Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal

Abstract

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.

Keywords: Lake Baikal; aerobic anoxygenic phototrophs; epilithon; neuston; plankton; pufM; rhodopsin; rhodopsin-containing bacteria.

Figure 1

Sampling stations. BK—sampling station off the Bol’shiye Koty settlement; G—sampling station off the Bol’shoye Goloustnoye settlement.

Figure 2

Similarities and differences between epilithon (G51, BK51, BK53), neuston (BK1, G1), and plankton (BK2, BK4, G2, G4) of Lake Baikal. Heatmap of 25 most represented OTUs_0.03 of 16S rRNA gene, UPGMA dendrogram and phylogenetic tree (A) and NMDS plot (B) based on the Bray-Curtis similarity matrix. Blue lines highlight water cluster of samples; green lines highlight epilithic biofilms cluster of samples. BK—samples taken off the Bol’shiye Koty settlement; G—samples taken off the Bol’shoye Goloustnoye settlement.

Figure 3

Taxonomic identification of 16S rRNA bacterial reads of epilithon (G51, BK51, BK53), neuston (BK1, G1), and plankton (BK2, BK4, G2, G4) of Lake Baikal at the class level.

Figure 4

Similarities and differences between AAPs of epilithon (G51, G52, BK51, BK53), neuston (BK1, G1), and plankton (BK2, BK4, G2, G4) of Lake Baikal. Heatmap of 25 most represented ESVs of pufM gene, UPGMA dendrogram and phylogenetic tree (A) and NMDS plot (B) based on the Bray-Curtis similarity matrix. Blue lines highlight water cluster of samples; green lines highlight epilithic biofilms cluster of samples. BK—samples taken off the Bol’shiye Koty settlement; G—samples taken off the Bol’shoye Goloustnoye settlement.

Figure 5

Taxonomic identification of pufM gene reads of epilithon (G5.1, G5.2, BK5.1, BK5.3), neuston (BK1, G1), and plankton (BK2, BK4, G2, G4) of Lake Baikal at the order level. BK—samples taken off the Bol’shiye Koty settlement; G—samples taken off the Bol’shoye Goloustnoye settlement.

Figure 6

Similarities and differences between epilithon (G51, G52, BK51, BK53), neuston (BK1, G1), and plankton (BK2, BK4, G2, G4) of Lake Baikal. Heatmap of the 25 most represented ESVs of rhodopsin gene, UPGMA dendrogram and phylogenetic tree (A) and NMDS plot (B) based on the Bray-Curtis similarity matrix. Red lines highlight water cluster of samples; green lines highlight epilithic biofilms cluster of samples. BK—samples taken off the Bol’shiye Koty settlement; G—samples taken off the Bol’shoye Goloustnoye settlement.

Figure 7

Taxonomic identification of rhodopsin gene reads of epilithon (G51, G52, BK51, BK53), neuston (BK1, G1), and plankton (BK2, BK4, G2, G4) of Lake Baikal at the phylum level. BK—samples taken off the Bol’shiye Koty settlement; G—samples taken off the Bol’shoye Goloustnoye settlement.

Figure 8

Maximum-Likelihood tree of 16S rRNA gene alignment with the closest homologues for the most abundant and potentially phototrophic OTUs. Circles and triangles are representing biotope type and colors are showing presence (blue and red) or absence (black) of the functional gene in reference organism (similarity 99–100%). The size of the circle/triangle corresponds to the number of sequences belonging to the OTU in the epilithic biofilm/water microbial communities, respectively.