Abstract:
: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.
journal_name
Nat Microbioljournal_title
Nature microbiologyauthors
Martínez Arbas S,Narayanasamy S,Herold M,Lebrun LA,Hoopmann MR,Li S,Lam TJ,Kunath BJ,Hicks ND,Liu CM,Price LB,Laczny CC,Gillece JD,Schupp JM,Keim PS,Moritz RL,Faust K,Tang H,Ye Y,Skupin A,May P,Muller EEL,Wilmdoi
10.1038/s41564-020-00794-8subject
Has Abstractpub_date
2021-01-01 00:00:00pages
123-135issue
1issn
2058-5276pii
10.1038/s41564-020-00794-8journal_volume
6pub_type
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