Master of Landscape Architecture / Department of Landscape Architecture,Regional and Community Planning / Blake Belanger / Resilience theory provides an approach for landscape architects to analyze systems and design adaptive environments. C.S. Holling created the theory in response to changing social-ecological systems (Holling 1973). Resilience is the ability of a system to adapt to disturbances and remain in the same state (Walker and Salt 2006). This report proposes a framework that applies resilience to site analysis. The goal of the Resilience Analysis Framework is to help designers address expected and unexpected threats to human well being on a global and local scale. The framework was created by synthesizing findings from a literature review and expert interviews. A literature review based the framework in theory. Interviews with professionals working on the Rebuild by Design (2013) competition grounded the framework in professional practice. The goal of the Rebuild by Design competition was to develop resilient solutions to the changing environment. Synthesizing findings from the literature review and expert interviews resulted in a five part framework. The five parts are: Stakeholder Engagement, System Description & Goal Establishment, System Analysis, System Report, and Prioritization. Stakeholder Engagement is a process that occurs throughout each part of the framework. It includes education, data collection, reporting, and feedback. The System Description & Goal Establishment part describes the basic properties of a system and establishes goals for the future of those properties. System Analysis is an in depth evaluation of the factors determining a system’s level of resilience. The System Report synthesizes the important information from the System Description & Goal Establishment and System Analysis parts. Prioritization performs the essential task of focusing a project by identifying high priority systems. The goals (from the System Description & Goal Establishment and System Analysis parts) for the high priority systems determine the primary goals for the project. These goals inform decisions during the site analysis/strategic planning phase of the design process. The framework was applied to Washington Square Park in Kansas City, Missouri. This application provided an example of how to apply the framework to a park analysis. This report’s main finding was a framework for building evidence to make resilient design decisions.

Master of Science / Division of Biology / John M. Blair / Temperate grasslands are among the most threatened biomes in the world, with the largest historical losses due to conversion to agricultural land. While much of this biome has already been converted, there is concern the last remaining remnants in North America will be converted in response to increasing demand for crops used for ethanol production. Thus, restoring grasslands post-anthropogenic disturbance is increasingly important for conserving grassland biodiversity. Two major challenges for prairie restorations are establishing the many subdominant and rarer species found in native prairie, and offsetting the typical decline in richness and diversity over time as restorations age. Repeated seed addition of targeted species is commonly used to override low and declining plant richness and diversity. While this is generally effective early in restoration (i.e., as communities are establishing), its effectiveness in later stages (i.e., when established communities are often losing diversity) remains unknown. I investigated plant community responses to combinations of resource manipulations and disturbances coupled with a seed addition in a 15-yr old restored grassland to test the hypothesis that spatial resource heterogeneity increases the rate of colonization into established prairie restoration communities. Seeds were added to a long-term restoration experiment involving soil depth manipulations (deep, shallow) crossed with nutrient manipulations (reduced N, ambient N, enriched N). Seedling emergence was generally low and only 8 of the 14 forb species added were detected in the first growing season. I found no effect of increased resource heterogeneity on the abundance or richness of seedlings. There was a significant nutrient effect (p<0.1, α=0.1) on seedling abundance, with higher emergence in the enriched N than the ambient N treatment. I also found unexpected nutrient effects on richness, diversity and Mean C (Mean C = Σ CoCi*Ai, where CoC=Coefficient of Conservatism and A=relative abundance of the ith species). All values, except Mean C, were higher in the enriched N treatment than in either the reduced or ambient N treatments. Mean C was lowest in the enriched N treatment, and highest in the whole-plot control, suggesting that the majority of species contributing to higher richness and diversity in the enriched N treatment were “weedier” species. In a separate experiment, I found no effect of small-scale disturbances (aboveground biomass removal or soil disturbance) on seedling abundance or seedling richness. I did find a marginal effect of disturbance type on seedling richness (p=0.11, α=0.1), with higher seedling richness in the soil disturbance than the aboveground biomass removal treatment. I did not find any disturbance effects on community response variables. These results indicate that recruitment from seed additions into well-established restored communities is relatively low in the first year following a seed addition, regardless of resource availability and heterogeneity. Follow-up studies to determine recruitment rates in subsequent years are needed to elucidate whether recruitment responses are driven more by individual species differences or by environmental mechanisms.

Doctor of Philosophy / Department of Biology / Jack F. Cully, Jr. / Dispersal remains one of the most important, yet least understood, life history traits. As the vehicle of gene flow among populations, dispersal can both relieve inbreeding depression and prevent local adaptation. Regionally, dispersal can stabilize or destabilize metapopulations, given its critical roles in disease transmission among populations as well as recolonization following local extinction events. Furthermore, in light of climate change and increasing habitat loss and fragmentation, the ability to navigate through unfamiliar, unsuitable habitat between populations is essential to the long-term survival of a species across its range. In my dissertation, I present a multi-scale investigation of factors affecting gene flow and disease transmission among populations of a keystone species and an agricultural pest of the North American prairie: the black-tailed prairie dog (Cynomys ludovicianus). Black-tailed prairie dogs are social, ground-dwelling squirrels that live in spatially isolated populations called colonies. First, we conducted a landscape genetic analysis of black-tailed prairie dogs throughout a large portion of their current range. Our estimates of gene flow indicate that the genetic neighborhood size of both male and female prairie dogs reaches 40-60 km within short-grass prairie, whereas colonies within mixed-grass prairie are more isolated. At a broad scale, we observed isolation-by-distance among colonies and great influence of grassland productivity on genetic connectivity; however, neither distance nor landscape characteristics greatly explained observed genetic differentiation among colonies separated by < 50 km. Last, we investigated whether landscape features could predict disease transmission patterns of sylvatic plague among colonies in short-grass prairie and found evidence that pastures act as corridors for plague transmission. Our results indicate that black-tailed prairie dogs are more resilient to habitat loss and fragmentation than other obligate grassland species and likely capable of transmitting sylvatic plague over long distances. Taken together, these studies illustrate how a multi-scale approach can reveal complexities of dispersal dynamics that would otherwise remain undetected.

Master of Science / Department of Biology / Keith B. Gido / Recognizing habitat needs of fishes across space and time is increasingly important for managing altered stream networks, such as in the Colorado River basin. Recent work on warm-water fishes suggest they might benefit from access to tributaries and their confluences. Fish movements or distributions within tributaries relative to distance from mainstem confluences in two streams with different network types (linear versus dendritic) were investigated in the San Juan River basin, USA. Upstream distance from the San Juan River resulted in species declines (Chaco Wash, linear network) or turnover (McElmo Creek, dendritic network). McElmo Creek movement patterns were likely attributed to spring spawning migrations of flannelmouth sucker (Catostomus latipinnis), spawning aggregations of razorback sucker (Xyrauchen texanus), foraging or refuge seeking by Colorado pikeminnow (Ptychocheilus lucius), and monsoon-related movements for channel catfish (Ictalurus punctatus) and razorback sucker. Razorback sucker and Colorado pikeminnow dominated movements at Chaco Wash, suggesting this backwater-like tributary supplied thermal or current refuge, foraging habitat, or both. Within McElmo Creek, a second study explored the importance of confluences by characterizing habitat use and movements of fishes at the junction of McElmo and Yellow Jacket creeks. Native fish dominated the confluence community composition. The reach downstream of the confluence had consistently higher abundances, species richness, and more frequent detections of tagged fishes relative to upstream reaches. Movement behaviors inferred by detection frequency of tagged fish among reaches surrounding the confluence differed among species. Small flannelmouth sucker (< 300 mm) and roundtail chub (Gila robusta) were commonly detected in Yellow Jacket Creek whereas large flannelmouth sucker (> 300 mm), bluehead sucker (C. discobolus), and channel catfish used McElmo Creek reaches. Monsoons increased McElmo Creek discharge which triggered upstream movements of channel catfish and displaced large flannelmouth sucker and bluehead sucker. Monsoons increased movements between McElmo and Yellow Jacket creeks by roundtail chub, small flannelmouth sucker, and black bullhead (Ameiurus melas). Combined, these two field studies emphasized using links between patterns and processes of tributary fish communities. Conservation, rehabilitation, and maintenance of connectivity and habitat heterogeneity at confluence zones likely can be a localized management strategy with expansive ecosystem effects.

Doctor of Philosophy / Division of Biology / Ari M. Jumpponen / Microorganisms are critically important for establishing and maintaining ecosystem properties and processes that fuel and sustain higher-trophic levels. Despite the universal importance of microbes, we know relatively little about the rules and processes that dictate how microbial communities establish and assemble. Largely, we rely on assumptions that microbial community establishment follow similar trajectories as plants, but on a smaller scale. However, these assumptions have been rarely validated and when validation has been attempted, the plant-based theoretical models apply poorly to microbial communities. Here, I utilized genomics-inspired tools to interrogate microbial communities at levels near community saturation to elucidate the rules and patterns of microbial community assembly. I relied on a community filtering model as a framework: potential members of the microbial community are filtered through environmental and/or biotic filters that control which taxa can establish, persist, and coexist. Additionally, I addressed whether two different microbial groups (fungi and bacteria) share similar assembly patterns. Similar dispersal capabilities and mechanisms are thought to result in similar community assembly rules for fungi and bacteria. I queried fungal and bacterial communities along a deglaciated primary successional chronosequence to determine microbial successional dynamics and to determine if fungal and bacterial assemblies are similar or follow trajectories similar to plants. These experiments demonstrate that not only do microbial community assembly dynamics not follow plant-based models of succession, but also that fungal and bacterial community assembly dynamics are distinct. We can no longer assume that because fungi and bacteria share small propagule sizes they follow similar trends. Further, additional studies targeting biotic filters (here, snow algae) suggest strong controls during community assembly, possibly because of fungal predation of the algae or because of fungal utilization of algal exudates. Finally, I examined various technical aspects of sequence-based ecological investigations. These studies aimed to improve microbial community data reliability and analyses.

Doctor of Philosophy / Department of Geography / Melinda Daniels / Geomorphic properties of streams are linked to ecosystem function through processes related to storage, transport, and other drivers regulating biogeochemical conditions. Disturbances altering the physical template of a stream are associated with cascading impacts on ecosystem function. However, few disturbances are studied at long time scales and so the legacy of such events and the implications for ecosystem structure and function are not well understood. This research investigates the role of historic tie-driving, a channel disturbance legacy, in shaping present-day stream channel conditions in the Rocky Mountain region and the associated implications for organic matter dynamics. Using a combination of geomorphic and riparian surveys, organic matter and vegetation sampling, and modeling, I show that components of mountain stream ecosystems have recovered from tie-driving at varying rates. First, I addressed how tie-driving has altered channel morphology and wood loading. Tie-driven streams are narrower, shallower, less rough, and have less wood than non-driven reference reaches. In a second study, I focused on differences in carbon storage within the stream and riparian area between tie-driven and non-driven streams. Carbon stored on the landscape represents a long-term component of the terrestrial carbon cycle and some, but not all, components have been impacted by tie-driving. Large instream wood, coarse downed wood, and fine downed wood were identified as carbon storage components that were significantly smaller in tie-driven stream-riparian corridors. Finally, I modeled whole stream ecosystem metabolism and tested whether abiotic drivers influenced variations in rates of gross primary productivity (GPP), ecosystem respiration (ER), and net ecosystem productivity (NEP). Results from this work suggest that rates of GPP were significantly different between tie-driven and non-driven streams and were partially explained by variations in light related to canopy structure. However, variations in ER and NEP were not significantly different between tie-driven and non-driven sites. Taken as a whole, this work shows that ecosystems bear the imprint of historic disturbances but individual ecosystem components recover at differing rates. Additionally, integrating stream hydro-geomorphic and ecological dynamics is an effective approach to understanding the impact of channel disturbances in shaping ecosystem function at a variety of spatial and temporal scales.

Master of Science / Division of Biology / Martha E. Mather / In contrast to well documented adverse impacts of large dams, little is known about how smaller low-head dams affect fish biodiversity. Over 2,000,000 low-head dams fragment United States streams and rivers and can alter biodiversity. The spatial impacts of low-head dams on geomorphology and ecology are largely untested despite how numerous they are. A select review of how intact low-head dams affect fish species identified four methodological inconsistencies that impede our ability to generalize about the ecological impacts of low-head dams on fish biodiversity. We tested the effect of low-head dams on fish biodiversity (1) upstream vs. downstream at dams and (2) downstream of dammed vs. undammed sites. Fish assemblages for both approaches were evaluated using three summary metrics and habitat guilds based on species occurrence in pools, riffles, and runs. Downstream of dams vs. undammed sites, we tested if (a) spatial extent of dam disturbance, (b) reference site choice, and (c) site variability altered fish biodiversity at dams. Based on information from geomorphic literature, we quantified the spatial extent of low-head dam impacts using width, depth, and substrate. Sites up- and downstream of dams had different fish assemblages regardless of the measure of fish biodiversity. Richness, abundance and Shannon’s index were significantly lower upstream compared to downstream of dams. In addition, only three of seven habitat guilds were present upstream of dams. Methodological decisions about spatial extent, and reference choice affected observed fish assemblage responses between dammed and undammed sites. For example, species richness was significantly different when comparing transects within the spatial extent of dam impact but not when transects outside the dam footprint were included. Site variability did not significantly influence fish response. These small but ubiquitous disturbances may have large ecological impacts because of their potential cumulative effects. Therefore, low-head dams need to be examined using a contextual riverscape approach. How low-head dam studies are designed has important ecological insights for scientific generalizations and methodological consequences for interpretations about low-head dam effects. My research provides a template on which to build this approach that will benefit both ecology and conservation.

Master of Science / Department of Biology / David C. Hartnett / The effects of bison activities on forb diversity and cover have been well-established, but less is known about how forb life history is altered by bison-mediated habitat changes. This study had three main objectives: 1) to evaluate the hypothesis that release from aboveground competition with grasses may contribute to the increased cover and diversity of forbs in prairie grazed by bison relative to ungrazed prairie, 2) to determine whether differences in forb reproductive effort between grazed and ungrazed habitats were size-dependent, and 3) to look for evidence of a trade-off between allocation to vegetative and sexual reproduction. The growth, biomass allocation, and sexual reproduction of six common unpalatable perennial species were measured and compared between bison-grazed and ungrazed tallgrass prairie burned at 2-year intervals: Ambrosia psilostachya, Artemisia ludoviciana, Baptisia australis, Psoralidium tenuiflorum, Solidago canadensis, and Vernonia baldwinii. Vegetative reproduction was also measured for B. australis¸ S. canadensis, and V. baldwinii. Light availability, canopy density and height, and percent cover of neighboring plants were measured in each studied individual’s immediate neighborhood and compared between habitats to establish the possibility of differing aboveground competition. Aboveground competition may be lower in bison-grazed habitats, as evidenced by differences in habitat characteristics and plant performance found in this study. In bison-present habitats, sexual reproduction was elevated for all six species and average plant size was greater for all species except A. psilostachya. Vegetative reproduction was not clearly different between habitats for all three species examined. Sexual reproduction increased with size for all species, and the relationship differed significantly between habitats for all species except A. psilostachya. Allocation to vegetative reproduction was not generally related to aboveground biomass, nor was there a clear trade-off between allocation to vegetative and sexual reproduction. The results of this study provide evidence that release from aboveground competition with grasses promotes the growth and sexual reproduction of the studied species of forb, and that differences in sexual reproduction are not entirely size-dependent. Patterns in allocation to vegetative reproduction were less clear and were not clearly tied to sexual reproductive allocation.

Doctor of Philosophy / Biology / Walter K. Dodds / Ari M. Jumpponen / Due to agricultural practices and urbanization, tallgrass prairie ecosystems have become threatened as < 5% of its historical coverage exists today. The small remainder of praire that does exist is further threatened by the encroachment of woody plant species. Woody plant encroachment may not only alter prairie ecosystem function, but also prairie microbial communities responsible for these functional processes. Further, prairies are high disturbance ecosystems, especially prairie streams which are hydrologically harsh. They support communities that frequently undergo succession due to recurring flood and drought conditions, yet little is known about the response of microbial communities to these disturbances. In my dissertation, I first address the degree of woody vegetation expansion in riparian corridors (parallel to streams) in watersheds with variable fire frequency and grazing. I found that the rate of riparian woody expansion declines with higher fire intervals and is not affected by grazing, but even annual burns may not prevent woody plant expansion in riparian zones from occurring. Second, I quantified the effect of using restorations of riparian corridors, through removal of woody plants, on physical, chemical, and microbial community (bacteria and fungi) dynamics across stream to upslope soils. Removal restoration causes a decrease in NH₄⁺ and soil water content, and causes streams and upslope soils to become similar in fungal community richness unlike forested landscapes. Bacterial communities were minimally impacted by removals, but were highly structured among stream to upslope soils due to multiple environmental gradients (i.e., pH, NO₃⁻, soil moisture). Lastly, I examined the successional development of biofilm-associated microbial communities in a prairie stream from both a functional and structural perspective. I found that biofilm microbes exhibited strong successional trajectories, with communities developing towards net autotrophy and therefore becoming reliant upon in-stream derived carbon. Further, bacterial communities displayed spatial differences, but much stronger temporal patterns in community composition were detected. These studies highlight how woody plant encroachment may influence stream ecosystems in addition to spatiotemporal trends in microbial community assembly.

Doctor of Philosophy / Department of Biology / Ari M. Jumpponen / Dark septate endophytes (DSE) are darkly pigmented microfungal ascomycetes commonly observed in the healthy plant roots. Studying the functional roles of DSE is challenging as fundamental information about their identity, nutritional requirements, host range or host preference are lacking. Objective 1: root colonizing fungi were isolated from Konza plants roots and DSE fungi were identified by testing Koch’s postulates using leek plants. Periconia macrospinosa and Microdochium sp., were identified as DSE as they produced microsclerotia and chlamydospores in the root cortex. Select DSE were tested for their enzymatic capabilities and ability to utilize nitrogen sources: fungi tested positive for amylase, cellulase, polyphenol oxidases and gelatinase. Periconia isolates utilized organic and inorganic nitrogen suggesting facultative biotrophic and saprotrophic habits. Objective 2: a Microdochium isolate and three Periconia isolates were screened on 16 plant species (six native grasses and forbs, four crops) in a resynthesis system to test host range. DSE colonized all plant species, albeit to varying degrees. Host biomass and nutritional levels to DSE colonization varied within and among host species confirming the broad host range. Based on % responsiveness to DSE colonization, a metric similar to ‘mycorrhizal dependency’, grasses responded positively, while forbs and crops responded negatively. To test this observed ‘host preference’ under natural conditions, Konza roots from seven grass and nine forb species were surveyed for DSE colonization. Grasses hosted 50% greater DSE than forbs, supporting the broad host range and host preference of DSE fungi. Objective 3: three conspecific Arabidopsis ecotypes, Col-0, Cvi-0 and Kin-1 were inoculated with 25 P. macrospinosa isolates in resynthesis system. The three ecotypes responded differently to inoculation: Col-0 and Cvi-0 responded negatively, while Kin-1 response was neutral. Despite the negative or neutral response, each ecotype responded positively to one or two isolates. The outcomes were along the mutualism-parasitism continuum precluding an unambiguous assignment to any particular life-style. This study shows that the outcomes along this continuum are dictated by host and fungal genotypes. However, the more important question about their function remains. Additional studies with Arabidopsis microarrays are likely to provide unique insights into the potential roles of DSE.