A novel and diverse group of Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

Abstract We have applied a long-read (PacBio CCS) metagenomic approach to analyze in depth the Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m. In addition to large (some complete) metagenome-assembled genomes, we have retrieved strong evidence of the presence of a novel and a likely endemic group of Patescibacteria inhabiting the bathypelagic realm. This novel group seems to possess extremely high intra-clade diversity akin to what happens with Patescibacteria at large but this takes place in an environment that has changed little in the last 25 million years. The enormous diversity detected within this group precludes assembly of complete genomes, albeit read binning and scaffolding indicate that they are similar to other Patescibacteria (i.e. parasites or symbionts) but they can synthesize most amino acids, likely reflecting the extremely oligotrophic habitat they inhabit. They have not been found anywhere else but one of the groups appears in small amounts in an oligotrophic alpine Lake Thun metagenome. We propose this novel group as Ca. Baikalibacteria. The recovery of MAGs via long-read metagenomics plus the use of long-read binning to uncover highly diverse “hidden” groups of prokaryotes are key strategies to move forward in ecogenomic microbiology.