Abundance and diversity of archaeal ammonia oxidizers in a coastal groundwater system

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 76 (2010): 7938-7948, doi:10.1128/AEM.02056-09.Nitrification, the microbially-catalyzed oxidation of ammonia to nitrate, is a key process in the nitrogen cycle. Archaea have been implicated in the first part of the nitrification pathway (oxidation of ammonia to nitrite), but the ecology and physiology of these organisms remain largely unknown. This work describes two different populations of sediment-associated ammonia-oxidizing archaea (AOA) in a coastal groundwater system on Cape Cod, Massachusetts. Sequence analysis of the ammonia monooxygenase subunit A gene (amoA) shows that one population of putative AOA inhabits the upper meter of the sediment where they may experience frequent ventilation with tidally-driven overtopping and infiltration of bay water supplying dissolved oxygen, ammonium and perhaps organic carbon. A genetically distinct population occurs deeper in the sediment, in a mixing zone between a nitrate- and oxygen-rich freshwater zone and a reduced, ammonium-bearing salt water wedge. Both of these AOA populations are coincident with increases in the abundance of Group I crenarchaeota 16S rRNA gene copies.Funding was provided by WHOI’s Coastal Ocean Institute to DRR and KLC, as well as funding from NSF/OCE project #05-24994 to KLC