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We analysed the relationship between the chemical complex (concentration of dissolved ions, nutrients, pH) and biological parameters (primary production, biomass of phytoplankton, abundance and activity of bacterial communities) at estuaries of rivers and coastal waters of Southern Baikal during the under-ice period. Correlation network analysis revealed CO2 to be the main limiting factor for the development of algae and microbial communities in the coastal zone of Lake Baikal. This study indicates that primarily reverse synthesis of bicarbonate and carbonate ions associated with the development of phytoplankton and accumulation of dissolved CO2 during photosynthesis regulates pH in the Baikal water. We did not detect the anthropogenic factors that influence the change in pH and acidification. Near the Listvyanka settlement (Lake Baikal, Listvennichnaya Bay), there was a great number of organotrophs and thermotolerant bacteria with low bacterioplankton activity and high concentration of organic carbon. This evidences eutrophication due to the influx of organic matter having an anthropogenic source. Nutrients produced during the bacterial destruction of this matter may explain the changes in bottom phytocenoses of Listvennichnaya Bay. [ABSTRACT FROM AUTHOR]

Microbiological and biogeochemical investigation of the water column of oligotrophic Lake Baikal at the sites of the K2 and Bolshoi mud volcanoes and the Gorevoy Utes oil seep was carried out in July 2013. Total microbial numbers (TMN), cell numbers of type I and type II methanotrophs, and methane concentrations were measured; the rate of methane oxidation was determined. Methane concentrations in Lake Baikal water column varied from 0.09 to 1 μL/L, while methane oxidation rates varied from 0.007 to 0.9 nL/(L day). The highest rates of methane oxidation were revealed in the near-bottom water horizons at the sites of the Bolshoy mud volcano and the Gorevoy Utes oil seep. These were the sites where the most pronounced anomalies in methane concentration were also detected. TMN varied from 0.123 × 10 to 1.64 × 10 cells/mL. Methanotrophic bacteria were revealed in the water column at all sites, their abundance did not always correlate with methane concentrations and the rates of methane oxidation. Methanotrophs constituted not more than 1.63% of the total microbial number, with their highest abundance in the upper 200 m of the water column. [ABSTRACT FROM AUTHOR]

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 Verrucomicrobia. Other groups, such as Actinobacteria and Proteobacteria, 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 Pelagibacter ubique strains, as well as a phage infecting the widespread freshwater bacterium Polynucleobacter IMPORTANCE 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 Pelagibacter-like (subtype I/II) genome. [ABSTRACT FROM AUTHOR]