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• 13101. [Article] Downstream rearing of juvenile Chinook salmon abundance, distribution and growth in the Upper Mainstem of the John Day River

  Abstract -- Juvenile spring Chinook (Oncorhynchus tshawytscha) emerge from the gravel in the late winter or early spring, and most follow a life history pattern known as Natal Reach Rearing (NRR) in which ...

  Citation × Citation Citation Abstract Copy Title: Downstream rearing of juvenile Chinook salmon abundance, distribution and growth in the Upper Mainstem of the John Day River Abstract -- Juvenile spring Chinook (Oncorhynchus tshawytscha) emerge from the gravel in the late winter or early spring, and most follow a life history pattern known as Natal Reach Rearing (NRR) in which juvenile fish remain in the stream reaches where they were spawned until their second spring of life when they start migrating towards the ocean (Healey 1991). However, in Columbia River tributaries, some juveniles have been observed following a Downstream Rearing (DSR) life history, in which they start moving downstream during their first spring towards other nursery habitats or perhaps ocean rearing (Copeland & Venditti 2009; Schroeder et al. 2016). Rearing in different habitats during their first year gives fish with these two life histories access to diverse food resources and, it is hypothesized that, this leads to different survival and growth advantages for these two groups. Differences in growth are of interest in efforts to conserve this threatened species because size is positively correlated to survival for salmon across multiple stages of their life cycle (Groot & Margolis 1991; Healey 1991; Quinn & Peterson 1996; Roni et al. 2012) Chinook salmon in the upper John Day River, Oregon, exhibit both NRR and DSR life history patterns. Fish following the DSR life history pattern are larger than NRR fish late in the spring, possibly due to factors such as higher fish density, lower stream productivity, and colder water temperatures in their natal reach than in the downstream reaches. However, this size advantage may be lost due to adverse summer conditions. Hot summer days combined with the withdrawal of water for agriculture lead to stream water temperatures well above lethal thresholds for salmon in many downstream reaches. DSR fish have been observed in tributaries of the mainstem John Day River, however their growth and survival during summer is unknown. Title: Downstream rearing of juvenile Chinook salmon abundance, distribution and growth in the Upper Mainstem of the John Day River Abstract -- Juvenile spring Chinook (Oncorhynchus tshawytscha) emerge from the gravel in the late winter or early spring, and most follow a life history pattern known as Natal Reach Rearing (NRR) in which juvenile fish remain in the stream reaches where they were spawned until their second spring of life when they start migrating towards the ocean (Healey 1991). However, in Columbia River tributaries, some juveniles have been observed following a Downstream Rearing (DSR) life history, in which they start moving downstream during their first spring towards other nursery habitats or perhaps ocean rearing (Copeland & Venditti 2009; Schroeder et al. 2016). Rearing in different habitats during their first year gives fish with these two life histories access to diverse food resources and, it is hypothesized that, this leads to different survival and growth advantages for these two groups. Differences in growth are of interest in efforts to conserve this threatened species because size is positively correlated to survival for salmon across multiple stages of their life cycle (Groot & Margolis 1991; Healey 1991; Quinn & Peterson 1996; Roni et al. 2012) Chinook salmon in the upper John Day River, Oregon, exhibit both NRR and DSR life history patterns. Fish following the DSR life history pattern are larger than NRR fish late in the spring, possibly due to factors such as higher fish density, lower stream productivity, and colder water temperatures in their natal reach than in the downstream reaches. However, this size advantage may be lost due to adverse summer conditions. Hot summer days combined with the withdrawal of water for agriculture lead to stream water temperatures well above lethal thresholds for salmon in many downstream reaches. DSR fish have been observed in tributaries of the mainstem John Day River, however their growth and survival during summer is unknown. Close

• 13102. [Article] The Response and Effect of Emergent Coastal Vegetation to Sedimentation and the Distribution of Coastal Vegetation Communities along Environmental Gradients

  Coastal marsh vegetation is an important component in maintaining marsh stability that is threatened by changes in sedimentation, sea level rise, natural and anthropogenic disturbances, and competition ...

  Citation × Citation Citation Abstract Copy Title: The Response and Effect of Emergent Coastal Vegetation to Sedimentation and the Distribution of Coastal Vegetation Communities along Environmental Gradients Author: Lemein, Todd Coastal marsh vegetation is an important component in maintaining marsh stability that is threatened by changes in sedimentation, sea level rise, natural and anthropogenic disturbances, and competition from invasive species. Vegetation has been demonstrated to reduce wave energy, increase sedimentation, and decrease erosion in tidal environments under a range of conditions. Similarities and differences between the morphology of vegetation species may play an important role in understanding the mechanism between vegetation, sedimentation, and wave energy. Diversity of species within vegetation communities has been shown to reduce the success of biological invasions from invasive species as well as increase the ability of the community to adapt to environmental changes such as inundation period (period of time vegetation is submerged partially or fully by water). The species present along coastal marshes and specifically at the interface between vegetated marsh and unvegetated mudflat provide an opportunity to better understand the interactions between vegetation and its physical setting. In this dissertation I focus on the species and vegetation communities that are present at this interface of the terrestrial and aquatic boundary to better understand how plant communities may be characterized, how they respond to disturbance, how they are distributed, and how they may influence the physical environment in which they grow. In Chapter two, I explore the ability to use image analysis and the lateral obstruction of vegetation to describe a species density, height and diameter and evaluate the tradeoffs in using image analysis over more traditional methods. In Chapter three, I evaluate the response of an emergent vegetation species, threesquare bulrush (Schoenoplectus pungens), to different depths of complete burial as could be expected from extreme storms, hurricanes, tsunamis, or restoration efforts involving sediment amendment. Chapter four describes the distribution of coastal marsh communities of the Laurentian Great Lakes along an elevational gradient beginning at the terrestrial and aquatic boundary, identifying patterns of wetland distribution, species composition, and exotic plant invasion. In Chapter five, I conclude the dissertation with an evaluation of the effects of two morphologically distinct species of emergent marsh vegetation, threesquare bulrush and Lyngbye’s sedge (Carex lyngbyei), on the sedimentation rate and variability in Tillamook Bay, OR and compare the results to the current understanding of vegetation-sediment feedback. In Chapter two, I found that for morphologically simple species, such as S. pungens, image analysis of lateral obstruction can be used to determine important morphological characteristics of a stand of vegetation including the mean stem height, density, and mean diameter. The method provides a description of the vertical variation in morphologic structure, providing a rapid analytic tool for exploring the effects of vegetation on wave and sediment interaction. However, I note that more morphologically complex species, such as sedges and grasses may not be as easily described using image analysis. In Chapter three, I determined that aboveground biomass of S. pungens would return to pre-disturbance levels following burial by up to 40 cm of mineral sediment after two years. Vegetation was observed to survive burials depths of up to 80 cm, although initially at much lower density. The aboveground height of stems were statistically similar to unburied controls after two years, which is important for the continuation of ecosystem services such as wave attenuation. The results suggest that S. pungens is capable of returning to pre-disturbance levels of biomass following large natural sedimentation events such as extreme storms, hurricanes, or tsunamis, and that burying portions of marshes with sediment as a restoration tool is not likely to harm the buried vegetation. In Chapter four I refine and describe 21 coastal vegetation communities in the Laurentian Great Lakes and the ecological gradients along which they are distributed. Latitude, agricultural intensity, site geomorphology, substrate, and water depth were found to be the significant variables that determined community distribution. Additionally, we observed an expansion of invasive plant species near areas of high anthropogenic activity such as farms and urban centers. In Chapter five, I found that there were species-specific differences in sedimentation rate and variability in Tillamook Bay, OR. Schoenoplectus pungens was found to retain more sediment than C. lyngbyei. Sedimentation rate was observed to be variable by location within the estuary. Two patterns of sediment accumulation were observed. The first occurred along vegetation gradients, with increased sedimentation farther into vegetation beds. In the second pattern, sediment accumulation was observed to be greatest at the marsh/mudflat boundary where vegetation was dense and then decreased with increasing depth into the vegetation. In conclusion, this dissertation explores the interaction of emergent wetland vegetation with environmental factors. Image analysis provides a new tool for rapid characterization of vegetation structure, a burial experiment documents Schoenoplectus pungens’ tolerance to sand burial, a field study at Tillamook, OR documents the relationship between sediment accumulation and emergent vegetation beds, and a wetland classification is developed for coastal wetlands along the Great Lakes, which includes plant communities dominated by S. pungens. Title: The Response and Effect of Emergent Coastal Vegetation to Sedimentation and the Distribution of Coastal Vegetation Communities along Environmental Gradients Author: Lemein, Todd Coastal marsh vegetation is an important component in maintaining marsh stability that is threatened by changes in sedimentation, sea level rise, natural and anthropogenic disturbances, and competition from invasive species. Vegetation has been demonstrated to reduce wave energy, increase sedimentation, and decrease erosion in tidal environments under a range of conditions. Similarities and differences between the morphology of vegetation species may play an important role in understanding the mechanism between vegetation, sedimentation, and wave energy. Diversity of species within vegetation communities has been shown to reduce the success of biological invasions from invasive species as well as increase the ability of the community to adapt to environmental changes such as inundation period (period of time vegetation is submerged partially or fully by water). The species present along coastal marshes and specifically at the interface between vegetated marsh and unvegetated mudflat provide an opportunity to better understand the interactions between vegetation and its physical setting. In this dissertation I focus on the species and vegetation communities that are present at this interface of the terrestrial and aquatic boundary to better understand how plant communities may be characterized, how they respond to disturbance, how they are distributed, and how they may influence the physical environment in which they grow. In Chapter two, I explore the ability to use image analysis and the lateral obstruction of vegetation to describe a species density, height and diameter and evaluate the tradeoffs in using image analysis over more traditional methods. In Chapter three, I evaluate the response of an emergent vegetation species, threesquare bulrush (Schoenoplectus pungens), to different depths of complete burial as could be expected from extreme storms, hurricanes, tsunamis, or restoration efforts involving sediment amendment. Chapter four describes the distribution of coastal marsh communities of the Laurentian Great Lakes along an elevational gradient beginning at the terrestrial and aquatic boundary, identifying patterns of wetland distribution, species composition, and exotic plant invasion. In Chapter five, I conclude the dissertation with an evaluation of the effects of two morphologically distinct species of emergent marsh vegetation, threesquare bulrush and Lyngbye’s sedge (Carex lyngbyei), on the sedimentation rate and variability in Tillamook Bay, OR and compare the results to the current understanding of vegetation-sediment feedback. In Chapter two, I found that for morphologically simple species, such as S. pungens, image analysis of lateral obstruction can be used to determine important morphological characteristics of a stand of vegetation including the mean stem height, density, and mean diameter. The method provides a description of the vertical variation in morphologic structure, providing a rapid analytic tool for exploring the effects of vegetation on wave and sediment interaction. However, I note that more morphologically complex species, such as sedges and grasses may not be as easily described using image analysis. In Chapter three, I determined that aboveground biomass of S. pungens would return to pre-disturbance levels following burial by up to 40 cm of mineral sediment after two years. Vegetation was observed to survive burials depths of up to 80 cm, although initially at much lower density. The aboveground height of stems were statistically similar to unburied controls after two years, which is important for the continuation of ecosystem services such as wave attenuation. The results suggest that S. pungens is capable of returning to pre-disturbance levels of biomass following large natural sedimentation events such as extreme storms, hurricanes, or tsunamis, and that burying portions of marshes with sediment as a restoration tool is not likely to harm the buried vegetation. In Chapter four I refine and describe 21 coastal vegetation communities in the Laurentian Great Lakes and the ecological gradients along which they are distributed. Latitude, agricultural intensity, site geomorphology, substrate, and water depth were found to be the significant variables that determined community distribution. Additionally, we observed an expansion of invasive plant species near areas of high anthropogenic activity such as farms and urban centers. In Chapter five, I found that there were species-specific differences in sedimentation rate and variability in Tillamook Bay, OR. Schoenoplectus pungens was found to retain more sediment than C. lyngbyei. Sedimentation rate was observed to be variable by location within the estuary. Two patterns of sediment accumulation were observed. The first occurred along vegetation gradients, with increased sedimentation farther into vegetation beds. In the second pattern, sediment accumulation was observed to be greatest at the marsh/mudflat boundary where vegetation was dense and then decreased with increasing depth into the vegetation. In conclusion, this dissertation explores the interaction of emergent wetland vegetation with environmental factors. Image analysis provides a new tool for rapid characterization of vegetation structure, a burial experiment documents Schoenoplectus pungens’ tolerance to sand burial, a field study at Tillamook, OR documents the relationship between sediment accumulation and emergent vegetation beds, and a wetland classification is developed for coastal wetlands along the Great Lakes, which includes plant communities dominated by S. pungens. Close

• 13103. [Article] An evaluation of soil warming for increased crop production

  In regions where soil temperatures limit plant growth, artificial soil warming may be an economically feasible practice. This hypothesis was evaluated in a soil warming experiment near Corvallis, Oregon. This ...

  Citation × Citation Citation Abstract Copy Title: An evaluation of soil warming for increased crop production Author: Rykbost, K. A. In regions where soil temperatures limit plant growth, artificial soil warming may be an economically feasible practice. This hypothesis was evaluated in a soil warming experiment near Corvallis, Oregon. This experiment was prompted by the observation that multiple use of waste heat discharged in the condenser cooling water of thermal power plants may become an important consideration in the development and siting of these plants. The thermal discharge might be used to achieve increased soil temperature by circulating warm water through a subsurface pipe network. Objectives of this investigation were: (1) to determine the effect, if any, of buried line heat sources on air temperatures within a crop canopy; (2) to determine the extent to which soil temperature can be elevated with buried line heat sources maintained at various temperatures; (3) to establish the effect of subsurface heating on soil water regimes and to evaluate a subsurface irrigation system as a means of maintaining high soil water content and hence high rates of heat transfer in the vicinity of heat sources; (4) to evaluate a theoretical model for prediction of energy dissipation rates; (5) to establish the yield response to soil warming for numerous crops; and (6) to evaluate the influence of subsurface heating on soil and air temperatures and crop production in a wood frame, plastic covered greenhouse. Six individually controlled electrical heating cables were used to simulate a buried pipe network. Thirteen different crops were grown on heated and unheated areas during the four years of this study. Air and soil temperatures were monitored at over 200 locations with thermistors. Readings were taken with a computerized digital data acquisition system. Soil water content was monitored with electrical resistance blocks. Energy inputs were measured for each heating cable with kilowatt-hour meters. Air temperatures at four heights above the soil surface over bare soil and in a field corn canopy were not appreciably affected by soil warming. Statistically significant temperature increases due to soil warming were observed but they were too small to be of consequence for crop growth. Soil temperatures in the upper 25 centimeters were more responsive to solar heating than to subsurface heating. Temperature increases due to soil warming were one to five degrees centigrade at the five centimeter depth, depending on heat source temperature, time of year, time of day and crop canopy conditions. A major portion of the root zone was maintained above 20 degrees centigrade during most of the growing season. The greatest temperature increases were observed on a plot where subsurface irrigation was used to maintain high soil water content near the heat sources. During the summer substantial soil drying occurred in the vicinity of the heat sources, particularly under a field corn crop. Thermal gradients prevented rewetting by sprinkler irrigation. A subsurface irrigation system maintained a wet soil near the heat sources throughout the growing season. The rate of heat loss from buried heat sources was found to respond to changes in depth and spacing of sources, source temperature, soil surface temperature and soil water content, as predicted by theoretical considerations. A high correlation between mean monthly air temperature and mean monthly heat loss rates was found. The results indicate that the area required to reduce the temperature of circulating warm water, from a 1,000 megawatt thermal power plant, by 10 degrees centigrade would range from 10,000 hectares in the winter to 20,000 hectares in the summer under Willamette Valley climatic conditions. This requirement could be reduced by design modifications or subsurface irrigation. A wide range in crop response to soil warming was observed for different crops and for some crops in different years. The results obtained with field corn and bush beans suggest that the response to soil heating depends on the degree of adversity to which the crop is subjected. When climatic conditions and management factors are optimum soil heating has a limited effect on crop yields. When one or more of these factors are limiting soil heating becomes more effective and greater yield responses occur. In nearly all cases soil warming resulted in more rapid germination and early growth, and earlier maturation. Double cropping of bush beans and double cropping with summer and winter annual forage crops appear to be feasible with soil warming. Yield increases due to soil warming were above 50 percent for several forage and vegetable crops. Several cropping sequences were suggested. Additional input from agricultural economists and engineers is needed to determine those crop combinations which will result in the greatest economic returns from a soil warming system. Soil heating did not result in higher air temperatures in a plastic covered greenhouse. Soil temperatures were substantially increased and this resulted in an increase in tomato production of 64 percent compared with a crop grown in the greenhouse with no soil warming. Strawberry yields did not respond to soil warming in greenhouse culture and this was attributed to high air temperatures due to solar heat trapping during daylight hours. The results of this investigation suggest that soil warming with condenser cooling waters from thermal power plants is feasible. Additional information is needed to evaluate the economic and engineering aspects of a soil warming system. It is unlikely that a soil warming system can fulfill all the needs of a thermal power plant cooling system. Additional studies to evaluate other beneficial uses of waste heat to be used in combination with a soil warming system will be required. Title: An evaluation of soil warming for increased crop production Author: Rykbost, K. A. In regions where soil temperatures limit plant growth, artificial soil warming may be an economically feasible practice. This hypothesis was evaluated in a soil warming experiment near Corvallis, Oregon. This experiment was prompted by the observation that multiple use of waste heat discharged in the condenser cooling water of thermal power plants may become an important consideration in the development and siting of these plants. The thermal discharge might be used to achieve increased soil temperature by circulating warm water through a subsurface pipe network. Objectives of this investigation were: (1) to determine the effect, if any, of buried line heat sources on air temperatures within a crop canopy; (2) to determine the extent to which soil temperature can be elevated with buried line heat sources maintained at various temperatures; (3) to establish the effect of subsurface heating on soil water regimes and to evaluate a subsurface irrigation system as a means of maintaining high soil water content and hence high rates of heat transfer in the vicinity of heat sources; (4) to evaluate a theoretical model for prediction of energy dissipation rates; (5) to establish the yield response to soil warming for numerous crops; and (6) to evaluate the influence of subsurface heating on soil and air temperatures and crop production in a wood frame, plastic covered greenhouse. Six individually controlled electrical heating cables were used to simulate a buried pipe network. Thirteen different crops were grown on heated and unheated areas during the four years of this study. Air and soil temperatures were monitored at over 200 locations with thermistors. Readings were taken with a computerized digital data acquisition system. Soil water content was monitored with electrical resistance blocks. Energy inputs were measured for each heating cable with kilowatt-hour meters. Air temperatures at four heights above the soil surface over bare soil and in a field corn canopy were not appreciably affected by soil warming. Statistically significant temperature increases due to soil warming were observed but they were too small to be of consequence for crop growth. Soil temperatures in the upper 25 centimeters were more responsive to solar heating than to subsurface heating. Temperature increases due to soil warming were one to five degrees centigrade at the five centimeter depth, depending on heat source temperature, time of year, time of day and crop canopy conditions. A major portion of the root zone was maintained above 20 degrees centigrade during most of the growing season. The greatest temperature increases were observed on a plot where subsurface irrigation was used to maintain high soil water content near the heat sources. During the summer substantial soil drying occurred in the vicinity of the heat sources, particularly under a field corn crop. Thermal gradients prevented rewetting by sprinkler irrigation. A subsurface irrigation system maintained a wet soil near the heat sources throughout the growing season. The rate of heat loss from buried heat sources was found to respond to changes in depth and spacing of sources, source temperature, soil surface temperature and soil water content, as predicted by theoretical considerations. A high correlation between mean monthly air temperature and mean monthly heat loss rates was found. The results indicate that the area required to reduce the temperature of circulating warm water, from a 1,000 megawatt thermal power plant, by 10 degrees centigrade would range from 10,000 hectares in the winter to 20,000 hectares in the summer under Willamette Valley climatic conditions. This requirement could be reduced by design modifications or subsurface irrigation. A wide range in crop response to soil warming was observed for different crops and for some crops in different years. The results obtained with field corn and bush beans suggest that the response to soil heating depends on the degree of adversity to which the crop is subjected. When climatic conditions and management factors are optimum soil heating has a limited effect on crop yields. When one or more of these factors are limiting soil heating becomes more effective and greater yield responses occur. In nearly all cases soil warming resulted in more rapid germination and early growth, and earlier maturation. Double cropping of bush beans and double cropping with summer and winter annual forage crops appear to be feasible with soil warming. Yield increases due to soil warming were above 50 percent for several forage and vegetable crops. Several cropping sequences were suggested. Additional input from agricultural economists and engineers is needed to determine those crop combinations which will result in the greatest economic returns from a soil warming system. Soil heating did not result in higher air temperatures in a plastic covered greenhouse. Soil temperatures were substantially increased and this resulted in an increase in tomato production of 64 percent compared with a crop grown in the greenhouse with no soil warming. Strawberry yields did not respond to soil warming in greenhouse culture and this was attributed to high air temperatures due to solar heat trapping during daylight hours. The results of this investigation suggest that soil warming with condenser cooling waters from thermal power plants is feasible. Additional information is needed to evaluate the economic and engineering aspects of a soil warming system. It is unlikely that a soil warming system can fulfill all the needs of a thermal power plant cooling system. Additional studies to evaluate other beneficial uses of waste heat to be used in combination with a soil warming system will be required. Close

• 13104. [Article] Molecular characterization of bacterial populations implicated in the anaerobic metabolism of toxic plant alkaloids from two different experimental and environmental sources

  There have been many studies that describe the protective degradation or metabolism of potentially harmful plant toxins, such as, mimosine from Leucaena leuconcephala, pyrrolizidine alkaloids from tansy ...

  Citation × Citation Citation Abstract Copy Title: Molecular characterization of bacterial populations implicated in the anaerobic metabolism of toxic plant alkaloids from two different experimental and environmental sources Author: Rattray, Rogan MacKay There have been many studies that describe the protective degradation or metabolism of potentially harmful plant toxins, such as, mimosine from Leucaena leuconcephala, pyrrolizidine alkaloids from tansy ragwort (Senecio jacobaea), oxalate and some mycotoxins by rumen microbes. There are many cases of plant-related toxicoses suffered by ruminant animals where there are no microbes known to offer protection. Ergot alkaloids produced by the endophytic fungus Neotyphodium coenophialum have been shown to cause the syndromes of fescue foot and summer slump in animals grazing tall fescue (Festuca arundinacea) grass varieties that carry the endophyte. Economic losses due to these diseases have been estimated to be about $1 billion per year. For this reason, it is economically desirable to find one or more microbes that could be introduced into the rumen environment to protect animals from fescue toxicosis and pyrrolizidine alkaloid toxicosis. Studies that have found protective microbes focused on identification of those microbes using mainly phenotyping and enrichment or isolation techniques. In the studies presented here, two different experimental and environmental systems were examined. Culture-independent molecular biology techniques were used to take advantage of differences found between bacteria in the 16S small ribosomal subunit gene as a means of characterizing diversity. Analytical chemistry techniques were used to place diversity observations in the context of function. Microbes within a consortia culture derived from the rumen of a sheep were previously shown to metabolize pyrrolizidine alkaloids found in the invasive weed, tansy ragwort. Thin layer chromatography was used to monitor microbial activity. The bacterial enrichment was characterized by molecular cloning techniques and by the molecular fingerprinting technique of denaturing gradient gel electrophoresis (DGGE). Phylogenetic analysis of the enrichment revealed that the consortium is composed of no more than five putative bacterial species which associated to the Anaerovibrio, Desulfovibrio, Megasphaera, Prevotella, and Synergistes generas. The DGGE results were directly compared to the cloning data by amplifying eight phylogenetically representative clones by polymerase chain reaction (PCR) and analyzing them by DGGE. Direct DGGE analysis of the enrichment displayed greater 16S diversity than the clone library used in this study, suggesting that at least one of the organisms present in the enrichment comprises less than 1% of the total cell population. Earthworms of the species Eisenia fetida are commonly used in the practice of vermicomposting. This is the process by which worms are used in a closed bin or pit, to aid in the breakdown of manure and other agricultural waste in order to generate highly fertile soil from the worm's digestive waste products, or cast. The worms were used in a two-treatment vermicompost experiment. One treatment was given tall fescue seed assayed to contain over 10,000 parts per billion of the endophyte toxin ergovaline (E+ treatment). The other treatment was used as a control and was given tall fescue seed with ergovaline amounts that fell below analytical levels of detection (E- treatment). Many of the worms originally introduced into the E+ treatment died off before a population of worms established itself as a productive vermicompost system. The success of this population of worms may be due to the presence of beneficial or protective microbes within their digestive tract. Digestive tracts were dissected and collected from worms of each treatment in February of 2007. The guts were homogenized and anaerobically cultured with and without added ergovaline. The disappearance of ergovaline and the stereo-isomer ergovalinine from worm-gut cultures was monitored daily by high-performance liquid chromatography (HPLC). DNA was purified from the same gut homogenate samples used for incubation experiments. Cloning of the 16S gene was applied to determine the identity of the bacteria present in the treatments during the month of February. The computational program Mr. Bayes was used to group restriction-fragment length polymorphism (RFLP) patterns based on their uniqueness. The program DOTUR was used to estimate the level of diversity based on ribotype distances. With the aim of encompassing the fullest amount of represented sequence diversity, these data were used to specifically select 192 clones from each 960 clone library. Selected clones were analyzed by sequencing the 16S insert. Clone sequences from both treatments made associations to bacterial 16S reference sequences in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes, Alpha, Beta, Gamma, Delta and Epsilon proteobacteria, Verrucomicrobia and unclassifed bacterial sequences. Four clones associated best with a plastid sequence derived from a green algae species. The global similarity between libraries indicated that the populations were not significantly different at the time of sampling. HPLC data showed no observable loss of ergovaline from incubations of E+ or E- worm treatment samples taken in February. Incubation experiments in December of 2006 using only E+ treatment worm guts had demonstrated the potential for microbial metabolism of ergovaline; however, no molecular work was done at that time. An integrative approach was taken to describe the function and bacterial composition of the two systems studied. The use of analytical chemistry techniques placed the observations of microbial diversity into context. Thin-layer chromatography was used to check that the ability of the pyrrolizidine alkaloid-degrading enrichment was still intact after being revived from long-term storage. This allowed for direct comparisons to earlier data published about the identity of microbes within these enrichments. HPLC data indicated that worm-gut homogenates characterized in February did not demonstrate the same metabolic activity as was observed during an incubation of gut material taken from E+ treatment worms in December. Since there was no previous molecular data to compare potential differences in bacterial diversity from these two time points, the molecular data collected in February will be used as a reference of the background population at a time when there was no metabolism of ergovaline. It is intended that the results of these studies will further the understanding of which microbes are involved in the metabolism of the particular compound of interest. In this way, steps may be made toward refining the culturing and propagation of desirable bacteria that may potentially serve as a treatment for ruminant animals challenged by the presence of either pyrrolizidine or ergot alkaloids in their diets. Title: Molecular characterization of bacterial populations implicated in the anaerobic metabolism of toxic plant alkaloids from two different experimental and environmental sources Author: Rattray, Rogan MacKay There have been many studies that describe the protective degradation or metabolism of potentially harmful plant toxins, such as, mimosine from Leucaena leuconcephala, pyrrolizidine alkaloids from tansy ragwort (Senecio jacobaea), oxalate and some mycotoxins by rumen microbes. There are many cases of plant-related toxicoses suffered by ruminant animals where there are no microbes known to offer protection. Ergot alkaloids produced by the endophytic fungus Neotyphodium coenophialum have been shown to cause the syndromes of fescue foot and summer slump in animals grazing tall fescue (Festuca arundinacea) grass varieties that carry the endophyte. Economic losses due to these diseases have been estimated to be about $1 billion per year. For this reason, it is economically desirable to find one or more microbes that could be introduced into the rumen environment to protect animals from fescue toxicosis and pyrrolizidine alkaloid toxicosis. Studies that have found protective microbes focused on identification of those microbes using mainly phenotyping and enrichment or isolation techniques. In the studies presented here, two different experimental and environmental systems were examined. Culture-independent molecular biology techniques were used to take advantage of differences found between bacteria in the 16S small ribosomal subunit gene as a means of characterizing diversity. Analytical chemistry techniques were used to place diversity observations in the context of function. Microbes within a consortia culture derived from the rumen of a sheep were previously shown to metabolize pyrrolizidine alkaloids found in the invasive weed, tansy ragwort. Thin layer chromatography was used to monitor microbial activity. The bacterial enrichment was characterized by molecular cloning techniques and by the molecular fingerprinting technique of denaturing gradient gel electrophoresis (DGGE). Phylogenetic analysis of the enrichment revealed that the consortium is composed of no more than five putative bacterial species which associated to the Anaerovibrio, Desulfovibrio, Megasphaera, Prevotella, and Synergistes generas. The DGGE results were directly compared to the cloning data by amplifying eight phylogenetically representative clones by polymerase chain reaction (PCR) and analyzing them by DGGE. Direct DGGE analysis of the enrichment displayed greater 16S diversity than the clone library used in this study, suggesting that at least one of the organisms present in the enrichment comprises less than 1% of the total cell population. Earthworms of the species Eisenia fetida are commonly used in the practice of vermicomposting. This is the process by which worms are used in a closed bin or pit, to aid in the breakdown of manure and other agricultural waste in order to generate highly fertile soil from the worm's digestive waste products, or cast. The worms were used in a two-treatment vermicompost experiment. One treatment was given tall fescue seed assayed to contain over 10,000 parts per billion of the endophyte toxin ergovaline (E+ treatment). The other treatment was used as a control and was given tall fescue seed with ergovaline amounts that fell below analytical levels of detection (E- treatment). Many of the worms originally introduced into the E+ treatment died off before a population of worms established itself as a productive vermicompost system. The success of this population of worms may be due to the presence of beneficial or protective microbes within their digestive tract. Digestive tracts were dissected and collected from worms of each treatment in February of 2007. The guts were homogenized and anaerobically cultured with and without added ergovaline. The disappearance of ergovaline and the stereo-isomer ergovalinine from worm-gut cultures was monitored daily by high-performance liquid chromatography (HPLC). DNA was purified from the same gut homogenate samples used for incubation experiments. Cloning of the 16S gene was applied to determine the identity of the bacteria present in the treatments during the month of February. The computational program Mr. Bayes was used to group restriction-fragment length polymorphism (RFLP) patterns based on their uniqueness. The program DOTUR was used to estimate the level of diversity based on ribotype distances. With the aim of encompassing the fullest amount of represented sequence diversity, these data were used to specifically select 192 clones from each 960 clone library. Selected clones were analyzed by sequencing the 16S insert. Clone sequences from both treatments made associations to bacterial 16S reference sequences in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes, Alpha, Beta, Gamma, Delta and Epsilon proteobacteria, Verrucomicrobia and unclassifed bacterial sequences. Four clones associated best with a plastid sequence derived from a green algae species. The global similarity between libraries indicated that the populations were not significantly different at the time of sampling. HPLC data showed no observable loss of ergovaline from incubations of E+ or E- worm treatment samples taken in February. Incubation experiments in December of 2006 using only E+ treatment worm guts had demonstrated the potential for microbial metabolism of ergovaline; however, no molecular work was done at that time. An integrative approach was taken to describe the function and bacterial composition of the two systems studied. The use of analytical chemistry techniques placed the observations of microbial diversity into context. Thin-layer chromatography was used to check that the ability of the pyrrolizidine alkaloid-degrading enrichment was still intact after being revived from long-term storage. This allowed for direct comparisons to earlier data published about the identity of microbes within these enrichments. HPLC data indicated that worm-gut homogenates characterized in February did not demonstrate the same metabolic activity as was observed during an incubation of gut material taken from E+ treatment worms in December. Since there was no previous molecular data to compare potential differences in bacterial diversity from these two time points, the molecular data collected in February will be used as a reference of the background population at a time when there was no metabolism of ergovaline. It is intended that the results of these studies will further the understanding of which microbes are involved in the metabolism of the particular compound of interest. In this way, steps may be made toward refining the culturing and propagation of desirable bacteria that may potentially serve as a treatment for ruminant animals challenged by the presence of either pyrrolizidine or ergot alkaloids in their diets. Close

• 13105. [Article] Agroforestry farming in American Samoa : a classification and assessment

  Agroforestry is a traditional farming practice in American Samoa that has helped to sustain the livelihood of the native population for centuries. These once self-sufficient islands have become economically ...

  Citation × Citation Citation Abstract Copy Title: Agroforestry farming in American Samoa : a classification and assessment Author: Tuitele-Lewis, Jeannette D. Agroforestry is a traditional farming practice in American Samoa that has helped to sustain the livelihood of the native population for centuries. These once self-sufficient islands have become economically dependent on U.S monies and other external resources during the past century. Dependency has caused a shift in the carrying capacity of the islands and has changed cultural attitudes regarding land use. This attitude is expressed on the landscape of changing agricultural and communal lands. Preserving traditional agroforestry practices and improving these systems may be important factors contributing to the future ecological, economic, and cultural sustainability of the territory. The goal of this study was to document and describe agroforestry farming in American Samoa in order to provide base-line information regarding the utilization of agroforestry species, agroforestry farming incentives and constraints, and current practices and systems. Thirty-eight farmers were randomly selected and farmer interviews and field surveys were conducted between the months of May-August 2003. Formal survey questions for the interview were divided into five major sections: woody species usage, livestock, inputs and soil, land tenure, and farmer demographics. Site selection corresponded with the participant farmers. Basic topographical information was collected for each site. Agroforestry practices mentioned during the interview process that were observed on site were documented. Each agroforestry site was placed into an initial classification type based on a visual assessment of plot size, species diversity, and vertical vegetative structure. Subplot data regarding species composition and vertical canopy structure was measured for each site. Data collection was divided into five vertical layers primarily by height: 1) low crop (<1.5m), 2) shrub/sapling (1.5-4m), 3) small tree (4-l0m), 4) large tree (10+m) and 5) climbing vines. For each subplot all ethnobotanically useful plant species were identified. Percent cover of useful species in each stratum layer was estimated and assigned one of seven percent cover classes. Subplot cover classes were averaged to obtain a single site estimate for each species in each stratum. Results from the farmer interviews suggest that agroforestry systems continue to be an important cultural and product resource in American Samoa. Although there is no longer the same level of dependency on these systems for meeting basic needs, agroforestry products continue to supplement household diets and are utilized for a variety of non-timber forest products and ecological services. Several agroforestry practices were observed among the farms in the study. However, the effectiveness of some of the practices including windbreaks, fallow, and erosion control was not optimal. This indicated that farmers could greatly benefit from institutionalized agroforestry practices such as appropriate spacing for wind filtration, improved fallow, and contour farming. Incentives and constraints for practicing agroforestry farming were identified. Some incentives included product variety, tradition, and a growing need for land-use efficiency. Identified constraints included time investment for production and poor labor resources, decreased profit when compared to mono-cultural farming, and the lack of planning prior to agroforestry implementation. The communal land tenure system acted as both an incentive and a disincentive for practicing agroforestry. The initial classification of agroforestry systems included home tree gardens, mixed crop plantations, transitional systems, and open canopy with dispersed tree systems. Agroforestry systems existed along an ecological complexity continuum, where complexity was measured by species diversity and vertical structure. A quantitative assessment of species composition and structure was used as a more objective approach to classifying local agroforestry systems. Non-metric multidimensional scaling was used to ordinate sites along a gradient based on species composition and structure. Several environmental and socio-economic variables were investigated to determine whether any of them demonstrated relationships with vegetative patterns. Species diversity, average number of canopy stratum layers, and elevation were three variables correlated with vegetative patterns. Sites that had high species diversity and were multi-structured were placed at the upper end of the gradient, while sites that had lower diversity with simple structure were generally placed at the lower end of the gradient. This supported the ecological complexity continuum. Less complex sites were associated with high elevations indicating that systems on the heavily populated lowland regions were more species rich and structurally diverse. The classification based on the cluster analysis indicated that distinct groups did not exist, as there was significant overlap. In general, groups derived from the cluster analysis were similar to those based on the visual assessment. One difference was that in the cluster analysis taro and gatae (Erythrina spp.) dominated sites emerged as a separate group. In addition, the cluster analysis was able to distinguish several subgroups within the mixed crop plantation type. No single socio-economic variable was correlated with vegetative patterns. This suggests that socio-economic variables do not determine vegetation in agroforestry systems and that human preference may be more of a driving factor than initially expected. It is likely that the availability of external resources allows for the selection of species within agroforestry systems to be based on choice rather than need. This trend is likely to increase as people become less dependent upon agroforestry systems to supplement needs. Traditional and institutionalized agroforestry systems have the potential to contribute to increasing self-sufficiency among American Samoan households. Because the importance of these systems is often not realized, the active promotion and education of agroforestry practices is essential. The classification of agroforestry systems provides an organizational framework for future research to build upon. The concept of the ecological complexity continuum where agroforestry systems fall along major points may be useful for answering socio-economic and ecological questions related to local agroforestry production. Title: Agroforestry farming in American Samoa : a classification and assessment Author: Tuitele-Lewis, Jeannette D. Agroforestry is a traditional farming practice in American Samoa that has helped to sustain the livelihood of the native population for centuries. These once self-sufficient islands have become economically dependent on U.S monies and other external resources during the past century. Dependency has caused a shift in the carrying capacity of the islands and has changed cultural attitudes regarding land use. This attitude is expressed on the landscape of changing agricultural and communal lands. Preserving traditional agroforestry practices and improving these systems may be important factors contributing to the future ecological, economic, and cultural sustainability of the territory. The goal of this study was to document and describe agroforestry farming in American Samoa in order to provide base-line information regarding the utilization of agroforestry species, agroforestry farming incentives and constraints, and current practices and systems. Thirty-eight farmers were randomly selected and farmer interviews and field surveys were conducted between the months of May-August 2003. Formal survey questions for the interview were divided into five major sections: woody species usage, livestock, inputs and soil, land tenure, and farmer demographics. Site selection corresponded with the participant farmers. Basic topographical information was collected for each site. Agroforestry practices mentioned during the interview process that were observed on site were documented. Each agroforestry site was placed into an initial classification type based on a visual assessment of plot size, species diversity, and vertical vegetative structure. Subplot data regarding species composition and vertical canopy structure was measured for each site. Data collection was divided into five vertical layers primarily by height: 1) low crop (<1.5m), 2) shrub/sapling (1.5-4m), 3) small tree (4-l0m), 4) large tree (10+m) and 5) climbing vines. For each subplot all ethnobotanically useful plant species were identified. Percent cover of useful species in each stratum layer was estimated and assigned one of seven percent cover classes. Subplot cover classes were averaged to obtain a single site estimate for each species in each stratum. Results from the farmer interviews suggest that agroforestry systems continue to be an important cultural and product resource in American Samoa. Although there is no longer the same level of dependency on these systems for meeting basic needs, agroforestry products continue to supplement household diets and are utilized for a variety of non-timber forest products and ecological services. Several agroforestry practices were observed among the farms in the study. However, the effectiveness of some of the practices including windbreaks, fallow, and erosion control was not optimal. This indicated that farmers could greatly benefit from institutionalized agroforestry practices such as appropriate spacing for wind filtration, improved fallow, and contour farming. Incentives and constraints for practicing agroforestry farming were identified. Some incentives included product variety, tradition, and a growing need for land-use efficiency. Identified constraints included time investment for production and poor labor resources, decreased profit when compared to mono-cultural farming, and the lack of planning prior to agroforestry implementation. The communal land tenure system acted as both an incentive and a disincentive for practicing agroforestry. The initial classification of agroforestry systems included home tree gardens, mixed crop plantations, transitional systems, and open canopy with dispersed tree systems. Agroforestry systems existed along an ecological complexity continuum, where complexity was measured by species diversity and vertical structure. A quantitative assessment of species composition and structure was used as a more objective approach to classifying local agroforestry systems. Non-metric multidimensional scaling was used to ordinate sites along a gradient based on species composition and structure. Several environmental and socio-economic variables were investigated to determine whether any of them demonstrated relationships with vegetative patterns. Species diversity, average number of canopy stratum layers, and elevation were three variables correlated with vegetative patterns. Sites that had high species diversity and were multi-structured were placed at the upper end of the gradient, while sites that had lower diversity with simple structure were generally placed at the lower end of the gradient. This supported the ecological complexity continuum. Less complex sites were associated with high elevations indicating that systems on the heavily populated lowland regions were more species rich and structurally diverse. The classification based on the cluster analysis indicated that distinct groups did not exist, as there was significant overlap. In general, groups derived from the cluster analysis were similar to those based on the visual assessment. One difference was that in the cluster analysis taro and gatae (Erythrina spp.) dominated sites emerged as a separate group. In addition, the cluster analysis was able to distinguish several subgroups within the mixed crop plantation type. No single socio-economic variable was correlated with vegetative patterns. This suggests that socio-economic variables do not determine vegetation in agroforestry systems and that human preference may be more of a driving factor than initially expected. It is likely that the availability of external resources allows for the selection of species within agroforestry systems to be based on choice rather than need. This trend is likely to increase as people become less dependent upon agroforestry systems to supplement needs. Traditional and institutionalized agroforestry systems have the potential to contribute to increasing self-sufficiency among American Samoan households. Because the importance of these systems is often not realized, the active promotion and education of agroforestry practices is essential. The classification of agroforestry systems provides an organizational framework for future research to build upon. The concept of the ecological complexity continuum where agroforestry systems fall along major points may be useful for answering socio-economic and ecological questions related to local agroforestry production. Close

• 13106. [Article] Science and efficacy of mild sodium hydroxide treatments in enzyme-based wheat straw-to-glucose processing

  The work described in this dissertation focused on chemistry related to the use of aqueous sodium hydroxide as a treatment in the processing of wheat straw. A major emphasis was the comprehensive evaluation ...

  Citation × Citation Citation Abstract Copy Title: Science and efficacy of mild sodium hydroxide treatments in enzyme-based wheat straw-to-glucose processing Author: Sophonputtanaphoca, Supaporn The work described in this dissertation focused on chemistry related to the use of aqueous sodium hydroxide as a treatment in the processing of wheat straw. A major emphasis was the comprehensive evaluation of straw component partitioning due to sodium hydroxide (NaOH) processing. This was evaluated over a range of NaOH concentrations (0­‐10%, w/v), all at 50°C, 5 h treatment period, and 3% solid loading. Solid and liquid phases resulting from NaOH treatments were evaluated. Total solids recovered in the NaOH­‐treated solid phase ranged from 47.4­‐88.0%. Overall carbohydrate recovery in the combined solid and liquid phases was negatively correlated with the alkali concentration of the treatment liquor. The glucan content of the NaOH‐treated solid phase ranged from 37.2­‐67.4%. Glucan recovery in the solid phase was relatively high in all cases, the minimum value being ~98%. Increasing amounts of xylan partitioned into the liquid phase as sodium hydroxide concentrations increased – it ranged from 31­‐83% of the xylan being recovered in the soluble phase. Carbohydrate analyses of the pretreated liquor revealed that the majority of carbohydrate loss from the solid fraction could be recovered in the liquid phase in form of oligomers and monomers due to alkaline degradation. The interconversion of glucose, fructose, and mannose under the alkaline condition played an important role in the presence of those sugars. Increase in NaOH concentration contributed to increase in amount of cellulose­‐derived and hemicellulose‐derived oligomers in the pretreated liquor. All oligomers except fructooligomers in NaOH pretreated liquor were higher than those found in water extraction at 50°C, 5 h. Total carbohydrate recovery from the solid and liquid fractions was as high as 99% for glucose and glucan in 5% NaOH treatment and 80‐95% for xylose and xylan in 1-­10% NaOH treatment. The presence of NaOH as extraction reagent dramatically induced lignin and ash removal from the pretreated solid with up to 63% acid insoluble lignin (AIL) and 87% ash extraction. Solid fractions resulting from NaOH pretreatments (up to 5% NaOH) were tested for their susceptibility to enzymatic saccharification using cellulase and cellulase/xylanase enzyme preparations. The cellulase/xylanase enzyme preparation was found to be more effective at cellulose saccharification than the cellulase enzyme preparation alone. Maximum glucose yield, which corresponded to the 5% NaOH treatment, was 82% over the standard 48 h saccharification period. Extended saccharifications times to 120 h showed that the conversion yield approached 90%. Sequential treatments of the straw (i.e. initial alkali treatment – first enzyme saccharification – second alkali treatment ‐ second enzyme treatment) revealed the NaOH treatment has the potential to render essentially all (~99%) of the straw glucan susceptible to enzyme saccharification. This suggests that the layered molecular arrangement of cellulose, hemicellulose, and lignin in the cell wall impacts biomass recalcitrance and glucan conversion yield. The other major focus of this dissertation research was the characterization of alkali neutralization, which occurs during the aqueous alkali processing of wheat straw. The approach taken was to evaluate the time course of alkali uptake and to determine the underlying nature of alkali uptake. The knowledge generated from this study is useful for understanding the nature of the alkali‐induced chemistry that is at the heart of alkali processing of agricultural byproducts, foods, and forest products. Alkali uptake/acid generation measurements were monitored for wheat straw suspensions at pH 11 and 30°C. The first phase of alkali uptake corresponded to the 30‐second time period over which the pH of the wheat straw suspension was adjusted from its original pH (~6.6) to pH 11. Alkali neutralization during this period was attributed to the instantaneous ionization of solvent accessible Bronstad acids. Following pH adjustment to 11.0, the time course of subsequent alkali uptake was recorded. The time course appeared biphasic. The early phase, which corresponded to the relatively rapid uptake of alkali, was evident during the first 24 hours. The later phase, which was characterized by the relatively slow uptake of alkali, was maintained for the length of the study (up to 96 hours). Alkali uptake during the early phase of the time course appears to be determined by the rate of hydrolysis of readily accessible esters – primarily acetic acid esters (acetyl groups). Alkali uptake during the later phase of the time course appears to be impacted by the rate of alkali penetration into the straw and the rate of production of alkali‐induced acid degradation products. The uptake of alkali in the pH adjustment phase was ~ 120 μEq per gram wheat straw, the uptake of alkali in the early phase of time course was ~ 1,064 μEq per gram wheat straw, and the rate of uptake in the later phase of the time course 6.10 μEq per gram wheat straw per hour. Amount of acetyl groups, ferulic acid, and p-­coumaric acid generated during 96-­h pretreatment revealed that they are major esters being hydrolyzed under the studied condition. Combined, these ester-­derived acids contributed up to ~ 28% of overall alkali uptake. In addition, alkaline degradation products quantified in this study showed additional ~ 28% contribution to the overall alkali uptake. Title: Science and efficacy of mild sodium hydroxide treatments in enzyme-based wheat straw-to-glucose processing Author: Sophonputtanaphoca, Supaporn The work described in this dissertation focused on chemistry related to the use of aqueous sodium hydroxide as a treatment in the processing of wheat straw. A major emphasis was the comprehensive evaluation of straw component partitioning due to sodium hydroxide (NaOH) processing. This was evaluated over a range of NaOH concentrations (0­‐10%, w/v), all at 50°C, 5 h treatment period, and 3% solid loading. Solid and liquid phases resulting from NaOH treatments were evaluated. Total solids recovered in the NaOH­‐treated solid phase ranged from 47.4­‐88.0%. Overall carbohydrate recovery in the combined solid and liquid phases was negatively correlated with the alkali concentration of the treatment liquor. The glucan content of the NaOH‐treated solid phase ranged from 37.2­‐67.4%. Glucan recovery in the solid phase was relatively high in all cases, the minimum value being ~98%. Increasing amounts of xylan partitioned into the liquid phase as sodium hydroxide concentrations increased – it ranged from 31­‐83% of the xylan being recovered in the soluble phase. Carbohydrate analyses of the pretreated liquor revealed that the majority of carbohydrate loss from the solid fraction could be recovered in the liquid phase in form of oligomers and monomers due to alkaline degradation. The interconversion of glucose, fructose, and mannose under the alkaline condition played an important role in the presence of those sugars. Increase in NaOH concentration contributed to increase in amount of cellulose­‐derived and hemicellulose‐derived oligomers in the pretreated liquor. All oligomers except fructooligomers in NaOH pretreated liquor were higher than those found in water extraction at 50°C, 5 h. Total carbohydrate recovery from the solid and liquid fractions was as high as 99% for glucose and glucan in 5% NaOH treatment and 80‐95% for xylose and xylan in 1-­10% NaOH treatment. The presence of NaOH as extraction reagent dramatically induced lignin and ash removal from the pretreated solid with up to 63% acid insoluble lignin (AIL) and 87% ash extraction. Solid fractions resulting from NaOH pretreatments (up to 5% NaOH) were tested for their susceptibility to enzymatic saccharification using cellulase and cellulase/xylanase enzyme preparations. The cellulase/xylanase enzyme preparation was found to be more effective at cellulose saccharification than the cellulase enzyme preparation alone. Maximum glucose yield, which corresponded to the 5% NaOH treatment, was 82% over the standard 48 h saccharification period. Extended saccharifications times to 120 h showed that the conversion yield approached 90%. Sequential treatments of the straw (i.e. initial alkali treatment – first enzyme saccharification – second alkali treatment ‐ second enzyme treatment) revealed the NaOH treatment has the potential to render essentially all (~99%) of the straw glucan susceptible to enzyme saccharification. This suggests that the layered molecular arrangement of cellulose, hemicellulose, and lignin in the cell wall impacts biomass recalcitrance and glucan conversion yield. The other major focus of this dissertation research was the characterization of alkali neutralization, which occurs during the aqueous alkali processing of wheat straw. The approach taken was to evaluate the time course of alkali uptake and to determine the underlying nature of alkali uptake. The knowledge generated from this study is useful for understanding the nature of the alkali‐induced chemistry that is at the heart of alkali processing of agricultural byproducts, foods, and forest products. Alkali uptake/acid generation measurements were monitored for wheat straw suspensions at pH 11 and 30°C. The first phase of alkali uptake corresponded to the 30‐second time period over which the pH of the wheat straw suspension was adjusted from its original pH (~6.6) to pH 11. Alkali neutralization during this period was attributed to the instantaneous ionization of solvent accessible Bronstad acids. Following pH adjustment to 11.0, the time course of subsequent alkali uptake was recorded. The time course appeared biphasic. The early phase, which corresponded to the relatively rapid uptake of alkali, was evident during the first 24 hours. The later phase, which was characterized by the relatively slow uptake of alkali, was maintained for the length of the study (up to 96 hours). Alkali uptake during the early phase of the time course appears to be determined by the rate of hydrolysis of readily accessible esters – primarily acetic acid esters (acetyl groups). Alkali uptake during the later phase of the time course appears to be impacted by the rate of alkali penetration into the straw and the rate of production of alkali‐induced acid degradation products. The uptake of alkali in the pH adjustment phase was ~ 120 μEq per gram wheat straw, the uptake of alkali in the early phase of time course was ~ 1,064 μEq per gram wheat straw, and the rate of uptake in the later phase of the time course 6.10 μEq per gram wheat straw per hour. Amount of acetyl groups, ferulic acid, and p-­coumaric acid generated during 96-­h pretreatment revealed that they are major esters being hydrolyzed under the studied condition. Combined, these ester-­derived acids contributed up to ~ 28% of overall alkali uptake. In addition, alkaline degradation products quantified in this study showed additional ~ 28% contribution to the overall alkali uptake. Close

• 13107. [Article] The optimal allocation of watershed conservation funding : a case study of the John Day River Basin, Oregon

  This study determines the optimal allocation of watershed conservation funds in the John Day River Basin, Oregon. Fund managers can use a variety of targeting schemes to allocate their limited resources. ...

  Citation × Citation Citation Abstract Copy Title: The optimal allocation of watershed conservation funding : a case study of the John Day River Basin, Oregon Author: Skelton, Katharine This study determines the optimal allocation of watershed conservation funds in the John Day River Basin, Oregon. Fund managers can use a variety of targeting schemes to allocate their limited resources. Depending on which targeting criteria is used, they may or may not be achieving the maximum environmental benefits per dollar expended, a policy goal that is increasingly being adopted for conservation programs. Previous studies have provided the theory behind this optimal allocation of funds, but none, to the researcher's knowledge, have attempted a case study to illustrate the optimal allocation of funds as well as the misallocations that could result. Watershed conservation policies are very important, especially here in the Pacific Northwest where salmonid populations are endangered. As stream temperatures are lowered, salmonid recruitment increases. Improvements in riparian vegetation provide stream shade and bank stability. Shade decreases stream temperatures by preventing solar radiation from reaching the stream, while bank stability allows streams to become narrower and deeper, with more vegetative overhang. Narrower streams have less surface area to come in contact with solar radiation and vegetative overhang provides additional shade. A simultaneous equation system was used to estimate stream temperature and fish recruitment models for the thirteen streams studied, classified into three environmental attribute clusters. Fish recruitment models were developed for rainbow trout, Chinook salmon and speckled dace. Marginal values for rainbow trout and Chinook salmon from previous studies were used to calculate the total marginal benefits to society from increasing cold-water salmonid species. The analytical models were the basis for determining the optimal fund allocation, after considering the cumulative, indirect and correlated benefits derived from improving riparian vegetation conditions. Policy managers and previous studies have failed to consider these additional environmental benefits, particularly jointly produced benefits. Two scenarios were determined for the optimal fund allocation, based on the riparian conditions of the surveyed stream reaches. The riparian conditions are reported using a vegetative use index from one (the worst conditions) to four (the best conditions). Under the first scenario, which assumes a full range of riparian conditions, Granite Creek should receive funding priority with $51,756 in marginal social benefits received from improving the streamside vegetative use rating from one to four, for one mile of stream. Deerdorff Creek and Reynolds Creek would be the next two streams to receive funding, respectively, both for a vegetative use improvement from one to two. The second scenario assumes that only vegetative conditions in the surveyed segments exist in the stream. Under these circumstances, only six of the thirteen streams would even be considered for funding, with Granite Creek again receiving priority. Improving the vegetative use rating in Granite Creek from three to four, for one stream mile, will produce $9355 in marginal social benefits. Murderer's Creek and Camp Creek would be the next streams to receive funding for a vegetative use improvement from three to four and one to two, respectively. In addition to determining the optimal fund allocation, discussion is included about the policy implications that would result from ignoring the cumulative, indirect and correlated benefits. For the fund misallocation discussion Granite Creek was assumed to be the stream that should be given funding priority for an improvement from three to four only, with Murderer's Creek and Camp Creek receiving funds second and third, respectively. If an on-site, physical criterion is used as the targeting criteria, such as stream temperatures or the riparian vegetation conditions, then the cumulative benefits will be ignored. Two possible misallocations could result when the cumulative effects are ignored. First, streams with very high temperatures may receive funding, even if improvements in the vegetative use index will not lower temperatures enough so that salmonids can survive. Second, streams that have temperatures below the optimal range for salmonids, but have poor riparian vegetation may be funded. Improving streamside vegetation in those streams would be a misallocation of funds. Targeting based on the highest stream temperature criteria would only consider the direct benefits received from improving streamside vegetation. Under a temperature- based targeting criteria, Alder Creek would be the first stream funded with Mountain and Murderer's Creek following. If we assume only two streams could be funded, then there will be a loss of almost all marginal benefits per stream mile. If the change in the stream temperatures is used as the targeting criteria, and indirect benefits are ignored, then Camp Creek would receive funding priority, with Mountain Creek, Granite Creek and Murderer's Creek following. If it is again assumed that only two streams could be funded, this targeting scheme would result in an approximate loss to society of up to 87 percent in marginal benefits, per stream mile Additionally, all of the indirect benefits need to be taken into consideration in order to optimally allocate funds. If Chinook salmon are ignored, and rainbow trout are the only cold-water species taken into account, then society will forgo around 50 percent of marginal social benefits, per stream mile. This is if we assume two streams are funded, and the South Fork is the second stream to receive funds, rather than Murderer's Creek. Granite Creek would still receive funding priority. Finally, correlated benefits, or warm-water species, need to be considered. In this study ignoring the warm-water species would not effect fund allocation, as a marginal social value for speckled dace was not found. Even if we assume the speckled dace is a proxy for warm-water sport fish, such as bass, and the correlated benefits are taken into consideration, funding priority would still be given to Granite Creek. However, under the same assumptions, if the correlated benefits are ignored in Camp Creek, then society will misallocate funds and lose a small portion of marginal social benefits per stream mile. This study points towards small, high elevation streams being given funding priority. Granite Creek should be the first stream to receive funds in the John Day River basin, when funds are optimally allocated. However, if not all of the environmental benefits are taken into consideration, different streams may be targeted. When a temperature-based targeting scheme is used, Alder Creek would be given funding priority, even though no marginal social benefits would be derived. If the change in stream temperatures is used, Camp Creek will receive funds, with a large loss to society in marginal benefits. If not all of the indirect benefits are considered, the South Fork will be funded over Murderer's Creek, and only half of the possible marginal benefits will be received. Finally, when correlated benefits were ignored, the fund allocation in this study was not affected. However, fund managers still have to consider the tradeoffs involved between warm and cold-water adapted fish species. This is especially true if warm-water sport fish or endangered species are the jointly produced benefits. Failing to include all of the environmental benefits that are produced when conservation programs are initiated will lead policy managers to target the wrong streams or basins, and misallocate funds. In addition, using the wrong criteria to prioritize watersheds will also lead managers to misallocate funds. Funds should be allocated so that the total value of environmental benefits is maximized, and not the total amount of resources saved. Title: The optimal allocation of watershed conservation funding : a case study of the John Day River Basin, Oregon Author: Skelton, Katharine This study determines the optimal allocation of watershed conservation funds in the John Day River Basin, Oregon. Fund managers can use a variety of targeting schemes to allocate their limited resources. Depending on which targeting criteria is used, they may or may not be achieving the maximum environmental benefits per dollar expended, a policy goal that is increasingly being adopted for conservation programs. Previous studies have provided the theory behind this optimal allocation of funds, but none, to the researcher's knowledge, have attempted a case study to illustrate the optimal allocation of funds as well as the misallocations that could result. Watershed conservation policies are very important, especially here in the Pacific Northwest where salmonid populations are endangered. As stream temperatures are lowered, salmonid recruitment increases. Improvements in riparian vegetation provide stream shade and bank stability. Shade decreases stream temperatures by preventing solar radiation from reaching the stream, while bank stability allows streams to become narrower and deeper, with more vegetative overhang. Narrower streams have less surface area to come in contact with solar radiation and vegetative overhang provides additional shade. A simultaneous equation system was used to estimate stream temperature and fish recruitment models for the thirteen streams studied, classified into three environmental attribute clusters. Fish recruitment models were developed for rainbow trout, Chinook salmon and speckled dace. Marginal values for rainbow trout and Chinook salmon from previous studies were used to calculate the total marginal benefits to society from increasing cold-water salmonid species. The analytical models were the basis for determining the optimal fund allocation, after considering the cumulative, indirect and correlated benefits derived from improving riparian vegetation conditions. Policy managers and previous studies have failed to consider these additional environmental benefits, particularly jointly produced benefits. Two scenarios were determined for the optimal fund allocation, based on the riparian conditions of the surveyed stream reaches. The riparian conditions are reported using a vegetative use index from one (the worst conditions) to four (the best conditions). Under the first scenario, which assumes a full range of riparian conditions, Granite Creek should receive funding priority with $51,756 in marginal social benefits received from improving the streamside vegetative use rating from one to four, for one mile of stream. Deerdorff Creek and Reynolds Creek would be the next two streams to receive funding, respectively, both for a vegetative use improvement from one to two. The second scenario assumes that only vegetative conditions in the surveyed segments exist in the stream. Under these circumstances, only six of the thirteen streams would even be considered for funding, with Granite Creek again receiving priority. Improving the vegetative use rating in Granite Creek from three to four, for one stream mile, will produce $9355 in marginal social benefits. Murderer's Creek and Camp Creek would be the next streams to receive funding for a vegetative use improvement from three to four and one to two, respectively. In addition to determining the optimal fund allocation, discussion is included about the policy implications that would result from ignoring the cumulative, indirect and correlated benefits. For the fund misallocation discussion Granite Creek was assumed to be the stream that should be given funding priority for an improvement from three to four only, with Murderer's Creek and Camp Creek receiving funds second and third, respectively. If an on-site, physical criterion is used as the targeting criteria, such as stream temperatures or the riparian vegetation conditions, then the cumulative benefits will be ignored. Two possible misallocations could result when the cumulative effects are ignored. First, streams with very high temperatures may receive funding, even if improvements in the vegetative use index will not lower temperatures enough so that salmonids can survive. Second, streams that have temperatures below the optimal range for salmonids, but have poor riparian vegetation may be funded. Improving streamside vegetation in those streams would be a misallocation of funds. Targeting based on the highest stream temperature criteria would only consider the direct benefits received from improving streamside vegetation. Under a temperature- based targeting criteria, Alder Creek would be the first stream funded with Mountain and Murderer's Creek following. If we assume only two streams could be funded, then there will be a loss of almost all marginal benefits per stream mile. If the change in the stream temperatures is used as the targeting criteria, and indirect benefits are ignored, then Camp Creek would receive funding priority, with Mountain Creek, Granite Creek and Murderer's Creek following. If it is again assumed that only two streams could be funded, this targeting scheme would result in an approximate loss to society of up to 87 percent in marginal benefits, per stream mile Additionally, all of the indirect benefits need to be taken into consideration in order to optimally allocate funds. If Chinook salmon are ignored, and rainbow trout are the only cold-water species taken into account, then society will forgo around 50 percent of marginal social benefits, per stream mile. This is if we assume two streams are funded, and the South Fork is the second stream to receive funds, rather than Murderer's Creek. Granite Creek would still receive funding priority. Finally, correlated benefits, or warm-water species, need to be considered. In this study ignoring the warm-water species would not effect fund allocation, as a marginal social value for speckled dace was not found. Even if we assume the speckled dace is a proxy for warm-water sport fish, such as bass, and the correlated benefits are taken into consideration, funding priority would still be given to Granite Creek. However, under the same assumptions, if the correlated benefits are ignored in Camp Creek, then society will misallocate funds and lose a small portion of marginal social benefits per stream mile. This study points towards small, high elevation streams being given funding priority. Granite Creek should be the first stream to receive funds in the John Day River basin, when funds are optimally allocated. However, if not all of the environmental benefits are taken into consideration, different streams may be targeted. When a temperature-based targeting scheme is used, Alder Creek would be given funding priority, even though no marginal social benefits would be derived. If the change in stream temperatures is used, Camp Creek will receive funds, with a large loss to society in marginal benefits. If not all of the indirect benefits are considered, the South Fork will be funded over Murderer's Creek, and only half of the possible marginal benefits will be received. Finally, when correlated benefits were ignored, the fund allocation in this study was not affected. However, fund managers still have to consider the tradeoffs involved between warm and cold-water adapted fish species. This is especially true if warm-water sport fish or endangered species are the jointly produced benefits. Failing to include all of the environmental benefits that are produced when conservation programs are initiated will lead policy managers to target the wrong streams or basins, and misallocate funds. In addition, using the wrong criteria to prioritize watersheds will also lead managers to misallocate funds. Funds should be allocated so that the total value of environmental benefits is maximized, and not the total amount of resources saved. Close

• 13108. [Article] The influence of climate change and restoration on stream temperature

  Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, ...

  Citation × Citation Citation Abstract Copy Title: The influence of climate change and restoration on stream temperature Author: Diabat, Mousa Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, and channel structure directly influence stream temperature. Numerous studies indicate that increased average air temperature during the past century has led to stream warming across the world. The trend of stream warming was also present in spring-fed watersheds, where summer flow has decreased. In addition, anthropogenic practices that alter the natural landscape and channel structure, such as forest management, agriculture, and mining contributed to stream warming. For example, deforested and unshaded stream reaches or dredged channels were warmer than shaded reaches and meandering streams. Stream temperatures in North American lotic habitats are of a specific concern due to their significant economic, cultural, and ecological value. With climate projections indicating that air temperature will only continue to rise throughout the 21st century, cold- or cool-water organisms, especially fishes, will be affected. Therefore, there is a strong need to better understand the impacts of changing climate, riparian landscape, and channel structure on a stream's heat budget. This may assist in restoring the historic thermal regime in impacted sites and mitigating the impacts of future climate change. This study looks into the relative influences of the different factors on a stream's heat budget with three manuscripts: one on stream temperature response to diel timing of air warming, one on stream temperature response to changes in air temperature, flow, and riparian vegetation, and one on stream temperature response to air warming and channel reconstruction. I used the software Heat Source version 8.05 to simulate stream temperature for all three analyses along the Middle Fork John Day River, Oregon USA. Two of the manuscripts were applied to an upper 37 km section of the Middle Fork John Day River (presented in chapter 2 and 3), where the third manuscript was applied to a 1.5-km section. The sensitivity analysis of stream temperature response to diel timing of air warming (Chapter 2: Diel Timing of Warmer Air under Climate Change Affects Magnitude, Timing, and Duration of Stream Temperature Change) was based on scenarios representing uniform air warming over the diel period, daytime warming, and nighttime warming. Uniform warming of air temperature is a simple representation of increases in the average daily or monthly temperatures generated by the 'delta method'. The delta method relies on adding a constant value to the air temperature time-series data. This constant value is the difference (delta) between base case average air temperatures and the projected one. Scenarios of daytime or nighttime warming represent conditions under which most of the warming of the air occurs during the daytime or the nighttime, respectively. I simulated the stream temperature response to warmer air conditions of +2 °C and +4 °C in daily average for all three cases of air warming conditions. The three cases of different diel distributions of air warming generated 7-day average daily maximum stream temperature (7DADM) increases of approximately +1.8 °C ± 0.1 °C at the downstream end of the study section relative to the base case. In most parts of the reach, the three distributions of air warming generated different ranges of stream temperatures, different 7DADM values, different durations of stream temperature changes, and different average daily temperatures. Changes of stream temperature were out of phase with imposed changes of air temperature. Therefore, nighttime warming of air temperatures would cause the greatest increase in maximum daily stream temperature, which typically occurs during the daytime. The sensitivity analysis of the relative influences of changes in air temperature, stream flow, and riparian vegetation on stream temperature (Chapter 3: Assessing Stream Temperature Response to Cumulative Influence of Changing Air Temperature, Flow, and Riparian Vegetation). This study summarized stream temperature simulation in 36 scenarios representing possible manifestations of 21st century climate conditions and land management strategies. In addition to existing conditions (base case) of flow, air temperature, and riparian vegetation, scenarios consisted of: two air temperature increases of 2 °C and 4 °C, two stream flow variations of +30% and -30%, three spatially uniform riparian vegetation conditions that create averages of effective shade 7%, 34%, and 79%, in addition to 14% for base case conditions. Results suggest that variation in riparian vegetation was the dominant factor influencing stream temperature because it regulates incoming shortwave radiation, the largest heat input to the stream, while variation in stream flow has a negligible influence. Results indicated that increasing the effective shade along the study section, particularly in the currently unshaded sections, could mitigate the influence of increasing air temperature, and would reduce stream temperature maxima below current values even under future climate conditions of warmer air. With the small influence it had, increasing stream flow reduced the 7DADM under low shade conditions. However, increasing stream flow showed counterintuitive results as it contributed to increasing stream temperature maxima when the stream was heavily shaded. The applied study examined the stream temperature response to restoration practices and their potential to mitigate the influence of warmer air conditions (Chapter 4: Estimating Stream Temperature Response to Restoring Channel and Riparian Vegetation and the Potential to Mitigate Warmer Air Conditions). This study focused on a 1.5 km section along the upper part of the Middle Fork John Day River that was modified due to past anthropogenic activities of mining for gold and timber harvest. Currently, the riparian vegetation of the study site is mostly shrubs and stands of short trees. Restoration designs call for the restoration of both the channel structure and replanting the riparian vegetation. Simulation results showed that the 7DADM was higher in the restored channel than the existing channel with both conditions of low and high effective shade conditions. However, a combined restoration practice of channel reconstruction and medium effective shade conditions reduced stream temperature maxima more than restoring riparian vegetation alone. In addition, results showed that restoring riparian vegetation was sufficient to mitigate the influence of warmer air on stream temperature, while restoring the channel alone is not. Heat budget analysis showed that heat accumulation during the daytime increased in the restored channel, which was longer, narrower, and deeper than the existing channel. It is important to emphasize that stream temperature is one of many goals that restoration activities aim to improve. Furthermore, differences in 7DADM among the different scenarios of restoration are negligible. Such small differences could hardly be measure. While this study examined a short section of 1.5 km, longer stream sections may increase the differences in 7DADM. Primary conclusions of this study are: 1) daily maxima of stream temperature will increase in response to increased air temperature regardless of the distribution of air warming during the diel cycle; 2) nighttime air warming caused a greater increase in stream temperature maximum than daytime warming; 3) riparian vegetation was the dominant factor on stream's heat budget, more than air temperature or stream flow; 4) restoring riparian vegetation mitigated the influence of warmer air; 5) restoring channel structure alone was not sufficient to lower temperature maxima; and 6) restoration project was most successful in improving degraded stream temperature when combined with channel reconstruction and improved riparian shade. Title: The influence of climate change and restoration on stream temperature Author: Diabat, Mousa Water temperature is an essential property of a stream. Temperature regulates physical and biochemical processes in aquatic habitats. Various factors related to climatic conditions, landscape characteristics, and channel structure directly influence stream temperature. Numerous studies indicate that increased average air temperature during the past century has led to stream warming across the world. The trend of stream warming was also present in spring-fed watersheds, where summer flow has decreased. In addition, anthropogenic practices that alter the natural landscape and channel structure, such as forest management, agriculture, and mining contributed to stream warming. For example, deforested and unshaded stream reaches or dredged channels were warmer than shaded reaches and meandering streams. Stream temperatures in North American lotic habitats are of a specific concern due to their significant economic, cultural, and ecological value. With climate projections indicating that air temperature will only continue to rise throughout the 21st century, cold- or cool-water organisms, especially fishes, will be affected. Therefore, there is a strong need to better understand the impacts of changing climate, riparian landscape, and channel structure on a stream's heat budget. This may assist in restoring the historic thermal regime in impacted sites and mitigating the impacts of future climate change. This study looks into the relative influences of the different factors on a stream's heat budget with three manuscripts: one on stream temperature response to diel timing of air warming, one on stream temperature response to changes in air temperature, flow, and riparian vegetation, and one on stream temperature response to air warming and channel reconstruction. I used the software Heat Source version 8.05 to simulate stream temperature for all three analyses along the Middle Fork John Day River, Oregon USA. Two of the manuscripts were applied to an upper 37 km section of the Middle Fork John Day River (presented in chapter 2 and 3), where the third manuscript was applied to a 1.5-km section. The sensitivity analysis of stream temperature response to diel timing of air warming (Chapter 2: Diel Timing of Warmer Air under Climate Change Affects Magnitude, Timing, and Duration of Stream Temperature Change) was based on scenarios representing uniform air warming over the diel period, daytime warming, and nighttime warming. Uniform warming of air temperature is a simple representation of increases in the average daily or monthly temperatures generated by the 'delta method'. The delta method relies on adding a constant value to the air temperature time-series data. This constant value is the difference (delta) between base case average air temperatures and the projected one. Scenarios of daytime or nighttime warming represent conditions under which most of the warming of the air occurs during the daytime or the nighttime, respectively. I simulated the stream temperature response to warmer air conditions of +2 °C and +4 °C in daily average for all three cases of air warming conditions. The three cases of different diel distributions of air warming generated 7-day average daily maximum stream temperature (7DADM) increases of approximately +1.8 °C ± 0.1 °C at the downstream end of the study section relative to the base case. In most parts of the reach, the three distributions of air warming generated different ranges of stream temperatures, different 7DADM values, different durations of stream temperature changes, and different average daily temperatures. Changes of stream temperature were out of phase with imposed changes of air temperature. Therefore, nighttime warming of air temperatures would cause the greatest increase in maximum daily stream temperature, which typically occurs during the daytime. The sensitivity analysis of the relative influences of changes in air temperature, stream flow, and riparian vegetation on stream temperature (Chapter 3: Assessing Stream Temperature Response to Cumulative Influence of Changing Air Temperature, Flow, and Riparian Vegetation). This study summarized stream temperature simulation in 36 scenarios representing possible manifestations of 21st century climate conditions and land management strategies. In addition to existing conditions (base case) of flow, air temperature, and riparian vegetation, scenarios consisted of: two air temperature increases of 2 °C and 4 °C, two stream flow variations of +30% and -30%, three spatially uniform riparian vegetation conditions that create averages of effective shade 7%, 34%, and 79%, in addition to 14% for base case conditions. Results suggest that variation in riparian vegetation was the dominant factor influencing stream temperature because it regulates incoming shortwave radiation, the largest heat input to the stream, while variation in stream flow has a negligible influence. Results indicated that increasing the effective shade along the study section, particularly in the currently unshaded sections, could mitigate the influence of increasing air temperature, and would reduce stream temperature maxima below current values even under future climate conditions of warmer air. With the small influence it had, increasing stream flow reduced the 7DADM under low shade conditions. However, increasing stream flow showed counterintuitive results as it contributed to increasing stream temperature maxima when the stream was heavily shaded. The applied study examined the stream temperature response to restoration practices and their potential to mitigate the influence of warmer air conditions (Chapter 4: Estimating Stream Temperature Response to Restoring Channel and Riparian Vegetation and the Potential to Mitigate Warmer Air Conditions). This study focused on a 1.5 km section along the upper part of the Middle Fork John Day River that was modified due to past anthropogenic activities of mining for gold and timber harvest. Currently, the riparian vegetation of the study site is mostly shrubs and stands of short trees. Restoration designs call for the restoration of both the channel structure and replanting the riparian vegetation. Simulation results showed that the 7DADM was higher in the restored channel than the existing channel with both conditions of low and high effective shade conditions. However, a combined restoration practice of channel reconstruction and medium effective shade conditions reduced stream temperature maxima more than restoring riparian vegetation alone. In addition, results showed that restoring riparian vegetation was sufficient to mitigate the influence of warmer air on stream temperature, while restoring the channel alone is not. Heat budget analysis showed that heat accumulation during the daytime increased in the restored channel, which was longer, narrower, and deeper than the existing channel. It is important to emphasize that stream temperature is one of many goals that restoration activities aim to improve. Furthermore, differences in 7DADM among the different scenarios of restoration are negligible. Such small differences could hardly be measure. While this study examined a short section of 1.5 km, longer stream sections may increase the differences in 7DADM. Primary conclusions of this study are: 1) daily maxima of stream temperature will increase in response to increased air temperature regardless of the distribution of air warming during the diel cycle; 2) nighttime air warming caused a greater increase in stream temperature maximum than daytime warming; 3) riparian vegetation was the dominant factor on stream's heat budget, more than air temperature or stream flow; 4) restoring riparian vegetation mitigated the influence of warmer air; 5) restoring channel structure alone was not sufficient to lower temperature maxima; and 6) restoration project was most successful in improving degraded stream temperature when combined with channel reconstruction and improved riparian shade. Close

• 13109. [Article] Comparative wintering ecology of two subspecies of sandhill crane : informing conservation planning in the Sacramento-San Joaquin River Delta region of California

  California's Central Valley agricultural landscapes provide several important wintering regions for Pacific Flyway sandhill crane (Grus canadensis) populations; however, the value of those regions is being ...

  Citation × Citation Citation Abstract Copy Title: Comparative wintering ecology of two subspecies of sandhill crane : informing conservation planning in the Sacramento-San Joaquin River Delta region of California Author: Ivey, Gary L. California's Central Valley agricultural landscapes provide several important wintering regions for Pacific Flyway sandhill crane (Grus canadensis) populations; however, the value of those regions is being compromised by urban expansion, other developments, and conversions to incompatible crop types. Greater (G. c. tabida) and lesser sandhill cranes (G. c. canadensis) both have special conservation status in California; the greater is listed as threatened and the lesser as a bird species of conservation concern by the state. However, basic information about their wintering ecology has been lacking to design biologically sound conservation strategies to maintain their wintering habitats. My study of sandhill cranes focused on one major Central Valley wintering region, the Sacramento-San Joaquin River Delta (Delta). I compared daily movements and winter site fidelity between the two sandhill crane subspecies, evaluated the timing of crane arrival and departure from the region, assessed foraging habitat choices, measured abundance and distribution in the Delta, documented the characteristics of roost sites, and developed habitat conservation models and decision tools for managers to facilitate habitat conservation and management. Both crane subspecies showed strong fidelity to my Delta study area. Foraging flights from roost sites were shorter for greaters than lesser (1.2 ± 0.4 km vs. 3.1 ± 0.1 km, respectively) and consequently, mean size of 95% fixed kernel winter home ranges was an order of magnitude smaller for greaters (1.9 ± 0.4 km² vs.21.9 ± 1.9 km², respectively). The strong site fidelity of greaters to roost complexes within landscapes in the Delta indicates that conservation planning targeted at maintaining and managing for adequate food resources around traditional roost sites can be effective for meeting sandhill crane habitat needs, while the scale of conservation differs by subspecies. I recommend that conservation planning actions consider all habitats within 5 km of a crane roost as a sandhill crane conservation "ecosystem unit." This radius encompasses 95% and 69% of the flights from roosts to foraging location (commuting flights) made by greaters and lessers, respectively. For lessers, a conservation radius of 10 km would encompass 90% of the commuting flights. Management, mitigation, acquisition, easement, planning, and farm subsidy programs intended to benefit cranes will be most effective when applied at these scales. Within these radii, conservation and management of wintering habitats should include creating both new roost and feeding areas to ensure high chances of successful use. Sandhill cranes used major crops and habitat types available in the landscapes surrounding their roost sites and focused most of their foraging in grain crops. They generally avoided dry corn stubble, selected dry rice stubble early in the season, and rarely used dry wild rice stubble. Tilled fields were also usually avoided but were occasionally used shortly after tillage. Mulched corn ranked high in comparison to other corn treatments while mulched rice use was used similarly to dry rice stubble. Both subspecies often highly favored cropland habitats when they were initially flooded. Cranes were attracted to new plantings of pasture and winter wheat. One important difference between the subspecies was that lessers used alfalfa which was generally avoided by greaters. Dry corn stubble was avoided while dry rice stubble was favored early in winter. If wildlife managers want to encourage winter field use by cranes they could provide incentives for favorable practices such as production of grain crops, reduction or delaying tillage and flooding of grain fields, provision of irrigations to some crop types, and increasing the practice of mulching of corn stubble. Of the 69 crane night roosts I identified, 35 were flooded cropland sites and 34 were wetland sites. I found that both larger individual roost sites and larger complexes of roost sites supported larger peak numbers of cranes. Water depth used by roosting cranes averaged 10 cm (range 3-21 cm, mode 7 cm) and was similar between subspecies. Roosting cranes avoided sites that were regularly hunted or had high densities (i.e., > 1 blind/5 ha) of hunting blinds. Roost site design and management should consider providing and maintaining large roost complexes (100 - 1000 ha) ideally in close proximity (< 5 km) to other roost sites, with large individual sites (> 5 ha) of mostly level topography, dominated by shallow water (5-10 cm depths). The fact that cranes readily use undisturbed flooded cropland sites makes this a viable option for creation of roost habitat. Because hunting disturbance can limit crane use of roost sites I suggest these two uses should not be considered compatible. However, if the management objective of an area includes waterfowl hunting, limiting hunting at low blind densities (i.e., < 1 blind/60 ha) and restricting hunting to early morning may be viable options for creating a crane-compatible waterfowl hunt program. Radio-marked sandhill cranes arrived in the Delta beginning 3 October, most arrived in mid-October, and the last radio-marked sandhill crane arrived on 10 December. Departure dates ranged from 15 January to 13 March. Mean arrival and departure dates were similar between subspecies. From mid-December through early-February in 2007-2008, the Delta population ranged from 20,000 to 27,000 sandhill cranes. Abundance varied at the main roost sites during winter, likely because sandhill cranes responded to changes in water and foraging habitat conditions. Sandhill cranes used an area of approximately 1,500 km² for foraging. Estimated peak abundance in the Delta was more than half the total number counted on recent Pacific Flyway midwinter surveys, indicating the Delta region is a key area for efforts in conservation and recovery of wintering sandhill cranes in California. Based on arrival dates, flooding of sandhill crane roost sites should be staggered with some sites flooded in early September and most sites flooded by early October. Maintaining flooding of at least some roost sites through mid-March would provide essential roosting habitat until most birds have departed the Delta region on spring migration. Not all 5-km radius ecosystem units are equal in their value to greater sandhill cranes, and the relative foraging value of a particular parcel within an ecosystem unit depends on the numbers of cranes using the focal roost site, the habitat choices they make, and the probability that they will fly to a particular parcel. Additionally, some ecosystem units overlap, and in these overlap zones, the probability of crane use is higher, because of additive effects. To provide a tool to allow managers to further refine management plans, I developed a model which allows more specific focus of crane conservation, mitigation and habitat management, using what my study revealed about greater sandhill cranes. This model considers the abundance of greaters at individual roost sites and the probability that they would fly to a given location. Sites closer to roosts had a higher probability of crane use. I calculated the probability that greaters would fly to a parcel within concentric 1-km intervals as a product of the proportion of commuting flights of individuals that reached that interval, and the proportion of all commuting flights that reached that interval. Within crane ecosystem units, it is important to protect the existing habitat from further loss and optimize foraging conditions for cranes. I provide a decision matrix to assist with plans to enhance existing crane landscapes, create new crane habitat areas or mitigate habitat losses. This matrix provides a framework for decision-making regarding enhancing sandhill crane foraging and roost site habitats. Wildlife managers could employ a variety of tools to conserve and manage crane habitats, including fee title acquisitions, private conservation easements, and specific cropland management actions to maintain crane-compatible conditions and high food values for cranes (possibly including providing unharvested food plots). My study has demonstrated that most cranes use a relatively small landscape surrounding their traditional roost sites and that they favor certain crops and post-harvest crop management practices for foraging. However, we need a better understanding of the actual carrying capacity for cranes in these crane management zones to ensure that managers can maintain these sites for cranes in the future. Title: Comparative wintering ecology of two subspecies of sandhill crane : informing conservation planning in the Sacramento-San Joaquin River Delta region of California Author: Ivey, Gary L. California's Central Valley agricultural landscapes provide several important wintering regions for Pacific Flyway sandhill crane (Grus canadensis) populations; however, the value of those regions is being compromised by urban expansion, other developments, and conversions to incompatible crop types. Greater (G. c. tabida) and lesser sandhill cranes (G. c. canadensis) both have special conservation status in California; the greater is listed as threatened and the lesser as a bird species of conservation concern by the state. However, basic information about their wintering ecology has been lacking to design biologically sound conservation strategies to maintain their wintering habitats. My study of sandhill cranes focused on one major Central Valley wintering region, the Sacramento-San Joaquin River Delta (Delta). I compared daily movements and winter site fidelity between the two sandhill crane subspecies, evaluated the timing of crane arrival and departure from the region, assessed foraging habitat choices, measured abundance and distribution in the Delta, documented the characteristics of roost sites, and developed habitat conservation models and decision tools for managers to facilitate habitat conservation and management. Both crane subspecies showed strong fidelity to my Delta study area. Foraging flights from roost sites were shorter for greaters than lesser (1.2 ± 0.4 km vs. 3.1 ± 0.1 km, respectively) and consequently, mean size of 95% fixed kernel winter home ranges was an order of magnitude smaller for greaters (1.9 ± 0.4 km² vs.21.9 ± 1.9 km², respectively). The strong site fidelity of greaters to roost complexes within landscapes in the Delta indicates that conservation planning targeted at maintaining and managing for adequate food resources around traditional roost sites can be effective for meeting sandhill crane habitat needs, while the scale of conservation differs by subspecies. I recommend that conservation planning actions consider all habitats within 5 km of a crane roost as a sandhill crane conservation "ecosystem unit." This radius encompasses 95% and 69% of the flights from roosts to foraging location (commuting flights) made by greaters and lessers, respectively. For lessers, a conservation radius of 10 km would encompass 90% of the commuting flights. Management, mitigation, acquisition, easement, planning, and farm subsidy programs intended to benefit cranes will be most effective when applied at these scales. Within these radii, conservation and management of wintering habitats should include creating both new roost and feeding areas to ensure high chances of successful use. Sandhill cranes used major crops and habitat types available in the landscapes surrounding their roost sites and focused most of their foraging in grain crops. They generally avoided dry corn stubble, selected dry rice stubble early in the season, and rarely used dry wild rice stubble. Tilled fields were also usually avoided but were occasionally used shortly after tillage. Mulched corn ranked high in comparison to other corn treatments while mulched rice use was used similarly to dry rice stubble. Both subspecies often highly favored cropland habitats when they were initially flooded. Cranes were attracted to new plantings of pasture and winter wheat. One important difference between the subspecies was that lessers used alfalfa which was generally avoided by greaters. Dry corn stubble was avoided while dry rice stubble was favored early in winter. If wildlife managers want to encourage winter field use by cranes they could provide incentives for favorable practices such as production of grain crops, reduction or delaying tillage and flooding of grain fields, provision of irrigations to some crop types, and increasing the practice of mulching of corn stubble. Of the 69 crane night roosts I identified, 35 were flooded cropland sites and 34 were wetland sites. I found that both larger individual roost sites and larger complexes of roost sites supported larger peak numbers of cranes. Water depth used by roosting cranes averaged 10 cm (range 3-21 cm, mode 7 cm) and was similar between subspecies. Roosting cranes avoided sites that were regularly hunted or had high densities (i.e., > 1 blind/5 ha) of hunting blinds. Roost site design and management should consider providing and maintaining large roost complexes (100 - 1000 ha) ideally in close proximity (< 5 km) to other roost sites, with large individual sites (> 5 ha) of mostly level topography, dominated by shallow water (5-10 cm depths). The fact that cranes readily use undisturbed flooded cropland sites makes this a viable option for creation of roost habitat. Because hunting disturbance can limit crane use of roost sites I suggest these two uses should not be considered compatible. However, if the management objective of an area includes waterfowl hunting, limiting hunting at low blind densities (i.e., < 1 blind/60 ha) and restricting hunting to early morning may be viable options for creating a crane-compatible waterfowl hunt program. Radio-marked sandhill cranes arrived in the Delta beginning 3 October, most arrived in mid-October, and the last radio-marked sandhill crane arrived on 10 December. Departure dates ranged from 15 January to 13 March. Mean arrival and departure dates were similar between subspecies. From mid-December through early-February in 2007-2008, the Delta population ranged from 20,000 to 27,000 sandhill cranes. Abundance varied at the main roost sites during winter, likely because sandhill cranes responded to changes in water and foraging habitat conditions. Sandhill cranes used an area of approximately 1,500 km² for foraging. Estimated peak abundance in the Delta was more than half the total number counted on recent Pacific Flyway midwinter surveys, indicating the Delta region is a key area for efforts in conservation and recovery of wintering sandhill cranes in California. Based on arrival dates, flooding of sandhill crane roost sites should be staggered with some sites flooded in early September and most sites flooded by early October. Maintaining flooding of at least some roost sites through mid-March would provide essential roosting habitat until most birds have departed the Delta region on spring migration. Not all 5-km radius ecosystem units are equal in their value to greater sandhill cranes, and the relative foraging value of a particular parcel within an ecosystem unit depends on the numbers of cranes using the focal roost site, the habitat choices they make, and the probability that they will fly to a particular parcel. Additionally, some ecosystem units overlap, and in these overlap zones, the probability of crane use is higher, because of additive effects. To provide a tool to allow managers to further refine management plans, I developed a model which allows more specific focus of crane conservation, mitigation and habitat management, using what my study revealed about greater sandhill cranes. This model considers the abundance of greaters at individual roost sites and the probability that they would fly to a given location. Sites closer to roosts had a higher probability of crane use. I calculated the probability that greaters would fly to a parcel within concentric 1-km intervals as a product of the proportion of commuting flights of individuals that reached that interval, and the proportion of all commuting flights that reached that interval. Within crane ecosystem units, it is important to protect the existing habitat from further loss and optimize foraging conditions for cranes. I provide a decision matrix to assist with plans to enhance existing crane landscapes, create new crane habitat areas or mitigate habitat losses. This matrix provides a framework for decision-making regarding enhancing sandhill crane foraging and roost site habitats. Wildlife managers could employ a variety of tools to conserve and manage crane habitats, including fee title acquisitions, private conservation easements, and specific cropland management actions to maintain crane-compatible conditions and high food values for cranes (possibly including providing unharvested food plots). My study has demonstrated that most cranes use a relatively small landscape surrounding their traditional roost sites and that they favor certain crops and post-harvest crop management practices for foraging. However, we need a better understanding of the actual carrying capacity for cranes in these crane management zones to ensure that managers can maintain these sites for cranes in the future. Close