Introduction to Geobiology

Xingliang Zhang, Department of Geology, Northwest University, Xi’an, China. Zisheng Guo, College of Life Sciences, Northwest University, Xi’an, China. Wei Liu, Northwest University Museum, Northwest University, Xi’an, China. Ruliang He, Department of Geology, Northwest University, Xi’an, China. Luoyang Li, College of Marine Geosciences, Ocean University of China, Qingdao, China. Weiduo Hao, Department of Geology, Northwest University, Xi’an, China.

• Preface xvAbout the Companion Website xvii1 Biological Diversity: A Geobiological Perspective 1Zisheng Guo and Xingliang Zhang1.1 Introduction 11.2 Classification of Biological Entities 21.2.1 Acellular Life 21.2.2 Domains of Cellular Life 41.2.2.1 The LUCA 51.2.2.2 The FECA and LECA 71.2.3 Kingdoms of Cellular Life 81.3 Diversity of Biological Metabolism 91.3.1 Metabolic Classification of Organisms 101.3.2 Photosynthesis 111.3.2.1 Pigments, Reactions, and Photosystems 111.3.2.2 Oxygenic Photosynthesis 111.3.2.3 Anoxygenic Photosynthesis 131.3.3 Nitrogen Fixation 151.3.4 Chemolithotrophy: Energy from Oxidation of Inorganics 161.3.4.1 Hydrogen-Oxidation: Using the Chemical Energy in H2 to Fix Carbon 171.3.4.2 Methanogenesis and Acetogenesis from CO2 Reduction 171.3.4.3 Oxidation of Reduced Sulfur Compounds 191.3.4.4 Iron Oxidation 211.3.4.5 Manganese Oxidation 221.3.4.6 Ammonia and Nitrite Oxidation: Nitrification 231.3.4.7 Anammox 251.3.5 Catabolism 261.3.5.1 Glycolysis and Fermentation 261.3.5.2 Aerobic Respiration 271.3.5.3 Nitrate Reduction and Denitrification 281.3.5.4 Microbial Manganese Reduction 291.3.5.5 Ferric Iron Reduction 301.3.5.6 Sulfate Reduction 321.3.5.7 Other Electron Acceptors 351.3.5.8 Methanogenesis 351.3.5.9 Methanotrophs and Methylotrophs 38References 392 Life in Extreme Environments 43Zisheng Guo and Xingliang Zhang2.1 Introduction 432.2 Diversity of Extreme Environments and Extremophiles 442.2.1 Extreme Environments 442.2.1.1 Extreme Ecosystems 442.2.1.2 Extreme Environmental Parameters 462.2.2 Phylogenic Diversity of Extremophiles 462.2.2.1 Extremophilic Prokaryotes 462.2.2.2 Extremophilic Eukaryotes 542.2.2.3 Extremophilic Viruses 552.3 Thermophiles 572.3.1 Phylogenic Diversity 572.3.2 Adaptive Strategies 582.4 Psychrophiles 592.4.1 Phylogenic Diversity 592.4.2 Adaptive Strategies 602.5 Acidophiles 622.5.1 Phylogenic Diversity 622.5.2 Adaptive Strategies 632.6 Alkaliphiles 632.6.1 Phylogenic Diversity 632.6.2 Adaptive Strategies 642.7 Halophiles 652.7.1 Phylogenic Diversity 662.7.1.1 Halophilic Archaea 662.7.1.2 Halophilic Bacteria 662.7.1.3 Halophilic Eukaryotes 662.7.2 Adaptive Strategies 672.7.2.1 Salt-in and -out Strategies 672.7.2.2 Other Strategies 682.8 Xerophiles 682.8.1 Low Water Activity Stress 682.8.2 Low Water Activity Habitats 692.8.3 Adaptive Strategies 692.9 Radiodurans 702.9.1 Discovery 702.9.2 Radiotolerant Organisms 702.9.3 Radiotolerant Mechanisms 712.10 Barophiles 722.10.1 Phylogenic Diversity 722.10.1.1 Barophilic Prokaryotes 722.10.1.2 Barophilic Eukaryotes 732.10.2 Adaptive Strategies 732.11 Tardigrades as a Model Animal for Astrobiology 742.11.1 Survival Strategies 742.11.2 Adaptations to Anhydrobiosis 762.11.3 Adaptations to Cryobiosis 772.11.4 Molecular Mechanisms of Radiation and ROS Tolerance 772.11.4.1 ROS Scavenging Mechanisms 782.11.4.2 DNA Repair Mechanisms 782.11.5 Tardigrades in Space 78References 793 Microbial Ecosystems 87Wei Liu and Xingliang Zhang3.1 Introduction 873.1.1 From Cell to Microbial Communities 873.1.2 Extracellular Polymeric Substances (EPS) 883.1.3 Preservation Potential 903.2 Biofilms and Microbial Mats 913.2.1 Biofilms 913.2.1.1 What Are Biofilms? 913.2.1.2 Why Learn About Biofilms? 923.2.1.3 Types of Biofilms 943.2.1.4 Development of Biofilms 943.2.1.5 Factors that Affect Biofilm Attachment and Growth 973.2.1.6 Fully Functioning Biofilm: Cooperate, Grow, and Spread 973.2.1.7 Biofilm Architecture 983.2.1.8 Biochemistry of Biofilm Bacteria 993.2.2 Microbial Mats 1003.2.2.1 Structure of Microbial Mats 1023.2.2.2 Morphology and Physical Behaviors 1043.2.2.3 Microenvironment Within the Microbial Mats 1043.2.2.4 Biogeochemistry of Microbial Mats 1063.3 Microbial Ecosystems on Earth 1073.3.1 Microbial Ecosystems in Marine Settings 1073.3.1.1 Basaltic Ocean Crust Ecosystems 1073.3.1.2 Hydrothermal Vent Ecosystems 1093.3.1.3 Cold Seep Ecosystems 1133.3.2 Microbial Ecosystems in Terrestrial Settings 1143.3.2.1 Glacier and Frozen Soil Systems 1143.3.2.2 Desert System 1163.3.2.3 Soil System 1193.3.2.4 Karst Cave System 1213.3.3 Microbial Ecosystems in Other Extreme Settings 1233.3.3.1 Extremely Acidic System 1233.3.3.2 High Saline-alkaline System 1253.3.3.3 Deep Subsurface System 1263.4 Microbial Ecosystem as a Model for Exploring Life Beyond 129References 1294 Earth as a System and Biogeochemical Cycles 135Weiduo Hao and Xingliang Zhang4.1 Introduction 1354.2 Earth System: An Overview 1354.2.1 A System Approach 1354.2.2 Energy Flows of the Earth System 1364.2.2.1 Law of Thermodynamics 1364.2.2.2 Earth’s Energy Budget 1364.2.2.3 Human Use of Energy Flows 1374.2.3 Three Key Traits of the Earth System 1384.2.3.1 Openness 1384.2.3.2 Integration 1394.2.3.3 Complexity 1394.3 Biogeochemical Cycles 1394.3.1 Concept 1394.3.1.1 Biomass Production 1394.3.1.2 Energy Source 1404.3.1.3 Terminal Electron Acceptors 1404.3.2 Element Abundance 1404.3.3 Carbon Cycle 1414.3.3.1 Carbon Reservoirs 1414.3.3.2 Flux: Withdrawal 1424.3.3.3 Flux: Addition 1434.3.3.4 Isotope Fractionation 1444.3.4 Oxygen Cycle 1464.3.4.1 O2 Reservoirs 1474.3.4.2 O2 Flux: Production 1484.3.4.3 O2 Flux: Consumption 1494.3.5 Nitrogen Cycle 1514.3.5.1 Reservoirs 1524.3.5.2 Flux 1524.3.5.3 Key Processes 1524.3.5.4 Isotope Fractionation 1544.3.6 Sulfur Cycle 1544.3.6.1 Reservoirs 1554.3.6.2 Flux 1564.3.6.3 Key Processes 1574.3.6.4 Organic Sulfur Compounds 1584.3.6.5 Isotope Fractionation 1594.3.7 Phosphorus Cycle 1624.3.7.1 Reservoirs 1624.3.7.2 Flux 1624.3.7.3 Bioavailability in Ecosystems 1644.3.7.4 P Supply and Sink 1644.3.7.5 Tectonic Controls on Global Phosphorus Cycle 1664.3.7.6 Human Impact on Global Phosphorus Cycle 1664.3.8 Iron Cycle 1674.3.8.1 Flux 1684.3.8.2 Key Processes 1694.4 Major Features of Biogeochemical Cycles 1704.4.1 Diversity of Pathways 1714.4.2 Variable Rates of Cycling 1714.4.3 The Effects of Human Activity 172References 1735 Biomineralization and Its Origin 177Luoyang Li and Xingliang Zhang5.1 Introduction 1775.2 Biominerals and Organominerals 1795.2.1 Concept and Unique Characteristics 1795.2.2 Major Groups of Biominerals 1815.2.2.1 Carbonate Biominerals 1825.2.2.2 Phosphate Biominerals 1845.2.2.3 Silica Biominerals 1855.2.2.4 Sulfate Biominerals 1865.2.2.5 Sulfide Biominerals 1865.2.2.6 Oxide and Hydroxide Biominerals 1875.2.2.7 Organominerals 1895.3 Classification of Biomineralization 1895.3.1 Biologically Influenced Mineralization (BFM) 1905.3.2 Biologically Induced Mineralization (BIM) 1915.3.3 Biologically Controlled Mineralization (BCM) 1925.3.3.1 Weakly vs. Strictly Biological-Controlled Mineralization 1925.3.3.2 Biologically Controlled Extracellular Mineralization 1935.3.3.3 Biologically Controlled Intercellular Mineralization 1935.3.3.4 Biologically Controlled Intracellular Mineralization 1945.4 Principle of Biomineralization 1955.4.1 Supersaturation and Nucleation 1955.4.2 Amorphous Phase and Solidification 1965.4.3 Hierarchical Organization 1985.4.4 Genetic and Molecular Systems 1995.4.5 Benefits and Costs 1995.4.6 Prokaryotic vs. Eukaryotic Biomineralization 2005.5 Origin and Evolution of Biomineralization 2015.5.1 History of Biomineralization Pathways 2015.5.2 On the Origin of Animal Skeletons 2025.5.3 Controls on the Onset of Biomineralization 2045.5.3.1 Co-option of Ancestral Biomineralization Toolkit 2045.5.3.2 Oxygen and Marine Redox 2055.5.3.3 Biomineralization as a Detoxification Mechanism 2055.5.3.4 Mineralogical Stability and Changing Seawater Chemistry 2065.5.3.5 The Rise of Biological Arm-Race 2085.5.4 Cambrian Animal Skeletonization: Insights from Molluscs 2085.5.4.1 Genetic Co-option Underpinning Shell Diversity 2095.5.4.2 Fossils and Oldest Molluscan Shells 2095.5.4.3 Mineralogy and Seawater Chemistry 2105.5.4.4 Microbial Attacks and Defensive Strategy 2125.6 Releasing Biomineralization Signatures from Fossils 2145.6.1 Diagenesis, Permineralization, and Phosphatization 2155.6.2 Recognizing Primary Biomineral Structures 2155.6.2.1 Identification of the Original Mineralogy 2155.6.2.2 Preservation of Skeletal Organic Matrix 2175.6.2.3 Primary Structures and Diagenetic Growths 2175.6.3 Biomineralization in Phylogenetic Systematics 2185.6.4 Skeletal Sediments and Paleoenvironmental Reconstruction 219References 2206 Biosedimentation 227Wei Liu and Xingliang Zhang6.1 Introduction 2276.2 Biogenic Sediments 2286.2.1 Carbonates 2296.2.1.1 Limestones are Biological Sediments 2306.2.1.2 Microbialites 2356.2.1.3 Methane-Seep Carbonates 2386.2.1.4 “Dolomite Problem” and Microbial Dolomite Models 2416.2.2 Siliceous Sediments 2436.2.2.1 Primary Sediments 2436.2.2.2 Formation of Chert 2456.2.3 Phosphatic Sediments 2476.2.3.1 Phosphorus Source 2486.2.3.2 Phosphorus Uptake 2486.2.3.3 Phosphorus Concentration 2496.2.3.4 Apatite Precipitation 2496.2.3.5 Microbial Structures in Phosphatic Rocks 2496.2.3.6 Grains and Groundmasses 2516.2.4 Iron Sediments 2516.2.4.1 Sedimentary Pyrite 2526.2.4.2 Banded Iron Formations 2536.3 Biological Diagenesis 2576.3.1 Biogeochemical Zonation of Sediment Column 2586.3.2 Diagenetic Mineralization 2616.3.2.1 Diagenetic Carbonate Minerals 2616.3.2.2 Diagenetic Phosphate Minerals 2626.3.2.3 Amorphous Silica 2626.4 Microbially Induced Sedimentary Structures 2626.4.1 Definition 2626.4.2 Classification 2636.4.3 Biological Processes in MISS Formation 2636.4.3.1 Growth 2636.4.3.2 Biostabilization 2686.4.3.3 Baffling and Trapping 2696.4.3.4 Binding 2696.4.3.5 Interference of Microbial Activities Interacting with Physical Environments 2696.4.4 Distribution and Preservation 2706.4.4.1 Temporal and Spatial Distribution 2706.4.4.2 Preservation and Recognition 2716.5 Astrobiological Implications 272References 2737 Bioerosion and Biological Weathering 279Ruliang He and Xingliang Zhang7.1 Introduction 2797.2 Bioerosion 2807.2.1 Macroborers 2827.2.1.1 Macroboring Groups 2827.2.1.2 Insight into Boring Sponges 2857.2.1.3 Insight into Boring Bivalves 2877.2.2 External Grazers and Scrapers (Raspers) 2897.2.3 Microborers 2927.2.3.1 Microbial Endolithic Groups 2927.2.3.2 Diverse Endolithic Habitats 2927.2.3.3 Geological Evolution of Microborings 2937.2.3.4 Geological and Astrobiological Implications 2947.3 Biological Weathering 2957.3.1 Biological Mechanisms That Enhance Rock Weathering 2957.3.1.1 Plant Roots 2957.3.1.2 Animals 2957.3.1.3 Microbial Communities 2967.3.2 Biological Weathering of Silicate Minerals and Rocks 2977.3.2.1 Feldspar 2987.3.2.2 Silica 2997.3.2.3 Mafic Rocks and Minerals 2997.3.3 Carbonate Weathering 3007.3.4 Sulfide Mineral Oxidation 3017.3.5 Insight into Lichen Weathering 3027.3.5.1 Physical Processes 3037.3.5.2 Biochemical Processes 3037.3.5.3 A Zone Model 3037.4 Soil as a Classic System of Biological Weathering 3047.4.1 Soil Development 3057.4.2 Horizons of Soil Profile 3067.4.3 Humus in Soils 307References 3078 Co-evolution of Life and Environment 311Xingliang Zhang8.1 Introduction 3118.2 Earth’s Earliest Records and Habitability 3138.2.1 Hadean (~4.567 to 4.031 Ga) 3138.2.1.1 Hadean Zircons and Implications 3138.2.1.2 Hadean Environment 3148.2.2 Archean (~4.031 to 2.5 Ga) 3158.2.2.1 Geological Record of Eoarchean (~4.031–3.6 Ga) 3168.2.2.2 Geological Record of Paleoarchean (3.6–3.2 Ga) 3188.2.2.3 Geological Record of Mesoarchean (3.2–2.8 Ga) 3208.2.2.4 Geological Record of Neoarchean (2.8–2.5 Ga) 3218.2.2.5 Archean Environment—Habitable for Prokaryotes 3228.3 Evolution of Atmosphere 3238.3.1 The Prebiotic Atmosphere 3248.3.2 The Atmosphere at the Time of Life Origin 3258.3.3 Atmospheric Greenhouse Gases and Long-term Climate Change 3258.3.3.1 The Faint Young Sun Paradox 3268.3.3.2 Atmospheric CO2 Concentrations in the Precambrian 3278.3.3.3 Methane-rich Atmosphere in the Precambrian 3298.3.3.4 Phanerozoic CO2 Concentrations 3308.3.4 The Rise of Atmospheric O2 3328.3.4.1 Net Accumulation of O2 in Atmosphere 3338.3.4.2 Constraints on Precambrian Atmospheric O2 Levels 3338.3.4.3 Evidence for the Paleoproterozoic Rise of Atmospheric O2 3358.3.4.4 Second Rise of Atmospheric O2 3378.3.4.5 Phanerozoic Variations of Atmospheric O2 3378.4 Evolution of the Ocean 3398.4.1 Origin of the Oceans 3408.4.2 Cooling of the Surface Ocean Temperature 3408.4.3 Salinity History of Ocean 3428.4.3.1 Total Salinity 3438.4.3.2 Secular Variations of SO42−, Ca2+, and Mg2+ Concentrations 3458.4.3.3 Bioavailability of Phosphorus and Nitrogen 3498.4.3.4 Bio-essential Trace Metals 3508.4.4 Evolution of Ocean Oxygenation 3518.5 Evolution of Biosphere 3538.5.1 The Origin of Life 3538.5.2 The Timing of Life Origin 3558.5.3 The Framework of Life History 3578.5.3.1 Prokaryotes Dominated the Biosphere for 2.0 Billion Years 3578.5.3.2 Eukaryotic Life Emerged Early and Diverged Late 3588.5.3.3 Multicellularity Across Lineages of the Life Tree 3608.5.3.4 The Cambrian Explosion of Animals 3618.5.3.5 The Development of Life on Land 3628.5.3.6 Phanerozoic Events 3648.5.4 Evolution of Metabolism 3678.6 A Summary: Four Billion Years Co-evolution to One Intelligent Species 369References 3739 Exploring Extraterrestrial Life 381Ruliang He and Xingliang Zhang9.1 Introduction 3819.2 Habitability and Habitable Zone 3819.2.1 Key Requirements for Habitability 3829.2.1.1 A Solvent 3829.2.1.2 Elements and Nutrients 3829.2.1.3 Energy 3839.2.1.4 Clement Physical and Chemical Conditions 3839.2.2 The Habitable Zone 3849.3 Potentially Habitable Worlds Beyond Earth 3859.3.1 Venus 3859.3.2 Mars 3869.3.2.1 A Brief Introduction to Mars 3869.3.2.2 Water on Mars 3879.3.2.3 Habitability of Mars 3929.3.2.4 Search for Extant Life in Subsurface of Mars 3929.3.3 Europa 3939.3.4 Enceladus 3959.3.5 Titan 3979.4 Detecting Life Beyond Earth 3999.4.1 Life Detection 3999.4.2 Biosignatures 4009.4.2.1 Physical Signals 4009.4.2.2 Chemical Signals 4009.4.3 Case Studies 4019.4.3.1 Viking Biological Investigation 4019.4.3.2 ALH84001 Martian Meteorite 4019.5 Lessons from Explorations 402References 403Glossary 405Index 415