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• 51. [Article] Mixed-Severity Fire Effects on Biological Legacies and Vegetation Response in Pseudotsuga Forests of Western Oregon's Central Cascades, USA

  Mixed-severity fire occurrence is increasingly recognized in Pseudotsuga forests of the Pacific Northwest, but questions remain about how tree mortality varies, and forest structure is altered, across ...

  Citation × Citation Citation Abstract Copy Title: Mixed-Severity Fire Effects on Biological Legacies and Vegetation Response in Pseudotsuga Forests of Western Oregon's Central Cascades, USA Author: Dunn, Christopher J. Mixed-severity fire occurrence is increasingly recognized in Pseudotsuga forests of the Pacific Northwest, but questions remain about how tree mortality varies, and forest structure is altered, across the disturbance gradient observed in these fires. Therefore, we sampled live and dead biological legacies at 45 one ha plots, with four 0.10 ha nested plots, stratified across an unburned, low, moderate and high-severity fire gradient. We used severity estimates based on differenced Normalized Burn Ratio (dNBR), and captured a disturbance gradient, but plots in our low-severity class underestimated fire effects because of misclassification or delayed mortality. We estimated probability of mortality for shade-intolerant (Douglas-fir, incense-cedar, sugar pine) and shade-tolerant (western hemlock, western redcedar, true fir) trees from 5,079 sampled trees and snags. The probability of mortality was higher for shade-tolerant species across all fire-severity classes, and decreased with increasing DBH except for western hemlock. Only large, shade-intolerant trees survived high-severity fire. Post-fire snag fall and fragmentation were estimated from 2,746 sampled snags and logs. The probability of snag fall decreased with increasing DBH for all species, and was positively correlated with fire severity, except for Douglas-fir that had a higher probability following low-severity fire. Snag fragmentation was positively correlated with DBH and fire severity for all species. We also estimated the coefficient of variation within- and among-plots by fire severity class, as well as across all sampled conditions. Structural attributes varied more within- than among-plots, likely a result of increasing sub-hectare patchy mortality as fire intensity increased. Although vertical and horizontal structural diversity increased at sub-hectare scales, the coefficient of variation was highest for all structural attributes when compared across all fire severity classes. Therefore, the range of fire effects observed in mixed-severity fires may be functionally important in creating structural complexity across landscapes, which is an important attribute of old-growth forests in the Pacific Northwest. Understory vegetation response to mixed-severity fires has not been characterized for these forests even though the majority of vegetation diversity is found in these vegetation layers. Therefore, we sampled forest structure (1000 m² circular plots) and understory vegetation (100 m² plots) at 168 collocated plots stratified across unburned, low, moderate and high-severity conditions 10 years (Tiller Complex) and 22 years (Warner Fire) post-fire. We focused on shrub species, but sampled forbs, graminoids, ferns and moss as functional groups. Offsite colonization and fire stimulated soil seedbanks increased the total species richness from 23 to 46. The life-history strategies of residual and colonizing species resulted in three dominant species response-curves to the magnitude of disturbance: 1) 'disturbance-sensitive', when relative abundance was highest in unburned plots and continued to decline with increasing fire severity, 2) 'disturbance-stimulated', when relative abundance was highest following low or moderate-severity fire and 3) 'disturbance-amplified', when relative abundance increased with increasing fire severity. Residual and colonizing species assemblages promoted five or six distinct understory communities, dominantly driven by legacy tree basal area rather than the proportion of basal area killed. Understory communities were rarely associated with one disturbance severity class as fire refugia, variation in overstory and understory fire severity, and compensatory conditions offset fire effects. Early-seral habitats were the most different from unburned forests, but were not the only post-fire conditions important across these burned landscapes. Interactions among live and dead forest structures following low or moderate-severity fire, and the vegetation response to these conditions, are also unique to the post-fire landscape and likely important for various wildlife species. Therefore, if ecological forestry paradigms focus dominantly on creating old-growth structure or early-seral habitats, they might exclude important conditions that contribute to the landscape structural complexity created by mixed-severity fires. Additionally, tree regeneration response to mixed-severity fires has not been characterized for these forests even though they offer insight into one aspect of the resilience of these ecosystems to disturbance. Therefore, we sampled forest structure (1000 m² circular plots) and regeneration dynamics (100 m² plots) at 168 collocated plots stratified across unburned, low, moderate and high-severity conditions 10 years (Tiller Complex) and 22 years (Warner Fire) post-fire. The largest marginal increase in tree mortality (stems ha⁻¹) occurred between unburned and low-severity fires, given preferential mortality of small trees and shade-tolerant species, but basal area mortality had the largest marginal increase moving from moderate to high-severity. Pairwise comparisons of legacy tree basal area between low and moderate-severity weren’t as significant as other comparisons, but did capture a gradient of increasing fire effects. Quadratic mean diameter and canopy base height were positively correlated with fire severity as incrementally larger trees were killed and canopy ascension followed. Regeneration density increased regardless of severity, relative to unburned forests (median density of 1,384 trees ha⁻¹), but the highest median density (16,220 trees ha⁻¹) followed low-severity fire at the Tiller Complex and moderate-severity fire (14,472 trees ha⁻¹) at Warner Fire. Plot-level average species richness was highest following these same fire severity classes, supporting the Intermediate Disturbance Hypothesis. Statistically distinct regeneration communities occurred across the fire severity gradient at both fire sites. The relative abundance of shade-tolerant tree species decreased as fire severity increased, except for a divergent response following stand-initiation at the Warner Fire. While divergent successional pathways were evident within a couple decades following stand-initiation, low or moderate-severity fires also modified successional trajectories and may be the most functionally important disturbance magnitude because it has the greatest potential to increase compositional and structural diversity. Incorporating mixed-severity fire effects into landscape management of Pseudotsuga forests could increase structural complexity at stand and landscape-scales. Title: Mixed-Severity Fire Effects on Biological Legacies and Vegetation Response in Pseudotsuga Forests of Western Oregon's Central Cascades, USA Author: Dunn, Christopher J. Mixed-severity fire occurrence is increasingly recognized in Pseudotsuga forests of the Pacific Northwest, but questions remain about how tree mortality varies, and forest structure is altered, across the disturbance gradient observed in these fires. Therefore, we sampled live and dead biological legacies at 45 one ha plots, with four 0.10 ha nested plots, stratified across an unburned, low, moderate and high-severity fire gradient. We used severity estimates based on differenced Normalized Burn Ratio (dNBR), and captured a disturbance gradient, but plots in our low-severity class underestimated fire effects because of misclassification or delayed mortality. We estimated probability of mortality for shade-intolerant (Douglas-fir, incense-cedar, sugar pine) and shade-tolerant (western hemlock, western redcedar, true fir) trees from 5,079 sampled trees and snags. The probability of mortality was higher for shade-tolerant species across all fire-severity classes, and decreased with increasing DBH except for western hemlock. Only large, shade-intolerant trees survived high-severity fire. Post-fire snag fall and fragmentation were estimated from 2,746 sampled snags and logs. The probability of snag fall decreased with increasing DBH for all species, and was positively correlated with fire severity, except for Douglas-fir that had a higher probability following low-severity fire. Snag fragmentation was positively correlated with DBH and fire severity for all species. We also estimated the coefficient of variation within- and among-plots by fire severity class, as well as across all sampled conditions. Structural attributes varied more within- than among-plots, likely a result of increasing sub-hectare patchy mortality as fire intensity increased. Although vertical and horizontal structural diversity increased at sub-hectare scales, the coefficient of variation was highest for all structural attributes when compared across all fire severity classes. Therefore, the range of fire effects observed in mixed-severity fires may be functionally important in creating structural complexity across landscapes, which is an important attribute of old-growth forests in the Pacific Northwest. Understory vegetation response to mixed-severity fires has not been characterized for these forests even though the majority of vegetation diversity is found in these vegetation layers. Therefore, we sampled forest structure (1000 m² circular plots) and understory vegetation (100 m² plots) at 168 collocated plots stratified across unburned, low, moderate and high-severity conditions 10 years (Tiller Complex) and 22 years (Warner Fire) post-fire. We focused on shrub species, but sampled forbs, graminoids, ferns and moss as functional groups. Offsite colonization and fire stimulated soil seedbanks increased the total species richness from 23 to 46. The life-history strategies of residual and colonizing species resulted in three dominant species response-curves to the magnitude of disturbance: 1) 'disturbance-sensitive', when relative abundance was highest in unburned plots and continued to decline with increasing fire severity, 2) 'disturbance-stimulated', when relative abundance was highest following low or moderate-severity fire and 3) 'disturbance-amplified', when relative abundance increased with increasing fire severity. Residual and colonizing species assemblages promoted five or six distinct understory communities, dominantly driven by legacy tree basal area rather than the proportion of basal area killed. Understory communities were rarely associated with one disturbance severity class as fire refugia, variation in overstory and understory fire severity, and compensatory conditions offset fire effects. Early-seral habitats were the most different from unburned forests, but were not the only post-fire conditions important across these burned landscapes. Interactions among live and dead forest structures following low or moderate-severity fire, and the vegetation response to these conditions, are also unique to the post-fire landscape and likely important for various wildlife species. Therefore, if ecological forestry paradigms focus dominantly on creating old-growth structure or early-seral habitats, they might exclude important conditions that contribute to the landscape structural complexity created by mixed-severity fires. Additionally, tree regeneration response to mixed-severity fires has not been characterized for these forests even though they offer insight into one aspect of the resilience of these ecosystems to disturbance. Therefore, we sampled forest structure (1000 m² circular plots) and regeneration dynamics (100 m² plots) at 168 collocated plots stratified across unburned, low, moderate and high-severity conditions 10 years (Tiller Complex) and 22 years (Warner Fire) post-fire. The largest marginal increase in tree mortality (stems ha⁻¹) occurred between unburned and low-severity fires, given preferential mortality of small trees and shade-tolerant species, but basal area mortality had the largest marginal increase moving from moderate to high-severity. Pairwise comparisons of legacy tree basal area between low and moderate-severity weren’t as significant as other comparisons, but did capture a gradient of increasing fire effects. Quadratic mean diameter and canopy base height were positively correlated with fire severity as incrementally larger trees were killed and canopy ascension followed. Regeneration density increased regardless of severity, relative to unburned forests (median density of 1,384 trees ha⁻¹), but the highest median density (16,220 trees ha⁻¹) followed low-severity fire at the Tiller Complex and moderate-severity fire (14,472 trees ha⁻¹) at Warner Fire. Plot-level average species richness was highest following these same fire severity classes, supporting the Intermediate Disturbance Hypothesis. Statistically distinct regeneration communities occurred across the fire severity gradient at both fire sites. The relative abundance of shade-tolerant tree species decreased as fire severity increased, except for a divergent response following stand-initiation at the Warner Fire. While divergent successional pathways were evident within a couple decades following stand-initiation, low or moderate-severity fires also modified successional trajectories and may be the most functionally important disturbance magnitude because it has the greatest potential to increase compositional and structural diversity. Incorporating mixed-severity fire effects into landscape management of Pseudotsuga forests could increase structural complexity at stand and landscape-scales. Close

• 52. [Article] Wildlife Health in Managed Forests : Immunity and Infectious Diseases in Wild Rodents of Oregon

  With continual and worldwide human population growth, our impact on the natural environment expands and intensifies every day. We consume natural resources, burn fossil fuels, and release toxic compounds ...

  Citation × Citation Citation Abstract Copy Title: Wildlife Health in Managed Forests : Immunity and Infectious Diseases in Wild Rodents of Oregon Author: Hanselmann, Rhea With continual and worldwide human population growth, our impact on the natural environment expands and intensifies every day. We consume natural resources, burn fossil fuels, and release toxic compounds into the air, water, and earth. We build roads that fragment the landscape, construct new settlements, and develop agricultural lands in previously undisturbed areas. And, we introduce non-native species, which compete with and/or prey on native ones. Our actions change the composition of ecosystems by effacing natural environments and decimating plant and animal populations. We have reached a time of unprecedented anthropogenic environmental change. And, while we recognize, and work feverishly to mitigate, countless consequences of our actions, we still lack a profound understanding of just as many of the corollaries of the environmental changes we provoke. One thing we do know is that human-induced changes in environmental conditions can affect health – from individual organisms, to plant and animal populations, all the way to the level of the ecosystem. Yet, the mechanisms underlying such adverse health outcomes are only partially understood. For instance, we know that alterations in the structure of plant and animal communities, the distribution and demographics of populations, and the abundance of individuals can influence the emergence or re-emergence of infectious diseases. Which species are present in a community, where, when, and in what numbers can all determine the dynamics of pathogens, lead to disease outbreaks, and provide opportunities for spillover into new species. However, given the many environmental-, population-, and organism-level factors involved, and the complexity by which these variables interact, detecting and predicting the ultimate consequences for the health of animal, including human, populations remains difficult. Wild animals play important roles in numerous infectious disease cycles, many of which are shared with humans. Considering this and the well-documented effects that human activity can have on wildlife populations, studying the impacts of anthropogenic environmental change on health in wildlife is highly relevant. To understand how human-induced environmental changes affect wildlife health and to make predictions about potential regional or even global consequences for the dynamics of infectious diseases, however, we first need to understand patterns at a local scale. Here, I describe variation in immune function in captive and wild rodent species native to managed forests in northwestern Oregon, and examine how intensive forest management practices affect these and other physiological processes, and the prevalence of infectious diseases, in a large-scale field experiment. In Chapter 2 of this dissertation, I present baseline data on simple immune parameters in an iconic inhabitant of old-growth forests in the Pacific Northwest, the red tree vole (Arborimus longicaudus). I show that both body condition and age are important for immune defenses in this species. Translating these findings to wild populations leads me to predict that degradation of habitat may affect red tree voles not only at the population scale, as is currently the case, but that less obvious consequences for the health of individuals surviving in disturbed or suboptimal habitat are also possible. It is important, therefore, that efforts to conserve this species consider adverse effects of present forest management practices on red tree vole health, as potentially increased disease susceptibility could have detrimental outcomes for this species. In Chapters 3 and 4, I took advantage of a rare and large-scale experiment to test my predictions regarding the negative consequences of habitat degradation for individual animals in more ubiquitous rodent species known for their resilience to environmental disturbance. I investigated the effects of intensive forest management on stress, health, and immunity (Chapter 3), and on the prevalence of infectious diseases transmissible to humans (Chapter 4) in deer mice (Peromyscus maniculatus), Townsend chipmunks (Tamias townsendii), and creeping voles (Microtus oregoni) inhabiting managed forest plots in northwestern Oregon. The experimental design employed allowed me to test the effect of regionally representative forest management practices on health and disease outcomes with important implications for public health. In Chapter 3, I present results which suggest that intensive forest management can have complex, but highly context-dependent effects on the health of wild deer mice. Intensive forest management can shape animals’ condition and reproductive activity, increase levels of stress hormone, and stimulate some but depress other immune responses. However, deer mice are only able to respond to the extreme stressor of this disturbance when underlying environmental conditions are favorable. When inhabiting inherently harsh habitat, mice appear unable to cope with additional disturbance imposed by intensive forest management, and only the fittest mice survive. Finally, in Chapter 4, I identify moderate prevalence of two important and potentially fatal human infections in rodents inhabiting managed forests in northwestern Oregon. In deer mouse populations, Sin Nombre virus was clustered spatially, and prevalence varied between years. But, in the focus of highest infection, the proportion of infected mice, albeit low, appeared to increase with intensity of forest management. For Leptospirosis, I found a similar pattern in creeping voles, but did not observe an association between infection prevalence and forest management in deer mice or chipmunks. I conclude that forest management may drive infectious disease patterns, but that the direction and magnitude of such effects depends on the host-pathogen system. Taken together, my findings indicate that wild animal health can suffer from declines in habitat quality associated with forest management. For a near-threatened species such as the red tree vole, decreases in the availability of food and nesting habitat have the potential to change susceptibility to infection, which could facilitate disease invasion and further threaten populations. For wild animals that serve as reservoirs for human infections, especially abundant and apparently resilient species, impaired health can drive the dynamics of pathogens and increase the risk of transmission to humans and other animals. Although many more questions remain, my work contributes to our understanding of the effects of anthropogenic environmental change for wildlife and human health. Title: Wildlife Health in Managed Forests : Immunity and Infectious Diseases in Wild Rodents of Oregon Author: Hanselmann, Rhea With continual and worldwide human population growth, our impact on the natural environment expands and intensifies every day. We consume natural resources, burn fossil fuels, and release toxic compounds into the air, water, and earth. We build roads that fragment the landscape, construct new settlements, and develop agricultural lands in previously undisturbed areas. And, we introduce non-native species, which compete with and/or prey on native ones. Our actions change the composition of ecosystems by effacing natural environments and decimating plant and animal populations. We have reached a time of unprecedented anthropogenic environmental change. And, while we recognize, and work feverishly to mitigate, countless consequences of our actions, we still lack a profound understanding of just as many of the corollaries of the environmental changes we provoke. One thing we do know is that human-induced changes in environmental conditions can affect health – from individual organisms, to plant and animal populations, all the way to the level of the ecosystem. Yet, the mechanisms underlying such adverse health outcomes are only partially understood. For instance, we know that alterations in the structure of plant and animal communities, the distribution and demographics of populations, and the abundance of individuals can influence the emergence or re-emergence of infectious diseases. Which species are present in a community, where, when, and in what numbers can all determine the dynamics of pathogens, lead to disease outbreaks, and provide opportunities for spillover into new species. However, given the many environmental-, population-, and organism-level factors involved, and the complexity by which these variables interact, detecting and predicting the ultimate consequences for the health of animal, including human, populations remains difficult. Wild animals play important roles in numerous infectious disease cycles, many of which are shared with humans. Considering this and the well-documented effects that human activity can have on wildlife populations, studying the impacts of anthropogenic environmental change on health in wildlife is highly relevant. To understand how human-induced environmental changes affect wildlife health and to make predictions about potential regional or even global consequences for the dynamics of infectious diseases, however, we first need to understand patterns at a local scale. Here, I describe variation in immune function in captive and wild rodent species native to managed forests in northwestern Oregon, and examine how intensive forest management practices affect these and other physiological processes, and the prevalence of infectious diseases, in a large-scale field experiment. In Chapter 2 of this dissertation, I present baseline data on simple immune parameters in an iconic inhabitant of old-growth forests in the Pacific Northwest, the red tree vole (Arborimus longicaudus). I show that both body condition and age are important for immune defenses in this species. Translating these findings to wild populations leads me to predict that degradation of habitat may affect red tree voles not only at the population scale, as is currently the case, but that less obvious consequences for the health of individuals surviving in disturbed or suboptimal habitat are also possible. It is important, therefore, that efforts to conserve this species consider adverse effects of present forest management practices on red tree vole health, as potentially increased disease susceptibility could have detrimental outcomes for this species. In Chapters 3 and 4, I took advantage of a rare and large-scale experiment to test my predictions regarding the negative consequences of habitat degradation for individual animals in more ubiquitous rodent species known for their resilience to environmental disturbance. I investigated the effects of intensive forest management on stress, health, and immunity (Chapter 3), and on the prevalence of infectious diseases transmissible to humans (Chapter 4) in deer mice (Peromyscus maniculatus), Townsend chipmunks (Tamias townsendii), and creeping voles (Microtus oregoni) inhabiting managed forest plots in northwestern Oregon. The experimental design employed allowed me to test the effect of regionally representative forest management practices on health and disease outcomes with important implications for public health. In Chapter 3, I present results which suggest that intensive forest management can have complex, but highly context-dependent effects on the health of wild deer mice. Intensive forest management can shape animals’ condition and reproductive activity, increase levels of stress hormone, and stimulate some but depress other immune responses. However, deer mice are only able to respond to the extreme stressor of this disturbance when underlying environmental conditions are favorable. When inhabiting inherently harsh habitat, mice appear unable to cope with additional disturbance imposed by intensive forest management, and only the fittest mice survive. Finally, in Chapter 4, I identify moderate prevalence of two important and potentially fatal human infections in rodents inhabiting managed forests in northwestern Oregon. In deer mouse populations, Sin Nombre virus was clustered spatially, and prevalence varied between years. But, in the focus of highest infection, the proportion of infected mice, albeit low, appeared to increase with intensity of forest management. For Leptospirosis, I found a similar pattern in creeping voles, but did not observe an association between infection prevalence and forest management in deer mice or chipmunks. I conclude that forest management may drive infectious disease patterns, but that the direction and magnitude of such effects depends on the host-pathogen system. Taken together, my findings indicate that wild animal health can suffer from declines in habitat quality associated with forest management. For a near-threatened species such as the red tree vole, decreases in the availability of food and nesting habitat have the potential to change susceptibility to infection, which could facilitate disease invasion and further threaten populations. For wild animals that serve as reservoirs for human infections, especially abundant and apparently resilient species, impaired health can drive the dynamics of pathogens and increase the risk of transmission to humans and other animals. Although many more questions remain, my work contributes to our understanding of the effects of anthropogenic environmental change for wildlife and human health. Close

• 53. [Article] Biological Soil Crusts of the Great Basin : An Examination of their Distribution, Recovery from Disturbance and Restoration

  We are at risk of losing the sagebrush steppe in the floristic Great Basin to the invasion of Bromus tectorum L., cheatgrass. The floristic Great Basin includes the Central Basin and Range, the Northern ...

  Citation × Citation Citation Abstract Copy Title: Biological Soil Crusts of the Great Basin : An Examination of their Distribution, Recovery from Disturbance and Restoration Author: Condon, Lea A. We are at risk of losing the sagebrush steppe in the floristic Great Basin to the invasion of Bromus tectorum L., cheatgrass. The floristic Great Basin includes the Central Basin and Range, the Northern Basin and Range, and the Snake River Plain. The Great Basin receives most of its precipitation as winter snow and experiences hot and dry summers. Early accounts of invasion by cheatgrass associated it with farming and grazing practices. The non-farmed areas in the region are still actively grazed and referred to as rangelands. On invaded sites, cheatgrass changes the flammability of fuels on invaded landscapes, across the Great Basin, from coarser fuels that are widely spaced to fine fuels that are continuous, filling interspaces between perennial plants. The fuel load created by cheatgrass regenerates annually. This has resulted in a change in the fire regime of the Great Basin from infrequent, small fires to more frequent large fires. In arid lands globally, soil interspaces between perennial plants are typically filled by biological soil crusts (biocrusts). This is also true for ecoregions in and surrounding the Great Basin. Biocrusts are known to influence many ecosystem processes that cheatgrass influences, specifically nutrient cycling and availability of soil moisture. However, little work has been done on biocrusts of the Great Basin and to my knowledge, no one had restored biocrusts within the Great Basin. I attempt to fill some of this knowledge "interspace" by relating biocrust presence to disturbances and cheatgrass invasion and to demonstrate the potential for biocrust restoration within this region. Previous work in eastern Oregon demonstrated relationships between declines in biocrusts and increases in cheatgrass with increasing grazing intensity, soil temperature, and decreasing soil moisture. Grazing intensity influences the cover of biocrusts as well as the abundance and composition of native bunchgrasses. Native bunchgrasses influence the interspace gap size between perennial herbaceous vegetation which is directly associated with the cover of cheatgrass. In a region where grazing records may be incomplete and may exist in various forms of data, having a simple indicator of grazing impacts would be useful. It is also crucial that we have an understanding of what leads to loss of site resistance to cheatgrass. This previous work suggested that cover of biocrusts, in addition to bunchgrass composition, were associated with increased site resistance to cheatgrass. In Chapter 2, I used current grazing records from a range of suspected grazing intensities, to examine the ability of both biocrusts and perennial vegetation to maintain site resistance to cheatgrass after fire. I examined the ability of mosses and lichens to maintain site resistance separately given that these are two very different kinds of organisms. Mosses are non-vascular plants and early colonizers of sites in primary succession. Lichens have a symbiotic relationship between a fungus and a photosynthesizing partner, a cyanobacteria, an algae or both. Using structural equation models, I corroborated that perennial vegetation and lichens are associated with increased site resistance to cheatgrass and that mosses are associated with and may facilitate both lichens and perennial herbaceous vegetation. Also in Chapter 2, I identified that burned sites were associated with increased grazing pressure by livestock as shown by increases in cow dung density and increases in gap size between perennial herbaceous vegetation. The Great Basin is managed for cover of perennial vegetation but it could also be managed for morphogroups of biocrusts. Considering morphogroups of biocrusts, which were shown in the Chapter 2 to be important for site resilience and resistance, I wanted to determine if there were site characteristics associated with biocrust distribution and recovery from disturbance, across the Great Basin. Outside of the Great Basin on the Columbia Plateau, others had found that mosses were still present on disturbed sites whereas lichens were often lost. In addition, biocrust species were more associated with soil properties than with grazing by livestock. Given that grazing by livestock and fire are common disturbances across the region, I wanted to know if the same relationships between biocrusts, soil properties and disturbance were true in the Great Basin. I found that cover of the lichen component of biocrusts was higher on sites that were both ungrazed and unburned. Factors related to disturbance characteristics were correlated with the recovery of biocrusts, even after accounting for time since fire. Factors related to disturbance, a composite of grazing and fire, were more important for structuring the cover and composition of morphogroups as opposed to environmental conditions. Lichens were the most sensitive morphogroup, compared to tall mosses, followed by short mosses which were favored by some disturbance but reduced in cover immediately after fire. Perennial grasses were also favored by some disturbance and perennial forbs did not show an obvious relationship with a disturbance gradient. Chapter 3 highlights that grazing by livestock and fire are common disturbances across the region so much so that the effects of one on the abundances of morphogroups could not be separated from the other. Given the observed contributions of biocrusts to site resilience and resistance, I wanted to know if we could restore biocrusts in the field. Others have grown mosses in a lab setting but this was the first study to restore mosses in the Great Basin. I tested the influence of factors that are commonly used in the field of restoration for facilitating plant establishment. I tested the influence of season of inoculation (fall versus spring), the addition of organic matter (in the form of jute net), irrigation (in the spring season) and the climatic setting of moss the collection sites (for moss propagation), in comparison to the experiment site (warm, dry versus cool, moist) on moss growth. I used two moss species: a ruderal (Bryum argenteum) and a later successional species (Syntrichia ruralis). Moss cover increased when the climatic setting of the collection site matched the experiment site. Mosses were facilitated by the addition of the organic jute netting, putting on most of their growth in winter. Although there is still a great deal of work to be done developing moss material for restoration and working out inoculation rates of moss fragments, similar to seeding rates, land managers have another tool to consider when rehabilitating sites after disturbance. Managing the Great Basin for biocrusts in the presence of grazing and fire will not only increase site resistance to cheatgrass but it will add to the conservation of ecosystem functions related to nutrient cycling, hydrologic cycling and soil erosion. Site resistance will be improved with increased periods of rest from grazing following fire. The lichen component of biocrusts is a more sensitive indicator of disturbance when compared with mosses or perennial vegetation but we are currently actively managing for perennial vegetation and not biocrusts. The moss component of biocrusts can be successfully restored in the Great Basin, without irrigation. This dissertation shows that land managers should consider a suite of organisms, in addition to perennial plants to achieve management goals and maintain site resistance to cheatgrass. Title: Biological Soil Crusts of the Great Basin : An Examination of their Distribution, Recovery from Disturbance and Restoration Author: Condon, Lea A. We are at risk of losing the sagebrush steppe in the floristic Great Basin to the invasion of Bromus tectorum L., cheatgrass. The floristic Great Basin includes the Central Basin and Range, the Northern Basin and Range, and the Snake River Plain. The Great Basin receives most of its precipitation as winter snow and experiences hot and dry summers. Early accounts of invasion by cheatgrass associated it with farming and grazing practices. The non-farmed areas in the region are still actively grazed and referred to as rangelands. On invaded sites, cheatgrass changes the flammability of fuels on invaded landscapes, across the Great Basin, from coarser fuels that are widely spaced to fine fuels that are continuous, filling interspaces between perennial plants. The fuel load created by cheatgrass regenerates annually. This has resulted in a change in the fire regime of the Great Basin from infrequent, small fires to more frequent large fires. In arid lands globally, soil interspaces between perennial plants are typically filled by biological soil crusts (biocrusts). This is also true for ecoregions in and surrounding the Great Basin. Biocrusts are known to influence many ecosystem processes that cheatgrass influences, specifically nutrient cycling and availability of soil moisture. However, little work has been done on biocrusts of the Great Basin and to my knowledge, no one had restored biocrusts within the Great Basin. I attempt to fill some of this knowledge "interspace" by relating biocrust presence to disturbances and cheatgrass invasion and to demonstrate the potential for biocrust restoration within this region. Previous work in eastern Oregon demonstrated relationships between declines in biocrusts and increases in cheatgrass with increasing grazing intensity, soil temperature, and decreasing soil moisture. Grazing intensity influences the cover of biocrusts as well as the abundance and composition of native bunchgrasses. Native bunchgrasses influence the interspace gap size between perennial herbaceous vegetation which is directly associated with the cover of cheatgrass. In a region where grazing records may be incomplete and may exist in various forms of data, having a simple indicator of grazing impacts would be useful. It is also crucial that we have an understanding of what leads to loss of site resistance to cheatgrass. This previous work suggested that cover of biocrusts, in addition to bunchgrass composition, were associated with increased site resistance to cheatgrass. In Chapter 2, I used current grazing records from a range of suspected grazing intensities, to examine the ability of both biocrusts and perennial vegetation to maintain site resistance to cheatgrass after fire. I examined the ability of mosses and lichens to maintain site resistance separately given that these are two very different kinds of organisms. Mosses are non-vascular plants and early colonizers of sites in primary succession. Lichens have a symbiotic relationship between a fungus and a photosynthesizing partner, a cyanobacteria, an algae or both. Using structural equation models, I corroborated that perennial vegetation and lichens are associated with increased site resistance to cheatgrass and that mosses are associated with and may facilitate both lichens and perennial herbaceous vegetation. Also in Chapter 2, I identified that burned sites were associated with increased grazing pressure by livestock as shown by increases in cow dung density and increases in gap size between perennial herbaceous vegetation. The Great Basin is managed for cover of perennial vegetation but it could also be managed for morphogroups of biocrusts. Considering morphogroups of biocrusts, which were shown in the Chapter 2 to be important for site resilience and resistance, I wanted to determine if there were site characteristics associated with biocrust distribution and recovery from disturbance, across the Great Basin. Outside of the Great Basin on the Columbia Plateau, others had found that mosses were still present on disturbed sites whereas lichens were often lost. In addition, biocrust species were more associated with soil properties than with grazing by livestock. Given that grazing by livestock and fire are common disturbances across the region, I wanted to know if the same relationships between biocrusts, soil properties and disturbance were true in the Great Basin. I found that cover of the lichen component of biocrusts was higher on sites that were both ungrazed and unburned. Factors related to disturbance characteristics were correlated with the recovery of biocrusts, even after accounting for time since fire. Factors related to disturbance, a composite of grazing and fire, were more important for structuring the cover and composition of morphogroups as opposed to environmental conditions. Lichens were the most sensitive morphogroup, compared to tall mosses, followed by short mosses which were favored by some disturbance but reduced in cover immediately after fire. Perennial grasses were also favored by some disturbance and perennial forbs did not show an obvious relationship with a disturbance gradient. Chapter 3 highlights that grazing by livestock and fire are common disturbances across the region so much so that the effects of one on the abundances of morphogroups could not be separated from the other. Given the observed contributions of biocrusts to site resilience and resistance, I wanted to know if we could restore biocrusts in the field. Others have grown mosses in a lab setting but this was the first study to restore mosses in the Great Basin. I tested the influence of factors that are commonly used in the field of restoration for facilitating plant establishment. I tested the influence of season of inoculation (fall versus spring), the addition of organic matter (in the form of jute net), irrigation (in the spring season) and the climatic setting of moss the collection sites (for moss propagation), in comparison to the experiment site (warm, dry versus cool, moist) on moss growth. I used two moss species: a ruderal (Bryum argenteum) and a later successional species (Syntrichia ruralis). Moss cover increased when the climatic setting of the collection site matched the experiment site. Mosses were facilitated by the addition of the organic jute netting, putting on most of their growth in winter. Although there is still a great deal of work to be done developing moss material for restoration and working out inoculation rates of moss fragments, similar to seeding rates, land managers have another tool to consider when rehabilitating sites after disturbance. Managing the Great Basin for biocrusts in the presence of grazing and fire will not only increase site resistance to cheatgrass but it will add to the conservation of ecosystem functions related to nutrient cycling, hydrologic cycling and soil erosion. Site resistance will be improved with increased periods of rest from grazing following fire. The lichen component of biocrusts is a more sensitive indicator of disturbance when compared with mosses or perennial vegetation but we are currently actively managing for perennial vegetation and not biocrusts. The moss component of biocrusts can be successfully restored in the Great Basin, without irrigation. This dissertation shows that land managers should consider a suite of organisms, in addition to perennial plants to achieve management goals and maintain site resistance to cheatgrass. Close

• 54. [Article] Historical change in channel form and riparian vegetation of the McKenzie River, Oregon

  This study examined channel structure and position and riparian vegetation and land use on the upper 70 km of the McKenzie River, Oregon in the 1940s, compared the 1940s conditions to present conditions, ...

  Citation × Citation Citation Abstract Copy Title: Historical change in channel form and riparian vegetation of the McKenzie River, Oregon Author: Minear, Paula J. This study examined channel structure and position and riparian vegetation and land use on the upper 70 km of the McKenzie River, Oregon in the 1940s, compared the 1940s conditions to present conditions, and explored the processes driving change in this system and the implications for aquatic habitat. The hydrologic record was analyzed, and field surveys were conducted and compared to historical habitat surveys. Riparian characteristics and channel features were digitized from aerial photographs from 1945/49 and 1986 and imported into Arcinfo GIS for analysis. Types of data digitized from the aerial photos included locations and length or area of wetted channel, active channel, tributaries, side channels, large woody debris, exposed gravel bars, roads, and dominant vegetation or land use within 200 m of the active channel. Construction of dams on the mainstem Mckenzie River and two major tributaries, Blue River and South Fork, in the 1960s has altered the flow regime and sediment supply to the mainstem Mckenzie, decreasing the frequency, mean and variation of peak flows, reducing the competence of flows to move existing bedload, and cutting off sediment from over half of the drainage area. Mean peak flows decreased 44% and competence of peak flows with a 2-yr recurrence interval declined approximately 29% after dams were constructed upriver. Adjustments to reduced sediment supply and flow alteration by dams in this system included 57% decrease in exposed gravel bars, 40% decrease in side channel length, and possible substrate coarsening (as compared to historical estimates). Channel straightening occurred in each of three instances of channel change during the study period, and sinuosity decreased one half of the amount needed to produce a straight channel in the most susceptible, unconstrained reach. Human actions prior to high flow events played a role in the direction of channel change in each case. Over the entire study area, 7% of the main channel changed position by 30 m or more and little or no change in channel position was noted in reaches constrained by valley floors. Additional channel constraint has been produced by road construction near the channel and riprapping for roads, bridges, and residences. Less large woody debris was observed in the 1986 channel than in the 1949 channel, indicating a reduction in pool-forming agents and channel roughness elements. Frequency of large pools ([greater than or equal to] 2 m depth and >40 m² area) decreased 19% over the study area. The greatest loss in pools (73%) was noted in the unconstrained reach that exhibited two areas of channel change and an increase in exposed gravel bars. Increased human use of the riparian area for roads and residential purposes has led to an increased fragmentation of the riparian landscape. Density of residential or developed patches within the riparian area has increased 215% as more and smaller areas are converted from natural vegetation to human use. Riparian area devoted to roads and residential uses has nearly doubled since the 1940s. Mean vegetation or land-use patch size has decreased from 2.2 ha to 1.6 ha as larger patches have been sub-divided, and patch and edge densities have increased. Agriculture and clearcuts for timber removal have decreased within the riparian area while continuing upslope. Riparian area in mature conifers has decreased 44% from levels in the 1940s while hardwoods have increased 45% in the riparian area. Future wood loading to the channel is reduced by a decline in mature riparian vegetation, especially mature conifers. Channel and riparian changes noted in this study have implications for fish populations. Channel straightening, reduction in side channels, and loss of pool-forming agents reduce habitat heterogeneity and off-channel refugia. Ecosystem management of watersheds requires evaluation of conditions across scales of time and space. The use of GIS in this study made it possible to detect changes in channel form and riparian conditions during four decades, along a 70-m channel and 90-m riparian area and to analyze the large data sets relevant to understanding functions and change in channels and riparian areas. Title: Historical change in channel form and riparian vegetation of the McKenzie River, Oregon Author: Minear, Paula J. This study examined channel structure and position and riparian vegetation and land use on the upper 70 km of the McKenzie River, Oregon in the 1940s, compared the 1940s conditions to present conditions, and explored the processes driving change in this system and the implications for aquatic habitat. The hydrologic record was analyzed, and field surveys were conducted and compared to historical habitat surveys. Riparian characteristics and channel features were digitized from aerial photographs from 1945/49 and 1986 and imported into Arcinfo GIS for analysis. Types of data digitized from the aerial photos included locations and length or area of wetted channel, active channel, tributaries, side channels, large woody debris, exposed gravel bars, roads, and dominant vegetation or land use within 200 m of the active channel. Construction of dams on the mainstem Mckenzie River and two major tributaries, Blue River and South Fork, in the 1960s has altered the flow regime and sediment supply to the mainstem Mckenzie, decreasing the frequency, mean and variation of peak flows, reducing the competence of flows to move existing bedload, and cutting off sediment from over half of the drainage area. Mean peak flows decreased 44% and competence of peak flows with a 2-yr recurrence interval declined approximately 29% after dams were constructed upriver. Adjustments to reduced sediment supply and flow alteration by dams in this system included 57% decrease in exposed gravel bars, 40% decrease in side channel length, and possible substrate coarsening (as compared to historical estimates). Channel straightening occurred in each of three instances of channel change during the study period, and sinuosity decreased one half of the amount needed to produce a straight channel in the most susceptible, unconstrained reach. Human actions prior to high flow events played a role in the direction of channel change in each case. Over the entire study area, 7% of the main channel changed position by 30 m or more and little or no change in channel position was noted in reaches constrained by valley floors. Additional channel constraint has been produced by road construction near the channel and riprapping for roads, bridges, and residences. Less large woody debris was observed in the 1986 channel than in the 1949 channel, indicating a reduction in pool-forming agents and channel roughness elements. Frequency of large pools ([greater than or equal to] 2 m depth and >40 m² area) decreased 19% over the study area. The greatest loss in pools (73%) was noted in the unconstrained reach that exhibited two areas of channel change and an increase in exposed gravel bars. Increased human use of the riparian area for roads and residential purposes has led to an increased fragmentation of the riparian landscape. Density of residential or developed patches within the riparian area has increased 215% as more and smaller areas are converted from natural vegetation to human use. Riparian area devoted to roads and residential uses has nearly doubled since the 1940s. Mean vegetation or land-use patch size has decreased from 2.2 ha to 1.6 ha as larger patches have been sub-divided, and patch and edge densities have increased. Agriculture and clearcuts for timber removal have decreased within the riparian area while continuing upslope. Riparian area in mature conifers has decreased 44% from levels in the 1940s while hardwoods have increased 45% in the riparian area. Future wood loading to the channel is reduced by a decline in mature riparian vegetation, especially mature conifers. Channel and riparian changes noted in this study have implications for fish populations. Channel straightening, reduction in side channels, and loss of pool-forming agents reduce habitat heterogeneity and off-channel refugia. Ecosystem management of watersheds requires evaluation of conditions across scales of time and space. The use of GIS in this study made it possible to detect changes in channel form and riparian conditions during four decades, along a 70-m channel and 90-m riparian area and to analyze the large data sets relevant to understanding functions and change in channels and riparian areas. Close

• 55. [Article] Comparing vegetation and soils of remnant and restored prairie wetlands in the northern Willamette Valley

  Native prairies of the Willamette Valley are considered among the rarest of Oregon's ecosystems (Clark and Wilson, 2001). As a result of agriculture conversion, urban development and cessation of native ...

  Citation × Citation Citation Abstract Copy Title: Comparing vegetation and soils of remnant and restored prairie wetlands in the northern Willamette Valley Author: Taylor, Sara M. Native prairies of the Willamette Valley are considered among the rarest of Oregon's ecosystems (Clark and Wilson, 2001). As a result of agriculture conversion, urban development and cessation of native burning, Willamette Valley prairies have become highly fragmented and invaded by non-native species, leaving little room for native plant diversity. Even though wetland prairie conservation and restoration has been a priority for many government agencies there is a need for research on what restoration techniques and management are necessary for increasing native species richness and abundance in remnant and restored wet prairie sites. In this research project, two studies were conducted. In the first study, data were collected on species presence and abundance from three 100m² randomized plots within three remnant wet prairies (Green Mountain, Gotter Prairie South, Knez) and three restored wet prairies (Hutchinson, Gotter Prairie North, Lovejoy) to answer the following research question, 'Are there differences between remnant and restored prairie plant communities with respect to the diversity and abundance of native species?' Analysis of variance and multivariate ordination techniques were used to assess the ecological differences between uncultivated, minimally-managed remnant wet prairies and newly-restored, highly managed wet prairies. Data on soils collected from agricultural sites (Westbrook, Zurcher, Gotter Prairie Ag), as well as the remnant and restored wet prairies mentioned above, were also used to compare soil quality and processes with the remnant and restored wetlands. Restored wet prairie had 23% higher native species cover than remnant prairie (p-value=0.089, N=6). Remnant and restored sites did not differ in native species richness (p-value=0.949, N=6). The relatively high per cent cover of native species at restored sites, (significant at the 10% level), suggests that land managers have successfully restored agricultural properties with an abundance of native species. The lack of significant difference in native species richness between remnant and restored sites also suggests that land managers have also been able to restore native plant diversity into former agricultural properties equivalent to some of the best intact remnant prairies within the Northern Willamette Valley in a short period of time (8 years or less). However, a non-metric scaling (NMS) ordination of the species matrix separated the remnant sites from the restored sites, suggesting that community composition distinguishes restored sites from remnants. The NMS results, which include environmental data in the analysis, also suggest that there is a positive correlation of percent soil moisture and percent soil organic matter associated with the remnant prairies and a positive correlation of management practices such as yearly chemical use, mowing, and clean crops, associated with the restored prairies. The location of Gotter Prairie North restoration within the ordination, between the remnant and restored sites, suggests an intermediate plant composition and soil quality. This could be attributed to intensive weed suppression and soil organic matter build up over time (8 years) in comparison to younger restored sites (3 and 4 years). Indicator species analysis identified many species with high indicator values (IVs) in the remnant prairies; Holcus lanatus, Deschampsia cespitosa, Carex densa and Phalaris arundinacea being the highest. The use of fire as a management tool produced only one species with a high IV (Camassia quamash). In the second study, three seeding treatments (Grass first, Grass and Forb together, Forb first) were compared within a 4 hectare experimental wet prairie unit to answer the research question „Which of the three seeding treatments used leads to the highest native species abundance and species richness?‟ Results from an analysis of variance indicated significant differences between treatments in native species richness for 2009 and 2010 (p-values=0.002 & 0.004 respectively) at the 5% level and native species abundance in 2010 only (p-value=0.099) at the 10% level. The Grass and Forb and Forb first treatments were highest in native species richness for 2009 and 2010, whereas the Grass and Forb and Grass first treatments were highest in native species abundance in 2010. A NMS ordination suggests that Juncus tenuis is one of the dominant species, in all seeding treatments, after one year of growth. Title: Comparing vegetation and soils of remnant and restored prairie wetlands in the northern Willamette Valley Author: Taylor, Sara M. Native prairies of the Willamette Valley are considered among the rarest of Oregon's ecosystems (Clark and Wilson, 2001). As a result of agriculture conversion, urban development and cessation of native burning, Willamette Valley prairies have become highly fragmented and invaded by non-native species, leaving little room for native plant diversity. Even though wetland prairie conservation and restoration has been a priority for many government agencies there is a need for research on what restoration techniques and management are necessary for increasing native species richness and abundance in remnant and restored wet prairie sites. In this research project, two studies were conducted. In the first study, data were collected on species presence and abundance from three 100m² randomized plots within three remnant wet prairies (Green Mountain, Gotter Prairie South, Knez) and three restored wet prairies (Hutchinson, Gotter Prairie North, Lovejoy) to answer the following research question, 'Are there differences between remnant and restored prairie plant communities with respect to the diversity and abundance of native species?' Analysis of variance and multivariate ordination techniques were used to assess the ecological differences between uncultivated, minimally-managed remnant wet prairies and newly-restored, highly managed wet prairies. Data on soils collected from agricultural sites (Westbrook, Zurcher, Gotter Prairie Ag), as well as the remnant and restored wet prairies mentioned above, were also used to compare soil quality and processes with the remnant and restored wetlands. Restored wet prairie had 23% higher native species cover than remnant prairie (p-value=0.089, N=6). Remnant and restored sites did not differ in native species richness (p-value=0.949, N=6). The relatively high per cent cover of native species at restored sites, (significant at the 10% level), suggests that land managers have successfully restored agricultural properties with an abundance of native species. The lack of significant difference in native species richness between remnant and restored sites also suggests that land managers have also been able to restore native plant diversity into former agricultural properties equivalent to some of the best intact remnant prairies within the Northern Willamette Valley in a short period of time (8 years or less). However, a non-metric scaling (NMS) ordination of the species matrix separated the remnant sites from the restored sites, suggesting that community composition distinguishes restored sites from remnants. The NMS results, which include environmental data in the analysis, also suggest that there is a positive correlation of percent soil moisture and percent soil organic matter associated with the remnant prairies and a positive correlation of management practices such as yearly chemical use, mowing, and clean crops, associated with the restored prairies. The location of Gotter Prairie North restoration within the ordination, between the remnant and restored sites, suggests an intermediate plant composition and soil quality. This could be attributed to intensive weed suppression and soil organic matter build up over time (8 years) in comparison to younger restored sites (3 and 4 years). Indicator species analysis identified many species with high indicator values (IVs) in the remnant prairies; Holcus lanatus, Deschampsia cespitosa, Carex densa and Phalaris arundinacea being the highest. The use of fire as a management tool produced only one species with a high IV (Camassia quamash). In the second study, three seeding treatments (Grass first, Grass and Forb together, Forb first) were compared within a 4 hectare experimental wet prairie unit to answer the research question „Which of the three seeding treatments used leads to the highest native species abundance and species richness?‟ Results from an analysis of variance indicated significant differences between treatments in native species richness for 2009 and 2010 (p-values=0.002 & 0.004 respectively) at the 5% level and native species abundance in 2010 only (p-value=0.099) at the 10% level. The Grass and Forb and Forb first treatments were highest in native species richness for 2009 and 2010, whereas the Grass and Forb and Grass first treatments were highest in native species abundance in 2010. A NMS ordination suggests that Juncus tenuis is one of the dominant species, in all seeding treatments, after one year of growth. Close

• 56. [Article] Using a species-centered approach to examine patterns and drivers of avian species richness in the Rogue Basin, Oregon

  The combined effects of habitat loss, degradation, and fragmentation pose a serious threat to Earth's biodiversity, imperiling even relatively common species. 'Habitat' is necessarily a species-specific ...

  Citation × Citation Citation Abstract Copy Title: Using a species-centered approach to examine patterns and drivers of avian species richness in the Rogue Basin, Oregon Author: Halstead, Katherine E. The combined effects of habitat loss, degradation, and fragmentation pose a serious threat to Earth's biodiversity, imperiling even relatively common species. 'Habitat' is necessarily a species-specific concept, and investigations of bird diversity relationships and subsequent efforts to prioritize conservation areas, are challenged by the difficulty of estimating complex habitat gradients for multiple species across broad spatial scales. Technologies such as fine-resolution remote sensing combined with enhanced species distribution modeling techniques hold promise for more accurate assessments of multi-species habitat distributions. In this research, I focused on forest bird species which utilize and/or are highly associated with threatened Oregon white oak and California black oak (Quercus garrayana and Q. kelloggii) vegetation types in the Rogue Basin of southwest Oregon. I created individual species distribution models (SDMs) for 48 bird species as a function of fine-resolution (30 x 30 m) remotely sensed land cover and other environmental variables using boosted regression tree (BRT) models. I then 'stacked' SDMs for spatially explicit regional estimates of multi-species avian richness. In my first chapter, I examined the potential for site-level species richness to be influenced by local vegetation and environmental conditions (e.g. the "local vegetation heterogeneity hypothesis") or by landscape-level dispersal potential (e.g. the "regional species pool hypothesis"). I summarized 'stacked' SDMs for indices of 1) habitat amount at a local scale relevant bird territory use and 2) habitat amount at a broad scale relevant to forest bird dispersal, and ask whether local- or landscape-scale habitat amount is relatively more important to site-level bird species richness. I hypothesized that greater importance of either habitat amount metric would indicate greater influence of local or landscape drivers to local richness. I found evidence that for a large pool of bird species with diverse habitat associations, landscape-scale habitat amount may be relatively more important to local (i.e., territory level) richness of forest birds than is local habitat amount. In contrast, for more specialized (i.e., oak-associated) guilds, local-scale habitat may be considerably more important than amount of habitat within the surrounding landscape. My results suggest the importance of local- and landscape-scale processes in structuring bird communities, supporting both 'local vegetation heterogeneity' and 'regional species pool' hypotheses. In my second chapter, I examined the relationships between landownership, oak vegetation distribution, and bird diversity, with the objective of determining which of five primary landownership types contribute most strongly to bird species habitat in the Rogue Basin. I asked whether individual bird species distributions and estimated richness are 'additive' or 'redundant' among land ownership types, hypothesizing that differences among owners will be apparent and related to the amount of oak-dominant vegetation held by each owner regionally. I found that estimated local mean species richness of oak-associated birds in private non-industrial (PNI) ownerships is approximately double that of other Rogue Basin public and private ownerships examined. This result may be driven by disproportionate PNI ownership of limited oak cover types, and/or by hypothesized variation in management goals and activities among owners which influence local vegetation structure. Relatively greater importance of territory-scale habitat to local oak-associated species richness suggests management for these species should maximize site-level habitat amount and quality. The importance of private non-industrial owners to oak-associated avian richness validates current focus on engaging private landowners in bird-focused oak conservation and restoration. Overall, my research links efforts to conserve avian habitat with efforts to understand multi-scale drivers of bird diversity, using a novel methodology that embraces the complexity of species' habitat gradients. Title: Using a species-centered approach to examine patterns and drivers of avian species richness in the Rogue Basin, Oregon Author: Halstead, Katherine E. The combined effects of habitat loss, degradation, and fragmentation pose a serious threat to Earth's biodiversity, imperiling even relatively common species. 'Habitat' is necessarily a species-specific concept, and investigations of bird diversity relationships and subsequent efforts to prioritize conservation areas, are challenged by the difficulty of estimating complex habitat gradients for multiple species across broad spatial scales. Technologies such as fine-resolution remote sensing combined with enhanced species distribution modeling techniques hold promise for more accurate assessments of multi-species habitat distributions. In this research, I focused on forest bird species which utilize and/or are highly associated with threatened Oregon white oak and California black oak (Quercus garrayana and Q. kelloggii) vegetation types in the Rogue Basin of southwest Oregon. I created individual species distribution models (SDMs) for 48 bird species as a function of fine-resolution (30 x 30 m) remotely sensed land cover and other environmental variables using boosted regression tree (BRT) models. I then 'stacked' SDMs for spatially explicit regional estimates of multi-species avian richness. In my first chapter, I examined the potential for site-level species richness to be influenced by local vegetation and environmental conditions (e.g. the "local vegetation heterogeneity hypothesis") or by landscape-level dispersal potential (e.g. the "regional species pool hypothesis"). I summarized 'stacked' SDMs for indices of 1) habitat amount at a local scale relevant bird territory use and 2) habitat amount at a broad scale relevant to forest bird dispersal, and ask whether local- or landscape-scale habitat amount is relatively more important to site-level bird species richness. I hypothesized that greater importance of either habitat amount metric would indicate greater influence of local or landscape drivers to local richness. I found evidence that for a large pool of bird species with diverse habitat associations, landscape-scale habitat amount may be relatively more important to local (i.e., territory level) richness of forest birds than is local habitat amount. In contrast, for more specialized (i.e., oak-associated) guilds, local-scale habitat may be considerably more important than amount of habitat within the surrounding landscape. My results suggest the importance of local- and landscape-scale processes in structuring bird communities, supporting both 'local vegetation heterogeneity' and 'regional species pool' hypotheses. In my second chapter, I examined the relationships between landownership, oak vegetation distribution, and bird diversity, with the objective of determining which of five primary landownership types contribute most strongly to bird species habitat in the Rogue Basin. I asked whether individual bird species distributions and estimated richness are 'additive' or 'redundant' among land ownership types, hypothesizing that differences among owners will be apparent and related to the amount of oak-dominant vegetation held by each owner regionally. I found that estimated local mean species richness of oak-associated birds in private non-industrial (PNI) ownerships is approximately double that of other Rogue Basin public and private ownerships examined. This result may be driven by disproportionate PNI ownership of limited oak cover types, and/or by hypothesized variation in management goals and activities among owners which influence local vegetation structure. Relatively greater importance of territory-scale habitat to local oak-associated species richness suggests management for these species should maximize site-level habitat amount and quality. The importance of private non-industrial owners to oak-associated avian richness validates current focus on engaging private landowners in bird-focused oak conservation and restoration. Overall, my research links efforts to conserve avian habitat with efforts to understand multi-scale drivers of bird diversity, using a novel methodology that embraces the complexity of species' habitat gradients. Close

• 57. [Article] The use of remote sensing for characterizing forests in wildlife habitat modeling

  Spatially explicit maps of habitat relationships have proven to be valuable tools for conservation and management applications including evaluating how and which species may be impacted by large scale ...

  Citation × Citation Citation Abstract Copy Title: The use of remote sensing for characterizing forests in wildlife habitat modeling Author: Vogeler, Jody C. Spatially explicit maps of habitat relationships have proven to be valuable tools for conservation and management applications including evaluating how and which species may be impacted by large scale climate change, ongoing fragmentation of habitat, and local land-use practices. Studies have turned to remote sensing datasets as a way to characterize vegetation for the examination of habitat selection and for mapping realized relationships across the landscape. Although the use of remote sensing in wildlife studies has increased in recent years, the use of these datasets is still limited and some data sources and methods are yet to be explored. The overall goal of this dissertation was to look at the state of the wildlife ecology discipline in the use of geospatial data for habitat mapping, and to advance this area through the fusion of remote sensing tools for the mapping of previously difficult to characterize forest metrics for inclusion in avian cavity-nester habitat models. Chapter 2 reviewed over 60 years of selected wildlife literature to examine the wildlife ecology disciple through historic trends and recent advances in the use of remote sensing for habitat characterization focusing on aspects of scale and the use of available technology. We discuss commonly used remote sensing data sources, point out recent advances in the use of geospatial data for characterizing forest wildlife habitat (the use of lidar data and the creation of spatially explicit habitat prediction maps), and provide future suggestions for increased utilization of available datasets (secondary lidar metrics and time series Landsat data). In chapters 3 and 4 we explored the use of remote sensing for characterizing forest components previously difficult to map across landscapes at scales relevant to local wildlife habitat selection. Chapter 3 found promise in the fusion of lidar structure and Landsat time series disturbance products in the modeling and mapping of post-fire snag and shrub distributions at fine scales and at size/cover thresholds relevant for habitat mapping applications for many wildlife species. The study was conducted within the 2003 B&B Fire Complex in central Oregon. Using 164 field calibration plots and remote sensing predictors, we modeled the presence/absence of snag classes (dbh ≥40cm, ≥50cm, and ≥75cm) and woody shrub cover resulting in 10m output predictive grid maps. Remote sensing predictors included various lidar structure and topography variables and Landsat time series products representing the pre-fire forest, disturbance magnitude, and current forest conditions. We were able to model and map all habitat metrics with acceptable predictive performance and low-moderate errors. The utility of these snag and shrub metrics for representing important nesting habitat features for a cavity-nesting species of conservation concern, the Lewis's Woodpecker (Melanerpes lewis), was demonstrated in Chapter 4. We were able to model nesting habitat with good accuracies according to multiple performance measures and then map realized relationships for this species of conservation concern in an identified source habitat type, providing a potential resource for local scale conservation and management efforts and adding to the regional knowledge of habitat selection for the Lewis's Woodpecker. To our knowledge, these chapters represent first attempts to fuse lidar and time series Landsat disturbance metrics in a post-fire landscape and for the mapping of snag and shrub distributions at scales relevant to avian cavity nesting habitat. Title: The use of remote sensing for characterizing forests in wildlife habitat modeling Author: Vogeler, Jody C. Spatially explicit maps of habitat relationships have proven to be valuable tools for conservation and management applications including evaluating how and which species may be impacted by large scale climate change, ongoing fragmentation of habitat, and local land-use practices. Studies have turned to remote sensing datasets as a way to characterize vegetation for the examination of habitat selection and for mapping realized relationships across the landscape. Although the use of remote sensing in wildlife studies has increased in recent years, the use of these datasets is still limited and some data sources and methods are yet to be explored. The overall goal of this dissertation was to look at the state of the wildlife ecology discipline in the use of geospatial data for habitat mapping, and to advance this area through the fusion of remote sensing tools for the mapping of previously difficult to characterize forest metrics for inclusion in avian cavity-nester habitat models. Chapter 2 reviewed over 60 years of selected wildlife literature to examine the wildlife ecology disciple through historic trends and recent advances in the use of remote sensing for habitat characterization focusing on aspects of scale and the use of available technology. We discuss commonly used remote sensing data sources, point out recent advances in the use of geospatial data for characterizing forest wildlife habitat (the use of lidar data and the creation of spatially explicit habitat prediction maps), and provide future suggestions for increased utilization of available datasets (secondary lidar metrics and time series Landsat data). In chapters 3 and 4 we explored the use of remote sensing for characterizing forest components previously difficult to map across landscapes at scales relevant to local wildlife habitat selection. Chapter 3 found promise in the fusion of lidar structure and Landsat time series disturbance products in the modeling and mapping of post-fire snag and shrub distributions at fine scales and at size/cover thresholds relevant for habitat mapping applications for many wildlife species. The study was conducted within the 2003 B&B Fire Complex in central Oregon. Using 164 field calibration plots and remote sensing predictors, we modeled the presence/absence of snag classes (dbh ≥40cm, ≥50cm, and ≥75cm) and woody shrub cover resulting in 10m output predictive grid maps. Remote sensing predictors included various lidar structure and topography variables and Landsat time series products representing the pre-fire forest, disturbance magnitude, and current forest conditions. We were able to model and map all habitat metrics with acceptable predictive performance and low-moderate errors. The utility of these snag and shrub metrics for representing important nesting habitat features for a cavity-nesting species of conservation concern, the Lewis's Woodpecker (Melanerpes lewis), was demonstrated in Chapter 4. We were able to model nesting habitat with good accuracies according to multiple performance measures and then map realized relationships for this species of conservation concern in an identified source habitat type, providing a potential resource for local scale conservation and management efforts and adding to the regional knowledge of habitat selection for the Lewis's Woodpecker. To our knowledge, these chapters represent first attempts to fuse lidar and time series Landsat disturbance metrics in a post-fire landscape and for the mapping of snag and shrub distributions at scales relevant to avian cavity nesting habitat. Close

• 58. [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