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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.


Principal component analysis of 30 metagenomes from five different environments based on frequencies of COG categories. A scatter plot of PCA-scores depicting variance of COG categories detected in different environmental metagenomes. In panel (A) COGs from Antarctic snow (cyan) are compared to temperate soil samples (red), sea water (green), and Antarctic microbial mat (orange). In panel (B) Arctic snow samples (violet) are included in comparison.
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Figure 4: Principal component analysis of 30 metagenomes from five different environments based on frequencies of COG categories. A scatter plot of PCA-scores depicting variance of COG categories detected in different environmental metagenomes. In panel (A) COGs from Antarctic snow (cyan) are compared to temperate soil samples (red), sea water (green), and Antarctic microbial mat (orange). In panel (B) Arctic snow samples (violet) are included in comparison.

Mentions: Recently, principal component analysis of the relative abundance of annotated reads of functional subsystems from Arctic surface snow metagenomes was presented and a conclusion was made that snow samples grouped together and were well-separated from other ecosystem metagenomes (Maccario et al., 2014). We repeated this analysis including our Antarctic snow metagenomes data. When Antarctic samples were substituted for Arctic samples used in the previous analysis, clear ecosystem clustering similar to the earlier reported result was obtained (Figure 4A), seemingly indicating commonalities of microbial communities of Antarctic snow. However, when Arctic snow metagenomic samples were also included, Antarctic samples became indistinguishable from soil and Antarctic microbial mat metagenomes; the free ocean water samples remained tightly clustered and separate, while the Arctic snow samples became very dispersed (Figure 4B).


Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow.

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

Principal component analysis of 30 metagenomes from five different environments based on frequencies of COG categories. A scatter plot of PCA-scores depicting variance of COG categories detected in different environmental metagenomes. In panel (A) COGs from Antarctic snow (cyan) are compared to temperate soil samples (red), sea water (green), and Antarctic microbial mat (orange). In panel (B) Arctic snow samples (violet) are included in comparison.
© Copyright Policy
Related In: Results  -  Collection

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Figure 4: Principal component analysis of 30 metagenomes from five different environments based on frequencies of COG categories. A scatter plot of PCA-scores depicting variance of COG categories detected in different environmental metagenomes. In panel (A) COGs from Antarctic snow (cyan) are compared to temperate soil samples (red), sea water (green), and Antarctic microbial mat (orange). In panel (B) Arctic snow samples (violet) are included in comparison.
Mentions: Recently, principal component analysis of the relative abundance of annotated reads of functional subsystems from Arctic surface snow metagenomes was presented and a conclusion was made that snow samples grouped together and were well-separated from other ecosystem metagenomes (Maccario et al., 2014). We repeated this analysis including our Antarctic snow metagenomes data. When Antarctic samples were substituted for Arctic samples used in the previous analysis, clear ecosystem clustering similar to the earlier reported result was obtained (Figure 4A), seemingly indicating commonalities of microbial communities of Antarctic snow. However, when Arctic snow metagenomic samples were also included, Antarctic samples became indistinguishable from soil and Antarctic microbial mat metagenomes; the free ocean water samples remained tightly clustered and separate, while the Arctic snow samples became very dispersed (Figure 4B).

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.