Theses and Dissertations

Permanent URI for this collectionhttps://hdl.handle.net/10217/100398

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Changes in functional structure of aquatic insect communities across environmental gradients in mountain streams
(Colorado State University. Libraries, 2024) Gutierrez, Carolina, author; Poff, N. LeRoy, advisor; Ghalambor, Cameron, advisor; Neuwald, Jennifer, committee member; Webb, Colleen, committee member
This study investigates the functional diversity of aquatic insect communities across environmental gradients within Rocky Mountain headwater streams, aiming to better understand how elevation, water temperature, and canopy cover shape the structure and dynamics of these communities. Functional diversity (FD) is defined here as the range, distribution, and relative abundance of organismal traits, which together provide deeper insight into ecosystem functionality than species diversity alone. FD was quantified through three primary metrics: functional richness (FRic), functional evenness (FEve), and functional divergence (FDiv), each capturing distinct aspects of how species contribute to ecosystem functioning. This multidimensional approach enables a nuanced examination of how aquatic insect communities respond to various environmental stressors and spatial constraints, particularly as altitudinal changes present unique challenges in terms of temperature variability and resource availability. Field data were collected from twenty-four stream sites distributed across elevation bands ranging from 1,500 to 3,500 meters. Sites were replicated in three different drainage systems to account for regional variation, with insect specimens collected and assessed for twenty functional traits. These traits included parameters such as voltinism (number of life cycles per year), adult lifespan, emergence synchronization, and dispersal ability, all of which are critical in determining an insect's role in the ecosystem. Canopy cover and water temperature were also measured to evaluate how localized microclimates and light availability influenced community composition. Results revealed a significant decline in functional richness with increasing elevation, with the steepest reductions observed in streams with sparse canopy cover. Functional richness was highest in areas where canopy cover ranged between 65-78%, and water temperature was between 8°C and 15°C, suggesting that moderate canopy cover and specific thermal conditions support more functionally diverse communities. Functional evenness and divergence, while showing less pronounced patterns, indicated that the most extreme trait values are critical for resilience in these systems, particularly under fluctuating environmental conditions. Trophic interactions further illustrate the importance of specific functional groups, such as predators, grazers, and filterers, in shaping community structure. The analysis of beta diversity demonstrated substantial turnover in functional traits across elevation gradients, emphasizing the heterogeneity of insect communities within low-order, high-altitude streams and reinforcing the role of environmental filtering in community assembly. These findings highlight the vulnerability of headwater stream ecosystems to environmental changes and underscore the importance of functional diversity metrics in ecological monitoring and conservation efforts. Overall, this study contributes to our understanding of how functional environmental gradients structure diversity and provides a foundation for comparative studies on functional diversity in tropical versus temperate mountain stream ecosystems, particularly in the context of global biodiversity conservation.
Open Access
Investigating the adaptive genetic landscape of global crop species
(Colorado State University. Libraries, 2024) Hein, Kirsten Marie, author; McKay, John, advisor; Morris, Geoffrey, committee member; Ross-Ibarra, Jeffrey, committee member; Schipanski, Meagan, committee member
Improving environmental adaptation in crops is essential for sustaining food security in the face of global climate change. Recent advances in high-throughput genomic sequencing and phenotyping technologies have enabled researchers to identify and validate the genetic factors shaping adaptation. In this dissertation, I investigated the genetic basis of environmental adaptation in global cereal crops, focusing on the staple crop, maize (Zea mays L.), and the orphan crop, tef (Eragrostis tef Zucc.). In Chapter 2, I employed a landscape genomics approach to identify the genetic and environmental drivers of adaptation in a georeferenced collection of Ethiopian tef. In Chapter 3, I utilized both forward and reverse genetic approaches to evaluate the precision of phenotype-genotype mapping across multiple phenotyping methods for quantifying root system architecture in field-excavated maize. In Chapter 4, I applied a functional genetics approach to characterize a novel gene model in maize predicted to regulate root system development and nitrogen capture under field conditions. Collectively, this work provides valuable insights into the complex relationships between phenotype, genotype, and environment, contributing to our understanding of adaptation in two distinct and vital crop systems.
Open Access
Crop domestication impacts on rhizosphere interactions and nitrogen acquisition
(Colorado State University. Libraries, 2024) Hwang, Siwook, author; Fonte, Steven J., advisor; Machmuller, Megan B., committee member; Crews, Timothy E., committee member; Wrighton, Kelly C., committee member; Boot, Claudia M., committee member
Synthetic nitrogen (N) fertilizer is an essential pillar of modern industrial agriculture. Production and application of synthetic N fertilizer, however, are two of the most expensive, energy intensive, and environmentally deleterious processes in agriculture. Therefore, alternative means of providing N in an agroecosystem are of great interest in sustainable agriculture. While many solutions – from cover cropping to intercropping – have been suggested over time it remains unclear if the modern high-yielding crops can thrive in these alternative N conditions. Decades of breeding under high synthetic N input as well as the inherently annual nature of these modern cereal crops may prevent them from fully taking advantage of these alternative N sources. In this dissertation, I explored the impact of domestication on crop rhizosphere interactions and N acquisition, in both retrospective and prospective terms. First, I investigated how modern maize (Zea mays subsp. mays), and its wild relative Teosinte (Zea mays subsp. parviglumis) differed in their ability to adapt to, and take up, cover crop residue N and synthetic N inputs. We designed a 13C (carbon)/15N dual isotope labeling experiment in which we compared the C allocation patterns of modern maize and teosinte in response to synthetic (urea) and organic (cover crop residue) forms of N. Teosinte responded to organic N by increasing its biomass root-to-shoot (R:S) ratio by 50% compared to synthetic N, while modern maize maintained the same biomass R:S ratios in both N treatments. Recent photosynthate R:S ratio (measured using 13C-CO2, 7 weeks after establishment) was greater in organic N than in synthetic N treatments for both modern maize and teosinte (91% and 37%; respectively). Label-derived dissolved organic C (DOC), representing recent rhizodeposits, was 2.5 times greater in the organic N treatments for both genotypes. Modern maize took up a similar amount of organic N as teosinte using different C allocation strategies. Our findings suggest that intensive breeding under high N input conditions has not affected this modern maize hybrid's access to organic N sources while improving its ability to take up synthetic N. Next, I shifted my focus to the novel perennial grains Kernza and perennial wheat. Kernza® is a domesticated intermediate wheatgrass (IWG, Thinopyrum intermedium). Perennial wheat is a hybrid between Kernza/IWG and modern annual durum wheat (Triticum turgidum subsp. durum). Kernza, in addition to being a perennial, may still possess beneficial belowground traits that may have been lost in modern cereals through millennia of aboveground-focused plant breeding. If so, such traits may be passed down to perennial wheat. To characterize root architecture, exudate profiles, and microbial communities of Kernza and perennial wheat in relation to annual wheat, I conducted a greenhouse experiment. We grew three genotypes/species (Kernza, perennial wheat, annual wheat) and collected their root exudates after 8 weeks of growth. The exudates were analyzed via LC-MS/MS for their chemical composition. We extracted DNA from rhizosphere soils and sequenced them for 16S and ITS profiles. Lastly, we scanned the roots to analyze root distribution across different diameter classes. We found that perennial wheat invested more heavily into very fine (< 250 µm) roots compared to annual wheat and Kernza. Perennial wheat also exuded at a greater rate of exudates per amount of root biomass. We suspect that the greater proportion of very fine roots in perennial wheat led to greater surface area and greater specific exudation rate, and that this may be related to hybrid vigor. We did not find evidence of a genotype effect on root exudate or microbial community composition. However, root exudates (overall metabolite profiles) significantly correlated with root architecture (distribution of root volume over different diameter classes) and the microbial community composition. These interactions represent a potential pathway through which plants can exert influence over the rhizosphere microbial community. Overall, these results emphasize the importance of root architecture in mediating belowground interactions. Understanding rhizosphere dynamics and the response to domestication and hybridization can guide further development of robust perennial cereal crops. In a third experiment, I studied how Kernza, perennial wheat, and annual responded to cereal-legume intercropping (biculture) in the field. To do so, we planted each of the three genotypes in monoculture or in biculture with alfalfa (Medicago sativa). We sampled their rhizosphere over two growing seasons and extracted soil DNA to construct rhizosphere 16S and ITS profiles. We hypothesized that 1) rhizosphere microbial community composition of annual wheat and Kernza will be most dissimilar from each other with perennial wheat intermediate, and 2) microbial community composition will shift in biculture, with the greatest change in Kernza and the smallest in annual wheat. We found that the rhizosphere 16S profiles differed significantly from the other two genotypes but the 16S profile of perennial wheat did not differ from that of annual wheat. Perennial wheat seemingly inherited microbial recruitment traits of its annual parent more so than its perennial parent's. Interestingly, inclusion of legumes led to the convergence, rather than divergence, of 16S profiles among genotypes. We postulate that the competitive pressure of alfalfa may have led to this convergence of 16S profiles across genotypes. The fungal community did not show evidence of genotype effect. However, the fungal community composition changed over two years in monoculture but not in biculture. This result implies that fungal community may become distinct over time if it is influenced by only one genotype (i.e., monoculture) rather than two (i.e., biculture). In conclusion, we found evidence of genotype-driven microbial community assembly that changed with legume's competitive pressure. The inheritability of microbial assembly was present but skewed towards the annual parent. Our study demonstrates the importance of including rhizosphere interactions in our evaluation of novel cereal crops in and out of cereal-legume biculture. In a final study, I investigated how rhizosphere microbial ecology of these three genotypes (Kernza, annual wheat, and perennial wheat) could be linked to their ability to acquire N from neighboring alfalfa plants. We designed a greenhouse study in which we planted all three cereals in monoculture or in biculture with alfalfa and used 15N leaf feeding technique to track the movement of N from alfalfa to cereals. In addition, we also extracted DNA from the soil and sequenced it for 16S rRNA profiles. Arbuscular mycorrhizal fungi (AMF) infection rate was also measured on all cereals and legumes. We hypothesized that: 1) annual wheat would produce the greatest biomass but Kernza would have highest proportion of legume derived N in its biomass, 2) all microbial communities will shift in biculture, with the greatest change in Kernza and the smallest in annual wheat, and 3) Kernza would have the highest rate of infection from AMF, especially in biculture. Surprisingly, we found no evidence of genotype or cropping system (monoculture or biculture) effect on either proportion or absolute amount of N derived from legume. We did find, however, that DOC concentration was higher in cereal rhizosphere grown in biculture than in monoculture, suggesting greater belowground investment in exudates when the grasses are grown with a legume. Despite this trend, annual wheat had much lower microbial biomass carbon (MBC) level in its rhizosphere compared to the perennials, in biculture. We contended that this may be due to substrate suitability of annual wheat's rhizodeposit. We also found that AMF infection rate was in fact the lowest in Kernza. Lastly, we found that 16S profiles of all three cereals shifted towards that of alfalfa in biculture. This trend might suggest microbial spillover, wherein rhizosphere microbial community of one genotype colonizes that of a neighboring plant, from alfalfa rhizosphere. Overall, we demonstrated that quantifying the N transfer in the rhizosphere can provide important insight into how these genotypes may be inducing changes in soil biogeochemistry in response to neighboring legumes. In summation, this dissertation provides links between crop genotype, root exudate chemistry and rate, microbial community assembly, and their biogeochemical consequences, in alternative N environments. Deepened understanding of how complex rhizosphere interactions may affect internal N cycling could be leveraged to further optimize these unique systems such as perennial cereal-legume biculture. In doing so, we will be one step closer to a more sustainable future, that is less reliant on synthetic N fertilizers.
Open Access
Adaptation to new and changing environments: from experiments to field studies
(Colorado State University. Libraries, 2024) Durkee, Lily F., author; Hufbauer, Ruth A., advisor; Ruegg, Kristen, committee member; Angeloni, Lisa, committee member; Melbourne, Brett A., committee member
In today's rapidly changing world, organisms are often exposed to new or challenging environments. Following environmental change, populations may experience one or more of the following outcomes: they may disperse to a new habitat, persist through phenotypic plasticity or adaptive evolution, or go extinct. Here, I focus on adaptive evolution as a mechanism for enabling populations to respond to different types of environmental change. Adaptation may be necessary in less mobile species, or in fragmented landscapes where dispersal corridors are not available. Insects can serve as excellent models for studying the evolutionary dynamics of populations, as their life cycles are relatively short and multiple generations can occur within a few years, enabling rapid adaptation. In this dissertation, I explore the impacts of a change in phenology (Chapter 1), a challenging environment (Chapter 2), and the presence of a mountain range (Chapter 3) on the adaptation of insect populations in both the laboratory (Chapters 1-2) and in the field (Chapter 3). To begin, I studied the effects of a phenology shift using experimental evolution. Climate change can affect the length and timing of seasons, which in turn can alter the time available for insects to complete their life cycles and successfully reproduce. Intraspecific hybridization between individuals from genetically distinct populations, or admixture, can boost fitness in populations experiencing environmental challenges. Admixture can particularly benefit small and isolated populations that may have high genetic load by masking deleterious alleles, thereby immediately increasing fitness, and by increasing the genetic variation available for adaptive evolution. To evaluate the effects of admixture on populations exposed to a novel life cycle constraint, I used the red flour beetle (Tribolium castaneum) as a model system. Distinct laboratory lineages were kept isolated or mixed together to create populations containing 1 to 4 lineages. I then compared the fitness of admixed populations to 1-lineage populations while subjecting them to a shortened generation time. After an initial decline in fitness in the new environment, the admixed populations demonstrated significantly greater fitness compared to the 1-lineage populations after three generations. The timing of the increase in fitness suggests that adaptation to the novel environmental constraint occurred, as opposed to the masking of deleterious alleles. In Chapter 2, I examined the effects of consistent immigration on the probability and timing of adaptation. Theory predicts that immigration can delay extinction and provide novel genetic material that can prevent inbreeding depression and facilitate adaptation. However, when potential source populations have not experienced the new environment before (i.e., are naive), immigration can counteract selection and constrain adaptation. This study evaluated the effects of immigration of naive individuals on adaptation in experimental populations of red flour beetles. Small populations were exposed to a challenging environment, and three immigration rates (0, 1, or 5 migrants per generation) were implemented with migrants from a benign environment. Following an initial decline in population size across all treatments, populations receiving no immigration gained a higher growth rate one generation earlier than those with immigration, illustrating the constraining effects of immigration on adaptation. After seven generations, a reciprocal transplant experiment found evidence for adaptation regardless of immigration rate. Thus, while the immigration of naive individuals briefly delayed adaptation, it did not increase extinction risk or prevent adaptation following environmental change. For Chapter 3, I shifted my focus from laboratory populations to natural populations. In nature, elevation gradients provide a way to study populations across a range of environmental conditions within relatively small spatial scales. Adaptation to the local habitat might occur in response to the unique selection pressures present at different elevations, resulting in distinct populations adapted to different environments. However, if there is high habitat connectivity, gene flow can slow or prevent adaptation while also maintaining genetic variation and large population sizes. In this chapter, I used genomics to investigate the interplay between selection and gene flow in butterfly populations collected from high (>2,500m) and low (<2,000m) elevations, both east and west of the Rocky Mountains. My study focused on the Rocky Mountain subspecies of the clouded sulfur butterfly (Colias philodice eriphyle Edwards). Weak, but statistically significant, patterns of population differentiation were apparent between butterflies collected east and west of the Rockies, and eastern butterflies harbored greater genetic diversity compared to those from the west. Additionally, FST values close to zero suggest gene flow was high among the collection sites. I used a redundancy analysis to show that the observed east-west differentiation may be largely driven by greater precipitation east of the Rockies, and I identified over 16,000 putatively adaptive loci and 3,000 candidate genes associated with the environmental variables that may underly adaptive traits. In summary, my dissertation research highlights that adaptation can occur with genetic mixing or immigration in less than 10 generations in the lab (Chapters 1-2) and that adaptation to different environments can be identified among well-connected populations in the field (Chapter 3). It is well documented that gene flow can help maintain genetic variation, particularly among fragmented populations. My results emphasize that gene flow does not impede natural selection (Chapters 2-3), and that mixing between distinct populations can even promote adaptation (Chapter 1). My findings, therefore, support the use of methods such as translocation and wildlife corridors to facilitate gene flow for sexually reproducing conservation targets.
Open Access
Avian influenza takes flight: host mobility, viral prevalence, and transmission at large spatial scales
(Colorado State University. Libraries, 2024) Berger, Brooke, author; Webb, Colleen, advisor; Miller, Ryan, committee member; Pepin, Kim, committee member; Gorsich, Erin, committee member; Koons, David, committee member
Many pathogens have large geographic distributions, but we currently have little ability to predict how they may change over time. Understanding what mechanisms drive the large-scale distributions and movements of pathogens is critical to designing effective surveillance programs, disease interventions, and predictive models of disease spread. Additionally, we lack information on what spatial scale these mechanisms are most important. In this dissertation we address one of the fundamental problems in ecology, the "problem of pattern and scale", in the context of disease prevalence and spatial transmission. Are the large-scale patterns we see emergent properties of many small-scale processes, or are they a product of large-scale processes themselves? We focused on the spatial distribution, prevalence and spatial transmission of influenza A virus in its endemic host, wild waterfowl. We used a zero-inflated Bayesian CAR model to determine if local environmental persistence of the virus or regional host migration were better predictors of large-scale patterns of prevalence. We found that an unweighted host migration network better predicted high and low values of prevalence than did local drivers. To understand how these factors impacted where IAV moves in the United States (US) we investigated how local-scale transmission and regional-scale host movements influence large-scale spatial transmission and our ability to detect these transmissions. We developed a Bayesian zero-inflated binomial network model to estimate the probability of spatial transmission between watersheds pairs. We found that regional host movement was the best predictor of spatial transmission and that Mallard ducks likely play a special role in moving the virus throughout the US. Viral movement patterns were closely associated with important waterfowl breeding and wintering habitats rather than flyways, as has been previously shown. In order to extend these analyses to other geographic areas and host species we need to construct continental scale host movement networks from movement data with differing spatial and temporal resolutions. We developed a method to simulate host movements from very few observations allowing us to match mark-recovery data to highly detailed satellite telemetry data. We used the biological information in the detailed movement data to estimate population posterior distributions of travel speed, turning angle, and direction. These quantities and an approximately Bayesian rejection scheme were used to simulate missing locations in the mark-recovery data with estimates of uncertainty. The method was validated with a telemetry dataset tracking the movement of Northern Pintail ducks, an important host of IAV. Movement networks constructed from simulated locations captured known population scale migration patterns of Pintail and exhibited similar higher order community structure. More broadly, this research contributes to our understanding of how host mobility impacts the prevalence and movement patterns of pathogens, and the spatial scale at which this mechanism is important. Our findings suggest that predicting the spread and spillover risk of IAV requires an understanding of where hosts move at the regional scale. In the future, as climate and land-use change alter the migration patterns of wild waterfowl, we can expect the distribution and movement patterns of IAV to shift as well.
Open Access
Human-carnivore conflict mitigation on ranchlands in the western United States and eastern Colombia
(Colorado State University. Libraries, 2024) Hyde, Matthew David, author; Crooks, Kevin, advisor; Breck, Stewart, advisor; Teel, Tara, committee member; Wittemyer, George, committee member; Young, Julie, committee member
Conflict between large carnivores and ranching livelihoods is a persistent challenge for carnivore conservation and management. Shifting societal views of large carnivore management at the end of the 20th century led to population recovery and, in some cases, reintroduction to their former range. Working lands, productive areas encompassing a matrix of human land use and natural land cover, are an important part of carnivore range as they provide vital habitat and connectivity between protected areas. However, large carnivores can have direct and indirect impacts to humans and human livelihoods on working lands through livestock depredation, increased labor to mitigate depredations, and in some cases risk to human safety. In the Western United States, the reintroduction of gray wolves (Canis lupus) and the recolonization of grizzly bears (Ursus arctos) are hailed as species recovery success stories but have been met with resistance from rural ranching communities. Wildlife managers, researchers, and other entities throughout the region seek to reduce livestock producers' burden of living with large carnivores while ensuring sustainable populations. On the plains of Eastern Colombia, jaguars (Panthera onca) are recolonizing former range after being nearly extirpated following centuries of conflict over livestock and the pelt trade in the mid-20th century. In Colombia, jaguars depredate livestock, but there is little government support for the implementation of prevention tools and no compensation for losses, leaving non-governmental organizations as the sole implementers of conflict mitigation. In both contexts, wildlife managers require tools and strategies to address livelihood impacts and incentivize human-carnivore coexistence. Development and evaluation of these methods is important to ensure that limited resources are being utilized effectively. In this dissertation, I examine human-carnivore conflict in the Western United States and Eastern Colombia through three lenses: population trends related to conservation interventions for large carnivores; evaluation of non-lethal conflict reduction tools; and the human dimensions of non-lethal mitigation. In Chapter 1, I examine jaguar population trends on a working ranch and wildlife tourism destination in Casanare, Colombia. We integrated nine years of camera trap data and tourist photos to estimate jaguar survival, abundance, and probability of tourist sightings through a Barker Robust Design mark-recapture model. We then used spatially explicit capture-recapture to estimate jaguar density and compare it to a 2014 estimate. We found that abundance increased from 5 ± 0.26 individuals in 2014 to 28 ± 2.7 in 2022, and density increased from 1.88 ± 0.87 per 100 km2 in 2014 to 3.80 ± 1.08 jaguars per 100 km2 in 2022. We estimated survival rate of 78 ± 0.08% for males and 80 ± 0.07% for females. The probability of a tourist viewing a jaguar increased from 0 ± 0.11% in 2014 to 40 ± 0.18% in 2020 before the Covid-19 pandemic. We provide the first robust estimates of jaguar survival and abundance on working lands. Our findings highlight the importance of productive lands for jaguar conservation and suggest that a tourism destination and working ranch can host an abundant population of jaguars when accompanied by conservation agreements and conflict interventions. Our analytical model that combines conventional data collection with tourist sightings can be applied to other species that are observed during tourism activities. In chapter 2, I evaluate the effectiveness of diversionary feeding—providing food caches to divert predators away from preying on livestock—to reduce depredations by reintroduced Mexican wolves in the US states of New Mexico and Arizona. We used data from the Mexican wolf recovery program from 2014-2021 in a Bayesian hierarchical model to evaluate whether diversionary feeding reduced livestock depredations by wolf packs and what factors correlated with depredations. Our model accounted for the non-detection of depredation events, given that some depredations are unencountered or unreported on extensive rangelands. We found that diversionary feeding reduced depredations on average by 0.78 ± 0.03 depredations (43.9%) per pack per year. Prey density was negatively correlated to depredations before diversionary feeding. Minimum pack size and annual livestock density were negatively correlated with depredations after diversionary feeding, while prey density was positively correlated. We estimated a mean of 63 ± 5.4% of depredations were detected with high variation between packs (40.4 ± 7.9 % – 74.0 ± 5.3%). Because detections were only two-thirds of model-estimated depredations in our study, our model could improve compensation and targeting of nonlethal tools to mitigate the financial burden of co-occurrence with wolves by elucidating factors that lead to lower detection and adjusting livestock loss compensation multipliers. Our results indicate diversionary feeding can reduce livestock depredations by wolves on large landscapes in the Western United States but is not a panacea for conflict reduction. In chapter 3, I examine the context of human tolerance for large carnivores before and after the implementation of electric fencing to reduce depredations by jaguars. Non-lethal mitigation is often implemented under the premise that ranchers' tolerance for large carnivores will increase once losses or reduced or eliminated. However, deep-rooted psychological and cultural factors can be equally, if not more, important for predicting tolerance. We conducted structured interviews in four communities in the Colombian Llanos to characterize conflict, identify predictors of retaliatory killings of jaguars, and evaluate the impact of a fencing intervention to increase tolerance. The social psychological variables from the theory of planned behavior were a better predictor of intention to kill a jaguar than past and expected livestock losses. The intervention did not increase tolerance, likely because self-selection bias led to a treatment group that was tolerant pre-intervention. Sixty percent of respondents reported moderate to severe livestock losses during year 1, highlighting the urgent need to identify broader mitigation strategies for livestock depredation. Positive attitudes and normative support in favor of retaliatory killings were pervasive, while 24% of respondents were intolerant—having positive attitudes of and intent to retaliate against a jaguar following the next livestock depredation. Our results suggest that a strategy focused only on reducing depredation is unlikely to reduce retaliatory killings, as losses are not the only driver of retaliation. The pervasiveness of livestock losses and support for retaliatory killings demonstrate a need for immediate action to reduce livelihood impacts and consider alternative, bottom-up approaches to conflict mitigation in the area. My research indicates that wildlife tourism and diversionary feeding are two strategies that can mitigate the livelihood impacts of large carnivore presence. Wildlife tourism on Colombian ranchlands provides tangible economic benefits to landowners to conserve jaguars, other wildlife, and their habitat. We observed an important population increase for the locally threatened jaguar, and conserving jaguar habitat likely has reverberating benefits for ecosystem services and other wildlife through prey hunting prohibitions. Further work is necessary, however, to understand the distribution of costs and benefits from jaguar tourism and population growth in the surrounding community to ensure equitable conservation outcomes. In addition, diversionary feeding proved to be an effective tool to reduce depredations by Mexican wolves in the Southwestern U.S. The integration of non-detection of depredation events in our analysis is an important contribution to carnivore management because it can elucidate uncompensated livelihood impacts which aggravate intolerance for carnivores. This tool could be applied to other populations of carnivores to mitigate losses and may be more easily deployed than some deterrents. Findings from my third chapter reinforce the importance of understanding the human dimensions of human-carnivore conflict prior to implementing conflict reduction strategies. Interventions based solely on livestock losses may be unsuccessful at reducing retaliatory killings if losses are not the only driver of intolerance of carnivores. Ultimately, human-carnivore conflicts and interventions to prevent them are nested with unique social, cultural, ecological, political, and economic context. The failure of interventions to recognize how carnivore behavior interacts with local human contexts may ultimately exacerbate conflict and lead to counterproductive mitigation strategies.
Open Access
Drought influences the plant microbiome community structure
(Colorado State University. Libraries, 2024) Bazany, Kathryn E., author; Trivedi, Pankaj, advisor; Leach, Jan, committee member; Wrighton, Kelly, committee member; Singh, Brajesh, committee member
Drought is predicted to increase in frequency and severity in many regions across the globe due to climate change. Plants must adapt to reduced water availability and increased temperatures, and much of this adaptation will be mitigated by the adaptations of the plant microbiome. Plant associated microbes provide a variety of beneficial functions to the plant host including the mitigation of plant abiotic stress. Given the relatively short timeframe by which microbes can evolve, we postulate that much of the rapid adaptation of the holobiont, the functioning unit of a plant and all its associated microbes, will be instigated by the microbes. In this dissertation, we demonstrate that (1) plant microbiome rhizosphere communities adjust in response to water deficit, (2) plant microbiome assembly in multiple niche compartments is influenced by water deficit, and (3) drought influences the plant microbiome in concert with AMF inoculation and the preexisting, native soil microbiome.
Open Access
A critical examination of obstacles and opportunities to building capacity for community engaged social-ecological research and management
(Colorado State University. Libraries, 2024) Hauptfeld, Kathrin "Rina" Simone, author; Newman, Gregory, advisor; Bruyere, Brett, committee member; Pejchar, Liba, committee member; Zarestky, Jill, committee member
This dissertation seeks to contribute to more equitable and effective local governance and research of social-ecological systems. Specifically, I investigated efforts to enhance the distribution of influence and capacity, particularly to historically marginalized actors. This required critical evaluation of factors that influence whether and how interventions to build influence and capacity do so. Chapter one introduces the theoretical framing to this research, my positionality, and an overview of chapter organization. In my first two manuscripts (Chapters 2 and 3), I research underexamined elements of public participation in scientific research (i.e., delegated local ecological monitoring) as a proposed tool for building community capacity for resource management, particularly in developing economies. I seek to understand local ecological monitoring from multiple levels of influence - both the perspectives of resource-dependent participants, as well as from the perspectives of the program implementers. Specifically, Chapter 2 seeks to understand the experience of participants (i.e., small-scale fisherfolk with a role in the management of marine protected areas in the Philippines) to investigate the narrative that local ecological monitoring empowers communities to manage their social-ecological systems. I find that monitoring programs largely failed to be adopted by local communities, and rather than empowering participants, were perceived as burdens and a reaffirmation of local hierarchies. My findings highlight the risks of uncritically applying 'participatory' approaches, and stress the need to recognize and design for the psycho-political contexts (e.g., agency) to achieve desired outcomes. In considering context, this study makes a novel contribution to the characterization of citizen science approaches, by distinguishing externally initiated programs in which monitoring is intended to become autonomous. In consideration of the failed outcomes in Chapter 2, Chapter 3 investigates the potential for win-win outcomes in citizen science by examining an understudied area - organizer rationales for engaging local participants in contributory programs in the Philippines. I find that organizer rationales for and perceptions of engaging participants were multiple, overlapping, and sometimes antagonistic, particularly regarding who is served, and who determines the objectives, suggesting that outcomes often framed as benefits in the literature may sometimes not benefit participants. To foster clarity and encourage reflexivity in citizen science programs, I map these findings onto the normative – substantive - instrumental typology of rationales to propose an adapted typology rooted in the realities of citizen science. Chapter 4 addresses the flip side of the participation equation by investigating how high- 'cost' community-oriented collaborative conservation practices are built and sustained among U.S. academics and practitioners. This retrospective program evaluation found that immersion into a community of practice, and obligations and opportunities to experiment with collaborative approaches fostered capacity - notably conviction for, awareness of, and comfort with collaborative conservation - resulting in long-term adoption of practice. The findings in these studies shed light on important obstacles and opportunities for enhancing efficacy and equity in community-engaged research and management endeavors increasingly sought in social-ecological systems. Notably, a pervasive thread to emerge from these chapters is the important role of intentional design using a systems-thinking approach, regarding linked social-ecological systems, multiple levels of influence, and temporal scales.
Open Access
Rare sugars in soils: insights on their presence, persistence, and potential for carbon sequestration
(Colorado State University. Libraries, 2024) Lemas, Stephanie, author; Boot, Claudia M., advisor; Conant, Richard, committee member; von Fischer, Joe, committee member; Levinger, Nancy E., committee member
Carbon (C) is a fundamental element in the biosphere, cycling through all its natural pools. However, due to human activity, the flux of C into the atmosphere has accelerated, impacting the climate in significant and consequential ways. Awareness of this has prompted world-wide research into different mitigation strategies, including both reducing the flux of C into the atmosphere and active carbon dioxide removal (CDR) from the atmosphere. Soil represents a substantial C reservoir with the capacity to store large amounts of C. Our research focuses on the role of chiral molecules, specifically rare sugars, to enhance the storage of C in soil. To assess the feasibility of this idea, we designed an experiment to test whether soil microorganisms were able to consume and respire 14 rare sugars. We found that some rare sugars showed very little or repressed respiration, but that most showed moderate or high respiration rates. This finding prompted the hypothesis that soil microorganisms have evolved the capacity to grow on rare sugars because those rare sugars are present in the soil. To test this, we designed another experiment to check for the presence of rare sugars, specifically rare hexoses, in soils. Hexose sugars are among the most important small molecules in nature, in part because they are essential sources of energy for most cells. D-glucose, the most abundant hexose, is well-known due to its roles in both cellular respiration and photosynthesis; however, D-glucose is far from the only hexose in nature. Plants and microorganisms produce not only D-glucose, but also D-fructose, D-galactose, and D-mannose, and they contribute these hexoses to soils in different proportions. These four hexoses are considered common in soil and have been incredibly well-studied, but they represent only a small fraction of the hexoses possible in soil systems. In this study, we used gas chromatography-mass spectrometry (GC-MS) to measure hexoses in diverse soils crowdsourced from across the contiguous United States. In addition to the four common hexoses, we identified a fifth hexose: a rare ketohexose corresponding to the overlapping retention times of psicose and tagatose ("PsiTag"). This rare ketohexose, or possible mixture of these two rare ketohexoses, was present in every soil we sampled. To the best of our knowledge, this is the first time a rare ketohexose has been identified in a soil extract. The ubiquitous presence of a rare hexose in soils shifts the paradigm and challenges the narrative about which hexoses are truly common. These two experiments explore the potential of rare sugars for soil C sequestration via bio-transformative CDR (BtCDR) by examining their presence and the persistence in soils. As a result of our investigation, we determined that each rare sugar falls into one of two categories: having high turnover in soil, and therefore low C sequestration potential, or having high recalcitrance in soil and high C sequestration potential. Experimental data suggest that PsiTag and L-fructose have high recalcitrance in soil, but that L-glucose has high turnover in soil. Further research is needed to verify these findings and explore additional rare sugars. Although preliminary data indicate that rare sugar monosaccharides would not serve as effective long-term C sinks in soil, we believe that rare sugars may have a yet unknown role to play in soil C dynamics. This thesis sheds new light into the previously uninvestigated presence of rare sugars in soil, their implications for sustainable C storage, and their potential contributions to a holistic approach to climate change mitigation.
Embargo
Subalpine seed dispersal capacity: understanding the role of disturbance adjacency in the context of post-fire recovery
(Colorado State University. Libraries, 2024) Crosby, Brynn, author; Rocca, Monique, advisor; Aplet, Gregory, committee member; Knapp, Alan, committee member; Fornwalt, Paula, committee member
There is a growing concern about the ability of forest systems to recover following recent large, high-severity wildfires. While such fires are a natural part of subalpine forests in the Southern Rockies, a warming climate and the interaction between wildfires and recent bark beetle outbreaks may be challenging forest resilience (the ability to return to pre-fire conditions). Seed production and dispersal – a critical process that mediates landscape recovery – is not yet well understood for systems having been impacted by beetle-kill, but is expected to decline. Therefore, the purpose of this research is to identify how a bark beetle outbreak in adjacent, unburned subalpine forest surrounding a high-severity burn patch shapes seed dispersal following a wildfire. Specifically, this study aims to understand how spruce beetle-kill and forest characteristics may influence seed production of Picea engelmannii (Engelmann spruce) in the unburned edge of wildfire and subsequent seed dispersal into a burned patch. In the summer of 2022, I installed 275 seed traps and quantified seed dispersal into high severity burn patches of the 2020 Cameron Peak Fire. I fit a series of Bayesian statistical models to estimate the role that spruce beetle severity and other characteristics of the unburned forest edge explained Engelmann spruce seed production and dispersal distance. Site beetle severity ranged from 6% beetle related mortality to 92% beetle related mortality. However, I found no evidence that this mortality had any significant influence on the quantity of seed collected or the distance seeds dispersed. Seeds were collected at all trap installation distances of every site burn patch, with roughly 3.3 Engelmann spruce seed per trap. There was no statistical difference between the average seed collected at each trap installation distance, meaning that the average quantity of seed collected at 15m from the unburned edge was not statistically different than the average seed collected at 100m from the unburned edge across sites. These findings suggest that spruce beetle kill does not necessarily have a limiting effect on seed production and seed dispersal as would be expected. In years of high seed production for Englemann spruce, forest characteristics which may commonly limit seed dispersal (e.g. tree height, slope, tree age, etc.) may have less of a limiting effect.
Open Access
The effect of multiple stressors on Kaua'i's forest birds: demography, health, and trophic cascades
(Colorado State University. Libraries, 2024) Romero, Ashley Cozette, author; Pejchar, Liba, advisor; Koons, David, committee member; Hart, Sarah, committee member
Island ecosystems harbor unparalleled biodiversity, providing habitat for a disproportionate share of the world's species relative to their area. Nevertheless, the vulnerability of islands to disturbances that result in negative consequences renders them among the most endangered environments. Bird populations on islands are particularly susceptible and often strongly affected by invasive species, habitat loss, climate change, and disease, all of which has resulted in widespread decline and extinction. In the Hawaiian Islands, native forest bird populations confront numerous threats, with the majority of remaining native bird populations classified as threatened, endangered, or teetering on the brink of extinction. To sustain and recover island bird populations, it is essential to understand the direct and indirect impacts of anthropogenic changes on forest bird populations, and to what degree each driver of change influences bird health, demographics, and habitat quality. The goals of this project were to quantify how various stressors influence the body condition and sex ratios of Kaua'i's forest birds, and to assess if primary and secondary forest regeneration processes that affect forest bird resource and habitat availability are influenced by invasive rodent control. To address these questions, I collected and analyzed three years of forest bird banding data in the Alaka'i Wilderness Preserve on Kaua'i's Island (Hawai'i, U.S.A.) from 2021 to 2023. Birds were banded in and outside of areas that have been subject to intensive rodent control for the past 5-9 years. I focused on four focal species of birds, three native and one non-native, and collected data to assess the body condition and sex of these captured birds. Mixed effects models were used to determine whether body condition was significantly associated with rodent control intensity on a local and landscape scale, malarial infection status, mean temperature during the peak mosquito breeding season, frequency of extreme rain events, canopy density, and topographic wetness index (TWI). Similarly, I used general linear models to test if rodent control intensity, malarial infection status, or date of capture was associated with a higher or lower likelihood of encountering a female. I found that body condition was negatively associated with positive malarial status for all but one of the focal species, and higher average temperatures and TWI were negatively associated with body condition for all species. None of the predictor variables evaluated were strong predictors of the sex of captured birds. To evaluate the effects of rodent control on forest regeneration processes that sustain bird habitat in the Alaka'i Wilderness Preserve, I examined whether rodent control was associated with changes in seed rain, fruiting density, and seedling emergence. Seed traps were established in February of 2023 and were checked periodically over a six-month period to obtain seed rain data from within and outside of areas of rodent control. Seeds collected from traps were identified to the lowest possible taxonomic level. During each visit to collect seed trap contents, the number of fruits on all fruiting plants within five meters of each seed rain trap was estimated. These estimates were used to calculate relative fruiting densities in treatment and reference plots. To examine seedling emergence, emergence plots in treatment and reference plots were cleared of all vegetation in July of 2022. I used Mixed Effects Models to compare seed rain, fruiting density, and seedling emergence between sites with and without rodent control and found no differences in seed rain, seedling emergence, or fruiting density within and outside of rodent control. My findings suggest that variables that are related to disease transmission may be more influential in predicting the health of forest birds than variables related to predation risk or food and resource availability. These findings also suggest that rodent control, at least at current levels of intensity, may not play a significant role in forest regeneration in Kaua'i's 'Alaka'i Plateau. Further research is needed to understand the effectiveness of rodent control in this system, but reducing the prevalence of avian malaria and mitigating climate change will be critical to alleviating sub-lethal effects on Kaua'i's forest birds. This study contributes to our understanding of the sometimes complex and synergistic effects of invasive predators, disease, forest structure, and climate on forest birds and the dynamics of insular ecosystems. My findings and approach could have implications for conservation and restoration in the many areas globally where rat invasion, climate change, and disease may interact to pose similar threats.
Open Access
Bald Eagle space use in an urbanizing landscape
(Colorado State University. Libraries, 2024) Middleton, Miranda, author; Pejchar, Liba, advisor; Conrey, Reesa, committee member; Boone, Randall, committee member
Rapid human population growth has led to an increase in urbanization globally. Urbanization extends beyond the boundaries of city limits to include the conversion of natural areas into energy production (such as coal, solar, and wind), the damming and diversion of rivers, and agriculture and forestry to feed and house urban residents. This land use change is a major driver of biodiversity loss and significantly impacts wildlife space use. While many species are unable to persist in urban environments, some species of raptors are frequently found using the urban matrix. Bald Eagles (Haliaeetus leucocephalus) are an iconic North American species that was once near extinction but are now commonly observed in and around cities. Here, I examined how urbanization influenced Bald Eagle home range size and habitat selection in the northern Front Range of Colorado, a semi-arid region currently experiencing rapid growth in both eagle and human populations. In my first chapter, I investigated home range size and core-use areas of 24 territorial Bald Eagles affixed with a GPS/GSM transmitter. Specifically, I examined home range size and core-use area at five different nest stages of the annual cycle (pre-nesting, incubation, nestling, post-fledge, and non-nesting) and for both sexes. Home ranges and core-use areas were created using a dynamic Brownian bridge movement model. I then used a mixed-effects linear regression model to identify the land cover characteristics influencing these areas. My research shows that Bald Eagle home ranges and core-use areas vary in size and are often discontinuous, frequently containing one to three separate areas. Home ranges were fifteen times or more larger than core-use areas. Smaller home ranges were positively correlated with water, herbaceous wetlands, and human development while greater canopy cover was associated with larger home ranges. Similarly, water was positively associated with smaller core-use areas while greater canopy cover was associated with larger core-use areas. Home ranges and core-use areas tended to be larger during the pre-nesting and non-nesting stages and smaller during the nestling and post-fledge stages, with these differences being more pronounced in females. Male home ranges were smallest during the post-fledge stage (43.89 km2 ± 98.67) and largest during the non-nesting stage (117.31 km2 ± 177.04). Females generally had smaller home ranges, which were smallest during the nestling stage (2.86 km2 ± 2.14) and largest during the incubation stage (70.31 km2 ± 183.48). In Chapter One, I mapped eagle home ranges throughout the annual cycle and analyzed what habitat features are associated with smaller home ranges, which may indicate higher quality habitat. In my second chapter I built on these findings to assess habitat selection within and beyond the home ranges calculated in chapter one. To examine habitat selection I used a logistic regression model during the same five nest stages, for both sexes, and at two different scales: within home range and within study area. My findings indicate that Bald Eagle habitat selection is influenced by nest stage, sex, spatial scale, land cover, and human development. Generally, eagles selected for herbaceous wetlands, grasslands, and habitats near water. They avoided agriculture and dense canopy cover. Overall eagles avoided development; however, they used low to moderately developed landscapes when in close proximity to water. Eagles had a higher probability of using developed areas within their home range than within the study area and during the incubation and nestling stages. Female eagles were also more likely to use developed areas than male eagles. At all nest stages, eagles were more likely to use areas with low levels of development than areas with high levels of development. My findings suggest that the space-use patterns of Bald Eagles are complex and vary throughout the annual cycle. Eagles are capable of thriving in urban environments, where their smaller home ranges suggest that they can find quality habitat. Conservation efforts in urbanizing regions should focus on protecting habitats close to water, in herbaceous wetlands, and with open canopy cover. It is also important to recognize that while Bald Eagles readily use urban environments with these habitat features, they prefer areas with low to moderate development. Additionally, conservation strategies should account for the fact that Bald Eagles have disconnected home ranges with critical foraging sites located away from their nests. Together, these recommendations could help guide policy and practice for sustaining Bald Eagle populations during their full annual cycle in urbanizing landscapes.
Embargo
Tropical forest root characteristics and responses to drying across environmental gradients
(Colorado State University. Libraries, 2024) Longhi Cordeiro, Amanda, author; Cusack, Daniela F., advisor; Ojima, Dennis, committee member; Cotrufo, M. Francesca, committee member; Conant, Richard, committee member
Fine roots represent the interface between plants and soils, and as such regulate all major biogeochemical cycles in terrestrial ecosystems, including tropical forests. Tropical forests play a crucial role in global carbon (C) cycling, largely due to their extensive root biomass and significant soil C stocks. However, these ecosystems have been experiencing more frequent severe droughts across some regions and are predicted to continue experiencing these extreme drought events in the future. This dissertation seeks to contribute to the understanding and synthesis of tropical root responses to drying in varying environmental conditions. In chapter 1, I gave an introduction about the importance of fine roots to ecosystem function and the impacts of drying in tropical forests. In chapter 2, I characterized root biomass, morphology, nutrient content, colonization to 1.2 meters depth as well as and arbuscular mycorrhizal fungal (AMF) to 20 cm depth in 32 plots across four distinct lowland Panamanian forests which are representative of the vast variation in soil fertility and mean annual precipitation (MAP) found across tropical forests. Root characteristics measurements, such as morphology and chemistry, at soil layers deeper than 30 cm have been rarely documented and to the best of knowledge this is the first study in tropical forests. I observed that that some root traits changed with soil depth similarly across sites while others had site-specific variation. I also observed larger variation at the soil surface and that morphological traits, in addition to root biomass can affect soil C stocks. In chapter 3, the effects of experimental and seasonal drying on fine root dynamics were explored using a partial throughfall reduction experiment across the same 32 plots as in chapter 2. I found that chronic drying impacted root biomass, productivity, morphology and arbuscular mycorrhizal fungi (AMF) colonization. Root biomass and characteristics also changed across seasons with different dynamics across depths. Chapter 4 focused on the effects of drought on tropical seedling development in a controlled chamber environment. I observed that drying decreased seedling growth, but high soil fertility and AMF inoculation mitigated these effects. I also observed changes in root morphology, leached C, new C allocation patterns, and aboveground traits in response to drought, but with usually interacting effects with fertility and AMF inoculation. Chapter 5 contributes a tropical root database (TropiRoot 1.0 database) with root data extracted from scientific papers across different countries and continents. Overall, this dissertation provides novel results and insights into the variation in root characteristics among tropical forests and their responses to climatic drying with interacting effects of fertility, symbionts and soil depth effects. It brings novel measurements that have never been published in tropical forest studies. In chapter 2, I found novel results about how different tropical forests had similar patterns of root variation with depth. It indicated differences in resources acquisition at the soil surface (likely for nutrients) and at deeper soil layers (likely for water) that are usually less investigated. I also showed a large variation of roots at surface soil across different forests that may influence forest responses to global change factors. In chapter 3, I supported some results across the literature such as drying decreasing root growth at the soil surface. However, I added new results such as drying decreasing root productivity at deeper soil layers, and changing root morphology and associations with symbionts probably to compensate the lower root growth. All together I observed that drying promoted changes in acquisition strategies and also that fertile forests may respond differently to drying. In chapter 4, I showed some clear tradeoffs in plant traits providing evidence that they are constantly changing in response to the environment. Also, I provided some novel results on the mechanisms, such as nutrient retention, on how mycorrhizal and fertility mitigated some negative effects of drying on plant growth. This aligns with the field study showing some possible resilience in the fertile forests to drying. The findings highlight the complex interactions between root traits and environmental conditions, offering important implications for predicting tropical forest responses to changing moisture and nutrient availability. All these chapters together provided a good understanding on how different forests respond to environmental changes. These impacts on soil C storage, links with root function and possible larger vulnerability of some forests are great topics for future studies.
Open Access
A modeling-experimental (ModEx) approach to advance understanding of global controls and microbial contributions to particulate and mineral-associated organic matter storage
(Colorado State University. Libraries, 2024) Hansen, Paige M., author; Cotrufo, M. Francesca, advisor; Schipanski, Meagan, committee member; Wallenstein, Matt, committee member; Trivedi, Pankaj, committee member
As soils are the largest terrestrial pool of carbon (C) and provision many ecosystem services, including nutrient cycling and maintenance of plant productivity, soil C sequestration represents a promising technology to help meet urgent needs to draw down atmospheric carbon dioxide (CO2) and prevent acceleration of climate change, as well as to help feed a rapidly growing global population. Given this, a comprehensive understanding of the mechanisms underpinning observed patterns of soil C storage is necessary to ensure a sustainable future for all. In response to this need, recent breakthroughs in our understanding of soil organic matter (SOM) dynamics have led to the development of multiple frameworks articulating how climate, soil, plant, and microbial properties interact with one another to control the formation of the two SOM constituents, particulate (POM) and mineral-associated organic matter (MAOM). Despite this, environmental controls that act on POM and MAOM storage at the global scale, as well as microbial functionality, is noticeably absent from our empirical understanding of SOM fraction formation and persistence. More advanced knowledge of these controls would enable more robust identification of where SOM is most vulnerable to loss, as well as more informed implementation of 'multi-pool' management practices aimed at enhancing C storage in both POM and MAOM. In this vein, this dissertation explores global controls on and microbial mediation of SOM dynamics at multiple scales through a combination of synthesis, modeling, and experimental (i.e., ModEx) approaches. Specifically, I first synthesized climate, soil property, and fraction C data to understand global controls on C storage in POM and MAOM. I then applied a previously developed individual-based model (Kaiser et al., 2015) to determine how emergent microbial community properties resulting from microbial social dynamics (i.e., interactions among microbes that produce enzymes at different rates) impact POM retention under varying degrees of MAOM saturation. Lastly, I investigated the relevance of hypothesized microbial copiotrophic and oligotrophic life history strategies to changes in POM and MAOM storage. Results from these projects indicate that global POM and MAOM storage is controlled by disparate suites of environmental variables, with POM being primarily controlled by variables that modulate microbial activity, and MAOM being controlled by a combination of C inputs and soil properties related to the potential to stabilize new MAOM. Additionally, flexible enzyme production in response to the availability of easily-assimilable, soluble substrates may contribute to POM retention under varying degrees of MAOM saturation and POM carbon:nitrogen ratio (C:N). However, variation in microbial function does not always result in changes in POM and MAOM storage – differences in growth rate, our proxy for copio- and oligotrophy, was unrelated to changes in POM and MAOM. Despite this, this dissertation indicates that microbial functions and environmental properties controlling microbial activity rates (i.e., controls on C outputs from the soil) mediate POM storage, but that MAOM is more reflective of C inputs to the soil. This indicates that microbial interventions to support soil C storage may want to focus on ecosystem-specific microbial manipulations that support community efficiency and modulate exo-enzyme production. In combination with other management strategies that increase soil C, these types of microbial interventions may help ensure that new soil C is retained in the soil for longer periods of time. Additionally, given that microbial activity is generally expected to increase with climate warming, these results indicate a premium need to preserve existing POM stocks.
Embargo
Isolation, interpretation, and implications of physical soil organic matter fractions in soil systems
(Colorado State University. Libraries, 2024) Leuthold, Samuel J., author; Cotrufo, M. Francesca, advisor; Lavallee, Jocelyn M., advisor; Mueller, Nathan, committee member; Schipanski, Meagan, committee member
Soil organic matter (SOM) is crucial to sustained ecosystem function, due to its role in regulating nutrient cycling, carbon (C) storage, and soil structure relevant to both food production and climate regulation. Since the early 1990s, physical fractionation methods have been used to separate bulk SOM into discrete components. The central aim of these methodologies is to simplify the complex heterogeneity of the bulk SOM pool by isolating fractions with more homogenous chemistries, formation pathways, and mechanisms of persistence. By understanding the relative distribution of C and nitrogen (N) among these various fractions, we gain appreciable insight into the mechanisms underlying fundamental soil biogeochemical processes. Despite their historic use, however, significant questions remain regarding the means of proper isolation and interpretation. This dissertation looks to these questions directly, reviewing and then interrogating the methods by which fractions separated before applying those fractionation schemes to answer key questions relating SOM to ecosystem function. The first section reviews the history and current state of physical fractionation methodologies, before using a triangulation of experimental evidence, including chemical, isotopic, and spectral indicators, to identify the best practices for laboratory use. These chapters advance our current understanding of SOM biogeochemistry by drawing an explicit link between the conceptual definitions of SOM fractions and the various procedural definitions that have been used historically. Across a range of soils representative of agricultural land in the United States, we show that fractionation methods that separate particulate organic matter (POM) fraction by density isolate fractions more in line with the conceptual definition of POM than the more frequently used size separation. This work aims to unify understanding across the field of soil biogeochemistry and allows for more robust analyses and modeling efforts. The subsequent chapters use this approach to investigate fundamental questions around SOM stability and persistence. The mineral associated organic matter (MAOM) fraction has long been understood to be relatively stable, with slower turnover times and a more homogenous composition as compared to POM. Its accumulation has thus been discussed as a target for climate change mitigation. We leveraged a unique long-term experimental site with archived samples stretching back over 60 years to test this assumption, aiming to identify a dynamic fraction of MAOM by comparing the SOM composition of plots that had not received organic inputs over the course of the experiment against plots that had received regular inputs for six decades. Our spectral and isotopic analyses showed that a dynamic fraction of the MAOM existed and was primarily composed of plant derived compounds. As the exchangeable MAOM pool was exhausted due to a lack of fresh C inputs, we found that the composition of the MAOM pool became more strongly dominated by microbial byproducts. This work represents useful evidence towards a holistic understanding of the dynamic nature of SOM, and forces reimagining of long-held paradigmatic views. One challenge in the current SOM biogeochemistry landscape is that often questions exist downstream of methodologies, such that the fractions that can be isolated drive the research that is conducted. By first identifying robust methodologies, in the second half of this dissertation we were able to ask specific questions about the link between SOM dynamics and ecosystem function. To this end, we pursued three different lines of inquiry: a field study in which the objective was to link the fractional distribution of C and N to yield stability in agricultural systems, a field study that seeks to understand the persistence dynamics of SOM over a decadal scale in grassland systems, and a laboratory incubation that aims to discern the relative contributions of POM and MAOM in regard to plant available N. The first field study used samples from 9 working farms across the Central United States to better understand how SOM might moderate the spatiotemporal stability of crop yields at the field scale. Yield instability is a major cause of economic and environmental distress in row crop systems, and regional studies have suggested that increasing SOM may be able to mitigate variation in yield across time and space. The chapter presented here is the first study that attempts to identify a mechanistic link between SOM fractions and yield stability. In disagreement with regional and county scale studies, we found that SOM abundance was not linked to increased yield stability in cropping systems. Rather, unstable yield zones had significantly higher SOM content than stable zones, particularly in regard to the POM fraction. This work indicates that at the subfield scale, interactions between climate, topography, and management may be driving spatial patterns of both yield stability and SOM accumulation. This is a key insight, implying that some of the relationships between SOM and agronomic outcomes are scale dependent, and highlighting the need for field scale work to maintain relevance to growers. The second field study produced novel insights, tracing isotopically enriched litter and pyrogenic organic matter (PyOM) through various SOM fractions over the course of a decade, one of the longest tracer experiments that has occurred in grassland ecosystems. We found that after 10 years, the majority of the remaining litter derived C and N inputs were stored in the MAOM fraction, a result well aligned with our hypotheses. Interestingly though, the litter derived MAOM fraction formed rapidly (~ 1 year) and persisted at a relatively similar concentration for the duration of the study. This suggests the potential for divergent persistence mechanisms of POM and MAOM, implying less inter-fraction transfer than previous frameworks have proposed and prompting re-evaluation of the mechanisms of MAOM formation and persistence. In contrast, the applied PyOM remained almost completely in the POM fraction over the 10-year period, reinforcing both the heterogeneity of the bulk SOM pool, and the myriad of persistence mechanisms that stabilize various SOM fractions. Given that PyOM is ubiquitous in soil regardless of burn history and can persist for hundreds of years, this result has critical importance for our understanding of turnover time of the POM fraction, and suggests that we may be underestimating the dynamic nature of POM when PyOM is not accounted for. Finally, in a lab incubation experiment, we took advantage of recent advances in isotopic measurement to prove recent theories around MAOM N accessibility. Whereas POM is often thought of as the fraction that provides nutrients in the short term, our two-week incubation showed that under certain conditions, the majority of plant available N may be derived from the MAOM fraction. This work validates proposed frameworks and is an important step towards understanding coupled C and N management in agroecosystems that could improve N use efficiency and increase producer sustainability. Overall, the work in this dissertation aims to provide a comprehensive overview of how fractions can and should be isolated, and the information gained via this fractionation. By clarifying and advancing methodology to quantify SOM components and the understanding of their contribution to critical soil functions for the sustainability of food production and the mitigation of climate change this dissertation represents a major step forward for the study, modeling and managing of SOM in agricultural systems.
Open Access
Bridging the gap between regenerative agriculture and the biological mechanisms controlling soil organic matter dynamics
(Colorado State University. Libraries, 2024) Prairie, Aaron, author; Cotrufo, M. Francesca, advisor; Fonte, Steven, committee member; Rosenzweig, Steven, committee member; Hall, Edward, committee member
This dissertation investigates the complex impacts of regenerative agriculture on soil organic matter (SOM) dynamics and soil fauna biodiversity, addressing a broad range of objectives from uncovering global patterns and policy needs to mechanistic understanding. Through global meta-analyses, policy evaluations, field studies, and mechanistic experiments, this research provides a comprehensive understanding of how regenerative practices influence soil health, carbon sequestration, and biodiversity. Chapter 2 aimed to understand global patterns through a meta-analysis quantifying the effects no-till (NT) and cropping system intensification significantly increase SOM, via impacts on both particulate organic matter (POM) and mineral-associated organic matter (MAOM). The analysis reveals that NT and cropping intensification synergize with integrated crop-livestock (ICL) systems to greatly enhance soil organic carbon (SOC) stocks, highlighting the potential of regenerative practices to mitigate climate change and promote soil health. Chapter 3 sought to evaluate the impacts of diversified agricultural systems on SOC, soil health, and yield across the United States. The findings indicate that diversified systems consistently show higher levels of SOC, improved soil health, and improved agronomic outcomes. The policy recommendations include increasing funding for soil health practices, supporting longer participation of producers in conservation programs, and tailoring these programs regionally to maximize their effectiveness. Chapter 4 focused on field-level impacts by examining the effects of varying degrees of regenerative practice adoption on SOM dynamics and soil fauna biodiversity in 22 farms within the Cheney Watershed, of central Kansas. By developing a Regenerative Farming Index (RFI), the study clearly links regenerative practices to increased carbon and nitrogen stocks in both POM and MAOM, and indicates a positive correlation between regenerative practices and soil biodiversity. Path analysis suggests that soil fauna indirectly influence SOM through their role in enhancing regenerative practices. Chapter 5 aimed to provide a mechanistic understanding of SOM dynamics by exploring the interactions between predatory mites and bacterivorous nematodes. The study highlights how these interactions shape microbial necromass accrual and MAOM formation. The findings underscore the importance of considering the entire soil food web in ecological studies to fully understand SOM formation and stabilization mechanisms. Overall, this dissertation advances the understanding of SOC dynamics under regenerative agriculture, providing valuable insights for sustainable soil management and climate change mitigation. By integrating global and local scales, it offers a holistic view of how regenerative practices can restore soil health and contribute to more resilient and productive agricultural systems.
Embargo
Cultivating collaborative adaptability in public lands social-ecological settings: linking theory, practice, and evaluation across cases and contexts
(Colorado State University. Libraries, 2024) Beeton, Tyler Andrew, author; Galvin, Kathleen, advisor; Cheng, Antony, committee member; Schultz, Courtney, committee member; Snodgrass, Jeffrey, committee member
Collaborative and adaptive forms of governance have become increasingly common in environmental management as they are claimed to help reduce conflict over resource management issues and uncertainty, increase trust, support shared understanding and buy-in for management actions, and facilitate social learning. In the USDA Forest Service, legal, regulatory, and bureaucratic challenges, and the increased emphasis on ecosystem management has increased the demand for, and investment in, collaboration as a tool to meet forest and fire management goals. Collaborative governance and adaptability scholarship has documented the key drivers and external conditions that influence collaboration, the internal dynamics that cultivate or constrain collaboration, and the outputs and outcomes of collaboration. Still, a number of research gaps remain that, if addressed, could advance the theory and practice of collaborative governance. First, the ways in which groups adapt and remain resilient to inevitable internal and external changes remains underexplored. Second, despite over twenty years of research in this space, relatively little is known about the configuration of, and relationship between, factors that comprise collaborative governance and adaptability. Third, collaboration is dynamic. As groups evolve, they create value in different ways, and their needs and priorities change. Thus, there is a need for periodic and ongoing assessments of how collaboration is working in local contexts, current challenges, and what adaptations are needed to improve collaborative processes and progress. This dissertation starts to address these research gaps and needs. I situated this work within the Collaborative Forest Landscape Restoration Program, a Forest Service-administered program first authorized in 2009 and reauthorized in 2019. The work presented in this dissertation was co-developed with the Southwest Ecological Restoration Institutes and the Forest Service Forest, Range Management, and Vegetation Ecology Program. Specifically, the work supported synthesis of lessons learned from the first 10 years of the CFLRP and the development of a standardized and longitudinal assessment of collaborative governance and adaptability for use in the CFLRP Common Monitoring Strategy. Broadly, my dissertation contributes to our understanding of the factors that facilitate or frustrate adaptation to inevitable change in collaborative settings. This is a critical line of inquiry given the increased and sustained investment in long-term collaborative environmental management in the United States and beyond. I employed a mixed-method analysis consisting of focus groups, program-wide surveys, and a systematic review, and I drew on the Integrative Framework for Collaborative Governance, collaborative adaptability and resilience literature, and organization theory to frame my analysis. In Chapter 2, I asked, how do collaborative governance regimes adapt to disruptions and what barriers constrained collaborative resilience? I found that collaboratives demonstrated the ability to mobilize social capital, learning, resources, and flexibility to respond to disruptions. Yet authority, accountability, and capacity complicated collaborative resilience. I conclude Chapter 2 with policy and practice recommendations to cultivate collaborative resilience moving forward. In Chapter 3, I developed and deployed a program-wide collaborative governance and adaptability assessment to all currently authorized CFLRP projects. I used a modified grounded theory approach to document and describe CFLRP project respondents' recommended actions and adaptations to improve collaborative processes and progress towards desired outcomes. Key recommendations included the need for: inclusive engagement throughout the process; institutional arrangements; resources and capacity; monitoring and social learning; trust, relationships, and commitment; external communication and outreach; and local autonomy in decision making. I discussed these findings in light of collaborative governance theory and practice and included relevant resources and actions that practitioners and funders of collaboratives and policy actors may consider to support collaboratives in working towards forest and fire management objectives. In chapter 4, I again used the program-wide CFLRP collaborative governance and adaptability assessment, and I used confirmatory factor analysis to test assumptions underlying the dimensional structure, reliability, and validity of measures thought to comprise collaborative governance and adaptability. I found that the components of collaborative governance and adaptability comprised six dimensions – principled engagement, shared motivation, leadership, resources, knowledge and learning, and institutional arrangements. As expected, several dimensions were significantly related, and the pattern of inter-factor relationships aligned with theoretical and empirical assumptions. We also found that the six dimensions represent statistically reliable, valid, and distinct measures that may be used to evaluate collaborative governance and adaptability. While our focus was on the CFLRP, the assessment can be adapted to other collaborative environmental governance contexts. Chapter 5 ends with a summary of findings, limitations of the work, and future research directions to address lingering questions about collaborative environmental governance.
Embargo
Quantifying and mapping tree mortality due to mountain pine bark beetles via analyses of remote sensing data in northern Colorado
(Colorado State University. Libraries, 2024) Taleb, Hamza A. S., author; Laituri, Melinda, advisor; Fassnacht, Steven, committee member; Leisz, Stephen, committee member; Grigg, Neil, committee member
In the past two decades, Mountain Pine Bark Beetle (MPBB) infestations have become more pervasive due to increasing temperatures and drought conditions related to climate change causing regional-scale mortality. Insect effects on tree die-off, fuels, and fire behavior can vary widely. A key problem in understanding insect-fire relationships is the lack of empirical maps that show interrelated changes in the distribution of insect infestations and fire zones over space and time. This study demonstrates an approach to tracking and mapping the spread of MPBB by analyses of vegetation indices calculated from Landsat TM data in the study site in northwestern Colorado. These indices were used for calculations in the Random Forest (RF) classifier algorithm and the Support Vector Machine (SVM) classifier algorithm to determine the presence or absence of MPBB and to illustrate the changes in the distribution of infestations with time. A comparison was made between the accuracy of the two classification algorithms (RF and SVM) in tracking and mapping the spread of MPBB. R2 has proved to be a reliable measure of accuracy of regression models. If the statistical accuracy of all the models, (RF vs. SVM and binary vs. regression) are compared, both the regression and binary models based on RF are more accurate. The results of this study can provide a useful tool for forest managers to make decisions about how changing conditions affect potential problems in forest management.
Open Access
Ecovoltaics and grassland responses to solar energy co-location
(Colorado State University. Libraries, 2024) Sturchio, Matthew Anders, author; Knapp, Alan K., advisor; Ocheltree, Troy, committee member; Schipanski, Meagan, committee member; Mueller, Nathan, committee member
The mitigation of climate change requires a transition to renewable sources of energy, and of all available options solar photovoltaic (PV) energy generation has the greatest potential to reduce CO2 emissions by the year 2030. Even so, ground mounted PV is land use intensive, and ideal locations for solar development often overlap with sensitive natural ecosystems and highly productive agricultural land. A scalable approach with potential to alleviate the land use tension created by solar development is the co-location of PV arrays and grassland ecosystems. While this approach has many positive implications for land sparing, the ecological consequences of PV presence above grassland ecosystems are not well understood. In this dissertation I discuss how the unique microenvironments created by PV arrays alter patterns of productivity, physiological response, and forage quality in a semi-arid grassland in Colorado, USA. I also outline a new approach to PV development, Ecovoltaics, that is informed by several fundamental ecological concepts. An Ecovoltaic approach to solar development co-prioritizes energy generation and ecosystem services by intentional design and management through all aspects of array development. With this work, I hope to inform a more sustainable future for solar energy.
Open Access
Population assessment of burrowing owls nesting on black-tailed prairie dog colonies in Colorado
(Colorado State University. Libraries, 2024) Albright, Sarah, author; Kendall, William, advisor; Conrey, Reesa, committee member; Pejchar, Liba, committee member; Boone, Randall, committee member
In North America, grassland birds have experienced steeper and more widespread declines than any other avian guild due to habitat loss resulting from grassland conversion to cropland, increasing urban and energy development, and climate change (Knopf 1994, Askins et al. 2007). The historical area of native grasslands has decreased by 62% since the 1800s and contributed to the loss of nearly 40% of grassland bird populations since 1966 (Wilsey et al. 2019). Heterogeneity in climate, grazing, and fire across the landscape have resulted in the existence of different grassland types that vary in structure and composition. The shortgrass prairie is the driest and warmest of the Great Plains grasslands and is dominated by low-growing perennial grasses, forbs, and shrubs. The shortgrass prairie provides vital nesting and foraging habitat for many grassland birds. In Colorado, approximately 50% of the historic shortgrass prairie has been converted to other land uses (Neely et al. 2006). The partial loss of shortgrass prairie habitat has ecological consequences including loss of native vegetation and decreases in populations of grassland species, including grassland birds. Black-tailed prairie dogs (Cynomys ludovicianus) are important drivers of ecosystem function in the shortgrass prairie because their colonial social structure, burrowing and foraging behaviors alter the landscape and provide areas of shorter vegetation and burrow systems that support increased biodiversity of animals and plants (Cully et al. 2010). Black-tailed prairie dogs function as a keystone species in shortgrass prairie ecosystems and create important breeding and foraging habitat for grassland birds including western burrowing owls (Athene cunicularia hypugaea: Smith and Lomolino 2004). The western burrowing owl is a small diurnal raptor that lives in grasslands, deserts, and other open habitats. It is a partially migratory species where populations in the southern parts of its range in the southwestern United States, Mexico, and portions of Central and South America are typically year-round residents. Migratory populations occur in the grasslands of North America, arriving in early spring to start breeding as far north as Canada and departing in late August to return to their wintering grounds in the southwestern United States and Mexico (Poulin et al. 2011). Burrowing owls typically nest in burrows dug by rodents such as prairie dogs and ground squirrels. In eastern Colorado, burrowing owls almost exclusively nest on black-tailed prairie dog colonies. Benefits of nesting on prairie dog colonies include increased predator detection from alarm calls, decreased predation due to the dilution effect, and reduced vegetation height. Black-tailed prairie dog populations have experienced an estimated decline of 90-98% since 1900 due to sylvatic plague outbreaks and habitat loss and alteration by human development (Miller et al. 1994, Desmond et al. 2000). Since prairie dog colonies provide critical habitat for burrowing owls and other species, population decline contributes to decreased availability of burrowing owl nesting habitat. Conservation status of the burrowing owl varies across its range. It is a species of conservation concern in the western United States, threatened in Mexico, and endangered in Canada (Sheffield 1997). The western burrowing owl is currently listed as a state-threatened species in Colorado and is designated as a Tier 1 Species of Greatest Conservation Need in Colorado's State Wildlife Action Plan (Colorado Parks and Wildlife 2015). The last burrowing owl population assessment in Colorado was conducted in 2005 (Tipton et al. 2008, 2009) and since then, only local surveys limited in spatial and temporal extent have been conducted. This has prompted the need for an updated population assessment of burrowing owls nesting in eastern Colorado, where the majority of Colorado's burrowing owls breed on black-tailed prairie dog colonies. In this study, we provide an updated status assessment for burrowing owls on Colorado's eastern plains and seek to expand the current understanding of which black-tailed prairie dog colony attributes have the highest value for burrowing owl occupancy, density, and productivity. We specifically examined how colony size, activity status, and vegetation characteristics influence these population parameters on 175 survey plots throughout eastern Colorado. We surveyed some of the same plots using similar methodology as Tipton et al. (2008, 2009) in their 2005 study, facilitating comparisons of burrowing owl populations 17–18 years later. The first chapter describes the distribution of burrowing owls nesting on black-tailed prairie dog colonies in eastern Colorado and serves to examine which black-tailed prairie dog colony characteristics drive the use of a colony by burrowing owls and the probability of successful reproduction. The second chapter focuses on burrowing owl density, productivity, and abundance in eastern Colorado to determine how many burrowing owls are present on occupied colonies and how productive they are on colonies where they do reproduce. The value of describing these components of burrowing owl populations in separate chapters comes from estimating and identifying the drivers of burrowing owl occupancy in chapter 1, then shifting to the finer scale of density to determine if the drivers of burrowing owl distribution are also driving density, productivity, and abundance. We used a black-tailed prairie dog colony shapefile prepared by the Colorado Natural Heritage Program for Colorado Parks and Wildlife in 2020 as our sampling frame. This shapefile includes polygons that represent black-tailed prairie dog colonies with digitized boundaries, created using imagery collected in 2019 by the National Agriculture Imagery Program (NAIP). We used a spatially balanced sampling design to select potential plots and selected new samples for each survey year (2022 and 2023) to maximize sample size and spatial coverage of the large study region. From early May through early August, we conducted four surveys on 175 plots in eastern Colorado, counting all burrowing owls seen, with two visits occurring prior to juvenile emergence and two occurring after. We estimated occupancy using a static multistate occupancy estimation model with two states: 'occupied' and 'occupied with successful reproduction'. We estimated density and abundance using distance sampling methods. We estimated productivity using a zero-inflated beta generalized linear model. We used occupancy data from Tipton et al. (2008) and dynamic occupancy models to evaluate burrowing owl local colonization and local extinction between 2005 and 2022 - 2023. Our analyses indicate that burrowing owl occupancy and density are highest in southern Colorado and lowest in northern Colorado. Colonies with higher prairie dog activity level had higher probability of reproduction and higher densities of adult burrowing owls. Vegetation height was the main driver of juvenile density such that colonies with taller vegetation supported lower densities of juvenile owls. We estimated burrowing owl occupancy to be 0.84 (95% CI [0.62, 0.95]) and probability of successful reproduction on occupied plots to be 0.86 (95% CI [0.70, 0.94]). We estimated an average density of 3.47 (95% CI [2.79, 4.15]) adult owls/km2 prior to juvenile emergence, 8.20 (95% CI [6.39, 10.00]) adult owls/km2 after juvenile emergence, and 18 juveniles/km2 (95% CI [13.86-23.66]). We expanded our density estimates to our sampling frame and estimated that there were 4,913 (95% CI [3,948-5,875]) adult owls prior to juvenile emergence, 11,613 (95% CI [5,333-17,893]) adult owls after juvenile emergence, and 26,580 (95% CI [19,623-33,537]) juvenile burrowing owls on black-tailed prairie dog colonies in eastern Colorado. We found that prairie dog activity had a positive effect on burrowing owl density, successful reproduction, and productivity regardless of prairie dog colony size. This indicates that burrowing owls are effectively utilizing and nesting on small prairie dog colonies in eastern Colorado, which could make them more resilient to breeding season habit loss, fragmentation, or degradation. In addition, we found that northern Colorado had lower burrowing owl occupancy and adult density, but had a similar probability of successful reproduction and juvenile density compared to south and central Colorado. If northern Colorado can sustain stable burrowing owl densities, burrowing owl populations may have enough successful reproduction to maintain stable populations. The covariates we investigated in this study did not adequately explain this spatial pattern. However, it is likely that differences in climate, prairie dog population dynamics, land use, or some other factor could cause differences in local habitat and breeding conditions across Colorado. The previous burrowing owl population assessment in eastern Colorado estimated burrowing owl occupancy to be 0.80 (95% CI [0.66-0.89]), density to be 3.04 adult owls/km2 (95% CI [2.15, 5.13]), and adult abundance to be 3,554 (95% CI [3,928-8,445]) owls in eastern Colorado. This suggests that overall, burrowing owl populations in eastern Colorado are relatively stable and are likely to remain stable if efforts continue to preserve the prairie dog colonies that are vital for burrowing owls during the breeding season. The burrowing owl is a state-threatened species in Colorado at the time of this thesis and thus we recommend future burrowing owl surveys to track population changes through time. Future monitoring efforts can help identify the drivers of burrowing owl population change and clarify the spatial patterns we found. These future efforts should occur more frequently than the ~17 year time period between this population assessment and the last assessment in 2005. We recommend conducting burrowing owl surveys every 5 years because it exceeds the time lag between black-tailed prairie dog colony local extinction and cessation of burrowing owl nesting. In addition, a 5 year time interval coincides with the timing of the Colorado Natural Heritage Program's black-tailed prairie dog mapping efforts in eastern Colorado, from which we constructed our sampling frame. Using updated mapping efforts is vital for monitoring efforts because it may decrease the probability that a plot selected from the sampling frame contains a prairie dog colony that has gone locally extinct. We recommend future efforts should select new plots to survey for burrowing owls in addition to resurveying a subset of the plots from this study. Revisiting sites from this study would be helpful in determining burrowing owl population trends through time, while selecting new plots can increase the spatial coverage of surveys. This 2-year study provides an updated status assessment of burrowing owl populations across the black-tailed prairie dog range in Colorado that will help calibrate burrowing owl population models incorporating prairie dog colony extent, inform future monitoring plans, and help guide conservation of keystone species and their communities.