Molecular and stable isotope methods to detect and measure anaerobic ammonium oxidation (anammox) in aquatic...

Numerous microbial processes transform nitrogen (N) but three anaerobic respiratory pathways remove fixed N from the environment: denitrification (nitrate conversion to N(2)), anaerobic ammonium oxidation (anammox; ammonium plus nitrite conversion to N(2)), and nitrite dependent methane oxidation (nitrite conversion to N(2)). Nitrification becomes a part of N removal processes as a supplier of nitrite (NO(2)(-)) and nitrate (NO(3)(-)) to anammox and denitrifying bacteria in anoxic water and sediments. It is important to detect and measure anammox and denitrification to understand biogeochemical N cycle and to estimate N removal potential in aquatic ecosystems. Denitrification has been extensively studied in many ecosystems to examine diversity and spatial and temporal dynamics of denitrifying communities as well as to understand its importance in regional and global N cycles. Nitrite dependent methane oxidation was recently discovered as a new pathway of removing fixed N and just started to examine its importance in different ecosystems. Anammox has undergone limited examination, although the number of studies is continuously increasing. There are many questions remaining in order to understand the factors controlling activities and community structures of anammox bacteria in different ecosystems. This chapter reviews both molecular and stable isotope methods to detect and measure anammox in anoxic sediments and water.