Classic story revised: lichens are fungus + algae + yeast (another fungus)

One of the classic stories of biology, taught to virtually every student, is the fact that what we call “lichens” are actually a combination of two very distantly related species: a species of alga and a species of fungus. (Sometimes the “alga” is really a species of cyanobacteria, formerly called “blue green algae” but not really algae.) It is offered as the paradigm of a true symbiosis, in which two species living together each provide something for the other. In the case of lichens, the alga provides the products of photosynthesis as nutrients, while the fungus provides structure, protection, nutrients, and moisture.  They’ve coevolved to the extent that while the algal partner can sometimes be found living freely on its own, the fungus is never found on its own. Finally, most (but not all) of the fungal partners in a lichen are ascomycetes (“sac fungi”)—a phylum in the fungal kingdom.

Lichens vary tremendously in their growth form depending on the partners; here are three examples taken from the Wikipedia article:




Well, this classic story has just been revised in a new online paper in Science by Toby Spribille et al. (reference below; free download). Spribille and his colleagues note that although this partnership has been described for decades, attempts to reconstruct a lichen in the lab by combining the fungal and algal partner always failed: researchers could simply not obtain the characteristic structure seen in nature. Their new paper gives an astounding result that may explain this failure: there’s a third partner in this symbiosis, and it’s yet another fungus—a yeast, which is a “basiodiomycete”, a different phylum that includes mushrooms and puffballs.

I’ll be brief.  Spribille et al. discovered the new partner when studying two lichens that looked very different (one produced an acid that made it yellow), but turned out to have the same algal and fungal partners. They were, in effect, the same species of lichen (though of course species delineation is tricky in this group). Why were they so different? They decided to study gene expression in the two forms using genes identified in ascomycetes and algae. No differences were found. But when they expanded their search to other types of fungi, they found that some basidiomycete genes were expressed in one form but not the other, even though no basidiomycetes were supposed to be there.

They then determined that other lichens also had a third basidiomycete partner, but one that differed among lichen “species”.  Although only 42 of the 56 sampled lichen genera had related basidiomycetes (indicating that the partnership may not be required in all lichens), they conclude that “basidiomycete fungi are ubiquitous and global associates of the world’s most speciose radiation of macrolichens.”

Finally, they visualized the cells, which was hard to do because they’re sparse and embedded in the lichen cortex (its skin). They finally managed to visualize the yeast cells, at first detected only by their gene transcripts, by “FISH” (fluorescent in situ hybridization) analysis: making RNA transcripts of the yeasts that hybridized to fluorescent molecules. And then they could see this:


Figure from paper. (A) B. fremontii, with (B) few FISH-hybridized live yeast cells at the level of the cortex. (C) B. tortuosa, with (D) abundant FISH-hybridized cortical yeast cells (scale bars, 20 μm).

The previous failure to detect the presence of another fungal partner may explain why scientists haven’t been able to synthesize lichens from their components: they were leaving out the third partner. 

And why wasn’t this partner detected before? The authors suggest that the genes in the new partner simply weren’t detected in the usual gene-sequencing procedures, which can be biased toward detecting genes present in greater numbers.

This shows that long-established stories can be drastically revised by new findings, and that the classic tale of this symbiosis may have to be revised a bit. It remains to be seen whether this new, third partner is actually required for the lichen to form, and, if so, if it really partakes in a symbiosis as well, giving stuff to its two partners and getting back from them. It could even be parasitic or neutral, or have a symbiosis with one of the two other partners and a different relationship with the other. To add the classic ending to scientific papers, “Much work remains to be done.”


Spribille, T. et al.  2016. Basidiomycete yeasts in the cortex of ascomycete macrolichens. Science.  Published online 21 JUL 2016 DOI: 10.1126/science.aaf8287


  1. ThyroidPlanet
    Posted July 25, 2016 at 11:10 am | Permalink


    • jimroberts
      Posted July 25, 2016 at 11:56 am | Permalink


  2. pck
    Posted July 25, 2016 at 11:15 am | Permalink

    It’s amazing how this didn’t come up earlier. Surely someone must have previously ground up some lichens and amplified 3 different marker gene sequences from the extracted DNA. You don’t need genes present in large numbers for that.

    • gravelinspector-Aidan
      Posted July 25, 2016 at 2:00 pm | Permalink

      Pick a marker gene.
      How many gene sequences are known which can be used as tags for detecting gene activity in an unknown sample? Hundreds of thousands, or millions?

    • Jeff J
      Posted July 26, 2016 at 7:08 am | Permalink

      I bet someone somewhere is kicking themselves for misidentifying the third partner as a contaminant.

      • Posted July 26, 2016 at 8:13 am | Permalink

        Maybe many people.

        • teacupoftheapocalypse
          Posted July 26, 2016 at 12:30 pm | Permalink

          Very likely many people, given the amount of yeast in the natural environment. Just ask anyone who bakes sourdough bread.

  3. Posted July 25, 2016 at 11:17 am | Permalink

    “To add the classic ending to scientific papers, ‘Much work remains to be done.'”

    LOL. I’ve got a few versions of that theme in my dissertation.

  4. Derek Freyberg
    Posted July 25, 2016 at 11:20 am | Permalink

    There’s an interesting article about this, and about Toby Spribille and his background, in a very recent Atlantic online, at

  5. Posted July 25, 2016 at 11:31 am | Permalink

    Nice work!

  6. rickflick
    Posted July 25, 2016 at 11:31 am | Permalink

    Another example of how our common understanding over decades is being overthrown. Small upgrades over time, like a Chinese water torture. This makes me nervous. Will I have to revise everything I ever learned? Well, probably eventually, I will, if I live long enough. I remember fondly course work in botany which spent a lot of time on algae and fungi. Discriminating species was a toughy. Now it looks like some wet chemistry will be required to get the names strait.

    • gravelinspector-Aidan
      Posted July 25, 2016 at 2:10 pm | Permalink

      This makes me nervous. Will I have to revise everything I ever learned?

      I went through this over a deccade ago as I tried dragging my biological knowledge into the 20th century by working through Margulis’ (& Schwartz) “Five Kingdoms” book. One chapter per phylum, 2-5 pages per chapter, 120-odd phyla. By the time I ran out of steam, 35-odd phyla in, at least 3 had been re-classified (IIRC one seeming multi-cellular “yeast” being recognised as an extremely degenerate metazoan – “higher” animal) … and I just lost heart.
      In the last decade the whole lot has been re-shuffled again. I don’t really try keeping up any more. There’s enough to keep up with on the rocks, and they don’t normally move around without an external force being involved.

      • rickflick
        Posted July 25, 2016 at 3:08 pm | Permalink

        As for rocks, I was in school when (1960s) continental drift was still taught as a bit iffy – even though Wegener had published on it in 1912, and many before him had different ideas. But, no, rocks don’t move on their own. The god Hades is responsible.

        • gravelinspector-Aidan
          Posted July 25, 2016 at 5:25 pm | Permalink

          We’re still getting over the shock of having to let catastophism back into polite society.
          Bumped into Professor Plagioclase today (you can guess what he had to drum into our skulls in the dim and distant past) ; it’s a small world, though not as small as Ceres

        • Bessemer Mucho
          Posted July 26, 2016 at 3:49 am | Permalink

          I can still remember my shock, as a college freshman who had been reading about seafloor spreading magnetic studies in Scientific American for years, being told by some geology grad students that there was nothing to it: their faculty advisor told them so.

    • Torbjörn Larsson
      Posted July 26, 2016 at 6:39 am | Permalink

      The problem with biology is that it has a life of its own.

      Not that other areas are much better. Good thing the brain-body system is plastic.

      By the way, Jerry’s article was excellent, I lichen it!

  7. Frank Wagner
    Posted July 25, 2016 at 11:38 am | Permalink

    I happened to visit the Field Museum in Chicago a few days ago and enjoyed a special exhibit there called Lichens: The Coolest Things You’ve Never Heard Of. It had a link for people to send pictures of lichens because there are so many unidentified species. I did not copy the link and the museum website doesn’t list it.

  8. Posted July 25, 2016 at 12:13 pm | Permalink

    That’s cool. Thanks for this post.

  9. Hempenstein
    Posted July 25, 2016 at 12:13 pm | Permalink

    Good thing the two-species version isn’t some Biblical revelation.

    • Mark Sturtevant
      Posted July 25, 2016 at 7:24 pm | Permalink

      Maybe the two-species version got left behind during the ‘Flood’.

  10. Posted July 25, 2016 at 12:15 pm | Permalink

    Fascinating. I have the 3rd kind of lichen growing on a tree and it makes lovely patterns. I have always liked lichens and mosses, tho the latter have been sadly neglected on this site.


    • Posted July 26, 2016 at 8:16 am | Permalink

      With their size, they are a challenge to photographers. My attempts have always failed miserably.

  11. Kevin
    Posted July 25, 2016 at 12:18 pm | Permalink

    Lichens are a true reminder of persistence and patience in nature. Taking their time, but they can be found just about anywhere on our planet. Amazing.

    • gravelinspector-Aidan
      Posted July 25, 2016 at 2:14 pm | Permalink

      What I like about them is the way that hundreds or thousands of years ago people were erecting calibration stations for lichen-based dating of exposed rock surfaces all over the world, with a useful range of representative local rock types, so that climate annd erosion analysis work can be done centuries later. Extremely foresighted.
      Of course, the constructors didn’t call them “dating calibration stations. Just “the cemetery”.

      • HaggisForBrains
        Posted July 26, 2016 at 4:43 am | Permalink

        🙂 From one who lives in a cemetery.

        • Diane G.
          Posted July 26, 2016 at 5:54 am | Permalink

          That sounds like an interesting story in itself!

          • HaggisForBrains
            Posted July 26, 2016 at 10:56 am | Permalink

            The neighbours are generally very quiet, but tend to get a bit rowdy towards the end of October 😉 I’m the gatekeeper; someone’s got to keep them in.

  12. Posted July 25, 2016 at 12:36 pm | Permalink

    One of the things I love about science is that the book is never closed.

  13. Posted July 25, 2016 at 12:46 pm | Permalink

    I echo the other posters in liking this post and my admiration for science.

    Carl Kruse

  14. Wayne Tyson
    Posted July 25, 2016 at 1:02 pm | Permalink

    Here’s what you get via the link.

    We’re sorry!

    “This special offer is no longer available, but we’d still love to have you as a member. Please click here to join AAAS today.

    “If you have questions about AAAS membership or would like additional information about joining, please contact Member Services at or by phone at +1-202-326-6417 or +1-866-434-2227 weekdays between the hours of 8:30 am ET and 5:00 pm ET.”

    I believe science should be equally available to all, and encourage publication only in open-source journals. You can get it free if you are faculty or student, but your university pays through the nose (or other orfice) for journal subscriptions (which, when they were only printed on expensive clay paper, but now, when they are uploaded once and sold many times), they are “profit centers” run, not by academics, but by MBA’s. Few of the “unwashed” or “unclean” non-academics can afford the download fees for everything they want to read, and certainly can’t afford a subscription to every journal they might like to consult.

    Yes, one could request a “reprint” from the author, but that is not very considerate of the author, who, in this age of web-connectedness, could be overwhelmed with such requests. Not considerate of we, the unclean, to do.

    AAAS should perhaps change its name to the American Association for the Retardation of Science–especially when it comes to “We, the retarded outcasts.”

    • Teresa Carson
      Posted July 25, 2016 at 1:40 pm | Permalink

      I think the assumption is that people who really need or want to see the original work will be affiliated with a university that subscribes to either the individual publication or a service that provides a number of scientific publications. That said, I feel your pain. It happens to me all the time. However, authors sometimes post their work on their own websites.

    • gravelinspector-Aidan
      Posted July 25, 2016 at 2:30 pm | Permalink

      For some months, the standard work-around for this has been to go to, paste in the URL of interest, and get the paper from there. Unfortunately, in the last week or so the “powers that be” seem to have shut down on this, and it’s alternatives at and …
      Can I find an alternative? Oh no, tell a lie, is up – probably just being attacked by the forces of for-profit publishing.
      You might need to exercise some educated guesses about what the Russian in the comments and instructions on the site means. It seems the programmers spend their time keeping the site up, not on UI trivia. I’ve only trivial Russian – too low to measure sensibly – but I can use it. And despite running a fairly tight ship on web security, I haven’t detected anything concerning about the site (they do overlay the PDFs with “we need funding” buttons, which upsets some of my security robots. But there doesn’t seem to be anything beyond an “we need funds” call behind it.
      If Elsevier and associates are struggling to get it shut down, then it’s probably doing something desirable to scientific publishing.
      There are also rumours of an ARXIV for “biology” gaining some traction. I don’t have any experience of that, but someone else might.

  15. Posted July 25, 2016 at 1:57 pm | Permalink

    I don’t collect spores, yeast and fungus, found this an interesting read.

  16. Posted July 25, 2016 at 2:07 pm | Permalink

    It’s my understanding that “yeasts” are polyphyletic, though the familiar ones like Saccharomyces cerevisiae are actually Ascomycetes.

  17. frankschmidtmissouri
    Posted July 25, 2016 at 2:13 pm | Permalink

    I sing the praises of yeasts
    They are quite remarkable beasts
    In wine, bread or lichen
    It’s always quite strikin’
    How important they are for a feast.

    (With apologies)

    • gravelinspector-Aidan
      Posted July 25, 2016 at 2:39 pm | Permalink

      Yours, or is there a yeast genus called Melania which you’re describing here?

  18. John Harshman
    Posted July 25, 2016 at 3:55 pm | Permalink

    A slight further complication: some lichen species contain both algae and cyanobacteria.

  19. keith cook + / -
    Posted July 25, 2016 at 5:38 pm | Permalink

    Symbiosis intrigue, I suffer from this and posts like this, scratch it quite nicely.

  20. W.Benson
    Posted July 25, 2016 at 9:44 pm | Permalink

    The discovery that lichens are often 3-species symbioses puts in stark light the relevance of the question of which species in a triad are obligatory symbionts. If any component species is a facultative symbiont, it cannot be selected to adapt strongly to the others or to evolve for the benefit of the association. Under these circumstances, how could a lichen, as a system, adapt to anything? It makes for an infernally intriguing situation.

  21. Posted July 26, 2016 at 2:24 am | Permalink



  22. Diane G.
    Posted July 26, 2016 at 3:34 am | Permalink

    As an NSF URP grantee (& botany major) way back in the day (very early ’70s) I was involved in the IBP Coniferous Forest Biome project; by the time my partner & I joined we were stuck with the only unclaimed flowchart box left, “Other Autotrophs.” This turned out to be the epiphytes–lichens, mosses, liverworts, et al–growing on old-growth Douglas Fir, which, as we documented, play a vital role in the NW CF biome ecology.

    I’ve been in love with lichens ever since and was thrilled to death when this research just recently hit the press.

  23. Posted July 26, 2016 at 6:27 am | Permalink

    Thanks for this article, Professor CC! I too love lichens and the lichen communities. I try to photograph them wherever I happen to travel.

    • Jeff J
      Posted July 26, 2016 at 7:18 am | Permalink

      I’d like to add a hearty ‘me too.’

      Occasionally our kind host kvetches that his well crafted science posts get far less attention than those addressing the hot topics. Personally, I really appreciate posts like this one. I just spent the last half hour learning cool things about lichens and now I can’t wait to pass them on to my kids tonight.

  24. Posted July 26, 2016 at 8:05 am | Permalink

    Reblogged this on The Logical Place.

  25. lovingyourselfweb
    Posted July 26, 2016 at 9:20 am | Permalink

    Great informative article. While reading this I went back to my school days and the memory of studying biology came back :).. Thanks for providing information… Hope soon it gets updated.

One Trackback/Pingback

  1. […] via Classic story revised: lichens are fungus + algae + yeast (another fungus) — Why Evolution Is True […]

%d bloggers like this: