Date: 09.12.2019

Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics

In aquatic microbial communities, the most abundant players, the viruses, remain unexplored. Some of them can infect and kill bacteria, those viruses are named bacteriophages or simply phages. Phages influence microbial community ecology affecting nutrient cycle.

A joint research team from the Department of Aquatic Microbial Ecology (Institute of Hydrobiology, BC, CAS) recently recovered complete genomes of  more than 2000 freshwater phages using over 100 public available metagenomic data and DNA-based methods. They describe different patterns of distributions in different seasons and depths phages in Římov Reservoir - Czech Republic and many viruses encoding genes that can help infected bacteria to survive very specific environmental stress.  The work was published in the Microbiome Journal.


Figure 1.Viral life strategies in freshwater environments. Left: The trojan horse strategy. A phage encoding the eukaryotic toxin ADP-ribosyltransferase (VIP2 family) infects a microbe that is then ingested by a eukaryotic predator (a flagellate is shown). In the phagolysosome the toxin is expressed and released after cell lysis into the phagolysosome from where it translocates to the cystosol. In the cytosol the toxin inhibits actino polymerization leading to cell death. Right: Phage-mediated ROS defense. (a-b) A phage encoding ROS-defense genes e.g. thioredoxin, glutaredoxin is ingested by a flagellate. (c-d) The damage produced to the microbe by the ROS present in the phagolysosome will be reduced by the expression of phage encoded genes, which will favour survival during the oxidative burst. (e) When the phage infected microbe is released outside, cell lysis by the phage can proceed.

Figure 2. Relative abundance of 1398 Řimov phages in 18 metagenomes. A heatmap of abundances is shown (coverage/Gb of metagenome normalized by Z-score). Phages are clustered by sample and abundance (average linkage, Spearman Rank correlation). Vertical bars on the right side indicate the classification of the clusters. Columns are annotated with the temperature, depth of the sample and the sampling date (RE = 0.5m and RH = 30m). Temperature color key is shown at bottom right.


For more detailed information, check the publication in the Microbiome Journal.

Kavagutti V., Andrei A., Mehrshad M., Salcher M., Ghai R. (2019) Phage-centric ecological interactions in aquatic ecosystems revealed through ultradeep metagenomics Microbiome 7: 135.
DOI: 10.1186/s40168-019-0752-0

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