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

Background Lake Baikal, the world's deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth the Ca. Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m. Results The retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group of Ca. Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to other Ca. Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria. Conclusion The recovery of 16S rRNA genes 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. The novel group possesses enormous intraclade diversity akin to what happens with Ca. Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million yearsFunding: This work was supported by grants “VIREVO” CGL2016-76273-P [AEI/FEDER, EU], and “FLEX3GEN” PID2020-118052 GB-I00 (cofounded with FEDER funds) from the Spanish Ministerio de Economia, Industria y Competitividad, and “HIDRAS3” PROMETEU/2019/009 from Generalitat Valenciana to FR-V. JMH-M was supported with a PhD fellowship from Margarita Salas program, cofounded by the Spanish Ministerio de Universidades and the European Union–Next Generation EU (2021/PER/00020). PJC-Y was supported by a Post-Doctoral Fellowship from Generalitat Valenciana (APOSTD/2019/009). TZ and AZ were supported by grant RSF 22-14-00084 from the Russian Academy of Sciences. The contribution of the crew and technicians of the RV Vereshchagin of the Irkutsk Limnological Institute is gratefully acknowledged