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Chapter 42 : Nitrogen Cycling in Aquatic Environments
This chapter focuses on the three core nitrogen cycling processes that are performed wholly or predominantly by prokaryotes: nitrogen fixation, nitrification, and denitrification. A phylogenetically and physiologically diverse array of bacteria and archaea carry out the process, using a highly conserved and complex suite of enzymes, in a variety of aquatic environments. Major advances in the study of nitrogen-fixing microbial populations in recent years have also occurred in the direction of assessing the potential importance of nitrogen fixers other than Trichodesmium. The ammoniaoxidizing bacteria (AOB) are considered to be strict autotrophs, while the nitrite-oxidizing bacteria (NOB) have a limited heterotrophic potential; growth of some strains is enhanced by metabolism of small organic acids. The most widely used approach for assessment of denitrifier diversity and community structure is based on the genes that encode nitrite reductase. Direct measurements of in situ denitrification rates in the open ocean are much rarer than those of nitrogen fixation. Recent advances in the study of the anammox process have highlighted how poorly conventional denitrification is understood, especially in the open ocean, and have focused attention on the need to improve methods for the direct in situ measurement of denitrification rates. Metagenomic approaches will allow us to link function, regulation, and population assessments by allowing us to identify multiple genes and operons and to link them to the identity of uncultivated organisms.