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

被引：8

作者：

Daffonchio, D ^{[1
]}

De Biase, A ^{[1
]}

Rizzi, A ^{[1
]}

Sorlini, C ^{[1
]}

机构：

[1] Univ Milan, DISTAM, I-20133 Milan, Italy

来源：

FEMS MICROBIOLOGY LETTERS | 1998年 / 164卷 / 02期

关键词：

Methanogenic Archaea; 16S rDNA variable region; interoperonic variability; length variability; polymerase chain reaction single-strand conformation polymorphism; identification;

D O I：

10.1016/S0378-1097(98)00246-8

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

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 2.611, Mb. wolfei DSMZ 2970, Methaosarcina 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. (C) 1998 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

引用

页码：403 / 410

页数：8

共 27 条

[1] PROPOSAL OF MINIMAL STANDARDS FOR DESCRIBING NEW TAXA OF METHANOGENIC BACTERIA [J].

BOONE, DR ;

WHITMAN, WB .

INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, 1988, 38 (02) :212-219

[2] Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii [J].

Bult, CJ ;

White, O ;

Olsen, GJ ;

Zhou, LX ;

Fleischmann, RD ;

Sutton, GG ;

Blake, JA ;

FitzGerald, LM ;

Clayton, RA ;

Gocayne, JD ;

Kerlavage, AR ;

Dougherty, BA ;

Tomb, JF ;

Adams, MD ;

Reich, CI ;

Overbeek, R ;

Kirkness, EF ;

Weinstock, KG ;

Merrick, JM ;

Glodek, A ;

Scott, JL ;

Geoghagen, NSM ;

Weidman, JF ;

Fuhrmann, JL ;

Nguyen, D ;

Utterback, TR ;

Kelley, JM ;

Peterson, JD ;

Sadow, PW ;

Hanna, MC ;

Cotton, MD ;

Roberts, KM ;

Hurst, MA ;

Kaine, BP ;

Borodovsky, M ;

Klenk, HP ;

Fraser, CM ;

Smith, HO ;

Woese, CR ;

Venter, JC .

SCIENCE, 1996, 273 (5278) :1058-1073

[3] A ONE-STEP MICROBIAL DNA EXTRACTION METHOD USING CHELEX-100 SUITABLE FOR GENE AMPLIFICATION [J].

DELAMBALLERIE, X ;

ZANDOTTI, C ;

VIGNOLI, C ;

BOLLET, C ;

DEMICCO, P .

RESEARCH IN MICROBIOLOGY, 1992, 143 (08) :785-790

[4]

Deutsche Sammlung von Mikroorganismen und Zellkulturen, 1989, CAT STRAINS

[5] THE RAPID DETECTION OF UNKNOWN MUTATIONS IN NUCLEIC-ACIDS [J].

GROMPE, M .

NATURE GENETICS, 1993, 5 (02) :111-117

[6] Isolation and identification of methanogen-specific DNA from blanket bog feat by PCR amplification and sequence analysis [J].

Hales, BA ;

Edwards, C ;

Ritchie, DA ;

Hall, G ;

Pickup, RW ;

Saunders, JR .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 1996, 62 (02) :668-675

[7] POLYMERASE CHAIN-REACTION AMPLIFICATION AND RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISM ANALYSIS OF 16S RIBOSOMAL-RNA GENES FROM METHANOGENS [J].

HIRAISHI, A ;

KAMAGATA, Y ;

NAKAMURA, K .

JOURNAL OF FERMENTATION AND BIOENGINEERING, 1995, 79 (06) :523-529

[8] PHYSICAL ORGANIZATION OF THE GENES FOR RIBOSOMAL-RNA IN METHANOCOCCUS-VANNIELII [J].

JARSCH, M ;

ALTENBUCHNER, J ;

BOCK, A .

MOLECULAR & GENERAL GENETICS, 1983, 189 (01) :41-47

[9] Methanogen flora of paddy soils in Japan [J].

Kudo, Y ;

Nakajima, T ;

Miyaki, T ;

Oyaizu, H .

FEMS MICROBIOLOGY ECOLOGY, 1997, 22 (01) :39-48

[10] Single-strand conformation polymorphism analysis of PCR-amplified ribosomal DNA internal transcribed spacers to differentiate species of Aspergillus section Flavi [J].

Kumeda, Y ;

Asao, T .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 1996, 62 (08) :2947-2952

← 1 2 3 →