Research on Nitrification and Related Processes, Part B

Research on Nitrification and Related Processes, Part B

1st Edition - May 4, 2011
This is the Latest Edition
  • Editor: Martin Klotz
  • Hardcover ISBN: 9780123864895
  • eBook ISBN: 9780123864901

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Description

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.

Key Features

  • 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

Readership

modelers, molecular ecologists, biogeochemists, ecophysiologists, geneticists and biochemists

Table of Contents

  • 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

Product details

  • No. of pages: 576
  • Language: English
  • Copyright: © Academic Press 2011
  • Published: May 4, 2011
  • Imprint: Academic Press
  • Hardcover ISBN: 9780123864895
  • eBook ISBN: 9780123864901

About the Serial Volume Editor

Martin Klotz