Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes

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Lichens are the archetypal symbiosis and the one for which the term was coined. Although application of shotgun sequencing techniques has shown that many lichen symbioses can harbour more symbionts than the canonically recognized fungus and photobiont, no global census of lichen organismal composition has been undertaken. Here, we analyze the genome content of 437 lichen metagenomes from six continents, and show that four bacterial lineages occur in the majority of lichen symbioses, at a frequency on par with algal photobionts. A single bacterial genus, Lichenihabitans , occurs in nearly one-third of all lichens sampled. Genome annotations from the most common lichen bacterial symbionts suggest they are aerobic anoxygenic photoheterotrophs and produce essential vitamins, but do not fix nitrogen. We also detected secondary basidiomycete symbionts in about two-thirds of analyzed metagenomes. Our survey suggests a core set of four to seven microbial symbionts are involved in forming and maintaining lichen symbioses.

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  1. Supplementary Table 1).

    I think it's important to include in this table the sequencing technology for each metagenome (example Illumina HiSeq PE 2x150bp sequencing) even though I could find that clicking through the SRA accessions, it helps to have it directly here especially because it seems a lot of the data comes from the 2019 UC Boulder study

  2. Supplementary Table 2).

    Something useful to add to this table and suggestion to Figure 2 for added metadata would be the # of contigs for each genome. I'm assuming most or all of these metagenomes were obtained from Illumina sequencing data and I would presume that a lot of the eukaryotic MAGs are going to be pretty fragmented and that's important information to include

  3. A striking potential metabolic complementarity to emerge from our annotations is the capacity of many frequent lichen bacteria to code for cofactors needed by one of the dominant eukaryotic symbionts

    I'm interpreting up to this point that functional annotation and pathway exploration was only performed for the bacterial genomes and not fungal/algal MAGs? Was this because of the difficult in performing ORF prediction/functional annotations without corresponding RNAseq data or something planned for the future? Because it would be interesting to see if the corresponding fungi have transporters for those cofactors

  4. Four bacterial families dominate lichen metagenomes

    It would be interesting to follow up for groups that are core such as Lichenihabitans if they are the same/different strains in these samples and if there are differences where those hotspots of diversity are relative to the lichen type

  5. Fig. 2.

    It would help provide additional context for these genomes if additional layers to the tree were added showing completeness, redundancy, genome size, etc. so it's easy to compare across the tree the quality of these genomes. This can be done with iTOL or EMPRESS as added metadata layers