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 – Scary nematode-eating forams and their amazing feet of doom

Poor, poor nematodes...

In the interests of public safety, I must reiterate once again what should be so painfully apparent from the last few posts on forams: If you ever find yourself shrunk to a milimetre or less, DO NOT fuck with forams. Ever.

It's a fairly known fact around these parts that [unicellular] forams can devour [multicellular] animals. But thus far we've just had giant tree forams like Notodendrodes show us the terrifying force of microbial nature. Notodendrodes is notably bigger than its prey, so the embarrassed metazoa have an excuse there. As for giant planktonic forams – well, those eat things only slightly larger than themselves, you may say. In which case you must be almost insatiable. But, as usual, there's more: rather small, unassuming Ammonia tepida devouring nematodes, copepods and gastropods unarguably larger than itself.

Like other forams, Ammonia uses its amazing reticulopodia (lit. "net-feet") to trap and entangle prey. Then, it penetrates its prey's exoskeleton or cuticle and forcefully rips apart the insides to shreds, bringing back phagocytosed chunks towards the main cell body for digestion. This process is creepy enough to warrant its own term: skyllocytosis (Bowser 1985 J Prootozool). All that's left behind is an empty cuticle with a hole. By the way, the prey are devoured within 24 hours. And apparently forams are pretty much always hungry. Imagine being violated by masses of dynamic and powerful net-like pseudopodia and torn to pieces from the inside. Doesn't sound fun. Feels good to be big, doesn't it?

Ammonia tepida vs. nematodes. c and d show before and after shots of one such encounter. Sometimes a second foram joins for a threesome. (Dupuy et al. 2010 J Foram Res)

As for copepods...the following sentence from the paper raises some concern: "Despite vigorous attempts to escape, copepods could not free themselves from the pseudopodial mesh."(Dupuy et al. 2010 J Foram Res) Most of us have seen copepods one time or another. For the world of their scale, they're quite strong. And yet they cannot escape. Neither can snails, whose shells are all that remains after a few hours. Have I mentioned foram reticulopodia are simply amazing?

Ammonia tepida vs. copepod (a) and juvenile snails (b,c). Note how the copepod is partially eaten already towards the right. d,e - SEM view of the ventral (umbilical) end of the foram. Little bumps (pustules) are thought to potentially act as 'teeth' and used to grind tests and cuticles. Some other forams are thought to do this with diatoms as well. (Dupuy et al. 2010 J Foram Res)

You may wonder how foram pseudopodia get to be so special. They possess many unique properties, many of which have yet to be understood. One of the more striking features is the rate of microtubule growth. While microtubules of animal cells grow at about 1-15µm/min, microtubule assembly in some forams can reach a stunning 12µm per second (Bowser & Travis 2002 J Foram Res). They manage this by possessing a unique third conformation of tubulin: helical filaments (in addition to the usual protofilaments/'tubes and free dimers).

Transformation of tubulin between helical filaments and free dimers appears to require no ATP, and thus would progress quite rapidly. Furthermore, tubulin of helical filaments can transform directly to the tubules, much faster than regular polymerisation from free dimers. The idea is that tubulin is stored in helical form (crystalised, if you will), and then transported to the site of active growth, and used for a quick and efficient supply of the growing 'tubes with fresh tubulin (Welnhofer & Travis 1996 Cell Motil Cytosk). Thus, it is perhaps not overly surprising that foraminiferan tubulins are highly diverged, suggesting selective pressure for the foram-specific modifications (Habura et al. 2005 MBE). This is yet another example of bizarre alterations by a protist of typically conservative aspects of eukaryotic biology.

SEMs of foram pseudopodia entrapping prey; in this case, Artemia. (Bowser et al. 1992 J Protozool)

To have an idea of what the microtubule cytoskeleton looks like in action, here's a stolen video of plant epidermis cortical microtubules marked with AtEB1:GFP:

In vivo timelapse of cortical microtubules marked with (+)-end binding GFP growing in a tobacco leaf epidermis. Picked this one because it has a scalebar (10µm) and a timestamp (in seconds; movie is sped up, but the whole thing lasts a minute); I do happen to have my own, but finding + editing them would be a pain right now. This should give you an idea of how dynamic the cytoskeleton really is, though keep in mind it's not the best example by far. Noticed interesting recent developments in the plant cell morphogenesis/cytoskeleton story, wish I had time to keep up. (Source: Brandner et al. 2008 Plant Physiol Movie S1)

Now for the video of foram microtubules growing and fluorescing in vivo... oh wait, there is none. =(

There are no foram model organisms. Yet. As far as I know, there's no genome yet either. That should be taken care of. And someone needs to figure out how to transform/transfect (genetically) the buggers too. "Must have pretty movies of rapid microtubule growth" should look great on a grant app. Seriously, it's even shiny and glowy and stuff. Don't they like things that look like cancer/immunology research? (And this is probably why they don't let me write grants yet; not that I'm in any hurry to become a bureaucrat...)

Another foram teaser: some species (eg. Rotaliella heterocaryotica) possess two types of nuclei – germline and somatic – just like ciliates. Actually, no one has any idea how much like ciliates they are, as very little molecular work has been done. Might be another case of crazy genomic dimorphism with ridiculous epigenetic machinery, etc.

Or, just like forams themselves, it may be something else altogether.

References
BOWSER, S. (1985). Invasive Activity of Allogromia Pseudopodial Networks: Skyllocytosis of a Gelatin/Agar Gel The Journal of Eukaryotic Microbiology, 32 (1), 9-12 DOI: 10.1111/j.1550-7408.1985.tb03005.x

Bowser, S. (2002). RETICULOPODIA: STRUCTURAL AND BEHAVIORAL BASIS FOR THE SUPRAGENERIC PLACEMENT OF GRANULORETICULOSAN PROTISTS The Journal of Foraminiferal Research, 32 (4), 440-447 DOI: 10.2113/0320440

BOWSER, S., ALEXANDER, S., STOCKTON, W., & DELACA, T. (1992). Extracellular Matrix Augments Mechanical Properties of Pseudopodia in the Carnivorous Foraminiferan Astrammina rara: Role in Prey Capture The Journal of Eukaryotic Microbiology, 39 (6), 724-732 DOI: 10.1111/j.1550-7408.1992.tb04455.x

Brandner, K., Sambade, A., Boutant, E., Didier, P., Mely, Y., Ritzenthaler, C., & Heinlein, M. (2008). Tobacco Mosaic Virus Movement Protein Interacts with Green Fluorescent Protein-Tagged Microtubule End-Binding Protein 1 PLANT PHYSIOLOGY, 147 (2), 611-623 DOI: 10.1104/pp.108.117481

Dupuy, C., Rossignol, L., Geslin, E., & Pascal, P. (2010). PREDATION OF MUDFLAT MEIO-MACROFAUNAL METAZOANS BY A CALCAREOUS FORAMINIFER, AMMONIA TEPIDA (CUSHMAN, 1926) The Journal of Foraminiferal Research, 40 (4), 305-312 DOI: 10.2113/gsjfr.40.4.305

Habura, A. (2005). Structural and Functional Implications of an Unusual Foraminiferal -Tubulin Molecular Biology and Evolution, 22 (10), 2000-2009 DOI: 10.1093/molbev/msi190

Carnivorous trees of the sea: Notodendrodes not as harmless as it looks

Remember Notodendrodes and the spicule tree? Don't they look so much like harmless trees sitting around sunbathing like their plant counterparts? Not all tree forams are harmless. The microscopic marine world is full of surprises, like trees waving around their long sticky network 'feet' to trap and devour any traveler that happens by. Here's some wonderful shots of Notodendrodes caught in the act:

The top left image shows a clump of Artemia caught by Notodendrodes, a big carnivorous tree foram. Note how the reticulopodia (pseudopodial networks) stretch between the branches like spiderwebs. Top right: SEM of the reticulopodial mesh of another species of Notodendrodes. Bottom: The tree foram in its natural setting, with a copepod attached (arrow). (Suhr et al. 2008 Mar Ecol Prog Ser)

There some nice foram videos on this YouTube page, including shots of reticulopodia and a fairly large foram moving about in situ. This movie by a Japanese researcher includes clips of Artemia being captured starting at 0:50.

Many forams are voracious predators, devouring anything from fellow protists to crustaceans and echinoderm and mollusc larvae. The following is Astrammina rara's rather impressive menu; all but two species were happily consumed:

However, not all forams are carnivorous. Some are mediocre at best at capturing prey, and some, like Crithionina, are quite bad. This suggests a range of feeding habits from detritovory to carnovory to omnivory. Note how Gromia (not a foram, despite looking vaguely similar; placement somewhat uncertain, though most likely either close to forams or a cercozoan) fails to capture any prey. Also, dead specimens failed to catch prey, indicating the capture is intentional and requires a fully functioning cell, and not an accidental adhesion to something sticky. In fact, there is evidence for specific targetting of certain prey, which wouldn't be much of a stretch as many forams are quite picky in choosing their test material.

I think this has some interesting – perhaps borderline philosophical – implications. Towards the end of the ciliate kleptoplasty post I mentioned how the traditional ecological terms often fail to describe the majority of life, which happens to be microscopic and play by some different rules. There's a greater problem in the approach of traditional ecology towards microbial life, however, and it even surfaced in a random chat with some ecology grad students. Namely, the treatment of all things microbial as the "bottom of the food web", ie. prey species created by evolution to feed cute fluffy animals. They have a similar attitude to plants as well: 'producers'. Fungi are 'decomposers'.

Probably to people tracking bird migration out in the field, such crude terms do just fine, and we all must make crude approximations somewhere (or drown in details). However, as in any simplification, there's always a danger of skimming over interesting outliers. I disagree with the blanket treatment of protists (and bacteria, and anything else) as the "bottom of the food web" for two reasons:

1. There are plenty of intricate interactions resulting in elaborate food webs (and, more generally, 'interaction webs'); a plethora of fascinating relationships is lost when one blurs them all into the 'prey for animals' category.

2. Feeding by animals forms but a very tiny part of the overall diversity of microbe-animal interactions. An ecological framework must account for symbionts (mutualists, parasites and commensals) along with predation. Toxoplasma, arguably the most successful parasite of vertebrates ever, is a wonderful example of 'lower trophic levels' leeching 'up' the food web and running the show. You can't really draw an arrow from a cat or human to the modest apicomplexan, as it doesn't really consume its slaves. But you can't really not draw that arrow. It's complicated.

(In fact, if organisms besides humans had Facebook, most of their relationship statuses would be set to "It's complicated". Groan all you want... =P)

Lastly, our forams mentioned above also have ecological consequences on the megafauna in their environments. Astrammina rara is benthic, meaning it lives on the ocean floor (or, technically, any substrate). Suhr et al (2008) mention past studies indicating lower-than-usual densities of marine fauna in particular areas; these areas seem to match up with Astrammina's distribution. Presumably, the effects of predation on small fauna and larvae can be seen on the larger scale.

Furthermore, the carnivorous forams seem to affect the survival strategies of the fauna around them (in hindsight, unsurprisingly): some echinoids have brood protection and settling strategies that may well have evolved in response to the lowly single celled protists they rightly fear. The authors suggest that the failure of Astrammina to capture larvae of the echinoid Acodontaster may be a result of the latter evolving a specific chemical defense against it.

The 'scum' from the bottom of the foodweb can come up to bite some 'higher' organisms in the ass – whodathunk?

Reference
Suhr, S., Alexander, S., Gooday, A., Pond, D., & Bowser, S. (2008). Trophic modes of large Antarctic Foraminifera: roles of carnivory, omnivory, and detritivory Marine Ecology Progress Series, 371, 155-164 DOI: 10.3354/meps07693