Karim Benzerara is Agrégé in Life and Earth Sciences and Director of Research at the CNRS, France. His research focuses on mineral/living interactions by combining microbiology and mineralogy.Christophe Thomazo is Agrégé in Life and Earth Sciences and Professor at the University of Burgundy, France. His research focuses on past and present biogeochemical cycles using stable isotopes.

• Introduction xiChristophe THOMAZO and Karim BENZERARAChapter 1 Weathering of Rocks by Living Organisms 1Bastien WILD and Damien DAVAL1.1 Rock weathering in the critical zone 11.2 Parameterization of mineral dissolution rates 21.3 Modeling rock chemical weathering in the critical zone 101.4 Mechanisms associated with microbial dissolution 171.5 Biotic weathering by microorganisms 191.6 What quantitative impact do living organisms have on mineral dissolution? 241.7 Conclusion 291.8 References 30Chapter 2 Biomineralization: The Formation of Minerals by Living Organisms 47Karim BENZERARA2.1 Introduction 472.2 Diversity of biominerals and biomineralizing organisms 502.3 Biomineral formation mechanisms 582.4 Impact of biomineralization on how the Earth functions 742.5 Impact of biomineralization on the functioning of living organisms 762.6 Evolutionary history of biomineralization processes 772.7 Applications of biomineralogy 792.8 Conclusion 812.9 References 81Chapter 3 Microbialites in the Fossil and Current Record 87 Emmanuelle VENNIN, Anthony BOUTON, Pierre BOUSSAGOL and Pieter T. VISSCHER3.1 Introduction 873.2 Microbialites: a continuous archive of Earth’s history 883.3 How microbialites are formed 983.4 Preservation of microbialites in the fossil record 1083.5 Examples illustrating the diversity of microbialites in current and fossil environments 1113.6 Conclusions 1153.7 References 116Chapter 4 Molecular Approaches for the Study of Phylogenetic and Functional Diversity of Living Organisms 129Miguel INIESTO, Ana GUTIÉRREZ-PRECIADO, Thomas BACCHETTA, David MOREIRA and Purificación LÓPEZ-GARCÍA4.1 Classifying and understanding living organisms 1294.2 Microbial diversity associated with microbialites 1374.3 Functions of microbial communities associated with microbialites 1434.4 Reconstruction of evolutionary history and inference of ancient traits 1464.5 Conclusions and perspectives 1504.6 References 151Chapter 5 Oxygen: A Major Geobiological Player 161Christophe THOMAZO5.1 Introduction 1615.2 Oxygen: origin and properties 1625.3 The geobiological history of oxygen on Earth 1705.4 Conclusion 1885.5 References 188Chapter 6 The Importance of Living Organisms in the Carbon and Nitrogen Cycles 197Alice PELLERIN and Magali ADER6.1 Biogeochemical cycles 1976.2 The carbon biogeochemical cycle 1986.3 The biogeochemical cycle of nitrogen 2086.4 General conclusions – from a geochemical cycle to a biogeochemical cycle: how to detect the appearance of the first biological fluxes of nitrogen and carbon? 2156.5 References 216Chapter 7 Modeling the Biosphere and Its Interactions with the Geosphere 219Guillaume LE HIR7.1 Introduction 2197.2 Response of the biosphere to current global changes 2237.3 Geosphere–biosphere interaction during the colonization of continents by plants 2347.4 How to model biosphere during mass extinctions? 2437.5 Conclusion 2507.6 References 251Chapter 8 Fluctuations in Biodiversity Over Geological Time: An Illustration of the Earth/Life Connection 257Arnaud BRAYARD8.1 Introduction 2578.2 History of Life – how to measure it in time and space? 2598.3 Extinctions and mass extinctions 2658.4 (Re)diversifications: some examples of interactions between the biosphere and the geosphere 2698.5 Conclusion 2768.6 References 277Conclusions 285Christophe THOMAZO and Karim BENZERARAList of Authors 291Index 293

Karim Benzerara is Agrégé in Life and Earth Sciences and Director of Research at the CNRS, France. His research focuses on mineral/living interactions by combining microbiology and mineralogy.Christophe Thomazo is Agrégé in Life and Earth Sciences and Professor at the University of Burgundy, France. His research focuses on past and present biogeochemical cycles using stable isotopes.

• Introduction xiChristophe THOMAZO and Karim BENZERARAChapter 1 Weathering of Rocks by Living Organisms 1Bastien WILD and Damien DAVAL1.1 Rock weathering in the critical zone 11.2 Parameterization of mineral dissolution rates 21.3 Modeling rock chemical weathering in the critical zone 101.4 Mechanisms associated with microbial dissolution 171.5 Biotic weathering by microorganisms 191.6 What quantitative impact do living organisms have on mineral dissolution? 241.7 Conclusion 291.8 References 30Chapter 2 Biomineralization: The Formation of Minerals by Living Organisms 47Karim BENZERARA2.1 Introduction 472.2 Diversity of biominerals and biomineralizing organisms 502.3 Biomineral formation mechanisms 582.4 Impact of biomineralization on how the Earth functions 742.5 Impact of biomineralization on the functioning of living organisms 762.6 Evolutionary history of biomineralization processes 772.7 Applications of biomineralogy 792.8 Conclusion 812.9 References 81Chapter 3 Microbialites in the Fossil and Current Record 87 Emmanuelle VENNIN, Anthony BOUTON, Pierre BOUSSAGOL and Pieter T. VISSCHER3.1 Introduction 873.2 Microbialites: a continuous archive of Earth’s history 883.3 How microbialites are formed 983.4 Preservation of microbialites in the fossil record 1083.5 Examples illustrating the diversity of microbialites in current and fossil environments 1113.6 Conclusions 1153.7 References 116Chapter 4 Molecular Approaches for the Study of Phylogenetic and Functional Diversity of Living Organisms 129Miguel INIESTO, Ana GUTIÉRREZ-PRECIADO, Thomas BACCHETTA, David MOREIRA and Purificación LÓPEZ-GARCÍA4.1 Classifying and understanding living organisms 1294.2 Microbial diversity associated with microbialites 1374.3 Functions of microbial communities associated with microbialites 1434.4 Reconstruction of evolutionary history and inference of ancient traits 1464.5 Conclusions and perspectives 1504.6 References 151Chapter 5 Oxygen: A Major Geobiological Player 161Christophe THOMAZO5.1 Introduction 1615.2 Oxygen: origin and properties 1625.3 The geobiological history of oxygen on Earth 1705.4 Conclusion 1885.5 References 188Chapter 6 The Importance of Living Organisms in the Carbon and Nitrogen Cycles 197Alice PELLERIN and Magali ADER6.1 Biogeochemical cycles 1976.2 The carbon biogeochemical cycle 1986.3 The biogeochemical cycle of nitrogen 2086.4 General conclusions – from a geochemical cycle to a biogeochemical cycle: how to detect the appearance of the first biological fluxes of nitrogen and carbon? 2156.5 References 216Chapter 7 Modeling the Biosphere and Its Interactions with the Geosphere 219Guillaume LE HIR7.1 Introduction 2197.2 Response of the biosphere to current global changes 2237.3 Geosphere–biosphere interaction during the colonization of continents by plants 2347.4 How to model biosphere during mass extinctions? 2437.5 Conclusion 2507.6 References 251Chapter 8 Fluctuations in Biodiversity Over Geological Time: An Illustration of the Earth/Life Connection 257Arnaud BRAYARD8.1 Introduction 2578.2 History of Life – how to measure it in time and space? 2598.3 Extinctions and mass extinctions 2658.4 (Re)diversifications: some examples of interactions between the biosphere and the geosphere 2698.5 Conclusion 2768.6 References 277Conclusions 285Christophe THOMAZO and Karim BENZERARAList of Authors 291Index 293

Karim Benzerara is Agrégé in Life and Earth Sciences and Director of Research at the CNRS, France. His research focuses on mineral/living interactions by combining microbiology and mineralogy.Christophe Thomazo is Agrégé in Life and Earth Sciences and Professor at the University of Burgundy, France. His research focuses on past and present biogeochemical cycles using stable isotopes.

• Introduction xiChristophe THOMAZO and Karim BENZERARAChapter 1 Weathering of Rocks by Living Organisms 1Bastien WILD and Damien DAVAL1.1 Rock weathering in the critical zone 11.2 Parameterization of mineral dissolution rates 21.3 Modeling rock chemical weathering in the critical zone 101.4 Mechanisms associated with microbial dissolution 171.5 Biotic weathering by microorganisms 191.6 What quantitative impact do living organisms have on mineral dissolution? 241.7 Conclusion 291.8 References 30Chapter 2 Biomineralization: The Formation of Minerals by Living Organisms 47Karim BENZERARA2.1 Introduction 472.2 Diversity of biominerals and biomineralizing organisms 502.3 Biomineral formation mechanisms 582.4 Impact of biomineralization on how the Earth functions 742.5 Impact of biomineralization on the functioning of living organisms 762.6 Evolutionary history of biomineralization processes 772.7 Applications of biomineralogy 792.8 Conclusion 812.9 References 81Chapter 3 Microbialites in the Fossil and Current Record 87 Emmanuelle VENNIN, Anthony BOUTON, Pierre BOUSSAGOL and Pieter T. VISSCHER3.1 Introduction 873.2 Microbialites: a continuous archive of Earth’s history 883.3 How microbialites are formed 983.4 Preservation of microbialites in the fossil record 1083.5 Examples illustrating the diversity of microbialites in current and fossil environments 1113.6 Conclusions 1153.7 References 116Chapter 4 Molecular Approaches for the Study of Phylogenetic and Functional Diversity of Living Organisms 129Miguel INIESTO, Ana GUTIÉRREZ-PRECIADO, Thomas BACCHETTA, David MOREIRA and Purificación LÓPEZ-GARCÍA4.1 Classifying and understanding living organisms 1294.2 Microbial diversity associated with microbialites 1374.3 Functions of microbial communities associated with microbialites 1434.4 Reconstruction of evolutionary history and inference of ancient traits 1464.5 Conclusions and perspectives 1504.6 References 151Chapter 5 Oxygen: A Major Geobiological Player 161Christophe THOMAZO5.1 Introduction 1615.2 Oxygen: origin and properties 1625.3 The geobiological history of oxygen on Earth 1705.4 Conclusion 1885.5 References 188Chapter 6 The Importance of Living Organisms in the Carbon and Nitrogen Cycles 197Alice PELLERIN and Magali ADER6.1 Biogeochemical cycles 1976.2 The carbon biogeochemical cycle 1986.3 The biogeochemical cycle of nitrogen 2086.4 General conclusions – from a geochemical cycle to a biogeochemical cycle: how to detect the appearance of the first biological fluxes of nitrogen and carbon? 2156.5 References 216Chapter 7 Modeling the Biosphere and Its Interactions with the Geosphere 219Guillaume LE HIR7.1 Introduction 2197.2 Response of the biosphere to current global changes 2237.3 Geosphere–biosphere interaction during the colonization of continents by plants 2347.4 How to model biosphere during mass extinctions? 2437.5 Conclusion 2507.6 References 251Chapter 8 Fluctuations in Biodiversity Over Geological Time: An Illustration of the Earth/Life Connection 257Arnaud BRAYARD8.1 Introduction 2578.2 History of Life – how to measure it in time and space? 2598.3 Extinctions and mass extinctions 2658.4 (Re)diversifications: some examples of interactions between the biosphere and the geosphere 2698.5 Conclusion 2768.6 References 277Conclusions 285Christophe THOMAZO and Karim BENZERARAList of Authors 291Index 293