Table 1.
Ribosomal subunit proteins of M. extorquens strain AM1 detected by MALDI-TOF/MS.
Figure 1.
WC-MS profiles of the type strains of Methylobacterium species, and dendrogram calculated by our method.
The spectra (m/z 2000–15,000) of relative intensity are shown as gel-like images using mMass 5.0 software [49]. Asterisks indicate the type strains showing similar spectra and are discussed in the text.
Figure 2.
Correlation of the WC-MS data using different culture conditions and correlation of similarity between WC-MS data and 16S rRNA gene sequences.
A. Mantel tests for similarities of WC-MS profiles of cells grown on R2A and methanol. B. Mantel tests for similarities of 16S rRNA gene and WC-MS on methanol. C. Enlarged image of B, showing combinations of the type strains sharing high 16S rRNA gene and WC-MS profile similarities.
Figure 3.
Biotyper-generated dendrogram based on WC-MS profile of the isolates.
Non-Methylobacterium isolates are indicated with asterisks (*), which were revealed by 16S rRNA gene sequencing. The closest 16S rRNA gene relatives were determined by pairwise similarity analysis using the EZtaxon server [42]. Note that strains 23e and 35a were previously identified as novel species (M. gnaphalii 23e(T) and M. oxalidis 35a(T), respectively).
Figure 4.
Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences (ca. 1.44 kb) of the Methylobacterium isolates (black) and Methylobacterium type strains (red).
Sequence alignment was carried out by SILVA Aligner [37] and analyzed with Kimura’s two-parameter algorithm (MEGA5) [38]. Tentative identifications by the EZtaxon site for the isolates are shown with pairwise similarity. Numbers at nodes are bootstrap percentages (based on 1000 resampled data sets); only values above 70% are shown. The sequence of Rhodopseudomonas palustris DSM123T (AB175650) was used as an outgroup. Note that strains 23e and 35a were previously identified as novel species (M. gnaphalii 23e(T) and M. oxalidis 35a(T), respectively). Bar: 0.01 substitutions per nucleotide position.