Metagenomic exploration of lichen thalli reveals novel viral communities

Lichens are a symbiotic relationship of an algal and/or cyanobacterial photobiont and a fungal mycobiont. Although typically described as a two-membered or three-membered symbiosis, culture-based and culture-free studies have revealed that lichen thalli also contain diverse communities of cryptic, but ubiquitous epilichenic and endolichenic fungi and bacteria. In terrestrial and aquatic systems, microbial cells are subject to viral infections that can alter host phenotypes as well as induce cell death. Here, for the first time, we explore the diversity and functional content of double-stranded DNA viruses in lichen thalli using whole genome shotgun sequencing. Sampling included eleven lichen species from two genera (Peltigera and Solorina) of which the mycobiont associates with cyanobacteria from the genus Nostoc as either the primary photobiont or as an additional nitrogen-fixing symbiont. In contrast to previous methods that use reference-based detection of viruses from mixed metagenomic assemblies, we used newly developed machine-learning approaches that are more likely to discover novel viruses. Such approaches are critical to the exploration of viral diversity and functions in understudied ecosystems such as lichen microbiomes. After stringent quality controls to remove host sequences, we found that every lichen thallus contains a diversity of viral sequences, the majority of which appear novel. Viral hosts included both the Nostoc cyanobiont as well as other bacterial lineages found in lichens. In total, we obtained > 50 circular bacteriophage genomes. Few viral sequences carried genes associated with a temperate lifestyle, suggesting cyanolichen-associated viruses may have a predominantly lytic life cycle. Overall, our findings confirm the presence of diverse viral communities within lichen thalli (lichen virome) and provide evidence that viruses may have a functional role within these complex symbiotic assemblages.