3 years ago

Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal.

Felipe H Coutinho, Pedro J Cabello-Yeves, Alexandra S Zakharenko, Tamara I Zemskaya, Francisco Rodriguez-Valera, Vadim V Blinov, Riccardo Rosselli
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 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 or Proteobacteria were in similar proportions as those found in other lakes. Genomes (and probably cells) tended to be of small size 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 Baltic Sea MAGs that, although 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, and 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 inverted temperature gradient (colder up) and decrease on 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 non-marine Pelagibacter-like (subtype I/II) genome.

Publisher URL: http://doi.org/10.1128/AEM.02132-17

DOI: 10.1128/AEM.02132-17

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