This Article Full Text Full Text (PDF) Other Versions of this Article: AEM.01676-06v1 73/1/101    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Hori, T. Articles by Conrad, R. Search for Related Content PubMed PubMed Citation Articles by Hori, T. Articles by Conrad, R. Agricola Articles by Hori, T. Articles by Conrad, R.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, January 2007, p. 101-109, Vol. 73, No. 1
0099-2240/07/$08.00+0     doi:10.1128/AEM.01676-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Identification of Acetate-Assimilating Microorganisms under Methanogenic Conditions in Anoxic Rice Field Soil by Comparative Stable Isotope Probing of RNA

Tomoyuki Hori,^1,2 Matthias Noll,^1, Yasuo Igarashi,² Michael W. Friedrich,¹ and Ralf Conrad^1*

Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str., D-35043 Marburg, Germany,¹ Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan²

Received 19 July 2006/ Accepted 17 October 2006

Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH₄ and/or CO₂. Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with ¹³C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25°C for 12 days, during which ¹³C-labeled acetate was added at a concentration of 500 µM every 3 days. ¹³C-labeled CH₄ and CO₂ were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate ¹³C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the ¹³C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a Geobacter sp. and an Anaeromyxobacter sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO₂ was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for Geobacter spp. and Anaeromyxobacter spp. under these conditions.

Published ahead of print on 27 October 2006.

Present address: Swiss Federal Institute of Technology (ETH Zürich), Institute of Terrestrial Ecology, Soil Biology, Universitätstr. 16, CH-8092 Zürich, Switzerland.