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, 8 (4), e59977

The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal

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The Structure of Microbial Community and Degradation of Diatoms in the Deep Near-Bottom Layer of Lake Baikal

Yulia R Zakharova et al. PLoS One.

Abstract

Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Microorganisms associated with the diatom Synedra acus in the near-bottom water layer of Lake Baikal.
(indicated by arrows). Epifluorescent microscopy, DAPI staining. Scale bar 50 µm.
Figure 2
Figure 2. Vertical distribution of microorganisms in bottom sediments of Lake Baikal.
(1) Number of diatom-associated bacteria, (2) total number of microorganisms.
Figure 3
Figure 3. Changes in the degree of preservation of diatom frustules in different layers of Lake Baikal bottom sediments.
(A, B) 0–1 cm. (C, D) 2–3 cm. (E, F) 6–7 cm. Scale bars: (A, C, E) 100 µm; (B, D, F) 10 µm.
Figure 4
Figure 4. Bacterial diversity in the near-bottom water layer of Lake Baikal, as characterized by rarefaction curves of OTUs defined at genetic distance levels of 0.01, 0.03, 0.05, and 0.07.
Figure 5
Figure 5. The structure of bacterial community in the near-bottom water layer of Lake Baikal.
Every taxonomic group presented in the dendrogram accounted for no less than 1% of the total number of sequence reads, with the width of branches being proportional to the number of identified reads. Values at the nodes show the number of OTU0.03 for a given taxon. The diagram at the bottom shows the proportions of OTU0.03 assigned to taxa of different ranks.
Figure 6
Figure 6. Bacterial isolates associated with the laboratory culture of S. acus.
A. johnsonii BW65UT1570 (A, F), M. adhaesivum BW66UT1570 (B), A. tumefaciens BW62UT1570 (D). The degradated siliceous frustules of diatom S. acus in cocultures with B. simplex BW64UT1570 (C), A. johnsonii BW65UT1570 (E). Axenic culture S. acus (G). Epifluorescent microscopy, DAPI staining (A, B); scanning electron microscopy (D, E, F, G). Scale bar: A, B and G, 50 µm; C, 40 µm; D, 10 µm; E, F, 5 µm.

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Grant support

This study was supported by the Russian Foundation for Basic Research (project no. 09-04-12231ofi-m) and by the Integration Project of the Siberian Branch of the Russian Academy of Sciences, no. 137 “Development of new approaches to process data generated by Next-generation sequencing machines.” The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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