Research on nitrification and related processes. Part A /

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. Prov...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Otros Autores: Klotz, Martin G. (Editor )
Formato: Electrónico eBook
Idioma:Inglés
Publicado: Amsterdam : Elsevier : Academic Press, [2011?], �2011.
Colección:Methods in enzymology ; v. 486.
Temas:
Nitrification.
Nitrogen cycle.
Cycle de l'azote.
Nitrification
Nitrogen cycle
TECHNOLOGY & ENGINEERING / Agriculture / General.
Acceso en línea:Texto completo
Texto completo
Tabla de Contenidos:
  • Section 1 Modeling
  • 1.Modeling the Role of Nitrification in Open Ocean Productivity and the Nitrogen Cycle / Andrew Yool
  • 1.Introduction
  • 2.Ocean Carbon Cycle
  • 3.Export Production and the f-Ratio
  • 4.Plankton Ecosystem Models
  • 5.Modeling Nitrification
  • 6.Operational Considerations
  • 7.Future Modeling
  • 8.Summary
  • Acknowledgments
  • References
  • 2.Continuous Cultivation and Thermodynamic Aspects of Niche Definition in the Nitrogen Cycle / Marc Strous
  • 1.Introduction
  • 2.A Minimal Model for Microbial Behavior
  • 3.Continuous Cultivation
  • Background and Experimental Approach
  • 4.Conclusion
  • Acknowledgments
  • References
  • Section 2 Cultivation and Cell Physiology
  • 3.Isolation, Cultivation, and Characterization of Ammonia-Oxidizing Bacteria and Archaea Adapted to Low Ammonium Concentrations / Hendrikus J. Laanbroek
  • 1.Introduction
  • 2.General Description of Cultivation Methods for Ammonia-Oxidizing Microorganisms
  • 3.Enrichment of Ammonia Oxidizers
  • 4.Isolation of Ammonia Oxidizers
  • 5.Characterization of Ammonia-Oxidizing Prokaryotes
  • References
  • 4.Cultivation, Detection, and Ecophysiology of Anaerobic Ammonium-Oxidizing Bacteria / Mike S. M. Jetten
  • 1.Introduction
  • 2.Enrichment of Anammox Bacteria as Planktonic Cell Suspensions
  • 3.Molecular Detection of Anammox Bacteria
  • 4.Conclusions
  • Acknowledgments
  • References
  • 5.Cultivation, Growth Physiology, and Chemotaxonomy of Nitrite-Oxidizing Bacteria / Andre Lipski
  • 1.Introduction
  • 2.Recipes for the Culture of NOB
  • 3.Cultivation Procedure
  • 4.Isolation
  • 5.Physiological Investigations
  • 6.Chemical Analyses
  • 7.Monitoring the Cultures
  • 8.Fatty Acid Analyses
  • Acknowledgments
  • References
  • 6.Surveying N2O-Producing Pathways in Bacteria / Lisa Y. Stein
  • 1.Introduction
  • 2.Bioinformatics
  • 3.Surveying Function
  • 4.Concluding Remarks
  • References
  • Section 3 Molecular Microbial Ecology and Processes Measurements
  • 7.Stable Isotope Probing with 18O-Water to Investigate Growth and Mortality of Ammonia Oxidizing Bacteria and Archaea in Soil / Egbert Schwartz
  • 1.Introduction
  • 2.Materials and Methods
  • 3.Calculation of Growth and Mortality Indices
  • 4.Results
  • 5.Discussion
  • 6.Conclusions
  • Acknowledgments
  • References
  • 8.Measuring Nitrification, Denitrification, and Related Biomarkers in Terrestrial Geothermal Ecosystems / Brian P. Hedlund
  • 1.Introduction
  • 2.General Considerations for Measurement of N-Cycle Activities in Terrestrial Geothermal Habitats
  • 3.Methods for Measuring Nitrification in Terrestrial Geothermal Habitats
  • 4.Methods for Measuring Denitrification in Terrestrial Geothermal Habitats
  • 5.Detection and Quantification of Potential Biomarkers for Thermophilic AOA and Denitrifying Thermus thermophilus
  • 6.Closing Remarks
  • Acknowledgments
  • References
  • 9.Determining the Distribution of Marine and Coastal Ammonia-Oxidizing Archaea and Bacteria Using a Quantitative Approach / Christopher A. Francis
  • 1.Introduction
  • 2.Methods for Measuring the Abundance of AOA and AOB Within Marine and Coastal Systems
  • 3.Methodological Considerations
  • 4.Targeting Specific Ecotypes: Quantifying Shallow and Deep Clades of Marine Water Column AOA
  • Acknowledgments
  • References
  • 10.15N-Labeling Experiments to Dissect the Contributions of Heterotrophic Denitrification and Anammox to Nitrogen Removal in the OMZ Waters of the Ocean / Marcel M. M. Kuypers
  • 1.Introduction
  • 2.Theoretical Description of 15N-Incubation Experiments
  • 3.In the Field: Supplementary Measurements
  • 4.In the Field: Incubation Experiments
  • 5.In the Lab: Mass Spectrometry Measurements
  • 6.Data Processing and Interpretation
  • 7.Common Pitfalls
  • 8.Concluding Remarks
  • Acknowledgments
  • References
  • 11.Assessment of Nitrogen and Oxygen Isotopic Fractionation During Nitrification and Its Expression in the Marine Environment / Caitlin Frame
  • 1.Introduction
  • 2.Methods
  • 3.Analytical Techniques
  • 4.Data Analysis
  • 5.Discussion
  • References
  • 12.Identification of Diazotrophic Microorganisms in Marine Sediment via Fluorescence In Situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-Nano SIMS) / Victoria J. Orphan
  • 1.Introduction
  • 2.Methods
  • 3.Concluding Remarks
  • Acknowledgments
  • References
  • 13.Measurement and Distribution of Nitrification Rates in the Oceans / B. B. Ward
  • 1.Introduction
  • 2.Nitrification Rate Measurements in Seawater (Table 13.1)
  • 3.Nitrification Rate Measurements in Sediments
  • 4.Distribution of Nitrification
  • References
  • 14.Construction of STOX Oxygen Sensors and Their Application for Determination of O2 Concentrations in Oxygen Minimum Zones / Donald Eugene Canfield
  • 1.Introduction
  • 2.STOX Sensor Principle
  • 3.Sensor Construction
  • 4.Electronics for STOX Sensors
  • 5.STOX Sensor Calibration and Performance
  • 6.Calculation of Oxygen Concentrations from STOX Data
  • 7.In Situ Deployment of STOX Sensors in OMZs
  • 8.Future Fast Response STOX Sensors
  • 9.Using STOX Sensors to Recalibrate Conventional Oxygen Sensors
  • Acknowledgments
  • References
  • 15.Regulation and Measurement of Nitrification in Terrestrial Systems / John M. Stark
  • 1.Introduction
  • 2.Diversity of the Nitrification Process in Terrestrial Environments
  • 3.Substrates and Products of Nitrification Reactions
  • 4.Controls on Nitrification Rates in Soil Environments
  • 5.Measurements of Nitrification in Terrestrial Environments
  • 6.Measurement of Nitrification Rates in Terrestrial Ecosystems
  • 7.Measurement of Nitrification Kinetics
  • 8.Nitrifier Population Size
  • 9.Modeling Approaches
  • 10.Future Advancements in Nitrification Rate Research in Terrestrial Environments
  • References
  • 16.Protocol for the Measurement of Nitrous Oxide Fluxes from Biological Wastewater Treatment Plants / Kartik Chandran
  • 1.Introduction
  • 2.Sampling Design for Full-Scale Monitoring
  • 3.Sampling Procedures: Headspace Gas Measurement
  • 4.Sampling Procedures: Measurement of Aqueous N2O Concentrations
  • 5.Sampling Procedures: Measurement of Advective Gas Flow Rate from Bioreactor Headspace
  • 6.Principles of Real-Time N2O Measurement
  • 7.Data Analysis: Determination of Fluxes
  • 8.Data Analysis: Determination of Emission Fractions
  • 9.Data Analysis: Calculation of N2O Emission Factors
  • 10.Standardization of Protocol and Comparison with Established Emissions Flux Measurement Methods
  • 11.N2O Emission Fluxes from Activated Sludge Processes
  • 12.Triggers for N2O Emission from Wastewater Treatment Operations
  • 13.Lab-Scale and Field-Scale Adaptation of Protocol N2O Emission Measurements
  • 14.Concluding Remarks
  • Acknowledgment
  • References
  • Section 4 Genetics, Biochemistry and Biogeochemistry
  • 17.Genetic Transformation of Ammonia-Oxidizing Bacteria / Lisa Y. Stein
  • 1.Introduction
  • 2.Transformation of AOB
  • 3.Gene Inactivation in AOB
  • 4.Use of Broad-Host Range Plasmids
  • 5.Strain Stability and Maintenance
  • 6.Conclusions
  • References
  • 18.Dissecting Iron Uptake and Homeostasis in Nitrosomonas europaea / Daniel J. Arp
  • 1.Introduction
  • 2.Use of Bioinformatics to Plan Fe-Related Studies
  • 3.Methods to Learn About the Physiological Responses to Fe Limitation
  • 4.Methods to Study Siderophore Uptake
  • 5.Genetic Complementation to Study fur Homologs
  • 6.Methods for Gene Inactivation of Fe Uptake Systems
  • 7.Lingering Questions that can be Answered by the Above Protocols
  • 8.Conclusion
  • References
  • 19.Production of Recombinant Multiheme Cytochromes c in Wolinella succinogenes / Jorg Simon
  • 1.Introduction
  • 2.Bacterial Cytochrome c Biogenesis Systems
  • 3.Recombinant Cytochrome c Production
  • 4.Cytochromes c in the Epsilonproteobacterium W. succinogenes
  • 5.Three Cytochrome c Heme Lyase Isoenzymes in W. succinogenes
  • 6.Heterologous Production of Cytochromes c in W.
  • succinogenes
  • 7.Conclusions and Perspectives
  • Acknowledgments
  • References
  • 20.Techniques for Investigating Hydroxylamine Disproportionation by Hydroxylamine Oxidoreductases / Angel Corona
  • 1.Introduction
  • 2.General Considerations
  • 3.Ammonia Concentration Determination
  • 4.Nitric Oxide Concentration Determination
  • 5.Nitrite Concentration Determination
  • 6.Nitrous Oxide and Dinitrogen Concentration Determination
  • References
  • 21.Liquid Chromatography
  • Mass Spectrometry-Based Proteomics of Nitrosomonas / Boran Kartal
  • 1.Introduction
  • 2.LC-MS/MS Instrument Setup
  • 3.Growth of N. eutropha C91 Pure Culture
  • 4.Sample Preparation
  • 5.C18 Reversed Phase LC-MS/MS Analysis
  • 6.Database Searches and Validation of Results
  • 7.Dataset Description and Protein Identification Example
  • 8.Conclusions
  • References
  • 22.The Geochemical Record of the Ancient Nitrogen Cycle, Nitrogen Isotopes, and Metal Cofactors / Jennifer B. Glass
  • 1.Introduction
  • 2.Reconstructing the Nitrogen Cycle and Associated Trace Metal Abundances through Time
  • 3.Determining Changes in the N-Cycle from the Geological Record of N Isotopes and Metal Availability
  • 4.Measurement
  • 5.Concluding Remarks
  • Acknowledgments
  • References.

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