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.

Part I. Modeling

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

Andrew Yool

2. Continuous cultivation and thermodynamic aspects of niche definition in the Nitrogen cycle

Stefanie Müller and Marc Strous

Part II. Cultivation and cell physiology

3. Isolation, cultivation, and characterization of ammonia-oxidizing bacteria and archaea adapted to low ammonium concentrations

Annette Bollmann, Elizabeth French and Hendrikus J. Laanbroek

4. Cultivation, Detection and Ecophysiology of Anaerobic Ammonium-Oxidizing Bacteria

Boran Kartal, Wim Geerts and Mike S. M. Jetten

5. Cultivation, growth physiology and chemotaxonomy of nitrite-oxidizing bacteria

Eva Spieck and André Lipski

6. Surveying N2O-Producing Pathways in Bacteria

Lisa Y. Stein

Part III. 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

Karen Adair and Egbert Schwartz

8. 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

9. Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach

Annika C. Mosier and Christopher A. Francis

10. 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

11. 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

12. 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

13. Measurement and Distribution of Nitrification Rates in the Oceans

B. B. Ward

14. 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

15. Regulation and measurement of nitrification in terrestrial systems

Jeanette M. Norton and John M. Stark

16. Protocol for the measurement of nitrous oxide fluxes from biological wastewater treatment plants

Kartik Chandran

Part IV. Genetics, Biochemistry and Biogeochemistry

17. Genetic Transformation of Ammonia-Oxidizing Bacteria

Luis A. Sayavedra-Soto and Lisa Y. Stein

18. Dissecting Iron Uptake and Homeostasis in Nitrosomonas europaea

Luis A. Sayavedra-Soto, Neeraja Vajrala, and Daniel J. Arp

19. Production of recombinant multiheme cytochromes c in Wolinella succinogenes

Melanie Kern and Jörg Simon

20. Techniques for Investigating Hydroxylamine Disproportionation by Hydroxylamine Oxidoreductases

A. Andrew Pacheco, Jennifer McGarry, Joshua Kostera and Angel Corona

21. 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

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

L.V. Godfrey1 and J.B. Glass