Biology of the Nitrogen Cycle

Cover......Page 1
Biology of the Nitrogen Cycle......Page 4
Copyright page......Page 5
Contents......Page 6
List of Contributors......Page 10
Preface......Page 14
Part I: Denitrification......Page 20
1.1 Introduction......Page 22
1.2 Proteins of denitrification......Page 23
1.3 Bioenergetics of denitrification......Page 26
1.4 Genes coding for enzymes of denitrification......Page 28
1.5 Regulation of transcription of the denitrification genes......Page 29
1.6 Regulatory networks in denitrifiers......Page 33
1.7 Concluding remarks......Page 37
References......Page 38
2.1 Introduction......Page 40
2.2 The membrane-bound NO3¯ -reductase (NarGHI)......Page 42
2.3 The Archaeal Nar system......Page 46
2.4 The periplasmic nitrate reductase (Nap)......Page 47
2.5 The assimilatory nitrate reductase (Nas)......Page 50
References......Page 53
3.1 Introduction......Page 56
3.2 Cd1 nitrite reductase......Page 57
3.3 Copper nitrite reductase......Page 67
References......Page 73
4.1 Introduction......Page 76
4.2 Structural variations in NORs......Page 77
4.3 Catalytic mechanism of NOR......Page 81
4.4 Comparison between catalysis by NOR and CcO......Page 82
References......Page 83
5.1 Introduction......Page 86
5.3 Enzyme structure and Cu centers......Page 87
5.4 Metal center assembly......Page 90
5.5 Gene patterns and dissemination of nos genes......Page 92
5.6 Evolutionary aspects......Page 94
5.7 Transport processes for Nos proteins......Page 96
5.8 Role of accessory flavoproteins......Page 97
References......Page 98
6.1 Introduction......Page 102
6.2 Denitrification in free-living rhizobia......Page 103
6.3 Denitrification in nodules......Page 105
References......Page 108
7.1 Dissimilatory nitrate reduction to ammonia, a process distinct from denitrification and nitrate assimilation......Page 112
7.2 The cytoplasmic pathway for nitrate dissimilation to ammonia......Page 114
7.3 The periplasmic pathway for respiratory reduction of nitrate to ammonia......Page 115
7.4 Regulation of the cytoplasmic and periplasmic pathways for nitrate reduction to ammonia......Page 118
7.5 Distribution of enzymes for nitrate reduction to ammonia and their ecological significance......Page 120
7.7 Current challenges and unanswered questions......Page 121
References......Page 122
Part II: Biological Nitrogen Fixation......Page 126
8.1 Which organisms fix N2?......Page 128
8.2 Nitrogenases......Page 130
8.3 MgATP and Mo-nitrogenase catalysis......Page 141
8.4 Genetics of N2-fixation......Page 142
8.6 Perspectives and future research......Page 144
References......Page 145
9.1. Introduction......Page 150
9.2 Environmental signals regulating expression of nitrogenases......Page 151
9.3 Levels of regulation of N2-fixation in proteobacteria and the central role of PII......Page 152
9.4 Transcriptional control of the nifA gene represents the first level of the regulatory cascade in diazotrophic proteobacteria......Page 154
9.5 NifA activates nif gene expression in concert with a specific sigma factor, RpoN......Page 155
9.6 Control of NifA activity represents the second level of the regulatory cascade......Page 156
9.7 Control of nitrogenase activity represents the third level of the regulatory cascade......Page 157
9.8 Regulation of alternative nitrogenases......Page 158
9.9 Regulation of N2-fixation in nonproteobacterial species......Page 159
9.10 Concluding remarks......Page 161
References......Page 162
10.1 Introduction......Page 166
10.2 An overview of nodule formation......Page 167
10.3 Molecular mechanisms of signal exchange......Page 170
10.4 Symbiotic nitrogen fixation and assimilation......Page 178
10.5 Conclusions......Page 180
References......Page 181
11.2 Actinorhizal symbioses......Page 184
11.3 Cyanobacterial symbioses......Page 188
References......Page 193
12.1 Introduction......Page 198
12.2 Non-symbiotic colonization of plants......Page 199
12.3 N2-fixing bacteria associated with plants......Page 200
12.4 Conclusion......Page 207
References......Page 208
13.1 Introduction......Page 212
13.2 Rate measurements......Page 213
13.3 Detecting N2 fixation potential and N2-fixing microorganisms......Page 218
References......Page 221
Part III: Other Reactions of the Nitrogen Cycle......Page 226
14.1 Introduction......Page 228
14.2 The general energetic problem faced by lithotrophic nitrifiers......Page 229
14.3 Denitrification reactions catalysed by nitrifiers......Page 237
14.4 Heterotrophic nitrification......Page 238
References......Page 239
15.1 Introduction......Page 242
15.2 Nitrifying microorganisms......Page 243
15.3 Community structure of nitrifiers in natural environments......Page 246
15.4 Factors influencing the ecology of nitrifying bacteria......Page 248
References......Page 260
16.1 Anammox: Discovery and introduction......Page 264
16.2 Enrichment of anammox biomass......Page 266
16.3 Physiology of anammox aggregates from the SBR......Page 267
16.4 Identification of the key player......Page 268
16.5 Ultrastructure of Brocadia anammoxidans......Page 272
16.7 Significance of anammox on a global scale......Page 273
16.8 Biochemistry and the role of environmental genomics......Page 275
16.9 The application of the anammox process......Page 276
16.10 Integration and perspectives......Page 277
References......Page 279
17.1 Introduction......Page 282
17.2 The NO3 ¯ and NO2 ¯ uptake systems......Page 286
17.3 Assimilatory NRs......Page 289
17.4 Assimilatory NiRs......Page 291
17.5 Regulation of NO3 ¯ assimilation......Page 293
References......Page 297
18.1 Introduction......Page 302
18.2 Physiology and molecular biology of nitrate uptake......Page 303
18.3 Assimilatory NO3 ¯ reduction in higher plants......Page 309
References......Page 314
19.1 Introduction......Page 322
19.2 Methods to assess proteolysis......Page 323
19.3 Tools to study the gene- and transcript pool of proteolytic organisms......Page 324
19.4 Investigation of proteolysis in terrestrial ecosystems......Page 325
References......Page 327
Part IV: Applications of Reactions of the Nitrogen Cycle, with Emphasis on Denitrification......Page 330
20.1 Introduction......Page 332
20.3 Genetic fingerprinting of denitrifier communities......Page 333
20.4 Quantification of denitrifier communities......Page 336
20.5 Examples of denitrifier communities in habitats......Page 338
20.6 Improving our ways to study denitrifiers in habitats......Page 341
References......Page 343
21.1 Nitrogen in agricultural systems......Page 350
21.2 Factors controlling denitrification in agricultural soils......Page 351
21.3 Agricultural consequences......Page 353
21.4 Environmental consequences of denitrification......Page 354
21.5 Quantification of denitrification losses......Page 356
21.6 Mitigation of denitrification activity in the field......Page 359
References......Page 360
22.1 Introduction......Page 362
22.2 Characteristics of the N-cycle in forest ecosystems......Page 363
22.3 Impact of increased nitrogen inputs on denitrification......Page 364
22.4 Nitrogen inputs affect forest microbial communities......Page 365
22.5 Environmental regulation of denitrification......Page 366
22.6 Species involved in denitrification......Page 367
22.7 Importance of denitrification for N2O-emissions......Page 368
22.8 Effect of forest type on denitrification......Page 369
22.9 Competition between plants and microorganisms......Page 370
22.10 The N2O:N2 ratio and in situ quantification......Page 371
22.11 Modelling......Page 372
References......Page 375
23.1 Introduction......Page 378
23.2 Wetlands as an environment for denitrification......Page 379
23.3 Molecular diversity of denitrifying bacteria......Page 380
23.4 Denitrification in riparian wetlands......Page 381
23.5 Denitrification in constructed wetlands......Page 382
23.6 Emission of nitrogen gases from wetlands......Page 383
References......Page 384
24.1 Introduction......Page 388
24.2 Low temperature......Page 389
24.3 Denitrification in halophilic environments......Page 391
References......Page 395
25.1 Introduction......Page 400
25.2 Product stoichiometry of denitrification......Page 401
25.3 Models of soil anaerobiosis as a regulator for denitrification......Page 403
25.4 Denitrification and N2O flux in soil biogeochemical models......Page 406
25.5 Microbial kinetics of denitrification in biogeochemical models......Page 408
References......Page 410
26.2 Associative bacteria are potentially beneficial to the health of plants......Page 416
26.4 The role of mycorrhizal fungi in mobilizing soil nutrients, in particular nitrogen......Page 418
26.5 The earthworm gut as a transient habitat for terrestrial denitrifiers......Page 420
References......Page 422
Index......Page 426
Colour Plate Section......Page 448