Search

Search Results

• 21. [Article] Examination of Human Impacts on the Biodiversity and Ecology of Lichen and Moss Communities

  Globally, more than half of the world's population is living in urban areas and it is well accepted that human activities (e.g. climate warming, pollution, landscape homogenization) pose a multitude of ...

  Citation × Citation Citation Abstract Copy Title: Examination of Human Impacts on the Biodiversity and Ecology of Lichen and Moss Communities Author: Prather, Hannah Marie Year: 2017 Globally, more than half of the world's population is living in urban areas and it is well accepted that human activities (e.g. climate warming, pollution, landscape homogenization) pose a multitude of threats to ecosystems. Largely, human-related impacts on biodiversity will hold consequences for larger ecological processes and research looking into human impacts on sensitive epiphytic lichen and moss communities is an emerging area of research. While seemingly small, lichen and moss communities exist on nearly every terrestrial ecosystem on Earth and contribute to whole-system processes (e.g. hydrology, mineral cycling, food web energetics) worldwide. To further examine human impacts on epiphytic communities, I conducted three studies examining urbanization and climate warming effects on epiphytic lichen and moss biodiversity and ecology. In the first study I revisited a historic urban lichen community study to assess how urban lichen communities have responded to regional air quality changes occurring over the last nearly two decades. I further investigated, for the first time, the biodiversity of urban tree canopy-dwelling lichen communities in a native coniferous tree species, Pseudotsuga menziesii. I found that urban parks and forested areas harbor a species rich community of lichens epiphytes. Further, I found evidence for the distinct homogenization of urban epiphytic lichen communities, suggesting that expanding beyond simplistic measures of biodiversity to consider community composition and functional biodiversity may be necessary when assessing the ecology and potential ecosystem services of epiphyte communites within urbanizing landscapes. Next, I present the first tall tree canopy study across a regional gradient of urbanization near Portland, Oregon, USA. I found that tall tree canopy epiphyte communities change dramatically along gradients of increasing urbanization, most notably by the transitioning of species functional groups from sensitive, oligotrophic species to a dominance of urban-tolerant, eutrophic species. The implications these dramatic shifts in species composition have on essential PNW ecosystem processes, like N-fixation and canopy microclimate regulation, is still not well understood and is difficult to formally evaluate. However, I find strong evidence that native conifer trees in urban areas may provide a diversity of essential ecosystem services, including providing stratified habitat for epiphyte communities and their associated micro arthropod communities and the scavenging of atmospherically deposited nutrients. Future work is needed to understand how losses in canopy N fixation and species with large biomass (both lichens and bryophytes) will affect nutrient and hydrologic cycling in the PNW region, which continue to undergo rapid growth and urbanization. The final chapter investigates the impacts of passive warming by Open Top Chambers (OTCs) in moss-dominated ecosystems located on the Western Antarctic Peninsula, an area of increasing climate warming. I compared species-specific temperature effects, moss canopy morphology, sexual reproductive effort and invertebrate communities between OTC and control moss communities for two moss species, Polytrichastrum alpinum and Sanionia uncinata, that make up over 65% of the terrestrial vegetative cover in the area. I found distinct reproductive shifts in P. alpinum under passive warming compared to controls. Moss communities under warming also had substantially larger total invertebrate communities than those in control moss communities, and invertebrate communities were significantly affected by moss species and moss reproductive effort. Further, substantial species-specific thermal differences among contiguous patches of these dominant moss species were revealed. These results suggest that continued warming will differentially impact the reproductive output of Antarctic moss species and is likely to dramatically alter terrestrial ecosystems dynamics from the bottom up. This combined work provides a diverse contribution to the field of epiphyte ecology and biology by providing new insights on how human impacts will affect epiphyte lichen and moss communities across diverse ecosystems, in light of a rapidly changing planet. Title: Examination of Human Impacts on the Biodiversity and Ecology of Lichen and Moss Communities Author: Prather, Hannah Marie Year: 2017 Globally, more than half of the world's population is living in urban areas and it is well accepted that human activities (e.g. climate warming, pollution, landscape homogenization) pose a multitude of threats to ecosystems. Largely, human-related impacts on biodiversity will hold consequences for larger ecological processes and research looking into human impacts on sensitive epiphytic lichen and moss communities is an emerging area of research. While seemingly small, lichen and moss communities exist on nearly every terrestrial ecosystem on Earth and contribute to whole-system processes (e.g. hydrology, mineral cycling, food web energetics) worldwide. To further examine human impacts on epiphytic communities, I conducted three studies examining urbanization and climate warming effects on epiphytic lichen and moss biodiversity and ecology. In the first study I revisited a historic urban lichen community study to assess how urban lichen communities have responded to regional air quality changes occurring over the last nearly two decades. I further investigated, for the first time, the biodiversity of urban tree canopy-dwelling lichen communities in a native coniferous tree species, Pseudotsuga menziesii. I found that urban parks and forested areas harbor a species rich community of lichens epiphytes. Further, I found evidence for the distinct homogenization of urban epiphytic lichen communities, suggesting that expanding beyond simplistic measures of biodiversity to consider community composition and functional biodiversity may be necessary when assessing the ecology and potential ecosystem services of epiphyte communites within urbanizing landscapes. Next, I present the first tall tree canopy study across a regional gradient of urbanization near Portland, Oregon, USA. I found that tall tree canopy epiphyte communities change dramatically along gradients of increasing urbanization, most notably by the transitioning of species functional groups from sensitive, oligotrophic species to a dominance of urban-tolerant, eutrophic species. The implications these dramatic shifts in species composition have on essential PNW ecosystem processes, like N-fixation and canopy microclimate regulation, is still not well understood and is difficult to formally evaluate. However, I find strong evidence that native conifer trees in urban areas may provide a diversity of essential ecosystem services, including providing stratified habitat for epiphyte communities and their associated micro arthropod communities and the scavenging of atmospherically deposited nutrients. Future work is needed to understand how losses in canopy N fixation and species with large biomass (both lichens and bryophytes) will affect nutrient and hydrologic cycling in the PNW region, which continue to undergo rapid growth and urbanization. The final chapter investigates the impacts of passive warming by Open Top Chambers (OTCs) in moss-dominated ecosystems located on the Western Antarctic Peninsula, an area of increasing climate warming. I compared species-specific temperature effects, moss canopy morphology, sexual reproductive effort and invertebrate communities between OTC and control moss communities for two moss species, Polytrichastrum alpinum and Sanionia uncinata, that make up over 65% of the terrestrial vegetative cover in the area. I found distinct reproductive shifts in P. alpinum under passive warming compared to controls. Moss communities under warming also had substantially larger total invertebrate communities than those in control moss communities, and invertebrate communities were significantly affected by moss species and moss reproductive effort. Further, substantial species-specific thermal differences among contiguous patches of these dominant moss species were revealed. These results suggest that continued warming will differentially impact the reproductive output of Antarctic moss species and is likely to dramatically alter terrestrial ecosystems dynamics from the bottom up. This combined work provides a diverse contribution to the field of epiphyte ecology and biology by providing new insights on how human impacts will affect epiphyte lichen and moss communities across diverse ecosystems, in light of a rapidly changing planet. Close

• 22. [Article] Community and ecosystem dynamics in remnant and restored prairies

  xiv, 166 p. : ill. A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number.

  Citation × Citation Citation Abstract Copy Title: Community and ecosystem dynamics in remnant and restored prairies Author: Pfeifer-Meister, Laurel, 1978- Year: 2009, 2008 xiv, 166 p. : ill. A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number. Title: Community and ecosystem dynamics in remnant and restored prairies Author: Pfeifer-Meister, Laurel, 1978- Year: 2009, 2008 xiv, 166 p. : ill. A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number. Close

• 23. [Article] The Schultz Fire : an interdisciplinary perspective on its history, management, and ecological effects

  This thesis examines the Schultz Fire as a case study to explain the complex history of fire suppression management in America’s forests, and to gain further understanding of how management practices have ...

  Citation × Citation Citation Abstract Copy Title: The Schultz Fire : an interdisciplinary perspective on its history, management, and ecological effects Author: Ranseen, Susanne N. This thesis examines the Schultz Fire as a case study to explain the complex history of fire suppression management in America’s forests, and to gain further understanding of how management practices have affected the increase in fire severity levels and how forests respond to such a disturbance. The thesis objectives were: (1) to analyze the causes of the fire severity of the Schultz Fire, especially: topography, fuels, or weather; (2); to examine the possible correlation between fire severity and tree density; (3) to investigate whether post-fire species richness was related to fire severity two years after the Schultz Fire; (4) to investigate whether post-fire plant species richness, plant cover, and tree regeneration was related to fire severity two years after the Schultz Fire; and (5) to interlink and convey how these factors relate to the history of fire management and policy and public perception. The history of fire related policy and management has significantly changed the dynamics of America's national parks and forests. Understanding the larger context of this history, both of national fire management and of the effects of language and perception on policy and public reaction, is part of understanding the Schultz Fire as a whole. Based on modeling, high winds combined with the presence of high surface fuel load were the main causes of the Schultz Fire's high fire severity levels. As fire severity increased there was a statistically significant increase in species richness. Severity level had little variation on percentage of cover by plants. No statistically significant relationship between tree density and fire severity levels was found. These findings underline the need for fuel treatments in southwest Ponderosa Pine forests, and effective cooperation between communities, managers, and ecologists. The Schultz Fire serves as an example in understanding the intricacies of how history affects the present and future of fire management. How fire has been managed and portrayed in the past has left an indelible mark on how fire is presently viewed. Without a clear understanding of the history of fire management and the role of fire in the ecology, future policies towards fire will be unable to account for and manage for the diversity of ecosystems and fires effects on those ecosystems across the United States. Title: The Schultz Fire : an interdisciplinary perspective on its history, management, and ecological effects Author: Ranseen, Susanne N. This thesis examines the Schultz Fire as a case study to explain the complex history of fire suppression management in America’s forests, and to gain further understanding of how management practices have affected the increase in fire severity levels and how forests respond to such a disturbance. The thesis objectives were: (1) to analyze the causes of the fire severity of the Schultz Fire, especially: topography, fuels, or weather; (2); to examine the possible correlation between fire severity and tree density; (3) to investigate whether post-fire species richness was related to fire severity two years after the Schultz Fire; (4) to investigate whether post-fire plant species richness, plant cover, and tree regeneration was related to fire severity two years after the Schultz Fire; and (5) to interlink and convey how these factors relate to the history of fire management and policy and public perception. The history of fire related policy and management has significantly changed the dynamics of America's national parks and forests. Understanding the larger context of this history, both of national fire management and of the effects of language and perception on policy and public reaction, is part of understanding the Schultz Fire as a whole. Based on modeling, high winds combined with the presence of high surface fuel load were the main causes of the Schultz Fire's high fire severity levels. As fire severity increased there was a statistically significant increase in species richness. Severity level had little variation on percentage of cover by plants. No statistically significant relationship between tree density and fire severity levels was found. These findings underline the need for fuel treatments in southwest Ponderosa Pine forests, and effective cooperation between communities, managers, and ecologists. The Schultz Fire serves as an example in understanding the intricacies of how history affects the present and future of fire management. How fire has been managed and portrayed in the past has left an indelible mark on how fire is presently viewed. Without a clear understanding of the history of fire management and the role of fire in the ecology, future policies towards fire will be unable to account for and manage for the diversity of ecosystems and fires effects on those ecosystems across the United States. Close

• 24. [Article] Complex Interactions Between Regional Dispersal of Native Taxa and an Invasive Species

  In the event of an environmental disturbance, dispersal of native taxa may provide species and genetic diversity to ecosystems, increasing the likelihood that there will be species and genotypes present ...

  Citation × Citation Citation Abstract Copy Title: Complex Interactions Between Regional Dispersal of Native Taxa and an Invasive Species Author: Strecker, Angela L., Arnott, Shelley E. Year: 2010 In the event of an environmental disturbance, dispersal of native taxa may provide species and genetic diversity to ecosystems, increasing the likelihood that there will be species and genotypes present that are less vulnerable to the disturbance. This may allow communities to maintain functioning during a disturbance and may be particularly important when the perturbation is novel to the system, such as the establishment of an invasive species. We examined how dispersal of native species may influence crustacean zooplankton communities in freshwater lakes invaded by the invertebrate predator, Bythotrephes longimanus. Using large enclosures, we experimentally tested the effect of dispersal on zooplankton community abundance, richness, and composition in (1) a community invaded by Bythotrephes, (2) the same community with the invader removed, and (3) a community that was never invaded. Dispersal increased zooplankton community abundance and richness; however, these effects were usually only significant in the invader-removed treatment. Dispersal tended to make the invader-removed communities more similar to never-invaded communities in abundance, richness, and composition. Dispersal had little effect on zooplankton abundance in the invaded community; however, richness significantly increased, and the community composition changed to resemble a never-invaded community by the end of the experiment. Our results have implications for understanding the role of dispersal during transitory states in communities. Dispersal of native taxa may be particularly important during the period between the arrival and broad-scale establishment of Bythotrephes, as dispersal through space or time (i.e., from resting eggs) may rapidly increase zooplankton abundance when the invader is absent or in low abundances. Overall, our results suggest that communities with strong local predatory and competitive interactions may be closed to immigration from colonists, but that invasive species may alter the conditions under which species can establish. These results have implications for the interaction of native and invasive species across broad spatial scales, as regional dispersal of native taxa may forestall the local extirpation of native species. In particular, transient phases that result from variable persistence of invaders within habitats or across a region may permit native colonists to successfully establish, and thus increase local and regional resistance to future disturbance. Title: Complex Interactions Between Regional Dispersal of Native Taxa and an Invasive Species Author: Strecker, Angela L., Arnott, Shelley E. Year: 2010 In the event of an environmental disturbance, dispersal of native taxa may provide species and genetic diversity to ecosystems, increasing the likelihood that there will be species and genotypes present that are less vulnerable to the disturbance. This may allow communities to maintain functioning during a disturbance and may be particularly important when the perturbation is novel to the system, such as the establishment of an invasive species. We examined how dispersal of native species may influence crustacean zooplankton communities in freshwater lakes invaded by the invertebrate predator, Bythotrephes longimanus. Using large enclosures, we experimentally tested the effect of dispersal on zooplankton community abundance, richness, and composition in (1) a community invaded by Bythotrephes, (2) the same community with the invader removed, and (3) a community that was never invaded. Dispersal increased zooplankton community abundance and richness; however, these effects were usually only significant in the invader-removed treatment. Dispersal tended to make the invader-removed communities more similar to never-invaded communities in abundance, richness, and composition. Dispersal had little effect on zooplankton abundance in the invaded community; however, richness significantly increased, and the community composition changed to resemble a never-invaded community by the end of the experiment. Our results have implications for understanding the role of dispersal during transitory states in communities. Dispersal of native taxa may be particularly important during the period between the arrival and broad-scale establishment of Bythotrephes, as dispersal through space or time (i.e., from resting eggs) may rapidly increase zooplankton abundance when the invader is absent or in low abundances. Overall, our results suggest that communities with strong local predatory and competitive interactions may be closed to immigration from colonists, but that invasive species may alter the conditions under which species can establish. These results have implications for the interaction of native and invasive species across broad spatial scales, as regional dispersal of native taxa may forestall the local extirpation of native species. In particular, transient phases that result from variable persistence of invaders within habitats or across a region may permit native colonists to successfully establish, and thus increase local and regional resistance to future disturbance. Close

• 25. [Article] The effects of multiple pathogens on amphibians in the Pacific Northwest

  The earth is undergoing a “biodiversity crisis” characterized by loss of populations, species, genetic diversity, and ecosystem services. Part of this crisis consists of population declines, extinctions, ...

  Citation × Citation Citation Abstract Copy Title: The effects of multiple pathogens on amphibians in the Pacific Northwest Author: Romansic, John M. The earth is undergoing a “biodiversity crisis” characterized by loss of populations, species, genetic diversity, and ecosystem services. Part of this crisis consists of population declines, extinctions, and increased incidence of deformities in amphibians. It is unknown whether deformities contribute to these declines. Many cases of population declines in amphibians are associated with infectious disease. Water molds (Oomycota: Oomycetes: Saprolegniales) (e.g. Achlya and Saprolegnia) may contribute to amphibian population declines whereas parasitic flatworms (Ribeiroia) appear to be major causes of amphibian deformities. I found that Saprolegnia can kill larval and newly-metamorphosed juvenile amphibians. In addition, I investigated synergistic effects of Saprolegnia and the environmental contaminant nitrate on survival of amphibian larvae. No synergisms were found. However, there was a less-than-additive interaction affecting one frog species. Saprolegnia killed Rana aurora (red-legged frog) larvae, but only when nitrate was not added, consistent with nitrate preventing Saprolegnia from killing R. aurora. I also tested for possible interactions among the pathogenic water mold A. flagellata, the pathogenic fungus Batrachochytrium dendrobatidis (BD), and the parasitic trematode Ribeiroia. No between-pathogen interactions were found, however, there were main effects of Ribeiroia and BD. Ribeiroia caused mortality and increased frequency of limb deformities. There were differences in the composition of deformity types between my study and previous work, suggesting that the relative frequencies of different deformity types produced by Ribeiroia may be context-dependent. Also, there was an overall effect of delayed development in Ribeiroia-exposed individuals. In addition, individuals that did not die or display limb deformities following Ribeiroia exposure had slower development than controls not exposed to Ribeiroia. Delayed development may contribute to the effects of Ribeiroia on amphibian populations. In contrast, BD sped up development, although there was no evidence of BD infection. These results are consistent with amphibian larvae responding to the presence of BD by increasing the rate of development. Hastened metamorphosis and dispersal from larval habitats may decrease the risk of BD infection or reduce BD infection load. Mortality of post-embryonic life stages from water molds and sublethal effects of Ribeiroia and BD on amphibian development may influence how these pathogens interact with amphibian populations. Title: The effects of multiple pathogens on amphibians in the Pacific Northwest Author: Romansic, John M. The earth is undergoing a “biodiversity crisis” characterized by loss of populations, species, genetic diversity, and ecosystem services. Part of this crisis consists of population declines, extinctions, and increased incidence of deformities in amphibians. It is unknown whether deformities contribute to these declines. Many cases of population declines in amphibians are associated with infectious disease. Water molds (Oomycota: Oomycetes: Saprolegniales) (e.g. Achlya and Saprolegnia) may contribute to amphibian population declines whereas parasitic flatworms (Ribeiroia) appear to be major causes of amphibian deformities. I found that Saprolegnia can kill larval and newly-metamorphosed juvenile amphibians. In addition, I investigated synergistic effects of Saprolegnia and the environmental contaminant nitrate on survival of amphibian larvae. No synergisms were found. However, there was a less-than-additive interaction affecting one frog species. Saprolegnia killed Rana aurora (red-legged frog) larvae, but only when nitrate was not added, consistent with nitrate preventing Saprolegnia from killing R. aurora. I also tested for possible interactions among the pathogenic water mold A. flagellata, the pathogenic fungus Batrachochytrium dendrobatidis (BD), and the parasitic trematode Ribeiroia. No between-pathogen interactions were found, however, there were main effects of Ribeiroia and BD. Ribeiroia caused mortality and increased frequency of limb deformities. There were differences in the composition of deformity types between my study and previous work, suggesting that the relative frequencies of different deformity types produced by Ribeiroia may be context-dependent. Also, there was an overall effect of delayed development in Ribeiroia-exposed individuals. In addition, individuals that did not die or display limb deformities following Ribeiroia exposure had slower development than controls not exposed to Ribeiroia. Delayed development may contribute to the effects of Ribeiroia on amphibian populations. In contrast, BD sped up development, although there was no evidence of BD infection. These results are consistent with amphibian larvae responding to the presence of BD by increasing the rate of development. Hastened metamorphosis and dispersal from larval habitats may decrease the risk of BD infection or reduce BD infection load. Mortality of post-embryonic life stages from water molds and sublethal effects of Ribeiroia and BD on amphibian development may influence how these pathogens interact with amphibian populations. Close

• 26. [Article] An edaphic study of the Mt. Pisgah Arboretum water garden, Coast Fork of the Willamette River

  Wetlands are widely identified as providing important and fundamental processes valuable for maintaining ecosystem health and diversity. Located in the southern Willamette Valley, the Mt. Pisgah Arboretum ...

  Citation × Citation Citation Abstract Copy Title: An edaphic study of the Mt. Pisgah Arboretum water garden, Coast Fork of the Willamette River Author: Bergen, Cameron Francis Wetlands are widely identified as providing important and fundamental processes valuable for maintaining ecosystem health and diversity. Located in the southern Willamette Valley, the Mt. Pisgah Arboretum contains some valuable remaining wetland habitat along the Coast Fork of the Willamette River. One goal of the Mt. Pisgah Arboretum is "to promote conservation, research, and awareness of ecology". To reach this goal, the Arboretum has identified the importance of maintenance and enhancement activities for onsite native habitats, including riparian and wetland habitats. Before restoration or enhancement activities can begin, it is essential to develop an understanding of current environmental conditions. The purpose of this research was to document both the characteristics and distribution of hydric soils and the hydrology, and to provide insight into the patterns and processes associated with a floodplain wetland. In this study, transect sampling of edaphic features was used to identify the distribution of hydric soils and the hydrologic nature of the Mt. Pisgah Arboretum Water Garden. Soil morphological data for particle size, matrix colors and redox features were evaluated and compared with observations of ground water hydrology, river hydrology and precipitation. Five stratigraphic units were identified underlying the Water Garden. A basalt Bedrock unit underlies the uplands associated with Mt. Pisgah and extends at least part way beneath the floodplain. The Clay unit was formed above the Bedrock unit, with some degree of encroachment onto the floodplain. Below 153 m are floodplain sediments, cobbles at depth, then a sand layer and silty clay loam at the surface. The Cobble unit overlaps the Bedrock unit at its base and is most likely Pleistocene age alluvium. The Sand unit is of Holocene age and is found only in the abandoned thalweg, tapering off laterally in both directions across the ancient channels. Draped above this all and slightly overlapping the upland Bedrock and Clay units, is the SiCL unit. The SiCL unit represents Holocene age alluvium, fine material deposited by slow moving water and overbank deposition. The Water Garden soils reflect this mosaic of parent materials on a complex slope. Water Garden soils sometimes met saturation requirements for hydric soils, but they did not always meet hydric soil indicator requirements. The hydrological data suggest that the soils in depressional areas of the Water Garden occupy a zone where water is exchanged between saturated sediments surrounding the channel of the Coast Fork and the channel itself. The hydrology of depressional areas with both ponded surface water and near surface saturation was principally the result of hyporheic upwelling. The soils in these depressional areas tended to form redox concentrations that met hydric soil indicator criteria. Hillslope soils in concave footslope positions exhibited hydrology indicating two separate zones of saturation, one near surface, the other at depth, related to infiltration and accumulation of precipitation. Few redoximorphic features were observed in hillslope soils, and the one hydric soil indicator that was used at these locations did not require redox. Accurate and detailed delineation of hydric soils on this landscape and clear determination of dominant sources of saturation provided an improved understanding of the complex nature of the Water Garden wetland. Results of this study show that hydric soils occupy both depressional and hillslope positions within the Water Garden. Delineation of a soil as hydric or non hydric was facilitated by the use of hydric soil indicator criteria, morphology and hydrology. This analysis provides the managers of the Mt. Pisgah Arboretum with an accurate representation of where hydric soils currently exist and the respective sources of saturation. With this information, managers are better equipped to develop restoration and enhancement options that better reflect the current environmental conditions in the Water Garden. Title: An edaphic study of the Mt. Pisgah Arboretum water garden, Coast Fork of the Willamette River Author: Bergen, Cameron Francis Wetlands are widely identified as providing important and fundamental processes valuable for maintaining ecosystem health and diversity. Located in the southern Willamette Valley, the Mt. Pisgah Arboretum contains some valuable remaining wetland habitat along the Coast Fork of the Willamette River. One goal of the Mt. Pisgah Arboretum is "to promote conservation, research, and awareness of ecology". To reach this goal, the Arboretum has identified the importance of maintenance and enhancement activities for onsite native habitats, including riparian and wetland habitats. Before restoration or enhancement activities can begin, it is essential to develop an understanding of current environmental conditions. The purpose of this research was to document both the characteristics and distribution of hydric soils and the hydrology, and to provide insight into the patterns and processes associated with a floodplain wetland. In this study, transect sampling of edaphic features was used to identify the distribution of hydric soils and the hydrologic nature of the Mt. Pisgah Arboretum Water Garden. Soil morphological data for particle size, matrix colors and redox features were evaluated and compared with observations of ground water hydrology, river hydrology and precipitation. Five stratigraphic units were identified underlying the Water Garden. A basalt Bedrock unit underlies the uplands associated with Mt. Pisgah and extends at least part way beneath the floodplain. The Clay unit was formed above the Bedrock unit, with some degree of encroachment onto the floodplain. Below 153 m are floodplain sediments, cobbles at depth, then a sand layer and silty clay loam at the surface. The Cobble unit overlaps the Bedrock unit at its base and is most likely Pleistocene age alluvium. The Sand unit is of Holocene age and is found only in the abandoned thalweg, tapering off laterally in both directions across the ancient channels. Draped above this all and slightly overlapping the upland Bedrock and Clay units, is the SiCL unit. The SiCL unit represents Holocene age alluvium, fine material deposited by slow moving water and overbank deposition. The Water Garden soils reflect this mosaic of parent materials on a complex slope. Water Garden soils sometimes met saturation requirements for hydric soils, but they did not always meet hydric soil indicator requirements. The hydrological data suggest that the soils in depressional areas of the Water Garden occupy a zone where water is exchanged between saturated sediments surrounding the channel of the Coast Fork and the channel itself. The hydrology of depressional areas with both ponded surface water and near surface saturation was principally the result of hyporheic upwelling. The soils in these depressional areas tended to form redox concentrations that met hydric soil indicator criteria. Hillslope soils in concave footslope positions exhibited hydrology indicating two separate zones of saturation, one near surface, the other at depth, related to infiltration and accumulation of precipitation. Few redoximorphic features were observed in hillslope soils, and the one hydric soil indicator that was used at these locations did not require redox. Accurate and detailed delineation of hydric soils on this landscape and clear determination of dominant sources of saturation provided an improved understanding of the complex nature of the Water Garden wetland. Results of this study show that hydric soils occupy both depressional and hillslope positions within the Water Garden. Delineation of a soil as hydric or non hydric was facilitated by the use of hydric soil indicator criteria, morphology and hydrology. This analysis provides the managers of the Mt. Pisgah Arboretum with an accurate representation of where hydric soils currently exist and the respective sources of saturation. With this information, managers are better equipped to develop restoration and enhancement options that better reflect the current environmental conditions in the Water Garden. Close

• 27. [Article] What is killing the corals? Viral and bacterial interrogations using metagenomics and microscopy

  Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, ...

  Citation × Citation Citation Abstract Copy Title: What is killing the corals? Viral and bacterial interrogations using metagenomics and microscopy Author: Soffer, Nitzan Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, bacteria, protists, and viruses. Environmental stressors and disease agents can perturb the delicate balance of the coral host and its microbiota, which can lead to disease. This ultimately results in reduced fitness and/or mortality. There are over 30 described coral disease signs, but with a few exceptions, little is known about their potential etiological agents. Without knowledge on the causes of these diseases, little can be done to mitigate future outbreaks. Chapter 1 of this dissertation provides examples for studying novel diseases in difficult to study organisms with the use of metagenomic tools. Armed with these metagenomic tools and electron microscopy, this dissertation aimed to determine potential pathogens in two coral diseases, White Plague disease (WP), and Growth Anomalies (GAs). First, I set to determine whether viruses may be involved in WP disease from a 2010 outbreak in the US Virgin Islands (USVI). In chapter 2, I compared viromes from 21 Montastraea annularis samples (7= Diseased, 7= Diseased=Bleached, 5= Bleached, 2= Healthy) and surrounding seawater (n=2). After comparing the viromes, I found that small circular REP- encoding eukaryotic ssDNA viruses (SCSDv) similar to circo and nano viruses were associated with WP diseased tissue, and thus potential pathogens. Electron microscopy confirmed the presence of viral particles, and absence of bacterial infection in WP diseased tissue. Even though it was likely that viruses are involved with WP it was still important to understand the changes in bacterial community and the roles of bacteriophages during WP coral infection to characterize opportunistic microbes. These questions were addressed in Chapter 3 where I described the bacterial communities and bacteriophage consortia associated with the USVI corals. I also constructed phage-bacteria networks to understand which phages may interact with bacteria of interest (those shown to be differentially abundant in Montastraea annularis of different health states). I determined that there was a range of interaction specificity across the different phages and bacteria. Chapter 4 aimed to elucidate a potential pathogen responsible for Growth Anomalies, a chronic disease resulting in skeletal deformities, loss of symbiotic algae and reduction of fitness in Hawaiin Porites lobata. By comparing microbial and viral metagenomes across health states I was able to determine any changes in composition from healthy and diseased corals. Overall, microbial communities and viral consortia did not vary across health states. The hypothesized Porites spp. symbiont Oceanspirillales was dominant in all libraries. However, relative abundances of taxa in the orders Vibrionales and Verrucomicrobiales were elevated in diseased compared to healthy corals and healthy appearing tissue of GA infected corals. In addition, bacterial functional pathways remained stable across health states, while signatures of virulence factors were elevated in diseased viromes from healthy. Lastly, chapter 5 summarized overall trends of microbes and viruses determined through the studies. In addition, suggestions for future studies were outlined. Overall, this dissertation revealed a potential viral pathogenic group for white plague disease, explored how phages can influence bacterial opportunists in corals of different health states, and determined bacterial orders and virulence factors that are associated with Growth Anomalies. This dissertation includes the first study to find an association between a viral group and coral disease. In addition, this dissertation contains the first (to date) phage-bacterial inferred network constructed from paired phage-bacteria metagenomes. Title: What is killing the corals? Viral and bacterial interrogations using metagenomics and microscopy Author: Soffer, Nitzan Corals have multiple roles in maintaining ocean health and are some of the world’s most diverse ecosystems. The coral animal is host to a multitude of taxa, including symbiotic dinoflagellate algae, fungi, bacteria, protists, and viruses. Environmental stressors and disease agents can perturb the delicate balance of the coral host and its microbiota, which can lead to disease. This ultimately results in reduced fitness and/or mortality. There are over 30 described coral disease signs, but with a few exceptions, little is known about their potential etiological agents. Without knowledge on the causes of these diseases, little can be done to mitigate future outbreaks. Chapter 1 of this dissertation provides examples for studying novel diseases in difficult to study organisms with the use of metagenomic tools. Armed with these metagenomic tools and electron microscopy, this dissertation aimed to determine potential pathogens in two coral diseases, White Plague disease (WP), and Growth Anomalies (GAs). First, I set to determine whether viruses may be involved in WP disease from a 2010 outbreak in the US Virgin Islands (USVI). In chapter 2, I compared viromes from 21 Montastraea annularis samples (7= Diseased, 7= Diseased=Bleached, 5= Bleached, 2= Healthy) and surrounding seawater (n=2). After comparing the viromes, I found that small circular REP- encoding eukaryotic ssDNA viruses (SCSDv) similar to circo and nano viruses were associated with WP diseased tissue, and thus potential pathogens. Electron microscopy confirmed the presence of viral particles, and absence of bacterial infection in WP diseased tissue. Even though it was likely that viruses are involved with WP it was still important to understand the changes in bacterial community and the roles of bacteriophages during WP coral infection to characterize opportunistic microbes. These questions were addressed in Chapter 3 where I described the bacterial communities and bacteriophage consortia associated with the USVI corals. I also constructed phage-bacteria networks to understand which phages may interact with bacteria of interest (those shown to be differentially abundant in Montastraea annularis of different health states). I determined that there was a range of interaction specificity across the different phages and bacteria. Chapter 4 aimed to elucidate a potential pathogen responsible for Growth Anomalies, a chronic disease resulting in skeletal deformities, loss of symbiotic algae and reduction of fitness in Hawaiin Porites lobata. By comparing microbial and viral metagenomes across health states I was able to determine any changes in composition from healthy and diseased corals. Overall, microbial communities and viral consortia did not vary across health states. The hypothesized Porites spp. symbiont Oceanspirillales was dominant in all libraries. However, relative abundances of taxa in the orders Vibrionales and Verrucomicrobiales were elevated in diseased compared to healthy corals and healthy appearing tissue of GA infected corals. In addition, bacterial functional pathways remained stable across health states, while signatures of virulence factors were elevated in diseased viromes from healthy. Lastly, chapter 5 summarized overall trends of microbes and viruses determined through the studies. In addition, suggestions for future studies were outlined. Overall, this dissertation revealed a potential viral pathogenic group for white plague disease, explored how phages can influence bacterial opportunists in corals of different health states, and determined bacterial orders and virulence factors that are associated with Growth Anomalies. This dissertation includes the first study to find an association between a viral group and coral disease. In addition, this dissertation contains the first (to date) phage-bacterial inferred network constructed from paired phage-bacteria metagenomes. Close

• 28. [Article] Forest macro-arthropods as potential indicators of ecosystem conditions in Western Idaho : an analysis of community composition, biological diversity, and community structure

  Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new ...

  Citation × Citation Citation Abstract Copy Title: Forest macro-arthropods as potential indicators of ecosystem conditions in Western Idaho : an analysis of community composition, biological diversity, and community structure Author: Ruby, Margaret E. Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new strategies and tools to help them assess their progress in maintaining healthy, productive and biologically diverse forests. Biomonitoring of select forest macro-arthropod species can provide useful information on the effects of management on forest biodiversity and ecosystem function. The purpose of this study was threefold: (1) to inventory the macro-arthropod community and important environmental variables in the Bear Creek and Indian Creek study area within the Payette National Forest (PNF) in Western Idaho; (2) to compare measures of community composition, diversity, and structure in forest macro-arthropod communities between patches of different sizes and treatment; and (3) to assist PNF managers in their ecosystem management efforts by providing principles to guide the use of macro-arthropods as indicators of changing forest conditions. Transects with pitfall traps were used to collect macro-arthropods at 22 sites in the Bear Creek and Indian Creek study area during the summer of 1994. Five forest patch types in Abies grandis habitat types were sampled. Intact forest patches of 100 or more hectares, and large patches of 50-100 hectares, ranged in age between 50 and 250 years old with multistoried structure. Small patches up to 10 hectares were remnants or fragments of formerly intact forest isolated by logging. A plantation patch was 15 years old with patchy understory and forb cover. Clearcut patches had little or no overstory, and variable understory, and forb layers. At each transect, soil samples were collected and six environmental descriptor variables were analyzed according to patch treatment and patch size. These site descriptors were: basal area (ft²/acre); percent canopy cover for the overstory, understory; and forb layers; litter depth (cm), and percent soil moisture content. Differences detected using an ANOVA and T-tests are discussed in the Results section. Arthropod community composition, diversity, and structure were described according to relative abundance, and four measures of diversity. They were also described by membership in seventeen orders and/or super-families; ten functional groups; two disperser classes (long or short distance); and three species indicator classes. A total of 5455 macro-arthropod individuals, representing 17 orders and/or super-families and 219 species were collected in the Bear Creek and Indian Creek study area. While macro-arthropod fauna relative abundance did not vary significantly by treatment (ANOVA p<0.3), it did vary significantly by patch size (ANOVA p<0.03). Fauna relative abundance was 35% greater in clearcut patches than in large patches (T-test p<0.09). Fauna relative abundance in small patches was twice that of intact (T-test p<0.03) and large (T-test p<0.02) patches. Taxonomic diversity (number of genera/taxa) of beetle, ant, and bug taxa differed significantly according to treatment type(each ANOVA p<0.05). For the top four taxa (beetles, ants, spiders, and bugs), taxonomic diversity was highest in the plantation and clearcut patches. Ants and bugs had their highest taxonomic diversity in the plantation patch (separate T-tests p<0.05) while the taxonomic diversity of beetles was highest in clear-cut patches (T-test p<0.05). Beetle and ant taxonomic diversity varied significantly by patch size (each ANOVA p<0.05). For beetles and bugs, small patches were twice as diverse as intact patches (separate T-tests p<0.04) and 1.5 times that of large patches. Ant diversity was similarly distributed amongst the patch sizes, with significant differences between small and intact and between small and large patches (separate T-tests p<0.05). Of the four species diversity measures employed, only two, [alpha] and JK1 (both measures of richness), were found to vary significantly by patch treatment and size. Evenness (E) and the Shannon Diversity Index (H') failed to detect differences in the majority of tests. Fauna [alpha] and JK1 differed significantly by treatment type (each ANOVA p<0.05). Richness in clearcut patches was nearly twice in intact and large patches, followed by plantation and large patches. Fauna [alpha] and JKl also differed significantly by patch size (each ANOVA p <0.001), with small patch fauna twice as rich as that in large and intact patches (separate T-tests p <0.01). Of the top four functional groups, predators were the most abundant and had the highest taxonomic diversity (number of genera/functional group), followed by herbivores, fungivores and parasites. Predators and herbivores showed increasing taxonomic diversity with decreasing patch size, from intact to large to small (ANOVA p< 0.05). Similarly, predators and herbivores exhibited increasing taxonomic diversity with increasing levels of management: from intact and large to plantation and clear-cuts (ANOVA p< 0.05). Predators and herbivores were most numerous in the managed and small patches. Fungivore taxonomic diversity was also highest in the small and managed patches, though neither patch size nor treatment differences were significant (ANOVA p<0.85). Parasite taxonomic diversity differed by patch size with highest generic diversity in the small patches (ANOVA p<0.l) and by treatment type with generic diversity highest in plantations and clearcuts followed in order by large and intact patches (ANOVA p<0.l). Twice as many genera were long distance dispersers as were short distance dispersers. Relative abundance of long distance dispersers varied significantly by patch treatment and patch size (each ANOVA p<0.0l). Long distance dispersers were most numerous in clear-cut patches, followed in order by plantation, small, large, and intact patches. Relative abundance of short distance dispersers was not significantly different between treatment types (ANOVA p<0.20) but was significantly different between patch sizes (ANOVA p<0.0l). Short distance dispersers were most numerous in small patches followed by plantation, large, and intact and least numerous in clearcut patches. An indicator species analysis of 121 Bear Creek and Indian Creek genera (Dufrene and Legendre 1997), revealed sub-groups of species with 75 to 100 percent "perfect indication" or affiliation for specific patch types. When intact and large patches were pooled and analyzed against all treated patches (plantation and clearcut patches), a list of 36 genera with 75 to 100 percent "perfect affiliation" for intact or large patches was produced (MRPP p<0.05). Small patches had 42 indicators with 75 to 100 percent "perfect indication" when compared with the pooled intact and large patches (MRPP p<0.l). Conclusions Macro-arthropod community composition, diversity and structure did vary, usually significantly, by patch treatment and size. Useful measures of generic diversity include richness estimators [alpha], [beta], and JK1. Examination of taxonomic diversity was also useful, especially for the more mobile arthropods. Pitfall traps provided copious data on the structure of the community in regards to predators and herbivores. Pitfalls, however, did not provide much information about the status of fungivores and parasites in the various different patches. Another trapping method such as the berlaise funnel, would likely provide more information about those functional groups which are likely operating at a finer scale of resolution than that tested by the pitfall trap. Employing both methods would provide a much better assessment of the community of arthropods living on the forest floor. The indicator species analysis program also provided very useful lists of species which are affiliated with particular patch conditions. Taken together, these measures could be adopted for use by forest managers to allow them to assess and monitor the effects of a management regime on the structure and composition of macro-arthropod communities as part of a comprehensive adaptive management plan. Title: Forest macro-arthropods as potential indicators of ecosystem conditions in Western Idaho : an analysis of community composition, biological diversity, and community structure Author: Ruby, Margaret E. Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new strategies and tools to help them assess their progress in maintaining healthy, productive and biologically diverse forests. Biomonitoring of select forest macro-arthropod species can provide useful information on the effects of management on forest biodiversity and ecosystem function. The purpose of this study was threefold: (1) to inventory the macro-arthropod community and important environmental variables in the Bear Creek and Indian Creek study area within the Payette National Forest (PNF) in Western Idaho; (2) to compare measures of community composition, diversity, and structure in forest macro-arthropod communities between patches of different sizes and treatment; and (3) to assist PNF managers in their ecosystem management efforts by providing principles to guide the use of macro-arthropods as indicators of changing forest conditions. Transects with pitfall traps were used to collect macro-arthropods at 22 sites in the Bear Creek and Indian Creek study area during the summer of 1994. Five forest patch types in Abies grandis habitat types were sampled. Intact forest patches of 100 or more hectares, and large patches of 50-100 hectares, ranged in age between 50 and 250 years old with multistoried structure. Small patches up to 10 hectares were remnants or fragments of formerly intact forest isolated by logging. A plantation patch was 15 years old with patchy understory and forb cover. Clearcut patches had little or no overstory, and variable understory, and forb layers. At each transect, soil samples were collected and six environmental descriptor variables were analyzed according to patch treatment and patch size. These site descriptors were: basal area (ft²/acre); percent canopy cover for the overstory, understory; and forb layers; litter depth (cm), and percent soil moisture content. Differences detected using an ANOVA and T-tests are discussed in the Results section. Arthropod community composition, diversity, and structure were described according to relative abundance, and four measures of diversity. They were also described by membership in seventeen orders and/or super-families; ten functional groups; two disperser classes (long or short distance); and three species indicator classes. A total of 5455 macro-arthropod individuals, representing 17 orders and/or super-families and 219 species were collected in the Bear Creek and Indian Creek study area. While macro-arthropod fauna relative abundance did not vary significantly by treatment (ANOVA p<0.3), it did vary significantly by patch size (ANOVA p<0.03). Fauna relative abundance was 35% greater in clearcut patches than in large patches (T-test p<0.09). Fauna relative abundance in small patches was twice that of intact (T-test p<0.03) and large (T-test p<0.02) patches. Taxonomic diversity (number of genera/taxa) of beetle, ant, and bug taxa differed significantly according to treatment type(each ANOVA p<0.05). For the top four taxa (beetles, ants, spiders, and bugs), taxonomic diversity was highest in the plantation and clearcut patches. Ants and bugs had their highest taxonomic diversity in the plantation patch (separate T-tests p<0.05) while the taxonomic diversity of beetles was highest in clear-cut patches (T-test p<0.05). Beetle and ant taxonomic diversity varied significantly by patch size (each ANOVA p<0.05). For beetles and bugs, small patches were twice as diverse as intact patches (separate T-tests p<0.04) and 1.5 times that of large patches. Ant diversity was similarly distributed amongst the patch sizes, with significant differences between small and intact and between small and large patches (separate T-tests p<0.05). Of the four species diversity measures employed, only two, [alpha] and JK1 (both measures of richness), were found to vary significantly by patch treatment and size. Evenness (E) and the Shannon Diversity Index (H') failed to detect differences in the majority of tests. Fauna [alpha] and JK1 differed significantly by treatment type (each ANOVA p<0.05). Richness in clearcut patches was nearly twice in intact and large patches, followed by plantation and large patches. Fauna [alpha] and JKl also differed significantly by patch size (each ANOVA p <0.001), with small patch fauna twice as rich as that in large and intact patches (separate T-tests p <0.01). Of the top four functional groups, predators were the most abundant and had the highest taxonomic diversity (number of genera/functional group), followed by herbivores, fungivores and parasites. Predators and herbivores showed increasing taxonomic diversity with decreasing patch size, from intact to large to small (ANOVA p< 0.05). Similarly, predators and herbivores exhibited increasing taxonomic diversity with increasing levels of management: from intact and large to plantation and clear-cuts (ANOVA p< 0.05). Predators and herbivores were most numerous in the managed and small patches. Fungivore taxonomic diversity was also highest in the small and managed patches, though neither patch size nor treatment differences were significant (ANOVA p<0.85). Parasite taxonomic diversity differed by patch size with highest generic diversity in the small patches (ANOVA p<0.l) and by treatment type with generic diversity highest in plantations and clearcuts followed in order by large and intact patches (ANOVA p<0.l). Twice as many genera were long distance dispersers as were short distance dispersers. Relative abundance of long distance dispersers varied significantly by patch treatment and patch size (each ANOVA p<0.0l). Long distance dispersers were most numerous in clear-cut patches, followed in order by plantation, small, large, and intact patches. Relative abundance of short distance dispersers was not significantly different between treatment types (ANOVA p<0.20) but was significantly different between patch sizes (ANOVA p<0.0l). Short distance dispersers were most numerous in small patches followed by plantation, large, and intact and least numerous in clearcut patches. An indicator species analysis of 121 Bear Creek and Indian Creek genera (Dufrene and Legendre 1997), revealed sub-groups of species with 75 to 100 percent "perfect indication" or affiliation for specific patch types. When intact and large patches were pooled and analyzed against all treated patches (plantation and clearcut patches), a list of 36 genera with 75 to 100 percent "perfect affiliation" for intact or large patches was produced (MRPP p<0.05). Small patches had 42 indicators with 75 to 100 percent "perfect indication" when compared with the pooled intact and large patches (MRPP p<0.l). Conclusions Macro-arthropod community composition, diversity and structure did vary, usually significantly, by patch treatment and size. Useful measures of generic diversity include richness estimators [alpha], [beta], and JK1. Examination of taxonomic diversity was also useful, especially for the more mobile arthropods. Pitfall traps provided copious data on the structure of the community in regards to predators and herbivores. Pitfalls, however, did not provide much information about the status of fungivores and parasites in the various different patches. Another trapping method such as the berlaise funnel, would likely provide more information about those functional groups which are likely operating at a finer scale of resolution than that tested by the pitfall trap. Employing both methods would provide a much better assessment of the community of arthropods living on the forest floor. The indicator species analysis program also provided very useful lists of species which are affiliated with particular patch conditions. Taken together, these measures could be adopted for use by forest managers to allow them to assess and monitor the effects of a management regime on the structure and composition of macro-arthropod communities as part of a comprehensive adaptive management plan. Close

• 29. [Article] Ecological effects of post-wildfire management activities (salvage-logging and grass-seeding) on vegetation composition, diversity, biomass, and growth and survival of Pinus ponderosa and Purshia tridentata

  Salvage-logging and artificial seeding of grass following wildfire are common practices in coniferous forests of the western United States, yet few studies have quantified the ecological effects of these ...

  Citation × Citation Citation Abstract Copy Title: Ecological effects of post-wildfire management activities (salvage-logging and grass-seeding) on vegetation composition, diversity, biomass, and growth and survival of Pinus ponderosa and Purshia tridentata Author: Sexton, Timothy Ogden Salvage-logging and artificial seeding of grass following wildfire are common practices in coniferous forests of the western United States, yet few studies have quantified the ecological effects of these post-fire activities. The effects of post-wildfire salvage-logging and grass-seeding on vegetation composition, aboveground biomass, and growth and survival of Pinus ponderosa and Purshia tridentata were quantified on the area burned by the 1992 Lone Pine Fire, Winema National Forest in the Klamath Basin, Oregon. Prior to the fire, the area was dominated by uneven-aged stands of Pinus ponderosa with Purshia tridentata and Stipa occidentalis in the understory. The fire was a stand-replacement disturbance, where the majority of trees, the herbaceous component, and crowns of understory shrubs were killed. Salvage logging resulted in a significant decrease in understory biomass, species richness, species diversity, and growth and survival of P. ponderosa and P. tridentata. In addition plant community composition was shifted from native forb dominance to grass dominance. In 1993, the understory biomass of salvage-logged sites was 38% of the aboveground biomass produced on nonsalvaged sites (322 kg ha^-1 vs 843 kg ha^-1). In 1994, salvage-logged sites produced only 27% of the biomass produced on nonsalvaged sites (402 kg ha^-1 vs 1468 kg ha^-1). Salvage-logging reduced species richness, species diversity, and altered species composition. The first and second years following logging, species richness was reduced by 13% (20 versus 23), and 30% (15 versus 22), respectively. In 1993 and 1994, native forb frequency on nonsalvaged sites was 80% and 77% respectively, while salvage-logged sites recorded 68% and 31% respectively. Conversely, graminoid frequency was significantly higher on salvage-logged sites. In 1994, native graminoid frequency was 35% in nonsalvaged sites and > 61% on salvage-logged sites. During the first two years following salvage-logging, mean height growth of naturally-regenerated Pinus ponderosa was significantly lower on salvaged sites (9.4 versus 7.8 cm yr^-1) as was density of natural Purshia tridentata seedlings (313 versus 530 seedlings ha^-1). Survival in salvage-logged treatments was 22% lower for planted Purshia tridentata seedlings (57% versus 45%). Height growth in salvage-logged treatments was 16% lower for planted Pinus ponderosa (4.4 versus 3.7 cm). Total aboveground biomass on nonsalvaged burned sites (controls) averaged 843 kg ha^-1 in 1993, and 1473 kg ha^-1 in 1994. In 1993, the first year following the fire, sites seeded to Secale cereale produced = 1995 kg ha^-1 total aboveground biomass; most of the biomass was S. cereale. Those seeded sites produced 89% less native forb biomass than controls (82 versus 780 kg ha^-1), and = 80% less native forb biomass than areas seeded to the native grasses Sitanion hystrix and Festuca idahoensis. In 1994, the second post-fire year, biomass on sites seeded to S. cereale was >1653 kg ha^-1, dominated by S. cereale. In 1994, no differences in total aboveground biomass were detected between S. cereale, F idahoensis, S. hystrix, and the Control, indicating that the erosion reducing benefits of grass-seeding did not last for more than one year. Treatments seeded with S. cereale produced 58% less native forb biomass than controls (350 versus 825 kg ha^-1). Seeding S. cereale also reduced by 69% the biomass ofStipa occidentalis, the most common native grass in the area (311 kg ha^-1 on control sites versus 96 kg ha^-1 on S. cereale sites). In 1993 and 1994, fewer species were recorded on S. cereale sites than on all other sites. Grass-seeded sites exhibited no significant differences in frequency of noxious weeds in either of the two years following wildfire and seeding, rejecting the hypothesis that grass-seeding reduces noxious weeds. However, native graminoid frequency was reduced on all grass-seeded treatments. There were no significant differences between grass-seeding treatments in height and density of natural P. ponderosa and P. tridentata seedlings or growth and survival of planted P. ponderosa and P. tridentata seedlings. While salvage-logging provides an economic benefit to local communities through the extraction of commercially valuable timber, there is an ecological cost. Reduction in ecosystem structure, production, species richness, diversity and alterations in species composition are important ecological consequences of salvage logging. In addition, this study demonstrates that salvage-logging retards the re-establishment and early growth of Pinus ponderosa and Purshia tridentata, two important wildfire restoration priorities. Grass-seeding also results in significant ecological changes. Alterations in ecosystem production, species richness, diversity and species composition are important ecological consequences of grass-seeding. Managers should consider these long-term influences on ecosystem composition and structure when faced with decisions concerning post-fire rehabilitation and management. Title: Ecological effects of post-wildfire management activities (salvage-logging and grass-seeding) on vegetation composition, diversity, biomass, and growth and survival of Pinus ponderosa and Purshia tridentata Author: Sexton, Timothy Ogden Salvage-logging and artificial seeding of grass following wildfire are common practices in coniferous forests of the western United States, yet few studies have quantified the ecological effects of these post-fire activities. The effects of post-wildfire salvage-logging and grass-seeding on vegetation composition, aboveground biomass, and growth and survival of Pinus ponderosa and Purshia tridentata were quantified on the area burned by the 1992 Lone Pine Fire, Winema National Forest in the Klamath Basin, Oregon. Prior to the fire, the area was dominated by uneven-aged stands of Pinus ponderosa with Purshia tridentata and Stipa occidentalis in the understory. The fire was a stand-replacement disturbance, where the majority of trees, the herbaceous component, and crowns of understory shrubs were killed. Salvage logging resulted in a significant decrease in understory biomass, species richness, species diversity, and growth and survival of P. ponderosa and P. tridentata. In addition plant community composition was shifted from native forb dominance to grass dominance. In 1993, the understory biomass of salvage-logged sites was 38% of the aboveground biomass produced on nonsalvaged sites (322 kg ha^-1 vs 843 kg ha^-1). In 1994, salvage-logged sites produced only 27% of the biomass produced on nonsalvaged sites (402 kg ha^-1 vs 1468 kg ha^-1). Salvage-logging reduced species richness, species diversity, and altered species composition. The first and second years following logging, species richness was reduced by 13% (20 versus 23), and 30% (15 versus 22), respectively. In 1993 and 1994, native forb frequency on nonsalvaged sites was 80% and 77% respectively, while salvage-logged sites recorded 68% and 31% respectively. Conversely, graminoid frequency was significantly higher on salvage-logged sites. In 1994, native graminoid frequency was 35% in nonsalvaged sites and > 61% on salvage-logged sites. During the first two years following salvage-logging, mean height growth of naturally-regenerated Pinus ponderosa was significantly lower on salvaged sites (9.4 versus 7.8 cm yr^-1) as was density of natural Purshia tridentata seedlings (313 versus 530 seedlings ha^-1). Survival in salvage-logged treatments was 22% lower for planted Purshia tridentata seedlings (57% versus 45%). Height growth in salvage-logged treatments was 16% lower for planted Pinus ponderosa (4.4 versus 3.7 cm). Total aboveground biomass on nonsalvaged burned sites (controls) averaged 843 kg ha^-1 in 1993, and 1473 kg ha^-1 in 1994. In 1993, the first year following the fire, sites seeded to Secale cereale produced = 1995 kg ha^-1 total aboveground biomass; most of the biomass was S. cereale. Those seeded sites produced 89% less native forb biomass than controls (82 versus 780 kg ha^-1), and = 80% less native forb biomass than areas seeded to the native grasses Sitanion hystrix and Festuca idahoensis. In 1994, the second post-fire year, biomass on sites seeded to S. cereale was >1653 kg ha^-1, dominated by S. cereale. In 1994, no differences in total aboveground biomass were detected between S. cereale, F idahoensis, S. hystrix, and the Control, indicating that the erosion reducing benefits of grass-seeding did not last for more than one year. Treatments seeded with S. cereale produced 58% less native forb biomass than controls (350 versus 825 kg ha^-1). Seeding S. cereale also reduced by 69% the biomass ofStipa occidentalis, the most common native grass in the area (311 kg ha^-1 on control sites versus 96 kg ha^-1 on S. cereale sites). In 1993 and 1994, fewer species were recorded on S. cereale sites than on all other sites. Grass-seeded sites exhibited no significant differences in frequency of noxious weeds in either of the two years following wildfire and seeding, rejecting the hypothesis that grass-seeding reduces noxious weeds. However, native graminoid frequency was reduced on all grass-seeded treatments. There were no significant differences between grass-seeding treatments in height and density of natural P. ponderosa and P. tridentata seedlings or growth and survival of planted P. ponderosa and P. tridentata seedlings. While salvage-logging provides an economic benefit to local communities through the extraction of commercially valuable timber, there is an ecological cost. Reduction in ecosystem structure, production, species richness, diversity and alterations in species composition are important ecological consequences of salvage logging. In addition, this study demonstrates that salvage-logging retards the re-establishment and early growth of Pinus ponderosa and Purshia tridentata, two important wildfire restoration priorities. Grass-seeding also results in significant ecological changes. Alterations in ecosystem production, species richness, diversity and species composition are important ecological consequences of grass-seeding. Managers should consider these long-term influences on ecosystem composition and structure when faced with decisions concerning post-fire rehabilitation and management. Close

• 30. [Article] Predictability and Constraints on the Structure of Ecological Communities in the Context of Climate Change

  Ecologists must increasingly balance the need for accurate predictions about how ecosystems will be affected by climate change, against the fact that making such predictions at the ecosystem-level may ...

  Citation × Citation Citation Abstract Copy Title: Predictability and Constraints on the Structure of Ecological Communities in the Context of Climate Change Author: Barner, Allison K. Ecologists must increasingly balance the need for accurate predictions about how ecosystems will be affected by climate change, against the fact that making such predictions at the ecosystem-level may be infeasible. Although information about responses of individual species to a changing environment is increasing, scaling such information to the community level is challenging. To date, predicting responses of ecological communities to climate change is constrained by limited theoretical and empirical knowledge about the response of communities and ecosystems to change. My dissertation addresses several knowledge gaps in our understanding of community structure under climate change. This research draws from a rich experimental tradition in the species-diverse model ecosystem of the US Pacific Northwest rocky intertidal to test ecological theory. In Chapter 2, I assessed whether the response of multiple species of coralline algae to global change could be predicted from basic first principles of chemistry, physiology, and ecology. Given the rate of global change, and the time-consuming process of experimentally determining species responses to climate change, I hypothesized that species can be grouped using existing theory, either by their evolutionary relatedness or by their ecological traits, such that climate responses are similar within a group. Such a scheme would greatly reduce the number of experiments needed to characterize species climate vulnerability, requiring the characterization of the response of groups of species to climate change, rather than individual species. Using a suite of five co-occurring species of intertidal articulated coralline algae (Corallina vancouveriensis, Corallina officinalis, Bossiella plumosa, Bossiella orbiginiana, and Calliarthron tuberculosum), I applied this framework to generate ten mutually exclusive hypotheses that could explain organismal response to ocean acidification, a consequence of global climate change that threatens marine calcifying species. I found that all species had similar responses to ocean acidification, and that responses were generally predicted by the body size of the individual. Despite the power that such a framework provides in understanding group-level response to climate change, predicting community-level response requires knowledge of how organisms affect one another. In Chapter 3, I quantified species interactions in a series of removal experiments to estimate the reciprocal effects between a canopy-forming intertidal kelp (Saccharina sessilis) and a suite of understory species that persist beneath the kelp canopy. This experiment was replicated in different oceanographic conditions across a large latitudinal gradient, as a step towards understanding how interactions might change with climate change. However, the experiment demonstrated that interactions between the canopy and understory were consistent among different environmental conditions. Furthermore, the strongest effect was that of understory species, particularly articulated coralline turf algae, on the canopy species. The coralline turf algae both facilitated the recruitment of the canopy species and buffered the canopy from abiotic stress during its adult life stage. Combining experimental results and observational surveys, a hypothesized interaction network for these species was constructed, highlighting the importance of direct and indirect species interactions in promoting species coexistence. A long-standing controversy in ecology is whether or not species interactions can be inferred from observational data, as opposed to from experimental tests. Although the rocky intertidal ecosystem is unique for its ease of experimental manipulation, quantifying species interactions experimentally is often difficult or impossible. As an alternative, many have turned to statistical methods to estimate species interactions from observational data, namely, from patterns in species pairwise co-occurrences. In Chapter 4, I examined these co-occurrence methods and their potential relationship to experimentally measured species interactions. I first used a suite of different co-occurrence methods to generate a set of predicted species interactions of macrophytes and invertebrates from observational surveys conducted in the rocky intertidal zone of Oregon. I then compared the predicted species interactions to the same pairwise species interactions determined experimentally and assembled from the literature. Overall, of the seven methods tested, each generated a different set of predicted species interactions from the same data, and all methods predicted interactions that did not match those in the experimental database. Thus, predicting species interactions from patterns in occurrence remains elusive. Importantly, much work remains to be done to understand the link between species co-occurrences and their actual interactions with one another on the landscape. A key limiting frontier in climate change ecology is determining the influence of species interactions on species distributions across the landscape, and the sensitivity of such interactions to changes in climate. Finally, in Chapter 5, I used theory from the published literature and knowledge from my previous chapters to make predictions the recovery of low rocky intertidal communities after a disturbance. The process of community development after disturbance has been studied in many ways, from the successional studies of the early 1900s, to modern community assembly theory. In recent years, a focus on the unpredictability of community assembly has emerged, paying particular attention to the role of historical contingency, or priority effects, in determining the recovery trajectory of a community. Priority effects occur when the arrival of a species after a disturbance inalterably changes the composition of the developing community, driving the assembly of widely different communities at a small spatial scale. I conducted a community assembly experiment in three different low intertidal zone community "types", each characterized by different dominant macrophyte species (Saccharina sessilis, Phyllospadix spp., and algal "turfs"). Replicating this experiment at six sites along the Oregon coast, I found that both regional and local dynamics constrain the recovery of communities after disturbance. Half of the time, the community returned to the state of the nearby community type. The remaining communities were influenced by priority effects that could be predicted based on 1) regional dynamics favoring some species over others, or 2) the timing of arrival of important facilitating species. Overall, understanding the dynamic relationship between the persistence of diverse communities and a changing environment remains one of the challenges of our time. My dissertation highlights some of the challenges in predicting the future composition of communities under climate change, but also provides some ways forward. Integration of experimental, theoretical, and observational studies builds the scaffolding of prediction, whereby understanding the constraints on species physiology, the interactions among species, and community assembly can help frame the context in which predictions are made. Title: Predictability and Constraints on the Structure of Ecological Communities in the Context of Climate Change Author: Barner, Allison K. Ecologists must increasingly balance the need for accurate predictions about how ecosystems will be affected by climate change, against the fact that making such predictions at the ecosystem-level may be infeasible. Although information about responses of individual species to a changing environment is increasing, scaling such information to the community level is challenging. To date, predicting responses of ecological communities to climate change is constrained by limited theoretical and empirical knowledge about the response of communities and ecosystems to change. My dissertation addresses several knowledge gaps in our understanding of community structure under climate change. This research draws from a rich experimental tradition in the species-diverse model ecosystem of the US Pacific Northwest rocky intertidal to test ecological theory. In Chapter 2, I assessed whether the response of multiple species of coralline algae to global change could be predicted from basic first principles of chemistry, physiology, and ecology. Given the rate of global change, and the time-consuming process of experimentally determining species responses to climate change, I hypothesized that species can be grouped using existing theory, either by their evolutionary relatedness or by their ecological traits, such that climate responses are similar within a group. Such a scheme would greatly reduce the number of experiments needed to characterize species climate vulnerability, requiring the characterization of the response of groups of species to climate change, rather than individual species. Using a suite of five co-occurring species of intertidal articulated coralline algae (Corallina vancouveriensis, Corallina officinalis, Bossiella plumosa, Bossiella orbiginiana, and Calliarthron tuberculosum), I applied this framework to generate ten mutually exclusive hypotheses that could explain organismal response to ocean acidification, a consequence of global climate change that threatens marine calcifying species. I found that all species had similar responses to ocean acidification, and that responses were generally predicted by the body size of the individual. Despite the power that such a framework provides in understanding group-level response to climate change, predicting community-level response requires knowledge of how organisms affect one another. In Chapter 3, I quantified species interactions in a series of removal experiments to estimate the reciprocal effects between a canopy-forming intertidal kelp (Saccharina sessilis) and a suite of understory species that persist beneath the kelp canopy. This experiment was replicated in different oceanographic conditions across a large latitudinal gradient, as a step towards understanding how interactions might change with climate change. However, the experiment demonstrated that interactions between the canopy and understory were consistent among different environmental conditions. Furthermore, the strongest effect was that of understory species, particularly articulated coralline turf algae, on the canopy species. The coralline turf algae both facilitated the recruitment of the canopy species and buffered the canopy from abiotic stress during its adult life stage. Combining experimental results and observational surveys, a hypothesized interaction network for these species was constructed, highlighting the importance of direct and indirect species interactions in promoting species coexistence. A long-standing controversy in ecology is whether or not species interactions can be inferred from observational data, as opposed to from experimental tests. Although the rocky intertidal ecosystem is unique for its ease of experimental manipulation, quantifying species interactions experimentally is often difficult or impossible. As an alternative, many have turned to statistical methods to estimate species interactions from observational data, namely, from patterns in species pairwise co-occurrences. In Chapter 4, I examined these co-occurrence methods and their potential relationship to experimentally measured species interactions. I first used a suite of different co-occurrence methods to generate a set of predicted species interactions of macrophytes and invertebrates from observational surveys conducted in the rocky intertidal zone of Oregon. I then compared the predicted species interactions to the same pairwise species interactions determined experimentally and assembled from the literature. Overall, of the seven methods tested, each generated a different set of predicted species interactions from the same data, and all methods predicted interactions that did not match those in the experimental database. Thus, predicting species interactions from patterns in occurrence remains elusive. Importantly, much work remains to be done to understand the link between species co-occurrences and their actual interactions with one another on the landscape. A key limiting frontier in climate change ecology is determining the influence of species interactions on species distributions across the landscape, and the sensitivity of such interactions to changes in climate. Finally, in Chapter 5, I used theory from the published literature and knowledge from my previous chapters to make predictions the recovery of low rocky intertidal communities after a disturbance. The process of community development after disturbance has been studied in many ways, from the successional studies of the early 1900s, to modern community assembly theory. In recent years, a focus on the unpredictability of community assembly has emerged, paying particular attention to the role of historical contingency, or priority effects, in determining the recovery trajectory of a community. Priority effects occur when the arrival of a species after a disturbance inalterably changes the composition of the developing community, driving the assembly of widely different communities at a small spatial scale. I conducted a community assembly experiment in three different low intertidal zone community "types", each characterized by different dominant macrophyte species (Saccharina sessilis, Phyllospadix spp., and algal "turfs"). Replicating this experiment at six sites along the Oregon coast, I found that both regional and local dynamics constrain the recovery of communities after disturbance. Half of the time, the community returned to the state of the nearby community type. The remaining communities were influenced by priority effects that could be predicted based on 1) regional dynamics favoring some species over others, or 2) the timing of arrival of important facilitating species. Overall, understanding the dynamic relationship between the persistence of diverse communities and a changing environment remains one of the challenges of our time. My dissertation highlights some of the challenges in predicting the future composition of communities under climate change, but also provides some ways forward. Integration of experimental, theoretical, and observational studies builds the scaffolding of prediction, whereby understanding the constraints on species physiology, the interactions among species, and community assembly can help frame the context in which predictions are made. Close