http://hdl.handle.net/1957/15880 2013-05-25T09:50:06Z http://hdl.handle.net/1957/34446 Drivers of arbuscular mycorrhizal fungal community composition in roots : hosts, neighbors, and environment Phillips, Wendy S. The vast majority of terrestrial plant species live in symbiosis with arbuscular mycorrhizal fungi (AMF). AMF and plants live in complex networks, with roots of individual plants hosting multiple AMF, and single AMF colonizing multiple plants concurrently. Through the exchange of resources, the two partners of this symbiosis can have great effects on each other, effects which can ripple through both communities. What determines the patterns of associations between the partners is still largely unknown. In this dissertation, I examine a variety of factors, and in particular host identity, that could drive the community composition of AMF in roots. I began by surveying the diversity of AMF in roots of 12 plant species at a remnant bunchgrass prairie in Oregon, U.S.A. (Chapter 2). To do that, I first designed new primers for use in polymerase chain reaction (PCR) to specifically amplify DNA from all Glomeromycota species. Using those primers, I found 36 distinct AMF phylogenetic groups, or operational taxonomic units (OTUs) in the roots from the prairie. The proportion of OTUs in the basal order Archaeosporales was greater than in many other environmental surveys. I also conducted an in silico analysis to predict how effectively previously published primers would detect the whole diversity of OTUs I detected. I then assayed AMF community composition in the roots of 50 plants from nine plant species (Chapter 3). To do that, I designed primers specific to 18 of the OTUs detected in the initial field survey and used them to test for the presence of each OTU in the roots individual plants. I used that data to test if AMF community composition in individual roots correlated with host identity, spatial distribution, or soil characteristics. I found host identity was associated with both the richness and the structure of root AMF communities, while spatial distribution and soil characteristics were not. Finally, I performed an experimental test of the effect of host identity and community context on AMF community assembly (Chapter 4). I grew plants from four native perennial plant species, including two common and two federally endangered plants, either individually or in a community of four plants (with one plant of each species). I analyzed the AMF community composition in the roots of all plants after 12 weeks of growth with exposure to a uniform mix of field soil as inoculum. I found that host species identity affected root AMF richness and community composition, and community context affected AMF richness. Only one of the endangered species was highly colonized by AMF, and I did not detect unique AMF communities associated with it. This dissertation provides information on the diversity of AMF at a remnant bunchgrass prairie, an ecosystem which has been the subject of very few studies of AMF. Although a complex mix of factors interact to determine AMF community composition in roots, this work provides strong evidence that host identity plays a major role in that process. Graduation date: 2013 2012-09-06T00:00:00Z http://hdl.handle.net/1957/33786 Defining agricultural sustainability in the Marys River region of Oregon Stanton, Michael (Michael Sean) This ethnographic study explores the social aspects of agricultural land-use in the Marys River region. The study seeks to understand how farmers define sustainability and how their views on agricultural issues help to define a sense of place and identity in the Marys River region, within the context of the globalized agricultural system. This project builds on past research utilizing the theory and praxis of political ecology, but also incorporates elements of bioregionalism to develop a theoretical model of regional political ecology for an integrated and multidisciplinary approach to answering the research questions. The study asks: 1) How do farmers in the Marys River region define agricultural sustainability? 2) What methods do farmers use to develop more sustainable agroecosystems? 3) What do farmers consider to be the most important issues in developing a more sustainable regional community within the globalized system of agriculture? A critical synthesis of information is developed establishing bioregional political ecology within the conceptual framework of the project. The study then describes the broad social and economic contexts that potentially shape and constrain farmer conceptualizations of sustainability, focusing on the contrast between the development and characteristics of the globalized system of industrial agriculture and more traditional systems-based methods considered to be alternative forms of agricultural production. The study then uses this conceptual framework to integrate an historical account describing the development of agriculture in the Marys River region with contemporary ethnographic information collected through participant observation and semi-structured interviews with farmers to provide a more holistic understanding of contemporary definitions of agricultural sustainability. This approach of integrating the qualitative information gathered from local farmers with historical and contemporary background information on land-use allowed for a better understanding of farmers' perspectives and definitions of sustainability. A principle finding from this research was that farmers throughout the Marys River region, regardless of farming styles and practices, consider sustainability primarily as the ability to continue farming into the extended future. Farmers' definitions of sustainability are inherently tied to the 'space' of the farm and these findings provide a common ground for dialogue among stakeholders with differing worldviews. This study helps to fill gaps in the existing literature on sustainability and agricultural land-use in the region; namely the perception and conceptualization of sustainability by its farmers. This more comprehensive understanding of how farmers relate to sustainability will help farmers, policymakers, and other institutions to better work together in making more informed decisions toward building stronger communities and developing a more sustainable bioregion within the global marketplace Graduation date: 2013 2012-09-18T00:00:00Z http://hdl.handle.net/1957/32957 Application of biomarker compounds as tracers for sources and fates of natural and anthropogenic organic matter in the environment Oros, Daniel R. Determination of the source and fate of natural (higher plant lipids, marine lipids, etc.) and anthropogenically (e.g., petroleum, coal emissions) derived hydrocarbons and oxygenated compounds in the environment was accomplished using gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) to characterize or identify molecular biomarkers to be utilized as tracers. The distributions and abundances of biomarkers such as straight chain homologous series (e.g., n-alkanes, n-alkanoic acids, n-alkan-2-ones, n-alkanols, etc.) and cyclic terpenoid compounds (e.g., sesquiterpenoids, diterpenoids, steroids, triterpenoids) were identified in epicuticular waxes from conifers of western North America (natural emissions). These biomarkers and their thermal alteration derivatives were also identified in smoke emissions from known vegetation sources (e.g., conifers, deciduous trees and grasses) and were then applied as tracers in soils, soils that contained wildfire residues and soil/river mud washout after wildfire burning. Where possible, the reaction pathways of transformation from the parent precursor compounds to intermediate and final alteration products were determined from GC-MS data. In addition, molecular tracer analysis was applied to air, water and sediment samples collected from a lacustrine setting (Crater Lake, OR) in order to determine the identities, levels and fates of anthropogenic (i.e., petroleum hydrocarbon contamination from boating and related activities) hydrocarbons in a pristine organic matter sink. This work demonstrated that biomarker tracer analysis is a useful tool for developing environmental management and pollution mitigation strategies. Graduation date: 2000 1999-09-24T00:00:00Z http://hdl.handle.net/1957/32595 Predicting channel stability in Colorado mountain streams using hydrobiogeomorphic and land use data : a cost-sensitive machine learning approach to modeling rapid assessment protocols Morét, Stephanie L. Natural resource data are typically non-linear and complex, yet modeling methods often utilize statistical analysis techniques, such as regression, that are insufficient for use on such data. This research proposes an innovative modeling method based on pattern recognition techniques borrowed from the field of machine learning. These techniques make no data distribution assumptions, can fit non-linear data, can be effective on a small data set, and can be weighted to include relative costs of different predictive errors. Rapid Assessment Protocols (RAPs) are commonly used to collect, analyze, and interpret stream data to assist diverse management decisions. A modeling method was developed to predict the outcome of a RAP in an effort to improve accurate prediction, weighted for cost-effectiveness and safety, while prioritizing investigations and improving monitoring. This method was developed using channel stability data collected from 58 high-elevation streams in the Upper Colorado River Basin. The purpose of the research was to understand the relationships of channel stability to several hydrobiogeomorphic features, easily derived from paper or electronic maps, in an effort to predict channel stability. Given that the RAP used was developed to evaluate channel stability, the research determined: 1) relationships between channel stability and major land-use and hydrobiogeomorphic features, and 2) if a predictive model could be developed to aid in identifying unstable channel reaches while minimizing costs, for the purpose of land management. This research used Pearson's and chi-squared correlations to determine associative relationships between channel stability and major land-use and hydrobiogeomorphic features. The results of the Pearson's correlations were used to build and test classification models using randomly selected training and test sets. The modeling techniques assessed were regression, single decision trees, and bagged (bootstrap aggregated) decision trees. A cost analysis / prediction (CAP) model was developed to incorporate cost-effectiveness and safety into the models. The models were compared based on their 1) performance and 2) operational advantages and disadvantages. A reliable predictive model was developed by integrating a CAP model, receiving operator characteristic curves, and bagged decision trees. This system can be used in conjunction with a GIS to produce maps to guide field investigations. Graduation date: 2001 2001-03-16T00:00:00Z