title: Advantages of functional single-cell isolation method over standard agar plate dilution method as a tool for studying denitrifying bacteria in rice paddy soil.
abstract: We recently established a method for isolating functional single cells from environmental samples using a micromanipulator (Functional single-cell (FSC) isolation), and applied it to the study of denitrifying bacteria in rice paddy soil (Ashida et al. 2010. Appl Microbiol Biotechnol 85:1211-1217). To further examine the advantages and possible disadvantages of the FSC method, we isolated denitrifying bacteria from the same rice paddy soil sample using both FSC and standard agar plate dilution (APD) methods and compared in this study. The proportion of denitrifying bacteria in the total isolates was more than 6-fold larger with FSC isolation (57.1%) compared with the APD method (9.2%). Denitrifying bacteria belonging to Alphaproteobacteria and Bacilli were commonly isolated using both methods, whereas those belonging to Betaproteobacteria, which had been found to be active in the denitrification-inductive paddy soil, were isolated only with the FSC method. On the other hand, Actinobacteria were only isolated using the APD method. The mean potential denitrification activity of the FSC isolates was higher than that of the APD isolates. Overall, FSC isolation was confirmed to be an excellent method for studying denitrifying bacteria compared with the standard agar plate dilution method.
authors.affiliation: Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. anisitom@mail.ecc.u-tokyo.ac.jp.
authors.forename: Tomoyasu
authors.initials: T
authors.lastname: Nishizawa
authors.forename: Kanako
authors.initials: K
authors.lastname: Tago
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Uei
authors.forename: Satoshi
authors.initials: S
authors.lastname: Ishii
authors.forename: Kazuo
authors.initials: K
authors.lastname: Isobe
authors.forename: Shigeto
authors.initials: S
authors.lastname: Otsuka
authors.forename: Keishi
authors.initials: K
authors.lastname: Senoo