The first stand-alone textbook for at least ten years on this increasingly hot topic in times of global climate change and sustainability in ecosystems.

Ecological biochemistry refers to the interaction of organisms with their abiotic environment and other organisms by chemical means. Biotic and abiotic factors determine the biochemical flexibility of organisms, which otherwise easily adapt to environmental changes by altering their metabolism. Sessile plants, in particular, have evolved intricate biochemical response mechanisms to fit into a changing environment. This book covers the chemistry behind these interactions, bottom up from the atomic to the system's level.

An introductory part explains the physico-chemical basis and biochemical roots of living cells, leading to secondary metabolites as crucial bridges between organisms and the respective ecosystem. The focus then shifts to the biochemical interactions of plants, fungi and bacteria within terrestrial and aquatic ecosystems with the aim of linking biochemical insights to ecological research, also in human-influenced habitats.

A section is devoted to methodology, which allows network-based analyses of molecular processes underlying systems phenomena.

A companion website offering an extended version of the introductory chapter on Basic Biochemical Roots is available at
http://www.wiley.com/go/Krauss/Nies/EcologicalBiochemistry

Gerd-Joachim Krauss is full Professor Emeritus for Ecological and Plant Biochemistry at the Martin-Luther-University of Halle, Germany, where he gained his PhD in plant biochemistry. He was responsible for research projects at the University of Sackville, Canada, the Bulgarian Academy of Sciences, Sofia, and Université de Pau/CNRS, Pau, France. His research interests are focused on metal stress response in plants and fungi, and the development of HPLC and coupling techniques.

Dietrich H. Nies is full Professor for Molecular Microbiology at the Martin-Luther-University of Halle, Germany. He began his academic career in Göttingen, carrying out his postdoc in Berlin and at the University of Illinois at Chicago. Professor Nies`s research centers on the interaction of bacteria with transition metals.

List of Contributors XVII

Foreword XXI

Preface XXIII

CompanionWebsite XXV

Part I: Basics of Life 1

1 Basic Biochemical Roots 3
Dietrich H. Nies

1.1 Chemistry and Physics of Life 3

1.2 Energy and Transport 3

1.3 Basic Biochemistry 4

2 Specialized PlantMetabolites: Diversity and Biosynthesis 15
Alain Tissier, Jörg Ziegler, and Thomas Vogt

2.1 Metabolite Diversity 15

2.2 Major Classes of Plant Specialized Compounds 16

2.3 Sites of Biosynthesis and Accumulation 33

2.4 Evolution of Specialized Pathway Genes 34

3 Evolution of SecondaryMetabolism in Plants 39
MichaelWink

3.1 Origins of Plant Secondary Metabolism 39

3.2 Evolutionary Alternatives 41

3.3 Endophytes, Symbiotic, and Ectomycorrhizal Fungi 45

Part II: Ecological Signatures of Life 49

4 Systematics of Life, Its Early Evolution, and Ecological Diversity 51
Dietrich H. Nies

4.1 Cellular Life Forms and Subcellular Parasites 51

4.2 Superkingdom Archaea 51

4.3 Superkingdom Bacteria 55

4.4 Superkingdom Eukaryota 59

5 Communities and Ecosystem Functioning 77
Heinz Rennenberg

5.1 Competition for, and Distribution of, Limiting Resources as a Means of Ecosystem Functioning 77

5.2 Joint Exploitation of Limiting Resources by Symbioses 79

5.3 Avoidance of Competition 89

5.4 Facilitation Mechanisms in Communities and Ecosystem Functioning 90

6 Food Chains and Nutrient Cycles 93
Felix Bärlocher and Heinz Rennenberg

6.1 Basic Concepts 93

6.2 Aquatic Systems 97

6.3 Terrestrial Systems 109

Part III: Biochemical Response to Physiochemical Stress (Abiotic Stress) 123

7 Information Processing and Survival Strategies 125
Ingo Heilmann

7.1 The Stress Concept--Plants and Their Environment 125

7.2 Plant Signal Transduction and the Induction of Stress Responses 126

7.3 Phytohormones 130

7.4 Other Signaling Molecules 141

7.5 Signal Transduction by Protein Phosphorylation 148

7.6 The Calcium Signaling Network 149

7.7 Stress-Induced Modulation of Gene Expression by microRNAs 150

8 Oxygen 155
Karl-Josef Dietz

8.1 Chemical Nature of Oxygen and Reactive Oxygen Species 155

8.2 Oxygen Metabolism 156

8.3 Oxygen Sensing 160

8.4 Antioxidant Defense 161

8.5 Reactive Oxygen Species in Abiotic Stresses 162

8.6 Reactive Oxygen Species in Biotic Interactions 164

8.7 Cell Signaling Function of Reactive Oxygen Species 165

9 Light 171
Thomas Kretsch

9.1 Principles of Light Detection and Photoreceptor Function 171

9.2 Sensing of UV-B Light 175

9.3 The LOV Domain: A Variable Molecular Building Block of Many Blue and UV-A Light Sensors 176

9.4 Cryptochromes 179

9.5 Phytochromes 180

9.6 Other Photoreceptor Systems 185

9.7 Flavonoid Biosynthesis in Plants -- a Model for a Light-Regulated Adaptation Process 185

10 Water 191
Wiebke Zschiesche and Klaus Humbeck

10.1 Water: the Essence of Life 191

10.2 Water Balance in Plants 192

10.3 Drought Stress 194

10.4 Cold Stress and Freezing 200

10.5 Salinity 201

10.6 Flooding Stress 205

11 Mineral Deficiencies 209

11.1 Mineral Requirement and Insufficiencies 209
Edgar Peiter

11.2 Carnivorous Plants and Fungi 224
Gerd-Joachim Krauss and Gudrun Krauss

12 Excess of Metals 237
Dietrich H. Nies, Eva Freisinger, and Gerd-Joachim Krauss

12.1 Properties of Transition Metals 237

12.2 Metal Transport through Cell Membranes 238

12.3 Biochemistry of the Minor Biometals: Essential, Desired, but Also Toxic 240

12.4 Biochemistry of Chemical ElementsWithout Known Biological Functions 244

12.5 Metal-Binding Peptides and Proteins Involved in Transition Metal Homeostasis 246

12.6 Interaction of Plants and Fungi with Metals 251

13 Xenobiotics from Human Impacts 259
Magali Solé and Dietmar Schlosser

13.1 Xenobiotics: from Emission to Cellular Uptake 259

13.2 Adverse Effects of Xenobiotics: from Cells to Ecosystems 265

13.3 Organismal Responses: Biochemical Elimination of Xenobiotics 268

Part IV: Organismal Interactions (Biotic Stress) 277

14 The Biofilm Mode of Life 279
Hans-Curt Flemming

14.1 What are Biofilms? 279

14.2 Environmental Roles of Biofilms 280

14.3 Life Cycle of Biofilms 281

14.4 Investigation of Biofilms 283

14.5 The Matrix: Extracellular Polymeric Substances 284

14.6 Communication in Biofilms 287

14.7 Enhanced Resistance of Biofilm Organisms 288

14.8 Emergent Properties of the Biofilm Mode of Life 290

15 Rhizosphere Interactions 293
Silvia D. Schrey, Anton Hartmann, and Rüdiger Hampp

15.1 Bacterial Communities in the Rhizosphere 294

15.2 Fungi of the Rhizosphere 303

15.3 Plant--Plant Interactions 306

16 Plant-Animal Dialogues 313
Susanne Preiß, Jörg Degenhardt, and Jonathan Gershenzon

16.1 The Flower Pollinator System 313

16.2 Ant--Plant--Fungus Mutualism, a Three-Way Interaction 319

16.3 Phenolics in the Interaction between Plant and Animals 320

16.4 Alkaloids in the Interaction between Plants and Animals 321

16.5 Terpenes in Plant Defense 325

Part V: The Methodological Platform 331

17 Sensing of Pollutant Effects and Bioremediation 333
Gerd-Joachim Krauss and Dietmar Schlosser

17.1 Pollutant Effect and Approaches to Characterize Exposure 333

17.2 Ecological Restoration and Bioremediation 335

17.2.1 Biological Ecosystem Components Mitigating Environmental Pollution 335

17.2.2 Present and Future Directions 338

18 The -Omics Tool Box 343
Dirk Schaumlöffel

18.1 Genomics 343

18.2 Transcriptomics 345

18.3 Proteomics 346

18.4 Metabolomics 356

18.5 Metallomics 360

19 Microscope Techniques and Single Cell Analysis 367
Bettina Hause and Gerd Hause

19.1 Visualization Principles 367

19.2 Preparation of Biological Materials 373

19.3 Detection Methods -- from Macromolecules to Ions 375

19.4 Single Cell Technologies 380

References 382

Further Reading 382

Glossary 383

Index 397