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• 131. [Article] Population genetics, ecology and evolution of a vertebrate metacommunity

  Population genetic structure is widespread in many organisms and can be found at small spatial scales. Fine-scale differentiation is the result of ecological and evolutionary processes working together ...

  Citation × Citation Citation Abstract Copy Title: Population genetics, ecology and evolution of a vertebrate metacommunity Author: Manier, Mollie Kim Population genetic structure is widespread in many organisms and can be found at small spatial scales. Fine-scale differentiation is the result of ecological and evolutionary processes working together to produce an overall pattern, but the relative importance of these factors in population differentiation is poorly understood. The goals of my research were to describe patterns of population genetic differentiation and to identify ecological and evolutionary factors important for population divergence. To this end, I investigated several aspects of genetic differentiation for three vertebrates in northern California. The focal species were the terrestrial garter snake (Thamnophis elegans) and the common garter snake (Thamnophis sirtalis) that occupy a series of ponds, lakes and flooded meadows in northern California. I found significant genetic differentiation and isolation by distance, as well as correlated patterns of pairwise divergence in both species. Independent estimates of effective population size and bi-directional migration rates also uncovered source-sink dynamics in both species that suggest frequent extinction-recolonization events within a metapopulation context. The generality of source-sink dynamics for an ecologically similar species within the same ecosystem was explored using a third species, B. boreas. I also identified ecological correlates of several population genetic parameters for all three species. Although F[subscript ST] were similar, B. boreas had larger effective population sizes, lower migration rates, lacked source-sink dynamics, and appeared to be in migration-drift equilibrium, indicative of a temporally stable population structure. A clustering analysis identified a series of block faults as a common barrier to dispersal for both garter snakes, and ecological correlates were found to be more similar among response variables than within species. I then compared degree of genetic differentiation at quantitative traits with that at neutral markers to infer strength of selection and adaptive divergence between two ecotypes of T. elegans. Selection on most traits was relatively weak, but strong diversifying selection was found for background coloration, total number of ventral scales and number of infralabials. Overall, my research documented ecological and evolutionary processes associated with population differentiation in a metacommunity and respresents an important contribution toward the unification of ecology and evolutionary biology. Title: Population genetics, ecology and evolution of a vertebrate metacommunity Author: Manier, Mollie Kim Population genetic structure is widespread in many organisms and can be found at small spatial scales. Fine-scale differentiation is the result of ecological and evolutionary processes working together to produce an overall pattern, but the relative importance of these factors in population differentiation is poorly understood. The goals of my research were to describe patterns of population genetic differentiation and to identify ecological and evolutionary factors important for population divergence. To this end, I investigated several aspects of genetic differentiation for three vertebrates in northern California. The focal species were the terrestrial garter snake (Thamnophis elegans) and the common garter snake (Thamnophis sirtalis) that occupy a series of ponds, lakes and flooded meadows in northern California. I found significant genetic differentiation and isolation by distance, as well as correlated patterns of pairwise divergence in both species. Independent estimates of effective population size and bi-directional migration rates also uncovered source-sink dynamics in both species that suggest frequent extinction-recolonization events within a metapopulation context. The generality of source-sink dynamics for an ecologically similar species within the same ecosystem was explored using a third species, B. boreas. I also identified ecological correlates of several population genetic parameters for all three species. Although F[subscript ST] were similar, B. boreas had larger effective population sizes, lower migration rates, lacked source-sink dynamics, and appeared to be in migration-drift equilibrium, indicative of a temporally stable population structure. A clustering analysis identified a series of block faults as a common barrier to dispersal for both garter snakes, and ecological correlates were found to be more similar among response variables than within species. I then compared degree of genetic differentiation at quantitative traits with that at neutral markers to infer strength of selection and adaptive divergence between two ecotypes of T. elegans. Selection on most traits was relatively weak, but strong diversifying selection was found for background coloration, total number of ventral scales and number of infralabials. Overall, my research documented ecological and evolutionary processes associated with population differentiation in a metacommunity and respresents an important contribution toward the unification of ecology and evolutionary biology. Close

• 132. [Article] The methodology, implementation,and analysis of the isotopic composition of soil respired CO₂ in forest ecological research

  Soils are the largest terrestrial pool of carbon, therefore it is critical to understand what controls soil carbon efflux to the atmosphere in light of current climate uncertainty. The primary efflux of ...

  Citation × Citation Citation Abstract Copy Title: The methodology, implementation,and analysis of the isotopic composition of soil respired CO₂ in forest ecological research Author: Kayler, Zachary Eric Soils are the largest terrestrial pool of carbon, therefore it is critical to understand what controls soil carbon efflux to the atmosphere in light of current climate uncertainty. The primary efflux of carbon from soil is soil respiration which is typically categorized into autotrophic and heterotrophic respiration. These two components have different responses to changes in the environment, thus necessitating a means to quantify the contributions of each. Natural abundance ¹³C can identify autotrophic and heterotrophic sources of respiration, but there is a paucity of research concerning the soil isotope methodology and the subsequent analysis. This dissertation documents my contributions to the advancement of understanding carbon metabolism in forest ecosystems of the Pacific Northwest through the use of the natural abundance carbon isotopic signature of soil respiration. The results of this research represent significant progress in the use of ¹³C in forest ecology. I show in a laboratory setting that a change in the isotopic signature of soil gas can take at least 48 hours to reach equilibrium. A change in the isotopic source of respiration is one mechanism behind non steady-state conditions while another mechanism is dynamic gas transport. I explored the impact of a negative pressure potential across the soil surface by inducing advection and found the isotopic signature of respiration to be 1‰ less than the theoretical steady-state value. I performed a source partitioning experiment in which I identified a highly depleted source of carbon contributing to respiration. I also considered the impacts of the potential errors associated with collecting and measuring isotopic samples on mixing-models currently used to identify the isotopic signature of respiration. I found that the effect of CO₂ and δ¹³C measurement error on large CO₂ concentration regime to be substantially different than small concentration regimes, necessitating a unique mixing-model and regression-model combination for estimating the isotopic signal of respiration. Finally, I built upon the progress made in the previous experiments and analyze almost two years of soil respiration and its isotopic signature to determine potential environmental and biological drivers. I found that: transpiration was highly correlated with both respiration and the carbon isotopic signature; soil moisture primarily influenced tree processes related to respiration; and I found evidence of soil respiration under isotopic non steady-state conditions. Title: The methodology, implementation,and analysis of the isotopic composition of soil respired CO₂ in forest ecological research Author: Kayler, Zachary Eric Soils are the largest terrestrial pool of carbon, therefore it is critical to understand what controls soil carbon efflux to the atmosphere in light of current climate uncertainty. The primary efflux of carbon from soil is soil respiration which is typically categorized into autotrophic and heterotrophic respiration. These two components have different responses to changes in the environment, thus necessitating a means to quantify the contributions of each. Natural abundance ¹³C can identify autotrophic and heterotrophic sources of respiration, but there is a paucity of research concerning the soil isotope methodology and the subsequent analysis. This dissertation documents my contributions to the advancement of understanding carbon metabolism in forest ecosystems of the Pacific Northwest through the use of the natural abundance carbon isotopic signature of soil respiration. The results of this research represent significant progress in the use of ¹³C in forest ecology. I show in a laboratory setting that a change in the isotopic signature of soil gas can take at least 48 hours to reach equilibrium. A change in the isotopic source of respiration is one mechanism behind non steady-state conditions while another mechanism is dynamic gas transport. I explored the impact of a negative pressure potential across the soil surface by inducing advection and found the isotopic signature of respiration to be 1‰ less than the theoretical steady-state value. I performed a source partitioning experiment in which I identified a highly depleted source of carbon contributing to respiration. I also considered the impacts of the potential errors associated with collecting and measuring isotopic samples on mixing-models currently used to identify the isotopic signature of respiration. I found that the effect of CO₂ and δ¹³C measurement error on large CO₂ concentration regime to be substantially different than small concentration regimes, necessitating a unique mixing-model and regression-model combination for estimating the isotopic signal of respiration. Finally, I built upon the progress made in the previous experiments and analyze almost two years of soil respiration and its isotopic signature to determine potential environmental and biological drivers. I found that: transpiration was highly correlated with both respiration and the carbon isotopic signature; soil moisture primarily influenced tree processes related to respiration; and I found evidence of soil respiration under isotopic non steady-state conditions. Close

• 133. [Article] Functional profiles of soil microbial communities in second-growth Douglas-fir forests of the Pacific Northwest

  Forests are one of the largest repositories of terrestrial C. Understanding factors that drive organic matter transformations and nutrient efflux from these systems is therefore highly important. Temperate ...

  Citation × Citation Citation Abstract Copy Title: Functional profiles of soil microbial communities in second-growth Douglas-fir forests of the Pacific Northwest Author: McGinnis, Megan L. Forests are one of the largest repositories of terrestrial C. Understanding factors that drive organic matter transformations and nutrient efflux from these systems is therefore highly important. Temperate forests are of particular significance due to the large fraction of C that is stored below ground in the soil. Characterizing nutrient transformations, especially for C and N, and factors that influence their mineralization is critical in managing these ecosystems sustainably. The objective of this study was to characterize the metabolic function of the soil microbial community as it relates to C and N cycling in managed second-growth Douglas-fir forests of the Pacific Northwest. In the first study, extracellular enzyme profiles were characterized and correlated with a wide range of environmental variables present at nine sites located in western Oregon and Washington. Enzyme profiles were also correlated with measures of microbial biomass and with C and N mineralization rates obtained from a two-month incubation. Sites varied significantly from one another in all enzymes. C-cycling enzymes were correlated with respired C, and N-cycling enzymes, in addition to phosphatase and oxidative enzymes, were correlated with released N. Enzyme profiles grouped similarly for sites of the same soil type. Abiotic factors such as CEC, EC, and cation concentrations were correlated strongly with many enzymes, suggesting that soil physical and chemical properties influence extracellular enzyme function. In the second study, a year-long soil microcosm incubation measured respired C as well as total released N: NO₃⁻, NH₄⁺, and dissolved organic N (DON). These cumulative mineralization measurements were fitted with kinetic models to characterize C and N cycling in the same nine soils. Mineralization rates, and their descriptive parameters derived from the models, were correlated with the same set of environmental characteristics and enzyme activities from the previous study. Total soil C and N, as well as microbial biomass, were strongly positively correlated with both C and N mineralization. However, abiotic factors such as soil chemical components also had significant effects. This, coupled with anomalous behavior noted in C mineralization in response to leaching treatments, may suggest substrate supply to microorganisms constrains much of C mineralization. N mineralization seemed strongly tied to biotic factors in addition to abiotic factors. Often in studies of N dynamics in soil, only mineralized N (NO₃⁻ and NH₄⁺) are examined; our study revealed that DON was the largest fraction of released N in these systems, and dynamics of DON in N cycle warrant further research. Together, these studies provide insights into factors that drive soil microbial community function across a broad range of site conditions for Douglas-fir dominated forests of the Pacific Northwest region and could serve as a baseline for future research. Title: Functional profiles of soil microbial communities in second-growth Douglas-fir forests of the Pacific Northwest Author: McGinnis, Megan L. Forests are one of the largest repositories of terrestrial C. Understanding factors that drive organic matter transformations and nutrient efflux from these systems is therefore highly important. Temperate forests are of particular significance due to the large fraction of C that is stored below ground in the soil. Characterizing nutrient transformations, especially for C and N, and factors that influence their mineralization is critical in managing these ecosystems sustainably. The objective of this study was to characterize the metabolic function of the soil microbial community as it relates to C and N cycling in managed second-growth Douglas-fir forests of the Pacific Northwest. In the first study, extracellular enzyme profiles were characterized and correlated with a wide range of environmental variables present at nine sites located in western Oregon and Washington. Enzyme profiles were also correlated with measures of microbial biomass and with C and N mineralization rates obtained from a two-month incubation. Sites varied significantly from one another in all enzymes. C-cycling enzymes were correlated with respired C, and N-cycling enzymes, in addition to phosphatase and oxidative enzymes, were correlated with released N. Enzyme profiles grouped similarly for sites of the same soil type. Abiotic factors such as CEC, EC, and cation concentrations were correlated strongly with many enzymes, suggesting that soil physical and chemical properties influence extracellular enzyme function. In the second study, a year-long soil microcosm incubation measured respired C as well as total released N: NO₃⁻, NH₄⁺, and dissolved organic N (DON). These cumulative mineralization measurements were fitted with kinetic models to characterize C and N cycling in the same nine soils. Mineralization rates, and their descriptive parameters derived from the models, were correlated with the same set of environmental characteristics and enzyme activities from the previous study. Total soil C and N, as well as microbial biomass, were strongly positively correlated with both C and N mineralization. However, abiotic factors such as soil chemical components also had significant effects. This, coupled with anomalous behavior noted in C mineralization in response to leaching treatments, may suggest substrate supply to microorganisms constrains much of C mineralization. N mineralization seemed strongly tied to biotic factors in addition to abiotic factors. Often in studies of N dynamics in soil, only mineralized N (NO₃⁻ and NH₄⁺) are examined; our study revealed that DON was the largest fraction of released N in these systems, and dynamics of DON in N cycle warrant further research. Together, these studies provide insights into factors that drive soil microbial community function across a broad range of site conditions for Douglas-fir dominated forests of the Pacific Northwest region and could serve as a baseline for future research. Close

• 134. [Article] Drivers of arbuscular mycorrhizal fungal community composition in roots : hosts, neighbors, and environment

  The vast majority of terrestrial plant species live in symbiosis with arbuscular mycorrhizal fungi (AMF). AMF and plants live in complex networks, with roots of individual plants hosting multiple AMF, ...

  Citation × Citation Citation Abstract Copy Title: Drivers of arbuscular mycorrhizal fungal community composition in roots : hosts, neighbors, and environment Author: Phillips, Wendy S. The vast majority of terrestrial plant species live in symbiosis with arbuscular mycorrhizal fungi (AMF). AMF and plants live in complex networks, with roots of individual plants hosting multiple AMF, and single AMF colonizing multiple plants concurrently. Through the exchange of resources, the two partners of this symbiosis can have great effects on each other, effects which can ripple through both communities. What determines the patterns of associations between the partners is still largely unknown. In this dissertation, I examine a variety of factors, and in particular host identity, that could drive the community composition of AMF in roots. I began by surveying the diversity of AMF in roots of 12 plant species at a remnant bunchgrass prairie in Oregon, U.S.A. (Chapter 2). To do that, I first designed new primers for use in polymerase chain reaction (PCR) to specifically amplify DNA from all Glomeromycota species. Using those primers, I found 36 distinct AMF phylogenetic groups, or operational taxonomic units (OTUs) in the roots from the prairie. The proportion of OTUs in the basal order Archaeosporales was greater than in many other environmental surveys. I also conducted an in silico analysis to predict how effectively previously published primers would detect the whole diversity of OTUs I detected. I then assayed AMF community composition in the roots of 50 plants from nine plant species (Chapter 3). To do that, I designed primers specific to 18 of the OTUs detected in the initial field survey and used them to test for the presence of each OTU in the roots individual plants. I used that data to test if AMF community composition in individual roots correlated with host identity, spatial distribution, or soil characteristics. I found host identity was associated with both the richness and the structure of root AMF communities, while spatial distribution and soil characteristics were not. Finally, I performed an experimental test of the effect of host identity and community context on AMF community assembly (Chapter 4). I grew plants from four native perennial plant species, including two common and two federally endangered plants, either individually or in a community of four plants (with one plant of each species). I analyzed the AMF community composition in the roots of all plants after 12 weeks of growth with exposure to a uniform mix of field soil as inoculum. I found that host species identity affected root AMF richness and community composition, and community context affected AMF richness. Only one of the endangered species was highly colonized by AMF, and I did not detect unique AMF communities associated with it. This dissertation provides information on the diversity of AMF at a remnant bunchgrass prairie, an ecosystem which has been the subject of very few studies of AMF. Although a complex mix of factors interact to determine AMF community composition in roots, this work provides strong evidence that host identity plays a major role in that process. Title: Drivers of arbuscular mycorrhizal fungal community composition in roots : hosts, neighbors, and environment Author: Phillips, Wendy S. The vast majority of terrestrial plant species live in symbiosis with arbuscular mycorrhizal fungi (AMF). AMF and plants live in complex networks, with roots of individual plants hosting multiple AMF, and single AMF colonizing multiple plants concurrently. Through the exchange of resources, the two partners of this symbiosis can have great effects on each other, effects which can ripple through both communities. What determines the patterns of associations between the partners is still largely unknown. In this dissertation, I examine a variety of factors, and in particular host identity, that could drive the community composition of AMF in roots. I began by surveying the diversity of AMF in roots of 12 plant species at a remnant bunchgrass prairie in Oregon, U.S.A. (Chapter 2). To do that, I first designed new primers for use in polymerase chain reaction (PCR) to specifically amplify DNA from all Glomeromycota species. Using those primers, I found 36 distinct AMF phylogenetic groups, or operational taxonomic units (OTUs) in the roots from the prairie. The proportion of OTUs in the basal order Archaeosporales was greater than in many other environmental surveys. I also conducted an in silico analysis to predict how effectively previously published primers would detect the whole diversity of OTUs I detected. I then assayed AMF community composition in the roots of 50 plants from nine plant species (Chapter 3). To do that, I designed primers specific to 18 of the OTUs detected in the initial field survey and used them to test for the presence of each OTU in the roots individual plants. I used that data to test if AMF community composition in individual roots correlated with host identity, spatial distribution, or soil characteristics. I found host identity was associated with both the richness and the structure of root AMF communities, while spatial distribution and soil characteristics were not. Finally, I performed an experimental test of the effect of host identity and community context on AMF community assembly (Chapter 4). I grew plants from four native perennial plant species, including two common and two federally endangered plants, either individually or in a community of four plants (with one plant of each species). I analyzed the AMF community composition in the roots of all plants after 12 weeks of growth with exposure to a uniform mix of field soil as inoculum. I found that host species identity affected root AMF richness and community composition, and community context affected AMF richness. Only one of the endangered species was highly colonized by AMF, and I did not detect unique AMF communities associated with it. This dissertation provides information on the diversity of AMF at a remnant bunchgrass prairie, an ecosystem which has been the subject of very few studies of AMF. Although a complex mix of factors interact to determine AMF community composition in roots, this work provides strong evidence that host identity plays a major role in that process. Close

• 135. [Article] Dynamic seascapes : a quantitative framework for scaling pelagic ecology and biogeochemistry

  Understanding and modeling microbial responses and feedbacks to climate change is hampered by a lack of a framework in the pelagic environment by which to link local mechanism to large scale patterns. ...

  Citation × Citation Citation Abstract Copy Title: Dynamic seascapes : a quantitative framework for scaling pelagic ecology and biogeochemistry Author: Kavanaugh, Maria T. Understanding and modeling microbial responses and feedbacks to climate change is hampered by a lack of a framework in the pelagic environment by which to link local mechanism to large scale patterns. Where terrestrial ecology draws from landscape theory and practice to address issues of scale, the pelagic seascape concept is still in its infancy. We have applied the patch mosaic paradigm of landscape ecology to the study of the seasonal and interannual variability of the North Pacific to facilitate comparative analysis between pelagic ecosystems and provide spatiotemporal context for eulerian time-series studies. Using multivariate, 13-year climatologies of sea surface temperature, photosynthetically active radiation, and chlorophyll a derived from remote sensing observations, we classified hierarchical seascapes at monthly and interannual scales. These dynamic, objectively-determined seascapes offer improved hydrographic coherence relative to oceanic regions with subjectively defined and static boundaries (Chapter 2) and represent unique biogeochemical functioning (Chapter 2) and microbial communities (Chapter3). Furthermore they provide consilience between satellite studies and in situ observations (Chapter 4) and allow for objective comparison of ecosystem forcing (Chapters, 4 and 5). In Chapter 2, we rigorously tested the assumption that satellite-derived seascapes describe regions of biogeochemical coherence. The seasonal cycle of the North Pacific was characterized at three levels of spatiotemporal hierarchy and broader relevance of monthly –resolved seascapes was assessed through analysis of variance (ANOVA) and multiple linear regression (MLR) analyses of nutrient, primary productivity, and pCO₂ data. Distinct nutrient and primary productivity regimes were well-characterized in the coarsest two levels of hierarchy (ANOVA, R² = 0.5-0.7). Finer scale partitioning was more relevant for pCO₂. MLR analyses revealed differential forcing on pCO₂ across seascapes and hierarchical levels and a 33 % reduction in mean model error with increased partitioning (from 18.5 µatm to 12.0 µatm pCO₂). In Chapter 3 we verified the seascapes with in situ collections of microbial abundance and structure. Flow cytometry data was collected from two long term time series and several cruises spanning thousand kilometers of the NE Pacific; these data allowed us to quantify spatiotemporal patterns. In addition, multiple response permutation analysis revealed differences in community structure across discrete seascapes, in terms of both absolute and relative abundances. Principal component analysis of the assemblage supported seascape divisions and revealed structure along environmental gradients with strong associations with chlorophyll a and sea surface temperature and, to a lesser extent, with mixed layer depth and mean photosynthetically active radiation in the mixed layer. Differences of assemblage structure between seascapes and strength of environmental forcing were strong in the subarctic and transition zones, but less pronounced in the subtropics, suggesting satellite-detected changes in bulk properties that may be associated with local physiology or interannual shifts in seascape boundaries. Based on the work presented in Chapter 4, we discovered that interannual shifts in the boundaries of a transition seascape and two distinct oligotrophic subtropical seascapes affect the variability observed at benchmark time series Station ALOHA; the latter two seascapes oscillate in their contributions to the expansion of the entire subtropics. On interannual scales, in situ phytoplankton abundance (as measured by chl-a), net primary productivity (NPP), and the relative abundance of eukaryotic phytoplankton and Synechococcus sp. increased during periods of encroachment by the transition seascape. Conversely, the relative abundance of Prochlorococcus increased and chl –a and NPP decreased when the highly oligotrophic seascape encroached on Station ALOHA. The dynamic range (~6 million km²) of subtropical expansion is born almost entirely by the transition zone - resulting in a transfer of ~1.2 Pg of total primary C production between a system primed for export production and one dominated by the microbial loop. In Chapter 5, we investigated multiple factors that contribute to the effectiveness of the biological pump in the transition seascape. Near-continuous measurements of net primary production (NPP), net community production (NCP) and several ecophysiological variables were collected in across subarctic, transition, and subtropical seascapes of the Northeast Pacific during August and September of 2008. Mesoscale processes and shifts in community structure contributed to high export efficiency in the subtropical seascape; the convergence of assemblage structure, high biomass, moderate NPP: NCP and high NCP contributed to biologically mediated air-sea exchange in the transition seascape. Furthermore, NPP and NCP were strongly spatially coupled in both the transition (r[subscript 1, 39]=0.70; p<0.0001) and subtropical seascapes (r[subscript 1, 45]= 0.68, p<0.0001), suggesting the possibility for empirical modeling efforts. This dissertation provides a first step to characterize the seascape variability in the NE Pacific and to understand the modulation of primary and export production in a critical transition region. The multivariate seascape approach described here provides spatiotemporal context for in situ studies and allows objective comparisons of systems' responses to climatic forcing. An integrated ocean observing system will require insight from in situ observations and experiments, ecosystem models, and satellite remote sensing. The results highlighted in this dissertation suggest that the pelagic seascape framework, through its capacity to scale both context and mechanism, may serve as an important and unifying component of such an observing system. Title: Dynamic seascapes : a quantitative framework for scaling pelagic ecology and biogeochemistry Author: Kavanaugh, Maria T. Understanding and modeling microbial responses and feedbacks to climate change is hampered by a lack of a framework in the pelagic environment by which to link local mechanism to large scale patterns. Where terrestrial ecology draws from landscape theory and practice to address issues of scale, the pelagic seascape concept is still in its infancy. We have applied the patch mosaic paradigm of landscape ecology to the study of the seasonal and interannual variability of the North Pacific to facilitate comparative analysis between pelagic ecosystems and provide spatiotemporal context for eulerian time-series studies. Using multivariate, 13-year climatologies of sea surface temperature, photosynthetically active radiation, and chlorophyll a derived from remote sensing observations, we classified hierarchical seascapes at monthly and interannual scales. These dynamic, objectively-determined seascapes offer improved hydrographic coherence relative to oceanic regions with subjectively defined and static boundaries (Chapter 2) and represent unique biogeochemical functioning (Chapter 2) and microbial communities (Chapter3). Furthermore they provide consilience between satellite studies and in situ observations (Chapter 4) and allow for objective comparison of ecosystem forcing (Chapters, 4 and 5). In Chapter 2, we rigorously tested the assumption that satellite-derived seascapes describe regions of biogeochemical coherence. The seasonal cycle of the North Pacific was characterized at three levels of spatiotemporal hierarchy and broader relevance of monthly –resolved seascapes was assessed through analysis of variance (ANOVA) and multiple linear regression (MLR) analyses of nutrient, primary productivity, and pCO₂ data. Distinct nutrient and primary productivity regimes were well-characterized in the coarsest two levels of hierarchy (ANOVA, R² = 0.5-0.7). Finer scale partitioning was more relevant for pCO₂. MLR analyses revealed differential forcing on pCO₂ across seascapes and hierarchical levels and a 33 % reduction in mean model error with increased partitioning (from 18.5 µatm to 12.0 µatm pCO₂). In Chapter 3 we verified the seascapes with in situ collections of microbial abundance and structure. Flow cytometry data was collected from two long term time series and several cruises spanning thousand kilometers of the NE Pacific; these data allowed us to quantify spatiotemporal patterns. In addition, multiple response permutation analysis revealed differences in community structure across discrete seascapes, in terms of both absolute and relative abundances. Principal component analysis of the assemblage supported seascape divisions and revealed structure along environmental gradients with strong associations with chlorophyll a and sea surface temperature and, to a lesser extent, with mixed layer depth and mean photosynthetically active radiation in the mixed layer. Differences of assemblage structure between seascapes and strength of environmental forcing were strong in the subarctic and transition zones, but less pronounced in the subtropics, suggesting satellite-detected changes in bulk properties that may be associated with local physiology or interannual shifts in seascape boundaries. Based on the work presented in Chapter 4, we discovered that interannual shifts in the boundaries of a transition seascape and two distinct oligotrophic subtropical seascapes affect the variability observed at benchmark time series Station ALOHA; the latter two seascapes oscillate in their contributions to the expansion of the entire subtropics. On interannual scales, in situ phytoplankton abundance (as measured by chl-a), net primary productivity (NPP), and the relative abundance of eukaryotic phytoplankton and Synechococcus sp. increased during periods of encroachment by the transition seascape. Conversely, the relative abundance of Prochlorococcus increased and chl –a and NPP decreased when the highly oligotrophic seascape encroached on Station ALOHA. The dynamic range (~6 million km²) of subtropical expansion is born almost entirely by the transition zone - resulting in a transfer of ~1.2 Pg of total primary C production between a system primed for export production and one dominated by the microbial loop. In Chapter 5, we investigated multiple factors that contribute to the effectiveness of the biological pump in the transition seascape. Near-continuous measurements of net primary production (NPP), net community production (NCP) and several ecophysiological variables were collected in across subarctic, transition, and subtropical seascapes of the Northeast Pacific during August and September of 2008. Mesoscale processes and shifts in community structure contributed to high export efficiency in the subtropical seascape; the convergence of assemblage structure, high biomass, moderate NPP: NCP and high NCP contributed to biologically mediated air-sea exchange in the transition seascape. Furthermore, NPP and NCP were strongly spatially coupled in both the transition (r[subscript 1, 39]=0.70; p<0.0001) and subtropical seascapes (r[subscript 1, 45]= 0.68, p<0.0001), suggesting the possibility for empirical modeling efforts. This dissertation provides a first step to characterize the seascape variability in the NE Pacific and to understand the modulation of primary and export production in a critical transition region. The multivariate seascape approach described here provides spatiotemporal context for in situ studies and allows objective comparisons of systems' responses to climatic forcing. An integrated ocean observing system will require insight from in situ observations and experiments, ecosystem models, and satellite remote sensing. The results highlighted in this dissertation suggest that the pelagic seascape framework, through its capacity to scale both context and mechanism, may serve as an important and unifying component of such an observing system. Close

• 136. [Article] Riparian litter inputs to streams in the central Oregon Coast Range

  Riparian zone vegetation can influence terrestrial and aquatic food webs through variations in the amounts, timing, and nutritional content of leaf and other litter inputs. Differences in vegetation composition ...

  Citation × Citation Citation Abstract Copy Title: Riparian litter inputs to streams in the central Oregon Coast Range Author: Hart, Stephanie K. Riparian zone vegetation can influence terrestrial and aquatic food webs through variations in the amounts, timing, and nutritional content of leaf and other litter inputs. Differences in vegetation composition and density, as well as riparian topography, may modulate the strength and quality of these inputs. Changes in inputs to small order streams affect the processes and condition of adjacent and downstream reaches based on the amount of particulate organic matter that is intercepted, retained, or exported. The central Oregon Coast Range provides an ideal opportunity to study how deciduous dominated and coniferous dominated riparian forests influence small streams within a matrix of managed riparian forests. In coastal Oregon riparian forests, we investigated lateral and vertical litter inputs to sixteen streams throughout a year and assessed how these inputs were influenced by density of deciduous dominated (mainly red alder (Alnus rubra)) or coniferous dominated (mainly Douglas-fir (Pseudotsuga menziesii)) overstory, understory, and lateral slope. Deciduous site vertical litter inputs (504 g m-2 yr-1 (95% CI: 447-562)) were estimated to exceed those from coniferous sites (394 g m-2 yr-1 (336-452)) by 110 g m-2 (29-192) over the full year. Annual lateral inputs (per meter of stream bank on one side) at deciduous sites (109 g m-1 yr-1 (76-143)) were estimated to be 47 g m-1 (1-95) more than coniferous sites (63 g m-1 yr-1 (29-97)). Annual inputs at coniferous sites were dominated by deciduous leaves, coniferous needles, and twig litter types. Deciduous leaves, deciduous-other, and small unidentifiable litter types dominated the annual inputs at deciduous sites. When evaluated temporally, November was the most pivotal month differentiating coniferous and deciduous site litter inputs. At deciduous sites, lateral litter movement increased with slope, but we did not see the same relationship for coniferous sites except in spring/summer months. Lateral inputs were quantitatively greatest in autumn months for both overstories, but were proportionately greater in winter. Regardless of slope, there was no indication that understory plants were obstructing annual lateral litter inputs or that annual lateral litter inputs were moving more than 5 m down slope. The percent nitrogen of annual total vertical litter was estimated to be 1.9% N (1.5-2.4) at deciduous sites and 1.2% N (0.8-1.7) at coniferous sites. Average % nitrogen of individual litter types were either greater in deciduous sites or not different among overstories, indicating that one can generally expect coniferous sites to have lower % N litter inputs overall. The annual nitrogen flux entering each meter-length (from above and both sides) of standard 4 m-wide streams at a deciduous sites (42 g N m-1 of stream) was twice that of coniferous sites (21 g N m-1 of stream). Annual total litter carbon flux into each meter-length of 4 m-wide streams was estimated to be 1154 g C m-1 of stream at deciduous sites and 880 g C m-1 of stream at coniferous sites. On average, autumn months (October-December) accounted for 46-59% of annual vertical C flux and 56-70% of annual vertical N flux at coniferous and deciduous sites. Our results suggest that red alder dominated riparian zones of the central Oregon Coast Range have significantly different quantity, timing, and quality of leaf litter inputs to streams than conifer dominated forests. Varied topography adjacent to streams with red alder dominated overstory has greater impact on the quantity, quality, and timing of total inputs than at coniferous sites. The cumulative effects from many small red alder dominated streams exporting to downstream reaches include more pronounced seasonality of litter delivery, with greater carbon and nitrogen loading annually, than expected from conifer dominated streams. Differences in overstory and topography in Oregon Coast Range riparian forests directly impact the delivery of nutrients and can affect the structure and composition of food webs in these ecosystems. Title: Riparian litter inputs to streams in the central Oregon Coast Range Author: Hart, Stephanie K. Riparian zone vegetation can influence terrestrial and aquatic food webs through variations in the amounts, timing, and nutritional content of leaf and other litter inputs. Differences in vegetation composition and density, as well as riparian topography, may modulate the strength and quality of these inputs. Changes in inputs to small order streams affect the processes and condition of adjacent and downstream reaches based on the amount of particulate organic matter that is intercepted, retained, or exported. The central Oregon Coast Range provides an ideal opportunity to study how deciduous dominated and coniferous dominated riparian forests influence small streams within a matrix of managed riparian forests. In coastal Oregon riparian forests, we investigated lateral and vertical litter inputs to sixteen streams throughout a year and assessed how these inputs were influenced by density of deciduous dominated (mainly red alder (Alnus rubra)) or coniferous dominated (mainly Douglas-fir (Pseudotsuga menziesii)) overstory, understory, and lateral slope. Deciduous site vertical litter inputs (504 g m-2 yr-1 (95% CI: 447-562)) were estimated to exceed those from coniferous sites (394 g m-2 yr-1 (336-452)) by 110 g m-2 (29-192) over the full year. Annual lateral inputs (per meter of stream bank on one side) at deciduous sites (109 g m-1 yr-1 (76-143)) were estimated to be 47 g m-1 (1-95) more than coniferous sites (63 g m-1 yr-1 (29-97)). Annual inputs at coniferous sites were dominated by deciduous leaves, coniferous needles, and twig litter types. Deciduous leaves, deciduous-other, and small unidentifiable litter types dominated the annual inputs at deciduous sites. When evaluated temporally, November was the most pivotal month differentiating coniferous and deciduous site litter inputs. At deciduous sites, lateral litter movement increased with slope, but we did not see the same relationship for coniferous sites except in spring/summer months. Lateral inputs were quantitatively greatest in autumn months for both overstories, but were proportionately greater in winter. Regardless of slope, there was no indication that understory plants were obstructing annual lateral litter inputs or that annual lateral litter inputs were moving more than 5 m down slope. The percent nitrogen of annual total vertical litter was estimated to be 1.9% N (1.5-2.4) at deciduous sites and 1.2% N (0.8-1.7) at coniferous sites. Average % nitrogen of individual litter types were either greater in deciduous sites or not different among overstories, indicating that one can generally expect coniferous sites to have lower % N litter inputs overall. The annual nitrogen flux entering each meter-length (from above and both sides) of standard 4 m-wide streams at a deciduous sites (42 g N m-1 of stream) was twice that of coniferous sites (21 g N m-1 of stream). Annual total litter carbon flux into each meter-length of 4 m-wide streams was estimated to be 1154 g C m-1 of stream at deciduous sites and 880 g C m-1 of stream at coniferous sites. On average, autumn months (October-December) accounted for 46-59% of annual vertical C flux and 56-70% of annual vertical N flux at coniferous and deciduous sites. Our results suggest that red alder dominated riparian zones of the central Oregon Coast Range have significantly different quantity, timing, and quality of leaf litter inputs to streams than conifer dominated forests. Varied topography adjacent to streams with red alder dominated overstory has greater impact on the quantity, quality, and timing of total inputs than at coniferous sites. The cumulative effects from many small red alder dominated streams exporting to downstream reaches include more pronounced seasonality of litter delivery, with greater carbon and nitrogen loading annually, than expected from conifer dominated streams. Differences in overstory and topography in Oregon Coast Range riparian forests directly impact the delivery of nutrients and can affect the structure and composition of food webs in these ecosystems. Close

• 137. [Article] Ultraviolet radiation as an environmental stressor of amphibians

  My thesis explored the effects of and potential mediating mechanisms for an important environmental stressor, ultraviolet-B (UVB) radiation. UVB radiation has negative effects on organisms in both terrestrial ...

  Citation × Citation Citation Abstract Copy Title: Ultraviolet radiation as an environmental stressor of amphibians Author: Bancroft, Betsy A. My thesis explored the effects of and potential mediating mechanisms for an important environmental stressor, ultraviolet-B (UVB) radiation. UVB radiation has negative effects on organisms in both terrestrial and aquatic systems. I used meta-analysis to quantify the effects of UVB radiation on a diversity of aquatic organisms (Chapter 2). UVB negatively affects aquatic organisms by reducing both survival and growth. In particular, UVB reduces growth of embryos more than any other life history stage. Some taxonomic groups may be more affected by UVB radiation than others. In our analysis, the growth of members of the kingdom Protozoa was suppressed by UVB radiation to a greater degree than any other kingdom. These analyses suggest that UVB is an important stressor in both freshwater and marine systems. Amphibians are a common component of freshwater systems and are experiencing world-wide population declines. These declines may be due to a number of causes including habitat loss, introduced species, global climate change, disease, toxic chemicals and UVB radiation. I used meta-analytic techniques to quantify the effects of UVB radiation on amphibians. By synthesizing the results of 41 articles on the effects of UVB radiation on amphibians (Chapter 3), I found a nearly 2-fold reduction in survival of amphibians exposed to UVB radiation. Salamanders (caudates) appear to be more susceptible to damage from UVB than frogs or toads (anurans). Moreover, survival of larvae was much lower than survival of embryos or metamorphic individuals under UVB radiation. In addition, I used factorial meta-analytic techniques to explore the interaction between UVB radiation and other stressors in amphibian habitats. UVB radiation acted synergistically with other stressors to reduce survival of amphibians. Behavioral avoidance of UVB radiation may help mediate the negative effects of UVB radiation on amphibians. In aquatic systems, behavioral avoidance usually requires movement out of shallow water, where UVB levels can be high, into deeper waters with lower UVB transmittance. However, these two microhabitats have very different thermal profiles, creating a trade-off between exploiting warm waters with high UVB levels and avoiding UVB by seeking cooler, deeper regions of ponds. I explored the microhabitat use of larvae of four species through a series of laboratory experiments, field experiments, and observational field transects at three different amphibian habitats (Chapter 4). Larvae did not avoid UVB radiation in either the laboratory or field experiments. Larvae in thermal gradients selected relatively high temperatures regardless of the UVB exposure at these temperatures. In field transects, salamander larvae were most common in deeper, cooler waters where UVB levels were lower. In contrast, anuran larvae were frequently observed in the warmer and shallower regions of each habitat. These regions also had the highest UVB levels, suggesting that anuran larvae are exposed to high levels of UVB due to thermoregulatory behavior. Behavioral avoidance of UVB radiation is not the only mechanism amphibians may use to prevent damage from UVB. Pigments such as melanin may allow larvae to exploit warm shallow waters by absorbing harmful UVB radiation before it causes cellular damage. I tested the efficacy of melanin as a photoprotective pigment in the larvae of two species, Rana cascadae and Pseudacris regilla (Chapter 5). I found no evidence of a photoprotective function for melanin in these larvae. In contrast, lighter colored tadpoles grew more under UVB radiation compared to darker colored tadpoles. Overall, exposure to UVB reduced survival of P. regilla larvae and reduced growth of R. cascadae larvae. Larvae of both of these species were frequently observed in very shallow water with intense solar radiation. This thesis emphasizes the importance of UVB radiation as an environmental stressor in aquatic habitats. Many aquatic organisms are negatively affected by UVB exposure. My thesis work quantitatively demonstrated that UVB radiation is one factor that reduces survival of amphibians and suggests that some species are exposed to high levels of UVB radiation in natural habitats. While UVB radiation is not the sole cause of amphibian population declines, my work suggests that UVB radiation is an important stressor for amphibians that should not be overlooked. In addition, UVB radiation is clearly an important stressor for many other aquatic organisms. Future work should consider the effects of UVB in aquatic systems, particularly the effects of UVB radiation on community structure and ecosystem function. Title: Ultraviolet radiation as an environmental stressor of amphibians Author: Bancroft, Betsy A. My thesis explored the effects of and potential mediating mechanisms for an important environmental stressor, ultraviolet-B (UVB) radiation. UVB radiation has negative effects on organisms in both terrestrial and aquatic systems. I used meta-analysis to quantify the effects of UVB radiation on a diversity of aquatic organisms (Chapter 2). UVB negatively affects aquatic organisms by reducing both survival and growth. In particular, UVB reduces growth of embryos more than any other life history stage. Some taxonomic groups may be more affected by UVB radiation than others. In our analysis, the growth of members of the kingdom Protozoa was suppressed by UVB radiation to a greater degree than any other kingdom. These analyses suggest that UVB is an important stressor in both freshwater and marine systems. Amphibians are a common component of freshwater systems and are experiencing world-wide population declines. These declines may be due to a number of causes including habitat loss, introduced species, global climate change, disease, toxic chemicals and UVB radiation. I used meta-analytic techniques to quantify the effects of UVB radiation on amphibians. By synthesizing the results of 41 articles on the effects of UVB radiation on amphibians (Chapter 3), I found a nearly 2-fold reduction in survival of amphibians exposed to UVB radiation. Salamanders (caudates) appear to be more susceptible to damage from UVB than frogs or toads (anurans). Moreover, survival of larvae was much lower than survival of embryos or metamorphic individuals under UVB radiation. In addition, I used factorial meta-analytic techniques to explore the interaction between UVB radiation and other stressors in amphibian habitats. UVB radiation acted synergistically with other stressors to reduce survival of amphibians. Behavioral avoidance of UVB radiation may help mediate the negative effects of UVB radiation on amphibians. In aquatic systems, behavioral avoidance usually requires movement out of shallow water, where UVB levels can be high, into deeper waters with lower UVB transmittance. However, these two microhabitats have very different thermal profiles, creating a trade-off between exploiting warm waters with high UVB levels and avoiding UVB by seeking cooler, deeper regions of ponds. I explored the microhabitat use of larvae of four species through a series of laboratory experiments, field experiments, and observational field transects at three different amphibian habitats (Chapter 4). Larvae did not avoid UVB radiation in either the laboratory or field experiments. Larvae in thermal gradients selected relatively high temperatures regardless of the UVB exposure at these temperatures. In field transects, salamander larvae were most common in deeper, cooler waters where UVB levels were lower. In contrast, anuran larvae were frequently observed in the warmer and shallower regions of each habitat. These regions also had the highest UVB levels, suggesting that anuran larvae are exposed to high levels of UVB due to thermoregulatory behavior. Behavioral avoidance of UVB radiation is not the only mechanism amphibians may use to prevent damage from UVB. Pigments such as melanin may allow larvae to exploit warm shallow waters by absorbing harmful UVB radiation before it causes cellular damage. I tested the efficacy of melanin as a photoprotective pigment in the larvae of two species, Rana cascadae and Pseudacris regilla (Chapter 5). I found no evidence of a photoprotective function for melanin in these larvae. In contrast, lighter colored tadpoles grew more under UVB radiation compared to darker colored tadpoles. Overall, exposure to UVB reduced survival of P. regilla larvae and reduced growth of R. cascadae larvae. Larvae of both of these species were frequently observed in very shallow water with intense solar radiation. This thesis emphasizes the importance of UVB radiation as an environmental stressor in aquatic habitats. Many aquatic organisms are negatively affected by UVB exposure. My thesis work quantitatively demonstrated that UVB radiation is one factor that reduces survival of amphibians and suggests that some species are exposed to high levels of UVB radiation in natural habitats. While UVB radiation is not the sole cause of amphibian population declines, my work suggests that UVB radiation is an important stressor for amphibians that should not be overlooked. In addition, UVB radiation is clearly an important stressor for many other aquatic organisms. Future work should consider the effects of UVB in aquatic systems, particularly the effects of UVB radiation on community structure and ecosystem function. Close