TABLE 3.

Survey of biogeochemically relevant genes in three complete and nine draft Roseobacter genomesa

Genome or parameterResult for:
AAnP genescox genespcaGHboxCsoxBnirS/KnasAphn genesvir genesdmdA
Genomes
    Complete
        Silicibacter pomeroyi DSS-3+++++++
        Silicibacter sp. strain TM1040+++++
        Jannaschia sp. strain CCS1++++++
    Draft
        Sulfitobacter sp. strain EE-36+++++
        Sulfitobacter sp. strain NAS-14.1++++++
        Roseovarius nubinhibens ISM+++++
        Roseovarius sp. strain 217+++++++++
        Oceanicola batsensis HTCC2597++++
        Oceanicola granulosus HTCC2516+
        Rhodobacterales bacterium HTCC2654+++++++
        Loktanella vestfoldensis SKA53++++
        Roseobacter sp. strain MED193+++++++
Parameters
    % of Roseobacter genomes25928325582550925050
    Experimental evidence (reference)NDYes (43)Yes (5)NDYes (21)Yes (Fig. S7)bYes (Fig. S4)bYes (Fig. S5)bNDYes (24)
    Ortholog in P. ubique HTCC1062NoNoNoNoNoNoNoNoNoYes
  • a The nine draft Roseobacter genomes include those for aerobic anoxygenic phototrophy (AAnP genes), carbon monoxide oxidation (cox genes), aromatic compound degradation (pcaGH and boxC), sulfur oxidation (soxB), denitrification (nirS/K), nitrate assimilation (nasA), phosphonate use (phn genes), type IV secretion (vir genes), and DMSP demethylase (dmdA). + indicates the presence of a homolog with an E value of ≤10−40 and amino acid percent sequence identity of ≥40%. Phenotypes that have been demonstrated experimentally for a Roseobacter strain are indicated by “yes.” ND, not determined. The presence of an ortholog in the genome of SAR11 member P. ubique is indicated.

  • b See the supplemental material.