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Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow.

Lopatina A, Medvedeva S, Shmakov S, Logacheva MD, Krylenkov V, Severinov K - Front Microbiol (2016)

Bottom Line: Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database.The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world.The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia.

ABSTRACT
The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

No MeSH data available.


Genus-level bacterial diversity in Antarctic snow samples based on PCR amplicon library. (A) Frequencies of reads corresponding to 20 most abundant genera present in all four samples are shown. For each genus, the height of color-coded bars reflects the percentage of corresponding reads in the entire sample from each station. (B) A heatmap comparing genus-level bacterial diversity and abundance for 255 genera detected in Antarctic snow samples. The colors show the extent of relatedness between the samples from each station as indicated in the legend.
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Figure 3: Genus-level bacterial diversity in Antarctic snow samples based on PCR amplicon library. (A) Frequencies of reads corresponding to 20 most abundant genera present in all four samples are shown. For each genus, the height of color-coded bars reflects the percentage of corresponding reads in the entire sample from each station. (B) A heatmap comparing genus-level bacterial diversity and abundance for 255 genera detected in Antarctic snow samples. The colors show the extent of relatedness between the samples from each station as indicated in the legend.

Mentions: Deeper taxonomic affiliation analysis at each site was next performed. 28, 20, 14, and 35% of 16S rRNA gene reads from, correspondingly, Druzhnaja, Progress, Mirnii, and Leningradskaja could not be affiliated to any known genus by the RDP tool. Results of the analysis of remaining reads are shown in Figure 3A, where abundances of 20 most prevalent genera are presented. The genus detected in the most abundance in any given sample was Flavobacterium, which comprised 39% of the sequences in the Progress library, followed by Hydrogenophaga (14%) and Ralstonia (7%). In the Druzhnaja sample, 16S rRNA genes from Janthinobacterium were dominant (27%), followed by Ralstonia (15%), and Pseudomonas (11%). In the Leningradskaja sample, 16S rRNA genes from Caulobacter (12%), Acinetobacter (10%), and Comamonas (9%) were most abundant. These genera were also the most abundant during clone library analysis (Lopatina et al., 2013) and in fact the abundance of genera in Druzhnaja and Leningradskaja stations, as revealed by cloning library and HTS approaches, was highly correlated (Pearson correlation coefficient of 0.8 and 0.9, respectively, data not shown). In Mirnii—rRNA gene sequences of Ralstonia (31%), Bacilariophyta (chloropast-containing diatoms) (24%), and Rudaea (8%) were the most dominant. There was no correlation of genera abundance or presence between samples from the four different stations: the Pearson correlation coefficient varied from 0.1 for Progress and Leningradskaja to 0.4 between Mirnii and Druzhnaja (Figure 3B).


Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow.

Lopatina A, Medvedeva S, Shmakov S, Logacheva MD, Krylenkov V, Severinov K - Front Microbiol (2016)

Genus-level bacterial diversity in Antarctic snow samples based on PCR amplicon library. (A) Frequencies of reads corresponding to 20 most abundant genera present in all four samples are shown. For each genus, the height of color-coded bars reflects the percentage of corresponding reads in the entire sample from each station. (B) A heatmap comparing genus-level bacterial diversity and abundance for 255 genera detected in Antarctic snow samples. The colors show the extent of relatedness between the samples from each station as indicated in the legend.
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Related In: Results  -  Collection

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Figure 3: Genus-level bacterial diversity in Antarctic snow samples based on PCR amplicon library. (A) Frequencies of reads corresponding to 20 most abundant genera present in all four samples are shown. For each genus, the height of color-coded bars reflects the percentage of corresponding reads in the entire sample from each station. (B) A heatmap comparing genus-level bacterial diversity and abundance for 255 genera detected in Antarctic snow samples. The colors show the extent of relatedness between the samples from each station as indicated in the legend.
Mentions: Deeper taxonomic affiliation analysis at each site was next performed. 28, 20, 14, and 35% of 16S rRNA gene reads from, correspondingly, Druzhnaja, Progress, Mirnii, and Leningradskaja could not be affiliated to any known genus by the RDP tool. Results of the analysis of remaining reads are shown in Figure 3A, where abundances of 20 most prevalent genera are presented. The genus detected in the most abundance in any given sample was Flavobacterium, which comprised 39% of the sequences in the Progress library, followed by Hydrogenophaga (14%) and Ralstonia (7%). In the Druzhnaja sample, 16S rRNA genes from Janthinobacterium were dominant (27%), followed by Ralstonia (15%), and Pseudomonas (11%). In the Leningradskaja sample, 16S rRNA genes from Caulobacter (12%), Acinetobacter (10%), and Comamonas (9%) were most abundant. These genera were also the most abundant during clone library analysis (Lopatina et al., 2013) and in fact the abundance of genera in Druzhnaja and Leningradskaja stations, as revealed by cloning library and HTS approaches, was highly correlated (Pearson correlation coefficient of 0.8 and 0.9, respectively, data not shown). In Mirnii—rRNA gene sequences of Ralstonia (31%), Bacilariophyta (chloropast-containing diatoms) (24%), and Rudaea (8%) were the most dominant. There was no correlation of genera abundance or presence between samples from the four different stations: the Pearson correlation coefficient varied from 0.1 for Progress and Leningradskaja to 0.4 between Mirnii and Druzhnaja (Figure 3B).

Bottom Line: Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database.The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world.The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia.

ABSTRACT
The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

No MeSH data available.