Monday, January 29, 2018

BacterioFiles 326 - Ciliate Symbionts Selected Separately

Euplotes ciliates
This episode: Learning about endosymbionts by comparing bacteria living inside eukaryotes to their free-living cousins!

Thanks to Dr. Vittorio Boscaro for his contribution!
Download Episode (9.7 MB, 10.6 minutes)

Show notes:
Microbe of the episode: Ancalochloris perfilievii

Journal Paper:
Boscaro V, Kolisko M, Felletti M, Vannini C, Lynn DH, Keeling PJ. 2017. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat Ecol Evol 1:1160.

Other interesting stories:
  • Wolbachia naturally found in mosquitoes inhibits malaria transmission (paper)
  • Group of 5 microbes help regulate Hydra's body contractions
  • In mice, fungi can function somewhat in place of gut bacteria (paper)
  • Bacteriophages get carried all over the body
  • Bacteria engineered to make boron-carbon bonds

  • Post questions or comments here or email to Thanks for listening!

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    Episode outline:

    • Background: Bacteria considered alive, viruses not
      • Virus requires host cell to do anything almost
      • Bacteria can live on their own, grow in lab cultures
        • Replicate themselves with own machinery
    • Obviously not always true though
      • Many pathogens and endosymbionts don’t replicate outside host
      • Most microbes haven’t been grown successfully in lab
      • Some don’t even have all machinery required
      • Ep 131, bacteria inside bacteria inside insects
    • Really a distinction between alive and not alive? Grey areas
    • What’s new: Now, Vittorio Boscaro, Martin Kolisko, Michele Felletti, Claudia Vannini, Denis Lynn, and Patrick Keeling, publishing in Nature Ecology & Evolution, have approached the question by studying free-living bacteria that are closely related to other bacteria living inside other microbes!
    • Polynucleobacter – abundant in some freshwater habitats
      • Can be grown in lab
    • Other strains live inside ciliate Euplotes
      • Ciliates need them, and they seem to need host (not cultivable, yet)
      • Different shapes from free-living
      • But very similar genetically; not easily separated into groups
    • Try to figure out how different strains evolved to get this result
    • Methods: Compared genome sequences from symbionts of 9 Euplotes strains
      • And 7 free-living Polynucleobacter
    • Found some differences
      • Symbiont genomes smaller and missing many important genes (or having pseudogenes)
    • Seems like direction goes from free-living to symbiont, not reverse
      • Otherwise would see free-living having pseudos in addition to re-acquired essential genes
    • Also found that symbionts arose multiple times
      • Not one free-living ancestor of all symbionts
      • But at least 8 free-living cells became symbionts
      • Euplotes all single ancestor though
      • How did they get new required symbiont? Must have gotten new while having one already
    • Couldn’t find any genes lacking in or present only in symbionts required for symbiosis
    • Free-living strains had almost 1500 core genes: present in all strains
      • Others found in some but not others
      • Symbionts all had 644 of these, but each had lost some of the others
      • Different for each strain
      • Remaining: related to fundamental metabolism (DNA, RNA, energy)
        • Gene loss was mostly random, not consistent
    • Summary: Polynucleobacter strains have become endosymbionts of the eukaryotic microbe Euplotes multiple times, fairly recently. They always lose gene functions in this process, but which genes are lost reveals interesting patterns and randomness
    • Applications and implications: Help understand process of becoming/acquiring endosymbionts
      • Important for many diverse aspects of life
      • Insects, other microbes, plants with chloroplasts
      • Even us, with mitochondria
    • Looked at which genes lost in symbionts and which remain
      • Can figure out new functions of genes by how they need to interact in symbiont
    • What do I think: Lots of things unclear about this relationship
      • What makes bacteria essential to hosts?
        • Synthesizing required nutrients, like in insects?
      • How are hosts sustaining their symbionts?
        • Providing source of nutrients?
      • How do new symbionts replace old ones?
        • Bacteria invade and kick out, or host ditches old and captures new?
        • The first author on the study, Dr. Vittorio Boscaro, describes his take on the interaction, and describes his findings: statement
    • Lots to learn about interesting interaction

    Symbionts, organisms living in close association to each other, are usually thought of as working together in perfect balance and harmony. But we think that in most cases, one of the partners is actually exploiting the other. In the system we studied, the bacterium Polynucleobacter is trapped by its host in an evolutionary dead end. The host needs the bacterium, but since there are many Polynucleobacter strains in the environment, it apparently just snatches new ones from time to time, replacing the previous symbiont. It’s a bad deal for the bacterium, but a good opportunity for researchers. Since the process happened over and over, and we could work on several independent host-symbiont lineages, we could observe the evolutionary events develop repeatedly, and figure out which things are predictable, and which are not. For example, we observe that all symbionts undergo genome reduction, but the exact order in which genes are lost is quite different. Also, we were able to quantitatively determine, for the first time, that genes are lost by genetic drift, i.e. the accumulation of deleterious substitutions that happens when selection is relaxed, and not by mutation pressure, which is an increase in the total number of mutations.


    1. Do you think with further study, this mechanism will be able to explain the evolutionary history of our mitochondria?

      1. I think studying endosymbionts like this could definitely help understand the process and genetic trends of various kinds better in general. I'm not sure extrapolating from this specific case to mitochondria would work too well, since we don't know exactly what these bacteria are doing to help these eukaryotes (which also already have their own mitochondria). But we do know some about mitochondrial genetics, that their genomes look like very degraded bacterial genomes but with some bacterial genes transferred to the host genome, thus making the mitochondria dependent on their host for basic function and such, which is interesting.

        Also, apparently Euplotes mitochondria are genetically interesting as compared to other ciliates:

    2. Do humans, animals, or plants have any other known endosymbionts other than mitochondria or chloroplasts?

      1. Definitely! Though none are as common or well-known or well-established in their hosts as mitochondria and chloroplasts, there are plenty of examples in different organisms.

        Aphids have an interesting relationship with bacteria called Buchnera: their diet is plant sap, which is rich in sugars but poor in protein, so these bacteria help by making essential amino acids the aphids can't make for themselves.

        Many insects have Wolbachia symbionts, some are more helpful than others but they have different effects depending on the specific relationship.

        The Wiki page is worth checking out for more examples: