Full text loading...
Chapter 1 : Nitrification: An Introduction and Overview of the State of the Field
Nitrogen is an essential element for life, a major component of proteins and nucleic acids. Cultivated ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) provided the basis for investigations into the physiology and biochemistry of nitrification for decades and supported the ecological inferences obtained from field studies. Most of this work was done on AOB, and even now, the NOB are much less studied in the environment. The discovery of novel organisms and novel pathways are the most important findings to be documented in the field of nitrification since the publication of the last monograph in 1986. But just as important, and absolutely critical to these discoveries, are the changes in the study and methodology of nitrification. Both independently and in parallel with these advances in the molecular biology of nitrification, major advances in understanding their biochemistry and regulation have also occurred in the last 25 years. Major insights about ammonia-oxidizing archaea (AOA) genomics and metabolic capabilities are discussed. Microbial ecology has been transformed into molecular ecology, so great has been the impact of molecular biological methods in the study of microbes in natural and managed systems. Ribosomal RNA and functional gene sequence data are now the standard for investigation of microbial diversity, distribution, and activity in the environment. These methods have made it possible to investigate environmental control of nitrification, regulation in response to changing conditions, the discovery of great uncultured diversity, and an understanding of succession and biogeography among functionally similar types.