Stein Research on Nitrification and Related Processes, Part B

1. Auflage 2011
ISBN: 978-0-12-386490-1
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 496, 576 Seiten

Reihe: Methods in Enzymology

The global nitrogen cycle is the one most impacted by mankind. The past decade has changed our view on many aspects of the microbial biogeochemical cycles, including the global nitrogen cycle, which is mainly due to tremendous advances in methods, techniques and approaches. Many novel processes and the molecular inventory and organisms that facilitate them have been discovered only within the last 5 to 10 years, and the process is in progress. Research on Nitrification and Related Processes, Part B provides state-of-the-art updates 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.

Stein, Lisa

Inhaltsverzeichnis

1;Front Cover;1
2;Research on Nitrification and Related Processes, Part B;4
3;Copyright;5
4;Contents;6
5;Contributors;14
6;Preface;20
7;Methods In Enzymology;22
8;Section One: Process Measurements in Natural Systems;52
8.1;Chapter 1: Strategies to Determine Diversity, Growth, and Activity of Ammonia-Oxidizing Archaea in Soil;54
8.1.1;1. Introduction;55
8.1.2;2. Common Methods;57
8.1.3;3. Community Composition and Diversity;66
8.1.4;4. Determining Growth and Abundance;72
8.1.5;5. Activity;74
8.1.6;6. Conclusions;80
8.1.7;References;82
8.2;Chapter 2: Responses of Aerobic and Anaerobic Ammonia/Ammonium-Oxidizing Microorganisms to Anthropogenic Pollution in Coastal...;86
8.2.1;1. Introduction;87
8.2.2;2. Selection of Sampling Sites and Physicochemical Characterization;89
8.2.3;3. Molecular Ecological Characterization;90
8.2.4;4. Community Structure Analyses;95
8.2.5;5. Relationship Between the Community Structure and Physicochemical Parameters;101
8.2.6;6. Relationships Between the Community Change and the Environments;105
8.2.7;7. Conclusions;106
8.2.8;Acknowledgments;107
8.2.9;References;107
8.3;Chapter 3: Molecular and Stable Isotope Methods to Detect and Measure Anaerobic Ammonium Oxidation (Anammox) in Aquatic Ecosystems;114
8.3.1;1. Introduction;115
8.3.2;2. Molecular Methods to Detect and Quantify Anammox Bacteria in Environmental Samples;117
8.3.3;3. Stable Isotope Methods to Measure Anammox Rates in Environmental Samples;128
8.3.4;Acknowledgments;135
8.3.5;References;135
8.4;Chapter 4: Nitrogen Mineralization and Assimilation at Millimeter Scales;142
8.4.1;1. Introduction;143
8.4.2;2. Microbial Habitats in Soil;143
8.4.3;3. Methodological Approaches;145
8.4.4;4. Conclusions;160
8.4.5;References;160
8.5;Chapter 5: Measurement of Carbon Dioxide, Methane, Nitrous oxide, and Water Potential in Soil Ecosystems;166
8.5.1;1. Introduction;167
8.5.2;2. Soil Gas Probes;173
8.5.3;3. Flux Estimates to the Atmosphere Using Recirculating Chambers;176
8.5.4;4. Data Analysis;176
8.5.5;5. Soil Profile Analysis;178
8.5.6;6. FTIR Calibration;179
8.5.7;7. Correlations Between Profile Concentrations and Surface Flux in Field Measurements;180
8.5.8;8. Correlations Between FTIR and Traditional Water Activity Measures;183
8.5.9;9. Common Issues During FTIR Measurement;183
8.5.10;10. Conclusions;185
8.5.11;Acknowledgments;186
8.5.12;References;186
8.6;Chapter 6: Source Determination of Nitrous Oxide Based on Nitrogen and Oxygen Isotope Tracing...;190
8.6.1;1. Introduction;191
8.6.2;2. Experimental Approach;194
8.6.3;3. Data Evaluation for Nitrous Oxide Source Determination;196
8.6.4;4. Application of the ERR Principle in Nitrate Source Determination;201
8.6.5;5. Discussion, Applications, and Future Directions;203
8.6.6;References;207
9;Section Two: Process Measurements in Biofilm Communities;212
9.1;Chapter 7: A Polyphasic Approach to Study Ecophysiology of Complex Multispecies Nitrifying Biofilms;214
9.1.1;1. Introduction;215
9.1.2;2. Microsensors;216
9.1.3;3. Microsensor Measurements;220
9.1.4;4. Estimation of Microbial Activities;220
9.1.5;5. Limitations of Microsensor Measurements;222
9.1.6;6. MAR-FISH;223
9.1.7;7. Methodology of MAR-FISH;223
9.1.8;8. Application of Microsensors and MAR-FISH to Nitrifying Biofilms;228
9.1.9;9. Ecophysiological Interaction Among Community Members;231
9.1.10;10. Conclusions;233
9.1.11;References;233
9.2;Chapter 8: In Situ Techniques and Digital Image Analysis Methods for Quantifying Spatial Localization Patterns of Nitrifiers...;236
9.2.1;1. Introduction;237
9.2.2;2. Theory of Spatial Arrangement Quantification by Digital Image Analysis;241
9.2.3;3. Protocols for the Spatial Arrangement Quantification of Nitrifiers;252
9.2.4;4. An Application Example: Spatial Analysis of Three Nitrifying Biofilm Populations;259
9.2.5;Acknowledgments;262
9.2.6;References;262
9.3;Chapter 9: Investigating Nitrosomonas europaea Stress Biomarkers in Batch, Continuous Culture, and Biofilm Reactors;268
9.3.1;1. Introduction;270
9.3.2;2. Identifying Stress Responses in Batch Bioreactors;273
9.3.3;3. Identifying Stress Responses in Continuous Growth Systems;284
9.3.4;4. Identifying Stress Responses in Biofilms;290
9.3.5;5. Conclusions;293
9.3.6;References;295
9.4;Chapter 10: Nitrification of Raw or Used Water Using Expanded Bed Biofilm Reactor Technology;298
9.4.1;1. Introduction;299
9.4.2;2. Design and Operation of EBBRs;303
9.4.3;3. Measurement of Nitrification Performance;310
9.4.4;4. Typical Bioreactor and Bioparticle Performance Data;313
9.4.5;5. Conclusions;316
9.4.6;References;317
9.5;Chapter 11: Ammonia-Oxidizing Bacteria in Wastewater;320
9.5.1;1. Introduction;321
9.5.2;2. Sampling;322
9.5.3;3. DNA Extraction;322
9.5.4;4. Quantitative PCR;323
9.5.5;5. Denaturing Gradient Gel Electrophoresis;324
9.5.6;6. Fluorescence In Situ Hybridization;326
9.5.7;7. Conclusion;334
9.5.8;References;335
10;Section Three: Genomics, Metagenomics and Transcriptomics;338
10.1;Chapter 12: Genomics for Key Players in the N Cycle...;340
10.1.1;1. Introduction: The Genomic Guinea Pigs;341
10.1.2;2. Want a Genome? Library Preparation First!;345
10.1.3;3. Sequencing a Genome from Start to Finish;348
10.1.4;4. Après Sequencing;357
10.1.5;5. Outlook: The Next Frontier;363
10.1.6;Acknowledgments;364
10.1.7;References;364
10.2;Chapter 13: Preparation of High-Molecular Weight DNA and Metagenomic Libraries from Soils and Hot Springs;370
10.2.1;1. Introduction;371
10.2.2;2. Protocols;375
10.2.3;3. Growing, Picking, Replicating, and Storage of the Fosmid Library;389
10.2.4;References;393
10.3;Chapter 14: Characterizing Bacterial Gene Expression in Nitrogen Cycle Metabolism with RT-qPCR;396
10.3.1;1. Why Study Bacterial Transformation of Reactive Nitrogen in the Environment?;397
10.3.2;2. Nucleic Acids as Markers of N-Metabolic Activity;398
10.3.3;3. Gene Expression in Bacteria That Facilitate Reactive Nitrogen Transformations;407
10.3.4;4. Future Directions of the Approach;415
10.3.5;Acknowledgments;416
10.3.6;References;417
10.4;Chapter 15: The Utility of Functional Gene Arrays for Assessing Community Composition, Relative Abundance, and Distribution...;424
10.4.1;1. Introduction;425
10.4.2;2. DNA Microarrays: Introduction to Microarrays;426
10.4.3;3. Probe Selection;426
10.4.4;4. Target Preparation;430
10.4.5;5. Array Printing, Hybridization, and Scanning;431
10.4.6;6. Factors That Influence Hybridization Results;432
10.4.7;7. Array Applications;435
10.4.8;8. Possibilities and Limitations;440
10.4.9;9. Detailed Protocol for Functional Gene Microarrays Using Oligonucleotide Probes;441
10.4.10;References;445
11;Section Four: Biochemistry and Proteomics;448
11.1;Chapter 16: Structure and Function of Formate-Dependent Cytochrome c Nitrite Reductase, NrfA;450
11.1.1;1. Introduction;451
11.1.2;2. Isolation of NrfA;452
11.1.3;3. Crystallization of NrfA and the NrfHA Complex;453
11.1.4;4. Structure Solution by Multiple-Wavelength Anomalous Dispersion;455
11.1.5;5. Structure of NrfA;456
11.1.6;6. Heme Group Arrangement;459
11.1.7;7. Active Site Architecture;461
11.1.8;8. Substrate Complexes, Activity Assays, and Reactivity;462
11.1.9;9. Reaction Mechanism;464
11.1.10;10. Electron Transfer Systems;466
11.1.11;Acknowledgments;469
11.1.12;References;469
11.2;Chapter 17: Detection and Characterization of a Multicopper Oxidase from Nitrosomonas europaea;474
11.2.1;1. Introduction;474
11.2.2;2. Identification, Detection, and Isolation;477
11.2.3;3. Characterization and Crystallization;481
11.2.4;Acknowledgments;482
11.2.5;References;482
11.3;Chapter 18: Assessing Variability in Gel-Based Proteomic Analysis of Nitrosomonas europaea;486
11.3.1;1. Introduction;487
11.3.2;2. Materials and Methods;491
11.3.3;3. Results and Discussion;496
11.3.4;Acknowledgments;511
11.3.5;References;511
11.4;Chapter 19: Nitrogen Metabolism and Kinetics of Ammonia-Oxidizing Archaea;516
11.4.1;1. Introduction;517
11.4.2;2. Strain Cultivation and Analytical Methods;519
11.4.3;3. Microrespirometry Setup;521
11.4.4;4. Stoichiometry and Kinetics of Ammonia Oxidation of N. maritimus and AOB;525
11.4.5;5. Variability of Kinetic Constants in AOB and AOA;531
11.4.6;6. Summary and Conclusions;533
11.4.7;Acknowledgments;534
11.4.8;References;534
12;Author Index;540
13;Subject Index;566
14;Colour Plate;576