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Applied and Environmental Microbiology, November 1999, p. 5050-5058, Vol. 65, No. 11
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Comparative Phylogenetic Assignment of Environmental Sequences
of Genes Encoding 16S rRNA and Numerically Abundant Culturable
Bacteria from an Anoxic Rice Paddy Soil
Ulf
Hengstmann,
Kuk-Jeong
Chin,
Peter H.
Janssen,
and
Werner
Liesack*
Max-Planck-Institut für terrestrische
Mikrobiologie, D-35043 Marburg, Germany
Received 29 April 1999/Accepted 5 August 1999
We used both cultivation and direct recovery of bacterial 16S rRNA
gene (rDNA) sequences to investigate the structure of the bacterial
community in anoxic rice paddy soil. Isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are
described in the accompanying paper (K.-J. Chin, D. Hahn, U. Hengstmann, W. Liesack, and P. H. Janssen, Appl. Environ.
Microbiol. 65:5042-5049, 1999). Here we describe the phylogenetic
positions of these strains in relation to 57 environmental 16S rDNA
clone sequences. Close matches between the two data sets were obtained for isolates from the culturable populations determined by the most-probable-number counting method to be large (3 × 107 to 2.5 × 108 cells per g [dry
weight] of soil). This included matches with 16S rDNA similarity
values greater than 98% within distinct lineages of the division
Verrucomicrobia (strain PB90-1) and the
Cytophaga-Flavobacterium-Bacteroides group (strains XB45
and PB90-2), as well as matches with similarity values greater than
95% within distinct lines of descent of clostridial cluster XIVa
(strain XB90) and the family Bacillaceae (strain SB45). In
addition, close matches with similarity values greater than 95% were
obtained for cloned 16S rDNA sequences and bacteria (strains DR1/8 and
RPec1) isolated from the same type of rice paddy soil during previous
investigations. The correspondence between culture methods and direct
recovery of environmental 16S rDNA suggests that the isolates obtained
are representative geno- and phenotypes of predominant bacterial groups
which account for 5 to 52% of the total cells in the anoxic rice paddy
soil. Furthermore, our findings clearly indicate that a dual approach
results in a more objective view of the structural and functional
composition of a soil bacterial community than either cultivation or
direct recovery of 16S rDNA sequences alone.
*
Corresponding author. Mailing address:
Max-Planck-Institut für terrestrische Mikrobiologie,
Karl-von-Frisch-Str., D-35043 Marburg, Germany. Phone: 49 (6421) 178 720. Fax: 49 (6421) 178 809. E-mail:
liesack{at}mailer.uni-marburg.de.

Present address: Department of Microbiology and Immunology,
University of Melbourne, Parkville, Victoria 3052,
Australia.
Applied and Environmental Microbiology, November 1999, p. 5050-5058, Vol. 65, No. 11
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
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