Fig 1.
Phylogeny of the Bacteroidota built with concatenated ribosomal proteins and labeled with clade names (classes, and orders within Bacteroidia) derived from GTDB-Tk.
The Chlorobia (formerly Chlorobi) are positioned as a class within the broader Bacteroidota phylum, and not as a separate phylum as previously thought.
Fig 2.
Phylogeny of the Chlorobia built with concatenated ribosomal proteins, with taxonomic assignments from GTDB-Tk and the presence of metabolic traits discussed in the text mapped on.
The presence of a Type 1 phototrophic reaction center is ubiquitous within the Chlorobia class, but other traits (such as the presence of a Cyc2 cytochrome protein associated with iron oxidation) have a more limited phylogenetic distribution and may be more derived traits that were acquired after the radiation of the phylum.
Fig 3.
Phylogenies of metabolic proteins discussed in the text; congruence of metabolic protein phylogenies with organismal phylogenies (e.g. those derived from concatenated ribosomal proteins such as in Fig 2) suggests vertical inheritance of traits from the last common ancestor, whereas incongruent topologies suggest a history of horizontal gene transfer of metabolic pathways.
A) Phylogeny of type 1 reaction centers, showing broad topological congruence with organismal relationships shown in Fig 2; together with the synapomorphic distribution of phototrophy in the Chlorobia, this suggests that phototrophy was acquired in stem group Chlorobia and has since been vertically inherited. B) Phylogeny of ATP citrate lyase, a key marker gene for the capacity for carbon fixation via the rTCA pathway. Phylogenetic relationships of this gene within the Chlorobia are congruent with organismal relationships, suggesting that this trait has been vertically inherited in most Chlorobi (with the exception of loss in aerobic members of the Chloroherpetonaceae). However, ATP citrate lyase in Chlorobi appears to be derived from genes of nitrite oxidizing bacteria (Nitrospirota and Nitrospinota), suggesting that this trait was acquired by Chlorobi via horizontal gene transfer after the radiation of nitrite oxidizers. C) Phylogeny of Cyc2 cytochrome proteins associated with iron oxidation in Chlorobi and Zetaproteobacteria. Cyc2 genes in the Chlorobi appear to be derived from those of Proteobacteria, suggesting that the capacity for iron oxidation was acquired by Chlorobi via horizontal gene transfer after the radiation of aerobic iron oxidizing bacteria.
Fig 4.
Best-estimate molecular clock estimate showing age of Chlorobi.
Node ages based on T03 constraints (omitting biomarkers) (Table 1, S1 Table, S3 and S4 Figs). The Bacteroidota phylum (highlighted in blue) is estimated to have radiated well after the Great Oxygenation Event ~2.3 Gya (vertical gray bar). Crown group Chlorobi (highlighted in light green) originated in Neoproterozoic time <1 Gya. All known photoferrotrophic Chlorobi are found in the Chlorobium genus (highlighted in dark green) which originated <300 Mya.
Table 1.
Molecular Clock estimates for key clades based on T03 constraints.