Reference : Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics...
Scientific journals : Article
Life sciences : Environmental sciences & ecology
http://hdl.handle.net/10993/51816
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics
English
Martinez Arbas, Susana mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology]
Narayanasamy, Shaman mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core]
Herold, Malte [> >]
Lebrun, Laura mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology]
Hoopmann, Michael R. [> >]
Li, Sujun [> >]
Lam, Tony J. [> >]
Kunath, Benoît J. [> >]
Hicks, Nathan D. [> >]
Liu, Cindy M. [> >]
Price, Lance B. [> >]
Laczny, Cedric Christian mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology]
Gillece, John D. [> >]
Schupp, James M. [> >]
Keim, Paul S. [> >]
Moritz, Robert L. [> >]
Faust, Karoline [> >]
Tang, Haixu [> >]
Ye, Yuzhen [> >]
Skupin, Alexander mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Integrative Cell Signalling]
May, Patrick mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core]
Muller, Emilie E. L. [> >]
Wilmes, Paul mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology]
2021
Nature Microbiology
Nature Publishing Group
6
1
123--135
Yes (verified by ORBilu)
International
2058-5276
London
United Kingdom
[en] Bacteriology ; Ecosystem ecology ; Metagenomics ; Microbiome ; Network topology
[en] Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
http://hdl.handle.net/10993/51816
10.1038/s41564-020-00794-8
https://www.nature.com/articles/s41564-020-00794-8
Number: 1 Publisher: Nature Publishing Group

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