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 >]
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 >]
* These authors have contributed equally to this work.
[en] CRISPR ; metagenomics ; activated sludge ; metatranscriptomics ; phages ; plasmids ; wastewater ; time series ; multi-omics
[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.