Field of Science

Amoeba: Much Wierder than You Think

Amoeba proteus extending pseudopodia to feed on a hapless ciliate. Note how the pseudopodia completely surround the ciliate, cutting off any escape, before they close in on it. A fantastic photo by Wim van Egmond - you owe it to yourself to visit that link.

I have been challenged (or at least, I think I have been challenged) to write some posts on amoebozoans, the clade of eukaryotes that includes such organisms as Amoeba and most slime moulds. As amoebozoans are unequivocally neat organisms, I'm happy to take up the challenge, but I thought Id start by focusing on the most famous amoebozoan genus of all, Amoeba itself. There are about five or so species of Amoeba (at least that I'm aware of), but most of what I'm going to say in this post applies equally to all of them. I think I'm safe in claiming that Amoeba is not just the most famous amoebozoan, it's also the most famous of all unicellular eukaryotes. Almost all general biology textbooks will include two examples of 'protists', and one of them will always be Amoeba (the other will be either Euglena or Paramecium). The funny thing about this ubiquity of the Amoeba exemplar, however, is that as unicellular protists go, Amoeba is actually (a) apparently not that common, and (b) seriously wierd*.

*Euglena and Paramecium aren't that typical either.

What makes Amoeba so odd? For a start, Amoeba is amoeboid* (kind of by definition, really). This might not seem so unusual at a glance (many micro-organisms are amoeboid), but the thing is that Amoeba is always amoeboid. It never possesses cilia. Many (if not most) other amoeboid eukaryotes transform into amoeboflagellates or flagellates for at least part of their life-cycle, or possess flagellated gametes, while the majority of unicellular eukaryotes are permanently flagellated**. Even among amoebozoans, cilia are not that unusual; they're still present in Breviata, Multicilia, Phalansterium, Mastigamoebidae, Pelomyxa and many Mycetozoa, though cilia have been entirely lost among amoebozoans at least nine times (Cavalier-Smith et al., 2004).

*Simply for the sake of avoiding confusion, I prefer to avoid the common use of the name "amoeba" to refer to any organism with an Amoeba-like morphology.

**A brief explanation about the terms "cilium" and "flagellum". Originally, the term "cilium" was used for small hair-like locomotory structures, usually present in large numbers, while "flagellum" referred to larger whip-like structures of which a cell would usually only have one or a few. As our knowledge of unicellular diversity broadened, the boundary between the two became increasingly blurred, and fundamentally they're all the same structure. On the other hand, "flagella" in bacteria, though superficially resembling flagella in eukaryotes, are structurally very different (eukaryote flagella are organelles formed of membrane-bound microtubules, while bacterial flagella are formed of a single protein strand). As a result, recent authors have tended to restrict the term "flagellum" to bacteria, and expand the term "cilium" to cover all eukaryote locomotory structures (a replacement term "undulipodium" never caught on [thankfully]). However, terms such as "flagellate" are still pretty well entrenched in their old sense.

Amoeba 'radiosa', photo by David Patterson & Aimlee Laderman. Despite the use of the name, there is not really such a species as 'Amoeba radiosa'. Rather, the name is used to indicate amoebae that have become detached from the substrate and are free-floating in the water column, where they abandon their usual flattened form and adopt a form with slender pseudopodia radiating from a spherical centre. Once they come back into contact with a solid surface, they will return to their normal morphology.

The second unusual thing about Amoeba (which is perhaps not unconnected to the first thing) is its reproductive habits. Most people are aware that Amoeba reproduce by division. That happens to be the only way that Amoeba reproduce (Chapman-Andresen, 1971); they are (so far as anyone knows) entirely asexual. While asexual reproduction is normal for many organisms, exclusively asexual lineages are something of a rarity. Most asexually reproducing organisms have more aphid-like life cycles - they reproduce asexually as long as conditions are favourable for doing so, but convert to sexual reproduction when times get tough. Even bacteria, which mostly don't engage in sexual reproduction per se, are able to engage in processes such as conjugation that still allow for gene flow.

And the third wierd thing about Amoeba has to be its genetics. Amoeba genomes are simply huge - the largest genomes known to exist, in fact. We humans have a genome that clocks in at a little under three billion base pairs of DNA. Amoeba proteus, the best-known species of Amoeba, has a genome containing closer to three hundred billion base pairs. And even that effort pales in comparison to Amoeba dubia, which carries around a whopping six hundred and seventy billion base pairs. That's right - the difference in genome size alone between the two species is larger than the total genome size of any other organism! The actual genetic structure of Amoeba, however, appears to be little-known. The genome of A. proteus is divided between more than five hundred chromosomes, which is hardly surprising considering its size. By means unknown, however, this enormous genome can be reduced to nearly a third of its normal size over the course of cell division (Parfrey et al., 2008). Presumably the normally polyploid amoeba jettisons excess chromosomes prior to division then recreates them from the remainder afterwards.

Amoeba proteus on the move (towards the top left of the photo). Note the knobbly bit at the bottom right corner. This is the uroid, and represents the trailing end of the cell. The form of the uroid has turned out to be surprisingly useful in identifying amoeboids. Another photo by David Patterson.

One other feature of the Amoeba nucleus is worth mentioning. The nucleus contains a number of stellate aggregations of condensed helical structures just inside the nuclear envelope that, when first observed, were not unreasonably thought to represent condensed chromosomes. However, further study showed that the nuclear helices were composed of a mixture of proteins and RNA (not DNA) and seemed to be able to be transported out of the nucleus into the surrounding cytoplasm (Minassian & Bell, 1976). The helices disappear over the course of cell division, but are regenerated afterwards. The exact function of these helices is still unknown. Minassian & Bell (1976) seem to have suggested (in a rather cagy way that would have allowed for ready back-tracking if they turned out to be wrong, and which I may have easily misinterpreted) that they could be related to ribosome formation. Gągola et al. (2003), in contrast, note the attachment of actin filaments to the helices, and imply that they may play a role in cell motility (Amoeba with removed nuclei are unable to move*, while amoeboid animals cells can continue to move even without their nuclei).

*Removing the nucleus from an Amoeba is as simple as slicing it in half.


Cavalier-Smith, T., E. E.-Y. Chao & B. Oates. 2004. Molecular phylogeny of Amoebozoa and the evolutionary significance of the unikont Phalansterium. European Journal of Protistology 40 (1): 21-48.

Chapman-Andresen, C. 1971. Biology of the large amoebae. Annual Review of Microbiology 25: 27-48.

Gągola, M., W. Kłopocka, A. Grębecki & R. Makuch. 2003. Immunodetection and intracellular localization of caldesmon-like proteins in Amoeba proteus. Protoplasma 222: 75-83.

Minassian, I., & L. G. E. Bell. 1976. Studies on changes in the nuclear helices of Amoeba proteus during the cell cycle. J. Cell Sci. 20: 273-287.

Parfrey, L. W., D. J. G. Lahr & L. A. Katz. 2008. The dynamic nature of eukaryotic genomes. Molecular Biology and Evolution 25 (4): 787-794.


  1. Three hundred billion base pairs. Holy crap.

    I knew Amoeba was weird, but didn't know just HOW weird. You'd think that for such a model organism we'd have some of this stuff figured out now.

    What an awesome enigma. What hath Emergence wrought?


  2. Fascinating post.

    I take it the ciliate can't come toward us or go away from us because the amoeba is squished flat on a slide? This probably seems trivial to you, but I haven't really thought much about how our popular images of microbes are based on ones which have been squished flat. It never occurred to me that it might have a different form (i.e., "radiosa") in 3D space.

  3. I share the relief that "undulipodium" hasn't caught on. Rationally, about the only fault with the word is it's a mouthful, but it just bugs me for some reason.

    How meaningful is the raw basepair count for polyploid nuclei? I mean, the total basepair count in a human is humongous - a polyploid protist just keeps its (much smaller) number of duplicates in the same sell. Of course, if Amoeba is 3ish-ploid, it's still got a much larger amount of irreducible genetic material than humans do, but the difference is not quite so vast, and it migh affect genome size ranking in other cases if duplicates are counted or not.

  4. I take it the ciliate can't come toward us or go away from us because the amoeba is squished flat on a slide?

    If I read the site that I got the picture from correctly, the amoeba will also cover the ciliate from above before it's finished. On the other hand, I don't think that the majority of ciliates and other acquatic micro-organisms normally swim freely through the water column. They're mostly concentrated on substrate surfaces, and if the ciliate doesn't have the wherewithal to swim straight upwards in the first place, then there's less problem for the amoeba.

    How meaningful is the raw basepair count for polyploid nuclei?

    I tried to make sure I was accounting for polyploidy - the next contender in total genome size I could find was Psilotum nudum (which I think is multiploid) with about 250 billion bp in total.

    As for the significance of this amount, I tried to find out but couldn't. Answering that would (for a start) require some sort of idea of just how much of what types of DNA the amoeba carries. Does it actually contain a proportionally high amount of functional genes, or is it loaded to the gunnels with stuff like transposons and microsatellites?

  5. Could there be a causal connection between the (presumable) amount of cruft in Amoeba's genome, and its total lack of sexual reproduction?

  6. The amoeboid with the biggest genome is sometimes called "Amoeba dubia", but the species' describer apparently decided ten years later to make it the type species of a new genus called Polychaos, which is one of my all-time favorite generic names. So today the critter is usually called Polychaos dubium.
    A few links:

  7. How can you slice a single-celled organism in half -- wouldn't the cytoplasm spill all over?

  8. The answer to that is hidden in the next post (second paragraph, excluding the footnote).

  9. After being a biology student for many four years, my teacher did not even mention this special characteristics of amoebas! Thanks for this post and I am waiting for more of these!

  10. Does anyone know (or have a reference to) the time a 670 Gbp cell might need to divide?

  11. I don't have the answer, but I would be surprised if dividing time was directly related to genome size. The cell's DNA doesn't all get replicated at the time of division; rather, replication happens while the cell is in interphase (the period of disassociated chromosomes between divisions). I expect that total genome size would only affect the obvious division time if it affects the time it takes to line the chromosomes up.

  12. At the rate of 20,000 base pairs replicated per second (which intuitively seems to be a rather high replication rate, even with many polymerases working in parallel), the time needed to replicate 670 Gbp is just over one year...
    Would it be reasonable to assume that the organism is "vulnerable" during division (or during interphase)?
    It appears as if in the polychaos case, the number of base pairs is estimated as a function of total chromosome weight, in pg. Could it be that the rather high polychaos estimate is due to an erroneous assumption regarding the relation chromosome weight/number of base pairs?


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