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.
Highlights
Denitrification is a microbial respiratory process where nitrate/nitrite are reduced in a stepwise manner to form the gaseous end products NO, N2O, and N2 (Zumft 1997)
We recently established a method for isolating functional single cells from environments using a micromanipulator (Functional single-cell (FSC) isolation), which we applied in studying denitrifying bacteria in rice paddy soil (Ashida et al 2010)
Strains belonging to the genera Bradyrhizobium and Bacillus were commonly obtained using both the FSC and agar plate dilution (APD) isolation methods
Summary
Denitrification is a microbial respiratory process where nitrate/nitrite are reduced in a stepwise manner to form the gaseous end products NO, N2O, and N2 (Zumft 1997). Denitrification of rice paddy soil was reported as. To overcome this situation, we recently established a method for isolating functional single cells from environments using a micromanipulator (Functional single-cell (FSC) isolation), which we applied in studying denitrifying bacteria in rice paddy soil (Ashida et al 2010). Oligotrophic denitrifying bacteria carrying previously uncharacterized functional gene sequences were isolated using the FSC method (Ishii et al 2010a). These studies clearly indicated the usefulness of the FSC isolation method as a tool for studying denitrifying bacteria in soil. The advantages and possible disadvantages of the FSC isolation method compared with the standard isolation method have not been well understood
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