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

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.

Diatom-Derived Polyunsaturated Aldehydes Are Unlikely to Influence the Microbiota Composition of Laboratory-Cultured Diatoms

“…It would be interesting to repeat this work with a higher spin speed to get a more comprehensive view of community dynamics. The microbial communities-dominated by the Proteobacteria, Bacteriodetes, Gammaproteobacteria and Escherichia/Shigella, also found in previous studies [24,58,61,62]-did change with growth phase and in response to PUA spiking, albeit at a relatively subtle level. Curiously, despite different Skeletonema species, including S. marinoi, having antimicrobial capacities [63][64][65], the strains of S. marinoi used had little to no effect on the microbiota, nor did the nitrate treatments.…”

Microbial dynamics during harmful dinoflagellate Ostreopsis cf. ovata growth: Bacterial succession and viral abundance pattern

“…cf. ovata bloom, however, Ilumatobacter phylotypes were the main representatives of Actinobacteria at maintenance/decline phase (Vanucci, Guidi, et al., ), as found in diatoms degradation processes (Bagatini et al., ; Zakharova et al., ). This finding suggests a more intimate relationship between Ilumatobacter and diatoms co‐occurring at the bloom rather than with O .…”

Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

“…At depths of more than 1000 m, a slight decrease in the content and flow rates of total organic carbon and nitrogen (Vologina and Sturm 2017) was observed. The study of microbial communities in Lake Baikal with molecular techniques and sequencing has been mostly focused on their diversity and structure in the trophogenic layer (Zakharova et al 2013;Mikhailov et al 2015) and surface subice waters (Bashenkhaeva et al 2015;Cabello-Yeves et al 2018). Other studies from the summer period showed that bacterial communities in deep-water samples (700 and 1400 m) were mainly represented by Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi (Glöckner et al 2000;Bel'kova et al 2003;Parfenova et al 2006;Zakharova et al 2013;Kurilkina et al 2016).…”

“…The study of microbial communities in Lake Baikal with molecular techniques and sequencing has been mostly focused on their diversity and structure in the trophogenic layer (Zakharova et al 2013;Mikhailov et al 2015) and surface subice waters (Bashenkhaeva et al 2015;Cabello-Yeves et al 2018). Other studies from the summer period showed that bacterial communities in deep-water samples (700 and 1400 m) were mainly represented by Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi (Glöckner et al 2000;Bel'kova et al 2003;Parfenova et al 2006;Zakharova et al 2013;Kurilkina et al 2016). The dynamics of physicochemical conditions throughout the water column and their relative stability in the deep layers appeared to be decisive factors that shape the pattern of bacterial communities in Lake Baikal (Kurilkina et al 2016).…”