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Comparison of Physiology and Genome-Wide Expression in Two Nitrosomonas Spp

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Comparison of Physiology and Genome-Wide Expression in Two Nitrosomonas Spp Comparison of physiology and genome-wide expression in two Nitrosomonas spp. under batch cultivation By Mohammad Ghashghavi A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science In Microbiology and Biotechnology Department of Biological Sciences University of Alberta © Mohammad Ghashghavi, 2014 Abstract: Ammonia oxidizing bacteria (AOB) play a central role in the nitrogen cycle by oxidizing ammonia to nitrite. Nitrosomonas europaea ATCC 19718 has been the single most studied AOB that has contributed to our understanding of chemolithotrophic ammonia oxidation. As a closely related species, Nitrosomonas eutropha C91 has also been extensively studied. Both of these bacteria are involved in wastewater treatment systems and play a crucial part in major losses of ammonium-based fertilizers globally. Although comparative genome analysis studies have been done before, change in genome-wide expression between closely related organisms are scarce. In this study, we compared these two organisms through physiology and transcriptomic experiments during exponential and early stationary growth phase. We found that under batch cultivation, N. europaea produces more N2O while N. eutropha consumes more nitrite. From transcriptomic analysis, we also found that there are selections of motility genes that are highly expressed in N. eutropha during early stationary growth phase and such observation was completely absent in N. europaea. Lastly, principle homologous genes that have been well studied had different patterns of expression in these strains. This study not only gives us a better understanding regarding physiology and genome-wide expression of these two AOB, it also opens a wide array of opportunities to further our knowledge in understanding other closely related species with regards to their evolution, physiology and niche preference. ii Acknowledgements: I would like to thank Dr. Lisa Stein for her full support and supervision throughout my graduate career. I’m very grateful for all the feedback during my Masters and throughout the writing of this thesis. I would also like to thank Albert Rosana in aiding with the laboratory work of this thesis. I would like to thank Kerim Kits as well for his continuous and constructive comments and support throughout my graduate career. Lastly, I would like to thank everyone in Dr. Stein’s lab and within the Department of Biological Sciences for their support. Furthermore, I would like to thank each and every professor at the Department of Biological Sciences that have helped throughout my career. I would also like to thank the University of Alberta for accepting me and providing me with the funds, through Teaching Assistantship, needed to complete my postgraduate degree. iii Table of Contents CHAPTER 1 INTRODUCTION ............................................................................................................... 1 1.1 THE EVOLUTION OF THE GLOBAL NITROGEN CYCLE ................................................................................... 1 1.2 THE HISTORY OF NITROGEN CYCLE EVOLUTION DURING THE ANOXIC ERA ............................................. 3 1.3 THE LINK BETWEEN METHANE AND AMMONIA OXIDATION ...................................................................... 6 1.4 TAXONOMY OF AMMONIA OXIDIZING BACTERIA ......................................................................................... 8 1.5 COMPLETE GENOME SEQUENCES OF AOB AND THEIR PROPERTIES ...................................................... 12 1.6 NITROSOMONAS EUROPAEA/NITROSOMONAS MOBILIS LINEAGE ............................................................ 14 1.7 GENERAL ISOLATION, ENRICHMENT, AND MAINTENANCE PROCEDURES ............................................ 18 1.8 ECOLOGY AND APPLICATION ........................................................................................................................ 21 1.9 THE BEGINNING OF NITRIFICATION FOCUSED RESEARCH........................................................................ 24 1.10 NITROSOMONAS EUROPAEA AND ITS GENOME ANALYSIS ....................................................................... 25 1.11 PRINCIPAL NITRIFICATION/DENITRIFICATION ENZYMES IN N. EUROPAEA ....................................... 27 1.12 NITROSOMONAS EUTROPHA AND ITS GENOME ANALYSIS ...................................................................... 32 1.13 MY THESIS PROJECT .................................................................................................................................... 37 CHAPTER 2 MATERIALS AND METHODS ...................................................................................... 39 2.1 CULTURE CARE AND PHYSIOLOGICAL MEASUREMENTS: .......................................................................... 39 2.2 RNA EXTRACTION: ........................................................................................................................................ 40 2.3 RRNA REMOVAL AND RNA PURIFICATION: .............................................................................................. 42 2.4 RNA ANALYSIS: .............................................................................................................................................. 43 CHAPTER 3 RESULTS .......................................................................................................................... 45 3.1 COMPARISON OF PHYSIOLOGY ..................................................................................................................... 45 3.2 GENE EXPRESSION IN N. EUROPAEA ............................................................................................................ 50 3.2.1 Metabolism ................................................................................................................................................... 50 3.2.2 Enzymes ......................................................................................................................................................... 53 3.2.3 Cellular processes ...................................................................................................................................... 55 3.2.4 Membrane proteins .................................................................................................................................. 56 3.2.5 Remaining categories .............................................................................................................................. 57 3.3 GENE EXPRESSION IN N. EUTROPHA ........................................................................................................... 58 3.3.1 Metabolism ................................................................................................................................................... 59 3.3.2 Enzymes ......................................................................................................................................................... 65 3.3.3 Cellular processes ...................................................................................................................................... 69 3.3.4 Environmental Information Processing ......................................................................................... 70 3.3.5 Bacterial Motility ...................................................................................................................................... 71 3.3.6 Remaining categories .............................................................................................................................. 72 3.4 GENE EXPRESSION COMPARISON BETWEEN N. EUROPAEA AND N. EUTROPHA ................................... 73 3.4.1 Metabolism ................................................................................................................................................... 75 3.4.2 Enzymes ......................................................................................................................................................... 77 3.4.3 Cellular processes ...................................................................................................................................... 77 3.4.4 Environmental information processing .......................................................................................... 78 3.4.5 Bacterial motility ...................................................................................................................................... 79 3.4.6 Membrane proteins, Iron-binding proteins and Human diseases ...................................... 80 CHAPTER 4 DISCUSSION .................................................................................................................... 83 4.1 SIMILARITIES AND DIFFERENCES IN GROWTH .......................................................................................... 83 4.2 SIMILARITIES AND DIFFERENCES IN NITRITE PRODUCTION AND O2 CONSUMPTION .......................... 86 4.3 SIMILARITIES AND DIFFERENCES IN N2O PRODUCTION .......................................................................... 90 4.4 GENOME-WIDE EXPRESSION ........................................................................................................................ 92 iv 4.5 BACTERIAL MOTILITY ................................................................................................................................... 95 4.6 EXPRESSION OF PRINCIPAL GENES .............................................................................................................
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