The dynamics of single stranded, positive sense RNA bacteriophages in the rumen virome

We studied a selection of single stranded (ss)RNA bacteriophages (Class Leviviricetes) in rumen samples from dairy cows. These phages are non-enveloped, positive sense bacteriophages infecting Gram-negative bacteria, e.g. Escherichia, Salmonella, Pseudomonas, or other Gammaproteobacteria. Leviviricetes phages have small genomes and are of interest, as they likely predate on commensal or pathogenic Gram-negative bacteria. These phages attach to retractile pili on the bacterial surface, characterising them as male- or sex/conjugation-dependent phages and may interfere with bacterial conjugation and antimicrobial resistance. We assembled 52 Leviviricetes sequence contigs with homology to reported Leviviricetes. Our findings indicate that the majority of these phage sequences are found in the rumen liquid rather than the solids fraction, that clearance rates are slow and consistent with rumen liquid clearance, and that abundance of individual phage contigs differ among cows and sampling times, consistent with dynamic bursts of replication and clearance. Some phage contigs were detected for up to 8 weeks, and considered part of a resident, dynamic virome, while other phage contigs become undetectable, suggesting transient infection. Our data may suggest a highly dynamic system, possibly caused by predator-prey interactions between a group of ssRNA bacteriophages and their bacterial hosts in the rumen of dairy cows.