Due to popular demand (does two count as popular?), I'm continuing with the Amoebozoa series (previous installments are here and here). The two major classifications of Amoebozoa that have been published in recent years are those of Cavalier-Smith et al. (2004) and Smirnov et al. (2005). While at first glance the two systems appear quite different, there are few real significant differences between them. Mostly it's a matter of different names being used for similar concepts, plus the Cavalier-Smith et al. classification assigns positions to a number of taxa that the more conservative Smirnov et al. classification is content to list as Amoebozoa incertae sedis. The Cavalier-Smith et al. classification divides amoebozoans between seven 'classes', which offers a good basis for dividing my posts. One of Cavalier-Smith et al.'s classes currently includes a single species, the strange (and not necessarily amoebozoan) Breviata anathema, which has previously been covered here and here, while the two classes of their infraphylum Mycetozoa (slime moulds) include the first three entries for this post here. So that leaves four classes that I haven't yet covered in detail. In the coming posts, I'll start with the Tubulinea, move to the Discosea, waft through the 'Variosea' and finish with the Archamoebae. And if that seems like a lot to you, just be glad I didn't choose to do my amoeboid series on Foraminifera - we could have been here well into the next century.
The "Tubulinea" of Smirnov et al. (2005) are the same grouping as the "Lobosea" of Cavalier-Smith et al. (2004). I prefer to use the name Tubulinea because Lobosea has been used in the past for a much larger grouping, effectively all amoebozoans except Mycetozoa and (sometimes) Archamoebae. Also, the name Tubulinea refers to one of the characteristic features of this group, the production of tubular rather than flattened pseudopodia, with cytoplasmic flow within the pseudopodia or entire cell along a single axis. All Tubulinea lack cilia at all stages of the life cycle. The Tubulinea include the Tubulinida (Amoeboidea of Cavalier-Smith et al.), Arcellinida, Copromyxidae, Leptomyxida and Echinamoeba, and both the papers cited above produced identical phylogenies for this class.
Echinamoeba forms the basalmost clade within the Tubulinea, together with the species 'Hartmannella' vermiformis (erroneous comments on the relationships of the family Hartmannellidae in Cavalier-Smith et al., 2004, are due to the use of H. vermiformis to represent Hartmannella; it wasn't until later that Smirnov et al., 2005, showed that H. vermiformis is not closely related to other Hartmannella species. The normal cell shape of Echinamoeba is "acanthopodian" - flattened with short, spinelike subpseudopodia (Smirnov & Goodkov, 1999); it only produces a more typically tubulinean cylindrical, monopodial form under particular conditions. The form it takes in these conditions is one produced by many amoeboids called the 'limax' form. Limax is a genus of slugs, and a microscopic slug is exactly what this form looks like. 'Hartmannella' vermiformis, on the other hand, is habitually worm-like, and has gained a certain notoriety as an unwitting vector for bacteria causing respiratory diseases in humans, particularly Legionnaire's disease (Brieland et al., 1997).
The Leptomyxida are the next group to branch off. The four genera of leptomyxidans - Leptomyxa, Rhizamoeba, Flabellula and Paraflabellula - resemble Echinamoeba by normally being flattened, and only adopting a tubular limax-like form occasionally. The normal form of Leptomyxa is reticulate, with a anastomosing net of pseudopodia. In the other three genera, the uroid (the trailing end of the moving cell) is adhesive, so when the cell is moving the posterior end is drawn out into smeared streaks. Rhizamoeba is monopodial, while the other two genera are fan-shaped. Paraflabellula produces short subpseudopodia from the anterior edge of the cell, Flabellula doesn't.
The Copromyxidae were placed by Cavalier-Smith et al. (2004) among the Tubulinea on the basis of their morphology (but were not represented in the molecular analysis), but were not even mentioned by Smirnov et al. (2005). Copromyxids include two little-studied genera, Copromyxa and Copromyxella. Cavalier-Smith et al. suggested that they are closer to Arcellinida and Tubulinida than other Tubulinea as these three groups are habitually rather than only intermittently tubular. Copromyxids differ from other Tubulinea in having a slime-mould type life cycle (I overlooked them in my earlier slime mould post). Life for copromyxids really is a pile of crap - their chosen habitat is animal dung. Fruiting bodies are produced by previously separate cells aggregating together to form a mound. Newly-arriving cells clamber over their confederates to reach the top of the pile, and the eventual result is a small, vaguely tree-like fruiting body (Bonner, 1982). Copromyxids are very similar in appearance to the non-amoebozoan acrasid slime moulds, and many earlier references combine the two.
The Arcellinida are the most speciose subgroup of Tubulinea (at least, as far as we know). Arcellinida are the testate Amoebozoa - they possess are hardened test of either secreted proteinaceous material or agglutinated mineral grains. The test is roughly vase-shaped, with a single opening through which the organism extends its pseudopodia. Phylogenetic studies (Nikolaev et al., 2005) confirm that the testate Amoebozoa form a monophyletic group (which, as I noted earlier, forms an interesting contrast to the polyphyletic testate Rhizaria), but the same cannot be said for proteinaceous- versus agglutinated-test formers, with lineages apparently switching between the two a number of times.
Finally, the Tubulinida includes Amoeba itself and its nearest and dearest (such as Chaos, Saccamoeba and true Hartmannella). Tubulinida differ from Echinamoeba and Leptomyxida in being permanently tubular, never flattened. The cell may move limax-wise as a single pseudopodium (Saccamoeba, Hartmannella, sometimes Amoeba) or may form multiple pseudopodia (Chaos, other times Amoeba). Both Cavalier-Smith et al. and Smirnov et al. placed Chaos and Amoeba closest to one another, and indeed phylogenetically mixed together. As the only difference between the two seems to be the number of nuclei (one in Amoeba, more in Chaos) it would perhaps not be surprising if one or the other, or both, turned out to be polyphyletic.
Finally, I'd like to end this post on a bit of speculation. In the first Amoebozoa post, I described the ridiculously large genome of Tubulinida species (thanks to commentor George X for pointing out that the species I referred to as Amoeba dubia is now known as Polychaos dubium). I tried to find if any studies had been done on the detailed genetic structure of these species, to see if there was any clue as to just why Tubulinida have such enormous genomes, but I couldn't find any. Indeed, when searching on Amoeba in Google Scholar, I was struck by the dates shown for most of the results - a significant proportion dating back to the period from the 1940s to the 1960s. It looks like Amoeba proteus, so popular as a model organism in the early days of cell biology due to its large size making it easy to observe and manipulate, may have since fallen in popularity. I can guess at some reasons why that might be - I get the impression that Amoeba's rarity makes it tricky to find, that it is difficult to maintain in culture once you do find it, and I wonder if, in a time when electron microscopy has become almost routine, Amoeba is large enough that its size has become a positive disadvantage rather than advantage.
In the absence of much information about Amoeba's genome beyond its size, speculation becomes ill-founded. The large size of the genome doesn't necessarily indicate a proportionally large number of genes - it could be that Amoeba is carrying a particularly heavy load of non-coding DNA. Also, the previously-mentioned cyclic nature of the Amoeba genome, with the amount of DNA increasing and decreasing over the course of the division cycle by a factor of nearly three (Parfrey et al., 1998), suggests that Amoeba proteus is at least hexaploid. Again, it might not be - perhaps instead of the entire genome being replicated three times, a smaller number of chromosomes are replicated many times (as we know happens with such things as B chromosomes in animals). But, with all those caveats, I still can't help wondering if the cyclic Amoeba genome is related to its unusual success as an asexual organism. Let us assume that the entire genome is replicated in the cell cycle, and that it is random which of the resulting replicate chromosomes gets retained and which disposed of prior to division. The result would be that the effective mutation rate of Amoeba would probably be noticeably higher than in organisms with more straightforward genetic cycles. Could this be what has allowed Amoeba to survive for so long seemingly without the benefit of recombination?
Bonner, J. T. 1982. Evolutionary strategies and developmental constraints in the cellular slime molds. American Naturalist 119 (4): 530-552.
Brieland, J. K., J. C. Fantone, D. G. Remick, M. LeGendre, M. McClain & N. C. Engleberg. 1997. The role of Legionella pneumophila-infected Hartmannella vermiformis as an infectious particle in a murine model of Legionnaire's disease. Infection and Immunity 65 (12): 5330-5333.
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.
Nesom, M., & L. S. Olive. 1972. Copromyxa arborescens, a new cellular slime mold. Mycologia 64 (6): 1359-1362.
Nikolaev, S. I., E. A. D. Mitchell, N. B. Petrov, C. Berney, J. Fahrni & J. Pawlowski. 2005. The testate lobose amoebae (order Arcellinida Kent, 1880) finally find their home within Amoebozoa. Protist 156: 191-202.
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.
Smirnov, A. V., & A. V. Goodkov. 1999. An illustrated list of basic morphotypes of Gymnamoebia (Rhizopoda, Lobosea). Protistology 1: 20-29.
Smirnov, A., E. Nassonova, C. Berney, J. Fahrni, I. Bolivar & J. Pawlowski. 2005. Molecular phylogeny and classification of the lobose amoebae. Protist 156: 129-142.