Applied Microbiology and Biotechnology

, Volume 99, Issue 13, pp 5547–5562 | Cite as

Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS

  • Dominik Ziegler
  • Joël F. Pothier
  • Julie Ardley
  • Romain Kouakou Fossou
  • Valentin Pflüger
  • Sofie de Meyer
  • Guido Vogel
  • Mauro Tonolla
  • John Howieson
  • Wayne Reeve
  • Xavier PerretEmail author
Applied genetics and molecular biotechnology


Accurate identification of soil bacteria that form nitrogen-fixing associations with legume crops is challenging given the phylogenetic diversity of root nodule bacteria (RNB). The labor-intensive and time-consuming 16S ribosomal RNA (rRNA) sequencing and/or multilocus sequence analysis (MLSA) of conserved genes so far remain the favored molecular tools to characterize symbiotic bacteria. With the development of mass spectrometry (MS) as an alternative method to rapidly identify bacterial isolates, we recently showed that matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) can accurately characterize RNB found inside plant nodules or grown in cultures. Here, we report on the development of a MALDI-TOF RNB-specific spectral database built on whole cell MS fingerprints of 116 strains representing the major rhizobial genera. In addition to this RNB-specific module, which was successfully tested on unknown field isolates, a subset of 13 ribosomal proteins extracted from genome data was found to be sufficient for the reliable identification of nodule isolates to rhizobial species as shown in the putatively ascribed ribosomal protein masses (PARPM) database. These results reveal that data gathered from genome sequences can be used to expand spectral libraries to aid the accurate identification of bacterial species by MALDI-TOF MS.


Bacterial fingerprints Phylogeny Cluster analysis Rhizobia Legume nodules GEBA-RNB 



This work was funded by the Swiss Commission for Technology and Innovation (CTI project 11225.1 PFLS_LS), the Swiss National Science Foundation (Grant Nos. 31003A-116591 and 31003A_146548), Mabritec, and Meat & Livestock Australia/Australian Wool Innovation Grant B.PSP.0013. We are grateful to Susana Brom, Sofie Goormachtig, Eric Giraud, Alessio Mengoni, Philip Poole, José-Enrique Ruiz-Sainz, and Maged Saad for providing a number of reference strains, Damiana Ravasi and Paola Decristophoris for assistance with DNA sequencing of a number of marker genes, and Antoine Huyghe for his help in generating Fig. 1.

Supplementary material

253_2015_6515_MOESM1_ESM.pdf (3.2 mb)
ESM 1 (PDF 3252 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Dominik Ziegler
    • 1
    • 2
  • Joël F. Pothier
    • 3
  • Julie Ardley
    • 4
  • Romain Kouakou Fossou
    • 1
  • Valentin Pflüger
    • 2
  • Sofie de Meyer
    • 4
  • Guido Vogel
    • 2
  • Mauro Tonolla
    • 1
    • 5
  • John Howieson
    • 4
  • Wayne Reeve
    • 4
  • Xavier Perret
    • 1
    Email author
  1. 1.Department of Botany and Plant Biology, Microbiology Unit, Sciences IIIUniversity of GenevaGeneva 4Switzerland
  2. 2.MabritecRiehenSwitzerland
  3. 3.Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources SciencesZurich University of Applied Sciences (ZHAW)WädenswilSwitzerland
  4. 4.Center for Rhizobium StudiesMurdoch UniversityMurdochAustralia
  5. 5.Laboratory of Applied Microbiology, Department of Environment Construction and DesignUniversity of Applied Sciences of Southern SwitzerlandBellinzonaSwitzerland

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