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UC San Diego Electronic Theses and Dissertations UC San Diego UC San Diego Electronic Theses and Dissertations Title Piggyback-the-Winner: lytic to temperate switching of viral communities Permalink https://escholarship.org/uc/item/0h34q8s4 Author Knowles, Benjamin Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO SAN DIEGO STATE UNIVERSITY Piggyback-the-Winner: lytic to temperate switching of viral communities A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biology by Benjamin William Knowles Committee in charge: University of California, San Diego Professor Eric Allen Professor Stuart Sandin San Diego State University Professor Forest Rohwer, Chair Professor Anca Segall, Co-Chair Professor Rob Edwards 2016 SIGNATURE PAGE The Dissertation of Benjamin William Knowles is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego San Diego State University 2016 iii DEDICATION I would like to dedicate this thesis to my Lady, Pearl Quijada. I’d dedicate it to the Cat too, but am loath to endorse her badness. I couldn’t have done it without you. iv EPIGRAPH “Is this a hickey or a bruise?” - Katy Perry “They don’t think it be like it do, but it does.” - Oscar Gamble v TABLE OF CONTENTS SIGNATURE PAGE .............................................................................................. iii DEDICATION ........................................................................................................ iv EPIGRAPH ............................................................................................................ v TABLE OF CONTENTS ........................................................................................ vi LIST OF ABBREVIATIONS .................................................................................. xi LIST OF FIGURES .............................................................................................. xiii LIST OF TABLES ................................................................................................. xv ACKNOWLEDGMENTS ..................................................................................... xvi VITA .................................................................................................................... xix ABSTRACT OF THE DISSERTATION ............................................................. xxvi INTRODUCTION OF THE DISSERTATION ......................................................... 1 REFERENCES .................................................................................................. 6 CHAPTER 1 .......................................................................................................... 8 March from the sea: a brief history of environmental phage ecology from marine to human system. .................................................................................. 8 ABSTRACT ....................................................................................................... 9 You won’t find what you’ve never seen ......................................................... 9 Advances with isolates ................................................................................ 11 vi Discoveries by epifluorescence ................................................................... 12 Massive bacteriocide by rapacious phages ................................................. 14 The tragic price of success .......................................................................... 16 Phage lysogeny and transduction ................................................................ 18 Enter the sequencer .................................................................................... 20 Sequencers with shotguns ........................................................................... 21 Archaeal viruses in the shadows ................................................................. 23 The Dark Matter ........................................................................................... 23 Phage metabolism ....................................................................................... 24 Connecting the ecological dots .................................................................... 26 Metagenomics goes rogue .......................................................................... 27 The future .................................................................................................... 29 ACKNOWLEDGEMENTS ............................................................................... 32 REFERENCES ................................................................................................ 33 FIGURES AND TABLES ................................................................................. 41 CHAPTER 2 ........................................................................................................ 45 Piggyback-the-Winner: lytic to lysogenic switches of viral communities ......... 45 INTRODUCTION ............................................................................................. 46 METHODS ...................................................................................................... 48 Viral and microbial counts ............................................................................ 48 Meta-analysis of cell and viral abundances ................................................. 49 Metaviromic sampling and processing ......................................................... 50 vii Bioinformatics .............................................................................................. 51 Bioinformatic code availability ...................................................................... 53 Incubation experiments ................................................................................ 54 Statistical analysis ....................................................................................... 55 RESULTS ........................................................................................................ 58 Viral and microbial abundance .................................................................... 58 Diversity and functional composition of microbial communities ................... 59 Viral and host abundances in other ecosystems ......................................... 61 Experimental manipulation of host growth rate ............................................ 62 Temperate genes, diversity, and virulence .................................................. 63 DISCUSSION .................................................................................................. 66 SUMMARY POINTS ........................................................................................ 68 ACKNOWLEDGEMENTS ............................................................................... 69 REFERENCES ................................................................................................ 70 FIGURES AND TABLES ................................................................................. 77 CHAPTER 3 ........................................................................................................ 89 Examination of induction-based evidence for host density-dependence of lysogeny suggests potentially novel drivers of natural viral communities ....... 89 INTRODUCTION ............................................................................................. 90 METHODS ...................................................................................................... 93 Published values .......................................................................................... 93 FCIC estimation ........................................................................................... 94 viii In situ studies ............................................................................................... 94 Dilution experiments .................................................................................... 95 Statistical analysis ....................................................................................... 96 RESULTS ........................................................................................................ 98 The global distribution of FCIC studies ........................................................ 98 Host density-dependence of FCIC across studies in published datasets .... 98 Host density-dependence of FCIC within studies in published datasets ..... 99 The distribution of published FCIC values ................................................. 100 The frequency of FCIC values ≤ 0 ............................................................. 100 Experimental manipulation and FCIC ........................................................ 102 DISCUSSION ................................................................................................ 105 Host density as a driver of FCIC in published datasets ............................. 105 Removing the ‘Unheard Third’ of FCIC values ≤ 0 .................................... 105 Induction in mixed communities vs. isolates .............................................. 106 Stochastic effects of dilution on FCIC ........................................................ 107 Dilution stochasticity and viral production assays: ..................................... 108 The Lurking Variable that drives of FCIC ..................................................
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