Biology of the Nitrogen Cycle
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Table of contents
- Cover
- Biology of the Nitrogen Cycleiii
- Copyright Pageiv
- Contentsv
- List of Contributorsix
- Prefacexiii
- Part I: Denitrification1
- Chapter 1. Introduction to the Biochemistry and Molecular Biology of Denitrification3
- 1.1 Introduction3
- 1.2 Proteins of denitrification4
- 1.3 Bioenergetics of denitrification7
- 1.4 Genes coding for enzymes of denitrification9
- 1.5 Regulation of transcription of the denitrification genes10
- 1.6 Regulatory networks in denitrifiers14
- 1.7 Concluding remarks18
- References19
- Chapter 2. The Prokaryotic Nitrate Reductases21
- 2.1 Introduction21
- 2.2 The membrane-bound NO3¯ -reductase (NarGHI)23
- 2.3 The Archaeal Nar system27
- 2.4 The periplasmic nitrate reductase (Nap)28
- 2.5 The assimilatory nitrate reductase (Nas)31
- 2.6 The eukaryotic nitrate reductases34
- References34
- Chapter 3. Nitrite Reductases in Denitrification37
- 3.1 Introduction37
- 3.2 Cd1 nitrite reductase38
- 3.3 Copper nitrite reductase48
- References54
- Chapter 4. Nitric Oxide Reductase: Structural Variations and Catalytic Mechanism57
- 4.1 Introduction57
- 4.2 Structural variations in NORs58
- 4.3 Catalytic mechanism of NOR62
- 4.4 Comparison between catalysis by NOR and CcO63
- References64
- Chapter 5. Nitrous Oxide Reductases67
- 5.1 Introduction67
- 5.2 Properties of N2O reductase68
- 5.3 Enzyme structure and Cu centers68
- 5.4 Metal center assembly71
- 5.5 Gene patterns and dissemination of nos genes73
- 5.6 Evolutionary aspects75
- 5.7 Transport processes for Nos proteins77
- 5.8 Role of accessory flavoproteins78
- References79
- Chapter 6. Denitrification in Rhizobia-Legume Symbiosis83
- 6.1 Introduction83
- 6.2 Denitrification in free-living rhizobia84
- 6.3 Denitrification in nodules86
- References89
- Chapter 7. The Dissimilatory Reduction of Nitrate to Ammonia by Anaerobic Bacteria93
- 7.1 Dissimilatory nitrate reduction to ammonia, a process distinct from denitrification and nitrate93
- 7.2 The cytoplasmic pathway for nitrate dissimilation to ammonia95
- 7.3 The periplasmic pathway for respiratory reduction of nitrate to ammonia96
- 7.4 Regulation of the cytoplasmic and periplasmic pathways for nitrate reduction to ammonia99
- 7.5 Distribution of enzymes for nitrate reduction to ammonia and their ecological significance101
- 7.6 Nitrate reduction to ammonia as an evolutionary link between nitrate assimilation and denitrific102
- 7.7 Current challenges and unanswered questions102
- References103
- Part II: Biological Nitrogen Fixation107
- Chapter 8. Physiology, Biochemistry, and Molecular Biology of Nitrogen Fixation109
- 8.1 Which organisms fix N2?109
- 8.2 Nitrogenases111
- 8.3 MgATP and Mo-nitrogenase catalysis122
- 8.4 Genetics of N2-fixation123
- 8.5 Regulation of N2-fixation125
- 8.6 Perspectives and future research125
- References126
- Chapter 9. Regulatory Cascades to Express Nitrogenases131
- 9.1. Introduction131
- 9.2 Environmental signals regulating expression of nitrogenases132
- 9.3 Levels of regulation of N2-fixation in proteobacteria and the central role of PII133
- 9.4 Transcriptional control of the nifA gene represents the first level of the regulatory cascade in135
- 9.5 NifA activates nif gene expression in concert with a specific sigma factor, RpoN136
- 9.6 Control of NifA activity represents the second level of the regulatory cascade137
- 9.7 Control of nitrogenase activity represents the third level of the regulatory cascade138
- 9.8 Regulation of alternative nitrogenases139
- 9.9 Regulation of N2-fixation in nonproteobacterial species140
- 9.10 Concluding remarks142
- References143
- Chapter 10. The Rhizobium-Legume Nitrogen-Fixing Symbiosis147
- 10.1 Introduction147
- 10.2 An overview of nodule formation148
- 10.3 Molecular mechanisms of signal exchange151
- 10.4 Symbiotic nitrogen fixation and assimilation159
- 10.5 Conclusions161
- References162
- Chapter 11. Plant Symbioses with Frankia and Cyanobacteria165
- 11.1 Introduction165
- 11.2 Actinorhizal symbioses165
- 11.3 Cyanobacterial symbioses169
- References174
- Chapter 12. Associative Nitrogen Fixation179
- 12.1 Introduction179
- 12.2 Non-symbiotic colonization of plants180
- 12.3 N2-fixing bacteria associated with plants181
- 12.4 Conclusion188
- References189
- Chapter 13. Measuring N2 Fixation in the Field193
- 13.1 Introduction193
- 13.2 Rate measurements194
- 13.3 Detecting N2 fixation potential and N2-fixing microorganisms199
- References202
- Part III: Other Reactions of the Nitrogen Cycle207
- Chapter 14. Biochemistry and Molecular Biology of Nitrification209
- 14.1 Introduction209
- 14.2 The general energetic problem faced by lithotrophic nitrifiers210
- 14.3 Denitrification reactions catalysed by nitrifiers218
- 14.4 Heterotrophic nitrification219
- References220
- Chapter 15. The Ecology of Nitrifying Bacteria223
- 15.1 Introduction223
- 15.2 Nitrifying microorganisms224
- 15.3 Community structure of nitrifiers in natural environments227
- 15.4 Factors influencing the ecology of nitrifying bacteria229
- 15.5 Conclusions241
- References241
- Chapter 16: Anammox245
- 16.1 Anammox: Discovery and introduction245
- 16.2 Enrichment of anammox biomass247
- 16.3 Physiology of anammox aggregates from the SBR248
- 16.4 Identification of the key player249
- 16.5 Ultrastructure of Brocadia anammoxidans253
- 16.6 Lipids of anammox bacteria254
- 16.7 Significance of anammox on a global scale254
- 16.8 Biochemistry and the role of environmental genomics256
- 16.9 The application of the anammox process257
- 16.10 Integration and perspectives258
- References260
- Chapter 17. Nitrate Assimilation in Bacteria263
- 17.1 Introduction263
- 17.2 The NO3 ¯ and NO2 ¯ uptake systems267
- 17.3 Assimilatory NRs270
- 17.4 Assimilatory NiRs272
- 17.5 Regulation of NO3 ¯ assimilation274
- 17.6 Concluding remarks278
- References278
- Chapter 18. Nitrate Assimilation in Plants283
- 18.1 Introduction283
- 18.2 Physiology and molecular biology of nitrate uptake284
- 18.3 Assimilatory NO3 ¯ reduction in higher plants290
- References295
- Chapter 19. Characterization of Proteolytic Microbes and Their Activities in Soils303
- 19.1 Introduction303
- 19.2 Methods to assess proteolysis304
- 19.3 Tools to study the gene- and transcript pool of proteolytic organisms305
- 19.4 Investigation of proteolysis in terrestrial ecosystems306
- References308
- Part IV: Applications of Reactions of the Nitrogen Cycle, with Emphasis on Denitrification311
- Chapter 20. Molecular Tools to Assess the Diversity and Density of Denitrifying Bacteria in Their Ha313
- 20.1 Introduction313
- 20.2 Molecular markers for denitrifying bacteria314
- 20.3 Genetic fingerprinting of denitrifier communities314
- 20.4 Quantification of denitrifier communities317
- 20.5 Examples of denitrifier communities in habitats319
- 20.6 Improving our ways to study denitrifiers in habitats322
- References324
- Chapter 21. Denitrification and Agriculture331
- 21.1 Nitrogen in agricultural systems331
- 21.2 Factors controlling denitrification in agricultural soils332
- 21.3 Agricultural consequences334
- 21.4 Environmental consequences of denitrification335
- 21.5 Quantification of denitrification losses337
- 21.6 Mitigation of denitrification activity in the field340
- References341
- Chapter 22. Denitrification and N-Cycling in Forest Ecosystems343
- 22.1 Introduction343
- 22.2 Characteristics of the N-cycle in forest ecosystems344
- 22.3 Impact of increased nitrogen inputs on denitrification345
- 22.4 Nitrogen inputs affect forest microbial communities346
- 22.5 Environmental regulation of denitrification347
- 22.6 Species involved in denitrification348
- 22.7 Importance of denitrification for N2O-emissions349
- 22.8 Effect of forest type on denitrification350
- 22.9 Competition between plants and microorganisms351
- 22.10 The N2O:N2 ratio and in situ quantification352
- 22.11 Modelling353
- 22.12 Austrian case – the missing nitrogen356
- References356
- Chapter 23. Denitrification in Wetlands359
- 23.1 Introduction359
- 23.2 Wetlands as an environment for denitrification360
- 23.3 Molecular diversity of denitrifying bacteria361
- 23.4 Denitrification in riparian wetlands362
- 23.5 Denitrification in constructed wetlands363
- 23.6 Emission of nitrogen gases from wetlands364
- References365
- Chapter 24. Organisms of the Nitrogen Cycle Under Extreme Conditions: Low Temperature, Salinity, pH369
- 24.1 Introduction369
- 24.2 Low temperature370
- 24.3 Denitrification in halophilic environments372
- References376
- Chapter 25. Nitrous Oxide Emission and Global Changes: Modeling Approaches381
- 25.1 Introduction381
- 25.2 Product stoichiometry of denitrification382
- 25.3 Models of soil anaerobiosis as a regulator for denitrification384
- 25.4 Denitrification and N2O flux in soil biogeochemical models387
- 25.5 Microbial kinetics of denitrification in biogeochemical models389
- References391
- Chapter 26. Interactions among Organisms that Result in Enhanced Activities of N-Cycle Reactions397
- 26.1 Introductory statement397
- 26.2 Associative bacteria are potentially beneficial to the health of plants397
- 26.3 Plants eating animals (carnivorous plants) to get access to an extra N-source399
- 26.4 The role of mycorrhizal fungi in mobilizing soil nutrients, in particular nitrogen399
- 26.5 The earthworm gut as a transient habitat for terrestrial denitrifiers401
- References403
- Index407
- Colour Plate SectionColour Pla
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
* 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