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Relationships Among Airborne Microbial Communities, Urban Land Uses and Vegetation Cover: Implications for Urban Planning and Human Health

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Relationships Among Airborne Microbial Communities, Urban Land Uses and Vegetation Cover: Implications for Urban Planning and Human Health RELATIONSHIPS AMONG AIRBORNE MICROBIAL COMMUNITIES, URBAN LAND USES AND VEGETATION COVER: IMPLICATIONS FOR URBAN PLANNING AND HUMAN HEALTH by GWYNHWYFER MHUIREACH A DISSERTATION Presented to the Department of Landscape Architecture and the Graduate School of the University of Oregon in partial fulfillment of the requirements for the degree of Doctor of Philosophy June 2018 DISSERTATION APPROVAL PAGE Student: Gwynhwyfer Mhuireach Title: Relationships Among Airborne Microbial Communities, Urban Land Uses and Vegetation Cover: Implications for Urban Planning and Human Health This dissertation has been accepted and approved in partial fulfillment of the requirements for the Doctor of Philosophy degree in the Department of Landscape Architecture by: Bart R. Johnson Chairperson Jessica L. Green Core Member Roxi Thoren Core Member Deb Johnson-Shelton Core Member G.Z. Brown Institutional Representative and Sara D. Hodges Interim Vice Provost and Dean of the Graduate School Original approval signatures are on file with the University of Oregon Graduate School. Degree awarded June 2018 ii © 2018 Gwynhwyfer Mhuireach This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs (United States) License. iii DISSERTATION ABSTRACT Gwynhwyfer Mhuireach Doctor of Philosophy Department of Landscape Architecture June 2018 Title: Relationships Among Airborne Microbial Communities, Urban Land Uses and Vegetation Cover: Implications for Urban Planning and Human Health Variation in exposure to environmental microbial communities has been implicated in the etiology of allergies, asthma and other chronic and immune disorders. In particular, preliminary research suggests that exposure to a high diversity of microbes during early life, for example through living in highly vegetated environments like farms or forests, may have specific health benefits, including immune system development and stimulation. In the face of rapidly growing cities and potential reductions in urban greenspace, it is vital to clarify our understanding of the relationship between vegetation and microbial communities so that we can better design cities that support human health. To explore whether and how urban airborne bacterial communities vary with the amount and structural diversity of nearby vegetation, I used passive air sampling and culture-independent microbial DNA sequencing combined with more traditional landscape architecture tools, including geographic information systems (GIS) and remote sensing data. The results indicated that locations with little vegetation (i.e., paved parking lots) were marked by significantly different bacterial composition from areas that were heavily vegetated (parks and forests). These differences were largely driven by taxonomic groups and indicator species that were enriched at certain sites. My work also shows that regional agricultural activities during the summer may have a substantial effect on airborne bacterial communities in the Eugene-Springfield metropolitan area (Oregon), specifically through elevated abundance of Sphingomonas faeni, a taxon previously isolated from hay dust. The second part of my work focused on building a conceptual bridge between scientific findings and potential design principles that can be tested in practical application. I performed iv a narrative review of vegetation-health, vegetation-microbe, and microbe-health relationships, which formed the foundation of a framework to translate scientific findings into design-relevant concepts. Strengthening this linkage between science and design will help ensure that research questions are relevant to design practice and that new scientific knowledge is accessible to designers. This dissertation includes previously published and unpublished co-authored material. v Curriculum Vitae NAME OF AUTHOR: Gwynhwyfer Mhuireach GRADUATE AND UNDERGRADUATE SCHOOLS ATTENDED: University of Oregon, Eugene, Oregon University of Washington, Seattle, Washington DEGREES AWARDED: Doctor of Philosophy, Landscape Architecture, 2018, University of Oregon Master of Science, Architecture, 2012, University of Oregon. Bachelor of Science, Biology (Ecology, Evolution and Conservation Track), 1999, University of Washington. AREAS OF SPECIAL INTEREST: Microbial Ecology Environmental Health PROFESSIONAL EXPERIENCE: Graduate Teaching Fellowship, Department of Landscape Architecture, 2012 - 2017. Graduate Research Fellowship, Energy Studies in Buildings Laboratory, 2012 - 2017. GRANTS, AWARDS, AND HONORS: University of Oregon Dissertation Research Fellowship, 2017 Travel grant, Department of Defense Microbiome Symposium, US Air Force Academy, Colorado Springs, CO, 2017. Travel grant, National Academies of Science, 3rd Meeting of Microbiomes of the Built Environment Committee, Irvine, CA, 2016. National Academies Fellow, graduated from National Academies Summer Institute on Undergraduate Education, Eugene, OR June 2015. EPA Science To Achieve Results (STAR) Fellowship, 2014. Invited participant, Evolution of Built Environment Microbiome Working Group, National Evolutionary Synthesis Center, Raleigh, NC, 2013. vi Donna V. Sundberg Scholarship in Architecture, 2011. PUBLICATIONS: Mhuireach, G., Johnson, B. R., Altrichter, A. E., Ladau, J., Meadow, J. F., Pollard, K. S., & Green, J. L. (2016). Urban greenness influences airborne bacterial community composition. Sci Total Environ, 571, 680–687. Brown, G.Z., Kline, J., Mhuireach, G., Northcutt, D. and Stenson, J., (2016). Making microbiology of the built environment relevant to design. Microbiome, 4(1), p.1. Martin, L. J., Adams, R. I., Bateman, A., Bik, H. M., Hawks, J., Mhuireach, G., … Dunn, R. R. (2015). Evolution of the indoor biome. Trends in Ecology & Evolution, 30(4), 223–232. Kembel, S. W., Meadow, J. F., O’Connor, T. K., Mhuireach, G., Northcutt, D., Kline, J., … Green, J. L. (2014). Architectural Design Drives the Biogeography of Indoor Bacterial Communities. PLOS ONE, 9(1), e87093. Meadow, J. F., Altrichter, A. E., Kembel, S. W., Kline, J., Mhuireach, G., Moriyama, M., … Bohannan, B. J. M. (2013). Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source. Indoor Air, 24(1), 41–48. Mhuireach, G., Bohannan, B. J. M., Brown, G. Z., Green, J. L., Jones, E., Kembel, S. W., … Womack, A. M. (2012). The relationship between ventilation energy use and indoor microbial communities. In Proceedings of the 10th International Conference on Healthy Buildings. Brisbane, Australia. vii Acknowledgments I profoundly and sincerely appreciate the assistance of Professor Bart Johnson, without whose penetrating insight and sustained enthusiasm this project would never have been completed. Doctor Jessica Green, my co-advisor, deserves special thanks for her extraordinary wisdom and for always having my best interests in mind. I am deeply grateful to Professor Roxi Thoren for her wonderful advice and genuine interest in designing urban landscapes for microbes. I would like to recognize Doctor Deborah Johnson-Shelton, my friend and collaborator, with whom I look forward to many new research endeavors. Professor G.Z. Brown, my long-time mentor, started me on this path and has been a guiding light throughout my graduate career; I appreciate and honor him more than I can express. I wish to thank all of the members, past and present, of the Biology and Built Environment (BioBE) Center and the larger international community of researchers studying microbiology of the built environment, who almost feel like family after working together and meeting at conferences for so many years. In particular, I am grateful to James Meadow, Joshua Ladau, Adam Altrichter, Clarisse Betancourt-Román, for their assistance with the microbiology aspects of my project and their patience in teaching me DNA processing and bioinformatics skills. My heartfelt thanks also goes out to all of the Energy Studies in Buildings staff and researchers, with whom I’ve shared many wonderful (and some stressful) times throughout my graduate career. I am deeply beholden to Kevin Van Den Wymelenberg, Director of ESBL and Co-Director of BioBE, for continuing to consider me part of the team and offer support during the final stages of my PhD. I also gratefully acknowledge the assistance of numerous volunteers in collecting microbial samples, as well as the public and private landowners, including the City of Eugene Parks and Open Space and Willamalane Park and Recreation District, who permitted the collection of samples on their land. My research was supported by the Department of Landscape Architecture at the University of Oregon, by the Biology and Built Environment Center, which was funded through generous grants from the Alfred P. Sloan Foundation, and by a Science to Achieve Results (STAR) viii Fellowship, #91769501-0, from the US Environmental Protection Agency. ix To Lyric and Cadence, who have coped with my graduate studies throughout their early years. All my love. x Table OF Contents Chapter Page I. INTRODUCTION ......................................................................................................................1 II. URBAN GREENNESS INFLUENCES AIRBORNE BACTERIAL COMMUNITY COMPOSITION .........................................................................................8 1. Introduction ..................................................................................................................................8 2. Materials & Methods ..............................................................................................................
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