First insight into the genome of an uncultivated crenarchaeote from soil

Achim Quaiser, Torsten Ochsenreiter, Hans-Peter Klenk, Arnulf Kletzin, Alexander H Treusch, Guido Meurer, Jürgen Eck, Christoph W Sensen, Christa Schleper

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we have constructed complex large-insert genomic libraries. Using archaea-specific 16S rRNA probes we have isolated a 34 kbp fragment from a 900 Mbp fosmid library of soil DNA. The clone contained a complete 16S/23S rRNA operon and 17 genes encoding putative proteins. Phylogenetic analyses of the rRNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ significantly from their previously studied uncultivated marine relatives. The protein encoding genes gave the first insights into the physiological potential of these organisms and can serve as a basis for future genomic and functional genomic studies.
OriginalsprogEngelsk
TidsskriftEnvironmental Microbiology
Vol/bind4
Udgave nummer10
Sider (fra-til)603-11
Antal sider8
ISSN1462-2912
StatusUdgivet - 2002

Fingeraftryk

Crenarchaeota
genomics
genome
Archaea
ribosomal RNA
rRNA Genes
gene
DNA
soil
genes
rRNA Operon
Proteins
protein
Genomic Library
proteins
genomic libraries
phylogenetics
phylogeny
DNA-directed DNA polymerase
operon

Citer dette

Quaiser, A., Ochsenreiter, T., Klenk, H-P., Kletzin, A., Treusch, A. H., Meurer, G., ... Schleper, C. (2002). First insight into the genome of an uncultivated crenarchaeote from soil. Environmental Microbiology, 4(10), 603-11.
Quaiser, Achim ; Ochsenreiter, Torsten ; Klenk, Hans-Peter ; Kletzin, Arnulf ; Treusch, Alexander H ; Meurer, Guido ; Eck, Jürgen ; Sensen, Christoph W ; Schleper, Christa. / First insight into the genome of an uncultivated crenarchaeote from soil. I: Environmental Microbiology. 2002 ; Bind 4, Nr. 10. s. 603-11.
@article{2fb5028043ce11df937d000ea68e967b,
title = "First insight into the genome of an uncultivated crenarchaeote from soil",
abstract = "Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we have constructed complex large-insert genomic libraries. Using archaea-specific 16S rRNA probes we have isolated a 34 kbp fragment from a 900 Mbp fosmid library of soil DNA. The clone contained a complete 16S/23S rRNA operon and 17 genes encoding putative proteins. Phylogenetic analyses of the rRNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ significantly from their previously studied uncultivated marine relatives. The protein encoding genes gave the first insights into the physiological potential of these organisms and can serve as a basis for future genomic and functional genomic studies.",
keywords = "Crenarchaeota, Genes, Bacterial, Genome, Bacterial, Genomic Library, Molecular Sequence Data, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Soil Microbiology",
author = "Achim Quaiser and Torsten Ochsenreiter and Hans-Peter Klenk and Arnulf Kletzin and Treusch, {Alexander H} and Guido Meurer and J{\"u}rgen Eck and Sensen, {Christoph W} and Christa Schleper",
year = "2002",
language = "English",
volume = "4",
pages = "603--11",
journal = "Environmental Microbiology",
issn = "1462-2912",
publisher = "Wiley-Blackwell",
number = "10",

}

Quaiser, A, Ochsenreiter, T, Klenk, H-P, Kletzin, A, Treusch, AH, Meurer, G, Eck, J, Sensen, CW & Schleper, C 2002, 'First insight into the genome of an uncultivated crenarchaeote from soil', Environmental Microbiology, bind 4, nr. 10, s. 603-11.

First insight into the genome of an uncultivated crenarchaeote from soil. / Quaiser, Achim; Ochsenreiter, Torsten; Klenk, Hans-Peter; Kletzin, Arnulf; Treusch, Alexander H; Meurer, Guido; Eck, Jürgen; Sensen, Christoph W; Schleper, Christa.

I: Environmental Microbiology, Bind 4, Nr. 10, 2002, s. 603-11.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - First insight into the genome of an uncultivated crenarchaeote from soil

AU - Quaiser, Achim

AU - Ochsenreiter, Torsten

AU - Klenk, Hans-Peter

AU - Kletzin, Arnulf

AU - Treusch, Alexander H

AU - Meurer, Guido

AU - Eck, Jürgen

AU - Sensen, Christoph W

AU - Schleper, Christa

PY - 2002

Y1 - 2002

N2 - Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we have constructed complex large-insert genomic libraries. Using archaea-specific 16S rRNA probes we have isolated a 34 kbp fragment from a 900 Mbp fosmid library of soil DNA. The clone contained a complete 16S/23S rRNA operon and 17 genes encoding putative proteins. Phylogenetic analyses of the rRNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ significantly from their previously studied uncultivated marine relatives. The protein encoding genes gave the first insights into the physiological potential of these organisms and can serve as a basis for future genomic and functional genomic studies.

AB - Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two-phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we have constructed complex large-insert genomic libraries. Using archaea-specific 16S rRNA probes we have isolated a 34 kbp fragment from a 900 Mbp fosmid library of soil DNA. The clone contained a complete 16S/23S rRNA operon and 17 genes encoding putative proteins. Phylogenetic analyses of the rRNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non-thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ significantly from their previously studied uncultivated marine relatives. The protein encoding genes gave the first insights into the physiological potential of these organisms and can serve as a basis for future genomic and functional genomic studies.

KW - Crenarchaeota

KW - Genes, Bacterial

KW - Genome, Bacterial

KW - Genomic Library

KW - Molecular Sequence Data

KW - Phylogeny

KW - RNA, Bacterial

KW - RNA, Ribosomal, 16S

KW - Soil Microbiology

M3 - Journal article

C2 - 12366755

VL - 4

SP - 603

EP - 611

JO - Environmental Microbiology

JF - Environmental Microbiology

SN - 1462-2912

IS - 10

ER -

Quaiser A, Ochsenreiter T, Klenk H-P, Kletzin A, Treusch AH, Meurer G et al. First insight into the genome of an uncultivated crenarchaeote from soil. Environmental Microbiology. 2002;4(10):603-11.