[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.
Disciplines :
Microbiology
Author, co-author :
Martinez Arbas, Susana ✱; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Narayanasamy, Shaman ✱; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Megeno S.A
Herold, Malte; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Lebrun, Laura ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Hoopmann, Michael R.; Institute for Systems Biology, Washington, USA
Li, Sujun; School of Informatics, Computing and Engineering, Indiana University, USA
Lam, Tony J.; School of Informatics, Computing and Engineering, Indiana University, USA
Kunath, Benoît ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Hicks, Nathan D.; TGen North, USA ; Harvard T.H. Chan, School of Public Health, USA
Liu, Cindy M.; TGen North, USA ; Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, USA
Price, Lance B.; TGen North, USA ; Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, USA
Laczny, Cedric Christian ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
Gillece, John D.; TGen North, USA
Schupp, James M.; TGen North, USA
Keim, Paul S.; TGen North, USA ; The Pathogen and Microbiome Institute, Northern Arizona University, USA
Moritz, Robert L.; Institute for Systems Biology, Washington, USA
Faust, Karoline; Laboratory of Molecular Bacteriology, KU Leuven, Belgium
Tang, Haixu; School of Informatics, Computing and Engineering, Indiana University, USA
Ye, Yuzhen; School of Informatics, Computing and Engineering, Indiana University, USA
Skupin, Alexander ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Integrative Cell Signalling
May, Patrick ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Bioinformatics Core
Muller, Emilie E. L.; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
Wilmes, Paul ; University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Systems Ecology
