The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes. The diversity of rhodopsin-containing bacteria in neuston and plankton of Lake Baikal was comparable to other studied water bodies. Bacteroidetes along with Proteobacteria were the prevailing phyla, and Verrucomicrobia and Planctomycetes were also detected. The number of rhodopsin sequences unclassified to the phylum level was rather high: 29% in the water microbiomes and 22% in the epilithon. Diversity of rhodopsin-containing bacteria in epilithic biofilms was comparable with that in neuston and plankton at the phyla level. Unweighted pair group method with arithmetic mean (UPGMA) and non-metric multidimensional scaling (NMDS) analysis indicated a distinct discrepancy between epilithon and microbial communities of water (including neuston and plankton) in the 16S rRNA, pufM and rhodopsin genes.

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Using the metagenomics approach and high throughput sequencing of the 16S rRNA gene amplicons, we studied the taxonomic diversity of nitrifying bacteria in microbial communities from epilithic biofilms and plankton of the littoral zone of Lake Baikal. The family Nitrosomonadaceae represents the diversity of ammonia-oxidizing bacteria; the genera Nitrospira (Nitrospirae) and Candidatus Nitrotoga (Gammaproteobacteria)-nitrite-oxidizing bacteria; and the phyla Nitrospinaeunidentified bacteria. Microbial communities from epilithic biofilms and the near-bottom water layer showed the highest diversity and those from the surface water layer-the lowest one. Among ammonia oxidizers, bacteria of the uncultured genus Ellin6067 (27 phylotypes) dominated and were ubiquitous, and among nitrite oxidizers-bacteria of the genus Nitrospira (7 phylotypes).