MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: Application to the identification of Lupinus nodulating strains

Sánchez-Juanes, Fernando; Ferreira, Laura; Vega, Pablo Alonso de la; Valverde, Ángel; Barrios, Milagros León; Rivas, Raúl; Mateos, Pedro F.; Martínez‐Molina, Eustoquio; González-Buitrago, José Manuel; Trujillo, Martha E.; Velázquez, Encarna

doi:10.1016/j.syapm.2013.09.003

Cited by 17 publications

(18 citation statements)

References 41 publications

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“…In contrast to the Ensifer, Mesorhizobium and Rhizobium genera, spectra of RPs calculated for bradyrhizobia showed significantly lower levels of similarity. This was not surprising given the heterogeneity of bradyrhizobial strains (Sánchez-Juanes et al 2013). Figure 1 also showed that in spite of only two isolates of distinct species selected to represent each of the Agrobacterium, Azorhizobium, Methylobacterium, and Microvirga genera, the clustering of theoretical RPs spectra was unambiguous.…”

Section: Using Deduced Ribosomal Proteins As Markers For Maldi-tof Msmentioning

confidence: 77%

“…These advantages, along with the proven accuracy of MALDI-TOF MS-based identification of bacteria, have revolutionized the routine identification of microorganisms to species and subspecies level in clinical diagnostic and food microbiological laboratories (Croxatto et al 2012;Mazzeo et al 2006). MALDI-TOF MS has also been shown to be an excellent tool for identification of diverse rhizobial species of Bradyrhizobium, Ensifer, Shinella, and Rhizobium applicable to large populations of isolates in ecological and taxonomic studies (Ferreira et al 2011;Sánchez-Juanes et al 2013). …”

Section: Discussionmentioning

confidence: 99%

“…MALDI-TOF MS offers the possibility of accurately resolving bacterial identity to the genus, species, and subspecies levels in some taxa and has successfully been applied to diverse rhizobial strains grown on solid media (Ferreira et al 2011;Sánchez-Juanes et al 2013;Ziegler et al 2012) and found inside legume nodules (Ziegler et al 2012). In most direct MALDI-TOF MS analyses, bacterial cells are lysed to release the intracellular proteins, which are then ionized and separated according to their mass-to-charge ratio (m/z) and recorded as distinct peaks, generating a complex spectrum, or fingerprint that is characteristic of a bacterial sample.…”

Section: Introductionmentioning

confidence: 99%

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

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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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.

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Section: Using Deduced Ribosomal Proteins As Markers For Maldi-tof Msmentioning

confidence: 77%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Ziegler

Pothier

Ardley

et al. 2015

Appl Microbiol Biotechnol

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“…The in-house databases helped researchers to achieve better identification results (Verroken et al, 2010; Ferreira et al, 2011; Calderaro et al, 2013, 2014a,b; Lau et al, 2013; Sánchez-Juanes et al, 2013; Vávrová et al, 2014; Warneke et al, 2014), but these databases remain inaccessible to other researchers. Development of an open access and universal database incorporating MALDI-TOF MS spectra of as many microorganisms as possible has been proposed as more appropriate than commercial and individual in-house databases (Mazzeo et al, 2006; Böhme et al, 2012).…”

Section: Development Of Maldi-tof Ms Spectral Databasementioning

confidence: 99%

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

2016

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Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.

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“…However, recent genome analyses confirmed that horizontal gene transfer and intergenic recombination often impaired taxonomic classification (Tian et al, 2012; Zhang et al, 2012). Given its potential to facilitate and expedite the exploration of rhizobial diversity in agricultural and natural ecosystems (Ziegler et al, 2012), matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) has become a rapid and reliable alternative to DNA sequencing for the identification of nodule isolates (Ferreira et al, 2011; Sánchez-Juanes et al, 2013) or their classification (Jia et al, 2015). In fact, MALDI-TOF MS was found to be so efficient in discriminating between closely related strains, that a large reference database covering all of the major rhizobial genera was established (Ziegler et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Two Major Clades of Bradyrhizobia Dominate Symbiotic Interactions with Pigeonpea in Fields of Côte d'Ivoire

et al. 2016

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In smallholder farms of Côte d'Ivoire, particularly in the northeast of the country, Cajanus cajan (pigeonpea) has become an important crop because of its multiple beneficial facets. Pigeonpea seeds provide food to make ends meet, are sold on local markets, and aerial parts serve as forage for animals. Since it fixes atmospheric nitrogen in symbiosis with soil bacteria collectively known as rhizobia, C. cajan also improves soil fertility and reduces fallow time. Yet, seed yields remain low mostly because farmers cannot afford chemical fertilizers. To identify local rhizobial strains susceptible to be used as bio-inoculants to foster pigeonpea growth, root nodules were collected in six fields of three geographically distant regions of Côte d'Ivoire. Nodule bacteria were isolated and characterized using various molecular techniques including matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) and DNA sequencing. These molecular analyses showed that 63 out of 85 nodule isolates belonged to two major clades of bradyrhizobia, one of which is known as the Bradyrhizobium elkanii super clade. Phylogenies of housekeeping (16S-ITS-23S, rpoB) and symbiotic (nifH) genes were not always congruent suggesting that lateral transfer of nitrogen fixation genes also contributed to define the genome of these bradyrhizobial isolates. Interestingly, no field-, plant-, or cultivar-specific effect was found to shape the profiles of symbiotic strains. In addition, nodule isolates CI-1B, CI-36E, and CI-41A that belong to distinct species, showed similar symbiotic efficiencies suggesting that any of these strains might serve as a proficient inoculant for C. cajan.

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MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: Application to the identification of Lupinus nodulating strains

Cited by 17 publications

References 41 publications

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

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

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

Two Major Clades of Bradyrhizobia Dominate Symbiotic Interactions with Pigeonpea in Fields of Côte d'Ivoire

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