Interspecific, intraspecific and interoperonic variability in the 16S rRNA gene of methanogens revealed by length and single-strand conformation polymorphism analysis

Daniele Daffonchio; Andrea De Biase; Aurora Rizzi; Claudia Sorlini

doi:10.1016/S0378-1097(98)00246-8

Interspecific, intraspecific and interoperonic variability in the 16S rRNA gene of methanogens revealed by length and single-strand conformation polymorphism analysis

Daniele Daffonchio^*, Andrea De Biase, Aurora Rizzi, Claudia Sorlini

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

Thirty-seven strains of mesophilic and thermophilic methanogenic Archaea, belonging to 30 species, were analyzed by length polymorphism (LP) and single-strand conformation polymorphism (SSCP) of an amplified 300-bp fragment of the 16S rRNA gene (Escherichia coli positions 9-331) including the variable regions V1 and V2. LPs and SSCPs were detected between species and between strains of the same species (Methanobacterium formicicum). LPs were found in Mb. formicicum DSMZ 3637, Mb. ivanovii DSMZ 2611, Mb. wolfei DSMZ 2970, Methanosarcina barkeri DSMZ 800, and Methanosaeta concilii DSMZ 3671, suggesting the presence of polymorphic 16S rRNA genes in the genome. We propose that LP and SSCP analysis of the 16S rRNA gene could be of practical help for strain identification. Copyright (C) 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

Original language	English (US)
Pages (from-to)	403-410
Number of pages	8
Journal	FEMS Microbiology Letters
Volume	164
Issue number	2
DOIs	https://doi.org/10.1016/S0378-1097(98)00246-8
State	Published - Jul 15 1998
Externally published	Yes

Keywords

16S rDNA variable region
Identification
Interoperonic variability
Length variability
Methanogenic Archaea
Polymerase chain reaction-single strand conformation polymorphism

ASJC Scopus subject areas

Microbiology
Molecular Biology
Genetics

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title = "Interspecific, intraspecific and interoperonic variability in the 16S rRNA gene of methanogens revealed by length and single-strand conformation polymorphism analysis",

abstract = "Thirty-seven strains of mesophilic and thermophilic methanogenic Archaea, belonging to 30 species, were analyzed by length polymorphism (LP) and single-strand conformation polymorphism (SSCP) of an amplified 300-bp fragment of the 16S rRNA gene (Escherichia coli positions 9-331) including the variable regions V1 and V2. LPs and SSCPs were detected between species and between strains of the same species (Methanobacterium formicicum). LPs were found in Mb. formicicum DSMZ 3637, Mb. ivanovii DSMZ 2611, Mb. wolfei DSMZ 2970, Methanosarcina barkeri DSMZ 800, and Methanosaeta concilii DSMZ 3671, suggesting the presence of polymorphic 16S rRNA genes in the genome. We propose that LP and SSCP analysis of the 16S rRNA gene could be of practical help for strain identification. Copyright (C) 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.",

keywords = "16S rDNA variable region, Identification, Interoperonic variability, Length variability, Methanogenic Archaea, Polymerase chain reaction-single strand conformation polymorphism",

author = "Daniele Daffonchio and {De Biase}, Andrea and Aurora Rizzi and Claudia Sorlini",

year = "1998",

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doi = "10.1016/S0378-1097(98)00246-8",

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T1 - Interspecific, intraspecific and interoperonic variability in the 16S rRNA gene of methanogens revealed by length and single-strand conformation polymorphism analysis

AU - Daffonchio, Daniele

AU - De Biase, Andrea

AU - Rizzi, Aurora

AU - Sorlini, Claudia

PY - 1998/7/15

Y1 - 1998/7/15

N2 - Thirty-seven strains of mesophilic and thermophilic methanogenic Archaea, belonging to 30 species, were analyzed by length polymorphism (LP) and single-strand conformation polymorphism (SSCP) of an amplified 300-bp fragment of the 16S rRNA gene (Escherichia coli positions 9-331) including the variable regions V1 and V2. LPs and SSCPs were detected between species and between strains of the same species (Methanobacterium formicicum). LPs were found in Mb. formicicum DSMZ 3637, Mb. ivanovii DSMZ 2611, Mb. wolfei DSMZ 2970, Methanosarcina barkeri DSMZ 800, and Methanosaeta concilii DSMZ 3671, suggesting the presence of polymorphic 16S rRNA genes in the genome. We propose that LP and SSCP analysis of the 16S rRNA gene could be of practical help for strain identification. Copyright (C) 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

AB - Thirty-seven strains of mesophilic and thermophilic methanogenic Archaea, belonging to 30 species, were analyzed by length polymorphism (LP) and single-strand conformation polymorphism (SSCP) of an amplified 300-bp fragment of the 16S rRNA gene (Escherichia coli positions 9-331) including the variable regions V1 and V2. LPs and SSCPs were detected between species and between strains of the same species (Methanobacterium formicicum). LPs were found in Mb. formicicum DSMZ 3637, Mb. ivanovii DSMZ 2611, Mb. wolfei DSMZ 2970, Methanosarcina barkeri DSMZ 800, and Methanosaeta concilii DSMZ 3671, suggesting the presence of polymorphic 16S rRNA genes in the genome. We propose that LP and SSCP analysis of the 16S rRNA gene could be of practical help for strain identification. Copyright (C) 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

KW - 16S rDNA variable region

KW - Identification

KW - Interoperonic variability

KW - Length variability

KW - Methanogenic Archaea

KW - Polymerase chain reaction-single strand conformation polymorphism

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Interspecific, intraspecific and interoperonic variability in the 16S rRNA gene of methanogens revealed by length and single-strand conformation polymorphism analysis

Abstract

Keywords

ASJC Scopus subject areas

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