Research on Nitrification and Related Processes, Part B

Preface

Strategies to Determine Diversity, Growth, and Activity of Ammonia-Oxidizing Archaea in Soil

1. Introduction

2. Common Methods

3. Community Composition and Diversity

4. Determining Growth and Abundance

5. Activity

6. Conclusions

Responses of Aerobic and Anaerobic Ammonia/Ammonium-Oxidizing Microorganisms to Anthropogenic Pollution in Coastal Marine Environments

1. Introduction

2. Selection of Sampling Sites and Physicochemical Characterization

3. Molecular Ecological Characterization

4. Community Structure Analyses

5. Relationship Between the Community Structure and Physicochemical Parameters

6. Relationships Between the Community Change and the Environments

7. Conclusions

Acknowledgments

Molecular and Stable Isotope Methods to Detect and Measure Anaerobic Ammonium Oxidation (Anammox) in Aquatic Ecosystems

1. Introduction

2. Molecular Methods to Detect and Quantify Anammox Bacteria in Environmental Samples

3. Stable Isotope Methods to Measure Anammox Rates in Environmental Samples

Acknowledgments

Nitrogen Mineralization and Assimilation at Millimeter Scales

1. Introduction

2. Microbial Habitats in Soil

3. Methodological Approaches

4. Conclusions

Measurement of Carbon Dioxide, Methane, Nitrous oxide, and Water Potential in Soil Ecosystems

1. Introduction

2. Soil Gas Probes

3. Flux Estimates to the Atmosphere Using Recirculating Chambers

4. Data Analysis

5. Soil Profile Analysis

6. FTIR Calibration

7. Correlations Between Profile Concentrations and Surface Flux in Field Measurements

8. Correlations Between FTIR and Traditional Water Activity Measures

9. Common Issues During FTIR Measurement

10. Conclusions

Acknowledgments

Source Determination of Nitrous Oxide Based on Nitrogen and Oxygen Isotope Tracing

1. Introduction

2. Experimental Approach

3. Data Evaluation for Nitrous Oxide Source Determination

4. Application of the ERR Principle in Nitrate Source Determination

5. Discussion, Applications, and Future Directions

A Polyphasic Approach to Study Ecophysiology of Complex Multispecies Nitrifying Biofilms

1. Introduction

2. Microsensors

3. Microsensor Measurements

4. Estimation of Microbial Activities

5. Limitations of Microsensor Measurements

6. MAR–FISH

7. Methodology of MAR–FISH

8. Application of Microsensors and MAR–FISH to Nitrifying Biofilms

9. Ecophysiological Interaction Among Community Members

10. Conclusions

In Situ Techniques and Digital Image Analysis Methods for Quantifying Spatial Localization Patterns of Nitrifiers and Other Microorganisms in Biofilm and Flocs

1. Introduction

2. Theory of Spatial Arrangement Quantification by Digital Image Analysis

3. Protocols for the Spatial Arrangement Quantification of Nitrifiers

4. An Application Example: Spatial Analysis of Three Nitrifying Biofilm Populations

Acknowledgments

Investigating Nitrosomonas europaea Stress Biomarkers in Batch, Continuous Culture, and Biofilm Reactors

Abbreviations

1. Introduction

2. Identifying Stress Responses in Batch Bioreactors

3. Identifying Stress Responses in Continuous Growth Systems

4. Identifying Stress Responses in Biofilms

5. Conclusions

Nitrification of Raw or Used Water Using Expanded Bed Biofilm Reactor Technology

1. Introduction

2. Design and Operation of EBBRs

3. Measurement of Nitrification Performance

4. Typical Bioreactor and Bioparticle Performance Data

5. Conclusions

Ammonia-Oxidizing Bacteria in Wastewater

1. Introduction

2. Sampling

3. DNA Extraction

4. Quantitative PCR

5. Denaturing Gradient Gel Electrophoresis

6. Fluorescence In Situ Hybridization

7. Conclusion

Genomics for Key Players in the N Cycle

1. Introduction: The Genomic Guinea Pigs

2. Want a Genome? Library Preparation First!

3. Sequencing a Genome from Start to Finish

4. Après Sequencing

5. Outlook: The Next Frontier

Acknowledgments

Preparation of High-Molecular Weight DNA and Metagenomic Libraries from Soils and Hot Springs

1. Introduction

2. Protocols

3. Growing, Picking, Replicating, and Storage of the Fosmid Library

Characterizing Bacterial Gene Expression in Nitrogen Cycle Metabolism with RT-qPCR

1. Why Study Bacterial Transformation of Reactive Nitrogen in the Environment?

2. Nucleic Acids as Markers of N-Metabolic Activity

3. Gene Expression in Bacteria That Facilitate Reactive Nitrogen Transformations

4. Future Directions of the Approach

Acknowledgments

The Utility of Functional Gene Arrays for Assessing Community Composition, Relative Abundance, and Distribution of Ammonia-Oxidizing Bacteria and Archaea

1. Introduction

2. DNA Microarrays: Introduction to Microarrays

3. Probe Selection

4. Target Preparation

5. Array Printing, Hybridization, and Scanning

6. Factors That Influence Hybridization Results

7. Array Applications

8. Possibilities and Limitations

9. Detailed Protocol for Functional Gene Microarrays Using Oligonucleotide Probes

Structure and Function of Formate-Dependent Cytochrome c Nitrite Reductase, NrfA

1. Introduction

2. Isolation of NrfA

3. Crystallization of NrfA and the NrfHA Complex

4. Structure Solution by Multiple-Wavelength Anomalous Dispersion

5. Structure of NrfA

6. Heme Group Arrangement

7. Active Site Architecture

8. Substrate Complexes, Activity Assays, and Reactivity

9. Reaction Mechanism

10. Electron Transfer Systems

Acknowledgments

Detection and Characterization of a Multicopper Oxidase from Nitrosomonas europaea

1. Introduction

2. Identification, Detection, and Isolation

3. Characterization and Crystallization

Acknowledgments

Assessing Variability in Gel-Based Proteomic Analysis of Nitrosomonas europaea

1. Introduction

2. Materials and Methods

3. Results and Discussion

Acknowledgments

Nitrogen Metabolism and Kinetics of Ammonia-Oxidizing Archaea

1. Introduction

2. Strain Cultivation and Analytical Methods

3. Microrespirometry Setup

4. Stoichiometry and Kinetics of Ammonia Oxidation of N. maritimus and AOB

5. Variability of Kinetic Constants in AOB and AOA

6. Summary and Conclusions

Acknowledgments