Phylogenetic trees

Fig. S1. Phylogenetic tree of the taxa used for comparative genomics analysis, including the 15 uncultured MAST species, using the 18S rDNA gene. The tree was generated with IQTREE using 1000 trees for topology and 1000 trees for bootstrapping. Five non-stramenopile taxa were used as outgroup. Eukaryotic species were assigned to a trophic lifestyle.

Fig. 5. Phylogenetic tree of microbial type I rhodopsins based on 207 protein sequences, including the new MASTs, showing the recognized groups and their prevalent function. Black dots indicate bootstrap support >80% over 1000 replicates. Stars highlight sequences recovered from co-assemblies.

Fig. S6. Phylogenetic tree of V-ATPases and the related F-ATPases genes constructed from recent bibliographical references (see Material and Methods). MASTs lineages are represented in orange. Values at nodes correspond to bootstraps > 80%.

Fig. S7. Phylogenetic tree of V-PPases genes constructed from recent bibliographical references (see Material and Methods). MASTs lineages are represented in orange. Values at nodes correspond to bootstraps > 80%.