Preface

ix

Introduction

xi

1

Bacterial Metabolism

1

1.1

General Considerations: Functional Properties of Bacteria

1

1.2

Bacterial Metabolism

4

1.3

Dissimilatory Metabolism

7

1.4

Assimilatory Metabolism

24

1.5

Bioenergecics of Microbial Metabolism

27

2

Transport Mechanisms

35

2.1

Physical Transport Mechanisms

36

2.2

Bacterial Motility and Sensory Motile Behaviour

45

3

Degradation of Organic Polymers and Hydrocarbons

49

3.1

Substrates and the Efficiency of Degradation

49

3.2

Hydrolytic Enzymes

52

3.3

Mineral Nutrients and Decomposition Rates of Plant Derived Detritus

53

3.4

Humic Material and Hydrocarbons

55

4

Comparison of Element Cycles

59

5

The Water Column

67

5.1

The Composition of Planktonic Prokaryote Communities

69

5.2

Organic Matter: Composition, Origin and Turnover

72

5.3

Suspended Particles: Formation and Coupling Between Plankton and Sediments

75

5.4

Bacteria and Cycling of N and P

78

5.5

The Fate of Bacterial Cells

79

5.6

Motile Chemosensory Behaviour

81

5.7

Stratified Water Columns

84

6

Biogeochemical Cycling in Soils

89

6.1

Soil Water as a Master Variable for Biogeochemical Cycling

93

6.2

Water Stress Physiology

97

6.3

Responses to Plant Organic Matter

109

6.4

Responses of Soil Biogeochemistry to Disturbance and Change

115

7

Aquatic Sediments

121

7.1

Vertical Zonation, Vertical Transport, and Mixing

122

7.2

Element Cycling in Sediments

128

7.3

Sediments in the Light

131

7.4

Microbial Mats

133

8

Microbial Biogeochemistry and Extreme Environments

143

8.1

Microbial Biology and Extreme Environments: An Overview

144

8.2

Biogeochemistry and Extreme Environments

147

8.3

Hypersalinc Microbial Mats as Model Extreme Environments

149

8.4

Sub-Surface Environments as Extreme Systems

153

8.5

Thermophiles and Hyperthermophiles in Extreme Environments

156

8.6

Additional Considerations

160

9

Symbiotic Systems

163

9.1

Symbiotic Polymer Degradation

165

9.2

Symbiotic N₂ Fixation

174

9.3

Autotrophic Bacteria as Symbionts

178

10

Microbial Biogeochemical Cycling and the Atmosphere

183

10.1

The Atmosphere as an Elemental Reservoir

184

10.2

Atmospheric Structure and Evolution

188

10.3

Synopsis of Trace Gas Biogeochemistry and Linkages to Climate Change

195

10.4

Trace Gas Dynamics and Climate Change: An Analysis of Methane Production and Consumption

211

11

Origins and Evolution of Biogeochemical Cycles

221

11.1

Biogeochemical Cycles and Thermodynamics

222

11.2

Pre-Biotic Earth and Mineral Cycles

226

11.3

The Earliest Life and its Origin

228

11.4

Precambrian Life and Precambrian Biogeochemical Cycling

231

Appendix 1

Thermodynamics and Calculation of Energy Yields of Metabolic Processes

237

Appendix 2

Phylogeny and Function in Biogeochemical Cycles

247

References

255

Index

293