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

Ziegler, Dominik; Pothier, Joël F.; Ardley, Julie; Kouakou Fossou, Romain; Pflüger, Valentin; de Meyer, Sofie; Vogel, Guido; Tonolla, Mauro; Howieson, John; Reeve, Wayne; Perret, Xavier

doi:10.1007/s00253-015-6515-3

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-1649

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS
Authors:	Ziegler, Dominik Pothier, Joël F. Ardley, Julie Kouakou Fossou, Romain Pflüger, Valentin de Meyer, Sofie Vogel, Guido Tonolla, Mauro Howieson, John Reeve, Wayne Perret, Xavier
DOI:	10.1007/s00253-015-6515-3 10.21256/zhaw-1649
Published in:	Applied Microbiology and Biotechnology
Volume(Issue):	99
Issue:	13
Page(s):	5547
Pages to:	5562
Issue Date:	18-Mar-2015
Publisher / Ed. Institution:	Springer
Publisher / Ed. Institution:	Berlin
ISSN:	0175-7598 1432-0614
Language:	English
Subjects:	Bacterial fingerprints; Phylogeny; Rhizobia; Legume nodules; GEBA-RNB; Cluster analysis
Subject (DDC):	570: Biology
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.
Further description:	Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)
URI:	https://digitalcollection.zhaw.ch/handle/11475/1649
Fulltext version:	Published version
License (according to publishing contract):	Licence according to publishing contract
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Natural Resource Sciences (IUNR)
Published as part of the ZHAW project:	MALDI-TOF MS for microorganism identification: from pattern recognition towards marker based approaches
Appears in collections:	Publikationen Life Sciences und Facility Management

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Ziegler, D., Pothier, J. F., Ardley, J., Kouakou Fossou, R., Pflüger, V., de Meyer, S., Vogel, G., Tonolla, M., Howieson, J., Reeve, W., & Perret, X. (2015). Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS. Applied Microbiology and Biotechnology, 99(13), 5547–5562. https://doi.org/10.1007/s00253-015-6515-3

Ziegler, D. et al. (2015) ‘Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS’, Applied Microbiology and Biotechnology, 99(13), pp. 5547–5562. Available at: https://doi.org/10.1007/s00253-015-6515-3.

D. Ziegler et al., “Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS,” Applied Microbiology and Biotechnology, vol. 99, no. 13, pp. 5547–5562, Mar. 2015, doi: 10.1007/s00253-015-6515-3.

ZIEGLER, Dominik, Joël F. POTHIER, Julie ARDLEY, Romain KOUAKOU FOSSOU, Valentin PFLÜGER, Sofie DE MEYER, Guido VOGEL, Mauro TONOLLA, John HOWIESON, Wayne REEVE und Xavier PERRET, 2015. Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS. Applied Microbiology and Biotechnology. 18 März 2015. Bd. 99, Nr. 13, S. 5547–5562. DOI 10.1007/s00253-015-6515-3

Ziegler, Dominik, Joël F. Pothier, Julie Ardley, Romain Kouakou Fossou, Valentin Pflüger, Sofie de Meyer, Guido Vogel, et al. 2015. “Ribosomal Protein Biomarkers Provide Root Nodule Bacterial Identification by MALDI-TOF MS.” Applied Microbiology and Biotechnology 99 (13): 5547–62. https://doi.org/10.1007/s00253-015-6515-3.

Ziegler, Dominik, et al. “Ribosomal Protein Biomarkers Provide Root Nodule Bacterial Identification by MALDI-TOF MS.” Applied Microbiology and Biotechnology, vol. 99, no. 13, Mar. 2015, pp. 5547–62, https://doi.org/10.1007/s00253-015-6515-3.