Bothe / Ferguson / Newton Biology of the Nitrogen Cycle

1. Auflage 2006
ISBN: 978-0-08-047133-4
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 452 Seiten

All organisms require nitrogen to live and grow. The movement of nitrogen between the atmosphere, biosphere, and geosphere in different forms is described by the nitrogen cycle. This book is an activity of the COST 856 Action on Denitrification. It covers all aspects of the N-cycle: chemistry, biology (enzymology, molecular biology), physics, applied aspects (greenhouse effect, N-pollution problems, practices in farming, in waste-water treatment, and more). In this book, leading editors offer the latest research available on dentrification (reduction of nitrates or nitrites commonly by bacteria- as in soil).
* Provides details on denitrification and its general role in the environment
* Offers latest research in N-Cycle and its reactions
* Discusses impacts on various environments: agriculture, wetlands, plants, waste-water treatment and more
* The only book available in the field since the last 20 years
* Contains 27 chapters written by internationally highly recognized experts in the field
* Covers all modern aspects, emphasizes molecular biology and ecology
* Written in an easily understandable way

Autoren/Hrsg.

Bothe, Hermann

Ferguson, Stuart

Newton, William E.

Inhaltsverzeichnis

1;Cover;1
2;Biology of the Nitrogen Cycle;4
3;Copyright Page;5
4;Contents;6
5;List of Contributors;10
6;Preface;14
7;Part I: Denitrification;20
7.1;Chapter 1. Introduction to the Biochemistry and Molecular Biology of Denitrification;22
7.1.1;1.1 Introduction;22
7.1.2;1.2 Proteins of denitrification;23
7.1.3;1.3 Bioenergetics of denitrification;26
7.1.4;1.4 Genes coding for enzymes of denitrification;28
7.1.5;1.5 Regulation of transcription of the denitrification genes;29
7.1.6;1.6 Regulatory networks in denitrifiers;33
7.1.7;1.7 Concluding remarks;37
7.1.8;References;38
7.2;Chapter 2. The Prokaryotic Nitrate Reductases;40
7.2.1;2.1 Introduction;40
7.2.2;2.2 The membrane-bound NO3¯ -reductase (NarGHI);42
7.2.3;2.3 The Archaeal Nar system;46
7.2.4;2.4 The periplasmic nitrate reductase (Nap);47
7.2.5;2.5 The assimilatory nitrate reductase (Nas);50
7.2.6;2.6 The eukaryotic nitrate reductases;53
7.2.7;References;53
7.3;Chapter 3. Nitrite Reductases in Denitrification;56
7.3.1;3.1 Introduction;56
7.3.2;3.2 Cd1 nitrite reductase;57
7.3.3;3.3 Copper nitrite reductase;67
7.3.4;References;73
7.4;Chapter 4. Nitric Oxide Reductase: Structural Variations and Catalytic Mechanism;76
7.4.1;4.1 Introduction;76
7.4.2;4.2 Structural variations in NORs;77
7.4.3;4.3 Catalytic mechanism of NOR;81
7.4.4;4.4 Comparison between catalysis by NOR and CcO;82
7.4.5;References;83
7.5;Chapter 5. Nitrous Oxide Reductases;86
7.5.1;5.1 Introduction;86
7.5.2;5.2 Properties of N2O reductase;87
7.5.3;5.3 Enzyme structure and Cu centers;87
7.5.4;5.4 Metal center assembly;90
7.5.5;5.5 Gene patterns and dissemination of nos genes;92
7.5.6;5.6 Evolutionary aspects;94
7.5.7;5.7 Transport processes for Nos proteins;96
7.5.8;5.8 Role of accessory flavoproteins;97
7.5.9;References;98
7.6;Chapter 6. Denitrification in Rhizobia-Legume Symbiosis;102
7.6.1;6.1 Introduction;102
7.6.2;6.2 Denitrification in free-living rhizobia;103
7.6.3;6.3 Denitrification in nodules;105
7.6.4;References;108
7.7;Chapter 7. The Dissimilatory Reduction of Nitrate to Ammonia by Anaerobic Bacteria;112
7.7.1;7.1 Dissimilatory nitrate reduction to ammonia, a process distinct from denitrification and nitrate assimilation;112
7.7.2;7.2 The cytoplasmic pathway for nitrate dissimilation to ammonia;114
7.7.3;7.3 The periplasmic pathway for respiratory reduction of nitrate to ammonia;115
7.7.4;7.4 Regulation of the cytoplasmic and periplasmic pathways for nitrate reduction to ammonia;118
7.7.5;7.5 Distribution of enzymes for nitrate reduction to ammonia and their ecological significance;120
7.7.6;7.6 Nitrate reduction to ammonia as an evolutionary link between nitrate assimilation and denitrification;121
7.7.7;7.7 Current challenges and unanswered questions;121
7.7.8;References;122
8;Part II: Biological Nitrogen Fixation;126
8.1;Chapter 8. Physiology, Biochemistry, and Molecular Biology of Nitrogen Fixation;128
8.1.1;8.1 Which organisms fix N2?;128
8.1.2;8.2 Nitrogenases;130
8.1.3;8.3 MgATP and Mo-nitrogenase catalysis;141
8.1.4;8.4 Genetics of N2-fixation;142
8.1.5;8.5 Regulation of N2-fixation;144
8.1.6;8.6 Perspectives and future research;144
8.1.7;References;145
8.2;Chapter 9. Regulatory Cascades to Express Nitrogenases;150
8.2.1;9.1. Introduction;150
8.2.2;9.2 Environmental signals regulating expression of nitrogenases;151
8.2.3;9.3 Levels of regulation of N2-fixation in proteobacteria and the central role of PII;152
8.2.4;9.4 Transcriptional control of the nifA gene represents the first level of the regulatory cascade in diazotrophic proteobacteria;154
8.2.5;9.5 NifA activates nif gene expression in concert with a specific sigma factor, RpoN;155
8.2.6;9.6 Control of NifA activity represents the second level of the regulatory cascade;156
8.2.7;9.7 Control of nitrogenase activity represents the third level of the regulatory cascade;157
8.2.8;9.8 Regulation of alternative nitrogenases;158
8.2.9;9.9 Regulation of N2-fixation in nonproteobacterial species;159
8.2.10;9.10 Concluding remarks;161
8.2.11;References;162
8.3;Chapter 10. The Rhizobium-Legume Nitrogen-Fixing Symbiosis;166
8.3.1;10.1 Introduction;166
8.3.2;10.2 An overview of nodule formation;167
8.3.3;10.3 Molecular mechanisms of signal exchange;170
8.3.4;10.4 Symbiotic nitrogen fixation and assimilation;178
8.3.5;10.5 Conclusions;180
8.3.6;References;181
8.4;Chapter 11. Plant Symbioses with Frankia and Cyanobacteria;184
8.4.1;11.1 Introduction;184
8.4.2;11.2 Actinorhizal symbioses;184
8.4.3;11.3 Cyanobacterial symbioses;188
8.4.4;References;193
8.5;Chapter 12. Associative Nitrogen Fixation;198
8.5.1;12.1 Introduction;198
8.5.2;12.2 Non-symbiotic colonization of plants;199
8.5.3;12.3 N2-fixing bacteria associated with plants;200
8.5.4;12.4 Conclusion;207
8.5.5;References;208
8.6;Chapter 13. Measuring N2 Fixation in the Field;212
8.6.1;13.1 Introduction;212
8.6.2;13.2 Rate measurements;213
8.6.3;13.3 Detecting N2 fixation potential and N2-fixing microorganisms;218
8.6.4;References;221
9;Part III: Other Reactions of the Nitrogen Cycle;226
9.1;Chapter 14. Biochemistry and Molecular Biology of Nitrification;228
9.1.1;14.1 Introduction;228
9.1.2;14.2 The general energetic problem faced by lithotrophic nitrifiers;229
9.1.3;14.3 Denitrification reactions catalysed by nitrifiers;237
9.1.4;14.4 Heterotrophic nitrification;238
9.1.5;References;239
9.2;Chapter 15. The Ecology of Nitrifying Bacteria;242
9.2.1;15.1 Introduction;242
9.2.2;15.2 Nitrifying microorganisms;243
9.2.3;15.3 Community structure of nitrifiers in natural environments;246
9.2.4;15.4 Factors influencing the ecology of nitrifying bacteria;248
9.2.5;15.5 Conclusions;260
9.2.6;References;260
9.3;Chapter 16: Anammox;264
9.3.1;16.1 Anammox: Discovery and introduction;264
9.3.2;16.2 Enrichment of anammox biomass;266
9.3.3;16.3 Physiology of anammox aggregates from the SBR;267
9.3.4;16.4 Identification of the key player;268
9.3.5;16.5 Ultrastructure of Brocadia anammoxidans;272
9.3.6;16.6 Lipids of anammox bacteria;273
9.3.7;16.7 Significance of anammox on a global scale;273
9.3.8;16.8 Biochemistry and the role of environmental genomics;275
9.3.9;16.9 The application of the anammox process;276
9.3.10;16.10 Integration and perspectives;277
9.3.11;References;279
9.4;Chapter 17. Nitrate Assimilation in Bacteria;282
9.4.1;17.1 Introduction;282
9.4.2;17.2 The NO3 ¯ and NO2 ¯ uptake systems;286
9.4.3;17.3 Assimilatory NRs;289
9.4.4;17.4 Assimilatory NiRs;291
9.4.5;17.5 Regulation of NO3 ¯ assimilation;293
9.4.6;17.6 Concluding remarks;297
9.4.7;References;297
9.5;Chapter 18. Nitrate Assimilation in Plants;302
9.5.1;18.1 Introduction;302
9.5.2;18.2 Physiology and molecular biology of nitrate uptake;303
9.5.3;18.3 Assimilatory NO3 ¯ reduction in higher plants;309
9.5.4;References;314
9.6;Chapter 19. Characterization of Proteolytic Microbes and Their Activities in Soils;322
9.6.1;19.1 Introduction;322
9.6.2;19.2 Methods to assess proteolysis;323
9.6.3;19.3 Tools to study the gene- and transcript pool of proteolytic organisms;324
9.6.4;19.4 Investigation of proteolysis in terrestrial ecosystems;325
9.6.5;References;327
10;Part IV: Applications of Reactions of the Nitrogen Cycle, with Emphasis on Denitrification;330
10.1;Chapter 20. Molecular Tools to Assess the Diversity and Density of Denitrifying Bacteria in Their Habitats;332
10.1.1;20.1 Introduction;332
10.1.2;20.2 Molecular markers for denitrifying bacteria;333
10.1.3;20.3 Genetic fingerprinting of denitrifier communities;333
10.1.4;20.4 Quantification of denitrifier communities;336
10.1.5;20.5 Examples of denitrifier communities in habitats;338
10.1.6;20.6 Improving our ways to study denitrifiers in habitats;341
10.1.7;References;343
10.2;Chapter 21. Denitrification and Agriculture;350
10.2.1;21.1 Nitrogen in agricultural systems;350
10.2.2;21.2 Factors controlling denitrification in agricultural soils;351
10.2.3;21.3 Agricultural consequences;353
10.2.4;21.4 Environmental consequences of denitrification;354
10.2.5;21.5 Quantification of denitrification losses;356
10.2.6;21.6 Mitigation of denitrification activity in the field;359
10.2.7;References;360
10.3;Chapter 22. Denitrification and N-Cycling in Forest Ecosystems;362
10.3.1;22.1 Introduction;362
10.3.2;22.2 Characteristics of the N-cycle in forest ecosystems;363
10.3.3;22.3 Impact of increased nitrogen inputs on denitrification;364
10.3.4;22.4 Nitrogen inputs affect forest microbial communities;365
10.3.5;22.5 Environmental regulation of denitrification;366
10.3.6;22.6 Species involved in denitrification;367
10.3.7;22.7 Importance of denitrification for N2O-emissions;368
10.3.8;22.8 Effect of forest type on denitrification;369
10.3.9;22.9 Competition between plants and microorganisms;370
10.3.10;22.10 The N2O:N2 ratio and in situ quantification;371
10.3.11;22.11 Modelling;372
10.3.12;22.12 Austrian case – the missing nitrogen;375
10.3.13;References;375
10.4;Chapter 23. Denitrification in Wetlands;378
10.4.1;23.1 Introduction;378
10.4.2;23.2 Wetlands as an environment for denitrification;379
10.4.3;23.3 Molecular diversity of denitrifying bacteria;380
10.4.4;23.4 Denitrification in riparian wetlands;381
10.4.5;23.5 Denitrification in constructed wetlands;382
10.4.6;23.6 Emission of nitrogen gases from wetlands;383
10.4.7;References;384
10.5;Chapter 24. Organisms of the Nitrogen Cycle Under Extreme Conditions: Low Temperature, Salinity, pH Value and Water Stress;388
10.5.1;24.1 Introduction;388
10.5.2;24.2 Low temperature;389
10.5.3;24.3 Denitrification in halophilic environments;391
10.5.4;References;395
10.6;Chapter 25. Nitrous Oxide Emission and Global Changes: Modeling Approaches;400
10.6.1;25.1 Introduction;400
10.6.2;25.2 Product stoichiometry of denitrification;401
10.6.3;25.3 Models of soil anaerobiosis as a regulator for denitrification;403
10.6.4;25.4 Denitrification and N2O flux in soil biogeochemical models;406
10.6.5;25.5 Microbial kinetics of denitrification in biogeochemical models;408
10.6.6;References;410
10.7;Chapter 26. Interactions among Organisms that Result in Enhanced Activities of N-Cycle Reactions;416
10.7.1;26.1 Introductory statement;416
10.7.2;26.2 Associative bacteria are potentially beneficial to the health of plants;416
10.7.3;26.3 Plants eating animals (carnivorous plants) to get access to an extra N-source;418
10.7.4;26.4 The role of mycorrhizal fungi in mobilizing soil nutrients, in particular nitrogen;418
10.7.5;26.5 The earthworm gut as a transient habitat for terrestrial denitrifiers;420
10.7.6;References;422
11;Index;426
12;Colour Plate Section;448