Biogeochemistry

Treatise on Geochemistry......Page 2
Executive Editor's Foreword......Page 3
8.01 The Early History of Life......Page 6
Strangeness and Familiarity---The Youth of the Earth......Page 7
Modeling---The Problem of Taking Fragments of Evidence and Rebuilding the Childhood of the Planet......Page 8
The Power of Biology: The Infinite Improbability Drive......Page 9
Building a Habitable Planet......Page 10
When and Where Did Life Start?......Page 12
The Archean Record......Page 13
The Physical State of the Archean Planet......Page 16
The Surface Environment......Page 18
Origin of Life......Page 19
RNA World......Page 20
The Last Common Ancestor......Page 22
A Hyperthermophile Heritage?......Page 24
Location of Early Biomes......Page 26
Methanogenesis: Impact on the Environment......Page 27
Geological Settings of the Early Biomes......Page 28
The Evolutionary Chain......Page 30
Anoxygenic Photosynthesis......Page 32
Oxygenic Photosynthesis......Page 33
Archean Oxygen......Page 34
The Ancestry of the Eucarya......Page 35
Possible Settings for the Eukaryote Endosymbiotic Event......Page 36
Water and Mud Stirring---Consequences......Page 37
Methane......Page 38
Feedback from the Biosphere to the Physical State of the Planet......Page 39
References......Page 40
Introduction......Page 45
Life and Rocks......Page 46
Mechanisms for Energy Conservation......Page 47
Extant Patterns of Metabolism......Page 49
Kinds of Phototrophs......Page 50
Lithotrophic Energy Sources......Page 51
Carbon Sources for Life......Page 52
Fermentative and Respiratory Metabolism......Page 53
Approaches Employing Genomics and Molecular Genetics......Page 54
Approaches Employing Geochemical and Geophysical Methods......Page 55
Overview......Page 61
References......Page 62
8.03 Sedimentary Hydrocarbons, Biomarkers for Early Life......Page 66
Biomarkers as Molecular Fossils......Page 67
Compound-specific Stable Isotopes......Page 69
Biomarkers as Maturity Indicators......Page 70
The Survival of Biomarkers with Increasing Temperature and Time......Page 71
Experimental approaches to biomarker and kerogen analysis......Page 73
n-Alkanes, Algaenans, and other Polymethylenic Biopolymers......Page 74
Alkyl Cyclohexanes and Cyclopentanes......Page 78
Isoprenoids......Page 79
Carotenoids......Page 82
Chlorophylls and Maleimides......Page 87
Sesquiterpanes (C15) and Diterpanes (C20)......Page 88
Hopanoids and other Pentacyclic Triterpanes......Page 90
Steroid Hydrocarbons......Page 94
Bacteria......Page 97
Archaea......Page 99
Eukarya......Page 100
Marine versus Lacustrine Conditions......Page 102
Paleotemperature and Paleolatitude Biomarkers......Page 103
Biomarkers in the Proterozoic (0.54--2.5Ga)......Page 104
Biomarkers Extracted from Archean Rocks (>2.5 Ga)......Page 105
References......Page 106
8.04 Biomineralization......Page 119
Outline of the Chapter......Page 120
Definitions and General Background on Biomineralization......Page 121
Calcium Carbonates......Page 122
Silica......Page 126
Bioapatite......Page 127
Iron Oxides and Hydroxides......Page 129
Sulfur Biomineralization......Page 131
Iron Biomineralization......Page 133
Carbonate Biomineralization......Page 136
Silica Biomineralization......Page 147
Plant Biomineralization......Page 154
Vertebrate Biomineralization......Page 160
Summary: Why Biomineralize?......Page 174
Chemical or Microbiomineralization Contributions......Page 176
References......Page 177
8.05 Biogeochemistry of Primary Production in the Sea......Page 187
A Primer on Redox Chemistry......Page 188
Chemoautotrophy......Page 189
Selective Forces in the Evolution of Photoautotrophy......Page 190
What are Photoautotrophs?......Page 191
Estimating Chlorophyll Biomass......Page 193
Estimating Net Primary Production......Page 196
Quantum Efficiency of NPP......Page 197
Export, New and ‘‘True New’’ Production......Page 198
Steady-state versus Transient State......Page 199
Nitrification......Page 200
Balance between Net Primary Production and Losses......Page 201
The Two Concepts of Limitation......Page 203
The Evolution of the Nitrogen Cycle......Page 204
Functional Groups......Page 205
Calcium Carbonate Precipitation......Page 206
Vacuoles......Page 207
High-nutrient, Low-chlorophyll Regions-Iron Limitation......Page 208
Linking Iron to N2 Fixation......Page 209
Other Trace-element Controls on NPP......Page 210
References......Page 211
8.06 Biogeochemistry of Terrestrial Net Primary Production......Page 216
What is NPP?......Page 217
The General Biochemistry of NPP......Page 218
The Basic Recipe for Carbon Gain......Page 221
CO2 Limitation......Page 222
Nitrogen Limitation......Page 223
Water Limitation......Page 224
Scaling of Carbon Gain......Page 225
Scaling of Controls over GPP......Page 226
Respiration......Page 228
Photosynthesis, Respiration, and NPP: Who is In Charge?......Page 229
Nutrient Use......Page 230
Nutrient Requirements......Page 231
Limitations by Different Nutrients......Page 232
Stoichiometry of NPP......Page 233
Uncoupling Mechanisms......Page 234
Recoupling Mechanisms......Page 237
Species Effects on Interactive Controls......Page 239
Vegetation Effects on Resources......Page 240
Species Effects on Disturbance Regime......Page 241
Summary......Page 242
References......Page 243
Introduction......Page 249
Composition of Decomposer Resources......Page 251
Roots......Page 252
Secondary Resources......Page 253
Soil Organic Matter......Page 254
Functional Ecology......Page 256
Soil Microorganisms......Page 258
Soil Fauna......Page 261
Interactions......Page 265
Litter Techniques......Page 266
SOM Techniques......Page 267
Detrital Processing......Page 268
Time Course of Litter Decomposition......Page 269
Leaching......Page 271
Catabolism......Page 273
Change in Nutrient Status......Page 278
Priming Effect on Native SOM......Page 280
Selective Preservation......Page 281
Condensation Models......Page 282
Control of Decomposition and Stabilization......Page 283
Decomposer Organisms......Page 284
Resource Quality......Page 288
Soil Characteristics......Page 291
Climate......Page 296
Multiple Constraints......Page 302
Modeling Approaches......Page 303
Conclusions......Page 305
References......Page 306
8.08 Anaerobic Metabolism: Linkages to Trace Gases and Aerobic Processes......Page 317
Overview of Anaerobic Metabolism......Page 319
Syntax of Metabolism......Page 321
Phototroph (Photolithoautotrophy) Diversity and Metabolism......Page 322
Chemotroph (Chemolithoautotrophy) Diversity and Metabolism......Page 324
Decomposition and Fermentation......Page 325
Polymer Degradation......Page 326
Fermentation......Page 328
Methane......Page 332
Methane in the Environment......Page 333
Methanogen Diversity and Metabolism......Page 334
Regulation of Methanogenesis......Page 335
Contributions of Acetotrophy versus Hydrogenotrophy......Page 339
Anaerobic Methane Oxidation......Page 342
Aerobic Methane Oxidation......Page 344
Wetland Methane Emissions and Global Change......Page 348
Nitrogen in the Environment......Page 350
Respiratory Denitrification......Page 351
Dissimilatory Nitrate Reduction to Ammonium (DNRA)......Page 357
Alternative Pathways to N2 Production......Page 359
Iron and Manganese in the Environment......Page 362
Iron and Manganese Geochemistry......Page 363
Microbial Reduction of Iron and Manganese......Page 364
Factors that Regulate Fe(III) Reduction......Page 366
Microbial Oxidation of Iron and Manganese......Page 371
Iron Cycling......Page 373
Sulfur Geochemistry......Page 374
Microbial Reduction of Sulfate......Page 375
Taxonomic Considerations......Page 377
Factors Regulating Sulfate Reduction Activity......Page 379
Microbial Reduction of Sulfur......Page 381
Disproportionation......Page 382
Sulfur Gases......Page 383
Microbial Oxidation of Sulfur......Page 386
Evidence of Competitive Interactions......Page 389
Mechanisms of Competition......Page 390
Contributions to Carbon Metabolism......Page 391
References......Page 392
Introduction......Page 425
The Carbon Cycle over Geologic Timescales......Page 426
Timescales of Carbon-cycle Change......Page 434
The Quaternary Record of Carbon-cycle Change......Page 435
Analysis of CO2 and CH4 in Ice Cores......Page 436
Holocene Carbon-cycle Variations......Page 440
Glacial/interglacial Carbon-cycle Variations......Page 444
Mechanisms of Gradual Geologic Carbon-cycle Change......Page 452
Model Simulations of Gradual Geologic Carbon-cycle Change......Page 455
Geologic Evidence for Phanerozoic Atmospheric CO2 Concentrations......Page 457
Abrupt Carbon-cycle Change......Page 459
The Precambrian Record of Carbon-Cycle Change......Page 460
References......Page 461
Introduction......Page 473
Reservoirs......Page 474
The Natural Flows of Carbon......Page 477
Changes Over the Period 1850-2000......Page 480
Changes Over the Period 1980-2000......Page 487
Terrestrial Mechanisms......Page 497
Oceanic Mechanisms......Page 505
Terrestrial......Page 506
Conclusion......Page 507
References......Page 508
Introduction......Page 514
The Oceans......Page 515
Freshwater Environments......Page 518
Photosynthesis......Page 519
Aerobic Cellular Respiration......Page 521
Macroscale Patterns of Aerobic Respiration......Page 522
Mineral Oxidation......Page 523
Iron and Sulfur Oxidation at the Oxic-Anoxic Transition......Page 524
Early Models......Page 525
The Archean......Page 527
The Proterozoic Atmosphere......Page 532
Phanerozoic Atmospheric O2......Page 538
Conclusions......Page 549
References......Page 551
Introduction......Page 555
The Initial Reaction: Nr Creation......Page 557
Atmosphere......Page 558
Nitrogen Reservoirs and Their Exchanges......Page 560
Terrestrial BNF-Natural......Page 561
Anthropogenic......Page 562
Nr Creation Rates from 1860 to 2000......Page 564
Introduction......Page 565
Nr Creation......Page 566
Nr Distribution......Page 567
Nr Conversion to N2......Page 568
Global Marine Nitrogen Budget......Page 569
Regional Nitrogen Budgets......Page 570
Introduction......Page 573
Terrestrial Ecosystems......Page 574
Aquatic Ecosystems......Page 575
Future......Page 576
References......Page 578
Introduction......Page 582
The Terrestrial Phosphorus Cycle......Page 584
Transport of Phosphorus from Continents to the Ocean......Page 588
The Marine Phosphorus Cycle......Page 589
Phosphorus Cycling in Terrestrial Ecosystems and Soils......Page 590
Phosphorus Cycling in Terrestrial Aquatic Systems: Lakes, Rivers and Estuaries......Page 591
Biogeochemistry and Cycling of Phosphorus in the Modern Ocean......Page 594
Phosphorus Cycling Over Long,Geologic Timescales......Page 627
References......Page 630
8.14 The Global Sulfur Cycle......Page 641
Isotopes......Page 642
Chemistry......Page 643
Sulfur in the Cosmos......Page 646
Sulfur on the Early Earth......Page 647
The Geological History of Sulfur......Page 649
Utilization and Extraction of Sulfur Minerals......Page 650
Deep-sea Vents......Page 651
Crater Lakes......Page 652
Origin of Life......Page 653
Sulfur Biomolecules......Page 654
Hydrogen Sulfide......Page 655
Organosulfides......Page 656
Surface and Groundwaters......Page 658
Marine Sediments......Page 659
Soils and Vegetation......Page 660
Hydrogen Sulfide......Page 661
Carbonyl Sulfide......Page 662
Dimethyl Sulfide......Page 663
Dimethylsulfoxide and Methanesulfonic Acid......Page 664
Sulfur Dioxide......Page 665
Deposition......Page 667
Combustion Emissions......Page 668
Acid Rain......Page 669
Water and Soil Pollutants......Page 670
Radiation Balance and Sulfate Particles......Page 671
Aircraft......Page 672
Conclusions......Page 673
References......Page 675
Appendix 1. Periodic Table of the Elements......Page 679
Appendix 2. Table of Isotopes......Page 680
Appendix 3. The Geologic Timescale......Page 684
Appendix 4. Useful Values......Page 685