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• 371. [Article] Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development

  While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of ...

  Citation × Citation Citation Abstract Copy Title: Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development Author: Henkel, Sarah K., Goldfinger, Chris While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of these devices and their complex mooring systems. Here I focus on characterizing benthic habitats and biological communities in offshore sedimentary and reef habitats where wind and wave energy facilities could be located. While little is known about species-habitat relationships and community processes in the depths and substrate types targeted for offshore renewable energy installation, an understanding of the natural dynamics of these systems is of utmost importance if we hope to forecast changes that might be brought about by wind and wave development. Since May 2010 we have conducted surveys of benthic habitats from northern California to Washington using a variety of techniques, providing baseline data on habitats and species potentially affected by wind and wave development, identifying species-habitat relationships, and quantifying spatial and temporal trends in species abundances and distributions. The first step in identifying and evaluating benthic communities is sonar mapping to determine depth and substrate types. In summer 2010 and 2011 six new offshore sites were mapped by the Seafloor Mapping and Plate Tectonics Lab at OSU using high-resolution multi-beam sonar and acoustic backscatter. In addition to the backscatter, Shipek grabs were taken in soft-bottom areas to collect sediment samples, which were run through a laser particle size analyzer (LDPSA) to determine actual grain size. Mapping began at the federal jurisdiction line and extended 9 – 12 miles offshore. Oregon and California have undertaken extensive mapping of state waters, so many areas have been mapped inshore of these sites as well. In summer 2011 and 2012, we visited 8 sites (6 newly mapped sites, one previously mapped, and one unmapped site) to collect a total of 153 cores using a 0.1 m2 box-corer. A sub-sample of sediment was collected from the corer and analyzed using the LDPSA; the rest was sieved through 1 mm mesh and all infaunal organisms were counted and identified. At each box core sampling station, CTD casts were conducted to obtain physical data describing the overlying water column for further habitat characterization. Unique infaunal invertebrate assemblages were found in sedimentary habitats at each of the Pacific Northwest shelf sites. Thus for renewable energy siting, it does not appear that baseline surveys conducted at one site can necessarily serve as a proxy for distant sites. However, some general trends were detected. Significantly different invertebrate assemblages were found in different depth ranges with a break at approximately 80 to 90 m depth; deeper sites exhibited greater diversity. Shallower sites had greater spatial heterogeneity in infaunal invertebrate assemblages than deeper sites; thus as monitoring protocols are developed we recommend that shallower sites be sampled more extensively in order to adequately characterize those communities. Molluscs seemed to be the most responsive to substrate type, with different assemblages found in pure sand, slightly muddy sand, and mostly silt/clay. In addition to sampling of sedimentary habitat, we conducted limited surveys of offshore reef habitats. Although it is unlikely that devices would be installed in these areas, reefs may be crossed by electrical cables, and changes in sediment transport due to ocean energy extraction or alterations of flow around large device arrays could lead to community impacts. The aim of this study was to describe baseline relationships between macroinvertebrate communities and habitat features against which to measure potential future impacts and to develop tools to predict community compositions of unsampled areas in the region based on substrate features. To date we have analyzed submersible dive video from three sites conducted in the mid-1990s. In the summers of 2011 and 2012, we visited these previously surveyed sites with an ROV. Analysis of submersible and ROV surveys indicated that two major substratum groups held different macroinvertebrate assemblages: moderate to high-relief rocky habitats and low-relief fine sediment habitats. The majority of macroinvertebrate taxa were associated with high-relief rocks; these taxa were further differentiated between flat and ridge rock habitats. Low-relief fine sediment habitat was most often associated with motile invertebrates. Within this habitat it appeared that fine-sediment substrata mixed with mud, boulders, or gravel each yield unique macro-invertebrate associations versus those found on uniformly mud or sand substrata. Latitude also was correlated with variation in macroinvertebrate assemblages. A major challenge will be detecting effects of wind and wave energy installations above the inherent natural variability in these systems. Decadal scale shifts in the California Current affect this ecosystem, with warm regimes and associated declines in planktonic production resulting in degradation of benthic community. On shorter timescales El Niño events can cause major, short-term disturbances. Off the Oregon coast, summer hypoxia events can have dramatic effects on benthic communities, and ocean acidification is an increasing concern. Thus, evaluation of this ecosystem must be made in the context of seasonal and climatic trends. Prior to installation of device arrays, baseline sampling is usually required as part of the permitting process. However, one-time sampling will not capture the variability of the system in a given area, and developers and regulators typically are not able to make the investment (in time or money) to repeatedly survey an area before development. Funding agencies rarely support long-term monitoring studies. Thus, finding support for repeated field sampling across time and space is especially challenging. The biggest issue facing wind and wave energy developers in the environmental arena is the high level of uncertainty regarding environmental effects. Without a substantial understanding of the natural dynamics of a system, it will be difficult to reduce that uncertainty. Title: Linking Habitat and Benthic Invertebrate Species Distributions in Areas of Potential Renewable Energy Development Author: Henkel, Sarah K., Goldfinger, Chris While the coastal waters of western North America hold great promise for wind and wave energy development, many concerns have been raised about the potential environmental impacts of the installation of these devices and their complex mooring systems. Here I focus on characterizing benthic habitats and biological communities in offshore sedimentary and reef habitats where wind and wave energy facilities could be located. While little is known about species-habitat relationships and community processes in the depths and substrate types targeted for offshore renewable energy installation, an understanding of the natural dynamics of these systems is of utmost importance if we hope to forecast changes that might be brought about by wind and wave development. Since May 2010 we have conducted surveys of benthic habitats from northern California to Washington using a variety of techniques, providing baseline data on habitats and species potentially affected by wind and wave development, identifying species-habitat relationships, and quantifying spatial and temporal trends in species abundances and distributions. The first step in identifying and evaluating benthic communities is sonar mapping to determine depth and substrate types. In summer 2010 and 2011 six new offshore sites were mapped by the Seafloor Mapping and Plate Tectonics Lab at OSU using high-resolution multi-beam sonar and acoustic backscatter. In addition to the backscatter, Shipek grabs were taken in soft-bottom areas to collect sediment samples, which were run through a laser particle size analyzer (LDPSA) to determine actual grain size. Mapping began at the federal jurisdiction line and extended 9 – 12 miles offshore. Oregon and California have undertaken extensive mapping of state waters, so many areas have been mapped inshore of these sites as well. In summer 2011 and 2012, we visited 8 sites (6 newly mapped sites, one previously mapped, and one unmapped site) to collect a total of 153 cores using a 0.1 m2 box-corer. A sub-sample of sediment was collected from the corer and analyzed using the LDPSA; the rest was sieved through 1 mm mesh and all infaunal organisms were counted and identified. At each box core sampling station, CTD casts were conducted to obtain physical data describing the overlying water column for further habitat characterization. Unique infaunal invertebrate assemblages were found in sedimentary habitats at each of the Pacific Northwest shelf sites. Thus for renewable energy siting, it does not appear that baseline surveys conducted at one site can necessarily serve as a proxy for distant sites. However, some general trends were detected. Significantly different invertebrate assemblages were found in different depth ranges with a break at approximately 80 to 90 m depth; deeper sites exhibited greater diversity. Shallower sites had greater spatial heterogeneity in infaunal invertebrate assemblages than deeper sites; thus as monitoring protocols are developed we recommend that shallower sites be sampled more extensively in order to adequately characterize those communities. Molluscs seemed to be the most responsive to substrate type, with different assemblages found in pure sand, slightly muddy sand, and mostly silt/clay. In addition to sampling of sedimentary habitat, we conducted limited surveys of offshore reef habitats. Although it is unlikely that devices would be installed in these areas, reefs may be crossed by electrical cables, and changes in sediment transport due to ocean energy extraction or alterations of flow around large device arrays could lead to community impacts. The aim of this study was to describe baseline relationships between macroinvertebrate communities and habitat features against which to measure potential future impacts and to develop tools to predict community compositions of unsampled areas in the region based on substrate features. To date we have analyzed submersible dive video from three sites conducted in the mid-1990s. In the summers of 2011 and 2012, we visited these previously surveyed sites with an ROV. Analysis of submersible and ROV surveys indicated that two major substratum groups held different macroinvertebrate assemblages: moderate to high-relief rocky habitats and low-relief fine sediment habitats. The majority of macroinvertebrate taxa were associated with high-relief rocks; these taxa were further differentiated between flat and ridge rock habitats. Low-relief fine sediment habitat was most often associated with motile invertebrates. Within this habitat it appeared that fine-sediment substrata mixed with mud, boulders, or gravel each yield unique macro-invertebrate associations versus those found on uniformly mud or sand substrata. Latitude also was correlated with variation in macroinvertebrate assemblages. A major challenge will be detecting effects of wind and wave energy installations above the inherent natural variability in these systems. Decadal scale shifts in the California Current affect this ecosystem, with warm regimes and associated declines in planktonic production resulting in degradation of benthic community. On shorter timescales El Niño events can cause major, short-term disturbances. Off the Oregon coast, summer hypoxia events can have dramatic effects on benthic communities, and ocean acidification is an increasing concern. Thus, evaluation of this ecosystem must be made in the context of seasonal and climatic trends. Prior to installation of device arrays, baseline sampling is usually required as part of the permitting process. However, one-time sampling will not capture the variability of the system in a given area, and developers and regulators typically are not able to make the investment (in time or money) to repeatedly survey an area before development. Funding agencies rarely support long-term monitoring studies. Thus, finding support for repeated field sampling across time and space is especially challenging. The biggest issue facing wind and wave energy developers in the environmental arena is the high level of uncertainty regarding environmental effects. Without a substantial understanding of the natural dynamics of a system, it will be difficult to reduce that uncertainty. Close

• 372. [Article] Vegetation and Small Mammal Responses to Western Juniper (Juniperus occidentalis) Control in Eastern Oregon

  Shrub-steppe ecosystems of western North America provide habitat for many wildlife species, are important components of public and private rangelands, and offer recreational opportunities for millions ...

  Citation × Citation Citation Abstract Copy Title: Vegetation and Small Mammal Responses to Western Juniper (Juniperus occidentalis) Control in Eastern Oregon Author: Morozumi, Corinne N. Shrub-steppe ecosystems of western North America provide habitat for many wildlife species, are important components of public and private rangelands, and offer recreational opportunities for millions of people. They are some of the most vulnerable ecosystems in the United States and have been altered by human activities such as livestock grazing, active fire suppression, conversion to agriculture, and urbanization of the west. Since the late 1800s woody encroachment of piñon-juniper species has also contributed to the loss of shrub-steppe habitat. Presently, land managers remove woody tree species in order to recover shrub-steppe although it is unclear how responses to these management activities differ due to site-specific conditions and existing woodland development. I studied post juniper-thinning responses in eastern Oregon at a wildlife area important as winter range for mule deer (Odocoileus hemionus). I investigated vegetative responses to western juniper (Juniperus occidentalis) thinning across a woodland development gradient and tested for interactive effects of juniper cutting and cattle exclusion. In addition, I explored plant and small mammal successional dynamics after juniper thinning and examined plant community responses within microhabitats created by the felled trees. I compared vegetative responses to juniper thinning as well as cattle exclusion among sites where juniper were subordinate (Phase I), co-dominant (Phase II), and dominant to shrubs and grasses (Phase III, sensu Miller et al. 2005). At the Phase I site, thinning did not increase herbaceous biomass while thinned plots at the Phase II site had 2.71 times more median herbaceous biomass (99.17% CI: 1.37 to 5.37 times more biomass) than unthinned plots. Conversely, herbaceous biomass at the Phase III juniper woodland site was 0.36 times lower in thinned plots when compared to unthinned plots (99.17% CI: 0.17 to 0.78 times less biomass). Unfortunately, many of the responses were driven by exotic species release. Where juniper were subordinate (Phase I), mean percent cover by exotic grass increased by 24.58 percentage points in thinned plots as compared to unthinned plots (98.30% CI: 0.27 to 48.90 percentage points higher). Thinning at the Phase II site increased mean exotic grass cover by an estimated 28.47 percentage points as compared to mean exotic cover in the same plots before treatment (98.30% CI: 4.15 to 52.79 percentage points higher cover). Median native bunchgrass cover at this site was 5.06 times greater after juniper treatment (99.7% CI: 1.78 to 14.35 times higher percent cover). I found few main or interactive effects of cattle exclosure after one year of treatment. Responses to grazing exclosure may take longer to develop. These results indicate that sites within the wildlife area respond differently to juniper management and that exotic grass control will be key to successful shrub-steppe recovery. In addition, I used a time-since-juniper thinning chronoseries consisting of plots cut in 2008, 2009, 2010, 2012, and an adjacent uncut control to explore how shrub-steppe flora and fauna are responding to juniper treatment through time. Shrub cover and seedling density were low in each plot. I recorded the highest seedling abundance (mean of 0.25 seedlings) in the uncut control plot. Median grass cover in the uncut control was 9.50% while in the most recently treated plot (2012) it was 26.75%. Small mammal relative abundance and diversity was low across all time-since-treatment plots though highest in the plot with the greatest time-since-treatment. Deer mouse (Peromyscus maniculatus) was the most abundant species in all plots and accounted for 70-95% of all unique captures. Least chipmunk (Tamias minimus) were present in the plot with greatest time-since-treatment indicating the potential recovery of key native shrubs since these small mammals perform an important seed dispersal role. I also investigated how potential microhabitats created by the felled juniper might support different plant communities. I assessed plant responses within zones created by 1) the felled tree (canopy zone), 2) the original duff zone, and 3) the between - tree interspace zone. The three zones had different plant community compositions as analyzed multivariately with non-metric multidimensional scaling (NMS). Canopy and duff zones were forb - dominated and had less exotic grass invasion while interspace zones were heavily invested with medusahead (Taeniatherum caput-medusae) and ventenata (Ventenata dubia). Exotic herbaceous productivity was lowest under the standing trees of the control plot and high in the interspace of all plots with juniper thinning. In the 2012 cut plot, grass cover was 27.90 percentage points less in the canopy zone compared to the interspace zone (98.75% CI: 17.64 to 38.16 percentage points less grass cover). In the uncut control, median native biomass was 2.08 times greater under the standing trees compared to the interspace (96.25% CI: 1.09 to 3.97 times more biomass). Results from the time-since-treatment chronoseries indicated that exotic grass dominance might be limiting shrub-steppe recovery. Active restoration of shrubs and native grasses may be necessary to address the dominance of exotic grass after juniper thinning. Positive signs of habitat recovery included small mammal responses though I was unable to calculate population estimates due to plot size. Title: Vegetation and Small Mammal Responses to Western Juniper (Juniperus occidentalis) Control in Eastern Oregon Author: Morozumi, Corinne N. Shrub-steppe ecosystems of western North America provide habitat for many wildlife species, are important components of public and private rangelands, and offer recreational opportunities for millions of people. They are some of the most vulnerable ecosystems in the United States and have been altered by human activities such as livestock grazing, active fire suppression, conversion to agriculture, and urbanization of the west. Since the late 1800s woody encroachment of piñon-juniper species has also contributed to the loss of shrub-steppe habitat. Presently, land managers remove woody tree species in order to recover shrub-steppe although it is unclear how responses to these management activities differ due to site-specific conditions and existing woodland development. I studied post juniper-thinning responses in eastern Oregon at a wildlife area important as winter range for mule deer (Odocoileus hemionus). I investigated vegetative responses to western juniper (Juniperus occidentalis) thinning across a woodland development gradient and tested for interactive effects of juniper cutting and cattle exclusion. In addition, I explored plant and small mammal successional dynamics after juniper thinning and examined plant community responses within microhabitats created by the felled trees. I compared vegetative responses to juniper thinning as well as cattle exclusion among sites where juniper were subordinate (Phase I), co-dominant (Phase II), and dominant to shrubs and grasses (Phase III, sensu Miller et al. 2005). At the Phase I site, thinning did not increase herbaceous biomass while thinned plots at the Phase II site had 2.71 times more median herbaceous biomass (99.17% CI: 1.37 to 5.37 times more biomass) than unthinned plots. Conversely, herbaceous biomass at the Phase III juniper woodland site was 0.36 times lower in thinned plots when compared to unthinned plots (99.17% CI: 0.17 to 0.78 times less biomass). Unfortunately, many of the responses were driven by exotic species release. Where juniper were subordinate (Phase I), mean percent cover by exotic grass increased by 24.58 percentage points in thinned plots as compared to unthinned plots (98.30% CI: 0.27 to 48.90 percentage points higher). Thinning at the Phase II site increased mean exotic grass cover by an estimated 28.47 percentage points as compared to mean exotic cover in the same plots before treatment (98.30% CI: 4.15 to 52.79 percentage points higher cover). Median native bunchgrass cover at this site was 5.06 times greater after juniper treatment (99.7% CI: 1.78 to 14.35 times higher percent cover). I found few main or interactive effects of cattle exclosure after one year of treatment. Responses to grazing exclosure may take longer to develop. These results indicate that sites within the wildlife area respond differently to juniper management and that exotic grass control will be key to successful shrub-steppe recovery. In addition, I used a time-since-juniper thinning chronoseries consisting of plots cut in 2008, 2009, 2010, 2012, and an adjacent uncut control to explore how shrub-steppe flora and fauna are responding to juniper treatment through time. Shrub cover and seedling density were low in each plot. I recorded the highest seedling abundance (mean of 0.25 seedlings) in the uncut control plot. Median grass cover in the uncut control was 9.50% while in the most recently treated plot (2012) it was 26.75%. Small mammal relative abundance and diversity was low across all time-since-treatment plots though highest in the plot with the greatest time-since-treatment. Deer mouse (Peromyscus maniculatus) was the most abundant species in all plots and accounted for 70-95% of all unique captures. Least chipmunk (Tamias minimus) were present in the plot with greatest time-since-treatment indicating the potential recovery of key native shrubs since these small mammals perform an important seed dispersal role. I also investigated how potential microhabitats created by the felled juniper might support different plant communities. I assessed plant responses within zones created by 1) the felled tree (canopy zone), 2) the original duff zone, and 3) the between - tree interspace zone. The three zones had different plant community compositions as analyzed multivariately with non-metric multidimensional scaling (NMS). Canopy and duff zones were forb - dominated and had less exotic grass invasion while interspace zones were heavily invested with medusahead (Taeniatherum caput-medusae) and ventenata (Ventenata dubia). Exotic herbaceous productivity was lowest under the standing trees of the control plot and high in the interspace of all plots with juniper thinning. In the 2012 cut plot, grass cover was 27.90 percentage points less in the canopy zone compared to the interspace zone (98.75% CI: 17.64 to 38.16 percentage points less grass cover). In the uncut control, median native biomass was 2.08 times greater under the standing trees compared to the interspace (96.25% CI: 1.09 to 3.97 times more biomass). Results from the time-since-treatment chronoseries indicated that exotic grass dominance might be limiting shrub-steppe recovery. Active restoration of shrubs and native grasses may be necessary to address the dominance of exotic grass after juniper thinning. Positive signs of habitat recovery included small mammal responses though I was unable to calculate population estimates due to plot size. Close

• 373. [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

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

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

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

• 375. [Article] Community profiles of ammonia oxidizers across high-elevation forest-to-meadow transects

  In recent years considerable interest has been shown in the diversity of ammonia-oxidizing bacteria in soil communities. The majority of the research has been carried out in Northern Europe where soils ...

  Citation × Citation Citation Abstract Copy Title: Community profiles of ammonia oxidizers across high-elevation forest-to-meadow transects Author: Mintie, Ann In recent years considerable interest has been shown in the diversity of ammonia-oxidizing bacteria in soil communities. The majority of the research has been carried out in Northern Europe where soils have received high atmospheric inputs of nitrogen over the past two centuries. In contrast, although much work has been conducted on nitrogen cycling processes in nitrogen limited forest ecosystems in western North America, no studies have examined the characteristics of ammonia-oxidizing communities in those environments. I was interested in measuring nitrification potential along a high-elevation temperate meadow-to-forest gradient, and characterizing the ammonia-oxidizing communities along that gradient using both molecular and culturing methods. Two experimental sites (Lookout and Carpenter) were chosen in the H.J. Andrews Experimental Forest, located in the western Cascade Range of Oregon, at elevations of approximately 1500 meters. Although nitrification potential rates (NPRs) between sites were not significantly different (P=0.544), variation was observed both within and between sites for specific vegetation types. NPRs were significantly lower in forest (F) soil samples than in meadow (M) soil samples, averaging 5 and 2% of meadow NPRs at Lookout and Carpenter, respectively. In meadow soil samples, most probable number (MPN) population densities of ammonia-oxidizers ranged from 0.6 to 2.6 x 10⁴ cells gram⁻¹ of oven dry soil and 0.9 x 10³ to 1.1 x 10⁵ cells g⁻¹ OD soil at Lookout and Carpenter, respectively. In forest soil samples, population densities ranged from undetectable to 1.1 x 10⁴ cells g⁻¹ OD soil, and 0.9 x 10² to 2.3 x 10³ cells g⁻¹ OD soil at Lookout and Carpenter, respectively. Microbial community DNA was amplified using primers to the ammonia monooxygenase subunit A. Terminal restriction fragments polymorphism analysis with three different restriction enzymes (CfoI, TaqI, and AluI) revealed community profiles dominated by Nitrosospira species. One fragment from CfoI (66 bp) and one fragment from AluI (392-bp) were prominent in 47 soil samples from both sites, and represented between 32 to 100% of the Genescan fragment analyses of PCR products. A full length fragment from AluI digests (491-bp), and three fragments from CfoI (68, 100, and 135- bp) were found sporadically in fewer soil sample T-RFLPs, and within those samples represented smaller percentages of total peak areas. The CfoI 135-bp fragment length was associated primarily with M and meadow/forest (M/F) soils where it was observed in approximately 58 and 100% of the respective transect locations. Eight isolates recovered from soil samples were analyzed using the same molecular methods as the field samples. The T-RFLP patterns of the isolates corresponded with many of those found in the community fingerprints. Four unique amoA sequences were identified among these isolates, including one that possessed the dominant T-RFLP amoA fingerprint in soil samples. This sequence shared 99.8% similarity with Nitrosospira sp. Ka4, a cluster 4 ammonia oxidizer isolated in Norway. Sequence analysis phylogenetically associated the other three isolates (with unique amoA sequences) near Nitrosospira sp. Nsp 1 and Nitrosospira briensis, both cluster 3 ammonia oxidizers. Cloning and sequencing of soil DNA confirmed that ammonia oxidizers with these amoA sequences were present in the soil samples. Two additional amoA sequences were identified in clones that were 95% similar and paraphylogenetically positioned between representatives of clusters 3 and 4. So far, these sequences have not been found in any of the isolates analyzed. Title: Community profiles of ammonia oxidizers across high-elevation forest-to-meadow transects Author: Mintie, Ann In recent years considerable interest has been shown in the diversity of ammonia-oxidizing bacteria in soil communities. The majority of the research has been carried out in Northern Europe where soils have received high atmospheric inputs of nitrogen over the past two centuries. In contrast, although much work has been conducted on nitrogen cycling processes in nitrogen limited forest ecosystems in western North America, no studies have examined the characteristics of ammonia-oxidizing communities in those environments. I was interested in measuring nitrification potential along a high-elevation temperate meadow-to-forest gradient, and characterizing the ammonia-oxidizing communities along that gradient using both molecular and culturing methods. Two experimental sites (Lookout and Carpenter) were chosen in the H.J. Andrews Experimental Forest, located in the western Cascade Range of Oregon, at elevations of approximately 1500 meters. Although nitrification potential rates (NPRs) between sites were not significantly different (P=0.544), variation was observed both within and between sites for specific vegetation types. NPRs were significantly lower in forest (F) soil samples than in meadow (M) soil samples, averaging 5 and 2% of meadow NPRs at Lookout and Carpenter, respectively. In meadow soil samples, most probable number (MPN) population densities of ammonia-oxidizers ranged from 0.6 to 2.6 x 10⁴ cells gram⁻¹ of oven dry soil and 0.9 x 10³ to 1.1 x 10⁵ cells g⁻¹ OD soil at Lookout and Carpenter, respectively. In forest soil samples, population densities ranged from undetectable to 1.1 x 10⁴ cells g⁻¹ OD soil, and 0.9 x 10² to 2.3 x 10³ cells g⁻¹ OD soil at Lookout and Carpenter, respectively. Microbial community DNA was amplified using primers to the ammonia monooxygenase subunit A. Terminal restriction fragments polymorphism analysis with three different restriction enzymes (CfoI, TaqI, and AluI) revealed community profiles dominated by Nitrosospira species. One fragment from CfoI (66 bp) and one fragment from AluI (392-bp) were prominent in 47 soil samples from both sites, and represented between 32 to 100% of the Genescan fragment analyses of PCR products. A full length fragment from AluI digests (491-bp), and three fragments from CfoI (68, 100, and 135- bp) were found sporadically in fewer soil sample T-RFLPs, and within those samples represented smaller percentages of total peak areas. The CfoI 135-bp fragment length was associated primarily with M and meadow/forest (M/F) soils where it was observed in approximately 58 and 100% of the respective transect locations. Eight isolates recovered from soil samples were analyzed using the same molecular methods as the field samples. The T-RFLP patterns of the isolates corresponded with many of those found in the community fingerprints. Four unique amoA sequences were identified among these isolates, including one that possessed the dominant T-RFLP amoA fingerprint in soil samples. This sequence shared 99.8% similarity with Nitrosospira sp. Ka4, a cluster 4 ammonia oxidizer isolated in Norway. Sequence analysis phylogenetically associated the other three isolates (with unique amoA sequences) near Nitrosospira sp. Nsp 1 and Nitrosospira briensis, both cluster 3 ammonia oxidizers. Cloning and sequencing of soil DNA confirmed that ammonia oxidizers with these amoA sequences were present in the soil samples. Two additional amoA sequences were identified in clones that were 95% similar and paraphylogenetically positioned between representatives of clusters 3 and 4. So far, these sequences have not been found in any of the isolates analyzed. Close

• 376. [Article] Response of soil microbial communities and nitrogen cycling processes to changes in vegetation inputs

  Changes in the type and amount of plant inputs can occur gradually, as with succession, or rapidly, as with harvesting or wildfire. With global change it is anticipated that both gradual and immediate ...

  Citation × Citation Citation Abstract Copy Title: Response of soil microbial communities and nitrogen cycling processes to changes in vegetation inputs Author: Brewer, Elizabeth Ann Changes in the type and amount of plant inputs can occur gradually, as with succession, or rapidly, as with harvesting or wildfire. With global change it is anticipated that both gradual and immediate scenarios will occur at increasing frequency. Changes in vegetation inputs alter the quality and quantity of soil organic matter inputs, thus influencing the composition of soil microbial communities and the nutrient cycles they mediate. Understanding the relationship of soil organic matter inputs on soil microbial communities and nutrient cycles will be beneficial in predicting responses to changes in vegetation inputs. During the last 100-150 years, the vegetation of the Rio Grande Plains of the United States has been shifting from grasslands/savannas to woodlands as the result of encroachment of N₂-fixing trees and their associated plant communities. The structure and diversity of soil microbial communities were examined under woody species and remnant grasslands. In addition, relationships between soil microbial communities and soil physical and chemical characteristics were explored. Soil microbial communities differed in soils under N₂-fixing trees and associated vegetation compared to remnant grasslands. Differences in both fungal and bacterial communities were anticipated with vegetation shifts; however, only fungal communities correlated with vegetation, whereas bacterial communities were influenced by spatial heterogeneity. Soil microbial N cycling was investigated in long-term (>10 years) organic matter manipulations in an old-growth forest, dominated by large Pseudotsuga menziesii (Mirb.) Franco (Douglas-fir). The objectives of this research were to: 1) determine if long-term organic matter manipulations in old-growth forests altered microbial N cycling, 2) determine the contribution of litter to N cycling, and 3) determine if litter quality (low C/N red alder and high C/N Douglas-fir) affected the contribution of litter-derived N to N transformations. Long-term organic matter manipulations were found to affect microbial C and N cycling, but to a lesser degree than anticipated. After 10 years of organic matter exclusions and additions, microbial communities in all treatments remained N limited, although N limitation was less severe in organic matter exclusion treatments. Adding leached litter to control and organic matter exclusion soils initially altered N processes but differences dissipated during a 151-day incubation. Litter quality had little impact on the N cycling and litter made modest contributions to N mineralization and nitrification. The exclusion of organic matter altered the functionality of the microbial community to access litter-derived N. Both the gradual establishment of woody clusters on grassland and abrupt manipulations of old-growth vegetation inputs elicited responses in microbial communities and N cycling. Although some responses were subtle, they nonetheless support the responsiveness and importance of microbial communities to soil processes. Understanding feedbacks among plant inputs, microbial communities and nutrient cycles will aid in predicting microbial, ecosystem, and global responses to vegetation changes. Title: Response of soil microbial communities and nitrogen cycling processes to changes in vegetation inputs Author: Brewer, Elizabeth Ann Changes in the type and amount of plant inputs can occur gradually, as with succession, or rapidly, as with harvesting or wildfire. With global change it is anticipated that both gradual and immediate scenarios will occur at increasing frequency. Changes in vegetation inputs alter the quality and quantity of soil organic matter inputs, thus influencing the composition of soil microbial communities and the nutrient cycles they mediate. Understanding the relationship of soil organic matter inputs on soil microbial communities and nutrient cycles will be beneficial in predicting responses to changes in vegetation inputs. During the last 100-150 years, the vegetation of the Rio Grande Plains of the United States has been shifting from grasslands/savannas to woodlands as the result of encroachment of N₂-fixing trees and their associated plant communities. The structure and diversity of soil microbial communities were examined under woody species and remnant grasslands. In addition, relationships between soil microbial communities and soil physical and chemical characteristics were explored. Soil microbial communities differed in soils under N₂-fixing trees and associated vegetation compared to remnant grasslands. Differences in both fungal and bacterial communities were anticipated with vegetation shifts; however, only fungal communities correlated with vegetation, whereas bacterial communities were influenced by spatial heterogeneity. Soil microbial N cycling was investigated in long-term (>10 years) organic matter manipulations in an old-growth forest, dominated by large Pseudotsuga menziesii (Mirb.) Franco (Douglas-fir). The objectives of this research were to: 1) determine if long-term organic matter manipulations in old-growth forests altered microbial N cycling, 2) determine the contribution of litter to N cycling, and 3) determine if litter quality (low C/N red alder and high C/N Douglas-fir) affected the contribution of litter-derived N to N transformations. Long-term organic matter manipulations were found to affect microbial C and N cycling, but to a lesser degree than anticipated. After 10 years of organic matter exclusions and additions, microbial communities in all treatments remained N limited, although N limitation was less severe in organic matter exclusion treatments. Adding leached litter to control and organic matter exclusion soils initially altered N processes but differences dissipated during a 151-day incubation. Litter quality had little impact on the N cycling and litter made modest contributions to N mineralization and nitrification. The exclusion of organic matter altered the functionality of the microbial community to access litter-derived N. Both the gradual establishment of woody clusters on grassland and abrupt manipulations of old-growth vegetation inputs elicited responses in microbial communities and N cycling. Although some responses were subtle, they nonetheless support the responsiveness and importance of microbial communities to soil processes. Understanding feedbacks among plant inputs, microbial communities and nutrient cycles will aid in predicting microbial, ecosystem, and global responses to vegetation changes. Close

• 377. [Article] Dead fuels and understory vegetation six years after a large mixed-severity wildfire in southwest Oregon

  Though the mixed-evergreen forests of the Klamath Siskiyous have a long history of large, mixed-severity fires, most research in this region has concentrated on the impacts of high-severity fire. Knowledge ...

  Citation × Citation Citation Abstract Copy Title: Dead fuels and understory vegetation six years after a large mixed-severity wildfire in southwest Oregon Author: Nathanson, Amy Though the mixed-evergreen forests of the Klamath Siskiyous have a long history of large, mixed-severity fires, most research in this region has concentrated on the impacts of high-severity fire. Knowledge of the ecological effects of low- and moderate-severity areas within mixed-severity fires is important because such areas may account for over half the landscape affected by a fire. The purpose of this study was to understand the relationship of fire severity with dead fuels and understory vegetation across a full range of fire severities. Study sites were located within and just outside the boundary of the 2002 Biscuit Fire, which burned 200,000 hectares in a mosaic of burn severities. Six years after the Biscuit Fire, the biomass and depth of litter and duff was lower on burned sites than unburned sites, and lowest on high-severity sites. This relationship was reversed for woody fuels >7.62 cm in diameter, where quantities were highest in high- and extreme-severity areas, though there was no evidence that quantities differed between low-severity and unburned sites. There was no evidence of a relationship between woody fuels 0.64-7.62 cm in diameter and fire severity, 6 years post-fire. There was no evidence that fuel quantities differed between sites that burned only in the Biscuit Fire with sites that also burned 15 years earlier in the 1987 Silver Fire. Fuel quantities and composition differed between burned and unburned sites, but these differences disappeared if litter and duff were not considered. Fuel classes were correlated with each other within three general size classes: small (litter, duff, and fuels <2.54 cm), medium (fuels 2.54-30 cm), and large (fuels >30 cm). There was little correlation between these size classes. Vegetation response also varied by fire severity, species, and height. Generally, density for tree seedlings <0.5 m was highest on low-severity sites and lowest on high-severity sites. For seedlings 0.5-1.37 m the relationship was reversed, with the highest seedling densities in high-severity areas. Specific seedling relationships to burn severity and other explanatory factors (e.g. shrub cover, elevation, precipitation, maxiumun August temperatures) varied by species and seedling height. Average seedling densities were above the minimum acceptable stocking levels of 333 trees per hectare (135 seedlings/acre) as identified in federal plans for the fire area. Shrub species richness and diversity did not vary with burn severity; however, shrub species and ground cover composition did differ with burn severity six years after the Biscuit Fire. The relationship of understory cover composition with burn severity aligned with species life history traits; fire-adapted, nitrogen-fixing species were more prevalent on high- and extreme-severity sites while species associated with low-severity fire or old-growth forests were more prevalent on low-severity or unburned sites. I found no evidence of difference in total graminoid or forb cover based on fire severity, but shrub quantities were lower on low-severity sites than on unburned, high-, and extreme-severity sites. This study reveals how fuel and vegetation vary across the full range of fire severities. It demonstrates that mixed-severity fires create a mix of ecological responses. It also provides a baseline for future studies, as the relationships between fire severity and fuels or vegetation may disappear or change in subsequent decades. Title: Dead fuels and understory vegetation six years after a large mixed-severity wildfire in southwest Oregon Author: Nathanson, Amy Though the mixed-evergreen forests of the Klamath Siskiyous have a long history of large, mixed-severity fires, most research in this region has concentrated on the impacts of high-severity fire. Knowledge of the ecological effects of low- and moderate-severity areas within mixed-severity fires is important because such areas may account for over half the landscape affected by a fire. The purpose of this study was to understand the relationship of fire severity with dead fuels and understory vegetation across a full range of fire severities. Study sites were located within and just outside the boundary of the 2002 Biscuit Fire, which burned 200,000 hectares in a mosaic of burn severities. Six years after the Biscuit Fire, the biomass and depth of litter and duff was lower on burned sites than unburned sites, and lowest on high-severity sites. This relationship was reversed for woody fuels >7.62 cm in diameter, where quantities were highest in high- and extreme-severity areas, though there was no evidence that quantities differed between low-severity and unburned sites. There was no evidence of a relationship between woody fuels 0.64-7.62 cm in diameter and fire severity, 6 years post-fire. There was no evidence that fuel quantities differed between sites that burned only in the Biscuit Fire with sites that also burned 15 years earlier in the 1987 Silver Fire. Fuel quantities and composition differed between burned and unburned sites, but these differences disappeared if litter and duff were not considered. Fuel classes were correlated with each other within three general size classes: small (litter, duff, and fuels <2.54 cm), medium (fuels 2.54-30 cm), and large (fuels >30 cm). There was little correlation between these size classes. Vegetation response also varied by fire severity, species, and height. Generally, density for tree seedlings <0.5 m was highest on low-severity sites and lowest on high-severity sites. For seedlings 0.5-1.37 m the relationship was reversed, with the highest seedling densities in high-severity areas. Specific seedling relationships to burn severity and other explanatory factors (e.g. shrub cover, elevation, precipitation, maxiumun August temperatures) varied by species and seedling height. Average seedling densities were above the minimum acceptable stocking levels of 333 trees per hectare (135 seedlings/acre) as identified in federal plans for the fire area. Shrub species richness and diversity did not vary with burn severity; however, shrub species and ground cover composition did differ with burn severity six years after the Biscuit Fire. The relationship of understory cover composition with burn severity aligned with species life history traits; fire-adapted, nitrogen-fixing species were more prevalent on high- and extreme-severity sites while species associated with low-severity fire or old-growth forests were more prevalent on low-severity or unburned sites. I found no evidence of difference in total graminoid or forb cover based on fire severity, but shrub quantities were lower on low-severity sites than on unburned, high-, and extreme-severity sites. This study reveals how fuel and vegetation vary across the full range of fire severities. It demonstrates that mixed-severity fires create a mix of ecological responses. It also provides a baseline for future studies, as the relationships between fire severity and fuels or vegetation may disappear or change in subsequent decades. Close

• 378. [Article] Woody riparian species patterns along northeast Oregon mountainous streams and the relationship to riparian capability

  Woody riparian vegetation is an essential component of riparian ecosystems, responsible in part for the maintenance of functional ecological processes. The plant community composition and distribution ...

  Citation × Citation Citation Abstract Copy Title: Woody riparian species patterns along northeast Oregon mountainous streams and the relationship to riparian capability Author: Yancey, Jennifer M. Woody riparian vegetation is an essential component of riparian ecosystems, responsible in part for the maintenance of functional ecological processes. The plant community composition and distribution provide an indication of the underlying mosaic of environmental attributes and processes. Restoration and management of riparian communities have been hindered by the lack of measurable criteria for the assessment of a riparian systems modified by human imposed infrastructures. The woody vegetation community offered a quantifiable indicator of the underlying mosaic of environmental, physical, and hydrological attributes, while allowing the investigation of the concept of riparian potential versus riparian capability. The examination of riparian condition was measured through the determination of species-environmental relationships along three mountainous channels in northeast Oregon. The physical and environmental attributes of channel morphology, hydrology, understory community composition, surface particle characteristics, and microclimate variables were quantified and analyzed in relation to the woody vegetation composition and distribution across the three separate streams and within flood-frequency elevation zones. The second component of the study evaluated and described methods for quantifying the concept of riparian capability, based on the measured species-environmental relationships and channel morphology. The evaluation of condition was measured against the reference baseline of Rosgen hierarchical classification and regional hydraulic geometry curves. Multivariate analyses indicated that vegetation transects grouped by stream and vegetation belt transects weakly grouped by flood zone, based on the species composition quantified within the vegetation transects and flood zones. Secondly, channel geometry, canopy cover, air temperature, channel particle size, understory composition attributes, and flood zone distance were found to be overall gradients, which described the variation in species composition across the three streams in northeast Oregon. Direct individual species-environmental relationship conclusions were weak due to the close clustering of species and multiple physical and environmental gradients. Riparian condition at the Grande Ronde River and North Fork Catherine Creek was determined to be functioning at riparian capability. Channel geometry measurements at the two stream reaches aligned with Rosgen stream type criteria and regional hydrologic curves, while species composition represented characteristics of potential natural communities. Meadow Creek was concluded to have departed from the highest attainable condition, thus riparian condition was less than capability. The results suggested that woody riparian vegetation response was a function the physical sttributes: channel morphological widths, bankfull, floodprone, 25-year flood width, valley width, channel sinuosity, and channel slope. Environmental attributes, floodplain canopy cover, air temperature, and understory composition, were further factors that influenced the woody riparian vegetation community variation. The results also suggested species richness and diversity were associated with specific physical and environmental attributes. Finally, the results provided the determination of riparian capability along montane streams in northeast Oregon and criteria acceptable for the determination of riparian capability. These criteria included the physical channel measurements assessed against Rosgen hierarchiecal classification and regional channel geometry curves; and woody vegetation presence and distribution assessed against potential natural community plant associations. Further research should be done across a variety of riparian systems to determine both indicator species and reference values for the physical and environmental attributes that could be utilized for the assessment of riparian capability. Title: Woody riparian species patterns along northeast Oregon mountainous streams and the relationship to riparian capability Author: Yancey, Jennifer M. Woody riparian vegetation is an essential component of riparian ecosystems, responsible in part for the maintenance of functional ecological processes. The plant community composition and distribution provide an indication of the underlying mosaic of environmental attributes and processes. Restoration and management of riparian communities have been hindered by the lack of measurable criteria for the assessment of a riparian systems modified by human imposed infrastructures. The woody vegetation community offered a quantifiable indicator of the underlying mosaic of environmental, physical, and hydrological attributes, while allowing the investigation of the concept of riparian potential versus riparian capability. The examination of riparian condition was measured through the determination of species-environmental relationships along three mountainous channels in northeast Oregon. The physical and environmental attributes of channel morphology, hydrology, understory community composition, surface particle characteristics, and microclimate variables were quantified and analyzed in relation to the woody vegetation composition and distribution across the three separate streams and within flood-frequency elevation zones. The second component of the study evaluated and described methods for quantifying the concept of riparian capability, based on the measured species-environmental relationships and channel morphology. The evaluation of condition was measured against the reference baseline of Rosgen hierarchical classification and regional hydraulic geometry curves. Multivariate analyses indicated that vegetation transects grouped by stream and vegetation belt transects weakly grouped by flood zone, based on the species composition quantified within the vegetation transects and flood zones. Secondly, channel geometry, canopy cover, air temperature, channel particle size, understory composition attributes, and flood zone distance were found to be overall gradients, which described the variation in species composition across the three streams in northeast Oregon. Direct individual species-environmental relationship conclusions were weak due to the close clustering of species and multiple physical and environmental gradients. Riparian condition at the Grande Ronde River and North Fork Catherine Creek was determined to be functioning at riparian capability. Channel geometry measurements at the two stream reaches aligned with Rosgen stream type criteria and regional hydrologic curves, while species composition represented characteristics of potential natural communities. Meadow Creek was concluded to have departed from the highest attainable condition, thus riparian condition was less than capability. The results suggested that woody riparian vegetation response was a function the physical sttributes: channel morphological widths, bankfull, floodprone, 25-year flood width, valley width, channel sinuosity, and channel slope. Environmental attributes, floodplain canopy cover, air temperature, and understory composition, were further factors that influenced the woody riparian vegetation community variation. The results also suggested species richness and diversity were associated with specific physical and environmental attributes. Finally, the results provided the determination of riparian capability along montane streams in northeast Oregon and criteria acceptable for the determination of riparian capability. These criteria included the physical channel measurements assessed against Rosgen hierarchiecal classification and regional channel geometry curves; and woody vegetation presence and distribution assessed against potential natural community plant associations. Further research should be done across a variety of riparian systems to determine both indicator species and reference values for the physical and environmental attributes that could be utilized for the assessment of riparian capability. Close

• 379. [Article] Overstory composition and stand structure shifts within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone

  Ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta var. murrayana) forests of south-central Oregon have been extensively researched over the last century. However, little information has ...

  Citation × Citation Citation Abstract Copy Title: Overstory composition and stand structure shifts within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone Author: Shuffield, Chaylon D. Ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta var. murrayana) forests of south-central Oregon have been extensively researched over the last century. However, little information has been reported on overstory composition and stand structure shifts associated with fire exclusion within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone. In recent time, the lack of disturbance history and quantitative information needed to reconstruct historic stand conditions has become a growing concern for many ecologists. The need to collect quantitative information from remnant old-growth stands is imperative to improve restoration activities, incorporate stand-level diversity, identify the degree of successional departure, and to ensure valuable data is archived for future reference and ecological analysis. In Chapter 1, an exhaustive search for published information on early land-use practices specific to our study area was performed to: (1) identify the degree of Native American influence on vegetation; (2) identify direct and indirect Euro-American disturbances involving the loss of natural processes; and (3) establish a reference period for appropriate representation of historic conditions. In Chapter 2, remnant old-growth stands were analyzed using dendrochronological techniques and statistical comparisons to quantify: (1) shifts in overstory composition and stand structure; (2) growth and development of ponderosa pine and lodgepole pine across time; and to (3) characterize the influence of climate and fire on species recruitment. Our analysis indicated successional trajectory shifts occurred shortly after the loss of Native American influence beginning around 1850 and associated affects of intensive grazing following 1880. Age reconstruction displayed an exponential pattern of recruitment between 1880 and 1950. Since 1850, our analysis revealed a reduction in average tree basal area growth and height development of understory ponderosa pine and lodgepole pine. Ponderosa pine greater than 150 years old accounted for less than 5.0% of the total contemporary density, but composed 45.0% of the total basal area. Lodgepole pine greater than 100 years old accounted for approximately 3.0% of the total contemporary density and composed 12.8% of the total basal area. Stand density for our study area averaged 25.3 trees per hectare for ponderosa pine greater than 53.3 centimeters diameter at 1.4 meters. We report low levels of lodgepole pine recruitment (2/hectare/decade) prior to 1880 and suggest the long-term development of less fire-resistant lodgepole pine has been favored since fire exclusion. Furthermore, contemporary settings support conditions associated to atypical mountain pine beetle outbreaks and fire behavior known to cause mortality of large diameter ponderosa pine. Restoration of remnant inter-mixed stands requires the aggressive removal of lodgepole pine and re-introduction of fire to provide long-term sustainability of ecosystem health and preservation of large diameter ponderosa pine. Title: Overstory composition and stand structure shifts within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone Author: Shuffield, Chaylon D. Ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta var. murrayana) forests of south-central Oregon have been extensively researched over the last century. However, little information has been reported on overstory composition and stand structure shifts associated with fire exclusion within inter-mixed ponderosa pine and lodgepole pine stands of the south-central Oregon pumice zone. In recent time, the lack of disturbance history and quantitative information needed to reconstruct historic stand conditions has become a growing concern for many ecologists. The need to collect quantitative information from remnant old-growth stands is imperative to improve restoration activities, incorporate stand-level diversity, identify the degree of successional departure, and to ensure valuable data is archived for future reference and ecological analysis. In Chapter 1, an exhaustive search for published information on early land-use practices specific to our study area was performed to: (1) identify the degree of Native American influence on vegetation; (2) identify direct and indirect Euro-American disturbances involving the loss of natural processes; and (3) establish a reference period for appropriate representation of historic conditions. In Chapter 2, remnant old-growth stands were analyzed using dendrochronological techniques and statistical comparisons to quantify: (1) shifts in overstory composition and stand structure; (2) growth and development of ponderosa pine and lodgepole pine across time; and to (3) characterize the influence of climate and fire on species recruitment. Our analysis indicated successional trajectory shifts occurred shortly after the loss of Native American influence beginning around 1850 and associated affects of intensive grazing following 1880. Age reconstruction displayed an exponential pattern of recruitment between 1880 and 1950. Since 1850, our analysis revealed a reduction in average tree basal area growth and height development of understory ponderosa pine and lodgepole pine. Ponderosa pine greater than 150 years old accounted for less than 5.0% of the total contemporary density, but composed 45.0% of the total basal area. Lodgepole pine greater than 100 years old accounted for approximately 3.0% of the total contemporary density and composed 12.8% of the total basal area. Stand density for our study area averaged 25.3 trees per hectare for ponderosa pine greater than 53.3 centimeters diameter at 1.4 meters. We report low levels of lodgepole pine recruitment (2/hectare/decade) prior to 1880 and suggest the long-term development of less fire-resistant lodgepole pine has been favored since fire exclusion. Furthermore, contemporary settings support conditions associated to atypical mountain pine beetle outbreaks and fire behavior known to cause mortality of large diameter ponderosa pine. Restoration of remnant inter-mixed stands requires the aggressive removal of lodgepole pine and re-introduction of fire to provide long-term sustainability of ecosystem health and preservation of large diameter ponderosa pine. Close

• 380. [Article] Characterization of fungal and bacterial communities associated with mat-forming ectomycorrhizal fungi from old-growth stands in the H.J. Andrews Experimental Forest

  Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to ...

  Citation × Citation Citation Abstract Copy Title: Characterization of fungal and bacterial communities associated with mat-forming ectomycorrhizal fungi from old-growth stands in the H.J. Andrews Experimental Forest Author: Hesse, Cedar N. Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to have increased microbial respiration rates and have been hypothesized to harbor unique assemblages of fungi and bacteria. The objectives of this dissertation were to characterize and examine the fungal and bacterial communities associated with EcM mats in old-growth forests of the H.J. Andrews Experimental Forest located in the Oregon Cascades. Additionally, this work assessed the application of traditional, emerging, and novel molecular sampling techniques for determining microbial communities of environmental samples. This research investigated the microbial communities associated with two common EcM mat genera found in old-growth Douglas fir stands in the Pacific Northwest; Piloderma (Atheliales, Basidiomycota) and Ramaria (Gomphales, Basidiomycota). Soil samples were collected from Piloderma and Ramaria mats and surrounding non- mat soil for molecular analysis of nucleic acids. First, a comparative study was conducted to determine the most appropriate rDNA molecular sampling technique for microbial community characterization. Two next-generation sequencing methods, Roche 454 pyrosequencing and Illumina-based environmental sequencing, the latter developed by the author, were compared to a more traditional sequencing approach, i.e., Sanger sequencing of clone libraries. These findings informed the subsequent sampling of the fungal ITS and bacterial 16S rDNA fragment with 454 pyrosequencing to determine the microbial communities within mat and non-mat soils. Second, this work utilized a pyrosequencing approach to explore fungal community structure in EcM mat and non-mat soils. This work concluded that differences in microbial communities do exist between Piloderma mat, Ramaria mat, and non-mat soils, but the differences are largely quantitative with relatively few distinct taxonomic shifts in microbial constituents. Piloderma, Ramaria and Russula, in addition to being the dominant taxa found on mycorrhizal root tips, were found to be the most abundant taxa in bulk soils within their respective mat types or non-mat sample. The background fungal communities within the EcM mats in this study exhibited considerable taxonomic overlap with the exception of Piloderma vs. non-mat comparisons; Russula species dominated nonmat soils but tended to be excluded or significantly underrepresented in Piloderma mats. Lastly, this study explored the bacterial communities associated with Piloderma and Ramaria mats using lower- coverage 454-Jr pyrosequencing. Bacterial communities exhibited significant structure as a function of mat-type, soil horizon and pH, but this finding should be interpreted with respect to the nonrandom distribution of Piloderma-mats in the O- horizon and the Ramaria-mats in the A-horizon, and the tendancy for EcM mats to be more acidic than surrounding soils. Nonetheless, the total microbial (bacterial and fungal) community was typically dominated by the mat-forming taxa, or Russula, in the case of non-mat soils. While the presence of Piloderma mats did enrich or restrict some bacterial groups, soil pH was also found to be a significant driver of bacterial richness and taxonomic diversity. Fungal and bacterial richness were also found to be positively related to one another, regardless of soil horizon or EcM mat type. This work, taken together, contributes to the understanding of hyperdiversity and heterogeneity of microbial communities of temperate forest soils and highlights the potential for fungal and bacterial communities to be influenced by the presence of EcM mats. Title: Characterization of fungal and bacterial communities associated with mat-forming ectomycorrhizal fungi from old-growth stands in the H.J. Andrews Experimental Forest Author: Hesse, Cedar N. Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to have increased microbial respiration rates and have been hypothesized to harbor unique assemblages of fungi and bacteria. The objectives of this dissertation were to characterize and examine the fungal and bacterial communities associated with EcM mats in old-growth forests of the H.J. Andrews Experimental Forest located in the Oregon Cascades. Additionally, this work assessed the application of traditional, emerging, and novel molecular sampling techniques for determining microbial communities of environmental samples. This research investigated the microbial communities associated with two common EcM mat genera found in old-growth Douglas fir stands in the Pacific Northwest; Piloderma (Atheliales, Basidiomycota) and Ramaria (Gomphales, Basidiomycota). Soil samples were collected from Piloderma and Ramaria mats and surrounding non- mat soil for molecular analysis of nucleic acids. First, a comparative study was conducted to determine the most appropriate rDNA molecular sampling technique for microbial community characterization. Two next-generation sequencing methods, Roche 454 pyrosequencing and Illumina-based environmental sequencing, the latter developed by the author, were compared to a more traditional sequencing approach, i.e., Sanger sequencing of clone libraries. These findings informed the subsequent sampling of the fungal ITS and bacterial 16S rDNA fragment with 454 pyrosequencing to determine the microbial communities within mat and non-mat soils. Second, this work utilized a pyrosequencing approach to explore fungal community structure in EcM mat and non-mat soils. This work concluded that differences in microbial communities do exist between Piloderma mat, Ramaria mat, and non-mat soils, but the differences are largely quantitative with relatively few distinct taxonomic shifts in microbial constituents. Piloderma, Ramaria and Russula, in addition to being the dominant taxa found on mycorrhizal root tips, were found to be the most abundant taxa in bulk soils within their respective mat types or non-mat sample. The background fungal communities within the EcM mats in this study exhibited considerable taxonomic overlap with the exception of Piloderma vs. non-mat comparisons; Russula species dominated nonmat soils but tended to be excluded or significantly underrepresented in Piloderma mats. Lastly, this study explored the bacterial communities associated with Piloderma and Ramaria mats using lower- coverage 454-Jr pyrosequencing. Bacterial communities exhibited significant structure as a function of mat-type, soil horizon and pH, but this finding should be interpreted with respect to the nonrandom distribution of Piloderma-mats in the O- horizon and the Ramaria-mats in the A-horizon, and the tendancy for EcM mats to be more acidic than surrounding soils. Nonetheless, the total microbial (bacterial and fungal) community was typically dominated by the mat-forming taxa, or Russula, in the case of non-mat soils. While the presence of Piloderma mats did enrich or restrict some bacterial groups, soil pH was also found to be a significant driver of bacterial richness and taxonomic diversity. Fungal and bacterial richness were also found to be positively related to one another, regardless of soil horizon or EcM mat type. This work, taken together, contributes to the understanding of hyperdiversity and heterogeneity of microbial communities of temperate forest soils and highlights the potential for fungal and bacterial communities to be influenced by the presence of EcM mats. Close