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PMID: 22189496 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice.

The ISME journal ·Vol. 6 ·No. 7 ·2012-07-00 ·Pages 1378-90

Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA

Abstract

The above- and below-ground parts of rice plants create specific habitats for various microorganisms. In this study, we characterized the phyllosphere and rhizosphere microbiota of rice cultivars using a metaproteogenomic approach to get insight into the physiology of the bacteria and archaea that live in association with rice. The metaproteomic datasets gave rise to a total of about 4600 identified proteins and indicated the presence of one-carbon conversion processes in the rhizosphere as well as in the phyllosphere. Proteins involved in methanogenesis and methanotrophy were found in the rhizosphere, whereas methanol-based methylotrophy linked to the genus Methylobacterium dominated within the protein repertoire of the phyllosphere microbiota. Further, physiological traits of differential importance in phyllosphere versus rhizosphere bacteria included transport processes and stress responses, which were more conspicuous in the phyllosphere samples. In contrast, dinitrogenase reductase was exclusively identified in the rhizosphere, despite the presence of nifH genes also in diverse phyllosphere bacteria.

MeSH Terms
Archaea/classification,genetics,isolation & purification,metabolism Bacteria/classification,genetics,isolation & purification,metabolism Carbon/metabolism Metagenome Methanol/metabolism Methylobacterium/classification,metabolism Oryza/metabolism,microbiology Proteome/analysis Rhizosphere
Chemicals
Proteome Carbon Methanol
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Knief Claudia
Institute of Microbiology, ETH Zurich, Zurich, Switzerland. knief@micro.biol.ethz.ch
Delmotte Nathanaël
Chaffron Samuel
Stark Manuel
Innerebner Gerd
Wassmann Reiner
von Mering Christian
Vorholt Julia A
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Article Info
Journal
The ISME journal
Abbr.
ISME J
ISSN
1751-7370
DOI
10.1038/ismej.2011.192
Email
knief@micro.biol.ethz.ch
Published
2012-07-00
Epub
2011-00-22
Pages
1378-90
Language
English
Region
England
NLM ID
101301086
PMCID
PMC3379629
Subset
IM
External Links
PubMed source DOI: 10.1038/ismej.2011.192 PMC Full Text View journal details
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