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The Factors That Influence Prokaryotic and Eukaryotic Community Structure in Indoor Dust

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The Factors That Influence Prokaryotic and Eukaryotic Community Structure in Indoor Dust The Factors that Influence Prokaryotic and Eukaryotic Community Structure in Indoor Dust by Sepideh Pakpour B.Sc. Shahid Beheshti University, Iran, 2006 M.Sc., McGill University, Canada, 2010 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE COLLEGE OF GRADUATE STUDIES (Biology) THE UNIVERSITY OF BRITISH COLUMBIA (Okanagan) December 2015 © Sepideh Pakpour, 2015 Abstract Buildings are complex ecological systems that support a high diversity of prokaryotic and eukaryotic communities. Since many of these organisms interact with humans and their activities, and adding the considerable amount of time modern humans spend indoors, it is critical to understand the taxonomic composition of indoor biota as well as the ecological processes and environmental factors that may influence their diversity and composition. In this thesis, I report on studies where I employed a Next-Generation DNA Sequencing technique, monitored 668 environmental factors and occupants’ activities, conducted advanced multivariate statistical analyses, and demonstrated that community composition of different organisms in indoor environments, including Fungi, Bacteria, and Animals may be influenced by different building characteristics, furnishings, type of occupants as well as their activities. In addition, this is the first study reporting the presence of Archaea in household dust as a common part of the indoor microbiota; however, the archaeal abundance in indoor environment was considerably lower than Bacteria, perhaps because of less available sources contributing to indoor Archaea or more environmental filtering preventing archaeal establishment in indoor environments. This also can be interpreted that the indoor archaeal assemblages are probably allochthonous for the most part (passive entrants of archaeal traces from different sources), in contrast, to those of the Bacteria which are a mixture of allochthonous and autochthonous (live and active inhabitants of dust). Finally, in a separate study with samples collected over a 20-year period, I found that the total airborne fungal spore count in outdoor air would likely increase significantly in future years as a result of climate change, indicating a likely rise in indoor fungal spore abundance as well. ii Overall, this study as one of the first to look for members of all domains of life in a single cohort study, has advanced our understanding of biological components of residential houses and illustrated how community composition of different organisms in the indoor environment may be influenced by different building characteristics, furnishing, and its occupants. I believe such comprehension of indoor ecology can help researchers design intervention studies to provide public health policy decision makers with new tools to improve the built environment. iii Preface This research was conducted at the University of British Columbia, Okanagan campus, under supervision of Dr. John Klironomos. The results of this research have been submitted in peer-reviewed journal articles and conference proceedings. A version of Chapter 1 and Chapter 2 will be submitted as a review journal article (S. Pakpour and J. Klironomos “A synopsis of indoor environment ecology”). This work was wholly drafted by S. Pakpour with editorial comments by Dr. John Klironomos. In addition, a version of some sections of the literature review in Chapter 2 has been published as a book chapter entitled “Micro-fungi in indoor environments: what is known and what is not”, and coauthors of this work are C. Yang, J. Klironomos, and D.W. Li. This In-Press work was partially drafted by S. Pakpour with editorial comments by Drs. J. Klironomos and D.W. Li. Chapter 3 – 6 are collaborative research projects between UBC and research teams of the Canadian Healthy Infant Longitudinal Development (CHILD) study. Dust samples for this research were collected by the research teams of the miniCHILD study in Vancouver, BC, Canada, and sent to S. Pakpour and J. Klironomos by T. Konya in Dr. J. Scott laboratory. A version of Chapter 3 has been submitted as a journal article (S. Pakpour, J. A. Scott, S. E. Turvey, J. R. Brook, T. K. Takaro, M. R. Sears, and J. Klironomos “The Relationship between Indoor Environmental Characteristics and Fungal Community Structure”, submitted to PLoS ONE). For this work, I conducted all the molecular experiments, bioinformatics and statistical analyses, and prepared the manuscript for publication. A preliminary version of this work was accepted as a conference presentation (S. Pakpour, J. Scott, S. Turvey, and J. Klirlonomos (2013) “The environmental determinants of fungal iv community structure in indoor dust”, The Canadian Society for Ecology and Evolution (CSEE), Kelowna, BC, Canada, May 2013). A version of Chapter 4 will be submitted as a journal article (S. Pakpour, J. A. Scott, S. E. Turvey, J. R. Brook, T. K. Takaro, M. R. Sears, and J. Klironomos “Influence of Occupants and Their Activities on Bacterial Communities in Residential Houses”). I conducted all the molecular analyses, bioinformatics and statistical analyses, and prepared the manuscript for publication. A version of Chapter 5 has been submitted as a journal article (S. Pakpour, J. A. Scott, S. E. Turvey, J. R. Brook, T. K. Takaro, M. R. Sears, and J. Klironomos “The relationship between housing characteristics and animal community composition in the dust of indoor environments”, submitted to Indoor Air). I conducted all the molecular analyses, bioinformatics and statistical analyses, and prepared the manuscript for publication. A version of Chapter 6 has been submitted as a journal article (S. Pakpour, J. A. Scott, S. E. Turvey, J. R. Brook, T. K. Takaro, M. R. Sears, and J. Klironomos “Archaea in the indoor environment and their relationship with housing characteristics”, submitted to FEMS Microbiology Ecology). I conducted all the molecular analyses, bioinformatics and statistical analyses, and prepared the manuscript for publication. A version of chapter 7 has been published in a journal article (S. Pakpour, D. W. Li, and , J. Klironomos (2014) “Relationships of fungal spore concentrations in the air and meteorological factors”, Fungal Ecology, 13: 130-134.), and accepted as a conference presentation and published as an extended abstract (S. Pakpour, D.W. Li, and J. Klironomos (2014) “Climatic drivers of airborne fungal spore concentrations in two North American v cities”, Indoor Air, Hong Kong, July 2014). For this study, I conducted the data analysis of test data and wrote the manuscript and the extended abstract. vi Table of Contents Abstract ....................................................................................................................................... ii Preface ....................................................................................................................................... iv Table of Contents ...................................................................................................................... vii List of Tables ........................................................................................................................... xiii List of Figures ........................................................................................................................... xv Acknowledgments ................................................................................................................. xxiii Dedication ............................................................................................................................... xxv Chapter 1: Introduction ............................................................................................................... 1 1.1 Objectives..................................................................................................................... 3 1.2 Outline of the Thesis .................................................................................................... 4 Chapter 2: Literature Review...................................................................................................... 6 2.1 Fungi and the Indoor Environment .............................................................................. 7 2.1.1 Fungal growth on construction and finishing materials ....................................... 9 2.1.2 Fungal products: Mycotoxins ............................................................................. 14 2.1.3 The indoor mycobiome and health problems ..................................................... 19 2.2 Bacteria and the Indoor Environment ........................................................................ 23 2.2.1 The indoor bacterial biota and health problems ................................................. 25 2.3 Animals and the Indoor Environment ........................................................................ 27 vii 2.3.1 Dust Mites ........................................................................................................... 27 2.3.2 Cockroaches ........................................................................................................ 28 2.4 Climate Change and the Indoor Environment ............................................................ 30 Chapter 3: The Relationship between Indoor Environmental Characteristics and Fungal Community Structure ............................................................................................................... 35 3.1 Overview ...................................................................................................................
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