Nakagawa et al. 10.1073/pnas.0700687104.

Supporting Information

Files in this Data Supplement:

SI Figure 5
SI Figure 6
SI Figure 7
SI Table 2
SI Figure 8
SI Table 3
SI Figure 9
SI Figure 10
SI Figure 11




SI Figure 5

Fig. 5. A 30-m tall sulfide mound in the Iheya North field (27°47' N 126° 53' E; water depth, 1,000 m) as an example of hydrothermal habitats where deep-sea vent e-Proteobacteria are dominantly detected.





SI Figure 6

Fig. 6. Circular diagrams of the Sulfurovum sp. NBC37-1 genome (A) and Nitratiruptor sp. SB155-2 genome (B). Locations of genomic islands shown in SI Fig. 9 and flagellar genes are shown outside circles. Outer circle, GC content; second and third circles, predicted coding regions on the plus and minus strands, respectively; fourth and fifth circles, RNA genes on the plus and minus strands, respectively. GC content was calculated by using a sliding window of 5 kb in steps of 2.5 kb. The color of predicted ORFs is based on COG functional categories.





SI Figure 7

Fig. 7. The sox gene clusters of representative sulfur oxidizers. Genes coding for homologous proteins are shown in the same colors. Sequences were retrieved from EMBL/GenBank.





SI Figure 8

Fig. 8. Negatively stained cells of Sulfurovum sp. NBC37-1 (A) and Nitratiruptor sp. SB155-2 (B). Cells were viewed with a transmission electron microscopy (JEM-1210 apparatus; JEOL).





SI Figure 9

Fig. 9. Genomic islands identified in the Sulfurovum sp. NBC37-1 genome (A) and Nitratiruptor sp. SB155-2 genome (B). The genomic islands were identified based on dinucleotide bias, codon bias, and GC content in addition to GC skew. DR, direct repeat; IR, inverted repeat; FtsZ, cell division protein FtsZ; TraD, TraI, and TraJ, conjugal transfer proteins.





SI Figure 10

Fig. 10. Phylogenetic tree based on amino acid sequences of PglB/Stt3. The scale bar represents the number of changes per position. Bootstrap values are based on 100 replicates.





SI Figure 11

Fig. 11. Relationships of various hydrogenases based on amino acid sequences of the small subunits. The GenBank/EMBL/DDBJ accession numbers or genomic IDs are shown in parentheses. The scale bar represents the number of changes per position. Hydrogenases of e-Proteobacteria are indicated as follows: red, deep-sea vent e-Proteobacteria; blue, other e-Proteobacteria.