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Among various biogeochemical processes in estuaries, nitrogen cycle invited much research interest in the last decade owing to its environmental significance, complexities of chemical transformations and microorganisms involved in the process. Nitrification (conversion of ammonia to nitrate via nitrite) is the key step in this process, and is modulated completely by microorganisms. This book documented the spatial and temporal variations in the distribution, and activity of nitrifying bacteria and archaea in the Cochin estuary, a monsoon driven tropical estuary located along the southwest coast of India. In the Cochin estuary, nitrification is modulated by the complex interplay between different nitrifiers and environmental variables which in turn is dictated by various hydrodynamic characteristics like fresh water discharge and seawater influx brought in by river water discharge and flushing.