Field of Science

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!


  1. where was this beach exactly?

  2. The very south end of Wreck Beach, by the marshy area, at low tide.

  3. Im out of my league, but the top pictures remind me of some parabasalids I've seen.

  4. I can't help you with the protists, but I am fascinated by what those bacteria are doing. My first hunch, that physical effects were involved, has still not *entirely* disappeared, as it all seems a bit too fast. I will try to ask one of the PIs, whose been involved in studying bacterial swarming for a few years.

  5. If you have big photosynthetic protists under the scope, you can see rings of bacteria arrange themselves around these cells at the optimal distance to get their favourite oxygen concentration.

  6. @The Lorax Perhaps not Parabasalians specifically, but they do seem to be excavates to me now -- counted 3-4 flagella while going over them frame-by-frame. Or maybe it was dividing. I'm really confused...

    @Lab Rat, @Rosie I have pictures of the bacterial phenomenon now, will post soon. There seemed to be no photosynthetic organism in that particular case, but I did wonder about that too.

  7. Your first mystery protist is a Rhynchobodo (or very similar kinetoplastid)

    Alastair Simpson.


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