Field of Science

Showing posts with label Ciliates. Show all posts
Showing posts with label Ciliates. Show all posts

Protistology Q&A on Reddit + gratuitous ciliate video

Earlier today I felt like procrastinating a little and posted a protistology IAmA thread on Reddit (basically threads where the opening poster answers questions, titles formatted like this: I Am A XYZ, Ask Me Anything). I expected a couple questions before the thread disappears forever into the obscurity of the great internet graveyard. Shockingly enough, apparently people actually care about science or something because I was typing away non-stop at a blizzard of questions for a few hours, until now. It was quite inspiring to see the type of questions people can come up with (even the basic badly-worded ones show that at least people care enough to ask), and learned a few things along the way too. Anyway, I'll come back to answer more stuff tomorrow, but here's the thread for the curious. Feel free to stop by and ask stuff! I find that sometimes the blog comment area can be a bit intimidating if you feel you have a dumb question, so you don't ask anything. Reddit dilutes that effect, and is quite a bit more anonymous.

Protistology Q&A on Reddit

And now to randomly show off a random Haptorian ciliate – meet Litonotus, a vicious predator armed with terrifying toxicysts, which you can see as long narrow things in its cytoplasm. Also note the two prominent macronuclei visible as clear-ish round areas in the cell. Litonotus is cool and all, but the bastard preys on creatures like Euplotes, which are kind of adorable (imagine Litonotus eats kittens...that's how bad it is). Nature is red in tooth cytostome and claw cilium indeed...

"Just another ciliate" – importance of sexy descriptions

ResearchBlogging.orgThere 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

Out in the field: freshwater microforay picture dump

I've probably accumulated about 10-20GB of protist pics by now. And a couple DV tapes' worth of video. Still got some work to do before I can catch up with my 80GB of Arabidopsis epidermis pictures (mostly of all sorts of mutilated stomata), but this is for fun rather than data, and thus accumulates much slower. Most of them are crap or uninteresting by now, but the others might as well get dumped here as raw data from 'field work'. The wonderful thing about microscopy is that the more you know, the more new things you observe, and the more interesting it gets. Eg. once you're no longer distracted by trying to identify unknown things, you pay more attention to behaviour. Anyway, I'll dump the photos in random installments here and there, hope there's at least something interesting for you from time to time.

To begin, a fuzzy ciliate of sorts. Prominent contractile vacuole, and I think in the left image I think you can make out its macronucleus or two. Can't see the mouth so IDing it is a bit difficult.


[to shave off some page loading time, the rest is below the jump (if it works)]

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.

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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).

Anoxic microforay part I: Aggregations and contractions

First I'll dump a few pictures of the strange bacterial swarming described in the earlier post, followed by some hawt ciliate action. First the bacterial swarming sequence; any suggestions/explanations/musings/factoids welcome and encouraged.

Stated the objectives used as opposed to magnification. No proper microscopist cares about mag anyway as it's rather meaningless. Also, I have no idea what the 'mag' is in this case anyway...the bacteria are small, about a couple microns or so. Sorry there are no timestamps - no idea how to put them on. Overall sequence spread out over about 5min. Phase contrast unless stated otherwise.


[Edit 20.08.10: Compressed pictures into a slideshow, thanks to Edward's helpful tips + tutorial; noticed the blog page is becoming harsh on the loading time, hope this helps]

EDIT 22.08.10 Moving pics to slideshow turned out more complicated than it should be, and don't have time to fix with an impending flight to internetlessness+vacation in a couple hours...really sorry, will fix + put up pictures ASAP once I get back!

I think the theory at the moment is that is may have something to do with optimal oxygen concentrations (ie low) towards the middle of the slide; oxygen would diffuse more at the edges of the cover slip, and this was an anoxic sample. However, it may have been near the centre as a coincidence; my sample size is kinda tiny here.

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Was recording Vorticella generating feeding currents in phase contrast when another obnoxious ciliate rudely interrupted the shoot; these three frames are consecutive, note how near-instantaneous the stalk contraction is!




Here's another one contracting, in DIC:
There are more photos to come, but processing and identifying them is time-consuming, and I'm still ridiculously behind on my actual work...so that should come later.

Sunday Protist - Assorted oddballs

As I scramble to finish a chapter before my supervisor notices his hiring mistake, instead of writing out a mini-review paper about a single group of sorts, I'll use the opportunity to point out a few of the oddballs I've accumulated lately. Many of them have just a single paper, or a passing mention and a reference to a paper I can't get easily (and that would likely be in some language I can't read to begin with...), and thus they don't really make good weekly protists by themselves. But yet, many are too cool to ignore mentioning.

Our first exhibit is a peculiar association between a coccolithophorid haptophyte (small phytoplankton), Reticulofenestra sessilis, and a centric diatom, Thalassiosira sp.:

The thing in the centre is the centric diatom. The scaley things around are the coccoliths, or calcified scales, of the haptophytes Reticulofenestra clustering around it. The exact nature of this relationship is unknown, though presumably beneficial for the haptophyte, as R.sesslis is found almost exclusively attached to diatoms. Image by from nannotax.org; original citation - Gaarder & Hasle 1962 Nyü Mag Bot (which doesn't exist online *gasp*)

Speaking of haptophytes, here's another cool-looking one. There is quite a bit to say about haptophytes overall, just too lazy to do it right now. There is a post in the making though...
Umbellosphaera. The things on the surface are its coccoliths, of which each individual is intricately crafted into a chanterelle/trumped-like shape. SEM on the left from a nice image repository/course supplement by Isao Inouye from U Tsukuba, one of the Meccas of protistology. (Website is in Japanese, unfortunately for [most of?] us. I really need to learn Japanese someday...) Image of single coccolith on the right from eol.org.

Now for an obligatory ciliate. Trichodina is a cute little peritrich (group that includes the coiled-stemmed-trumpet Vorticella) that deserves more attention than just a pretty picture, but its looks can't wait to be exposed. Both the top and bottom sides have cilia, and the creature is like a miniature robotic vacuum cleaner, vacuuming the fish gills (or other substrates, like jellyfish) of bacteria and various other prey that accumulate there. In doing so, it causes fish disease, but the cute lil' thing didn't mean to!
Left: Trichodina 'vacuuming' fish gills (source). Middle: DIC image of the Trichodina 'sucker' (surprisingly from National Geographic, of all places). Right: Drawing of the ciliate. (HJ Clark 1866 Am J Sci) Will surely come back to it someday!

And last for today, this little critter is absolutely adorable. There's actually quite a bit to say about it, but I'm not gonna do it because some other blogger is far more qualified to write it up. Perhaps after the conference season calms down a little, said blogger could share their wonderful stories with us...
Apusomonas proboscidea. To paraphrase Opisthokont, 'cute Apusomonas' would be redundant. You see that little protrusion at the top? It wiggles 'spastically' as the critter crawls forward along its flagellum. If you're really keen check out the movies in this recent paper on apusomonads (TC-S alert!). Left: Karpov & Myl'nikov 1989 Zoologicheskiy Zhurnal (in Russ.) Right: Flemming Ekelund at ToLWeb (Apusomonas is really tiny...)

That's it for today. Am going out of town until middle of next week, will likely lack internet (eeek, how will I live?!), so if comments are mysteriously ignored, that's why.

Criminally photosynthetic: Myrionecta, Dinophysis and stolen plastids

ResearchBlogging.orgThe microbial world is full of vicious beasts. Yes, much of microbial life is cute and cuddly in one way or another. But that doesn't stop many of them from making wolverines seem docile by comparison. There is an entire mafia out there built around...organ theft; including some multicellular players as well, in case you thought animals were saintly. Today we'll look at some famous thieving masterminds of the plastid black market, but keep in mind that there are many more fascinating relationships involving keeping entire organisms or their parts alive within the host, and vastly more oddities that have still escaped human attention (not hard to do, actually).

Let's start off the messy subject with a pretty diagram summarising the major plastid hoarding events of the [moderately] distant past:
Pac-Man!* Today all we need to do is appreciate the overall big picture: there were numerous symbiotic events and by about tertiary endosymbiosis, it gets messy. Not pictured are the cases of more-or-less transient kleptoplasty (plastid-theft), which would do serious harm to the readability and aesthetic qualities of this diagram. (Keeling 2004 Am J Bot; free access) For those keen on extra gory details of plastid endosymbiosis, see this recent review.
*If somebody were to make a game of Pac-Man: Endosymbiosis Edition...


Today's plastidial saga will involve an arduous journey from the cyanobacterium to the red algal endosymbiont of the cryptomonad, to the subsequent ingestion by a ciliate and a dinoflagellate. In fact, just keep in mind that the cryptomonad itself is the result of a hungry heterotroph getting a habit of devouring red algae and developing a case of terminal indigestion, ultimately gaining a plastid and plastid-targetting genes in its own nucleus. The cryptomonad in particular happens to be really awesome in another way: it actually still retains the original, eukaryotic, red algal nucleus of its former prey! That nucleus has been badly shrunk in the wash, and the genome is essentially on crack, but that's a long story for some other day.

Just so you get an idea of what a cryptomonad roughly looks like:

Cryptomonas. Note its very diminutive size. Source: Micro*scope.

We're about to move on to the sleazy thieving ciliates and dinoflagellates. But first, we must establish how kleptoplasty (lit. plastid theft) differs from endosymbiosis. To clarify, I use 'symbiosis' as a general term for an intimate interaction between two different species, including parasitism, mutualism and commensalism. Thus, an endosymbiont needn't feel the same way about the relationship as its host, and very often doesn't. Keep in mind that it is often not very obvious which exact category the symbiosis falls into, as nature doesn't particularly care for our naming fetish.

Endosymbiosis, in the context of organelles and other intracellular stuff, typically entails the complete engulfment of another organism by the cell. Once gene transfer occurs between the genomes of the two organisms, some declare the endosymbiont is now officially an organelle. The endosymbiont-organelle debate is old, stale and utterly pointless; thus, as I have declared in a previous post, I like to call plastids and mitochondria 'endosymbionts' and the more questionable cases, like Perkinsela, 'organelles'. That way, I can piss off just about everyone. Ha!

Then there is the much-awaited plastid theft, where only the plastid itself of the failed endosymbiont is retained, with the rest of it typically digested away. The katablepharid Hatena which Labrat wrote a wonderful post about (as well as Merry at Small Things Considered), is a striking case of kleptoplasty (and only discovered this past decade!). The intensity of kleptoplasty, as well as endosymbiosis, vary greatly from transient plastids (or endosymbionts) that are not essential to the host, to mostly permanent plastids or endosymbionts that are retained indefinitely, capable of reproducing on their own, and completely obligatory for the host's survival. This is nicely summarised in this diagram from a recent review on acquired photosynthesis by Stoeker et al 2009:

Two ways to get a plastid: 1) steal a plastid-bearing alga and lock it in your basement keep it alive within you (endosymbiosis); 2) mug the alga, steal its plastid and try to keep it alive yourself. Along the two paths lie multitudes of intermediate steps different in the persistence of the plastid (how long it lasts) and how dependent the host is upon it. (Stoecker et al. 2009 Aquat Microbiol Ecol)

In the endosymbiotic pathway, nucleomorphs (and the original plastidial prokaryotic genome) suggest the permanent associations we know among the 'normal' algae come from the endosymbiotic path, as there is evidence for whole host retention at some point. However, the data do not entirely rule out some independent secondary plastid acquisition via kleptoplasty rather than endosymbiosis. As for tertiary plastidial symbionts, it gets fun. The classic persistent cases like Kryptoperidinium tend to have a whole endosymbiont, nucleus and all, so the endosymbiotic pathway is also more likely, cut things like Dinophysis, on the other hand, are just weird.

Now, at last, our long-awaited thief: the ciliate Myrionecta rubra (=Mesodinium rubrum):

Myrionecta rubra (originally Mesodinium rubrum); c - cirri; ChC - chloroplast complexes; ECB - equatorial ciliary band (Taylor et al. 1969 Nature) Right: SEM of Myrionecta by Takayama Haruyoshi (more awesome micrographs here)

As you can see, this ciliate bears plastids - a rather non-ciliate activity. In fact, if you slice it up, you'll find that the plastids are very carefully arranged at the periphery:

N - cryptomonad nucleus; M - ciliate macronucleus (note the difference in chromatin organisation); note how the plastids are not only predominantly on the cell periphery but also tend to all face outward! (Oakley & Taylor 1978 Biosyst)

The ciliate captures a cryptophyte, takes its plastids -- along with the nucleomorphs, pyrenoids and other plastid-associated stuff, as well as cryptomonad mitochondria -- and packages them up in their own little compartments. Furthermore, the nucleus is also retained and consistently packaged in an entirely separate package from the plastids. Quite remarkably, the cryptomonad nucleus remains transcriptionally active! (Apparently, Elio beat me to it in 2007. Grrr) Presumably, maintaining an active host nucleus would help keep the plastids functional longer.

Oddly enough, I have difficulties finding anything on the exact process of crypto acquisition - I initially thought it just phagocytoses them, but a friend of mine studying weird plastid aquisition thinks they may actually employ myzocytosis - sucking out the contents of its prey through a 'straw', like many other alveolates do: this may explain the segregation and separate enveloping of the plastid and crypto nucleus. This would require Myrianecta to be quite fast and well-coordinated; the speed is there as it tends to jump instead of moving gradually (details here).


There is a plot twist to this story. A stroke of irony, or poetic justice, or karma if you're into such things. The thieving ciliate itself gets mugged...by a dinoflagellate!

At first glance, Dinophysis caudata is a normal photosynthetic dino, which isn't particularly surprising as roughly half of them are (most with their own plastids). Dinophyceans are quite trippy morphologically, which made it even more frustrating that Dinophysis appeared impossible to culture, despite being photosynthetic. For a while, no one could figure out what exactly was wrong with it. Turns out, its plastids aren't its own, and are rather cryptomonad-like. Great, so it kleptoplasties the cryptos, let's just grow it in a jar full of them! Again, no luck - for some reason, Dinophysis appeared incapable of ingesting the cryptomonads!

It was all rather perplexing until someone figured out the problem in the 2000's, publishing the first successful culturing attempt in 2006 (Park et al. 2006 Aquat Microbiol Ecol). Here's what was missing:

Dinophysis (the jug-like thing with a conspicuous flagellum) sucking the plastids out of Myrionecta, who's rolled up into a small, whimpering ball by this point. (Park et al. 2006 Aquat Microbiol Ecol)

Not only is Dinophysis caudata a stinkin' thief, but it can't even do the primary stealing itself - the dino requires Myrionecta to do all the dirty work of packaging up the plastids. But it gets messier. First, a summary of the plastid's plight:

Dinophysis ingests plastids from the ciliate Myrionecta, who in turn stole them from a cryptomonad. Who, if you recall, obtained it a long time ago as a red algal endosymbiont. Who, of course, obtained the original plastid as a cyanobacterial symbiont. I think it ends there though. That poor cyanobacterial genome has been through a lot! (Wisecaver & Hackett 2010 BMC Genomics)

Now, whether Dinophysis also bears proper plastids of its own is up to heated debate at the moment. It looks like I'm not the only one thoroughly confused by it, and sorting out this issues is slightly beyond the responsibilities of a mere blogger at the moment, so let's leave this part of the story explicitly vague. It seems like Dinophysis may somehow supplement its own stock with the stolen plastids, as it appears to have plastid-targetting genes in its own genome (Wisecaver & Hackett 2010 BMC Genomics). However, there are also cases of Dinophysis carrying plastids that appeared very non-cryptomonad, and most likely to be of dinoflagellate origin (Garcia-Cuetos et al. 2009 Harmful Algae).

The chaos is quite understandable: it is actually very difficult to determine the nature of a relationship between two organisms, especially on the microscopic scale, and especially when one is inside another. It's often hard to distinguish a permanent from a transient relationship, and a mutualistic from a parasitic one. While there is strong direct evidence that the dino sucks plastids out of Myrionecta, that does not necessarily mean all of its plastids originated there. Or that it lacks its own (though that would make sense). Or more importantly, that the various research teams are even looking at the same bloody organism! Speaking of which, Myrionecta and Dinophysis appear to be in a 'bit' of taxonomic mess too, so I'll just let the professionals fight it out amongst themselves.

While that's going on, one cannot help but wonder how many such 'unconventional' relationships there really are. Food webs are not as direct as people think, the once one peers a little further than the usual stereotyped interactions (predator, parasite, prey, producer, whatever), ecology actually becomes an interesting (admittedly, fascinating!) subject. On that note, I think we should really be careful when trying to force terrestrial and macroscopic ecological terms onto the microbial world -- and by careful, I think we should perhaps come up with a system specialised for microbial life from the very beginning. While we seldom see one animal rip out an organ of another and keep it alive for itself, organelle theft is actually not all that uncommon. Life on the cellular level is weird to us, and many traditional terms simply fail to describe it.

There's a whole black market of utterly bizarre microbial interactions out there. We are only scratching the surface.


References
Garcia-Cuetos, L., Moestrup, �., Hansen, P., & Daugbjerg, N. (2010). The toxic dinoflagellate Dinophysis acuminata harbors permanent chloroplasts of cryptomonad origin, not kleptochloroplasts Harmful Algae, 9 (1), 25-38 DOI: 10.1016/j.hal.2009.07.002

Johnson, M. (2010). The acquisition of phototrophy: adaptive strategies of hosting endosymbionts and organelles Photosynthesis Research DOI: 10.1007/s11120-010-9546-8

Johnson, M., Oldach, D., Delwiche, C., & Stoecker, D. (2007). Retention of transcriptionally active cryptophyte nuclei by the ciliate Myrionecta rubra Nature, 445 (7126), 426-428 DOI: 10.1038/nature05496

Keeling, P. (2004). Diversity and evolutionary history of plastids and their hosts American Journal of Botany, 91 (10), 1481-1493 DOI: 10.3732/ajb.91.10.1481

OAKLEY, B., & TAYLOR, F. (1978). Evidence for a new type of endosymbiotic organization in a population of the ciliate Mesodinium rubrum from British Columbia Biosystems, 10 (4), 361-369 DOI: 10.1016/0303-2647(78)90019-9

Park, M., Kim, S., Kim, H., Myung, G., Kang, Y., & Yih, W. (2006). First successful culture of the marine dinoflagellate Dinophysis acuminata Aquatic Microbial Ecology, 45, 101-106 DOI: 10.3354/ame045101

Stoecker, D., Johnson, M., deVargas, C., & Not, F. (2009). Acquired phototrophy in aquatic protists Aquatic Microbial Ecology, 57, 279-310 DOI: 10.3354/ame01340

TAYLOR, F., BLACKBOURN, D., & BLACKBOURN, J. (1969). Ultrastructure of the Chloroplasts and Associated Structures within the Marine Ciliate Mesodinium rubrum (Lohmann) Nature, 224 (5221), 819-821 DOI: 10.1038/224819a0

Wisecaver, J., & Hackett, J. (2010). Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata BMC Genomics, 11 (1) DOI: 10.1186/1471-2164-11-366

Ciliate-in-a-test-tube

Who said test-tube babies were 'unnatural'?

Undella hyalina, a tintinnid ciliate. Tintinnids craft wonderful loricas out of organic materials, often studding them with bits of random gunk (but not in this case).
http://www.obs-vlfr.fr/gallery/album316/undellopsis_hyalina

There's something quite adorable about a ciliate who willingly crawls into a test-tube by itself. In fact, it actually makes its own test-tube. If only all the protists could just grown their own flasks, fill them with optimal media, and culture themselves*...

More to come soon!

*Technically, they do culture themselves, quite successfully too. Just not in conditions convenient for researchers...

Sunday Protist -- Blue Mats of the deep sea: Folliculinopsis

ResearchBlogging.orgFar, far away, in the land of eternal darkness along the base of the deep sea hydrothermal vents of the Juan de Fuca Ridge lie stretches of surface covered by 'blue mats'.
These blue mats are produced by yet another tube-forming denizen of the hydrothermal vents. To non-tube-dwellers like us they may even look vaguely reminiscent of the much more famous giant tube worms, and the concept is quite similar up until that point.

However, if you look inside a tube with its live host, something distinctly non-annelid peers out:

This creature is, in fact, a ciliate - a relative of the elegant Folliculina (referred to in the good ol' days as the "bottle-animalcule"), Folliculinopsis sp., a heterotrich like the giant Stentor:

Folliculinopsis. The two long 'wings' or 'ears' sticking out are its peristomal lobes, which can be seen in the preceding SEM. (Ji et al. 2004 J Ocean Univ China)

Folliculinopsis is host to countless bacterial symbionts; in fact so lushly the bacteria thrive on it that one can barely see the ciliate beneath them! Presumably, these bacteria may be involved in chemical defense, protection from the rather toxic surrounding environment or assist in metabolism. Symbiosis with prokaryotes seems to be fairly common for eukaryotes living awkward (extreme) environments, in large part because prokaryotes are simply amazing at biochemistry unlike their metabolically-challenged nucleated counterparts.

SEMs and TEM of symbiotic bacteria on Folliculinopsis sp. The lorica is covered mostly with filamentous bacteria (top left) whereas the surface of the ciliate is entirely covered with coccoid and rod-shaped episymbionts (bottom two SEMs). Moreover, the inside of the ciliate is full of bacteria-containing vacuoles, as seen in the TEM (near the cortex). (Kouris et al. 2007 Mar Ecol)

In another folliculinid, Eufolliculina, the surface of the peristomal lobes has a peculiar feature: short membrane-covered pins at the base of each cilium. Mulisch (1991 Cell Tissue Res) proposes these pins may act as sensory organelles, perhaps to transmit oriented mechanical stimuli. The cilia have a swelling at the level of the pin, filled with peculiar granular particles with potential involvement in calcium regulation (as you may recall from intro-level physiology, Ca2+ is quite popular in signaling systems). Similar cilium-pin complexes have also been found in other folliculinids, suggesting it may be a shared feature.

Cilia with sensory pegs at the base (arrows). (Mulisch 1991 Cell Tissue Res)

The cilium-peg complex reminds me of sensory hairs or sensilla on insects. Mulisch relates it to the hydrozoan cnidocil in the cnidocyst, or the stereocilia (microvili) at the base of the kinocilium in vertebrate sensory hair bundles. Perhaps this is yet another instance of ultimate convergence, as there is ultimately a finite number of ways particular functions can be performed, and evolution's random walks are bound to chance upon some more than once.

The biology of protist sensory mechansims and overall behaviour is still vast, mysterious, murky territory desperately in need of serious investigation. Unicellular organisms have complex behaviours just like multicellular ones, and are no more 'mere automatic responders to stimuli' than we are (due to our cumbersome complexity, much more random noise tends to creep in; perhaps where creativity comes from...); somehow, without a brain or even a nervous system, many unicellular organisms are nevertheless quite capable of performing complex behaviours in response to various stimuli.

This topic was quite popular in the early 20th century, but seems to have been largely abandoned today (in unicellular organisms). Considering the volumes of papers published daily on cell motility in tissue cultures, would it be too much to ask for some investigation of more intelligent cell types, ie. those that also act as entire organisms? Surely a ciliate must be much more fascinating to work with than some confused helpless cells ripped out of context in some suspension? There's enough work to do in this corner of science to keep us busy for many more years to come...!

On that note, the sun is rising. I should respond to the stimulus. By sleeping... (spent a few more hours scratching my head over some potential centrohelids...freaking gaps in the literature are really annoying, especially when you can't access half of it as it lies under piles of dust in some obscure obsolete journals that have been forgotten for the past five decades or so. Fun times.

References:
Ji, D., Lin, X., & Song, W. (2004). Complementary notes on a ‘well-known’ marine heterotrichous ciliate, Folliculinopsis producta (Wright, 1859) Frauré-Fremiet, 1936 (Protozoa, ciliophora) Journal of Ocean University of China, 3 (1), 65-69 DOI: 10.1007/s11802-004-0011-1

Kouris, A., Kim Juniper, S., Frébourg, G., & Gaill, F. (2007). Protozoan?bacterial symbiosis in a deep-sea hydrothermal vent folliculinid ciliate (Folliculinopsis sp.) from the Juan de Fuca Ridge Marine Ecology, 28 (1), 63-71 DOI: 10.1111/j.1439-0485.2006.00118.x


Mulisch, M. (1991). Ultrastructure and membrane topography of special ciliary organelles in the ciliate Eufolliculina uhligi (Protozoa) Cell and Tissue Research, 265 (1), 145-150 DOI: 10.1007/BF00318148

Sunday Protist -- Tachyblaston: A suctorian parasite of suctorians

ResearchBlogging.org[it's totally still Sunday in someone's mind somewhere...right?]

Reading old protistology books can be quite a frustrating exercise: image you come across a really cool-looking organism, try to follow up on what happened to it since, and discover it's only been written up once in the distant past and neglected ever since. This happens to a very annoying percentage of organisms described in those older books (newer books tend to forget the phantom and near-phantom species). Now this organism in particular at least has a very detailed source behind it, but alas! ...in German. I saw it in Grell's (1973) Protozoology, and the original description comes from... Grell 1950 . The former I have an English copy of, the latter I do not. So don't expect much detail.

Ecologists often lump microorganisms together as 'decomposers' (at least in undergrad courses); those of us living in a different scale of things beg to differ. From an intro ecology text, you get the idea that ecology somehow ceases to happen once you reach a certain size or phylum, and everything's just a part of this amorphous blob that exists to recycle nutrients so that the rest of us can live on. Shockingly enough, this amorphous blob has a whole ecosystem of its own, complete with predators and photosynthesisers and those who do both, as well as parasites and mutualist endosymbionts and saprophytes, etc. They interact with each other in ways not in the slightest less interesting than fluffy animals. In the microscopic world, cells become bodies that, just like ours, can get hunted, infected or benefited by some other organism. Or host a pile of commensals (who do exist, by the way, by similar arguments that Nearly Neutral Theory employs for mutations)

*Zoological ecologists also tend to treat plants as 'those things that exist for animals to eat', which annoys the hell out of anyone dealing with plants. On the first day of ecology the instructor causally mentioned that 'plants don't do much in the way of behaviour', and thus the course will largely ignore them. I expressed disagreement after class, noting there is little fundamentally different between a plant biochemical response leading to, say, discharge of toxins or some regulatory change, and an animal biochemical response leading to observable [to our eye] mechanical change. Yeah, this is why I have difficulty talking to the more 'traditional' biologists sometimes...but that is completely off-topic.

Remember how crabs can sometimes be covered in sea anemonies? Many smaller crustaceans can often be covered in organisms superficially resembling miniature sea anemonies - namely, Suctorians - highly derived (=weird) ciliates covered in miniature tentacles. Suctorians also reproduce by budding, as opposed to conventional symmetrical mitosis employed by the canonical ciliate. Just like sea anemonies and other cnidarians, suctorians also have stalked and swarming forms, like the polyp vs. medusa destinction in the former. Which is quite unsurprising, really, as aquatic sessile organisms usually use specialised free-swimming forms to spread. But still another cool bit of ultimate convergence discussed a couple posts ago.

Top: A copepod covered in suctorians; an SEM of Ephelota gemmipara from the copepod. (Fernandez-Leborans et al. 2005 J Nat Hist) Bottom: Ephelota superba, suctorian episymbiont of Antarctic krill. Quite reminiscent of an anthozoan. (Stankovic et al. 2002 Polar Biol)

Now, imagine a microscopic sea anemone being parasitised by another. I'm not sure whether there are any cnidarian parasites of other cnidarians (wouldn't be too surprised), so the analogy stops around here. The awesome does not, however: parasites are never truly simple. Tachyblaston's infancy consists of finding an Ephelota, attaching itself and piercing the cell membrane to leech off the cytoplasm. Over time, the entire cell can become filled with parasites. During this stage, the parasite buds to produce swarmers.

Tachyblaston invading Ephelota cell body. Right: Tachyblaston budding. (Grell 1950 Z.Protistenk)

Afterwards, the swarmers swim around and attach themselves to an Ephelota stalk, where they themselves form a stalked cup structure. There the parasite buds multiple times, yielding a cup full of Tachyblaston, which is subsequently emptied as the buds (this time with a single thick tentacle, according to Martin 1909) evacuate and crawl up the stalk toward the main cell body of Ephelota to infect it and start the cycle over.
Left: Swarmers. The stage that actually sort of looks like a ciliate... Middle: Full 'cup' of Tachyblaston in stalked stage. Right: Empty cup after all (Grell 1950 Z.Protistenk)

To summarise Tachyblaston's life cycle, the cell-penetrating parasites of the Ephelota cell body bud to form swarmers, which, in addition to reminding us of suctorians' ciliate leanings, find another Ephelota and attach themselves to the stalk, forming a cup which they fill up by budding again, finally releasing single-tentacled forms that crawl up the stalk to the next victim. How's that for unicellular organisms having 'primitive' differentiation capabilities?

Overview of the whole life cycle of Tachyblaston. Oh the tentacles... (Grell 1950 Z.Protistenk)

Tachyblaston's original description by Martin 1909:380 J Cell Sci can be found here. The parasite was very distinctive due to a major refringent particle of unknown origin or function present within each Tachyblaston cell. The genus name reflects the extraordinary speed with which the parasite epidemic can sweep over an entire population of Ephelota, which end up a decimated forest of bare stalks. Creepy.

And last but not least, here's an obligatory tree to orient ourselves phylogenetically:

Tachyblaston and Ephelota are both suctorians in Phyllopharyngea, which contains some other bizarre (and somewhat obscure) creatures like Chonotrichs. (Gong et al. 2008 JEM)

PS: Blogging about ciliates is very difficult. They are too damn distracting - you start reading about one and come across ten others you suddenly must look up, and so on. About as bad as Wikipedia. Actually, since looking these things up is now actually relevant to my day job, the distractions get worse as I feel compelled to write down and follow anything potentially related to work. Just in case. Apparently, sort of using blogger as a reference manager... hence the exploding drafts folder. Sigh.

References:
Fernandez-Leborans, G., Freeman, M., Gabilondo, R., & Sommerville, C. (2005). Marine protozoan epibionts on the copepod Lepeophtheirus salmonis , parasite of the Atlantic salmon Journal of Natural History, 39 (8), 587-596 DOI: 10.1080/00222930400001525

GONG, J., GAO, S., ROBERTS, D., AL-RASHEID, K., & SONG, W. (2008).
n. sp. (Ciliophora, Phyllopharyngea, Cyrtophoria): Morphological Description and Phylogenetic Analyses Based on SSU rRNA and Group I Intron Sequences
Journal of Eukaryotic Microbiology, 55 (6), 492-500 DOI: 10.1111/j.1550-7408.2008.00350.x


Grell, K. (1950). Der Generationswechsel des parasitischen Suktors Tachyblaston ephelotensis Martin Zeitschrift f�r Parasitenkunde, 14 (5) DOI: 10.1007/BF00260027

Martin, CH (1909). Some Observations on Acinetaria: Part I.—The " Tinctin-kbrper " of Acinetaria and the Conjugation of Acineta papillifera. Quarterly journal of microscopical science, 53 (2), 351-389