We investigated the quantities and phylogenies of amoA genes of ammonia-oxidizing archaea (AOA) belonging to Crenarchaeota and ammonia-oxidizing bacteria (AOB) belonging to Betaproteobacteria in water columns and deep-ocean cold seep sediment in the northeastern Japan Sea with a competitive PCR (cPCR) assay. Water samples were collected at depths of 2000 m and 2956 m. Sediment samples were collected where white bacterial mats had developed. The cPCR analysis revealed five to ten times more AOA

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... han betaproteobacterial AOB in both the water columns and sediment. The abundance of the crenarchaeotal amoA gene was estimated at 6×10 1 and 3×10 2 copies ml −1 in the water columns at depths of 2000 m and 2956 m, and 1×10 8 and 1×10 7 copies g −1 in pelagic brown sediment and black sediment, respectively. Most archaeal amoA clones from water column at 2000 m fell into the Deep Marine Group. Most archaeal amoA clones from pelagic brown sediment were less closely related to known environmental clones. Moreover, incubation experiments revealed nitrite production at 4°C and 10°C. The results indicate that psychrophilic AOA and AOB may be responsible for nitrification in the deep-ocean region of the northeastern Japan Sea.