Abstract
Microbial single-cell genomics represents an innovative approach to study microbial diversity and symbiosis. It allows us to recover genomes of microbes possessing specific features of our interest, or detect relationships between microbes found in close proximity to each other (one microbe inside of the other or microbes attached to each other). It can be used for linking phages with their bacterial hosts in different kinds of environmental samples, which often contain an enormous diversity of yet uncultured bacterial species and novel bacteriophages. In the typical microbial single-cell genomics workflow, fluorescence-activated cell sorting (FACS) is used to collect bacterial cells of interest, based on their cell size, internal granularity, or fluorescence. Femtograms of DNA from each sorted particle are then amplified up to the quantities required by the standard sequencing library preparation kits. Single-cell assemblies then reveal presence of phages in sorted bacterial cells. In case of highly abundant viral species, single-cell genomics can be coupled with metagenomics (shotgun sequencing of the total microbial community), which can provide insights into the bacteria-bacteriophage population fluctuations in time or space. In this chapter, we explain the details of uncovering relationships between bacteriophages and their hosts coming from so-called viral or bacterial dark matter.