemostats containing the Point Mugu (PM) culture were maintained using an influent containing tetrachloroethene (PCE) as an electron acceptor and lactate as a fermenting electron donor. One of these chemostats, PM-5L, was used as a control, while the influent to the PM-2L chemostat was amended with sulfate on an equal electron-equivalent basis to PCE. The effluent composition of these two chemostats was monitored over time, and periodic batch rate tests and molecular analyses were performed with cells harvested from the chemostat to elucidate the changes in performance and microbial composition within the chemostat culture. A numerical model based on Monod kinetics with competitive inhibition was developed to fit data from batch PCE-to-ethene rate tests by simultaneously solving for the k[subscript m]X parameters of each CAH dechlorination step given a standard set of Ks values. Non-linear regression of multi-equilibrium VC Monod test data provided the Monod parameters (k[subscript m]X and K[subscript s]) for VC dechlorination. These parameters were used to quantify changes in dechlorinating performance of each chemostat over time and compare the performance of the two chemostats. The effluent chemical composition of the PM-5L chemostat appeared to be steady after approximately six residence times, with 1120 μM PCE being transformed to 98% ethene and 2% VC, H₂ tensions remaining between 2-3 nM, acetate around 4.3 mM, and biomass around 23 mg protein/L. Batch rate tests during this time showed rapid rates of transformation for all CAHs, agreeing well with chemostat performance. The k[subscript m]X parameters derived from the PCE-to-ethene data and the pseudo-mixed order rate coefficient of VC dechlorination determined through multi-equilibrium VC Monod tests also remained essentially constant over the one-year period of study. Changes in the PM-2L chemostat performance following the initiation of sulfate reduction were observed. Sulfate reduction began almost immediately after its addition to the chemostat, and total sulfide concentrations rose to 100-300 μM. Chemostat performance with respect to CAH and H₂ concentrations was roughly steady over approximately 250 days, with PCE being dechlorinated to 9 μM cis-DCE, 230 μM VC, and 860 μM ethene under H₂ tensions around 4 nM. Total protein levels nearly doubled during this period, increasing from 25 to 47 mg protein/L. Sulfate reduction then rapidly increased to completion, resulting in 620-720 μM dissolved sulfide and a decrease in the H₂ concentration to 2 nM. At this time, the extent of PCE dechlorination also decreased to 280, 760, and 80 μM cis-DCE, VC, and ethene, respectively. Batch rate tests showed a decrease in all chlorinated ethene reduction rates; however, VC dechlorination was the most effected by sulfate reduction, showing a 97% reduction in rate following sulfate addition. Multi-equilibrium VC rate tests were impossible to conduct following the sharp increase in sulfate reduction in the chemostat due to lack of measurable dechlorination over a days' time. A simple chemostat model employed Monod kinetics for the series of CAH reactions to determine the steady-state extent of dechlorination in the chemostat predicted by the best-fit kinetic parameters of each PCE-to-ethene rate test. The extent of dechlorination was well-modeled for the PM-5L chemostat when a H₂ limitation factor of 0.3 was applied to the rate of each CAH. Using a dual Monod kinetic model with H₂ as the electron donor, the limitation factor corresponded with a half-velocity coefficient (K[subscript H]) of 4.6 nM. When this same K[subscript H] was used to model the PM-2L chemostat, a greater extent of dechlorination was predicted than what was observed in the chemostat, possibly suggesting other inhibitory factors of dechlorination were present in the PM-2L chemostat. DNA and RNA analyses of cells periodically harvested from the chemostat were performed by Ian P.G. Marshall at Stanford University. His work revealed shifts in the chemostats' Dehalococcoides population over time. Analysis of the PM-5L culture using the H2ase chip he developed and a clone library of hupL genes showed that the Dehalococcoides population was predominately related to strains BAV-1 or CBDB1/GT and did not undergo a significant shift over time. Clone libraries constructed for cells harvested from the PM-2L chemostat revealed two shifts in the chemostat Dehalococcoides population. A genetically homogenous strain relative of BAV-1 was eliminated following a decline in chemostat H2 tensions from around 27 nM to 2 nM and a corresponding increase in dehalogenation efficiency. In a second shift, a strain 195 relative outcompeted the CBDB1/GT relatives following enhanced sulfate reduction. A general decrease in the Dehalococcoides concentration within the chemostat culture was also suggested by qPCR analysis of Dehalococcoides 16S genes. These molecular results correlated well with the decline in VC reduction rates reported in batch kinetic tests given the characteristic co-metabolic VC reduction of the dominant strain 195 relative and overall lower concentrations of Dehalococcoides. Our work suggests that sulfate reduction in the anaerobic chemostat environment caused a shift in the dechlorinating microbial population to a strain with less efficient VC reduction. This shift was also accompanied by a decline in Dehalococcoides concentration within the culture. Both of these factors contributed to the decline in chlorinated ethene transformation rates observed through batch rate tests. Competition for H₂ was not expected to be the primary cause for the changes observed in the PM-2L chemostat. Long-term batch tests involving the control culture are proposed to elucidate whether sulfide or other factors of sulfate reduction are responsible for this shift, and to confirm the suspected role of H₂ competition between dechlorination and sulfate reduction in the chemostat-grown PM culture. Title: Kinetic and molecular effects of sulfate reduction on a dechlorinating culture under chemostat growth conditions Author: Berggren, Dusty Rose V. Chlorinated ethenes are common groundwater contaminants that may be treated through in-situ bioremediation. Relationships between the reducing environment, available electron donors and acceptors, reaction kinetics, and microbial community composition must be further understood to successfully engineer remediation schemes in the complex subsurface environment. This thesis work investigated the effect of sulfate reduction on a dehalogenating culture grown under very controlled conditions. Two chemostats containing the Point Mugu (PM) culture were maintained using an influent containing tetrachloroethene (PCE) as an electron acceptor and lactate as a fermenting electron donor. One of these chemostats, PM-5L, was used as a control, while the influent to the PM-2L chemostat was amended with sulfate on an equal electron-equivalent basis to PCE. The effluent composition of these two chemostats was monitored over time, and periodic batch rate tests and molecular analyses were performed with cells harvested from the chemostat to elucidate the changes in performance and microbial composition within the chemostat culture. A numerical model based on Monod kinetics with competitive inhibition was developed to fit data from batch PCE-to-ethene rate tests by simultaneously solving for the k[subscript m]X parameters of each CAH dechlorination step given a standard set of Ks values. Non-linear regression of multi-equilibrium VC Monod test data provided the Monod parameters (k[subscript m]X and K[subscript s]) for VC dechlorination. These parameters were used to quantify changes in dechlorinating performance of each chemostat over time and compare the performance of the two chemostats. The effluent chemical composition of the PM-5L chemostat appeared to be steady after approximately six residence times, with 1120 μM PCE being transformed to 98% ethene and 2% VC, H₂ tensions remaining between 2-3 nM, acetate around 4.3 mM, and biomass around 23 mg protein/L. Batch rate tests during this time showed rapid rates of transformation for all CAHs, agreeing well with chemostat performance. The k[subscript m]X parameters derived from the PCE-to-ethene data and the pseudo-mixed order rate coefficient of VC dechlorination determined through multi-equilibrium VC Monod tests also remained essentially constant over the one-year period of study. Changes in the PM-2L chemostat performance following the initiation of sulfate reduction were observed. Sulfate reduction began almost immediately after its addition to the chemostat, and total sulfide concentrations rose to 100-300 μM. Chemostat performance with respect to CAH and H₂ concentrations was roughly steady over approximately 250 days, with PCE being dechlorinated to 9 μM cis-DCE, 230 μM VC, and 860 μM ethene under H₂ tensions around 4 nM. Total protein levels nearly doubled during this period, increasing from 25 to 47 mg protein/L. Sulfate reduction then rapidly increased to completion, resulting in 620-720 μM dissolved sulfide and a decrease in the H₂ concentration to 2 nM. At this time, the extent of PCE dechlorination also decreased to 280, 760, and 80 μM cis-DCE, VC, and ethene, respectively. Batch rate tests showed a decrease in all chlorinated ethene reduction rates; however, VC dechlorination was the most effected by sulfate reduction, showing a 97% reduction in rate following sulfate addition. Multi-equilibrium VC rate tests were impossible to conduct following the sharp increase in sulfate reduction in the chemostat due to lack of measurable dechlorination over a days' time. A simple chemostat model employed Monod kinetics for the series of CAH reactions to determine the steady-state extent of dechlorination in the chemostat predicted by the best-fit kinetic parameters of each PCE-to-ethene rate test. The extent of dechlorination was well-modeled for the PM-5L chemostat when a H₂ limitation factor of 0.3 was applied to the rate of each CAH. Using a dual Monod kinetic model with H₂ as the electron donor, the limitation factor corresponded with a half-velocity coefficient (K[subscript H]) of 4.6 nM. When this same K[subscript H] was used to model the PM-2L chemostat, a greater extent of dechlorination was predicted than what was observed in the chemostat, possibly suggesting other inhibitory factors of dechlorination were present in the PM-2L chemostat. DNA and RNA analyses of cells periodically harvested from the chemostat were performed by Ian P.G. Marshall at Stanford University. His work revealed shifts in the chemostats' Dehalococcoides population over time. Analysis of the PM-5L culture using the H2ase chip he developed and a clone library of hupL genes showed that the Dehalococcoides population was predominately related to strains BAV-1 or CBDB1/GT and did not undergo a significant shift over time. Clone libraries constructed for cells harvested from the PM-2L chemostat revealed two shifts in the chemostat Dehalococcoides population. A genetically homogenous strain relative of BAV-1 was eliminated following a decline in chemostat H2 tensions from around 27 nM to 2 nM and a corresponding increase in dehalogenation efficiency. In a second shift, a strain 195 relative outcompeted the CBDB1/GT relatives following enhanced sulfate reduction. A general decrease in the Dehalococcoides concentration within the chemostat culture was also suggested by qPCR analysis of Dehalococcoides 16S genes. These molecular results correlated well with the decline in VC reduction rates reported in batch kinetic tests given the characteristic co-metabolic VC reduction of the dominant strain 195 relative and overall lower concentrations of Dehalococcoides. Our work suggests that sulfate reduction in the anaerobic chemostat environment caused a shift in the dechlorinating microbial population to a strain with less efficient VC reduction. This shift was also accompanied by a decline in Dehalococcoides concentration within the culture. Both of these factors contributed to the decline in chlorinated ethene transformation rates observed through batch rate tests. Competition for H₂ was not expected to be the primary cause for the changes observed in the PM-2L chemostat. Long-term batch tests involving the control culture are proposed to elucidate whether sulfide or other factors of sulfate reduction are responsible for this shift, and to confirm the suspected role of H₂ competition between dechlorination and sulfate reduction in the chemostat-grown PM culture. Close

• 3680. [Article] Interactive Genetic Algorithms for watershed planning : an investigation of usability and human-centered design

  Degradation of watersheds is a major concern in areas where adverse climate effects and unsustainable use of the natural resources have caused extensive stresses to watershed systems (e.g., increased floods, ...

  Citation × Citation Citation Abstract Copy Title: Interactive Genetic Algorithms for watershed planning : an investigation of usability and human-centered design Author: Piemonti, Adriana Debora Degradation of watersheds is a major concern in areas where adverse climate effects and unsustainable use of the natural resources have caused extensive stresses to watershed systems (e.g., increased floods, increased droughts, worsened in-stream water quality) through the years. While considerable efforts are being made to generate technical solutions that focus on plans of spatially-distributed conservation practices (e.g., Wetlands, Filter Strips, Grassed Waterways, Crop Management practices, etc.) for restoration of existing conditions in the watersheds, adoption and implementation of these solutions require a better understanding of constraints faced by affected stakeholders and decision makers. Participatory modeling and design approaches have, as a result, become popular in the recent past to support a community's engagement during the modeling process and during development of potential scenarios of plans (or, design alternatives). And now, with new and ongoing developments in Web 2.0 technologies, there is an even greater need for research that examines how large number of stakeholders can be engaged in the development of design alternatives via the internet-based, decision support environments. The overarching goal of this research is to investigate how stakeholder participation ("humans") and Interactive Genetic Algorithms ("computer") can be coupled in a web-based watershed decision support system (DSS) called WRESTORE (Watershed REstoration using Spatio Temporal Optimization of REsources- http://wrestore.iupui.edu/), in order to generate user-preferred design alternatives of distributed conservation practices on a watershed landscape. An important component of this goal is to also improve the understanding of how human behavior on the graphical user interface (GUI) of the DSS can be observed and evaluated in real-time, and then learned from to further improve the performance of the underlying search algorithm. Four specific objectives were addressed in this work to accomplish the overall goal: • Objective 1: Observe interactions of multiple users with the GUI of a web-based watershed DSS (WRESTORE, http://wrestore.iupui.edu/) during interactive search experiments, and then use Usability metrics (response times, clicking events and confidence levels) to evaluate the differences and similarities in user behaviors and interactions. • Objective 2: Examine relationships between the type of users (e.g., stakeholders versus surrogates), the Usability metrics, and patterns in the watershed-scale plans of conservation practices generated by the multi-objective Interactive Genetic Algorithm embedded in WRESTORE. • Objective 3: Examine relationships between the type of users, the Usability metrics, and patterns in the user-preferred, sub-basin-scale plans of conservation practices generated by the multi-objective Interactive Genetic Algorithm embedded in WRESTORE. • Objective 4: Develop and test novel human-guided search operators that adaptively learn for patterns in user-preferred alternatives generated by the multi-objective Interactive Genetic Algorithm, and, as a result, improve the convergence rate of the search algorithm for generating design alternatives that conserve these learned patterns. Results show that there is a clear difference on how different types of users interact with the Interactive Optimization system. The observed relationship between confidence levels, time spent on a task, and number of mouse clicking events, indicated that participants who were able to use the WRESTORE GUI to gather more information and had a higher rate of time per number of clicks, tended to increase their levels of self-confidence in their own feedback. Also, when engaging with watershed stakeholders versus non-stakeholders (or, surrogates), 67% of the stakeholder participants steadily increased their average self-confidence levels as they continued to interact with the tool, in contrast to only 29% of surrogate participants who also showed an increase in their self-confidence levels through time. Such usability and confidence level evaluations provide assessments on which participant was potentially generating reliable feedback data for the search algorithm to use. An analysis of design alternatives generated by the individuals in both stakeholder and non-stakeholder groups showed that a majority (67%) of the stakeholder participants found a higher percentage (on and average 52%) of preferred design alternatives via the interactive search process. Also, users who were focused on assessing the suitability of design alternatives for the entire watershed trended to demonstrate a bias for one of the watershed-scale objective functions. In contrast, users, who were focused on assessing the suitability of design alternatives at only a few local sub-basins in the watershed, did not demonstrate any clear bias for any one of the watershed-scale objective functions. Additionally, patterns were observed in the design of decision alternatives generated by the human-centered search process, which further divulged potential user preferences related to the decision space for example, whether a specific participant preferred a certain practice over another, or a certain location over another for a specific practice. Finally, to improve the convergence rates of the Interactive Genetic Algorithm in WRESTORE, we investigated whether observed patterns in decisions (especially, when users were focused on local sub-regions of the watershed) can be used to improve the search for user-desire designs. A novel Interactive Genetic Algorithm with adaptive, human-guided, selection, crossover and mutation operators was proposed. The new algorithm was tested with six types of simulated participants (three deterministic and three probabilistic users) developed from the feedback data of three real participants. Results of search experiments with the novel adaptive IGA operators indicated a faster convergence than the default IGA, for two out of three deterministic simulated users. However, none of the probabilistic user showed a convergence different than the default values. This indicates that while current results indicate promise, there is need for additional research on adaptive, human-guided IGA operators, especially when noisy/stochastic users participate in the search. Additionally, adaptation of search operators have the potential to improve convergence rates when participatory design is done via Interactive Genetic Algorithms. Title: Interactive Genetic Algorithms for watershed planning : an investigation of usability and human-centered design Author: Piemonti, Adriana Debora Degradation of watersheds is a major concern in areas where adverse climate effects and unsustainable use of the natural resources have caused extensive stresses to watershed systems (e.g., increased floods, increased droughts, worsened in-stream water quality) through the years. While considerable efforts are being made to generate technical solutions that focus on plans of spatially-distributed conservation practices (e.g., Wetlands, Filter Strips, Grassed Waterways, Crop Management practices, etc.) for restoration of existing conditions in the watersheds, adoption and implementation of these solutions require a better understanding of constraints faced by affected stakeholders and decision makers. Participatory modeling and design approaches have, as a result, become popular in the recent past to support a community's engagement during the modeling process and during development of potential scenarios of plans (or, design alternatives). And now, with new and ongoing developments in Web 2.0 technologies, there is an even greater need for research that examines how large number of stakeholders can be engaged in the development of design alternatives via the internet-based, decision support environments. The overarching goal of this research is to investigate how stakeholder participation ("humans") and Interactive Genetic Algorithms ("computer") can be coupled in a web-based watershed decision support system (DSS) called WRESTORE (Watershed REstoration using Spatio Temporal Optimization of REsources- http://wrestore.iupui.edu/), in order to generate user-preferred design alternatives of distributed conservation practices on a watershed landscape. An important component of this goal is to also improve the understanding of how human behavior on the graphical user interface (GUI) of the DSS can be observed and evaluated in real-time, and then learned from to further improve the performance of the underlying search algorithm. Four specific objectives were addressed in this work to accomplish the overall goal: • Objective 1: Observe interactions of multiple users with the GUI of a web-based watershed DSS (WRESTORE, http://wrestore.iupui.edu/) during interactive search experiments, and then use Usability metrics (response times, clicking events and confidence levels) to evaluate the differences and similarities in user behaviors and interactions. • Objective 2: Examine relationships between the type of users (e.g., stakeholders versus surrogates), the Usability metrics, and patterns in the watershed-scale plans of conservation practices generated by the multi-objective Interactive Genetic Algorithm embedded in WRESTORE. • Objective 3: Examine relationships between the type of users, the Usability metrics, and patterns in the user-preferred, sub-basin-scale plans of conservation practices generated by the multi-objective Interactive Genetic Algorithm embedded in WRESTORE. • Objective 4: Develop and test novel human-guided search operators that adaptively learn for patterns in user-preferred alternatives generated by the multi-objective Interactive Genetic Algorithm, and, as a result, improve the convergence rate of the search algorithm for generating design alternatives that conserve these learned patterns. Results show that there is a clear difference on how different types of users interact with the Interactive Optimization system. The observed relationship between confidence levels, time spent on a task, and number of mouse clicking events, indicated that participants who were able to use the WRESTORE GUI to gather more information and had a higher rate of time per number of clicks, tended to increase their levels of self-confidence in their own feedback. Also, when engaging with watershed stakeholders versus non-stakeholders (or, surrogates), 67% of the stakeholder participants steadily increased their average self-confidence levels as they continued to interact with the tool, in contrast to only 29% of surrogate participants who also showed an increase in their self-confidence levels through time. Such usability and confidence level evaluations provide assessments on which participant was potentially generating reliable feedback data for the search algorithm to use. An analysis of design alternatives generated by the individuals in both stakeholder and non-stakeholder groups showed that a majority (67%) of the stakeholder participants found a higher percentage (on and average 52%) of preferred design alternatives via the interactive search process. Also, users who were focused on assessing the suitability of design alternatives for the entire watershed trended to demonstrate a bias for one of the watershed-scale objective functions. In contrast, users, who were focused on assessing the suitability of design alternatives at only a few local sub-basins in the watershed, did not demonstrate any clear bias for any one of the watershed-scale objective functions. Additionally, patterns were observed in the design of decision alternatives generated by the human-centered search process, which further divulged potential user preferences related to the decision space for example, whether a specific participant preferred a certain practice over another, or a certain location over another for a specific practice. Finally, to improve the convergence rates of the Interactive Genetic Algorithm in WRESTORE, we investigated whether observed patterns in decisions (especially, when users were focused on local sub-regions of the watershed) can be used to improve the search for user-desire designs. A novel Interactive Genetic Algorithm with adaptive, human-guided, selection, crossover and mutation operators was proposed. The new algorithm was tested with six types of simulated participants (three deterministic and three probabilistic users) developed from the feedback data of three real participants. Results of search experiments with the novel adaptive IGA operators indicated a faster convergence than the default IGA, for two out of three deterministic simulated users. However, none of the probabilistic user showed a convergence different than the default values. This indicates that while current results indicate promise, there is need for additional research on adaptive, human-guided IGA operators, especially when noisy/stochastic users participate in the search. Additionally, adaptation of search operators have the potential to improve convergence rates when participatory design is done via Interactive Genetic Algorithms. Close