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This volume 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.

Table of Contents

Part I. Modeling



Modelling the role of nitrification in open 1 ocean productivity and the nitrogen cycle
Andrew Yool

Continuous cultivation and thermodynamic aspects of niche definition in the Nitrogen cycle
Stefanie Müller and Marc Strous

Part II. Cultivation and cell physiology

Isolation, cultivation, and characterization of ammonia-oxidizing bacteria and archaea adapted to low ammonium concentrations
Annette Bollmann, Elizabeth French and Hendrikus J. Laanbroek

Cultivation, Detection and Ecophysiology of Anaerobic Ammonium-Oxidizing Bacteria
Boran Kartal, Wim Geerts and Mike S. M. Jetten

Cultivation, growth physiology and chemotaxonomy of nitrite-oxidizing bacteria
Eva Spieck and André Lipski

Surveying N2O-Producing Pathways in Bacteria
Lisa Y. Stein

Part III. Molecular Microbial Ecology And Processes Measurements

Stable isotope probing with 18O-water to investigate growth and mortality of ammonia oxidizing bacteria and archaea in soil
Karen Adair and Egbert Schwartz

Measuring Nitrification, Denitrification, and Related Biomarkers in Terrestrial Geothermal Ecosystems
Jeremy A. Dodsworth, Bruce Hungate, José R. de la Torre, Hongchen Jiang, and Brian P. Hedlund

Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach
Annika C. Mosier and Christopher A. Francis

15N-labeling experiments to dissect the contributions of heterotrophic denitrification and anammox to nitrogen removal in the OMZ waters of the ocean
Moritz Holtappels, Gaute Lavik, Marlene M. Jensen and Marcel M.M. Kuypers

Assessment of nitrogen and oxygen isotopic fractionation during nitrification and its expression in the marine environment
Karen L. Casciotti, Carolyn Buchwald, Alyson E. Santoro, and Caitlin Frame

Identification of Diazotrophic Microorganisms in Marine Sediment Via Fluorescence in situ Hybridization Coupled to Nanoscale Secondary Ion Mass Spectrometry (FISH-NanoSIMS)
Anne E. Dekas and Victoria J. Orphan

Measurement and Distribution of Nitrification Rates in the Oceans
B. B. Ward

Construction of STOX Oxygen Sensors and Their Application for Determination of O2 Concentrations in Oxygen Minimum Zones
Niels Peter Revsbech, Bo Thamdrup, Tage Dalsgaard and Donald Eugene Canfield

Regulation and measurement of nitrification in terrestrial systems
Jeanette M. Norton and John M. Stark

Protocol for the measurement of nitrous oxide fluxes from biological wastewater treatment plants
Kartik Chandran

Part IV. Genetics, Biochemistry and Biogeochemistry

Genetic Transformation of Ammonia-Oxidizing Bacteria
Luis A. Sayavedra-Soto and Lisa Y. Stein

Dissecting Iron Uptake and Homeostasis in Nitrosomonas europaea
Luis A. Sayavedra-Soto, Neeraja Vajrala, and Daniel J. Arp

Production of recombinant multiheme cytochromes c in Wolinella succinogenes
Melanie Kern and Jörg Simon

Techniques for Investigating Hydroxylamine Disproportionation by Hydroxylamine Oxidoreductases
A. Andrew Pacheco, Jennifer McGarry, Joshua Kostera and Angel Corona

Liquid chromatography - mass spectrometry based proteomics of Nitrosomonas
Hans J.C.T. Wessels, Jolein Gloerich, Erwin van der Biezen, Mike S. M. Jetten and Boran Kartal

The Geochemical Record of the Ancient Nitrogen Cycle, Nitrogen Isotopes and Metal Co-factors

L.V. Godfrey1 and J.B. Glass