Molecular analysis of the ammonia oxidizing bacterial community in the surface soil layer of a Japanese paddy field

Ammonia oxidation to nitrite is the key part in the nitrification–denitrification process that occurs in the oxic–anoxic interface of paddy fields and is, therefore, an important component of the nitrogen cycle. Ammonia oxidation is carried out by autotrophic ammonia oxidizing bacteria (AOB). In this study, we investigated the AOB community in the surface paddy soil layer using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing methods using amoA-specific primers targeting a partial stretch of the gene that encodes ammonia monooxygenase A (amoA). DGGE bands with eight different levels of mobility were obtained from the surface soil. The DNA sequences of five bands were identified. All DNA sequences were closely related to Nitrosospira spp. and no Nitrosomonas-like AOB were identified. The deduced amino acid sequences of the five retrieved DGGE bands were closely related (99–100%) to previously published amoA amino acid sequences of the cultured strains Nitrosospira Ka3 and Nitrosospira CT2F. A phylogenetic tree based on the amoA amino acid sequence revealed that all five AOB sequences were grouped within the amoA cluster 1.