this is a fascinating line of inquiry, and comes down to the methods of detection being insufficiently fine-grain. it's challenging to tell apart all of the pi

this is a fascinating line of inquiry, and comes down to the methods of detection being insufficiently fine-grain. it's challenging to tell apart all of the pieces in a metagenomic sample except through assembly. A "viral plasmid" like you describe would go unnoticed simply because it would map to another sequence assembly. there's indication of high copy-number plasmids in bacteria sometimes. not sure if anyone has looked to see if any of those are kept in the outside of the cell. usually imaged cells are washed very well before imaging, otherwise background is off the charts...