Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal

Abstract

We present a metagenomic study of Lake Baikal (East Siberia). Twosamples 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 generatemetagenome-assembled genomes (MAGs) that are representative of the microbes liv-ing in this special environment. Compared with freshwater bodies studied around theworld, Lake Baikal had an unusually high fraction of Verrucomicrobia. Other groups, suchas Actinobacteria and Proteobacteria, were in proportions similar to those found in otherlakes. The genomes (and probably cells) tended to be small, presumably reflecting theextremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineagesrecruiting very little from other water bodies and are distantly related to other freshwa-ter microbes. Despite their novelty, they showed the closest relationship to genomesdiscovered by similar approaches from other freshwater lakes and reservoirs. Some ofthem were particularly similar to MAGs from the Baltic Sea, which, although it is brack-ish, connected to the ocean, and much more eutrophic, has similar climatological condi-tions. Many of the microbes contained rhodopsin genes, indicating that, in spite of thedecreased light penetration allowed by the thick ice/snow cover, photoheterotrophycould be widespread in the water column, either because enough light penetrates orbecause the microbes are already adapted to the summer ice-less conditions. We havefound a freshwater SAR11 subtype I/II representative showing striking synteny with Pe-lagibacter ubique strains, as well as a phage infecting the widespread freshwater bacte-rium Polynucleobacter.