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MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae.

Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Velázquez E - PLoS ONE (2011)

Bottom Line: Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae.Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences.The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

View Article: PubMed Central - PubMed

Affiliation: Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain.

ABSTRACT
Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

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Neighbour-joining phylogenetic tree based on nodC gene sequences (about 860 nt) showing the position of representative strains from each biovar analysed in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 5 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.
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pone-0020223-g007: Neighbour-joining phylogenetic tree based on nodC gene sequences (about 860 nt) showing the position of representative strains from each biovar analysed in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 5 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.

Mentions: For example, within genus Rhizobium, R. leguminosarum contains three biovars: viciae, trifolii and phaseoli [31], [38], perfectly distinguishable on the basis of their nodC gene sequences (figure 7). However MALDI-TOF MS analysis showed that strains with housekeeping genes close to R. leguminosarum USDA 2370T (RVS11, RPVF18 and ATCC 14480) [29], [38], [39] matched with score values higher than 2 with this strain with independence to the biovar they belong to (figure 7). Likewise, the strains FL27 from biovar gallicum [45] and PhD12 from biovar phaseoli [21] carrying divergent nodC genes (figure 7) matched with R. gallicum R602spT with score values higher than 2 (Table 2F). The same was found in R. lusitanum whose strains P1-7T and P3-13 have phylogenetically distant nodC genes (figure 7) but they matched with a score value of 2.314 (Table 2F).


MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae.

Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Velázquez E - PLoS ONE (2011)

Neighbour-joining phylogenetic tree based on nodC gene sequences (about 860 nt) showing the position of representative strains from each biovar analysed in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 5 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3105015&req=5

pone-0020223-g007: Neighbour-joining phylogenetic tree based on nodC gene sequences (about 860 nt) showing the position of representative strains from each biovar analysed in this study.Bootstrap values calculated for 1000 replications are indicated. Bar, 5 nt substitution per 100 nt. Accesion numbers from Genbank are given in brackets.
Mentions: For example, within genus Rhizobium, R. leguminosarum contains three biovars: viciae, trifolii and phaseoli [31], [38], perfectly distinguishable on the basis of their nodC gene sequences (figure 7). However MALDI-TOF MS analysis showed that strains with housekeeping genes close to R. leguminosarum USDA 2370T (RVS11, RPVF18 and ATCC 14480) [29], [38], [39] matched with score values higher than 2 with this strain with independence to the biovar they belong to (figure 7). Likewise, the strains FL27 from biovar gallicum [45] and PhD12 from biovar phaseoli [21] carrying divergent nodC genes (figure 7) matched with R. gallicum R602spT with score values higher than 2 (Table 2F). The same was found in R. lusitanum whose strains P1-7T and P3-13 have phylogenetically distant nodC genes (figure 7) but they matched with a score value of 2.314 (Table 2F).

Bottom Line: Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae.Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences.The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

View Article: PubMed Central - PubMed

Affiliation: Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain.

ABSTRACT
Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

Show MeSH