Lake Baikal is the deepest lake in the world. Its depth provides the only bathypelagic (> 1000 m deep) freshwater habitat on Earth and its oxic, ultra-oligotrophic features make it a freshwater counterpart of the deep ocean. Here we have analyzed metagenomes from 1250 and 1350 m deep samples and built 231 metagenome-assembled genomes (MAGs). We detected high fractions of Thaumarchaeota (ca. 20% of 16S rRNA reads) and members of the candidate phyla radiation (CPR) (3-4.5%). Among the MAGs, we obtained ammonia-oxidizing archaea (AOA, Nitrosopumilaceae) and bacteria (AOB, Nitrosomonadaceae), and nitrite-oxidizers (Nitrospirae) indicating very active nitrification. A new clade of freshwater SAR202 Chloroflexi and methanotrophs (Methyloglobulus) were also remarkably abundant, the latter reflecting a possible role of methane oxidation as well. Novel species of streamlined and cosmopolitan bacteria such as Ca. Fonsibacter or acI Actinobacteria were more abundant at the surface but also present in deep waters. Conversely, CPRs, Myxococcales, Chloroflexi, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) archaea, or Gammaproteobacteria were found only in bathypelagic samples. We noted various important taxonomic and metabolic differences between deep aphotic region of Lake Baikal and marine waters of similar depth: Betaproteobacteriales, CPR, and DPANN superphylum were only found in bathypelagic Baikal, while Deltaproteobacteria, Gammaproteobacteria, or Alphaproteobacteria prevailed in oceanic samples. The genes mediating ammonia and methane oxidation, aromatic compound degradation, or alkane/methanesulfonate monooxygenases were detected in higher numbers in deep Baikal compared to their oceanic counterparts or its own surface. Overall, depth seems to be less relevant than salinity in configuring the microbial community.

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.

Background Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. Results Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. Conclusions These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance.