Research on Nitrification and Related Processes, Part A

1. Auflage 2011
ISBN: 978-0-12-381295-7
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 485, 608 Seiten, Web PDF

Reihe: Methods in Enzymology

State-of-the-art update on methods and protocols dealing with the detection, isolation and characterization of macromolecules and their hosting organisms that facilitate nitrification and related processes in the nitrogen cycle as well as the challenges of doing so in very diverse environments. - Provides state-of-the-art update on methods and protocols - Deals with the detection, isolation and characterization of macromolecules and their hosting organisms - Deals with the challenges of very diverse environments

Autoren/Hrsg.

Inhaltsverzeichnis

1;Front Cover;1
2;Methods in Enzymology: Research on Nitrification and Related Processes, Part A;4
3;Copyright;5
4;Contents;6
5;Contributors;14
6;Preface;20
7;Methods in Enzymology;22
8;Section One: Modeling;52
8.1;Chapter 1: Modeling the Role of Nitrification in Open Ocean Productivity and the Nitrogen Cycle;54
8.1.1;1. Introduction;55
8.1.2;2. Ocean Carbon Cycle;55
8.1.3;3. Export Production and the f-Ratio;58
8.1.4;4. Plankton Ecosystem Models;63
8.1.5;5. Modeling Nitrification;66
8.1.6;6. Operational Considerations;73
8.1.7;7. Future Modeling;75
8.1.8;8. Summary;78
8.1.9;Acknowledgments;79
8.1.10;References;79
8.2;Chapter 2: Continuous Cultivation and Thermodynamic Aspects of Niche Definition in the Nitrogen Cycle;84
8.2.1;1. Introduction;84
8.2.2;2. A Minimal Model for Microbial Behavior;86
8.2.3;3. Continuous Cultivation-Background and Experimental Approach;94
8.2.4;4. Conclusion;101
8.2.5;Acknowledgments;101
8.2.6;References;101
9;Section Two: Cultivation and cell physIology;104
9.1;Chapter 3: Isolation, Cultivation, and Characterization of Ammonia-Oxidizing Bacteria and Archaea Adapted to Low Ammonium Con;106
9.1.1;1. Introduction;107
9.1.2;2. General Description of Cultivation Methods for Ammonia-Oxidizing Microorganisms;108
9.1.3;3. Enrichment of Ammonia Oxidizers;114
9.1.4;4. Isolation of Ammonia Oxidizers;119
9.1.5;5. Characterization of Ammonia-Oxidizing Prokaryotes;123
9.1.6;Appendix A Identification of Ammonia Oxidizers Based on 16S rRNA and Functional Genes;128
9.1.7;Appendix B Measurement of NH4+, NO2-, and NO3-;132
9.1.8;References;135
9.2;Chapter 4: Cultivation, Detection, and Ecophysiology of Anaerobic Ammonium-Oxidizing Bacteria;140
9.2.1;1. Introduction;141
9.2.2;2. Enrichment of Anammox Bacteria as Planktonic Cell Suspensions;144
9.2.3;3. Molecular Detection of Anammox Bacteria;148
9.2.4;4. Conclusions;155
9.2.5;Acknowledgments;155
9.2.6;References;156
9.3;Chapter 5: Cultivation, Growth Physiology, and Chemotaxonomy of Nitrite-Oxidizing Bacteria;160
9.3.1;1. Introduction;161
9.3.2;2. Recipes for the Culture of NOB;163
9.3.3;3. Cultivation Procedure;165
9.3.4;4. Isolation;167
9.3.5;5. Physiological Investigations;169
9.3.6;6. Chemical Analyses;172
9.3.7;7. Monitoring the Cultures;172
9.3.8;8. Fatty Acid Analyses;175
9.3.9;Acknowledgments;178
9.3.10;References;178
9.4;Chapter 6: Surveying N2O-Producing Pathways in Bacteria;182
9.4.1;1. Introduction;183
9.4.2;2. Bioinformatics;186
9.4.3;3. Surveying Function;194
9.4.4;4. Concluding Remarks;198
9.4.5;References;199
10;Section Three: Molecular microbial Ecology and processes measurements;204
10.1;Chapter 7: Stable Isotope Probing with 18O-Water to Investigate Growth and Mortality of Ammonia Oxidizing Bacteria and Archae...;206
10.1.1;1. Introduction;207
10.1.2;2. Materials and Methods;209
10.1.3;3. Calculation of Growth and Mortality Indices;211
10.1.4;4. Results;212
10.1.5;5. Discussion;216
10.1.6;6. Conclusions;218
10.1.7;Acknowledgments;218
10.1.8;References;219
10.2;Chapter 8: Measuring Nitrification, Denitrification, and Related Biomarkers in Terrestrial Geothermal Ecosystems;222
10.2.1;1. Introduction;223
10.2.2;2. General Considerations for Measurement of N-Cycle Activities in Terrestrial Geothermal Habitats;228
10.2.3;3. Methods for Measuring Nitrification in Terrestrial Geothermal Habitats;230
10.2.4;4. Methods for Measuring Denitrification in Terrestrial Geothermal Habitats;238
10.2.5;5. Detection and Quantification of Potential Biomarkers for Thermophilic AOA and Denitrifying Thermus thermophilus...;244
10.2.6;6. Closing Remarks;249
10.2.7;Acknowledgments;249
10.2.8;References;249
10.3;Chapter 9: Determining the Distribution of Marine and Coastal Ammonia-Oxidizing Archaea and Bacteria Using a Quantitative...;256
10.3.1;1. Introduction;257
10.3.2;2. Methods for Measuring the Abundance of AOA and AOB Within Marine and Coastal Systems;260
10.3.3;3. Methodological Considerations;264
10.3.4;4. Targeting Specific Ecotypes: Quantifying Shallow and Deep Clades of Marine Water Column AOA;265
10.3.5;Acknowledgments;268
10.3.6;References;269
10.4;Chapter 10: 15N-Labeling Experiments to Dissect the Contributions of Heterotrophic Denitrification and Anammox to Nitrogen...;274
10.4.1;1. Introduction;275
10.4.2;2. Theoretical Description of 15N-Incubation Experiments;278
10.4.3;3. In the Field: Supplementary Measurements;284
10.4.4;4. In the Field: Incubation Experiments;288
10.4.5;5. In the Lab: Mass Spectrometry Measurements;291
10.4.6;6. Data Processing and Interpretation;294
10.4.7;7. Common Pitfalls;299
10.4.8;8. Concluding Remarks;300
10.4.9;Acknowledgments;300
10.4.10;References;301
10.5;Chapter 11: Assessment of Nitrogen and Oxygen Isotopic Fractionation During Nitrification and Its Expression in the Marine...;304
10.5.1;1. Introduction;305
10.5.2;2. Methods;310
10.5.3;3. Analytical Techniques;313
10.5.4;4. Data Analysis;315
10.5.5;5. Discussion;323
10.5.6;References;326
10.6;Chapter 12: Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence In Situ Hybridization Coupled...;332
10.6.1;1 Introduction;333
10.6.2;2 Methods;336
10.6.3;3 Concluding Remarks;351
10.6.4;Acknowledgments;352
10.6.5;References;352
10.7;Chapter 13: Measurement and Distribution of Nitrification Rates in the Oceans;358
10.7.1;1. Introduction;359
10.7.2;2. Nitrification Rate Measurements in Seawater;361
10.7.3;3. Nitrification Rate Measurements in Sediments;369
10.7.4;4. Distribution of Nitrification;370
10.7.5;References;371
10.8;Chapter 14: Construction of STOX Oxygen Sensors and Their Application for Determination of O2 Concentrations in Oxygen...;376
10.8.1;1. Introduction;377
10.8.2;2. STOX Sensor Principle;378
10.8.3;3. Sensor Construction;379
10.8.4;4. Electronics for STOX Sensors;383
10.8.5;5. STOX Sensor Calibration and Performance;384
10.8.6;6. Calculation of Oxygen Concentrations from STOX Data;386
10.8.7;7. In Situ Deployment of STOX Sensors in OMZs;388
10.8.8;8. Future Fast Response STOX Sensors;390
10.8.9;9. Using STOX Sensors to Recalibrate Conventional Oxygen Sensors;390
10.8.10;Acknowledgments;391
10.8.11;References;391
10.9;Chapter 15: Regulation and Measurement of Nitrification in Terrestrial Systems;394
10.9.1;1. Introduction;395
10.9.2;2. Diversity of the Nitrification Process in Terrestrial Environments;396
10.9.3;3. Substrates and Products of Nitrification Reactions;397
10.9.4;4. Controls on Nitrification Rates in Soil Environments;398
10.9.5;5. Measurements of Nitrification in Terrestrial Environments;401
10.9.6;6. Measurement of Nitrification Rates in Terrestrial Ecosystems;402
10.9.7;7. Measurement of Nitrification Kinetics;408
10.9.8;8. Nitrifier Population Size;412
10.9.9;9. Modeling Approaches;412
10.9.10;10. Future Advancements in Nitrification Rate Research in Terrestrial Environments;413
10.9.11;References;413
10.10;Chapter 16: Protocol for the Measurement of Nitrous Oxide Fluxes from Biological Wastewater Treatment Plants;420
10.10.1;1. Introduction;421
10.10.2;2. Sampling Design for Full-Scale Monitoring;421
10.10.3;3. Sampling Procedures: Headspace Gas Measurement;424
10.10.4;4. Sampling Procedures: Measurement of Aqueous N2O Concentrations;427
10.10.5;5. Sampling Procedures: Measurement of Advective Gas Flow Rate from Bioreactor Headspace;427
10.10.6;6. Principles of Real-Time N2O Measurement;428
10.10.7;7. Data Analysis: Determination of Fluxes;428
10.10.8;8. Data Analysis: Determination of Emission Fractions;429
10.10.9;9. Data Analysis: Calculation of N2O Emission Factors;429
10.10.10;10. Standardization of Protocol and Comparison with Established Emissions Flux Measurement Methods;430
10.10.11;11. N2O Emission Fluxes from Activated Sludge Processes;432
10.10.12;12. Triggers for N2O Emission from Wastewater Treatment Operations;433
10.10.13;13. Lab-Scale and Field-Scale Adaptation of Protocol N2O Emission Measurements;434
10.10.14;14. Concluding Remarks;434
10.10.15;Acknowledgments;434
10.10.16;References;435
11;Section Four: Genetics, Biochemistry and Biogeochemistry;438
11.1;Chapter 17: Genetic Transformation of Ammonia-Oxidizing Bacteria;440
11.1.1;1 Introduction;441
11.1.2;2 Transformation of AOB;442
11.1.3;3 Gene Inactivation in AOB;444
11.1.4;4 Use of Broad-Host Range Plasmids;449
11.1.5;5 Strain Stability and Maintenance;450
11.1.6;6 Conclusions;450
11.1.7;References;451
11.2;Chapter 18: Dissecting Iron Uptake and Homeostasis in Nitrosomonas europaea;454
11.2.1;1. Introduction;455
11.2.2;2. Use of Bioinformatics to Plan Fe-Related Studies;457
11.2.3;3. Methods to Learn About the Physiological Responses to Fe Limitation;458
11.2.4;4. Methods to Study Siderophore Uptake;469
11.2.5;5. Genetic Complementation to Study fur Homologs;472
11.2.6;6. Methods for Gene Inactivation of Fe Uptake Systems;473
11.2.7;7. Lingering Questions that can be Answered by the Above Protocols;474
11.2.8;8. Conclusion;476
11.2.9;References;476
11.3;Chapter 19: Production of Recombinant Multiheme Cytochromes c in Wolinella succinogenes;480
11.3.1;1. Introduction;481
11.3.2;2. Bacterial Cytochrome c Biogenesis Systems;484
11.3.3;3. Recombinant Cytochrome c Production;486
11.3.4;4. Cytochromes c in the Epsilonproteobacterium W. succinogenes;486
11.3.5;5. Three Cytochrome c Heme Lyase Isoenzymes in W. succinogenes;490
11.3.6;6. Heterologous Production of Cytochromes c in W. succinogenes;490
11.3.7;7. Conclusions and Perspectives;493
11.3.8;Acknowledgments;494
11.3.9;References;494
11.4;Chapter 20: Techniques for Investigating Hydroxylamine Disproportionation by Hydroxylamine Oxidoreductases;498
11.4.1;1. Introduction;499
11.4.2;2. General Considerations;501
11.4.3;3. Ammonia Concentration Determination;505
11.4.4;4. Nitric Oxide Concentration Determination;508
11.4.5;5. Nitrite Concentration Determination;509
11.4.6;6. Nitrous Oxide and Dinitrogen Concentration Determination;511
11.4.7;References;513
11.5;Chapter 21: Liquid Chromatography-Mass Spectrometry-Based Proteomics of Nitrosomonas;516
11.5.1;1. Introduction;517
11.5.2;2. LC-MS/MS Instrument Setup;519
11.5.3;3. Growth of N. eutropha C91 Pure Culture;520
11.5.4;4. Sample Preparation;521
11.5.5;5. C18 Reversed Phase LC-MS/MS Analysis;522
11.5.6;6. Database Searches and Validation of Results;523
11.5.7;7. Dataset Description and Protein Identification Example;527
11.5.8;8. Conclusions;530
11.5.9;References;530
11.6;Chapter 22: The Geochemical Record of the Ancient Nitrogen Cycle, Nitrogen Isotopes, and Metal Cofactors;534
11.6.1;1. Introduction;535
11.6.2;2. Reconstructing the Nitrogen Cycle and Associated Trace Metal Abundances through Time;540
11.6.3;3. Determining Changes in the N-Cycle from the Geological Record of N Isotopes and Metal Availability;543
11.6.4;4. Measurement;548
11.6.5;5. Concluding Remarks;550
11.6.6;Acknowledgments;550
11.6.7;References;550
12;Author Index;558
13;Subject Index;584
14;Colour plate;600