Table 2.
Comparison of genomic features among Ca. Sedimenticola endophacoides, free-living Sedimenticola spp. (Flood et al. 2015; Louie et al. 2016), and bacterial symbionts, including the lucinid thioautotrophic symbiont clade A (Petersen et al. 2016; Konig et al. 2016), a vesicomyid clam gill symbiont (Ca. Ruthia Magnifica; Roeselers et al. 2010), a solemyid clam gill symbiont (Dmytrenko et al. 2014), bathymodiolin mussel gill symbionts (Bathymodiolus septemdierum and Bathymodiolus thermophilus; Ikuta et al. 2016; Ponnudurai et al. 2017), deep-sea tubeworm trophosomal symbionts (Ridgeia piscesae, Riftia pachyptila and Tevnia jerichonana; Gardebrecht et al. 2012; Perez and Juniper 2016), a marine nematode ectosymbiont (Ca. Thiosymbion oneisti; Petersen et al. 2016), and a deep-sea scaly-foot snail esophageal gland symbiont (Nakagawa et al. 2014).
| Function | Ca. Sedimenticola endophacoides | S. thio-taurini | S. selenati-reducens | Ca. Thio-diazotropha endoloripes | Ca. Thio-diazotropha endolucinida | Ca. Ruthia magnifica | Solemya velum symbiont | Bathymodiolus spp. symbionts | Deep-sea tubeworm symbionts | Ca. Thiosymbion oneisti | Crysomallon squamiferum symbiont |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Sulfur oxidation | Sqr type VI | Sqr types I and VI | Sqr types I, III and VI | Sqr type I | Sqr type I | Sqr types I and VI | Sqr type I | ||||
| Hydrogen oxidation | Groups 1 and 2b (NAD-dependent) Ni-Fe hydrogenase | Groups 1 and 2a Ni-Fe hydrogenase | − |
Groups 1 and 2b (NAD-dependent) Ni-Fe hydrogenase |
Groups 1 and 2a Ni-Fe hydrogenase | − | Groups 1 and 2a Ni-Fe hydrogenase | ||||
| Carbon fixation | RuBisCo II | RuBisCO Iaq and II | RuBisCo Iaq | RuBisCo Iaq and II | RuBisCO II | RuBisCO Iaq | RuBisCO Iaq | RuBisCO II | RuBisCO Iaq | RuBisCO Iaq and II | |
| Nitrogen fixation | − | + | − | + | + | − | − | − | − | + | − |
| Assimilatory nitrate and nitrite reduction | − | − | − | + | − | − | − | + | + | + | + |
| Urea hydrolysis | + | + | − | + | − | − | + | − | − | + | − |
| Oxygen respiration | cbb3 type terminal oxidase | cbb3, aa3 and cytochrome d ubiquinol oxidases | cbb3 and aa3 type terminal oxidases | cbb3, aa3 and cytochrome d ubiquinol oxidases | |||||||
‘+’ denotes a feature annotated in a genome while ‘−’ denotes a feature not yet sequenced in a genome
Sqr sulfide:quinone oxidoreductase, RuBisCO ribulose-1,5-bisphosphate carboxylase/oxygenase