Figure 1.
Genome binning of the dominant population with a plot of assembly contigs (based on coverage versus GC ratio).
The circles represent the contigs with the size of the square root of their length. Clusters of contigs with similar color present potential genome bins, and contigs cluster with a coverage of approximately 80 (enclosed with black line) were collected for genome binning in this study.
Figure 2.
Phylogeny of phylotypes affiliated with the candidate phylum SBR1093.
This phylogenetic tree is constructed with 16S rRNA gene sequences based on the neighbor-joining method with Jukes and Cantor distances. The main clades with nodes supported by a bootstrap value of >50% are labeled and marked with different background colors (Clade I green, Clade II blue, Clade III yellow, Clade IV pink and Clade V purple). The phylotypes derived from different sources are labeled with the following: dark red, activated sludge; orange, soil; blue, sediments; dark green, ocean crust; pink, lava; purple, seawater; green, mine tailings; brown, marine organisms; black, others. The phylotype SRB1093 HKSP obtained in this study is enclosed with a solid red line, whereas the first reported phylotype is enclosed with a red dashed line. The scale bar represents 0.05 nucleotide substitutions per site.
Figure 3.
Putative metabolic pathway of SBR1093 HKSP (based on the genetic analysis).
Carbon fixation with the HPHB cycle is used for the biomass synthesis via the transfer of acetyl-CoA to the citrate cycle or gluconeogenesis, and the genes responsible for each step are marked with green words. Intermediates connected with colored lines represent different metabolic pathways.
Table 1.
Genes responsible for the HPHB cycle in the identified genomes and their identity with those in SBR1093.
Figure 4.
Phylogenetic tree of 4-hydroxybutyryl-CoA dehydratase proteins.
The 4-hydroxybutyryl-CoA dehydratases in this draft genome and others in identified autotrophic Achaea were retrieved from NCBI to build the phylogenetic tree. The hosts of these marked (in bold) are suspected autotrophic microbes that undergo the HPHB cycle. The number in front of the taxonomy presents the accession number in NCBI. The tree topography and evolutionary distances are given via the neighbor-joining method with a Poisson correction. The numbers at the nodes indicate the percentage bootstrap values for the clade of this group in 1,000 replications. The scale bar represents a difference of 0.1 substitutions per site.