Saccharimonadia in the Plankton of Ancient Lakes (Baikal and Hovsgol)

Saccharimonadia were analyzed in Lakes Baikal and Hovsgol using metagenomic sequencing approaches. Twenty-two metagenome-assembled genomes (MAGs) were reconstructed, including 20 from Lake Baikal and 2 from Lake Hovsgol. The two Hovsgol MAGs formed distinct phylogenetic branches: one grouped with a Baikal ubiquitous/surface-associated lineage, while the other clustered with a Baikal MAG lacking depth-stratified data. In contrast, a monophyletic, deep-water clade was identified in Lake Baikal and showed no close genomic relatives outside the lake. Genes involved in DNA repair, defense mechanisms, and host interaction were enriched in deep MAGs, whereas surface-associated MAGs carried higher abundances of genes related to phage interactions, amino acid metabolism, protein synthesis, cell division, and cell wall biosynthesis.