Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism
Open Access
- 15 October 2021
- journal article
- research article
- Published by Oxford University Press (OUP) in ISME Communications
- Vol. 1 (1), 1-4
- https://doi.org/10.1038/s43705-021-00060-w
Abstract
Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine-learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences predicts numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.This publication has 19 references indexed in Scilit:
- Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant PathogensJournal of Virology, 2016
- VirSorter: mining viral signal from microbial genomic dataPeerJ, 2015
- Patterns and ecological drivers of ocean viral communitiesScience, 2015
- Modeling ecological drivers in marine viral communities using comparative metagenomics and network analysesProceedings of the National Academy of Sciences of the United States of America, 2014
- Lichens—a new source or yet unknown host of herbaceous plant viruses?European Journal of Plant Pathology, 2013
- Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiomeEnvironmental Microbiology, 2011
- LichensCurrent Biology, 2009
- A Phylogenetic Estimation of Trophic Transition Networks for Ascomycetous Fungi: Are Lichens Cradles of Symbiotrophic Fungal Diversification?Systematic Biology, 2009
- Exploring the Vast Diversity of Marine VirusesOceanography, 2007
- Bacterial photosynthesis genes in a virusNature, 2003