Preface xv About the Companion Website xvii 1 Biological Diversity: A Geobiological Perspective 1 Zisheng Guo and Xingliang Zhang 1.1 Introduction 1 1.2 Classification of Biological Entities 2 1.2.1 Acellular Life 2 1.2.2 Domains of Cellular Life 4 1.2.

2.1 The LUCA 5 1.2.2.2 The FECA and LECA 7 1.2.3 Kingdoms of Cellular Life 8 1.3 Diversity of Biological Metabolism 9 1.

3.1 Metabolic Classification of Organisms 10 1.3.2 Photosynthesis 11 1.3.2.1 Pigments, Reactions, and Photosystems 11 1.3.

2.2 Oxygenic Photosynthesis 11 1.3.2.3 Anoxygenic Photosynthesis 13 1.3.3 Nitrogen Fixation 15 1.3.

4 Chemolithotrophy: Energy from Oxidation of Inorganics 16 1.3.4.1 Hydrogen-Oxidation: Using the Chemical Energy in H2 to Fix Carbon 17 1.3.4.2 Methanogenesis and Acetogenesis from CO2 Reduction 17 1.3.

4.3 Oxidation of Reduced Sulfur Compounds 19 1.3.4.4 Iron Oxidation 21 1.3.4.5 Manganese Oxidation 22 1.

3.4.6 Ammonia and Nitrite Oxidation: Nitrification 23 1.3.4.7 Anammox 25 1.3.5 Catabolism 26 1.

3.5.1 Glycolysis and Fermentation 26 1.3.5.2 Aerobic Respiration 27 1.3.5.

3 Nitrate Reduction and Denitrification 28 1.3.5.4 Microbial Manganese Reduction 29 1.3.5.5 Ferric Iron Reduction 30 1.3.

5.6 Sulfate Reduction 32 1.3.5.7 Other Electron Acceptors 35 1.3.5.8 Methanogenesis 35 1.

3.5.9 Methanotrophs and Methylotrophs 38 References 39 2 Life in Extreme Environments 43 Zisheng Guo and Xingliang Zhang 2.1 Introduction 43 2.2 Diversity of Extreme Environments and Extremophiles 44 2.2.1 Extreme Environments 44 2.2.

1.1 Extreme Ecosystems 44 2.2.1.2 Extreme Environmental Parameters 46 2.2.2 Phylogenic Diversity of Extremophiles 46 2.2.

2.1 Extremophilic Prokaryotes 46 2.2.2.2 Extremophilic Eukaryotes 54 2.2.2.3 Extremophilic Viruses 55 2.

3 Thermophiles 57 2.3.1 Phylogenic Diversity 57 2.3.2 Adaptive Strategies 58 2.4 Psychrophiles 59 2.4.1 Phylogenic Diversity 59 2.

4.2 Adaptive Strategies 60 2.5 Acidophiles 62 2.5.1 Phylogenic Diversity 62 2.5.2 Adaptive Strategies 63 2.6 Alkaliphiles 63 2.

6.1 Phylogenic Diversity 63 2.6.2 Adaptive Strategies 64 2.7 Halophiles 65 2.7.1 Phylogenic Diversity 66 2.7.

1.1 Halophilic Archaea 66 2.7.1.2 Halophilic Bacteria 66 2.7.1.3 Halophilic Eukaryotes 66 2.

7.2 Adaptive Strategies 67 2.7.2.1 Salt-in and -out Strategies 67 2.7.2.2 Other Strategies 68 2.

8 Xerophiles 68 2.8.1 Low Water Activity Stress 68 2.8.2 Low Water Activity Habitats 69 2.8.3 Adaptive Strategies 69 2.9 Radiodurans 70 2.

9.1 Discovery 70 2.9.2 Radiotolerant Organisms 70 2.9.3 Radiotolerant Mechanisms 71 2.10 Barophiles 72 2.10.

1 Phylogenic Diversity 72 2.10.1.1 Barophilic Prokaryotes 72 2.10.1.2 Barophilic Eukaryotes 73 2.10.

2 Adaptive Strategies 73 2.11 Tardigrades as a Model Animal for Astrobiology 74 2.11.1 Survival Strategies 74 2.11.2 Adaptations to Anhydrobiosis 76 2.11.3 Adaptations to Cryobiosis 77 2.

11.4 Molecular Mechanisms of Radiation and ROS Tolerance 77 2.11.4.1 ROS Scavenging Mechanisms 78 2.11.4.2 DNA Repair Mechanisms 78 2.

11.5 Tardigrades in Space 78 References 79 3 Microbial Ecosystems 87 Wei Liu and Xingliang Zhang 3.1 Introduction 87 3.1.1 From Cell to Microbial Communities 87 3.1.2 Extracellular Polymeric Substances (EPS) 88 3.1.

3 Preservation Potential 90 3.2 Biofilms and Microbial Mats 91 3.2.1 Biofilms 91 3.2.1.1 What Are Biofilms? 91 3.2.

1.2 Why Learn About Biofilms? 92 3.2.1.3 Types of Biofilms 94 3.2.1.4 Development of Biofilms 94 3.

2.1.5 Factors that Affect Biofilm Attachment and Growth 97 3.2.1.6 Fully Functioning Biofilm: Cooperate, Grow, and Spread 97 3.2.1.

7 Biofilm Architecture 98 3.2.1.8 Biochemistry of Biofilm Bacteria 99 3.2.2 Microbial Mats 100 3.2.2.

1 Structure of Microbial Mats 102 3.2.2.2 Morphology and Physical Behaviors 104 3.2.2.3 Microenvironment Within the Microbial Mats 104 3.2.

2.4 Biogeochemistry of Microbial Mats 106 3.3 Microbial Ecosystems on Earth 107 3.3.1 Microbial Ecosystems in Marine Settings 107 3.3.1.1 Basaltic Ocean Crust Ecosystems 107 3.

3.1.2 Hydrothermal Vent Ecosystems 109 3.3.1.3 Cold Seep Ecosystems 113 3.3.2 Microbial Ecosystems in Terrestrial Settings 114 3.

3.2.1 Glacier and Frozen Soil Systems 114 3.3.2.2 Desert System 116 3.3.2.

3 Soil System 119 3.3.2.4 Karst Cave System 121 3.3.3 Microbial Ecosystems in Other Extreme Settings 123 3.3.3.

1 Extremely Acidic System 123 3.3.3.2 High Saline-alkaline System 125 3.3.3.3 Deep Subsurface System 126 3.4 Microbial Ecosystem as a Model for Exploring Life Beyond 129 References 129 4 Earth as a System and Biogeochemical Cycles 135 Weiduo Hao and Xingliang Zhang 4.

1 Introduction 135 4.2 Earth System: An Overview 135 4.2.1 A System Approach 135 4.2.2 Energy Flows of the Earth System 136 4.2.2.

1 Law of Thermodynamics 136 4.2.2.2 Earth''s Energy Budget 136 4.2.2.3 Human Use of Energy Flows 137 4.2.

3 Three Key Traits of the Earth System 138 4.2.3.1 Openness 138 4.2.3.2 Integration 139 4.2.

3.3 Complexity 139 4.3 Biogeochemical Cycles 139 4.3.1 Concept 139 4.3.1.1 Biomass Production 139 4.

3.1.2 Energy Source 140 4.3.1.3 Terminal Electron Acceptors 140 4.3.2 Element Abundance 140 4.

3.3 Carbon Cycle 141 4.3.3.1 Carbon Reservoirs 141 4.3.3.2 Flux: Withdrawal 142 4.

3.3.3 Flux: Addition 143 4.3.3.4 Isotope Fractionation 144 4.3.4 Oxygen Cycle 146 4.

3.4.1 O2 Reservoirs 147 4.3.4.2 O2 Flux: Production 148 4.3.4.

3 O2 Flux: Consumption 149 4.3.5 Nitrogen Cycle 151 4.3.5.1 Reservoirs 152 4.3.5.

2 Flux 152 4.3.5.3 Key Processes 152 4.3.5.4 Isotope Fractionation 154 4.3.

6 Sulfur Cycle 154 4.3.6.1 Reservoirs 155 4.3.6.2 Flux 156 4.3.

6.3 Key Processes 157 4.3.6.4 Organic Sulfur Compounds 158 4.3.6.5 Isotope Fractionation 159 4.

3.7 Phosphorus Cycle 162 4.3.7.1 Reservoirs 162 4.3.7.2 Flux 162 4.

3.7.3 Bioavailability in Ecosystems 164 4.3.7.4 P Supply and Sink 164 4.3.7.

5 Tectonic Controls on Global Phosphorus Cycle 166 4.3.7.6 Human Impact on Global Phosphorus Cycle 166 4.3.8 Iron Cycle 167 4.3.8.

1 Flux 168 4.3.8.2 Key Processes 169 4.4 Major Features of Biogeochemical Cycles 170 4.4.1 Diversity of Pathways 171 4.4.

2 Variable Rates of Cycling 171 4.4.3 The Effects of Human Activity 172 References 173 5 Biomineralization and Its Origin 177 Luoyang Li and Xingliang Zhang 5.1 Introduction 177 5.2 Biominerals and Organominerals 179 5.2.1 Concept and Unique Characteristics 179 5.2.

2 Major Groups of Biominerals 181 5.2.2.1 Carbonate Biominerals 182 5.2.2.2 Phosphate Biominerals 184 5.2.

2.3 Silica Biominerals 185 5.2.2.4 Sulfate Biominerals 186 5.2.2.5 Sulfide Biominerals 186 5.

2.2.6 Oxide and Hydroxide Biominerals 187 5.2.2.7 Organominerals 189 5.3 Classification of Biomineralization 189 5.3.

1 Biologically Influenced Mineralization (BFM) 190 5.3.2 Biologically Induced Mineralization (BIM) 191 5.3.3 Biologically Controlled Mineralization (BCM) 192 5.3.3.1 Weakly vs.

Strictly Biological-Controlled Mineralization 192 5.3.3.2 Biologically Controlled Extracellular Mineralization 193 5.3.3.3 Biologically Controlled Intercellular Mineralization 193 5.3.

3.4 Biologically Controlled Intracellular Mineralization 194 5.4 Principle of Biomineralization 195 5.4.1 Supersaturation and Nucleation 195 5.4.2 Amorphous Phase and Solidification 196 5.4.

3 Hierarchical Organization 198 5.4.4 Genetic and Molecular Systems 199 5.4.5 Benefits and Costs 199 5.4.6 Prokaryotic vs. Eukaryotic Biomineralization 200 5.

5 Origin and Evolution of Biomineralization 201 5.5.1 History of Biomineralization Pathways 201 5.5.2 On the Origin of Animal Skeletons 202 5.5.3 Controls on the Onset of Biomineralization 204 5.5.

3.1 Co-option of Ancestral Biomineralization Toolkit 204 5.5.3.2 Oxygen and Marine Redox 205 5.5.3.3 Biomineralization as a Detoxification Mechanism 205 5.

5.3.4 Mineralogical Stability and Changing Seawater Chemistry 206 5.5.3.5 The Rise of Biological Arm-Race 208 5.5.4 Cambrian Animal Skeletonization: Insights from Molluscs 208 5.

5.4.1 Genetic Co-option Underpinning Shell Diversity 209 5.5.4.2 Fossils and Oldest Molluscan Shells 209 5.5.4.

3 Mineralogy and Seawater Chemistry 210 5.5.4.4 Microbial Attacks and Defensive Strategy 212 5.6 Releasing Biomineralization Signatures from Fossils 214 5.6.1 Diagenesis, Permineralization, and Phosphatization 215 5.6.

2 Recognizing Primary Biomineral Structures 215 5.6.2.1 Identification of the Original Mineralogy 215 5.6.2.2 Preservation of Skeletal Organic Matrix 217 5.6.

2.3 Primary Structures and Diagenetic Growths 217.