We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Other groups, such as and , were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with strains, as well as a phage infecting the widespread freshwater bacterium Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine-like (subtype I/II) genome.

The composition of bacterial communities in Lake Baikal in different hydrological periods and at different depths (down to 1515 m) has been analyzed using pyrosequencing of the 16S rRNA gene V3 variable region. Most of the resulting 34 562 reads of the Bacteria domain have clustered into 1693 operational taxonomic units (OTUs) classified with the phyla Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, Acidobacteria and Cyanobacteria. It has been found that their composition at the family level and relative contributions to bacterial communities distributed over the water column vary depending on hydrological period. The number of OTUs and the parameters of taxonomic richness (ACE, Chao1 indices) and diversity (Shannon and inverse Simpson index) reach the highest values in water layers. The composition of bacterial communities in these layers remains relatively constant, whereas that in surface layers differs between hydrological seasons. The dynamics of physicochemical conditions over the water column and their relative constancy in deep layers are decisive factors in shaping the pattern of bacterial communities in Lake Baikal.

We investigated upwelling events in the pelagic area of Lake Baikal that developed during summer stratification (July-November) using a combination of in situ and satellite observations. These upwellings appear in the centres of local cyclonic macrovortices with compensatory downwelling located on their periphery in coastal areas. The average duration of upwelling events was 5 weeks, with an observed maximum of 16 weeks. The most stable upwellings in Southern Baikal and over the Academician Ridge covered areas of up to 4,400 km 2 (59 % of Southern Baikal's surface) and 1,550 km 2 , respectively. Water was ascending in the upwelling zones at velocities of 1 9 10 -4 to 1.2 9 10 -2 cm s -1 . Temperature differences of 1-4°C and 2-13°C were observed between the downwelling and upwelling zones in the epilimnion and metalimnion, respectively. On the surface of the lake, water temperature can drop 4-7°C for water ascending from depths of 10-75 m, but the observed thickness of the layer within which water was ascending reached a depth of 280 m in August-September and 380 m in October; i.e. the ascending water included the entire upper layer (0-300 m). Geostrophic currents reached up to 24-38 cm s -1 on the boundary between up-and downwelling zones (usually 5-7 km offshore), but did not exceed 6-10 cm s -1 in the centres of upwelling zones.Comparison with other large lakes of the world is carried. This study is important for understanding the upwelling process that develops in Lake Baikal during summer stratification and can influence the heterogeneity of nutrients and primary production.