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• 1. [Article] Mosby Creek Limiting Factors Analysis and Restoration Plan

  Abstract -- The Mosby Creek Limiting Factors Analysis (Rapid Bio-Assessment) assessed stream conditions for native salmonids and prioritized projects of benefit to spring Chinook, cutthroat trout, rainbow ...

  Citation × Citation Citation Abstract Copy Title: Mosby Creek Limiting Factors Analysis and Restoration Plan Abstract -- The Mosby Creek Limiting Factors Analysis (Rapid Bio-Assessment) assessed stream conditions for native salmonids and prioritized projects of benefit to spring Chinook, cutthroat trout, rainbow trout, and Pacific lamprey in this high-priority, free-flowing stream in the Coast Fork Willamette Watershed. To gain access to private properties adjacent to the 75 miles of surveyed streams, the applicant conducted landowner outreach and coordinated two years of continuous temperature data collection by volunteers. The contractor conducted a modified limiting factors analysis and a snorkel survey in the Mosby Creek main stem and tributaries up to 6 percent gradient. The resulting study results include a prioritized restoration plan that has been shared with local landowners and restoration partners and used for restoration planning. Title: Mosby Creek Limiting Factors Analysis and Restoration Plan Abstract -- The Mosby Creek Limiting Factors Analysis (Rapid Bio-Assessment) assessed stream conditions for native salmonids and prioritized projects of benefit to spring Chinook, cutthroat trout, rainbow trout, and Pacific lamprey in this high-priority, free-flowing stream in the Coast Fork Willamette Watershed. To gain access to private properties adjacent to the 75 miles of surveyed streams, the applicant conducted landowner outreach and coordinated two years of continuous temperature data collection by volunteers. The contractor conducted a modified limiting factors analysis and a snorkel survey in the Mosby Creek main stem and tributaries up to 6 percent gradient. The resulting study results include a prioritized restoration plan that has been shared with local landowners and restoration partners and used for restoration planning. Close

• 2. [Article] An Evaluation of the Nontarget Effects of Transgenic Bacillus thuringiensis Maize on Arbuscular Mycorrhizal Fungi in the Soil Ecosystem

  My dissertation research examined the effect of the cultivation of insect-resistant Bacillus thuringiensis (Bt) maize on the soil environment with a goal of understanding how to obtain a balance between ...

  Citation × Citation Citation Abstract Copy Title: An Evaluation of the Nontarget Effects of Transgenic Bacillus thuringiensis Maize on Arbuscular Mycorrhizal Fungi in the Soil Ecosystem Author: Cheeke, Tanya Elizabeth Amy Year: 2013 My dissertation research examined the effect of the cultivation of insect-resistant Bacillus thuringiensis (Bt) maize on the soil environment with a goal of understanding how to obtain a balance between technological advancement and maintenance of a healthy soil ecosystem. Although Bt plants may help to reduce pesticide use, conferring benefits to farm workers and the environment, there are still unresolved questions about how the cultivation of Bt plants affects soil organisms. For this dissertation project, I used 14 different genotypes of Bt maize and non-Bt maize (Zea mays) to investigate the effects of transgenic Bt plants on the colonization ability, abundance, and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) in the soil ecosystem over time. My greenhouse studies demonstrated that Bt maize plants exhibited reduced AMF colonization across multiple Bt genotypes and that effects were most pronounced when fertilizer levels were limited and spore density was high. In addition, I found that although differences in AMF colonization between Bt and non-Bt maize were difficult to detect in the field, spore density was reduced in Bt field plots after just one growing season. When I tested the effect of plot history on AMF and plant growth, I found that Bt and non-Bt maize plants had higher leaf chlorophyll content when grown in plots previously cultivated with the same maize line as the previous year, indicative of a positive feedback effect. I also examined potential mechanisms contributing to the reduced AMF colonization observed in Bt maize in greenhouse studies and determined that follow-up experiments should continue to investigate differences in root apoplastic invertase activity and root permeability in Bt and non-Bt maize. Future investigations would also benefit from examining potential differences in root exudate profiles and volatile organic compounds between Bt and non-Bt cultivars. Taken together, my dissertation results suggest that, while difficult to detect in the field, reductions in AMF colonization in Bt maize roots may be ecologically significant as they could lead to a decrease in the abundance of AMF propagules in the soil over time, potentially impacting soil structure and function in areas where Bt crop cultivation is high. Title: An Evaluation of the Nontarget Effects of Transgenic Bacillus thuringiensis Maize on Arbuscular Mycorrhizal Fungi in the Soil Ecosystem Author: Cheeke, Tanya Elizabeth Amy Year: 2013 My dissertation research examined the effect of the cultivation of insect-resistant Bacillus thuringiensis (Bt) maize on the soil environment with a goal of understanding how to obtain a balance between technological advancement and maintenance of a healthy soil ecosystem. Although Bt plants may help to reduce pesticide use, conferring benefits to farm workers and the environment, there are still unresolved questions about how the cultivation of Bt plants affects soil organisms. For this dissertation project, I used 14 different genotypes of Bt maize and non-Bt maize (Zea mays) to investigate the effects of transgenic Bt plants on the colonization ability, abundance, and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) in the soil ecosystem over time. My greenhouse studies demonstrated that Bt maize plants exhibited reduced AMF colonization across multiple Bt genotypes and that effects were most pronounced when fertilizer levels were limited and spore density was high. In addition, I found that although differences in AMF colonization between Bt and non-Bt maize were difficult to detect in the field, spore density was reduced in Bt field plots after just one growing season. When I tested the effect of plot history on AMF and plant growth, I found that Bt and non-Bt maize plants had higher leaf chlorophyll content when grown in plots previously cultivated with the same maize line as the previous year, indicative of a positive feedback effect. I also examined potential mechanisms contributing to the reduced AMF colonization observed in Bt maize in greenhouse studies and determined that follow-up experiments should continue to investigate differences in root apoplastic invertase activity and root permeability in Bt and non-Bt maize. Future investigations would also benefit from examining potential differences in root exudate profiles and volatile organic compounds between Bt and non-Bt cultivars. Taken together, my dissertation results suggest that, while difficult to detect in the field, reductions in AMF colonization in Bt maize roots may be ecologically significant as they could lead to a decrease in the abundance of AMF propagules in the soil over time, potentially impacting soil structure and function in areas where Bt crop cultivation is high. Close

• 3. [Article] The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations

  Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number ...

  Citation × Citation Citation Abstract Copy Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Title: The Response of Zooplankton Communities in Montane Lakes of Different Fish Stocking Histories to Atmospheric Nitrogen Deposition Simulations Author: Brittain, Jeffrey Thomas Year: 2015 Freshwater ecosystems are subject to a wide variety of stressors, which can have complex interactions and result in ecological surprises. Non-native fish introductions have drastically reduced the number of naturally fishless lakes and have resulted in cascading food web repercussions in aquatic and terrestrial habitats. Additional anthropogenic influences that result from increases in global airborne emissions also threaten wildlife habitat. Atmospheric nitrogen deposition has been recognized as an anthropogenic contributor to acidification and eutrophication of wilderness ecosystems. Planktonic communities have shown declines in response to predation and shifts in composition as a result of nutrient inputs and acidification, both of which are potential fates of nitrogen deposition. This study identified the response of zooplankton communities from two lakes (fish present vs. absent) in Mount Rainier National Park to manipulations simulating an episodic disturbance event in mesocosms. The experiment used a 2 x 2 factorial design with acid and nitrogen treatments. Treatments resulted in significantly elevated nitrogen and decreased pH conditions from control mesocosms over 42 days, indicating that the treatment effects were achieved. Results indicate that zooplankton communities from lakes with different food web structure respond differently to the singular effects of acid and nitrogen addition. Surprisingly, the interaction of the two stressors was related to increases in community metrics (e.g., abundance, biomass, body size, richness, and Shannon-Weiner diversity) for both lake types. This work can aid management decisions as agencies look to restore more aquatic montane habitats to their historic fishless states, and assess their abilities to recover and afford resistance to atmospheric pollution. Close

• 4. [Article] The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem

  Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of ...

  Citation × Citation Citation Abstract Copy Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Title: The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem Author: Diemer, Geoffrey Scott Year: 2014 Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere. Close

• 5. [Article] Interactions Among Fuel Management, Species Composition, Bark Beetles, and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin

  Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their ...

  Citation × Citation Citation Abstract Copy Title: Interactions Among Fuel Management, Species Composition, Bark Beetles, and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin Author: Scheller, Robert M., Kretchun, Alec M., Loudermilk, E. Louise, Hurteau, Matthew D., Weisberg, Peter J., Skinner, Carl Year: 2017 Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their long-term interactions with future climate change are poorly understood. Droughts and the associated moisture deficit contribute to the onset of bark beetle outbreaks although outbreak extent and severity is dependent upon the density of host trees, wildfire, and forest management. Our objective was to estimate the effects of climate change and bark beetle outbreaks on ecosystem carbon dynamics over the next century in a western US forest. Specifically, we hypothesized that (a) bark beetle outbreaks under climate change would reduce net ecosystem carbon balance (NECB) and increase uncertainty and (b) these effects could be ameliorated by fuels management. We also examined the specific tree species dynamics—competition and release—that determined NECB response to bark beetle outbreaks. Our study area was the Lake Tahoe Basin (LTB), CA and NV, USA, an area of diverse forest types encompassing steep elevation and climatic gradients and representative of mixed-conifer forests throughout the western United States. We simulated climate change, bark beetles, wildfire, and fuels management using a landscape-scale stochastic model of disturbance and succession. We simulated the period 2010–2100 using downscaled climate projections. Recurring droughts generated conditions conducive to large-scale outbreaks; the resulting large and sustained outbreaks significantly increased the probability of LTB forests becoming C sources over decadal time scales, with slower-than-anticipated landscape-scale recovery. Tree species composition was substantially altered with a reduction in functional redundancy and productivity. Results indicate heightened uncertainty due to the synergistic influences of climate change and interacting disturbances. Our results further indicate that current fuel management practices will not be effective at reducing landscape-scale outbreak mortality. Our results provide critical insights into the interaction of drivers (bark beetles, wildfire, fuel management) that increase the risk of C loss and shifting community composition if bark beetle outbreaks become more frequent. Title: Interactions Among Fuel Management, Species Composition, Bark Beetles, and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin Author: Scheller, Robert M., Kretchun, Alec M., Loudermilk, E. Louise, Hurteau, Matthew D., Weisberg, Peter J., Skinner, Carl Year: 2017 Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their long-term interactions with future climate change are poorly understood. Droughts and the associated moisture deficit contribute to the onset of bark beetle outbreaks although outbreak extent and severity is dependent upon the density of host trees, wildfire, and forest management. Our objective was to estimate the effects of climate change and bark beetle outbreaks on ecosystem carbon dynamics over the next century in a western US forest. Specifically, we hypothesized that (a) bark beetle outbreaks under climate change would reduce net ecosystem carbon balance (NECB) and increase uncertainty and (b) these effects could be ameliorated by fuels management. We also examined the specific tree species dynamics—competition and release—that determined NECB response to bark beetle outbreaks. Our study area was the Lake Tahoe Basin (LTB), CA and NV, USA, an area of diverse forest types encompassing steep elevation and climatic gradients and representative of mixed-conifer forests throughout the western United States. We simulated climate change, bark beetles, wildfire, and fuels management using a landscape-scale stochastic model of disturbance and succession. We simulated the period 2010–2100 using downscaled climate projections. Recurring droughts generated conditions conducive to large-scale outbreaks; the resulting large and sustained outbreaks significantly increased the probability of LTB forests becoming C sources over decadal time scales, with slower-than-anticipated landscape-scale recovery. Tree species composition was substantially altered with a reduction in functional redundancy and productivity. Results indicate heightened uncertainty due to the synergistic influences of climate change and interacting disturbances. Our results further indicate that current fuel management practices will not be effective at reducing landscape-scale outbreak mortality. Our results provide critical insights into the interaction of drivers (bark beetles, wildfire, fuel management) that increase the risk of C loss and shifting community composition if bark beetle outbreaks become more frequent. Close

• 6. [Article] PCR-Activated Cell Sorting as a General, Cultivation-Free Method for High-Throughput Identification and Enrichment of Virus Hosts

  Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present ...

  Citation × Citation Citation Abstract Copy Title: PCR-Activated Cell Sorting as a General, Cultivation-Free Method for High-Throughput Identification and Enrichment of Virus Hosts Author: Lim, Shaun W., Lance, Shea T., Stedman, Kenneth M., Abate, Adam R. Year: 2017 Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages by modifying the PCR primers used for detection. Moreover, this technique allows quantification of free phage particles, as benchmarked against the “gold standard” of virus enumeration, the plaque assay. Title: PCR-Activated Cell Sorting as a General, Cultivation-Free Method for High-Throughput Identification and Enrichment of Virus Hosts Author: Lim, Shaun W., Lance, Shea T., Stedman, Kenneth M., Abate, Adam R. Year: 2017 Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed. This allows targeted recovery of all possible host species in a diverse population associated with a specific phage, and can be easily targeted to identify the hosts of different phages by modifying the PCR primers used for detection. Moreover, this technique allows quantification of free phage particles, as benchmarked against the “gold standard” of virus enumeration, the plaque assay. Close

• 7. [Article] Disequilibrium of Fire-prone Forests Sets the Stage for a Rapid Decline in Conifer Dominance during the 21st Century

  As trees are long-lived organisms, the impacts of climate change on forest communities may not be apparent on the time scale of years to decades. While lagged responses to environmental change are common ...

  Citation × Citation Citation Abstract Copy Title: Disequilibrium of Fire-prone Forests Sets the Stage for a Rapid Decline in Conifer Dominance during the 21st Century Author: Serra-Diaz, Josep M., Maxwell, Charles, Lucash, Melissa S., Scheller, Robert M., Laflower, Danelle M., Miller, Adam D., Tepley, Alan J., Epstein, Howard E., Anderson-Teixeira, Kristina J., Thompson, Jonathan R. Year: 2017 As trees are long-lived organisms, the impacts of climate change on forest communities may not be apparent on the time scale of years to decades. While lagged responses to environmental change are common in forested systems, potential for abrupt transitions under climate change may occur in environments where alternative vegetation states are influenced by disturbances, such as fire. The Klamath mountains (northern California and southwest Oregon, USA) are currently dominated by carbon rich and hyper-diverse temperate conifer forests, but climate change could disrupt the mechanisms promoting forest stability– regeneration and fire tolerance— via shifts in the fire regime in conjunction with lower fitness of conifers under a hotter climate. Understanding how this landscape will respond to near-term climate change (before 2100) is critical for predicting potential climate change feedbacks and to developing sound forest conservation and management plans. Using a landscape simulation model, we estimate that 1/3 of the Klamath could transition from conifer forest to shrub/hardwood chaparral, triggered by an enhanced fire activity coupled with lower post-fire conifer establishment. Such shifts were more prevalent under higher climate change forcing (RCP 8.5) but were also simulated under the climate of 1950-2000, reflecting the joint influences of early warming trends and historical forest legacies. Our results demonstrate that there is a large potential for loss of conifer forest dominance—and associated carbon stocks and biodiversity-- in the Klamath before the end of the century, and that some losses would likely occur even without the influence of climate change. Thus, in the Klamath and other forested landscapes subject to similar feedback dynamics, major ecosystem shifts should be expected when climate change disrupts key stabilizing feedbacks that maintain the dominance of long-lived, slowly regenerating trees. Title: Disequilibrium of Fire-prone Forests Sets the Stage for a Rapid Decline in Conifer Dominance during the 21st Century Author: Serra-Diaz, Josep M., Maxwell, Charles, Lucash, Melissa S., Scheller, Robert M., Laflower, Danelle M., Miller, Adam D., Tepley, Alan J., Epstein, Howard E., Anderson-Teixeira, Kristina J., Thompson, Jonathan R. Year: 2017 As trees are long-lived organisms, the impacts of climate change on forest communities may not be apparent on the time scale of years to decades. While lagged responses to environmental change are common in forested systems, potential for abrupt transitions under climate change may occur in environments where alternative vegetation states are influenced by disturbances, such as fire. The Klamath mountains (northern California and southwest Oregon, USA) are currently dominated by carbon rich and hyper-diverse temperate conifer forests, but climate change could disrupt the mechanisms promoting forest stability– regeneration and fire tolerance— via shifts in the fire regime in conjunction with lower fitness of conifers under a hotter climate. Understanding how this landscape will respond to near-term climate change (before 2100) is critical for predicting potential climate change feedbacks and to developing sound forest conservation and management plans. Using a landscape simulation model, we estimate that 1/3 of the Klamath could transition from conifer forest to shrub/hardwood chaparral, triggered by an enhanced fire activity coupled with lower post-fire conifer establishment. Such shifts were more prevalent under higher climate change forcing (RCP 8.5) but were also simulated under the climate of 1950-2000, reflecting the joint influences of early warming trends and historical forest legacies. Our results demonstrate that there is a large potential for loss of conifer forest dominance—and associated carbon stocks and biodiversity-- in the Klamath before the end of the century, and that some losses would likely occur even without the influence of climate change. Thus, in the Klamath and other forested landscapes subject to similar feedback dynamics, major ecosystem shifts should be expected when climate change disrupts key stabilizing feedbacks that maintain the dominance of long-lived, slowly regenerating trees. Close

• 8. [Article] The Interplay Between Landscape Structure and Biotic Interactions

  Landscape structure and biotic interactions are closely linked. We identify five aspects of landscape structure that contribute to the co-occurrence of species and restrict or enable different types of ...

  Citation × Citation Citation Abstract Copy Title: The Interplay Between Landscape Structure and Biotic Interactions Author: Zarnetske, Phoebe, Baiser, Benjamin, Strecker, Angela L., Record, Sydne, Belmaker, Jonathan, Tuanmu, Mao-Ning Year: 2017 Landscape structure and biotic interactions are closely linked. We identify five aspects of landscape structure that contribute to the co-occurrence of species and restrict or enable different types of biotic interactions: patch size and habitat amount, isolation of patches, barriers to dispersal and movement, persistence of landscape structure, and landscape complexity. In addition, these aspects of landscape structure influence the strength and outcome of biotic interactions. Whereas most research focuses on the effects of the abiotic environment on species and their biotic interactions, research on foundation species and ecosystem engineers demonstrates the important influence of biotic interactions on landscape structure itself, including effects on landscape complexity, extent of habitat, and the structure of landscape features. In this review, we describe ecological theories that lay the foundation for interplay between landscape structure and biotic interactions, and summarize these connections across an array of interacting species in freshwater, marine, and terrestrial systems. We end with suggestions for integrating the fields of landscape ecology and community ecology to better understand the connections between landscape structure and biotic interactions and better predict their dynamics in light of global change. Title: The Interplay Between Landscape Structure and Biotic Interactions Author: Zarnetske, Phoebe, Baiser, Benjamin, Strecker, Angela L., Record, Sydne, Belmaker, Jonathan, Tuanmu, Mao-Ning Year: 2017 Landscape structure and biotic interactions are closely linked. We identify five aspects of landscape structure that contribute to the co-occurrence of species and restrict or enable different types of biotic interactions: patch size and habitat amount, isolation of patches, barriers to dispersal and movement, persistence of landscape structure, and landscape complexity. In addition, these aspects of landscape structure influence the strength and outcome of biotic interactions. Whereas most research focuses on the effects of the abiotic environment on species and their biotic interactions, research on foundation species and ecosystem engineers demonstrates the important influence of biotic interactions on landscape structure itself, including effects on landscape complexity, extent of habitat, and the structure of landscape features. In this review, we describe ecological theories that lay the foundation for interplay between landscape structure and biotic interactions, and summarize these connections across an array of interacting species in freshwater, marine, and terrestrial systems. We end with suggestions for integrating the fields of landscape ecology and community ecology to better understand the connections between landscape structure and biotic interactions and better predict their dynamics in light of global change. Close

• 9. [Article] Testing the Ecological and Physiological Factors Influencing Reproductive Success in Mosses

  As non-vascular, early land plants with an aquatic ancestry, mosses do not regulate internal water conditions separate from that of their environment and as a result, evolved mechanisms to survive in a ...

  Citation × Citation Citation Abstract Copy Title: Testing the Ecological and Physiological Factors Influencing Reproductive Success in Mosses Author: Shortlidge, Erin Elizabeth Year: 2014 As non-vascular, early land plants with an aquatic ancestry, mosses do not regulate internal water conditions separate from that of their environment and as a result, evolved mechanisms to survive in a terrestrial world out of water. Yet, there is a widely accepted dogma that moss reproductive success is solely dependent on rainfall events carrying swimming, bi-flagellate sperm across the landscape to reproductively mature and receptive female mosses--but this classic view of moss reproduction may be too simplistic. In this dissertation I test the assumptions of reproductive limitation in mosses and present novel findings in a basal, yet understudied terrestrial plant mating system. I find evidence of environmental desiccation tolerance in moss sperm, thus offering the potential for stress-tolerant gametes on the landscape possibly suited for various transport vectors, reminiscent of a pollen grain. To investigate the broad evolutionary implications of this newfound complexity in moss sexual reproduction, I tested classic tenets of plant-pollinator theory on the ancient mosses and their ubiquitous microarthropod inhabitants. Experimental results show that mosses and microarthropods are engaged in a "pollination-like" syndrome guided by sex-specific volatile cues that differentially affect microarthropod behavior. These data indicate an existing complex mutualistic relationship and provides new evidence of sexually dimorphic investment by male and female mosses into reproductive success. Further, these data put forth the idea that female mosses challenge an inherent mate limitation by investing into reproductive assurance via maintaining a relationship with microarthropods. Experimental work further confirms a role for invertebrates in moss reproductive success and tests mutualism theory through ongoing experiments. Such experiments include an assessment of moss genetic diversity, paternity, and male fitness traits as it relates to mosses with or without the presence of microarthropods, thereby testing for fitness benefits gained by mosses possibly engaged in a transport mutualism with microarthropods. I further tested mutualism, community ecology and moss sexual reproduction concepts in extreme geothermal moss populations living at the edges of inhabitable Earth, and results show that even geothermal moss canopies are diverse and host differential and abundant life. In a first field test of mutualism I found that although extreme heat stress may constrain sexual reproduction in mosses, a correlation between within-population moss genetic diversity and microarthropod abundances exists. To further examine mosses in extreme environments, and how these environments may constrain sexual reproductive success, I evaluated the effects of simulated warming on Antarctic moss physiology and reproductive biology. Data indicates that simulated warming relieves mosses of physiological stress, and results in a greater investment into primary productivity and sexual reproduction. These data support the hypothesis that with less stress, sexual reproduction is increased. Mosses are an ideal system by which to understand organisms that exist in environments ranging from the mesic to the extreme, in the laboratory and the field and even in the classroom, where the small functioning ecosystem of mosses can be used for discovery-based biology education as described in the Mosscosms curriculum. This work contributes significantly to the field of bryophyte and plant biology by revealing novel insights into the biotic and abiotic drivers of sexual reproduction in mosses. Title: Testing the Ecological and Physiological Factors Influencing Reproductive Success in Mosses Author: Shortlidge, Erin Elizabeth Year: 2014 As non-vascular, early land plants with an aquatic ancestry, mosses do not regulate internal water conditions separate from that of their environment and as a result, evolved mechanisms to survive in a terrestrial world out of water. Yet, there is a widely accepted dogma that moss reproductive success is solely dependent on rainfall events carrying swimming, bi-flagellate sperm across the landscape to reproductively mature and receptive female mosses--but this classic view of moss reproduction may be too simplistic. In this dissertation I test the assumptions of reproductive limitation in mosses and present novel findings in a basal, yet understudied terrestrial plant mating system. I find evidence of environmental desiccation tolerance in moss sperm, thus offering the potential for stress-tolerant gametes on the landscape possibly suited for various transport vectors, reminiscent of a pollen grain. To investigate the broad evolutionary implications of this newfound complexity in moss sexual reproduction, I tested classic tenets of plant-pollinator theory on the ancient mosses and their ubiquitous microarthropod inhabitants. Experimental results show that mosses and microarthropods are engaged in a "pollination-like" syndrome guided by sex-specific volatile cues that differentially affect microarthropod behavior. These data indicate an existing complex mutualistic relationship and provides new evidence of sexually dimorphic investment by male and female mosses into reproductive success. Further, these data put forth the idea that female mosses challenge an inherent mate limitation by investing into reproductive assurance via maintaining a relationship with microarthropods. Experimental work further confirms a role for invertebrates in moss reproductive success and tests mutualism theory through ongoing experiments. Such experiments include an assessment of moss genetic diversity, paternity, and male fitness traits as it relates to mosses with or without the presence of microarthropods, thereby testing for fitness benefits gained by mosses possibly engaged in a transport mutualism with microarthropods. I further tested mutualism, community ecology and moss sexual reproduction concepts in extreme geothermal moss populations living at the edges of inhabitable Earth, and results show that even geothermal moss canopies are diverse and host differential and abundant life. In a first field test of mutualism I found that although extreme heat stress may constrain sexual reproduction in mosses, a correlation between within-population moss genetic diversity and microarthropod abundances exists. To further examine mosses in extreme environments, and how these environments may constrain sexual reproductive success, I evaluated the effects of simulated warming on Antarctic moss physiology and reproductive biology. Data indicates that simulated warming relieves mosses of physiological stress, and results in a greater investment into primary productivity and sexual reproduction. These data support the hypothesis that with less stress, sexual reproduction is increased. Mosses are an ideal system by which to understand organisms that exist in environments ranging from the mesic to the extreme, in the laboratory and the field and even in the classroom, where the small functioning ecosystem of mosses can be used for discovery-based biology education as described in the Mosscosms curriculum. This work contributes significantly to the field of bryophyte and plant biology by revealing novel insights into the biotic and abiotic drivers of sexual reproduction in mosses. Close

• 10. [Article] Field Evaluation of Arbuscular Mycorrhizal Fungal Colonization in Bacillus thuringiensis Toxin-Expressing (Bt) and Non-Bt Maize

  The cultivation of genetically engineered Bacillus thuringiensis toxin-expressing (Bt) maize continues to increase worldwide, yet the effects of Bt crops on arbuscular mycorrhizal fungi (AMF) in soil are ...

  Citation × Citation Citation Abstract Copy Title: Field Evaluation of Arbuscular Mycorrhizal Fungal Colonization in Bacillus thuringiensis Toxin-Expressing (Bt) and Non-Bt Maize Author: Cheeke, Tanya E., Cruzan, Mitchell B., Rosenstiel, Todd N. Year: 2013 The cultivation of genetically engineered Bacillus thuringiensis toxin-expressing (Bt) maize continues to increase worldwide, yet the effects of Bt crops on arbuscular mycorrhizal fungi (AMF) in soil are poorly understood. In this field experiment, we investigated the impact of seven different genotypes of Bt maize and five corresponding non-Bt parental cultivars on AMF and evaluated plant growth responses at three different physiological time points. Plants were harvested 60 days (active growth), 90 days (tasseling and starting to produce ears), and 130 days (maturity) after sowing, and data on plant growth responses and percent AMF colonization of roots at each harvest were collected. Spore abundance and diversity were also evaluated at the beginning and end of the field season to determine whether the cultivation of Bt maize had a negative effect on AMF propagules in the soil. Plant growth and AMF colonization did not differ between Bt and non-Bt maize at any harvest period, but AMF colonization was positively correlated with leaf chlorophyll content at the 130-day harvest. Cultivation of Bt maize had no effect on spore abundance and diversity in Bt versus non-Bt plots over one field season. Plot had the most significant effect on total spore counts, indicating spatial heterogeneity in the field. Although previous greenhouse studies demonstrated that AMF colonization was lower in some Bt maize lines, our field study did not yield the same results, suggesting that the cultivation of Bt maize may not have an impact on AMF in the soil ecosystem under field conditions. Title: Field Evaluation of Arbuscular Mycorrhizal Fungal Colonization in Bacillus thuringiensis Toxin-Expressing (Bt) and Non-Bt Maize Author: Cheeke, Tanya E., Cruzan, Mitchell B., Rosenstiel, Todd N. Year: 2013 The cultivation of genetically engineered Bacillus thuringiensis toxin-expressing (Bt) maize continues to increase worldwide, yet the effects of Bt crops on arbuscular mycorrhizal fungi (AMF) in soil are poorly understood. In this field experiment, we investigated the impact of seven different genotypes of Bt maize and five corresponding non-Bt parental cultivars on AMF and evaluated plant growth responses at three different physiological time points. Plants were harvested 60 days (active growth), 90 days (tasseling and starting to produce ears), and 130 days (maturity) after sowing, and data on plant growth responses and percent AMF colonization of roots at each harvest were collected. Spore abundance and diversity were also evaluated at the beginning and end of the field season to determine whether the cultivation of Bt maize had a negative effect on AMF propagules in the soil. Plant growth and AMF colonization did not differ between Bt and non-Bt maize at any harvest period, but AMF colonization was positively correlated with leaf chlorophyll content at the 130-day harvest. Cultivation of Bt maize had no effect on spore abundance and diversity in Bt versus non-Bt plots over one field season. Plot had the most significant effect on total spore counts, indicating spatial heterogeneity in the field. Although previous greenhouse studies demonstrated that AMF colonization was lower in some Bt maize lines, our field study did not yield the same results, suggesting that the cultivation of Bt maize may not have an impact on AMF in the soil ecosystem under field conditions. Close