Quantitative Viral Ecology

Acknowledgments xi Preface xiii I VIROLOGY: AN ECOLOGICAL PERSPECTIVE 1 1. What Is a Virus? 3 1.1. What Is a Virus? 3 1.2. Dimensions of Viral Biodiversity 7 1.3. Summary 22 2. Viral Life History Traits 24 2.1. Life History Traits in Ecology 24 2.2. Viral Life Cycle 25 2.3. Traits Associated with Lysis 28 2.4. Traits Associated with Lysogeny 39 2.5. Extracellular Traits 46 2.6. Summary 52 II POPULATION AND EVOLUTIONARY DYNAMICS OF VIRUSES AND THEIR MICROBIAL HOSTS 55 3. Population Dynamics of Viruses and Microbes 57 3.1. On Measurements and Models 57 3.2. Viruses and the "Control" of Microbial Populations 58 3.3. Viruses and Oscillatory Dynamics 74 3.4. Linking Microscopic Details with Dynamics 84 3.5. Summary 88 4. Evolutionary Dynamics of Viruses or Microbes, but Not Both 89 4.1. Viruses and the Nature of Mutation 89 4.2. The Effects of Viruses on Host Evolution 98 4.3. The Effects of Hosts on Viral Evolution 110 4.4. Summary 123 5. Coevolutionary Dynamics of Viruses and Microbes 125 5.1. From Sensitivity Relations to Coevolution 125 5.2. Toward "Novel" Coevolution: On the Probability of Compensating Mutations 129 5.3. The Effect of Coevolution on Host and Viral Population Dynamics 137 5.4. Ecological Effects on the Coevolutionary Dynamics of Types and Traits 146 5.5. Summary 159 III VIRAL ECOLOGY IN THE OCEANS: A MODEL SYSTEM FOR MEASUREMENT AND INFERENCE 161 6. Ocean Viruses: On Their Abundance, Diversity, and Target Hosts 163 6.1. Ways of Seeing 163 6.2. Counting Viruses in the Environment 165 6.3. Estimating Viral Diversity 175 6.4. Virus-Microbe Infection Networks 186 6.5. Summary 199 7. Virus-Host Dynamics in a Complex Milieu 201 7.1. Rosenblueth and Wiener's Cat 201 7.2. Many Viruses and Many Hosts 203 7.3. Nutrients and the Viral "Shunt" 213 7.4. Viruses and Grazers 219 7.5. Summary 235 8. The Future of Quantitative Viral Ecology 236 8.1. Current Challenges, in Theory 236 8.2. On the Future of Quantitative Viral Ecology 239 TECHNICAL APPENDIXES 245 A. Viral Life History Traits 247 A.1. Measuring Viral Life History Traits: A Quantitative Perspective 247 A.2. A Core Technique: The Plaque Assay 248 A.3. Protocols for Life History Trait Estimation 254 B. Population Dynamics of Viruses and Microbes 258 B.1. Host-Associated Life History Traits 258 B.2. Linear Stability Analysis of a Nonlinear Dynamical System 259 B.3. Implicit Resource Dynamics as a Limit of Explicit Resource Dynamics 269 B.4. On Poisson Processes and Mean Field Models 270 B.5. A Note on Simulating Dynamical Systems 272 B.6. Analysis of a Population Dynamics Model with Reinfection of Infected Hosts 276 C. Evolutionary Dynamics of Viruses or Microbes, but Not Both 278 C.1. Models of Independent Mutations Arising in the Growth of Populations 278 C.2. Invasion Criterion for Mutant Viruses with Distinct Life History Traits 280 C.3. Deriving the Canonical Equation of Adaptive Dynamics 281 C.4. Simulating Evolutionary Dynamics 283 D. Ocean Viruses: On Their Abundance, Diversity, and Target Hosts 286 D.1. Protocol for Automatic Estimation of Virus-Like Particles from Digital Images Derived from Epifluorescence Microscopy 286 E. Virus-Host Dynamics in a Complex Milieu 288 E.1. A Multitrophic Model to Quantify the Effects of Marine Viruses on Microbial Food Webs and Ecosystem Processes 288 Bibliography 293 Index 319