Succession and community composition of ammonia-oxidizing archaea and bacteria in bulk soil of a Japanese paddy field

• Published in: Soil science and plant nutrition (Tokyo) Vol. 56; no. 2; pp. 212 - 219
• Main Authors: Fujii, C., Nihon Univ., Fujisawa, Kanagawa (Japan), Nakagawa, T, Onodera, Y, Matsutani, N, Sasada, K, Takahashi, R, Tokuyama, T
• Format: Journal Article
• Language: English
• Published: Oxford, UK Taylor & Francis Group 01.04.2010; Blackwell Publishing Ltd; Taylor & Francis Ltd
• Subjects: ammonia-oxidizing archaea; ammonia-oxidizing bacteria; AMMONIUM; amoA; AMONIO; Archaea; BACTERIA; ECOLOGICAL SUCCESSION; Floods; Genes; http://www.fao.org/aos/agrovoc#c_2464; http://www.fao.org/aos/agrovoc#c_32634; http://www.fao.org/aos/agrovoc#c_36167; http://www.fao.org/aos/agrovoc#c_4039; http://www.fao.org/aos/agrovoc#c_5472; http://www.fao.org/aos/agrovoc#c_5498; http://www.fao.org/aos/agrovoc#c_765; JAPAN; JAPON; MICRO-ORGANISME DU SOL; Microbiology; MICROORGANISMOS DEL SUELO; nitrification; Oryza sativa; OXIDACION; OXIDATION; OXYDATION; PADDY SOIL; SOIL MICROORGANISMS; Soil sciences; SOL DE RIZIERE; SUCCESSION ECOLOGIQUE; SUCESION ECOLOGICA; SUELO DE ARROZALES
• ISSN: 0038-0768; 1747-0765
• DOI: 10.1111/j.1747-0765.2010.00449.x

The present study describes succession in the abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the upland and flooded bulk soils of a Japanese rice paddy field over 2 years using a quantitative polymerase chain reaction of both crenarchaeotal and betaproteobacterial ammonia monooxygenase alpha subunit (amoA) genes. A marked increase in the abundance of AOA amoA gene was observed in upland bulk soil after plowing, drainage and rice harvesting. A marked increase was also observed in the abundance of AOB amoA gene after plowing. The abundances of both AOA and AOB amoA genes in flooded bulk soil decreased immediately after flooding. During the middle period of flooding, the abundance of AOA amoA gene increased slightly in the flooded bulk soil. As the flooding subsided, the abundance of AOA amoA gene decreased, whereas that of AOB amoA gene increased. The AOA amoA gene sequences were affiliated with two phylogenetic clusters previously found in marine and soil environments. Both Nitrosospira-like and Nitrosomonas-like clones were detected. Our results revealed that there was a difference in the succession of abundances between AOA and AOB amoA genes in Japanese bulk paddy soil.