Research on Nitrification and Related Processes, Part A (eBook)

Front Cover 1
Methods in Enzymology: Research on Nitrification and Related Processes, Part A 4
Copyright 5
Contents 6
Contributors 14
Preface 20
Methods in Enzymology 22
Section One: Modeling 52
Chapter 1: Modeling the Role of Nitrification in Open Ocean Productivity and the Nitrogen Cycle 54
1. Introduction 55
2. Ocean Carbon Cycle 55
3. Export Production and the f-Ratio 58
4. Plankton Ecosystem Models 63
5. Modeling Nitrification 66
6. Operational Considerations 73
7. Future Modeling 75
8. Summary 78
Acknowledgments 79
References 79
Chapter 2: Continuous Cultivation and Thermodynamic Aspects of Niche Definition in the Nitrogen Cycle 84
1. Introduction 84
2. A Minimal Model for Microbial Behavior 86
3. Continuous Cultivation-Background and Experimental Approach 94
4. Conclusion 101
Acknowledgments 101
References 101
Section Two: Cultivation and cell physIology 104
Chapter 3: Isolation, Cultivation, and Characterization of Ammonia-Oxidizing Bacteria and Archaea Adapted to Low Ammonium Con 106
1. Introduction 107
2. General Description of Cultivation Methods for Ammonia-Oxidizing Microorganisms 108
3. Enrichment of Ammonia Oxidizers 114
4. Isolation of Ammonia Oxidizers 119
5. Characterization of Ammonia-Oxidizing Prokaryotes 123
Appendix A Identification of Ammonia Oxidizers Based on 16S rRNA and Functional Genes 128
Appendix B Measurement of NH4+, NO2-, and NO3- 132
References 135
Chapter 4: Cultivation, Detection, and Ecophysiology of Anaerobic Ammonium-Oxidizing Bacteria 140
1. Introduction 141
2. Enrichment of Anammox Bacteria as Planktonic Cell Suspensions 144
3. Molecular Detection of Anammox Bacteria 148
4. Conclusions 155
Acknowledgments 155
References 156
Chapter 5: Cultivation, Growth Physiology, and Chemotaxonomy of Nitrite-Oxidizing Bacteria 160
1. Introduction 161
2. Recipes for the Culture of NOB 163
3. Cultivation Procedure 165
4. Isolation 167
5. Physiological Investigations 169
6. Chemical Analyses 172
7. Monitoring the Cultures 172
8. Fatty Acid Analyses 175
Acknowledgments 178
References 178
Chapter 6: Surveying N2O-Producing Pathways in Bacteria 182
1. Introduction 183
2. Bioinformatics 186
3. Surveying Function 194
4. Concluding Remarks 198
References 199
Section Three: Molecular microbial Ecology and processes measurements 204
Chapter 7: Stable Isotope Probing with 18O-Water to Investigate Growth and Mortality of Ammonia Oxidizing Bacteria and Archae... 206
1. Introduction 207
2. Materials and Methods 209
3. Calculation of Growth and Mortality Indices 211
4. Results 212
5. Discussion 216
6. Conclusions 218
Acknowledgments 218
References 219
Chapter 8: Measuring Nitrification, Denitrification, and Related Biomarkers in Terrestrial Geothermal Ecosystems 222
1. Introduction 223
2. General Considerations for Measurement of N-Cycle Activities in Terrestrial Geothermal Habitats 228
3. Methods for Measuring Nitrification in Terrestrial Geothermal Habitats 230
4. Methods for Measuring Denitrification in Terrestrial Geothermal Habitats 238
5. Detection and Quantification of Potential Biomarkers for Thermophilic AOA and Denitrifying Thermus thermophilus... 244
6. Closing Remarks 249
Acknowledgments 249
References 249
Chapter 9: Determining the Distribution of Marine and Coastal Ammonia-Oxidizing Archaea and Bacteria Using a Quantitative... 256
1. Introduction 257
2. Methods for Measuring the Abundance of AOA and AOB Within Marine and Coastal Systems 260
3. Methodological Considerations 264
4. Targeting Specific Ecotypes: Quantifying Shallow and Deep Clades of Marine Water Column AOA 265
Acknowledgments 268
References 269
Chapter 10: 15N-Labeling Experiments to Dissect the Contributions of Heterotrophic Denitrification and Anammox to Nitrogen... 274
1. Introduction 275
2. Theoretical Description of 15N-Incubation Experiments 278
3. In the Field: Supplementary Measurements 284
4. In the Field: Incubation Experiments 288
5. In the Lab: Mass Spectrometry Measurements 291
6. Data Processing and Interpretation 294
7. Common Pitfalls 299
8. Concluding Remarks 300
Acknowledgments 300
References 301
Chapter 11: Assessment of Nitrogen and Oxygen Isotopic Fractionation During Nitrification and Its Expression in the Marine... 304
1. Introduction 305
2. Methods 310
3. Analytical Techniques 313
4. Data Analysis 315
5. Discussion 323
References 326
Chapter 12: Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence In Situ Hybridization Coupled... 332
1 Introduction 333
2 Methods 336
3 Concluding Remarks 351
Acknowledgments 352
References 352
Chapter 13: Measurement and Distribution of Nitrification Rates in the Oceans 358
1. Introduction 359
2. Nitrification Rate Measurements in Seawater 361
3. Nitrification Rate Measurements in Sediments 369
4. Distribution of Nitrification 370
References 371
Chapter 14: Construction of STOX Oxygen Sensors and Their Application for Determination of O2 Concentrations in Oxygen... 376
1. Introduction 377
2. STOX Sensor Principle 378
3. Sensor Construction 379
4. Electronics for STOX Sensors 383
5. STOX Sensor Calibration and Performance 384
6. Calculation of Oxygen Concentrations from STOX Data 386
7. In Situ Deployment of STOX Sensors in OMZs 388
8. Future Fast Response STOX Sensors 390
9. Using STOX Sensors to Recalibrate Conventional Oxygen Sensors 390
Acknowledgments 391
References 391
Chapter 15: Regulation and Measurement of Nitrification in Terrestrial Systems 394
1. Introduction 395
2. Diversity of the Nitrification Process in Terrestrial Environments 396
3. Substrates and Products of Nitrification Reactions 397
4. Controls on Nitrification Rates in Soil Environments 398
5. Measurements of Nitrification in Terrestrial Environments 401
6. Measurement of Nitrification Rates in Terrestrial Ecosystems 402
7. Measurement of Nitrification Kinetics 408
8. Nitrifier Population Size 412
9. Modeling Approaches 412
10. Future Advancements in Nitrification Rate Research in Terrestrial Environments 413
References 413
Chapter 16: Protocol for the Measurement of Nitrous Oxide Fluxes from Biological Wastewater Treatment Plants 420
1. Introduction 421
2. Sampling Design for Full-Scale Monitoring 421
3. Sampling Procedures: Headspace Gas Measurement 424
4. Sampling Procedures: Measurement of Aqueous N2O Concentrations 427
5. Sampling Procedures: Measurement of Advective Gas Flow Rate from Bioreactor Headspace 427
6. Principles of Real-Time N2O Measurement 428
7. Data Analysis: Determination of Fluxes 428
8. Data Analysis: Determination of Emission Fractions 429
9. Data Analysis: Calculation of N2O Emission Factors 429
10. Standardization of Protocol and Comparison with Established Emissions Flux Measurement Methods 430
11. N2O Emission Fluxes from Activated Sludge Processes 432
12. Triggers for N2O Emission from Wastewater Treatment Operations 433
13. Lab-Scale and Field-Scale Adaptation of Protocol N2O Emission Measurements 434
14. Concluding Remarks 434
Acknowledgments 434
References 435
Section Four: Genetics, Biochemistry and Biogeochemistry 438
Chapter 17: Genetic Transformation of Ammonia-Oxidizing Bacteria 440
1 Introduction 441
2 Transformation of AOB 442
3 Gene Inactivation in AOB 444
4 Use of Broad-Host Range Plasmids 449
5 Strain Stability and Maintenance 450
6 Conclusions 450
References 451
Chapter 18: Dissecting Iron Uptake and Homeostasis in Nitrosomonas europaea 454
1. Introduction 455
2. Use of Bioinformatics to Plan Fe-Related Studies 457
3. Methods to Learn About the Physiological Responses to Fe Limitation 458
4. Methods to Study Siderophore Uptake 469
5. Genetic Complementation to Study fur Homologs 472
6. Methods for Gene Inactivation of Fe Uptake Systems 473
7. Lingering Questions that can be Answered by the Above Protocols 474
8. Conclusion 476
References 476
Chapter 19: Production of Recombinant Multiheme Cytochromes c in Wolinella succinogenes 480
1. Introduction 481
2. Bacterial Cytochrome c Biogenesis Systems 484
3. Recombinant Cytochrome c Production 486
4. Cytochromes c in the Epsilonproteobacterium W. succinogenes 486
5. Three Cytochrome c Heme Lyase Isoenzymes in W. succinogenes 490
6. Heterologous Production of Cytochromes c in W. succinogenes 490
7. Conclusions and Perspectives 493
Acknowledgments 494
References 494
Chapter 20: Techniques for Investigating Hydroxylamine Disproportionation by Hydroxylamine Oxidoreductases 498
1. Introduction 499
2. General Considerations 501
3. Ammonia Concentration Determination 505
4. Nitric Oxide Concentration Determination 508
5. Nitrite Concentration Determination 509
6. Nitrous Oxide and Dinitrogen Concentration Determination 511
References 513
Chapter 21: Liquid Chromatography-Mass Spectrometry-Based Proteomics of Nitrosomonas 516
1. Introduction 517
2. LC-MS/MS Instrument Setup 519
3. Growth of N. eutropha C91 Pure Culture 520
4. Sample Preparation 521
5. C18 Reversed Phase LC-MS/MS Analysis 522
6. Database Searches and Validation of Results 523
7. Dataset Description and Protein Identification Example 527
8. Conclusions 530
References 530
Chapter 22: The Geochemical Record of the Ancient Nitrogen Cycle, Nitrogen Isotopes, and Metal Cofactors 534
1. Introduction 535
2. Reconstructing the Nitrogen Cycle and Associated Trace Metal Abundances through Time 540
3. Determining Changes in the N-Cycle from the Geological Record of N Isotopes and Metal Availability 543
4. Measurement 548
5. Concluding Remarks 550
Acknowledgments 550
References 550
Author Index 558
Subject Index 584
Colour plate 600