Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal


We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near–bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.

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The authors gratefully acknowledge Irkutsk Supercomputer Center of SB RAS for providing the access to HPC-cluster «Akademik V.M. Matrosov». We also thank to Ivan Sidorov, system administrator of HPC-cluster, for help in performing computations.


The work was supported by the State Task for Limnological Institute SB RAS No. 0345–2016–0007, the ofi-m RFBR grant No 17-29-05040 and mol-a RFBR grant No 18-34-00442.

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Correspondence to Aleksandra S. Zakharenko.

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Fig. S1

Rarefaction curves (PNG 265 kb)

Fig. S2

Phylogenetic tree of the phylum Cyanobacteria based on the analysis of nucleotide sequences of the V2–V3 regions of the 16S rRNA gene obtained from the total DNA of water column of Lake Baikal. The tree was constructed using the neighbor-joining (NJ) method. Bootstrap analysis provided probability assessment of individual nodes; the values above 60% are shown. The scale is 0.01 (PNG 173 kb)

Fig. S3

Phylogenetic tree of the phylum Verrucomicrobia based on the analysis of nucleotide sequences of the V2–V3 regions of the 16S rRNA gene obtained from the total DNA of water column of Lake Baikal. The tree was constructed using the neighbor-joining (NJ) method. Bootstrap analysis provided probability assessment of individual nodes; the values above 60% are shown. The scale is 0.01 (PNG 1125 kb)

File S1

Reference taxonomy of pmoA sequence fragments (TAXONOMY 265 kb)

File S2

Reference alignment of pmoA sequence fragments (FNA 8691 kb)

High resolution image (TIF 759 kb)

High resolution image (TIF 636 kb)

High resolution image (TIF 3354 kb)

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Zakharenko, A.S., Galachyants, Y.P., Morozov, I.V. et al. Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal. Microb Ecol 78, 269–285 (2019).

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  • Water column
  • Diversity
  • Methanotrophic
  • Methylotrophic bacteria
  • Lake Baikal