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 Perret
Applied genetics and molecular biotechnology

Abstract

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.

Keywords

Bacterial fingerprints Phylogeny Cluster analysis Rhizobia Legume nodules GEBA-RNB 

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
  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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