TABLE 3.
Summary of key metabolic pathways in the genomesa
| Function | ES-1 | ES-2 | Gallionellaceae (KS-Tueb) | Gallionellaceae (KS-Mad) | Bradyrhizobium | Comamonadaceae | Rhizobium | Rhodanobacter |
|---|---|---|---|---|---|---|---|---|
| Carbon metabolism | ||||||||
| CBB reductive pentose phosphate cycle | + | + | + | + | + | − | + | + |
| Glycolysis (Embden-Meyerhof pathway) | + | + | + | + | + | + | + | + |
| Pyruvate oxidation to acetyl-CoA through pyruvate dehydrogenase | + | + | + | + | + | + | + | + |
| Citrate cycle (TCA cycle, Krebs cycle) | + | + | + | + | + | + | (+) | + |
| Pentose phosphate pathway | + | + | + | + | + | +/−b | (+) | + |
| Glyoxylate cycle | − | − | − | − | + | + | − | + |
| Nitrogen metabolism | ||||||||
| Nitrogen fixation, nitrogen → ammonia | + | − | − | − | − | − | − | − |
| Ammonification, nitrate/nitrite → ammonia | + | − | − | − | + | − | + | − |
| Nitrification, ammonia → nitrite | − | − | − | − | − | − | − | − |
| Denitrification | ||||||||
| Nitrate → nitrite | − | − | + | + | + | + | (+) | + |
| Nitrite → nitric oxide | + | − | + | + | + | + | + | (+) |
| Nitric oxide → nitrous oxide | + | + | − | − | + | + | (+) | + |
| Nitrous oxide → nitrogen gas | − | − | − | − | + | + | + | (+) |
| Complete denitrification | No | No | No | No | Yes | Yes | Yes | Yes |
| Hydrogen metabolism | ||||||||
| Group 1, uptake [NiFe]-hydrogenase | + | − | + | + | − | − | + | − |
| Group 3, bidirectional cytoplasmic [NiFe]-hydrogenase | + | + | + | + | + | − | − | − |
| Group 4, H2-evolving, energy-conserving [NiFe]-hydrogenases | + | + | + | + | + | − | + | + |
| Sulfur metabolism | ||||||||
| Assimilatory sulfate reduction | + | + | + | + | + | + | + | + |
| Dissimilatory sulfate reduction | + | − | − | − | − | − | − | − |
| Thiosulfate oxidation by SOX complex | + | − | − | − | + | + | + | − |
| Phosphorus metabolism | ||||||||
| Phosphonate transport system | − | + | − | − | + | − | + | + |
| Phosphonoacetate degradation | + | + | + | + | + | + | + | + |
| High-affinity phosphate transport system | + | + | + | + | + | + | + | + |
| Low-affinity phosphate transporters | + | + | − | − | + | + | − | + |
| Polyphosphate accumulation and degradation | + | + | + | + | + | + | (+) | + |
| Alkaline phosphatase | − | − | − | − | + | − | + | − |
| Oxidative phosphorylation | ||||||||
| Complex I, NADH:quinone oxidoreductase | + | + | + | + | + | + | + | + |
| Complex II, succinate dehydrogenase | + | + | + | + | + | + | + | + |
| Complex III, cytochrome bc1 complex | + | − | + | + | + | + | + | + |
| Alternative complex III (ACIII) | + | + | − | − | − | − | − | − |
| aa3-type cytochrome c oxidase | − | − | + | + | + | + | + | + |
| Cytochrome bd ubiquinol oxidase | + | + | − | − | − | − | + | + |
| cbb3-type cytochrome c oxidase | + | + | + | + | + | + | + | + |
| F-type ATPase | + | + | + | + | + | + | + | + |
| V-type ATPase | + | − | − | − | − | − | − | − |
a
+, a complete pathway is present; −, a pathway is absent; (+), the missing gene(s) in that pathway was found in the metagenome and can be assigned to that genome based on fold coverage and sequence homology.
b
+/−, the oxidative phase of the pentose phosphate pathway is present, but the nonoxidative phase is absent.