Clickable Tree of Eukaryotes (Katz Lab)

For a while I've been contemplating on considering to con someone into making a clickable tree for me, allowing one to zoom in and click genus names leading to further info/pictures/whatever. Of course, I'd be far too lazy to actually execute such a project, especially given my lack of programming skills, and lack of faith in the stability of current phylogenies... luckily, I recently discovered some nice people already took care of that, and produced a really awesome tree:

The genus names lead to their respective Micro*scope pages (with pictures)! (Parfrey and Katz, http://www.science.smith.edu/departments/Biology/lkatz/EuTree2009/Eutree09.html; relevant literature: Parfrey et al. 2006 PLoS Genet, 2010 Syst Biol)

This is the eukaryotic tree of life sensu Katz Lab. Being on the opposite side of the continent, the people here have some differing opinions on the subject (my diagram – seriously due for an update – kind of reflects local influences). As you may have noticed from the bounty of polytomies (multiple branches at a single node indicating uncertainty in branching order), the Parfrey and Katz tree is quite conservative, which is probably a good thing. For pedagogical purposes, however, I still think it's better to go ahead with the supergroups, while mentioning the frailty of some, as it helps organise the organisms and dispells the common notion of Protista being just an amorphous grab-bag of microbial crap that doesn't fit. They run the show, it is WE who 'don't fit'...

For research purposes, one must strive to keep track of the certainty of each and every piece of data or hypothesis one works with. Of course, that's overwhelming to n00bs people outside the field, so the shakiness of some models tends to be glossed over. Also, most people don't care.

Speaking of things normal people don't care about, I was quite shocked by the disappearance of Archaeplastida as a clade -- the locals give off the impression Archaeplastida is among the healthier of the supergroups. Excavates, on the other hand, are acknowledged to be somewhat 'meh' as a clade by some of the people working on them. Hacrobia is rumoured to be practically dead anyway, so I'm just keeping that label for the sake of categorising things that may at best turn out to be paraphyletic (which I'm ok with informally), or at worst, grotesquely polyphyletic in ways that would make Heliozoa and Rhizopodia cry. Also, the Stramenopiles are sister to Rhizaria as opposed to Alveolata ("our" order goes (Rhiz,(Stram,Alv))). I find that weird. Although, on the second though, why the hell not. But local folklore has it that Stram+Alv are a pretty solid grouping. Then again, local folklore sings praises to the Chromalveolate Hypothesis... As an innocent, defenseless cell biologist, I'll just hide in the corner until this blows over...

Also, note that the tattered remnants of the 'supergroups' themselves are horribly politomised. Recall how the animal phylogeny tends to have a comb-like branch structure along the 'base' -- ie, among the earlier divergence events, only one group went on to diversify in ways we notice. Then, shortly before the Cambrian diversification event ('explosion' my ass), a bunch of divergences happened that later did lead to multiple lineages that became diverse, in ways we notice. But prior to that, it seems that animal evolution proceeded at a fairly "gradual" pace, according to some anyway. In terms of extant descendants anyway. But in any case, there are ample opportunities for an illiterate journalist (or scientist) to commit the "primitive animal" fallacy.

This error comes much more difficult in the eukaryotic evolution scenario, that is, if only those illiterates knew a thing or two about the modern phylogenies. This is because apparently, very few early-branching 'undiversified' taxa exist, if none at all. Hard to explain without a tree to show, but it seems like the major eukaryotic supergroups rapidly exploded, either soon after the origin of eukaryotes, or all the earlier-diverging clades disappeared without a trace.

This is a question of the 'tempo and mode' of evolution -- the rate and extent of diversification. It's a rather fuzzy concept, as it's quite difficult to establish what diversity is and how to measure it. Considering we biologists don't even know what a species is (and linguists, I'm told, know not what a word (or language), is...), comparing diversity is very difficult. There are some vague tendencies, but that's all they are. Or so it seems anyway -- perhaps I missed something. I guess it's hard to compare the extent of diversity when you reject ranked taxonomy. Zoologists, at least in the past, have used phyla as an indicator, which were somewhat based on the body plan. Whether it's a valid indicator is a whole other topic, but we lack such luxuries in the microbial realm anyway. This topic deserves a proper post someday...

What I was trying to get at, before almost drowning in caveats and disclaimers there, is that the major clades of eukaryotes have arisen rapidly and seem to have left no residual 'basal'/'stem' taxa, making it very difficult to resolve the relationships between them. Resolving recent 'explosions' is quite doable, as is resolving more gradual evolution in the distant past...rapid explosions in the distant past are one hell of a bitch to deal with, which is why much of the deep phylogeny remains a mystery.

How I managed to go off on this tangent eludes me. I see trees, I start chatting about them, ain't nothin' I can do 'bout that.

It being the start of the school year accompanied by an ominous influx of undergrad cooties *shudder*, I'm going to be on slow blogging mode for another week or so. So use that tree to entertain yourselves -- in fact, this tree and ToLweb make my blogging kind of redundant =P (shhh...) Fear not, since I still need to feel useful from time to time, my protists shall keep on coming.

Relevant papers to the Parfrey & Katz tree: (should be accessible)
Parfrey, L., Barbero, E., Lasser, E., Dunthorn, M., Bhattacharya, D., Patterson, D., & Katz, L. (2006). Evaluating Support for the Current Classification of Eukaryotic Diversity PLoS Genetics, 2 (12) DOI: 10.1371/journal.pgen.0020220

Parfrey, L., Grant, J., Tekle, Y., Lasek-Nesselquist, E., Morrison, H., Sogin, M., Patterson, D., & Katz, L. (2010). Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Systematic Biology DOI: 10.1093/sysbio/syq037

Hiatus until 01 Sep + MORE random doodles!

Flying out very soon, for an underserved vacation smack in the middle of "OMG I don't have "all summer" anymore!!1! *flailing arms*" season. This is what happens when you let parents buy tickets for you. On the other hand, I really need the extra money so I can blow it all on my GREs. Yay.

So before I go and ditch you guys for a week and a half (really, I'd rather be here, blogging and working! =/), I'd like to share something from...my bedroom ^^. I know, how risqué...! This naughty piece is a part of my...wall. That's right, my wall is covered in very shameful things, like even more protist doodles:

No, I don't actually need a life. It's all over my wall anyway.

Anyway, I'll be back 01 Sep. Hopefully the blogging will pick up then, as I'm beginning to discover that regardless how nicely undergrad-free it is, summer is just not conducive to extreme productivity or anything. Quite annoying, actually. Must compensate in fall.

[rant] Some asshat recalled the two specific books I was gonna bring home and read on my vacation to get two major sections of the chapter finished before it becomes evident how little I got done this month... and those aren't books of which you find many similar works lying about -- one of them is the ONLY book on the subject since the 1800's, and I absolutely cannot get by without it. So yeah, thanks, whoever it was. Not that they were supposed to know or anything. But I still retain the right to be irrationally pissed off about it. So much for catching up over the vacation. Now I'm really screwed come September. [/rant]

Must head off to airport soon... have a happy end of August, everyone!

Protist doodles

I like doodling things from time to time, especially protists. The fun aside, it's actually a nice way to acquaint oneself with how the look and behave. With protists, you get the choice of portraying the internal structures, as if viewing in transmission light microscopy, or only the surfaces, as if through SEM. Both are fun, although the former works better with ink doodles and the latter best suited for more serious shaded drawings, in my opinion. Anyway, a while ago I got home after reading and writing about Hacrobians all day, grabbed a beer and went doodling. From memory. Note that a lot of ultrastructure descriptions were read and incorporated into my work that day. Can anyone identify the organisms portrayed?

The image on the right comes from fucking around with a couple filters in ImageJ, and the result was kinda trippy. I smoothened the image, ran Find Edges on it and inverted the colours.
Oh, the image on the left was also post-processed: the original was a photo of a strip of paper with the drawings lying atop a horrible background, which was some random research paper that happened to be beneath it. The strip of paper was horribly slanted, and thus the background had to be edited out by hand, meaning I had to up the contrast until the drawing background was entirely evenly white, so I could blank out the background behind it. I really dislike post-processing besides cropping and slight change of brightness+contrast, but had little choice there. Thought I'd run this disclaimer anyway.

Post-it notes are fun to doodle on too. This is a fairly old one:

And a random trypanosome from a while ago: (the closest I'll ever get to biomedicine, ha!)

There's more, but they require being photographed or scanned, and that takes effort.

Also, I have a few posts in the making featuring protist-y things by people who can actually do art, so stay tuned. Also, if you know of some awesome protist/microbial/biology/sciencey, please do mention it here!

Ok, retreating back into my cave to work on blog posts as well as my actual writing stuff. Yay, guilt-zone!

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.

Random picture dump: Parabasalid mitosis

I actually went out and did stuff this weekend. Like, non-protist stuff involving geographical locations outside the lab. Incidentally, this weekend also happened to be about the hottest this summer, and heat and I aren't the best of friends. Reading isn't particularly fun on a headache, so I went over my random protist videos and got more screenshots. Most of them should end up in the upcoming 'microforay' sometime soon, but I also found something cool from an adventure way back in May. Not enough material for a microforay, but still wanted to dump it somewhere.

Had to do some stuff with termite (local Zootermopsis) gut symbionts, so I dumped them under DIC for fun. There was the usual gang: Streblomastix, Trichomitopsis, Trichonympha and miscellaneous smaller things. Watching Trichonymphas (they're big and cute enough to be a count noun) can get quite addicting, and the guilt from being responsible for their inevitable death by oxygen poisoning compels you to acquaint yourself with every individual on the slide. At that point, I noticed something was odd about the way some of them moved. Furthermore, their anterior ends appeared strange...as if there were two "heads"!

(Once again, apologies for the crappy image quality, but this is the best I can do until I actually have the time to sit down and learn the program.)

OMG, cell division! I still find dividing cells utterly awesome, even just conceptually - it's as if unicellular organisms regularly undergo a "Siamese twin" phase! This is especially evident in organisms who continue to move about and beat their flagella during division, thereby making the two-individuals-in-one concept even more apparent. The cell(s?) usually move(s) around in a fairly incoherent manner at that point, although that might depend on the species too.

Anyway, what's that thing in the middle, between the two "heads"?

As you may have guessed, that thing is indeed the nucleus in mitosis, with spindle fibres all over. With chromosomes. Roughly like these figures from Cleveland (1960 J Protozool):

Top: Whole Trichonympha in early anaphase. Bottom: Close-up of mitotic nucleus. The chromosomes are separated as the thick central spindle grows, pushing apart the centrioles which pull chromosomes along with them via the astral rays. (Cleveland 1960 J Protozool)

Parabasalian mitosis can be quite weird and awesome, but that's a topic for another day. At the moment, I can't even crop properly anymore...ignore that random line in 9a. Just thought I'd share pictures of weird organisms doing cool things.

Oh, and if I ever catch these critters mating, you'll hear it. Potentially even literally ^^

Microfieldwork and a couple mystery critters

My work-related productivity ran aground lately, and thus I feel too guilty to blog. I should probably sort out the stuff I get paid to do first, and until then, do not qualify for having "spare time", especially since I already did too much of that this weekend by going on a random sampling foray:

My friend apparently saw a bubbling pool with a nice stench of sulfur on a local beach, so we went hunting for extremophiles. She had just borrowed A Field Guide to Bacteria, and finally realised that microbial life is many orders of magnitude more awesome than anything easily visible to the naked eye. Far more exciting than her sticklebacks anyway =P (joking! please don't lynch me, fish people!)

Anyway, naturally our fieldwork had to be accompanied by the first rain in over a month, and we got soaked while wading through salty mud in search of the elusive bubbling pool. Unfortunately, the pool seems to have disappeared. Furtunately, the stench of sulfur hasn't. Nor has the blackish-greyish unappetising-looking gunk, or the patches of bright green algae. Being biologists, the yuckier and smellier the gunk, the more excited we got, and the more happily we sampled away. Now I have a plate of anoxic goo sitting on my bench -- could be a great teaching tool for training one not to open random plates and sniff them. Biologists are immune to such lessons, of course, especially microbiologists, who seem to be irresistibly attracted to nasty smelly stuff.

Anyway, gunk hit the slide and on the scope it went (the slide, not the gunk). It was AMAZING. I have found an excavate paradise! At least four varieties of diplomonads I could see! Swarms of bodonids and heterotrophic euglenids! For the saner people, there were loads of bacteria to oogle at too. For some reason, many assume all prokaryotes are too tiny to be detected by a light scope, but that is entirely not true -- you can see bacteria swimming around, even under low mag. Resolving inner structures is obviously nearly impossible (except for Epulopiscium), but you can definitely watch the cells themselves swimming around for hours, and see plenty of morphological diversity.

On the topic of bacteria, next time you put a coverslip on a rich anoxic sample (at least of the very surface layer, but maybe planktonic/benthic samples work too), wait a bit and go towards somewhere in the centre of the slide on medium mag. With phase contrast, you can even go to low mag. Somewhere on the slide, there may be a giant swarming ball of bacteria! The ball gets bigger and bigger as more bacteria accumulate inside, and becomes slightly visible to the naked eye! After a few minutes, the ball collapses into an ever-expanding ring, which keeps growing until it reaches the edges of the coverslip, by which point many of the bacteria die.

What's going on there? I've been told it's probably aerotaxis - microaerophilic/anaerobic bacteria scurrying the hell away from the poisonous oxygenated slide edges (while their aerophilic counterparts often form borders along the edges, if you look carefully after a few minutes). Thus, the bacteria eventually congregate in the local minimum of oxygen concentration, and form a ball. What is interesting is why this ball then collapses into a ring -- do some anaerobes produce oxygen waste, and thus poison their immediate vicinity? Alternatively, could they be secreting some other toxic product and fleeing from it? Seems like this is something that should have been well studied (and well-modeled - mathematical biologists love this kind of stuff, don't they? They get to whip out their gradients and differential equations and other fun stuff), but my unproductivity guilt stops me from looking it up myself ^^

Anyway, plenty of cool stuff has been seen, including a particularly weird flagellate that swims around in a corkscrew fashion and has a warped cell body morphology too difficult to describe at the moment. Might anyone know what it is? It's not too common, around 1-2 cells/slide, and seems to enjoy lower planktonic/benthic areas more than the surface. Roughly 10-15um, I'd say. Anyway, I grabbed some pics:

Sorry for the awful quality -- they're crude screenshots of stills from video, as the scope in question lacks a normal camera and I've yet to figure out how to use the software...those pixels have been through a lot. Be nice to them. The resolution abuse really bothers me though, so I'll try not to look at them myself...

Any ideas? Anoxic dense marine intertidal sediment, ~10um big, swims in a corkscrew fashion. Slightly more refractile than nearby bodonids and diplomonads of similar size. Two cells depicted above.

I'll get more images from the anoxic samples once the unproductivity guilt issue gets taken care of, but that flagellate has been nagging me too much. But in addition to excavates and this mysterious thing, there's also loads of cool ciliates, Naegleria (I think!), dinoflagellates, amoebozoans, and cercozoans. Speaking of which:

In addition to the anoxic wonderland, I also went on a grueling field work expedition to a nearby stagnant ditch-pond thing, an arduous journey that took me 10min including stair-climbing and door-opening. And the potential threat of being bitten by a feral stickleback or some roaming drunk undergrad. I almost sympathise with the field biologists - it is dangerous and difficult work, after all. Especially once the beer runs out.

Anyway, got loads of sample, dumped it into a petri dish, floated coverslips on it. I heard of this technique where coverslips are floated for a while and stuff grows on them, so I had to try it out. Was sort of relevant to my work too, to see how well it would work for an undergrad lab. Fairly quickly, you get 'benthic' ciliates crawling all over it. Curiously, the neuston (air-water interface layer) is full of benthic-looking things growing upside down on it. Amoebae crawl under the water (air?) surface, hypotrich ciliates 'walk' on it. While neuston has been studied a fair bit lately (under the glamour word "biofilms"), the protist component has, as usual, been entirely ignored, save for a couple old papers. Upside-down forest of stalked choanoflagellates, bicoecids and various ochrophytes? Hard to believe, eh?

This doesn't simulate the air-water interface per se, but the cover slips do show how easily small floating life can grow upside down and not even care. After about 4 days, you start seeing some really cool stuff, like this peculiar cercozoan:

Peculiar cercozoan. Freshwater 'pond' sample, collected in early August, cover slip floated on sample for about 4 days. Organism growing on the cover slip glass.
The doughnut-shaped thing is the nucleus with the large nucleolus (I think - plenty of cercozoans do that anyway), the large circle beneath that is the contractile vacuole. From the cell body proper to the shell/test/lorica opening leads some strange 'neck' structure with longitudinal striations. From the shell extend numerous branched filopodia exhibiting bidirectional streaming of granules (extrusomes?) and what appears to be bacterial prey (the large-ish lump in a filopodium near the shell)

I doubt this is a freshwater foram, as the foram reticulopodia look quite different (less thin, and fuse together a lot). There are apparently freshwater gromiids (remember the giant track-leaving Gromia in the news a couple years ago?), but something feels off about its pseudopodia -- they don't appear to anastamose (fuse together) in the ones I saw. Alternatively, I thought it could be a Granofilosean cercozoan, like Limnofila(Bass et al. 2009 Protist fig 5) or something, but those lack tests, so that's stupid. And now I'm all out of ideas. Would appreciate some help from anyone into this kind of thing =D (could also be an stramenopile amoeba, not a cercozoan...a thraustochytrid, perhaps? Cell body structure doesn't seem right; also, do thraustrochytrids do bidirectional streaming of granules and prey?)

I probably lost most of my readers by about there. Sorry about that, but I really want to know what these things are! They nag me! In my sleep! (seriously -- never read a detailed taxonomy paper, especially a Cavalier-Smith taxonomy paper, along with a beer just before going to sleep; so many gliding amoeboflagellates went through my head last night...creepy. Unless you like that kind of thing. Looking forward to my bedtime beer + Cavalier-Smith paper tonight =D)

Anyway, my guilt is back, so I must go and read stuff so I can finally make progress in writing stuff. I'm still alive and blogging though, and hopefully will get back on track soon ^^ And you have some more protist pictures (and maybe even videos!) to look forward to!

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

Mystery Micrograph #22

[originally posted on 18.06.10 1:45am]
[EDIT 23.07.10: Btw, this mystery micrograph is still unsolved. Get crackin'. Ask questions if you need to.]

Apologies for the delay. To buy myself some time, I'll make it a really hard one this time. Like, a TEM. Bwahahaa. I'll give you a hint: these are not moth antennae.

Scalebars: 1um. To be referenced later.

Ultrastructure is particularly evil. Because it shows cells (cell slices) as they are, rather than how the researcher or artist thinks they are.

[25.06.10 HINT]: These structures are a synapomorphy/unique shared feature of one specific group of organisms.

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

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