Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%–40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.

中文翻译：

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地衣共生体（Umblicaria phaea）宏基因组中的病毒多样性：完整的病毒基因组、推定的宿主和海拔分布

病毒可以通过启动水平基因转移、影响宿主表型或扩大宿主的生态位在共生关系中发挥关键作用。然而，关于共生生物中病毒多样性和分布的知识仍然难以捉摸。在这里，我们使用深度测序的宏基因组 DNA（PacBio Sequel II；两个个体）与群体基因组学方法（Pool-seq；11 个群体，550 个个体）配对来了解地衣Umbilicaria phaea中的病毒分布。我们评估（i）地衣菌体中的病毒多样性，（ii）假定的病毒宿主（真菌，藻类，细菌）和（iii）沿两个复制的海拔梯度的病毒分布。我们鉴定了五种新型病毒，与已知病毒具有 28%–40% 的氨基酸同一性。它们暂时属于花椰菜病毒科、肌病毒科、足病毒科和蜘蛛病毒科. 我们的分析表明，Caulimovirus 与地衣的绿藻光生物（Trebouxia）有关，其余病毒与细菌宿主有关。我们没有在真菌生物中检测到病毒序列。Caulimovirus 丰度随着海拔的升高而降低，这种模式反映在宿主该病毒的特定藻类谱系中。噬菌体显示出特定人群的模式。我们的工作首次全面深入地了解与地衣全生物相关的病毒，并提出病毒宿主和环境在构建病毒分布中的相互作用。