Marine Microforay – foram and a thecofilosean party

Apologies for disappearing for a while – had an interview, finals and then my arm decided to temporarily rediscover RSI-like symptoms just when I had a term paper to write, so I had to lay off extraneous typing for a while. Then I realised just how much of my life depends on typing, and losing that ability would not only make me worthless and unemployable, but also unable to communicate with many of my friends who happen to be inconveniently dispersed around the globe. So yeah, I should probably stop casually dismissing ergonomics about now...as should you, if you haven't already!

I've accumulated another batch of microscopic findings, this time from marine samples. By the looks of it, I might be moving to the Midwest soon, and thus be deprived of my ocean (and mountains *sob*), so I figured that focusing on marine protists while I have the chance would be a good idea. Swampy pondwater is available pretty much anywhere anyway.

From time to time, you can be lucky enough to find a foram shell in the sediments around here. Live forams can be found too, but much more rarely – I have a couple, but still need to process the videos. This is not a snail:

Foram. Wreck Beach. 20x obj, DIC except for last image, which is in phase.

To save loading time, the rest are below the fold.

Reticulose amoeba: cells can be fine nets too

Again, the protist kingdom is a special paradise for a cell biologist: as soon as one steps outside the plant and animal kingdoms (and yeast), diversity of cellular forms and structures explodes beyond reason. Cells can also take the shape of a fine net with no obvious cell body proper:

Cover slip floated ~ 1wk on marine sample from intertidal silt at Stanley Park. (40x obj, DIC and phase, resp.)
EDIT: Confirmed Filoreta.

Almost overlooked it thinking it was just slide gunk. Amoebae suffer all too often from that fate – apparently Parvamoeba, one of the most common and ubiquitous amoebae, was only described in the early 90's (Rogerson 1993 EJP) because it was tiny and no one noticed.

Could be something like Filoreta sp. (Rhizarian), but something feels off about it. Filoreta doesn't seem to stretch cytoplasm between filopodia like this specimen does. Maybe it's more like the amoebozoan Corallomyxa and Stereomyxa, or stramenopile Leukarachnion. Then again, amoebae are notoriously dynamic in their morphology. Something that's a far bigger issue in the microbial world is the necessity of getting a sense of the morphotype range of a species; one specimen doesn't quite cut it as it does for animal taxonomy.

In fact, perhaps instead of the ridiculious (for us) ICZN and ICBN requirements for submission of material for curation (many species neither like being cultured nor preserve all that well on a slide), for microbial species there should be a requirement for additional images of different specimens, if possible, to try to capture some of the morphological range. But then again, I'm not a taxonomist, so what do I know.

Right, midterm... (hey, at least I procrastinate productively!)

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)]

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!