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PMID: 9252585 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Detection and in situ identification of representatives of a widely distributed new bacterial phylum.

FEMS microbiology letters ·Vol. 153 ·No. 1 ·1997-08-01 ·Pages 181-90

Ludwig W, Bauer SH, Bauer M, Held I, Kirchhof G, Schulze R, Huber I, Spring S, Hartmann A, Schleifer KH

Abstract

16S rRNA gene libraries were prepared by polymerase chain reaction amplification and cloning from soil samples taken periodically from a field with genetically modified plants. Sequence analyses of the cloned rDNAs indicated that 140 of them clustered apart from known bacterial phyla. Based on 31 full sequences a new phylum could be defined. It includes Holophaga foetida, 'Geothrix fermentans' and Acidobacterium capsulatum as the only cultured species so far. Therefore, this line of descent was named the Holophagal Acidobacterium phylum. About 50 published partial sequences of cloned rDNAs retrieved from soil, freshwater sediments or activated sludge from different continents indicate the occurrence of further representatives of this phylum. Two specific hybridization probes were constructed for members of one of four subclusters. A careful data analysis revealed the importance and problems of identifying and dealing with artefacts such as chimeric structure when defining new phylogenetic groups based mainly upon cloned amplified rDNAs. For the first time, the presence of bacterial cells representing this group could be shown in soil, sediment, activated sludge and lake snow by in situ hybridization.

MeSH Terms

Bacteria/classification,genetics Cloning, Molecular Gene Library In Situ Hybridization, Fluorescence/methods Molecular Sequence Data Phylogeny RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA Soil Microbiology

Chemicals

RNA, Ribosomal, 16S

Authors & Affiliations

10 authors, click to expand affiliations / ORCID

Ludwig W

Lehrstuhl für Mikrobiologie, Technische Universität München, Germany. ludwig@mikro.biologie.tu-muenchen.de

Bauer S H

Bauer M

Held I

Kirchhof G

Schulze R

Huber I

Spring S

Hartmann A

Schleifer K H

Article Info

Journal

FEMS microbiology letters

Abbr.

FEMS Microbiol Lett

ISSN

0378-1097

DOI

10.1111/j.1574-6968.1997.tb10480.x

ludwig@mikro.biologie.tu-muenchen.de

Published

1997-08-01

Pages

181-90

Language

English

Region

England

NLM ID

7705721

Subset

Databases

GENBANK

Z95707, Z95708, Z95709, Z95710, Z95711, Z95712, Z95713, Z95714, Z95715, Z95716, Z95717, Z95718, Z95719, Z95720, Z95721, Z95722, Z95723, Z95724, Z95725, Z95726, Z95727, Z95728, Z95729, Z95730, Z95731, Z95732, Z95733, Z95734, Z95735, Z95736

External Links

PubMed source DOI: 10.1111/j.1574-6968.1997.tb10480.x View journal details

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Detection and in situ identification of representatives of a widely distributed new bacterial phylum.

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