About the Author ix Preface xi About the Companion Website xiii 1 Setting the Scene 1 1.1 The Physical and Chemical Environment of the MMFW 2 1.2 Competitive and Defensive Characteristics of Biological Actors in the MMFW 9 1.2.1 Prokaryotes 11 1.2.2 Protists 12 1.2.

2.1 Flagellates 13 1.2.2.2 Diatoms 16 1.2.2.3 Ciliates 18 1.

2.3 Metazoan Top Predators on the MMFW 19 1.2.3.1 Copepods 19 1.2.3.2 Euphausiids (Krill) 20 1.

2.3.3 Appendicularians 21 1.2.3.4 Rotifers 21 1.2.4 Viruses 21 1.

3 New Methods and New Concepts: Paradigm Shifts in Our Understanding of the Mmfw 23 References 28 2 Control Mechanism in Food Chains and Food Webs 37 2.1 Top-Down and Bottom-Up Control in Food Chain 37 2.2 Biomass Versus Growth Rate Limitation 38 2.3 New, Regenerated, and Export Production. What Determines N T ? 40 2.4 Using an Idealized Mathematical Model to Illustrate the Effects of Food Chain Closure, Stability, Recycling, Defence, Fitness, and Trade-Off 42 2.4.1 Properties of the Steady State 43 2.

4.2 Food Web Closure 44 2.4.3 Biomasses and Mass Transfer Rates Scale Differently with Nutrient Content N T 45 2.4.4 Transients and Stability 45 2.5 Fitness and Trade-Off 47 2.6 Monod and Droop Models for Microbial Growth 48 2.

7 Competition and Coexistence 50 2.7.1 Bottom-Up-Driven Coexistence 50 2.7.2 Top-Down-Driven Coexistence 50 2.7.3 Pentagon Structures 54 2.8 KtW as a Factor in the Evolution of Present-Day MMFW 55 References 57 3 The Microscale: Microbial Movement and Encounters 59 3.

1 α-Parameters and Encounter Kernels 60 3.1.1 What Is the Secret Behind the Diatom Success? 65 3.1.2 Predator and Prey Interactions 66 3.2 Temperature Sensitivity of the MMFW 67 References 68 4 MinMod, a Minimum Model for the MMFW 71 4.1 Model Structure and Philosophy 72 4.2 Model Behaviour 73 4.

2.1 Food Web Closure, Characteristic Time Scales and the Difference Between Drivers and Variables 73 4.2.2 The Cascading Effect from Copepods 74 4.2.3 Bacteria-Diatom Balance and Competition for Mineral Nutrients 75 4.3 The Mathematical Formulation 77 4.3.

1 The Steady States 81 4.3.1.1 Different States According to Diatom Status 81 4.3.1.2 Steady States with C-Limited Bacteria 83 4.3.

2 The Transients 84 4.4 The Importance of Model ''Transparency'' 85 References 86 5 Prokaryote Diversity and Flux Partitioning 87 5.1 On Fitness, Species Dominance and Evolutionary Stable Communities 90 5.2 The Structuring Effect of Prokaryote Predator Defence 92 5.3 The Structuring Effect of Defence Against Viruses 94 5.3.1 Virus Abundance and Flux Partitioning 95 5.3.

2 Viruses, Diversity and Flux Partitioning 103 5.3.3 Host-Virus Arms Races and Experimental Evolution 107 5.4 Species and Strain Diversity, and Flux Partitioning in a One-Species Host-Virus-Predator System 111 5.4.1 Diversity, and Flux Partitioning in a Mixed Prokaryote Community 116 5.5 A Summarizing Hypothesis for How Trade-offs Determines Prokaryote Diversity 125 References 126 6 The Role of Competition and Defence Microbial Genome Organization 131 6.1 Prokaryote Species in Natural Habitats Are not Clonal 131 6.

2 An Enigmatic Outlier? The Huge Genome of Dinoflagellates 133 References 134 7 Element Cycles and Ecological Stoichiometry of the MMFW 137 7.1 Ocean Nutrient Content and N : P Ratio 138 7.2 The Si-Cycle 139 7.3 The C-Cycle 140 7.4 Genetic Consequences of Nutrient Limitation 143 References 144 8 Basin Scale Drivers of the MMFW 147 8.1 The Arctic 148 8.1.1 Physical Conditions 148 8.

1.2 The Arctic Microbial Food Web 149 8.2 The Mediterranean Sea 152 8.2.1 Circulation and Oligotrophication 152 8.2.2 Why Is the Mediterranean P-Limited? 153 8.2.

3 Using the Oligotrophication Gradient to Explore the Pelagic Carbon Cycle 154 8.3 Iron Limitation and HNLC Regions 158 References 160 9 MMFW in the Ocean''s Interior 165 9.1 Missing Energy Source or Technical Measurement Problems? 166 9.2 Protistan Predators in the Ocean''s Interior 169 9.3 Prokaryote Diversity and Viruses in the Aphotic Ocean 170 9.4 Connections to the Upper Part of the Pelagic Food Web 171 References 173 10 Power Laws and Fractal Properties 175 10.1 Equal Mass in Each Decadal Size Class in the Food Chain? 176 10.2 Size and Metabolic Rates 177 References 179 11 Applied Aspects 181 11.

1 Marine Pathogens, A Product of Coincidental Evolution? 181 11.2 Bioremediation 183 11.3 Eutrophication 185 11.3.1 Food Web Effects: The Example of Shallow Lake Restoration 185 11.3.2 Coastal Eutrophication. The Interplay Between Land Use, Runoff and Hydrography 186 11.

3.3 Climate Change 189 References 193 12 Some Aspects of MMFW That Are Not Included in MinMod 199 12.1 Complications in the Left Pentagon 199 12.1.1 Mixotroph Protists 199 12.1.2 Picoautotrophs 200 12.1.

3 Coccolithophores 201 12.2 Complications in the Right Pentagon 201 12.2.1 Dinoflagellates 201 12.3 Alternative Pathways? Bypass and Tunnelling 202 References 202 13 Other Perspectives 205 13.1 Similarities and Differences in Terrestrial Systems 205 13.2 A Final Comment: Competition and Defence from an Anthropocentric Perspective 207 References 208 Appendix 211 Index 213.