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

Scaled protists and bloated distractions

Ok, I was gonna just post this picture as filler, and then suddenly got sucked into the microbial biogeography debate – you know, "is everything everywhere?" etc. So I was going to write up a quick blurb on that, but it somehow grew out of control. As I don't have time for such epic digressions at this moment, esp w a promised post quite overdue, amidst other stuff, I'll just shelve that for later and simply post the pretty picture instead. Enjoy this lineup of protists scaled to the size of a pinhead:

How many protists can dance atop a pin? (Finlay 2002 Science)
I'm going to try to vaguely identify them, from left to right: Chaos sp.; Stentor sp.; some random amoebozoan; Amoeba sp.; Loxodes? man I suck at this; Bursaria sp.?; Paramecium sp.; Mayorella sp.?; a euglyphid; another bloody ciliate; Strombidium; Difflugia-like thing; Euplotes; Ophryscolex-like; heterotrophic euglenid; heterotrophic euglenid again (Peranema); het eugl (Entosiphon or Petalomonas), Chlamydomonas? too small; ?, pedinellid-like thing?; Bodo, non-descript small unknown flagellate? Bodo., last two look like those tiny non-photosynthetic stramenopiles everyone ignores.

This tangent was initiated by working on that long overdue post, by the way. Apparently, one graph is enough to lead me on a massive multi-window-tab-explosion journey into the wild unknowns, even if it involves ecology. Maybe this is why it's taking me like four months to write a single freaking chapter. I'm not sure the free version of Mendeley was meant to handle hundreds upon hundreds of references. Let's see what it does once I hit a thousand, which will be soon. At least researching flagellar root apparatuses doesn't typically lead me to Hooke's description of the first cell, unlike one particular reader here =P (who needs to update, by the way...)

Oh, and submit to the carnivals! The more posts I have, the lest posts I'd have to fake, and the less I must rickroll you with fake links...

Mystery Micrograph #25

The last one was cracked by 'Anonymous', suspiciously close to a well-known dinoflagellate lab... it was a Warnowiid ocelloid, which is pretty much the coolest thing ever. I shall definitely blog about it someday. Been procrastinating with it because I'm not sure I can do it justice. In short, it's an image-forming camera eye...of a unicellular alga. If only these things weren't present at about one individual per cubic metre of seawater...argh!

Onto the next one. Tell me what's going on here:

TEM; 2 - 2300x 3 - 3400x. To be referenced later.

Gluttonous amoeba

Was looking through some freshwater pond samples one day, and saw this amoeba (Polychaos?) which has managed to engulf an entire Phacus (a photosynthetic euglenid)!

How it managed to ensnare the Phacus with its pseudopodia is beyond me. Phacus is perfectly capable of swimming away. Then again, amoebae are actually kinda scary...

Or what if this euglenid wasn't actually being digested, and would have eventually become a permanent endosymbiont, forming a brand new lineage of photosynthetic amoebozoans with tertiary plastids? And just as this miracle was about to happen, some asshole biologist captures the poor amoeba and kills it. Oh well.

Call for submissions for MolBiol Carnival! (and CoE)

Have you written about fancy little molecules doing something biological lately? Have you written about biologists doings something molecular? Do you have pretty gels to show off, in a polite manner as to not offend those of us who chronically fail at PCR? Have you aligned some proteins into pretty super-neat colourful blocks screaming OCD! to the rest of the world? And written about it?

If so, you should submit your post to the high Impact Factor MolBiol Carnival. That way, not only will your wonderful exhibit be hosted amid members of the world's awesomest kingdom, but you'd reach a much wider readership than you would through Obscure Journal of Experimental Molecular Shit No-one Understands Anyway (Aka Journal of HAHAHA YOU'RE NOT IN CANCER RESEARCH SO WE DON'T CARE ABOUT YOU) And you thought that post was going to Nature, eh? What are you, an undergrad summer intern? ;-)
You can even cross-submit to the Carnival of Evolution, as evolution cannot be properly studied without molecular biology (Ha, suck on that, ecologists!*)

Was all of the above too much text for you? Too confusing? Lemme rephrase that:

CLICK HERE and SUBMIT YOUR POST to MolBiol Carnival NOW. Please ;) Scheduled for 01 Nov, 2010, here; please have the submissions in by 31 Oct. Make 'em spooky if you'd like.

Are you happy now, Alejandro?

*I'm perfectly cool with ecologists. I even have a friend who is one. It's kind of like the token 'gay friends' of flaming fundie Republicans. Except that I'm not actually an ecologist** myself. ;-)

** Please don't tell my cell biology peeps I'm applying to a graduate program with "ecology" in its title...I would get shunned by the entire field.

Speaking of evolution, Carnival of Evolution is alive and kicking too. You should submit. Next one is also 01 Nov at Byte Size Biology, and even though it won't be as cool as ours, it will still be totally awesome and the perfect place for you evolution posts.

Incidentally, I should probably write some real posts. Haven't done that in a while...

Cute Peritrich and random update

As alluded to earlier, I've been swept away by midterms and applications. Now that the midterms are done, got the rest of the ever-growing to-do list to take care of. Oh dear. Currently working on: a chapter, research proposal for fellowship, applications and that long-overdue write-up of Mike Lynch's seminar. Fear not, I have not forgotten. Just haven't figured out a way to reproduce by fragmentation yet...

So enjoy a random pretty Peritrich ciliate (think Vorticella) - Apocarchesium, a sizeable clump of vorticella-like bodies atop a single contractile stalk:

Forest of trumpets, on a single stalk. Scalebar - 100µm. (Norf & Foissner 2010 JEM)

And since this paper is by the great Wilhelm Foissner, it includes the obligatory sexy drawings:

Everything you need to know to identify Apocarchesium. (Norf & Foissner 2010 JEM)

That one's actually modest by his standards. There's some truly amazing descriptive drawings by him out there. Possibly worthy of a whole post. Eventually. Especially since he has described a freaking insane number of various ciliates, and possibly other protists. But before that, prior obligations.


Meanwhile, I like to recommend this awesome NAS Sackler Colloquium talk by Julius Lukeš accompanying Lukeš et al. 2009 PNAS on convergent evolution between Alveolates (namely, dinoflagellates) and Euglenozoans. Go watch and savour the amazing genomic evolutionary madness contained therein.

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.

---
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).

Mystery Micrograph #24

Ok, last one was too easy – Braarudosphaera, a rather polyhedral coccolithophorid (haptophyte) which serves as strong evidence that our Creator was a D&D geek. Apparently he/she/it liked their tabletop RPGs microscopic. Who knew.

Time for an evil one, then. Oh, how can one be evil with micrographs...oh right, TEMs! Those tend to drive everyone crazy. Bwahahaha...

Oh what could this be? If only you knew... (to be referenced later)

Have fun! Again, if you're some sort of protistologist and immediately recognise what this is, stay the hell away. Stand back and savour some painful guesswork first – see, everyone wins!

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

Mystery Micrograph #23

...and they're back! (last one was a TEM of Joenoides' sexy parabasal fibres)

Let's see what you've got on this sucker:

(to be referenced later)

Several people excluded from this one. You know who you are.