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Searching For Predominant Soil Bacteria: 16S RDNA Cloning Versus Strain Cultivation.

Felske, Wolterink, van Lis R, de Vos WM, Akkermans
Published 1999 · Medicine, Biology

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The predominant bacteria in Dutch grassland soils, as identified by direct DNA extraction, PCR amplification of 16S rDNA and subsequent cloning and sequencing, were compared to the most abundant culturable bacteria. The 16S rDNAs of the strains from a comprehensive cultivation campaign were compared to some of the predominant cloned sequences by temperature gradient gel electrophoresis (TGGE). Four ribotypes were selected that were found to be abundant in the clone library: two closely related Bacillus-like sequences, a representative from the Verrucomicrobiales cluster and an uncultured member of the Actinobacteria. Using a variety of cultivation approaches a total of 659 pure cultures were isolated. Initially, approximately 8% of all isolates matched any of these ribotypes by same migration speed of their 16S rDNA amplicons on TGGE. However, sequencing analysis of matching isolates indicated that their 16S rDNA sequences were clearly different from the cloned sequences representing the fingerprint bands. Comparing the cultivation approach and the molecular 16S rDNA analysis from the same soil sample, there was no correlation between the collection of cultured strains and the 16S rDNA clone library.
This paper references
Rapid silver staining and recovery of PCR products separated on polyacrylamide gels.
C. Sanguinetti (1994)
Application of denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis for studying soil microbial communities.
H. Heuer (1997)
Recursion relation generation of probability profiles for specific‐sequence macromolecules with long‐range correlations
D. Poland (1974)
Repression of nitrification in soils under a climax grassland vegetation
A. Stienstra (1994)
In Situ Detection of an Uncultured Predominant Bacillus in Dutch Grassland Soils
A. Felske (1998)
Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions.
C. Kuske (1997)
Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation.
J. Borneman (1997)
Molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations.
H. Rheims (1996)
Screening for Genetic Diversity of Isolates of Anaerobic Fe(II)-oxidizing Bacteria Using DGGE and Wh
B. Buchholz-Cleven (1997)
Evaluation of denaturing gradient gel electrophoresis in the detection of 16S rDNA sequence variation in rhizobia and methanotrophs
T. Vallaeys (1997)
Computational simulation of DNA melting and its application to denaturing gradient gel electrophoresis.
L. Lerman (1987)
Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats.
J. Staley (1985)
Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment.
W. Liesack (1992)
A comprehensive set of sequence analysis programs for the VAX
J. Devereux (1984)
Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils
Felske (1998)
Molecular microbial diversity of an agricultural soil in Wisconsin.
J. Borneman (1996)
Principal-Components and Factor Analysis for the Description of Microbial Populations
T. Rosswall (1978)
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
R. Amann (1995)
[Biochemical characterization of Bacillus benzoevorans sp. nov., a new filamentous, sheathed mesophilic species, degrading various aromatic acids and phenols].
F. Pichinoty (1984)
[Morphology and cytology of Bacillus benzoevorans, a new filamentous, sheathed mesophilic species, degrading various aromatic acids and phenols].
F. Pichinoty (1984)
Molecular phylogenetic analysis of a soil microbial community in a soybean field
T. Ueda (1995)
Phylogeny of the Main Bacterial 16S rRNA Sequences in Drentse A Grassland Soils (The Netherlands)
A. Felske (1998)
Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis.
U. Nübel (1996)
Viable but nonrecoverable stage of Salmonella enteritidis in aquatic systems.
D. Roszak (1984)
Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts.
V. Rosenbaum (1987)
Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils.
A. Felske (1997)
High diversity in DNA of soil bacteria.
V. Torsvik (1990)
Detection and in situ identification of representatives of a widely distributed new bacterial phylum.
W. Ludwig (1997)
Direct ribosome isolation from soil to extract bacterial rRNA for community analysis.
A. Felske (1996)

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