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Applied and Environmental Microbiology, June 2002, p. 3067-3075, Vol. 68, No. 6
0099-2240/02/$04.00+0 DOI: 10.1128/AEM.68.6.3067-3075.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Influence of Different Cultivars on Populations of Ammonia-Oxidizing Bacteria in the Root Environment of Rice
Aurelio M. Briones,1 Satoshi Okabe,2 Yoshiaki Umemiya,3 Niels-Birger Ramsing,4 Wolfgang Reichardt,5 and Hidetoshi Okuyama1*Laboratory of Environmental Molecular Biology, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810,1 Department of Urban and Environmental Engineering, Graduate School of Engineering, Hokkaido University, Sapporo 060-0813,2 Laboratory of Plant Nutrition and Soil Science, National Institute of Fruit Tree Science, Tsukuba, Ibaraki 305-8605, Japan,3 Department of Microbial Ecology, Aarhus University, DK-8000 Aarhus C, Denmark,4 Crop, Soil, and Water Sciences Division, International Rice Research Institute, Los Baños 4031, Philippines5
Received 20 September 2001/ Accepted 28 February 2002
Comparisons of the activities and diversities of ammonia-oxidizing bacteria (AOB) in the root environment of different cultivars of rice (Oryza sativa L.) indicated marked differences despite identical environmental conditions during growth. Gross nitrification rates obtained by the 15N dilution technique were significantly higher in a modern variety, IR63087-1-17, than in two traditional varieties. Phylogenetic analysis based on the ammonium monooxygenase gene (amoA) identified strains related to Nitrosospira multiformis and Nitrosomonas europaea as the predominant AOB in our experimental rice system. A method was developed to determine the abundance of AOB on root biofilm samples using fluorescently tagged oligonucleotide probes targeting 16S rRNA. The levels of abundance detected suggested an enrichment of AOB on rice roots. We identified 40 to 69% of AOB on roots of IR63087-1-17 as Nitrosomonas spp., while this subpopulation constituted 7 to 23% of AOB on roots of the other cultivars. These results were generally supported by denaturing gradient gel electrophoresis of the amoA gene and analysis of libraries of cloned amoA. In hydroponic culture, oxygen concentration profiles around secondary roots differed significantly among the tested rice varieties, of which IR63087-1-17 showed maximum leakage of oxygen. The results suggest that varietal differences in the composition and activity of root-associated AOB populations may result from microscale differences in O2 availability.
* Corresponding author. Mailing address: Laboratory of Environmental Molecular Biology, Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan. Phone: 81-11-706-4523. Fax: 81-11-706-2347. E-mail: hoku{at}ees.hokudai.ac.jp.
Applied and Environmental Microbiology, June 2002, p. 3067-3075, Vol. 68, No. 6
0099-2240/02/$04.00+0 DOI: 10.1128/AEM.68.6.3067-3075.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
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