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

The ISME Journal
Claudia KniefJulia A Vorholt


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.


Mar 9, 2013·Environmental Science & Technology·Yan JiaYong-Guan Zhu
Jan 5, 2014·Environmental Science & Technology·Yan JiaYong-Guan Zhu
Apr 12, 2012·Applied and Environmental Microbiology·Robert BrankatschkHelmut Bürgmann
Nov 8, 2012·PloS One·Rémi PeyraudJulia A Vorholt
Oct 1, 2014·Nature Reviews. Genetics·David S GuttmanPaul Schulze-Lefert
Jul 11, 2013·BioMed Research International·Constantinos MoulasDimitrios G Karpouzas
Aug 11, 2012·Bioscience, Biotechnology, and Biochemistry·Hiroyuki IguchiYasuyoshi Sakai
Apr 17, 2014·Trends in Biotechnology·Terrence H BellEtienne Yergeau
Feb 5, 2013·Annual Review of Plant Biology·Davide BulgarelliPaul Schulze-Lefert
Feb 21, 2014·The ISME Journal·Lucas W MendesSiu M Tsai
Oct 31, 2015·International Journal of Molecular Sciences·Nele WeyensStanislaw W Gawronski
Jan 19, 2016·Frontiers in Microbiology·Ravindra Pal Singh, C R K Reddy
Jan 23, 2016·Frontiers in Microbiology·Björn BreidenbachMarc G Dumont
Jan 1, 2015·Microorganisms·Hiroyuki IguchiYasuyoshi Sakai
Dec 30, 2015·Plant Physiology and Biochemistry : PPB·Youry PiiTanja Mimmo
Jan 22, 2015·Proceedings of the National Academy of Sciences of the United States of America·Joseph EdwardsVenkatesan Sundaresan
Feb 26, 2015·Proceedings of the National Academy of Sciences of the United States of America·Marcel G A van der Heijden, Klaus Schlaeppi
Jan 19, 2016·Trends in Plant Science·Eva Oburger, Hannes Schmidt
Jul 1, 2015·Trends in Plant Science·Maria VivasBernard Slippers
Mar 24, 2016·Trends in Microbiology·Julia A Schwartzman, Edward G Ruby
Aug 13, 2014·Molecular Ecology·Anastasia BraginaGabriele Berg
Mar 27, 2016·Journal of Biotechnology·Christina A MüllerGabriele Berg
Mar 29, 2016·Current Opinion in Biotechnology·Feth El Zahar HaicharWafa Achouak
Sep 4, 2015·Molecular Ecology·Anastasia BraginaGabriele Berg
May 15, 2015·Journal of Applied Microbiology·J A McGarveyR Hnasko
May 20, 2014·Microbial Biotechnology·Jackson Z LeeJohn R Spear
Apr 14, 2016·Journal of Environmental Science and Health. Part. B, Pesticides, Food Contaminants, and Agricultural Wastes·Ok K KooSteven C Ricke
Apr 9, 2015·Environmental Science and Pollution Research International·Ana R LopesOlga C Nunes


Nov 14, 2000·Journal of Bacteriology·Julia A VorholtRudolf K Thauer
Nov 15, 2000·FEMS Microbiology Reviews·Werner LiesackN P Revsbech
Nov 15, 2000·FEMS Microbiology Reviews·A BruneH Cypionka
May 26, 2001·Applied and Environmental Microbiology·G Eller, P Frenzel
Oct 27, 2001·Applied and Environmental Microbiology·A ElbeltagyK Minamisawa
Apr 27, 2002·Applied and Environmental Microbiology·Tillmann Lueders, Michael W Friedrich
Apr 11, 2003·Biochimica Et Biophysica Acta·Christopher Anthony, Paul Williams
Nov 25, 2003·Analytical Chemistry·Alexey I NesvizhskiiRuedi Aebersold
Jul 16, 2004·Journal of Proteome Research·Wenhong ZhuJohn R Yates
May 25, 2005·Journal of Experimental Botany·José-Miguel BareaConcepción Azcón-Aguilar
Jul 8, 2005·Applied and Environmental Microbiology·Claudia KniefAmnat Chidthaisong
Jul 14, 2005·Environmental Microbiology·Vasiliki AnestiAnn P Wood
Aug 18, 2005·Environmental Microbiology·Claudia Knief, Peter F Dunfield
Apr 6, 2006·Bioinformatics·Ryota Suzuki, Hidetoshi Shimodaira
Apr 22, 2006·International Journal of Systematic and Evolutionary Microbiology·Cindy H NakatsuYoichi Kamagata
Jul 29, 2006·Environmental Microbiology·Yahai LuRalf Conrad
Dec 5, 2006·Proceedings of the National Academy of Sciences of the United States of America·Christoph H HagemeierUlrich Ermler
Mar 3, 2007·Annual Review of Biochemistry·Amanda S Hakemian, Amy C Rosenzweig
Jan 8, 2009·International Journal of Systematic and Evolutionary Microbiology·Munusamy MadhaiyanTong-Min Sa
Jan 28, 2009·Environmental Microbiology·Pravin Malla ShresthaWerner Liesack
Jun 2, 2009·Systematic and Applied Microbiology·Liqin WuYahai Lu
Oct 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Nathanaël DelmotteJulia A Vorholt
Dec 15, 2010·Journal of Proteome Research·Haibin WangWen-Xiong Lin

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