caa a22 4500 605505942 CHVBK 20210128100624.0 cr unu---uuuuu 210128e20150701xx s 000 0 eng 10.1007/s00253-015-6515-3 doi (NATIONALLICENCE)springer-10.1007/s00253-015-6515-3 Ribosomal protein biomarkers provide root nodule bacterial identification by MALDI-TOF MS [Elektronische Daten] [Dominik Ziegler, Joël Pothier, Julie Ardley, Romain Fossou, Valentin Pflüger, Sofie de Meyer, Guido Vogel, Mauro Tonolla, John Howieson, Wayne Reeve, Xavier Perret] 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. Springer-Verlag Berlin Heidelberg, 2015 Bacterial fingerprints nationallicence Phylogeny nationallicence Cluster analysis nationallicence Rhizobia nationallicence Legume nodules nationallicence GEBA-RNB nationallicence Ziegler Dominik Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut Pothier Joël Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences (ZHAW), Grüental, P.O. Box, CH-8820, Wädenswil, Switzerland aut Ardley Julie Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut Fossou Romain Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut Pflüger Valentin Mabritec, Lörracherstrasse 50, CH-4125, Riehen, Switzerland aut de Meyer Sofie Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut Vogel Guido Mabritec, Lörracherstrasse 50, CH-4125, Riehen, Switzerland aut Tonolla Mauro Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut Howieson John Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut Reeve Wayne Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut Perret Xavier Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut Applied Microbiology and Biotechnology Springer Berlin Heidelberg 99/13(2015-07-01), 5547-5562 0175-7598 99:13<5547 2015 99 253 https://doi.org/10.1007/s00253-015-6515-3 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00253-015-6515-3 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Ziegler Dominik Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut NATIONALLICENCE 700 1- Pothier Joël Environmental Genomics and Systems Biology Research Group, Institute for Natural Resources Sciences, Zurich University of Applied Sciences (ZHAW), Grüental, P.O. Box, CH-8820, Wädenswil, Switzerland aut NATIONALLICENCE 700 1- Ardley Julie Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut NATIONALLICENCE 700 1- Fossou Romain Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut NATIONALLICENCE 700 1- Pflüger Valentin Mabritec, Lörracherstrasse 50, CH-4125, Riehen, Switzerland aut NATIONALLICENCE 700 1- de Meyer Sofie Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut NATIONALLICENCE 700 1- Vogel Guido Mabritec, Lörracherstrasse 50, CH-4125, Riehen, Switzerland aut NATIONALLICENCE 700 1- Tonolla Mauro Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut NATIONALLICENCE 700 1- Howieson John Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut NATIONALLICENCE 700 1- Reeve Wayne Center for Rhizobium Studies, Murdoch University, Murdoch, Australia aut NATIONALLICENCE 700 1- Perret Xavier Department of Botany and Plant Biology, Microbiology Unit, Sciences III, University of Geneva, 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland aut NATIONALLICENCE 773 0- Applied Microbiology and Biotechnology Springer Berlin Heidelberg 99/13(2015-07-01), 5547-5562 0175-7598 99:13<5547 2015 99 253