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

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 co...

Full description

Saved in:
Bibliographic Details
Published in:Applied microbiology and biotechnology 2015-07, Vol.99 (13), p.5547-5562
Main Authors: Ziegler, Dominik, Pothier, Joël F, Ardley, Julie, Fossou, Romain Kouakou, Pflüger, Valentin, de Meyer, Sofie, Vogel, Guido, Tonolla, Mauro, Howieson, John, Reeve, Wayne, Perret, Xavier
Format: Article
Language:English
Subjects:
Applied Genetics and Molecular Biotechnology
Bacteria
Bacteria - chemistry
Bacteria - classification
Bacteria - genetics
Bacterial Proteins - genetics
Biodiversity
Biomarkers
Biomarkers - analysis
Biomedical and Life Sciences
Biotechnology
Cluster Analysis
Conserved sequence
crops
desorption
DNA, Ribosomal - chemistry
DNA, Ribosomal - genetics
Gene sequencing
genes
Genetic aspects
Genetic markers
Genomes
Ionization
Ions
Legumes
Life Sciences
Mass spectrometry
Mass spectroscopy
Microbial Genetics and Genomics
Microbiology
microsymbionts
Molecular Sequence Data
multilocus sequence typing
Nitrogen fixation
Nitrogenation
Nodules
Nucleotide sequence
nucleotide sequences
Phylogeny
Physiological aspects
Proteins
Ribosomal proteins
Ribosomal Proteins - analysis
ribosomal RNA
RNA, Ribosomal, 16S - genetics
Root Nodules, Plant - microbiology
rRNA 16S
Sequence analysis
Sequence Analysis, DNA
Soil bacteria
Soil Microbiology
Soil microorganisms
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization - methods
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:0175-7598
1432-0614
DOI:10.1007/s00253-015-6515-3