Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow

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.

Microbes influence the biogeochemical and optical properties of maritime Antarctic snow

“…The results described above reveal an active snowpack microbial ecosystem which is notable for an autotrophic biomass dominated by the snow algae and a bacterial community dominated by Proteobacteria and Bacteroidetes. The microbial community therefore shares some characteristics with those observed in better known Alpine and Arctic snow ecosystems [e.g., Amato et al , ; Harding et al , ; Hell et al , ; Larose et al , ], as well as snows in the vicinity of Russian Antarctic research stations [ Lopatina et al , ]. For example, the importance of the Sphingobacteria, Flavobacteria, and Betaproteobacteria in coastal snows of the present study is similar to that described in snow lying upon soil in coastal Svalbard [ Larose et al , ].…”

Long-term genomic coevolution of host-parasite interaction in the natural environment

“…Studies on a related bacterium, Flavobacterium psychrophilum , have discovered inactive CRISPR systems across multiple strains 49 , but also high variability between metagenomic samples from nature 50 . In F. columnare , we report two active CRISPR loci: C1, a type II-C system and C2, a recently identified RNA-targeting type VI-B system.…”

Dynamics of Escherichia coli type I‐E CRISPR spacers over 42 000 years

“…; Lopatina et al . ). To minimize biases due to variations in individual repeat sequences, primers used for amplification were designed based on a repeat Logo determined with WebLogo 3.0 (Crooks et al .…”