Table 1.
Features of Thermus aquaticus Y51MC23.
Fig 1.
Molecular phylogenetic analysis of Thermus species by maximum likelihood method using 16S rRNA gene sequences.
The tree with the highest log likelihood (-3496.7463) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches.
Fig 2.
Features of the Thermus aquaticus Y51MC23 chromosome and plasmids.
Tracks from outside to inside: CDs forward strand, CDs reverse strand, tRNA genes, rRNA genes, prophage, CRISPRs, GC plot, and GC skew. Prepared using DNA Plotter software [46].
Fig 3.
Identification of four Thermus aquaticus Y51MC23 plasmids by PFGE.
Genomic DNA extracts showed a distinct pulsed field gel electrophoresis banding pattern whose sizes closely match 4 contigs with specific coverage depths that do not map to the primary chromosomal contig. The sizes of these bands (arrows) match actual contig lengths from the finished genome assembly (14.4, 16.6, 69.9, and 78.7 kb respectively), suggesting that the material in the bands is of linear form. The native form of these putative plasmids is presumed to be circular.
Table 2.
Thermus aquaticus Y51MC23 genome summary.
Table 3.
Comparison of RAST annotations of Thermus chromosomes.
Fig 4.
Synteny plot of the closed and finished T. aquaticus Y51MC23 genome versus T. scotoductus SA-01.
Table 4.
Predicted Transporter systems present in the T. aquaticus Y51MC23 genome.
Fig 5.
Diagram of Y51MC23 prophage 1 and 2 versus Thermus sp. 2.9 prophage synteny.
Annotated ORFs are shown as block arrows for Thermus aquaticus prophage 1 (top), prophage 2 (center), and Thermus sp. 2.9 (bottom). Gold indicates hypothetical ORFs; Green indicates ORFs shared between all three prophage; magenta indicates ORFs specific to prophage 1; blue indicates ORFs shared between prophage 2 and TSP2.9 prophage; orange indicates regions that differ between prophage 2 and TSP2.9 prophage. The 3,652 bp region of nucleic acid identity between prophage 1 and 2 is indicated in brick-red color. Amino acid identity between pairs of encoded proteins are indicated in small circles as determined by blastp.
Table 5.
CRISPR elements found in T. aquaticus Y51MC23.
Fig 6.
Micrograph of Thermus aquaticus Y51MC23 cells from aerobic cultures.
Culture samples were stained with SYTO® 9 fluorescent stain in sterile water (Molecular Probes). Dark field fluorescence microscopy was performed using a Nikon Eclipse TE2000-S epifluorescence microscope at 2000× magnification and a high-pressure Hg light source.
Fig 7.
Micrograph of Thermus aquaticus Y51MC23 from anaerobic cultures.
Culture sample was stained with SYTO® 9 fluorescent stain in sterile water (Molecular Probes). Dark field fluorescence microscopy was performed using a Nikon Eclipse TE2000-S epifluorescence microscope at 200X magnification (left) or 2000X magnification (right) and a high-pressure Hg light source (484 nm excitation and 500 nm emission filters).
Fig 8.
Micrograph of Thermus aquaticus Y51MC23 round body found in anaerobic cultures.
Clockwise from left to right, views through a single large round body. Culture samples were stained with SYTO® 9 fluorescent stain in sterile water (Molecular Probes).
Fig 9.
Micrograph of Thermus aquaticus Y51MC23 layered structure in anaerobic culture.
Clumps of cells were re-suspended in sterile water and stained with SYTO® 9 (green fluroescence) using 484 nm excitation and 500 nm emission filters (left panel) or propidium iodide (red fluorescence) using 536 nm excitation and 617 nm emission filters (right panel). Dark field fluorescence microscopy was performed using a Nikon Eclipse TE2000-S epifluorescence microscope at 2000X magnification and a high-pressure Hg light source.
Fig 10.
Formation of highly fluorescent spheres in Y51MC23 culture.
Clockwise from top left. 1. Schematic of proposed mechanism of sphere formation. 2. Elongated cell (A) and swollen regions (B, C). 3. Highly fluorescent spheres (D). Culture samples were stained with SYTO® 9 fluorescent stain in sterile water (Molecular Probes).
Fig 11.
Peptidoglycan staining of Y51MC23 culture.
Clumps of cells were re-suspended in sterile water and stained with SYTOX Green (green fluroescence) using 484 nm excitation and 500 nm emission filters (right panel) or Texas Red-X dye–labeled WGA (red fluorescence) using 536 nm excitation and 617 nm emission filters (left panel). Dark field fluorescence microscopy was performed using a Nikon Eclipse TE2000-S epifluorescence microscope at 2000X magnification and a high-pressure Hg light source.