"Just another ciliate" – importance of sexy descriptions

There are species descriptions, and then there are species descriptions. All too often, you come across a mention of some obscure but ridiculously cool-looking organism, with only a very scant description of what it looks like and what it does. Much less often, you can come across yet-another-new-species (usually of a ciliate), but a particularly nicely described one. Again, those super nice descriptions tend to be of ciliates, largely due to the likes of Wilhelm Foissner and his academic offspring. Descriptive detail can only make species more interesting, and eventually of great potential to be useful for science. (Conversely, many a taxon has been rendered invalid due to poor description)

A sexy description is also a great way to lure readers into noticing your otherwise garden variety new species. Case in point – I see this random IJSEM paper on a couple new marine ciliate Frontonia species – nothing too earth shattering. Being rather compulsive about skimming over any mention of a protist I see in the literature, I click. Being rather lazy and a shallow-minded picture-loving type, I head straight for the figures. Unexpectedly, they dazzle me with sexiness. Desperate for something easy to blog about for the next little while (impending interview, exams, end-of-term chaos, etc), I suddenly find your otherwise-routine new species description quite exciting and blog about it. Here, Frontonia mengi and F.magna get screentime largely thanks to their authors.

Some of us in science are that simple minded. If more people realised that and preyed upon our ilk with shiny pictures, think how much more presentable science as a whole would be!

(That said, no amount of gloss and shine can make your data more or less wrong. But it can, and does, dazzle some of us into overlooking a flaw or three...)

Actually, the above was just a long-winded elaborate excuse to post ciliate porn. Ah, check out the kineties on that ass!

Frontonia mengi. See text. (Fan et al. 2010 IJSEM)

Well, those were mostly just shots of its oral ciliature, but close enough. The root structures of the cilia are highlighted with silver nitrate and carbonate staining, yielding the pretty staining effect. a-c section through the 'mouth'; d shows the "membranelle" around the 'mouth'. e shows the area behind the mouth; arrowhead points to the cytopyge. 'Cytopyge'? Well, a cell's gotta get rid of its waste somehow, and ciliates actually have the cellular analogue of an asshole. Not the socially dysfunctional kind. So yeah, look at that ass. g shows detail of the cortex, h is the overall view of the ventral ciliature. At i, the rows of cilia "stitch together" at the 'anterior suture'. k shows the germline micronucleus (Mi) and somatic macronucleus (Ma).

Now for some delicious DIC:

Frontonia mengi. See text. (Fan et al. 2010 IJSEM)

Crisp DIC intoxicates me. The seductive allure of polarisation-derived faux-3D relief is nearly impossible to resist, especially when you have the fine complex cell of a ciliate. In fact, good DIC is often better than staining, since you don't have to fix (kill) anything. Unfortunately in the case of some larger ciliates, some degree of squishing must be done otherwise the sample is too damn thick for crisp DIC. I think the gist of microscopy can be summarised as the never-ending compromise between care of specimen and care of the optical setup. The most powerful microscopy generally requires total destruction of the specimen, whereas the most natural and undisturbed data can only be attained with simple techniques and weak optics. It's like the Heisenberg principle of microscopy: the more accurately you determine the state of your specimen, the more mangled your specimen gets.

I digress. In the above plate, a-e show general views of several individuals of F.mengi. Remember my rant a couple posts ago about the usefulness of depicting morphotypical (shape type) variation? I hope it is evident here how that can be useful. For example, if only figure a was published, one could be mislead to consider that large vacuole a characteristic feature of this particular ciliate species. The other four images, however, show that to be a feature of just that specimen instead (non-contractile vacuoles, in this case). Furthermore, the authors even invluded a table of morphometric data, measuring the body dimensions and some visible subcellular details (like numbers of kineties and nuclear size) of 23 individuals.

The arrow in 1b points to a contractile vacuole – one could just make out the channel leading to the cell's exterior for expelling its contents. f-g show sections of the mouth, live. h shows detail of the cell surface, the oral apparatus quite visible (as is the cytopyge). i details the cytopharyngeal rods, which are specialised structures this genus of ciliates employs to devour long strands of algae. The characteristically massive ciliate nuclei are visible in j – the arrow points to the macronucleus while the arrowhead points to the micronucleus. No staining necessary, fuck yah.

Frontonia, like many ciliates, is also armed and dangerous. The surface is loaded with extrusomes (k), which can fire leaving a trail, much like the cryptomonad ejectisomes (l). m and n show the contractile vacuole and its exit pore, respectively. The contractile vacuole is necessary for osmotic regulation, especially in freshwater species, and is somewhat analogous in function to our kidneys.

The second species, Frontonia magna, is also well-described. In these specimens, one can make out the algal filament and its constituents – particularly in b, e and f. Like F.menga, it's also loaded with extrusomes (h). I particularly like i, which shows the ciliature of the anterior suture. It's quite hawt.

Frontonia magna. See text. (Fan et al. 2010 IJSEM)

Of course, no description is properly complete (in my opinion) without drawings to accompany the micrographs. Drawings highlight the important features observed by the authors, and are useful in combining information gathered from multiple sections and imaging techniques in a convenient summary. Making an accessible visual summary of a huge pile of microscopy data is no easy task, and is very much an art.

Continuing with F.magna, a summarises the ventral view of a typical individual. b provides a sketch of the sutures, without the distracting detail. c shows the side view, along with the contractile vacuole. d shows the relative sizes and positions of the nuclei. e, again, emphasises variation – it shows the various ways a cell appears after overeating with algal filaments protruding all over the place. It's amazing how hard prey can try to make their predator look like an entirely new freaking domain of life, by stretching it out and colouring it in all sorts of funny ways. A similar phenomenon has been responsible for an entire mistaken genus, Ouramoeba, in the otherwise totally awesome Leidy 1874 work on amoebae. The algal prey is detailed in g, while h details the cilia around the oral apparatus.

Frontonia magna See text. (Fan et al. 2010 IJSEM)

Of course, no species description these days is complete without a healthy phylogeny, and Fan et al. got that covered too. I feel I've stolen more than enough figures already, so I'll just say their Frontonia spp. fit snugly within Peniculia, a group including the famous Paramecium, and the two species are sister to each other. There's also a composition of drawings from multiple sources for other members of this genus, so this paper is a nice current reference for Frontonia, if you ever wake up one morning needing one. Believe me, these cravings may strike at the oddest hour.

Anyway, I just thought these figures really deserve to see the light of day, and not just remain buried away in what will very soon be just the back issues of a microbial systematics journal. While some may look down on routine-seeming research like basic species descriptions for they do not provide a fancy high-level synthesis or anything, but ultimately, these fancy high-level syntheses are built on lower-ranking papers like these, and cannot exceed the quality of their constituents. It is primary 'basic' literature like this that forms the foundation of science; without species descriptions, without "yet another gene/genome/tree/whatever", there will be nothing to base the more glamorous studies on. This is why impact factor is a load of bullshit, and anyone whose hands itch to oppress "low impact" science should be kept the hell away from research funding strategies, for they obviously have no fucking clue how research works in the first place. Grrr. How can anyone vote against a species description as awesome as Fan et al. 2010 above?

Reference
Fan, X., Chen, X., Song, W., Al-Rasheid, K., & Warren, A. (2010). Two new marine Frontonia species, F. mengi spec. nov. and F. magna spec. nov. (Protozoa; Ciliophora), with notes on their phylogeny based on SSU rRNA gene sequence data INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY DOI: 10.1099/ijs.0.024794-0

Dermamoeba – Having your coat and eating it too

We've been neglecting the micro-squishies lately (filose amoebae ain't proper squishies – too many fine protrusions in the way). Amoebozoa is a eukaryotic supergroup comprised of predominantly lobose amoebae, meaning their pseudopods are rounded and not fine and pointy (like those in the preceding post's organism – Filoreta). Aside from the test-bearing Arcellinids, amoebozoans tend to be naked amoebae ('gymnamoebae'), like the well-known Amoeba proteus, often erroneously referred to as a 'primitive', 'simple' or 'ancient' organism. "Naked amoeba" is a bit of a misnomer – while they don't lug rocks and heavy dishware around like testate amoebae, they generally carry some sort of cover, as most cells do. Gymnamoebae just pack light. Some, like Cochliopodium, dress themselves in intricate scales, while others, like many Vannellids, are covered in thin, pointy glycostyles. Dermamoeba, in turn, wears a thick, heavy coat.

5-8 Dermamoeba going about its business (n – nucleus, cv – contractile vacuole). 9 – Dermamoeba lounging about in cysts (c) upon devouring some algae (chain-forming diatom or some Trebonema-like thing). Nom nom nom. (Smirnov et al. 2011 EJP)

Dermamoeba's fine coat consists of thick bi-layered glycocalyx (a covering of fluffy sugar-proteins), sometimes with additional 'dense matter' lining the cell membrane. Upon encystation, an extra layer, the cell wall, is formed, but the contraption is thick enough without it already, at about half a micron.

EM sections through the intense Dermamoeba cell coat. m – cell membrane, gl – glycocalyx, adm – 'arrangement of dense material' (ie, "we don't know"). The glycocalyx often forms pretty patterns when sectioned. (15 is part of a Golgi body) (Smirnov et al. 2011 EJP)

This thick coat poses some problems of its own. Amoebae eat by engulfing prey with their pseudopods – and this involves some degree of nudity and cell membrane exposure. Half a micron of glycocalyx wouldn't be particularly flexible, and and not much fun to digest. Dermamoeba has to nibble on its coat before the meal. Upon contacting prey (typically algae), the amoeba forms a concave food cup around it, from the centre of which the cell coat gradually disappears. As the food cup deepens, the prey is pulled in to meet its doom via thick bundles of actin microfilaments spanning much of the cell – another unusual feature of this process. The prey is consequently engulfed for eventual digestion. As a result, the prey-containing vacuole has no glycocalyx for the amoeba to choke on (or rather, presumably, waste energy digesting).

Diagram of Dermamoeba's unusual feeding procedure. After the algal prey (al) is contacted by the amoeba (am), the glycocalyx (gl) is digested and the prey is drawn in by thick actin microfilament bundles (mf). The resulting food vacuole (fv) is conveniently devoid of coat material. (Smirnov et al. 2011 EJP)

And here the food cup is 'live', or was before some electron microscopist brutally murdered it in osmic acid and sliced it up:

EM sections through prey (al) being engulfed by the amoeba (am). Note the disappearance of the glycocalyx (gl) at the centre of the invagination. (Smirnov et al. 2011 EJP)

How do some of the other coat-bearing amoebae get around their irremovable clothing? Without going into much detail (amoebozoan surface coverings are really cool...), the glycostyle-bearing Pellita simple sticks small 'subpseudopodia' through it for both moving about and feeding. In fact, some propose that the glycostyles may help it move by reducing the surface area in contact with the substrate – keeping the sticky cell membrane away on stilts.

Top left: Pellita walking on stilts of glycostyles (depicted at the right). Bottom: extruding sub-feet across stilts for feeding. (Smirnov & Kudryavtsev 2005 EJP)

I'm decidedly avoiding amoebozoan systematics here. Christopher Taylor did a nice overview of it at the Catalogue of Organisms a while back, but keep in mind that some of the groups did jump around since then, and the phylogenies are in the works. Maybe if more people cared, the taxonomy could be resolved sooner...

PS: My committee* has voted to remove "Sunday Protist" from Sunday Protist titles, since:
a) They seldom come out on Sundays anyway (lulz); and
b) Takes up too much valuable headline real estate. Since we bloggers are supposedly playing pseudo-journalists or something, might as well play it right... ;-)
(and c) Structure and I aren't the best of friends.)

* Given how inefficient my brain is at accomplishing anything, I've concluded it can only be composed of a close neural approximation of a committee. Explains the indecisiveness as well. Probably requires a double majority to pass any major decisions, and hence is about as effective as the Californian government. Without the sovereign debt crisis, fortunately.

References
SMIRNOV, A., & KUDRYAVTSEV, A. (2005). Pellitidae n. fam. (Lobosea, Gymnamoebia) – a new family, accommodating two amoebae with an unusual cell coat and an original mode of locomotion, n.g., n.sp. and comb. nov European Journal of Protistology, 41 (4), 257-267 DOI: 10.1016/j.ejop.2005.05.002

Smirnov AV, Bedjagina OM, & Goodkov AV (2011). Dermamoeba algensis n. sp. (Amoebozoa, Dermamoebidae) – An algivorous lobose amoeba with complex cell coat and unusual feeding mode European Journal of Protistology : 10.1016/j.ejop.2010.12.002

Sunday Protist – Trimastix marina

Before we begin, two things about [current] Trimastix marina – it has four flagella (not three) and is found in freshwater. The taxonomic author, Saville-Kent, is a bit notorious for some rather sketchy descriptions, and Trimastix is one of his 'trophies'. That said, it may be that Kent did actually see a three-flagellated and/or marine thing like this and it just hasn't been found or published yet. But for the time being, feel free to point and laugh at the double misnomer.

This past fall I dumped a bunch of leaves in a dish and kept them wet for a while. Turns out, the abundance and diversity of microbes and meiofauna thriving in that pile of dead leaves in your yard is quite amazing – all sorts of ciliates, myxomycetes (slime moulds), tardigrades, rotifers, springtails, flagellates, amoebae – you name it. Some of this world can be seen with a simple dissecting scope; it helps to put a coverslip or some other piece of glass on the wet leaves to see better. This coverslip is also great for investigating what lives on the surface of the rotting leaves. The other impressive detail was how quickly the leaf tissues rot away, after a couple months leaving little more than the bare skeleton of the vascular system. Dead leaves are the whale falls of the terrestrial microbiome.

Rotting tissues tend to have relatively low oxygen concentrations, and thus host some unique organisms. Among them was this peculiar flagellate that simply screamed "EXCAVATE" at the top of its lungs, but I couldn't quite figure out what it was:

Trimastix marina. The cell body is about 25-30µm, with a prominent anterior flagellum sticking out in front, and three smaller flagella trailing behind. The nucleus is the little blob at the very anterior tip of the cell, in front of a large circular food vacuole. At the very posterior tip is the contractile vacuole characteristic of freshwater things in general. Along the side of the cell is an exceptionally conspicuous groove, through which one of the recurrent flagella runs – a characteristic feature of excavates. Anoxic, leaf litter moistened with ample water for a couple of weeks. 40x obj, DIC

The part that screamed "EXCAVATE" at me was the distinctive groove (namesake of the supergroup) along the side of the cell. You can often discern it in other excavates like Jakobids, Retortamonads and Carpediemonas-like organisms (CLOs; hey, it beats "Clade B"...), but here you don't even have to look hard. Curiously, the closely related oxymonads (see Streblo, Saccinobaculus) seem to have lost the groove, but that's another story.

Overview of 'basic' excavate cell types. Trimastix marina is the very distinctive one in the bottom middle. There's something distinctive and cute about its thick anterior flagellum and the way it moves. (Simpson et al. 2002 JEM)

Thus far, Trimastix may seem like your garden variety peculiar flagellate. But there's something universally eukaryotic you might have difficulty finding – a proper mitochondrion.

I mentioned earlier the sample was somewhat anoxic. It wasn't irrelevant, because I've never seen anything like this critter in regular pondwater or well-aerated soil. Like many of its excavate relatives, Trimastix has lost the necessity to maintain the elaborate complexity of aerobic pathways and their accompanying structures, like cristae. Furthermore, it lacks a mitochondrial genome. This led to the conclusion that Trimastix lacks anything mitochondrial altogether, and may have diverged prior to mitochondrial endosymbiosis – a perfectly reasonable assumption given the data at the time. This landed Trimastix (along with the better-known sister Oxymonads) a position in then-subkingdom/phylum Archezoa (Cavalier-Smith 1983)
[NB: Archezoa = 'beginning/early animals', not ArchaEzoa, which would be 'ancient animals'. He seems particular about that.]

Trimastix wasn't a major player in the Archezoa Hypothesis (wherein 'amitochondriate' lineages are contemporary representatives of pre-endosymbiotic eukaryotes) since it's rather obscure, but was still a piece of the puzzle. Eventually, better phylogenetic techniques and improved taxon sampling destroyed the Archezoa Hypothesis, particularly as mitochondrial genes and derived organelles (such as mitosomes and hydrogenosomes) were found. Trimastix's mitochondrial genes were found later than those of other anaerobes, perhaps owing to its obscurity – but they're there: mitochondrion-targetting genes in the nuclear genome (Hampl et al. 2008 PLoS ONE). Furthermore, the aftermath of mitochondrial reduction looks like a generic double-membrane bound blob in electron micrographs (Hampl & Simpson 2008 in Hydrogenosomes and Mitosomes: Mitochondria of Anaerobic Eukaryotes) – no wonder it was so hard to find!

All that's left of Trimastix's mitochondrion, as the eons of anaerobic existence devoured its need to maintain one. It is uncertain whether it produces hydrogen gas – which would make it a hydrogenosome rather than a mitosome – though at least some of the necessary genes seem to be present in the nuclear genome. (Hampl & Simpson 2008)

As an aside, there's no known case yet of a reduced mitochondrion that simply disappeared – in addition to aerobic respiration, eukaryotes have also become dependent upon it for some other vital metabolic pathways, such as those involving the Fe-S cluster. In fact, in at least one species of microsporidia, ATP is imported into the mitochondrial relic in order to keep the key metabolic pathways running. (I vaguely recall having written about this before, somewhere...)

Lastly, Trimastix is host to some lateral gene transfer for its glycolytic pathway – it appears to have picked up and replaced at least four of the eukaryotic genes with bacterial versions (Stechmann et al. 2006 BMC Evol Biol). There was a discussion somewhere on the blogosphere lately (Coyne's blog, IIRC) about the relative importance of LGT – it sure as hell does happen in eukaryotes as well, though not crazy enough to wreak havoc on the phylogenies.


And the rain hasn't stopped yet. But I can't skip a second night of sleep... as much as I'd love to keep blogging about stuff.

References
Hampl, V., Silberman, J., Stechmann, A., Diaz-Triviño, S., Johnson, P., & Roger, A. (2008). Genetic Evidence for a Mitochondriate Ancestry in the ‘Amitochondriate’ Flagellate Trimastix pyriformis PLoS ONE, 3 (1) DOI: 10.1371/journal.pone.0001383

Hampl, V, & Simpson, AGB (2008). Possible Mitochondria-Related Organelles in Poorly-Studied “Amitochondriate” Eukaryotes HYDROGENOSOMES AND MITOSOMES: MITOCHONDRIA OF ANAEROBIC EUKARYOTES DOI: 10.1007/7171_2007_107

SIMPSON, A., RADEK, R., DACKS, J., & O'KELLY, C. (2002). How Oxymonads Lost Their Groove: An Ultrastructural Comparison of Monocercomonoides and Excavate Taxa The Journal of Eukaryotic Microbiology, 49 (3), 239-248 DOI: 10.1111/j.1550-7408.2002.tb00529.x

Stechmann, A., Baumgartner, M., Silberman, J., & Roger, A. (2006). The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic BMC Evolutionary Biology, 6 (1) DOI: 10.1186/1471-2148-6-101

Sunday Protist – Gromia: beautiful predatory grapes of the sea

And we're back. The protists and I, that is. Well, the protists never quite went anywhere but you know what I mean...

You may have heard of Gromia a couple years ago when it hit the news by leaving tracks on the ocean floor resembling Ediacaran trace fossils (tracks). Or perhaps not; I tend to get overly excited the one time a year some protist makes the news. The giant (3cm) track-leaving Gromia in question sounded even cooler as it came from the great deep sea; other species of Gromia are in fact quite content with the more familiar shallow waters as well, crawling on the holdfasts of kelp in addition to thriving in the ice cold polar waters of McMurdo Sound (Antarctica), where the vibrantly colourful first specimen below comes from:

Gromia, from various locales including Antarctica (A), Madeira in the Atlantic (B) and Guam (C). Big and colourful, what's not to like there? Scalebars: A - 1mm; B - 0.5mm; C - 0.1mm (Burki et al. 2002 Protist)

For some time, there has been considerable confusion between Gromia and the cruelly similarly-named foraminiferan Allogromia, bad enough to warrant a Nature paper (Hedley 1958). At first glance, they do appear somewhat similar: a sizeable grape-like blob of a test surrounded by a mass of fine pseudopodia. While foram pseudopodia form a rather elaborate and extensive network of doom and terror for anything they come in contact with, Gromia uses more modest non-fusing alternative of pseudopodia. Thus, prior to molecular data, it was often considered a sort of a precursor to the more grown-up real forams, and assumed to have a rather simple test. They could hardly be more wrong, both with the assumed relation to forams and the simplicity of its test.

Typically (using that word rather loosely), a protist test consists of the plasma membrane covered by some sort of an organic matrix (often sugary proteins and protein-y sugars), followed by the deposited structural material, be it agglutinated bits of rock from the environment (often carefully and specifically selected) or secreted calcium carbonate, siliceous scales or something else entirely. To my knowledge, the process of selecting material for the test in agglutinating species, and formation of the test in general, is still quite poorly understood. There is some understanding of how diatoms and some coccolithophorids build their extracellular wonders, but most amoebae have been largely ignored, even the more 'famous' representatives like the forams, euglyphids and arcellinids. The Allogromia mentioned earlier has the organic (non-calcified, non-agglutinated) test characteristic of Allogromiids at large, who form a vast paraphyletic sea of diversity from which the more popular lineages arise – the Protista of the foram world, if you will.

Gromia also carries an organic test, hence the confusion with Allogromiids. But its test turns out to be a bit more elaborate, with an inner lining consisting of up to ten layers of odd honeycomb membranes, the whole thickness of the structure penetrated by multitudes of pores. The test surface is sometimes covered by attached bacteria (Aranda da Silva & Gooday 2009 DSR II). Furthermore, rather than simply a hole in the wall, its opening is surrounded by a complicated oral capsule which acts as a valve or a trap door: when the pseudopodia are withdrawn, the opening closes. One seldom thinks of movable structural parts on the microscopic level, but here you go:

The structure of Gromia's test and oral capsule, in that order. The figure on the right shows a pseudopodium gradually protruding through the closed aperture. (Hedley & Bertaud 1962 J Protozool; Mazei & Tsiganov 2006 in Presnovodniye Rakoviye Amyobi (in Rus.))

The pores make the test surface look quite pretty in reflected light:

The giant deep sea Gromia sphaerica; note the complex test surface structure with prominent perforations. (Matz et al. 2008 Curr Biol)

To make these mysterious 'grapes' of the sea even sexier, they are known to have sex. Upon conjugation, flagellated gametes are exchanged between the parents, producing amoeboid diploid swarmers that ultimately form a new test and complete the cycle. The parental shell and all the work that went into building one is abandoned in this process. Both forams and gromiids are 'mortal' in our sense – they spend a period of time building a body that eventually becomes abandoned by the next generation. Organisms like many flagellates, for example, are somewhat 'immortal' in that the cell is never abandoned between generations, but rather split up and shared by mostly clonal offspring. Extra structural complexity often bears the curse of losing 'immortality'.

Gromia's life cycle. (Arnold 1966 J Protozool)

Gromia shares some strangeness with giant deep sea Xenophyophores (forams): they like to live in their own excrement. This may sound disturbing, but they're still fairly microscopic, so their shit is of a rather more chemical character. Curiously, both Xenophyophores and Gromia tend to lean toward the upper end of the protist size range, perhaps partly aided by their inability or lack of desire to part with their faeces – these faecal pellets, so-called stercomata, appear to play a structural role in the Xenophyophores, and may well contribute to structure in Gromiids as well. Waste accumulation is not too grave a problem for these organisms due to their habit of generating clouds of swarmers that ditch the parental shell forever.

As alluded to earlier, gromiids are fairly distantly related to forams, and definitely evolved their elaborate test independently. For some time, gromiids were thought to be closely related to filose amoebae with shells, ie cercozoan euglyphids and such. Turns out, while not too close to the euglyphids, Gromia is a cercozoan (Burki et al. 2002 Protist), and tends towards the endomyxean side with the plant parasite phytomyxids, vicious vampyrellid amoebae and the ornate haplosporidia. In other words, things that look little like them, aside from a tendency to form thin pseudopodia.

Gromiids probably have a bigger story to tell, as environmental sequence data reveal swaths of cryptic diversity, and new species are still being described from the deep sea as well as polar waters (eg. Rothe et al. 2009 Zool J Linn Soc; Gooday & Bowser 2004 Protist; Rothe et al. 2011 Polar Biol; and Aranda da Silva et al. 2006 Mar Biol for diversity porn). As for their ecological niche, the gromiids seem to play a similar role to allogromiids and other forams – versatile predators preying on algae and anything else that gets caught in their feet.

Aww, they even grow on trees! Gromia schmoozing with a tree-shaped foram, Pelosina, possibly in some sort of a symbiotic relationship. (Gooday & Bowser 2004 Protist)

Hopefully back to more regular blogging now. Quality of writing is at the mercy of my irritating writer's block, you have been warned...

References
Aranda da Silva, A., & Gooday, A. (2009). Large organic-walled Protista (Gromia) in the Arabian Sea: Density, diversity, distribution and ecology Deep Sea Research Part II: Topical Studies in Oceanography, 56 (6-7), 422-433 DOI: 10.1016/j.dsr2.2008.12.027

Silva, A., Pawlowski, J., & Gooday, A. (2005). High diversity of deep-sea Gromia from the Arabian Sea revealed by small subunit rDNA sequence analysis Marine Biology, 148 (4), 769-777 DOI: 10.1007/s00227-005-0071-9

ARNOLD, Z. (1966). Observations on the Sexual Generation of Gromia oviformis Dujardin The Journal of Eukaryotic Microbiology, 13 (1), 23-27 DOI: 10.1111/j.1550-7408.1966.tb01863.x

Zach M. Arnold (1952). Structure and Paleontological Significance of the Oral Apparatus of the Foraminiferoid Gromia oviformis Dujardin Journal of Paleontology, 26 (5), 829-831

BURKI, F. (2002). Phylogenetic Position of Dujardin inferred from Nuclear-Encoded Small Subunit Ribosomal DNA Protist, 153 (3), 251-260 DOI: 10.1078/1434-4610-00102

[Fuck this, the browser crashed TWICE and I'm not finding all the links again. Not tonight anyway. URLs are in the post.]

Sunday Protist - A sampling of Cercozoa Part I

This post grew out of proportion, so I'm splitting it into two or three parts, to cater to our ever-shortening attention spans (mine included)...

[Warning: Taxonomy. Of the harshest kind: involves Cavalier-Smith]

At the moment, among my favourite supergroups is Rhizaria (tree). Rhizaria is generally where all the obscure, interesting, and outright weird eukaryotes get sent by molecular data these days. The group itself is fairly recent, having been formally spewed out declared by Cavalier-Smith in 2002, as a fusion of Cercozoa and Retaria(=forams and 'radiolarians'), as well as Heliozoa and Apusozoa, apparently because they had "a centrosomal core or radiating microtubules and two microtubular roots and soft surface, typically with reticulopodia." (TC-S 2002 IJSEM:297) Don't worry, I don't really know what that means either. That is, those are fairly common traits in many non-Rhizarians, even according to the TC-S 2002 classification.

The name derives from the group's inclusion of many members of the then-defunct "Rhizopods" ('root-feet' - members typically had thin, branchy pseudopodia). Since then, Heliozoa died a horrible death with its limbs strewn all over the tree (Nikolaev et al. 2004 PNAS) and [many] Apusozoa now seem to enjoy their privileged life as the putative basal Opisthokonts (or their sisters). Ironically, many of the "Heliozoa" did return to Cercozoa later. Obligatory TC-S Diagram:

The birth of Rhizaria. As the young supergroup struggles to open its eyes to the world for the first time, it is confronted by the glaring faces of frustrated readers threatening to ban the author from ever birthing another taxon, for the sake of global sanity. Yet, despite its weak, fragile synapomorphies, the newborn supergroup, heavily-medicated by state-of-the-art molecular phylogenies, rises to become a bona fide citizen of the taxonomic world. For now. As all other life forms on earth, the higher taxa themselves are mortal. (diagram slightly modified (red box added) from Cavalier-Smith 2002 IJSEM)

"Radiolarians" (Acantharians+Taxopodids+Polycystines) and Forams (more generally, Granuloreticulosea) are massively diverse, complicated and awesome, but Cercozoa are more obscure to non-protistologists, and are a rather weird assemblage of stuff. I think the Amoebozoan taxon "Variosea" would have been quite fitting for them, were it not taken by amoebae instead. Cercozoa is older than Rhizaria, but not by much - it was formally established by Cavalier-Smith in 1998 (Biol Rev) as a modified successor of Rhizopoda:

"The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some ‘ rhizopods ’ and is therefore renamed Cercozoa" (TC-S 1998 BiolRev:203)

Of course, that was Tom's version of Rhizopoda to begin with. Taxonomy gets very fun when different people at different times mean different things by the same name. Can't seem to find the etymology of Cercozoa, but the formal description reads pretty much like 'miscellaneous eukaryotes with thin pseudopodia'. And that they are.

While Cercozoa was initially based loosely on morphology and sketchy data from the dawn of molecular phylogenetics, it mostly survived intact over the years, and grew further (with various things shaved off too, of course). The original members were Phytomyxids (incl. the plant pathogen Plasmodiophora), Reticulofilosa (basically, Chlorarachniophytes) and Monadofilosa (Cercomonas, Gymnophrys, Euglypha and Spongomonas are given as original examples). Curiously, all of them survived the onslaught of molecular reality (or so we hope...). Stuff has been added, like Ascetosporea (paramyxids and haplosporidia; added in TC-S 2002 IJSEM) and the gromiids, as well as various obscure incertae sedis orphans and a few refugees from 'Heliozoa'.

Eventually, the Cercozoa got 'sistered' to the forams (Keeling 2001 MBE) by ACTIN phylogenies, which got taxonomically recognised in the TC-S 2002 IJSEM revision of The Book of Tom by declaring the holy union of Retaria (forams and rads) and Cercozoa as Rhizaria. Going overboard as usual by adding in Heliozoa and Apusozoa, of course. We're talking about the mad taxonomist here ;-) (now someone needs to make that into a pop culture phenomenon to rival mad scientists..."And along comes the evil mad taxonomist...and RENAMES EVERYTHING!" *cue spooky music*) The group still lacks any solid synapomorphies (shared derived characters); the situation is such that even the use of obscure ultrastructural elements has been attempted, such as Cavalier-Smith's "transitional nonagonal fibre" (TC-S 2008 Protist) – even one of his own past students has no idea what he meant there!

And a whole bunch of other stuff happened but I think that was enough Historical Taxonomy (would make the most popular course evar, srsly) for...the month. Ok, so have we lost everyone yet? Or have the wiser ones employed the high art of The Scrollbar and skimmed accordingly? In any case, I'd like to very briefly and shallowly run over a few of the major cercozoans to give you a taste of the phylum, and just how diverse and varied it is. Things will be skipped, including, quite possibly, The Most Interesting Thing Ever Because You Studied it for the Past Ten Years. Apologies in advance. TMITEBYSiftPTY will get its chance, someday.

Some phylogeny and taxonomy sources: TC-S & Chao 2003; Bass & TC-S 2004; Bass et al. 2005; Pawlowski & Burki 2009; Chantangsi et al. 2010.

(L: Pawlowski & Burki 2009; R: Chantangsi et al. 2010)

To be continued in Part II – Endomyxa.

References
Bass D, & Cavalier-Smith T (2004). Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). International journal of systematic and evolutionary microbiology, 54 (Pt 6), 2393-404 PMID: 15545489

BASS, D. (2005). Polyubiquitin Insertions and the Phylogeny of Cercozoa and Rhizaria Protist, 156 (2), 149-161 DOI: 10.1016/j.protis.2005.03.001

CAVALIER-SMITH, T. (1998). A revised six-kingdom system of life Biological Reviews of the Cambridge Philosophical Society, 73 (3), 203-266 DOI: 10.1017/S0006323198005167

Cavalier-Smith T (2002). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International journal of systematic and evolutionary microbiology, 52 (Pt 2), 297-354 PMID: 11931142

Cavalier-Smith, T., & Chao, E. (2003). Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution Journal of Molecular Evolution, 56 (5), 540-563 DOI: 10.1007/s00239-002-2424-z

CAVALIERSMITH, T., LEWIS, R., CHAO, E., OATES, B., & BASS, D. (2008). Morphology and Phylogeny of Sainouron acronematica sp. n. and the Ultrastructural Unity of Cercozoa Protist, 159 (4), 591-620 DOI: 10.1016/j.protis.2008.04.002

Chantangsi, C., Hoppenrath, M., & Leander, B. (2010). Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions Molecular Phylogenetics and Evolution, 57 (2), 518-527 DOI: 10.1016/j.ympev.2010.07.007

Keeling PJ (2001). Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Molecular biology and evolution, 18 (8), 1551-7 PMID: 11470846

Nikolaev, S. (2004). From the Cover: The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes Proceedings of the National Academy of Sciences, 101 (21), 8066-8071 DOI: 10.1073/pnas.0308602101

PAWLOWSKI, J., & BURKI, F. (2009). Untangling the Phylogeny of Amoeboid Protists Journal of Eukaryotic Microbiology, 56 (1), 16-25 DOI: 10.1111/j.1550-7408.2008.00379.x

Sunday Protist - Ciliate-in-a-basket: Dictyocysta

Crazy days this week (and possibly next), so a short one. This tintinnid ciliate has a particularly beautiful lorica:

SEM of Dictyocysta in its lorica. Scalebar = 40µm (Agatha 2010 J Euk Microbiol)

Tintinnids construct their loricas out of proteins and polysaccharides, and some species attach matter from their surroundings. There's a few interesting stories involving them, but I still need to finish the post on that. Tintinnids are only very distantly related to Folliculinids, and both evolved their loricae independently from each other. Several other lineages of ciliates also construct tests, but Tintinnids and Folliculinids are the most prominent ones. And have cool names.

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Two midterms this week, midterm and lab exam the week after, writing my GREs in three weeks, blankly staring at grad school apps and trying to find a way to justify my existence in 500 words or less for the personal statements (You must be so jealous of me, I know). Also need to finish a bunch of stuff for work – was too distracted this past week.

Blogging-wise, I'm hosting the upcoming MolBiol Carnival; you should submit early and often so that I don't have to fake data posts. Faking posts is baaaad. Don't make do it. Here's the link to save me from immoral temptations: LINK. <-- click there and submit to the carnival. (intentionally ambiguous, mwahaha) I'll also be writing up a very interesting seminar talk involving molecular biol, mutation, genomes, introns, popgen and really cool evolution stories. The topics are a bit intense, so it may take me a while to understand it in a way that's not outright wrong, but very soon there'll be a continuation of my non-adaptive evolution series. To get you more excited, the speaker in question is Michael Lynch!

Oh, and I will finish Part III of In Defense of Constructive Neutral Evolution as soon as I can get around to it. Apparently some of you actually do care, so I must return the favour =D

Not enough time in the day to get everything done. Damn you, physics! (I'd imagine that slowing down Earth's revolutions would have drastic side effects wiping out all cumbersome macroscopic life in an instant. Prokaryotes, and possibly even unicellular protists, wouldn't mind much though).

Sunday Protist – Nematode-hunting amoebae: Theratromyxa

A couple posts ago we saw how ecological relationships may refuse to obey the laws of their kingdoms: protists can hunt crustaceans. Protists can also farm bacteria, animals can parasitise unicellular protists, plants can parasitise fungi, fungi can hunt animals, animals can steal plastids and photosynthesise, as well as steal algae for their embryos, fungi parasitise protists, and perhaps plants may even feast on the occasional bacterium or two (though that's yet to be confirmed). It seems neither the organisms in question nor evolution itself received the memo wherein "plants photosynthesise, animals hunt, fungi decompose, protists are generic microbial slime subservient to all the former". Probably forget to staple cover sheets to their TPS reports as well.

In the predatory foram case, you may be shrugging your shoulders and remarking that those forams are pretty damn huge anyway, so it's not that incredible. Alright, I'll grant you that. But what about a fairly small single-celled amoeba tackling nematodes in the soil?

Life cycle of Theratromyxa, involving predation on food a little too large for its size followed by long-term digestion and slumber in cysts. Not a bad lifestyle. (Sayre 1973 J Nematol; Sayre & Wergin 1989 Can J Microbiol)

Imagine you're living your life as a diminutive nematode, and suddenly a small creepy-looking branchy amoeba crawls toward you. Shivers descend down your non-existent spine as the amoeba extends its slender pseudopodia all over your body and gradually engulfs it. Your writhe in terror, but to no avail, for the creepy monster who just moments before appeared tiny and insignificant now has you inside a digestive vacuole full of acid and unfriendly enzymes. If you were lucky, some of your companions were engulfed along with you, so while packed in like sardines, you still have company. You wonder whether this is payback for all the evil you had wrought upon those poor plant roots. Little do you know your entire plight has been carefully planned by your self-proclaimed overlords from another phylum, just to get pretty pictures in the end:

Light micrographs (left; Sayre 1973 J Nematol) and SEM of Theratromyxa (right; Sayre & Wergin 1989 Can J Microbiol). Image 6 shows quite nicely how Theratromyxa captures the nematode. This looks rather similar in principle to the feeding veil of dinoflagellate Protoperidium. Sometimes the amoeba can capture several nematodes at once. SEM shows amoeba enveloping a nematode.

Theratromyxa has been considered for use as a biological control agent for the root-knot nematode (a very tiny group of nematodes, G. Meloidogyne. However, it wasn't particularly effective as excystment was rather slow, and there was no known method of speeding it up. Apparently, anastamosis (joining of numerous pseudopodia/amoebae) has been reported in previous studies, but Sayre 1973 did not observe any. But there still is the possibility of several Theratromyxa individuals (or their relatives) also ganging up on larger prey, as some other protists are known to do (eg. centrohelids cooperating in hunting larger ciliates).

Theratromyxa is a Vampyrellid, a group of rather frightening amoebae, likely in the Endomyxa clade of Cercozoans/Rhizarians (see Pawlowski & Burki 2009 JEM; Parfrey et al. 2010 Syst Biol) (AFAIK, endomyxans are cercozoans, but considering the amount of stuff that's gradually settling in Endomyxa, perhaps the definition of cercozoa is bound to change eventually. I like 'Cercozoa' better than 'Filosea', the other subgroup of cercozoans; ie, it'd be nice to ditch 'Filosea', replace it with 'Cercozoa' and make Endomyxa not Cercozoans. Confused? Don't worry – just taxonomic musings.) Some other Vampyrellids are notorious for poking holes in fungi (Anderson & Patrick 1980 Soil Biol Biochem) and algae (life cycle), and then devouring the cells within. Not a very happy thought if you're a filamentous alga.

By the way, some cercozoan amoeboflagellates can gang up on larger nematodes too, but I'll save that for another day.

References
Sayre RM (1973). Theratromyxa weberi, An Amoeba Predatory on Plant-Parasitic Nematodes. Journal of nematology, 5 (4), 258-64 PMID: 19319347

Sayre, R., & Wergin, W. (1989). Morphology and fine structure of the trophozoites of Theratromyxa weberi (Protozoa: Vampyrellidae) predacious on soil nematodes Canadian Journal of Microbiology, 35 (5), 589-602 DOI: 10.1139/m89-094

Sunday Protist - Farming forams: a case of protistan agriculture

"WTF, it's Friday already!" Friday? What Friday? You saw nothing.

My previous two Sunday Protist attempts got derailed. With the first one, noticed there was quite a bit to say about them, and decided to postpone it for later as it was a big topic (and unrelated to my current work). Then I picked something relevant to my day job, y'know, two birds one stone, etc. And somehow that led me to paleontology. A warzone in paleontology. Complete and total clusterfuck. With potential inaccuracies here and there that I now need to sort out. Whilst we wait, I'll just do something quick: a case of a foraminiferan apparently growing bacteria and then eating them in perhaps one of the most non-human farming enterprises ever! (leafcutter ants are pretty much human at that phylogenetic distance...)

Textularia blocki lives on seagrass. Many forams have interesting associations with seaweeds, ranging from internal parasitism to epiphytic attachment, usually via secretions of sulfated mucopolysaccharides, a fairly common material in the extracellular matrix. T.blocki, however, is a freely motile foram. It leaves peculiar 'grazing traces' as it crawls along the seagrass, without damaging the tissue beneath it:

Left: T.blocki with grazing traces on blade of seagrass. Right: (Langer & Gehring 1993 J Foram Res)

As made evident in the diagram, the traces consist of two parallel 'walls', consisting of pale whitish adhesive material, presumably containing mucopolysaccharides, devoid of sand grains or other contaminants. Curiously, some forams carried sand grains along, without depositing them. These secretions are formed by pseudopodia, or the 'business' part of the foram: an intricate network of reticulated feet with amazing cytoskeletal properties. When these secretions are left alone in seawater for 48h, a lush garden of bacteria sprung up specifically along the secretion traces:

Bacterial gardens along the foraminiferan secretion traces. Note the relatively clean surface of the leaf outside the secretions, supporting that it is the adhesive mucous that attracts bacterial accumulation (Langer & Gehring 1993 J Foram Res)

When released back into the medium containing the seagrass lined with traces, the forams approach the nearest trace and follow along it, suggesting they use some form of chemical sensing to determine where the secretions are and how they are oriented. The speed is then reduced, suggesting the foram is then busy grazing on their bacterial harvest.

Thus, a 'mere' single celled organism can produce organised tracks of nutritious material, wait for their bacterial crop to grow, and subsequently harvest it. We like to think we invented agriculture. The more biologically-oriented among us point out leafcutter ant fungus gardens and aphid farming. Yet, agriculture has also evolved on the unicellular scale in a small humble foraminiferan living among blades of seagrass. Humbling, isn't it?

Interestingly, a similar behaviour has been described gastropods like slugs and limpets, as their mucous also attracts bacterial growth. Convergence: when a good thing is chanced upon multiple times, it will likely be kept by several lineages independently. This applies to language and cultural evolution as well as that of biological organisms.


We tend to have a deep conviction that cells are dumb blobs of goo, incapable of any sort of behaviour besides basic phototaxis or whatever. We think cells are just simple chemical response machines – which is true. But ultimately, so are we. There is no fundamental distinction between human social dynamics and the adventures of a crawling amoeba. The difference is all in the quantity and complexity of interactions – the higher the complexity, the more random (stochastic) the system appears (and to an extent, is). While I must concede that in terms of the number of components and pathways involved, human or ant behaviours are more complex than that of an amoeba, that does not mean the proverbial amoeba 'lacks' behaviour entirely.

I've mentioned the cellular behaviour stuff before, probably too often for regular readers. Apparently, that idea needs restating though. Also, as a cell biologist, I find it quite...well, pleasing. It's nice that, ultimately, my subjects are no more or less machine-like than humans or plants. Furthermore, where I was heading with this originally, I think part of our notion of cells being 'stupid' comes from the obsession with our own cells. Animal cells are, in fact, quite simple and developmentally retarded. The cause is cell specialisation driven by multicellularity. Eg. an epithelial cell can now afford to lose the ability to hunt around for prey, it no longer needs to coordinate movement in any sophisticated manner, the life cycle can be simplified to terminal differentiation.

Curiously, a similar problem plagues modern science and engineering: overspecialisation means that one must no longer have the same level of foundational education to survive, and thus we end up arguably knowing more about less, or perhaps knowing the same about less. I can suck at math or chemistry and get away with it. In the old days, people had to actually have a broader base just to function. Conversely, there was also less information floating around. Which is more efficient? Just as multicellularity vs. unicellularity, each system has its merits and drawbacks. So it's hard to tell.

A while back I found a paper on cellular complexity in multicellular vs. unicellular organisms that needs to be discussed in greater detail eventually...


---Random Link---
ChrisM over at the wonderful Echinoblog (about the cooler deuterostomes; ok, hemichordates and ascidians are cool too) wrote about sperm-eating ciliates infesting starfish.

Lots of things like sperm. For example, Monocystis is a gregarine with a penchant for earthworm sperm – infection rates are so high that if you slice up a worm from your backyard and smear the contents of its seminal vesicles on a slide, the chances are pretty good that you'll find some. And by 'some', I mean, LOTS. So if you're ever in the mood for some apicomplexans, all you need is an earthworm, a blade and a scope. There are parasites in pretty much anything and everything, so if you go around examining various animals, you may well find loads of cool protistan denizens in them. Many of which could be undescribed and, perhaps, new to science.

Reference
Langer, M., & Gehring, C. (1993). Bacteria farming; a possible feeding strategy of some smaller motile Foraminifera The Journal of Foraminiferal Research, 23 (1), 40-46 DOI: 10.2113/gsjfr.23.1.40