On the other hand, some forams (colloquial for foraminifera) take advantage of homes that were already constructed by their amoeboid brethren. Forams reproduce by splitting up into many, many little ‘baby’ forams, after which the mother shell is abandoned. Thus, the ocean floor is completely littered by empty shells accumulated over the eons. Incidentally, a ton of research has been done on fossil forams, as they are good indicators for assessing geological layers — something that oil and gas companies seem to care about for some mysterious reason. The actual biology of living forams remains largely ignored, which I find tragic. But a fair bit is known about their diversity, and what they can do (as opposed to how they do it), leading us back to hermit crabs. Well, their microscopic analogues.

First off, we’ll look at a bryozoan-like foram test user — Placopsilinella. By bryozoan-like, I mean similar to the colonial encrustations on seaweeds, rocks and other surfaces one can find in the ocean. Except these forams aren’t colonial, but similar concept of chambers constructed on top of something else. I think it looks kind of neat: (has an echinoderm feel to it)

This specimen comes from a study of deep sea forams by Gooday et al. (2013, Mar Biol Res), which is conveniently open access — so you can read it. The rest of the forams in question are internal dwellers, taking over empty rooms in vacant housing. Maybe they do drugs in there too, who knows. The orange thing in the image below is Hospitella, inhabiting an empty Globigerinid (planktonic foram) test. It’s orange naturally, and looks rather un-foram-like. The chambers are connected by tubes, which also lead outside the opening. The amoeba itself occupies the space inside its chambers, as well as extruding a network of pseudopods outside its home, feeding on unfortunate prey who swim by. The pseudopods can’t be seen here because the samples have to be fixed(=killed) before examination — deep sea research is difficult that way. The squatter has a flexible organic wall, whereas the host shell is calcareous, meaning it contains calcite. It turns out that glycerol dissolves that, so you can see the soft-shelled inhabitants of calcareous forams in nude!

This is not the first time Hospitella has been seen: it was described by a German scientist, Rhumbler, in 1911 (back in the day when descriptive biology was popular… sigh). It was still orange, and full of tubules. If you’re into old literature (with drawings!), this volume on forams is excellent — although in German. But the pics are pretty, and this guy saw a lot of pretty badass stuff. There is another volume on the biology of forams, with really nice plates at the back, from which the following images are extracted. And if you’re really interested in extensively procrastinating with whatever you have to do, there are more volumes on other marine organisms from the same expedition.

Of course, Gooday et al. themselves extracted those images, which I only noticed after going through the work myself. So y’all get a double dose. Below are more pictures of Hospitella, with C and D showing the organism once again in vivo. The scanning electron micrographs show detail of the flexible test, namely its flexibility, as well as a cross-section of its wall.

Below are some more scanning EMs of another specimen. The first image shows the intact host cell, as well as the inhabitant’s tube to the outside world. B through D show the inhabitant after the loss of its home, with the glimpse of a chamber in C showing stercomata, or hard (sometimes structural) grains of its fecal matter. E and F show more shots of the critter inhabiting its home, in cross section of both.

Gooday et al. also describe a new squatter genus, Incola — apparently derived from  inculta, or Latin for ‘neglected’. That description applies to far more than one foram… The new squatter has a stark difference from Hospitella – its test is agglutinated, or composed of small particles stuck together. It somehow finds and uses coccoliths (recall that it has a network of pseudopods outside the test), the algal scales mentioned above, to supplement its construction. It’s arguably a less lazy squatter than Hospitella, doing some of its own remodeling after moving in.

Looks a little like a potter wasp’s nest!

A shell so good is hard to resist for other creatures also. Forams can be home for everything from mutualistic algae to parasitic nematodes. The study of living organisms consistently points back to a tendency for every available space and niche to be occupied by something or other — not only on the macroscopic scale, but especially on the micro one. It’s a theme found in human societies as well — any available occupation and viable livelihood tends to be filled sooner or later by one of us trying to make ends meet in life. In way, we too spawn host environments and symbiotic relationships with each other — some mutualistic, some parasitic… and some simply commensal. One’d hope the former would be most common, but evolution has no morals — arguably, social evolution included.

And, of course, squatting is not unknown to us. Building a house inside a house, however… hmm, probably someone has, somewhere, but never heard of it. Perhaps the closest analogy would be the Pueblo cities in caverns like Mesa Verde, though those caverns weren’t constructed by anyone. So yeah, it thus follows that forams are awesome — of course!

Oh, I should probably mention a minor detail: Giardia is notorious for giardiasis — also known as beaver fever — a nasty disease obtained from drinking outdoor — and otherwise contaminated — water, especially from slow-moving streams and water downstream of dead animals, faeces, etc. To normal, well-balanced people, this means Giardia is to be avoided at all costs, and that research must be done to either get rid of it or make the sickness marginally more bearable. To a protist nut, the clinical importance means we can have a better understanding of a phylogenetically unique and fascinating model organism. Excavates, the group containing Giardia, are diverse but not particularly well-understood. Naegleria and trypanosomes are fellow opportunists and parasites, respectively, who bring ire upon humans and attract scientific funding. Giardia is on the other branch of the most basic divide between groups of Excavates, however — closer to the enigmatic parabasalids and oxymonads of the termite gut. Oh, and they’re also literally double cells — two nuclei, and two sets of four flagella, in a mirrored arrangement. What more can a cell biologist want?

An impressive scanning EM collage of Giardia in division. (Nohýnková et al. 2006 Euk Cell; free access) Isn’t it cute?

As far as parasites go, Giardia has quite a simple overall lifestyle (PS: if you’re an instructor and make your students memorise parasitic life cycles — you are a sadist! ;p). Sex has not been observed, though some evidence hints that it might perhaps happen. Essentially, Giardia spends its life either lying in wait as a cyst, or leaving the cyst and swimming towards intestinal walls, attaching among the villi with a specialised suction plate. There it sits and feeds on the host’s tasty juices, like glucose. Apparently, intestines don’t really like having uninvited things attached to them, and all hell breaks loose. Not that the parasite is of a particularly friendly disposition either.

They’re cute under lasers too. Confocal image of Giardia: microtubules in red, the two nuclei in blue.  (Sagolla et al 2006 J Cell Sci; free access)

Being highly derived — as a result of their phylogenetic position as well as parasitism — Giardia has unusual genome structure and cell biology. Giardia is both Golgi- and actin-challenged. The Golgi bodies are extremely reduced, and for a long time were thought to be absent altogether — though now it is known that their derived form is necessary for cyst formation (Faso et al. 2012 Cell Microbiol). Actin is present in a single copy, and a really weird one at that. Major standard actin-binding proteins are absent altogether (Paredez et al. 2011 PNAS; free access), including the motor protein myosin (you might know it from muscles). The cell skeleton component actin is present in all eukaryotes, and plays a major role in things like growth and amoeboid movement. Curiously, a number of typically non-actin-regulating proteins have been found to be recruited to actin in Giardia — an example of functional replacement, possibly one that then enabled the loss typical actin-associated proteins (last part is speculation on my part).

Here’s an excellent electron micrograph showing the structure of the middle of the cell, with four of the flagella exposed. Note the finely-spaced contours on the lower left, fine enough to appear to form a diffraction grating at low resolution. More on that in a bit!

Image shamelessly stolen from: Cande Lab website/Images (by Joel Mancuso). Image modified by slight unsharp mask and then halving the size.

Before I go on to ultrastructure, I must mention an important note — it is commonly stated, even in scientific literature, that Giardia is ancient. This is not the case: the statement is based on old data from the 90s, which were based on outdated phylogenetic techniques. This misconception dates back to the Archezoa Hypothesis, wherein a mitochondrion was gradually growing in sophistication along the anaerobic deep-branching eukaryotes (on the “bottom” of the tree), until it reached its canonical complexity at the base of the divergence of more ‘normal’ eukaryotes — like algae, ciliates and the “crown” group of Fungi, Animals and Plants.

In the early 2000s, this hypothesis fell apart as newer tree-building techniques were better at resolving highly derived (unusual) critters, and all of the mitochondrially-challenged anaerobes were placed in the midst of mitochondria-bearing groups. Furthermore, mitochondrial genes were found in each of those anaerobes, confirming that proper genome-bearing mitochondria came first. Thus, Giardia is in no way unusually ancient, any more so than the other eukaryotes, and is claimed as such out of pure inertia. Public service announcement over.

Suction is used for attachment, but it is still not entirely clear how that suction (negative pressure) is generated (House et al. 2011 PLoS Path; free access). Remember the first electron micrograph above, and the very fine lines at the bottom left? These are part of a section of the sucker plate(=ventral disk, more technically). Those bands are made of cytoskeletal elements, and are thought to be the stuff that generates suction — namely, microtubules. Giardia, despite (because of?) its modest actin repertoire, has an elaborate microtubular cytoskeleton. The ultimate focus of this post (I stick to ‘short’ introductions, y’see), an electron tomography study by Schwartz et al. (2012 PLoS ONE; free access), reveals the most in-depth information about this complex organelle’s structure seen thus far.

Electron tomography(ET) uses thicker sections than classical transmission electron microscopy, and renders 3D reconstructions within those sections by imaging it from different directions. This allows structures to to be inferred in 3D without losing as much data to sectioning — though a bit of resolution does get sacrificed. The 3D sections are then assembled to form a computer model of the whole organism, or its chunks of interest. ET has already recently revealed plenty of structures that were previously unseen or misinterpreted — it’s not always obvious whether and where one blob meets up with another in thin-section electron microscopy. And pretty models are generated — I will post some more later. As a deeply serious scientist, I like pretty pictures =)

The microtubules are nucleated(=rooted) at the centre of the disk, and extend outwards in a loose spiral towards the edge. Atop the microtubules (ie, facing away from the bottom surface), ‘microribbons’ protrude into the cytoplasm. The ‘tubes and ribbons are spaced closer together towards the edge. The figure above shows the microtubule arrangement and polarity (their have a rapidly growing+shrinking and a slowly shrinking end, roughly speaking), and how they inferred it (don’t worry about that). I find it curious that while the cell is obsessively symmetrical, the disk itself is arranged in a spiral. Additionally, since the microtubules are uncapped at the slowly-shrinking end (often some protein is squished onto there to stop the shrinking) — are the ‘tubes in the disk highly dynamic, constantly forming, growing in a spiral and losing their shrinking end, being replaced with younger microtubules? You’d probably need superresolution live cell confocal microscopy for that. Would love to see the movies!

The next figure shows an insanely zoomed-in 3D reconstruction of a section of the microtubule-microribbon complex. The circular part comes from the microtubule being sliced across. It maps some individual proteins and major structures of the complex, and the point here that you care about is that it’s complex, and you can figure out where individual proteins go. The lowercase ‘g’ means it’s Giardia‘s version of the protein, while MAPs and MIPs are creatively-named Microtubule-Associated Proteins and Microtubule Inner Proteins, respectively.  How they assemble is an even more exciting process, but don’t ask me. I’m in awe of how much structure can be seen in electron tomography!

In addition to presenting a stunning reconstruction of a complex protist structure, this paper presents a novel imagining technique (not the tomography, but the technical way they used it), which I’ll keep in mind for further reference, just in case. Reconstructing complicated 3D structures is kind of a fun thing, and shows us once again how far from simple both cell and protistan biology are!

Focus article: Schwartz CL, Heumann JM, Dawson SC, Hoenger A (2012) A Detailed, Hierarchical Study of Giardia lamblia’s Ventral Disc Reveals Novel Microtubule-Associated Protein Complexes. PLoS ONE 7(9): e43783. doi:10.1371/journal.pone.0043783

As usual, it falls upon myself to amend such cosmological oversights. But that’s fine — I’ve spent a huge chunk of my childhood creating fantasy cultures and mythologies studying hard and doing homework, so making stuff up is sort of my forte — very useful in science. Adapting extant styles to your cultures is incredibly fun in itself, and seeing how various things can be seen in other ways. I’ll begin with 8 — one for each supergroup (slightly outdated now, but this isn’t supposed to be a scientific reference). It’s also a good number to fit with Buddhist motifs, as 4s and 8s are kind of central to their plot. Anyway, serendipitously, a friend happened to have  a couple books on Tibetan symbols and motifs lying about — a deadly distraction. So I’ve been practicing and doodling a bit. These are mostly sketches; hopefully better versions will follow someday.

The first one is supposed to represent a microsporidian — a highly reduced single-celled fungal parasite (with the smallest nuclear genome in all of Eukarya!). The flame is supposed to represent the awesomeness and/or terror of parasitism (depending on your view, I guess); the coil at the top is the polar tube, via which the parasite injects itself into unfortunate cells. On the bottom is an ever-so-slightly stylised nucleus.  We’ll have this represent fungi for now.

The euglyphid below was one of the first protist zodiac figures I’ve done. Euglyphids are scaly testate amoebae, with spines — which are straight in nature, but why should I care? This will serve the Rhizaria (though I do want to do a foram too).

Then I doodled a haptophyte — marine alga with elaborate calcium carbonate scales it builds and secretes. The thing at the top is a haptonema —  food is caught by it, aggregated into a ball, and once the ball of food is big enough… the haptonema reaches around and inserts it into the posterior end for phagocytosis. So a haptophyte eats with its ass. A tough topic to discuss with a straight face…

Unrelated to the zodiac, I’ve been reading about dileptid ciliates — notable for wiggling about a trunk or proboscis loaded with miniature missiles; upon a brushing contact with prey, those missiles cause it to… explode. Then the dileptid drinks its cell juice. Why swallow your food when you can just blow it up? Further inspiration came from two facts: a) dileptids eat rotifers when they can (photgraphic evidence present in literature); and b) apparently the skinny base of the trunk in a regular dileptid was not enough for Paradileptus, who felt the need to construct a sizeable pouch around its mouth. Like a carnivorous version of a Basking shark, perhaps?

And here I was playing around with a new toy — 9B graphite stick. Amoebae are hard/fun to shade (depending on how nice you expect it to look — starting with low standards is advised.)

I definitely haven’t abandoned the Pacific Northwest stylisation of protists either! Just very, very distracted, as always. Anyway, that’s it for the progress update on the procrastinatory doodling front.

Remember our testate amoeba friends, the arcellinids? Here is a pair of Arcellas (Arcellae?) in the midst of division. Organic tests(=”shells”) rust over time, as in they turn yellow and then brown with oxidation. Based on that, you can tell that the newer test is on the bottom, as they start out clear. These cells have almost finished dividing, with a lingering cytoplasmic bridge barely connecting the two, between their mouthes (ok, ‘oral apertures’). Mouth-to-mouth division. The three tiny round things at the top end of the cytoplasmic bridge look like the last organelles that will be transferred over to the younger cell — perhaps a few mitochondria, based on their size. Don’t worry, there’s already plenty that have been transferred to the younger cell already!

To split, arcellinids need to orient themselves on their sides, perpendicular to the surface. They do this by producing gas bubbles that increase bouyancy at one end and cause them to re-orient. The bubble at the bottom of the younger cell could be a remnant of that, or could be just a contractile vacuole — can’t tell from this image. Next to it is a nucleus with a very obvious nucleolus. The top cell has one too. After separating and returning to their default upright position, the two amoebae will probably be quite hungry, and go on with their ploy to devour pretty much anything they can get on top of. There are documentations of arcellinids feasting on nematodes and rotifers, but more on that sometime later. This specimen is from a pond sample, although they thrive in soil as well.

(Photo by Edward Mitchell and Jerry Kudenov (U of Alaska, Anchorage). Courtesy of Edward Mitchell)

The above shell, reminiscent of medieval scale armour, was built by an Assulina species, a member of the Euglyphid clan. Euglyphids are thin-footed(=filose) amoebae notable for their orderly construction and secretion of siliceous scales. To push the construction (or even bricklaying!) analogy a bit further yet, the scales are held together by the cement between them. The shapes and arrangement of scales is characteristic of each species, meaning their formation is strictly regulated and not all that random. As soon as you see something morphologically prominent being not random in biology, your first instinct should be to do drugs. On the cells. This can help reveal some of the cellular components involved in the process, but much more importantly — generates freaks. And if you’re a cell biologist, freaks are fun!

So, back to coffee. *sip* This is what caffeine does to our neat and organised Assulina species:

Oh no, our euglyphid has gone out in public completely disheveled! This is from a study by O. Roger Anderson (who also happens to be the god of forams and radiolarians), where Assulina was treated with 5mM of caffeine (Anderson 1995 J Morphol) — for a comparison, drip coffee typically has 3.5-4mM, from a back of the envelope calculation. The scales become crooked, and you can see pieces of cement (the long gooey stuff) horribly misplaced atop the scales. On top of that, some of the scales end up standing perpendicular to the surface altogether!

The scales are made by a membrane system associated with the Golgi apparatus. Presumably, a template is laid down (I don’t know how in the case of Euglyphids, but coccolithophorids (algae with calcareous scales) use a protein-cellulose structure first), and the containing vesicle can then be seen with silica-depositive vesicles fusing with it. This silica gradually accumulates, and the scale matures. It is then delivered towards the mouth of the cell during cell division, where an entirely new test is constructed from scratch, opposite of the older cell. (I wonder if they can repair the test too…). In short, membrane dynamics and the Golgi are essential for scale formation. On the left are scales made by a healthy amoeba:

In addition to neurology magic (I suck at vertebrate biology, go talk to Scicurious instead), caffeine disrupts the Golgi function and membrane trafficking. In plants, caffeine treatments disrupt the cell plate formation, where cellulose-containing vesicles fuse to form the wall between the cells — this produces some really fun freaks! (don’t water your plants with coffee, by the way). If building things within a cell is so dependent on membrane gymnastics, you can imagine that a membrane-trafficking inhibitor might not be the best friend of quality there. And that is exactly the case on the right of the above image — the vesicles are bloated and disorderly, while their contents fare no better.

In the caffeine-treated euglyphids, the scale vesicle struggles to control the shape of its contents. Scales become thicker, rounder, and marred by an irregular surface — along with some organic gunk on the surface, perhaps the cement. There’s a closeup of the weirdness:

The control of the direction of scales upon deposition is also lost — some are perpendicular, while others are inverted altogether. There is a malfunction in whatever mechanism ensures the vesicles are oriented correctly while releasing their scales into the daughter test. The Golgi apparatus itself develops some impressively large tubules which are invisible in normal cells. These can be seen as regularly packed circles near the nucleus in the picture below:

So think of these poor unkempt creatures next time you have your coffee. And I would be particularly wary of bricklayers with a mug. Or armourers, for that matter.

The follow-up question regards what other psychoactive substances do to the amoeba’s construction capabilities. Out of purely academic interests, for example: THC, psilocybin, LSD and LSA, mescaline, DMT… once again, out of entirely theoretical curiosity. Environment Canada has already explored this topic with spiders, but the research field just BEGS for a greater phylogenetic diversity. Furthermore, perhaps testate amoebae and other protists can be used to explore further psychoactive (and, for actual academic research, cytoactive) chemicals. Here’s a guaranteed fundable grant application waiting to be written, for anyone who’s bored (or eager to rise to the heights of scientific and humanitarian contribution!).

Spending hours at the ‘scope helps get a three dimensional visualisation of the microbial world; ultimately, microscopy becomes akin to wandering around in the woods and being a naturalist, immersed in an intuitive world with volume. The only thing that’s missing is sound. (I wonder if protists make sounds…) It’s fun to try to transmit some of that three dimensional world into art, since we can’t really see it otherwise. You can pretend you’re a naturalist sketching in the forest, trying to go for realism (with artistic license):

Or even more artistic license:

Cartoonised 3D Paramecium. Next victim is a euglyphid (testate amoeba), below: (couldn’t figure out how to incorporate the surface scales with this style)

Or you can go full-on stylised. Since I did my undergrad in the Northwest, and the upcoming big protist conference is in Vancouver, been trying to replicate the local First Nations art styles. First attempt: Telonema, a marine flagellate (though I’ve seen one in freshwater…).

Trimastix, an excavate occasionally found in soil and rotting leaves:

(Upon request, Trimastix prints are available here.)

And sometimes you can just be silly

That’s it for now; don’t want to exhaust my meager collection right away

(And feel free to contact me if you’d like to use anything, I’ll be happy to help!)

Luckily, a sampling of the alien world has been recently unveiled as a permanent exhibit at the San Francisco Exploratorium. Kevin Carpenter, a former member of the Keeling Lab (responsible for quite a bit of termite gut research), is notable for being exceptionally skilled with Scanning Electron Microscopy of protists. You can find some images from the exhibit on his site. It appears that the Exploratorium seems to have a live exhibit of termites and their denizens. So if you happen to be in the Bay Area, be aware that there is now a place to pay homage to some of the few eukaryotes who can digest hardly-edible cellulose.

Here’s a shrunken sample of the documented alien world — a Saccinobacculus (“snake-in-a-bag”) with a bacteria-laden butt of Barbulonympha in the background. Click on  either of them for a further journey in the termite (and roach) gut!

This Mayorella‘s (?) nucleus is smiling and wishing you a very happy day =) The auspicious pattern is formed by heterochromatin clumps. To the right of the nucleus is a contractile vacuole — devoid of any emotion this time. Cells do speak to you from time to time. In your head. Pareidolia is fun!

The amoeba, in this case a large Amoeba proteus, first comes along a ciliate and attaches itself to it. Frontonia often hang out in the detritus on the bottom, and are thus especially prone to encounter amoebae. The amoeba rides the frantic ciliate while extending its pseudopods, and eventually attaches itself to a surface, anchoring the ciliate to its doom. The pseudopods continue to extend, and form a cytoplasmic ring that constricts and begins to pinch the ciliate into two halves. The ring extends into a tube as it exerts more pressure, and the ciliate is ultimately torn in half: one half engulfed and stuffed into a food vacuole, the other half swimming away (but mortally wounded). The dying half will probably be shortly sucked dry by scavenging Coleps ciliates. The terrifying ciliate predator has met its end, by an organism often used colloquially to represent slowness, laziness and general weakness.

Eight minutes. In eight minutes a large, tough ciliate is cleaved in half by a squishy meek-looking beast. As with other members of its group, Peniculids (including Paramecium), Frontonia has a fairly stiff cortex (or “skin”), and plenty of turgor pressure within to make it relatively rigid. In fact, they manage to contain bent cyanobacterial filaments — which, you can probably imagine, exert quite a bit of tension themselves. Imagine the force the cytoplasmic ring must exert to pinch the ciliate apart! Furthermore, Amoeba proteus is a generalist, and does not specilialise in Frontonia or even ciliates. It eats everything from bacteria to small flagellates and large ciliates… to nematodes and rotifers. Yes, rotifers. Each of those prey requires a different strategy to capture them, and the amoeba is smart enough to know which one to use (presumably using chemical signals). In other words, as I probably mentioned too many times before… single cells do have behaviours! (as an aside — much like spiders, some of whom apparently make silky nets to trap certain prey! (article here) [/irrelevant fact])

Much like a python after devouring a small sheep, the amoeba requires about four days of digestion to negotiate the [half of] Frontonia. I wonder if in the wild, it finds a place to hide and rest during the process. After such a feat, it surely deserves to.

You can see a clear, slightly bubbly, macronucleus — a thick wad of its own DNA. Beneath the nucleus is a freshly engulfed diatom — you can tell it’s fresh by its intact state, particularly of its plastids. Above the nucleus is an example of what will soon happen to it — dissolve in acid and enzymes of a digestive vacuole. This vacuole will soon be recycled back to the surface to dispose of the victim’s remains. The membrane becomes part of the cell surface, and then “spent” as phagocytic vacuoles (newly minted food vacuoles) form at the mouth. A protist’s circulatory system can be a little more exciting than ours, in a way.

Here’s a labelled version for clarification:

I haven’t quite figured out the identity of the refractile crystaline blob near the centre, above the “mouth” (inside a vacuole). If anyone knows — I’d love to hear it!

*yawn* Not the most flashy micrograph you’ve ever seen, most likely. But it’s still kinda cool, I think: here, you can see bacterial division! This is a stalked bacterium, possibly Caulobacter or something like it — a major model for bacterial morphogenesis, or shape-formation. At the very bottom of the stalk is a faint thickening resembling a holdfast. The constriction of the cell body is cell division in progress, via budding. The new cell is a flagellated ‘swarmer’. Unfortunately, the flagellum that should extrude from the upper (swarmer) cell isn’t visible here — perhaps it’s too fine and moves too quickly.

A quick glimpse of the Caulobacter lifestyle can be seen in this review by Hughes et al. 2012 (paywalled). When a swarmer settles, it grows a stalk and soon begins budding to produce swarmers (offspring, essentially). Apparently, once a stalk is formed, the bacterium is attached to the surface for life. If the chosen surface goes awry for whatever reason, it is up to the swarmer cells to detect something is wrong (via presence of leaking DNA from dead colleagues) and not settle down there.

Were I an organised person, perhaps I’d make one day a week a bacterial day — while protists are my first obsession, I feel not enough attention is given to bacteria from a morphological and cell biological perspective. Too many people speak of them as chemical. pathogenic or ecological agents, faceless and formless, just blobs with DNA sequences. Most bacteria have been cursed by their size: too small for light microscopy to reveal much, while electron microscopy comes with severe preparation artefacts, meaning one can’t really see what a cell does live under EM. You get indirect (while awesome!) suggestions, at best. Luckily, with the development of super-resolution light microscope, the classical 200nm theoretical resolution limit (closer to about half a micron in practice) is finally being crossed, and microscopy can reveal tiny features in still-living bacterial cells! An example of what can be seen with light these days can be seen in this image from Yves Brun’s lab. A little bit more detailed than my stalked blob above, eh?

Pretty much every photosynthetic eukaryote you see shares one single common origin of plastid endosymbiosis, with the exception of a testate amoeba — Paulinella chromatophora, which has one or two recently reduced cyanobacteria (‘cyanelles’, again) of a separate origin. There is a relatively large interest (reads: a couple labs) in Paulinella in hopes that studying it will reveal something about how plastid endosymbiosis works, as well as some insights to how the other (main) symbiosis event happened. Eukaryotes have thus domesticated cyanobacteria on at least two separate occasions, and seem to be doing fairly well with their stolen agriculture industry.

Evidently, I don’t post enough creepy things around here, so here’s an attempt to make up for it. Stockfish are outdoor dried cod, and was traditionally the main export of rural maritime villages in northern Norway. The seaside villages are covered in cod drying racks and dessicated cod, accompanied by a wonderful smell. Or an awful smell if fish rotting in the sun isn’t a part of your culture (in Russia we salt and dry our river fish — delicious! Good with beer too). The heads are chopped off in the process, and used to scare tourists. I find them adorable.

Notice how “rotting” was mentioned above. The inner microbiologist in you might immediately jump up at the sight of that wonderful word, and with good reason. These stockfish photos might not be so frivolous after all — the drying process involves microbial action! Some of us who love fermented foods also have an unhealthy obsession with plugging random delicious things into Google Scholar and seeing if there’s anything on their microbiology and biochemistry. Stockfish aren’t as widespread as some other fermented things (like beer, perhaps), but — as you might expect — studies have been done on the microbiology of [properly] decaying cod. Not many though.

According to Valdimarsson & Guðbjörnsdóttir (2008 J App Microbiol), the fermentation process begins with Moraxella and Acinetobacter bacteria.       The fish are then further ripened with a Lactobacillus plantarum-type bacterium. As suggested by the name, Lactobacillus are lactic acid bacteria (Kleerebezem et al. 2003 PNAS), often found in things like fermented dairy and pickles, giving them that deliciously sour flavour. Lactic acid producers are generally desired in food fermentation, due to improving taste and also taking up resources before undesirable bacteria get to them. Fermentation is essentially an ecosystem management process — you who thrives and who is kept out by altering environmental conditions, as well as the stuff present in the food itself. Being of Eastern European origin, I find that practically everything tastes better after having passed through the metaphorical ‘digestive tracts’ of a vibrant microbial ecosystem!

This works in coastal Nordic areas because the temperature and humidity there is amenable to this particular cocktail of bacteria; even so, in unusually wet drying conditions (Valdimarsson & Guðbjörnsdóttir 2008 J App Microbiol), an “off” taste appears and the stockfish becomes of low quality — most likely as a result of a different microbial collective thriving there. As climate conditions vary from region to region, so does the bacterial diversity, and the types of fermented products that can or cannot come from that area — leading to a rather fascinating case of an interplay of microbiology and geography dramatically influencing what we eat around the world. Curiously, a big chunk of the stockfish end up in Portugal and rehydrated as bacalhau (bacalao in Spain). While cod can be caught off the Iberian coast, it does not appear that it can be dried there in a stockfish kind of way. A case of trade established not only due to differing flora and fauna found in respective countries, but their microbial ecosystems as well. The microbial biome on the chilly Norwegian coast plays an active role in their economy, regardless of whether people are aware of its existence.

Microbioanthropology(?) is kind of fascinating — and, again, delicious!

The fish pictured above ain’t cod but is among the first things that greets you in the tourist info centre in Moskenes. I’m not sure what fish it is, but it sure wants to be frightening!

It’s also quite pretty. We’ll look at specific weird organisms some other time, but for now — a couple general views of a particularly dense mat from a sewage treatment pool. A prime tourist destination, hands down!

Perhaps the next time you encounter a putrid odour, think for a moment about its makers and their worlds alien to our oxygen-tuned smell receptors.

The entire cell is arranged radially around a central organising unit, the centroplast, from which the cytoskeletal framework of the axopod emerges. The cytoplasm is organised more or less concentrically — immediately around the centroplast is an “exclusion zone” devoid of organelles, followed by a sphere of Golgi bodies,  curiously oriented with their maturing end (where stuff comes out of) inward rather than outward. Around the Golgi layer is the endoplasmic reticulum as well as the nucleus tucked in between the axopods. The remarkable thing here is that a ‘typical’ cell is oriented with the nucleus near the centre, followed by the endoplasmic reticulum and then golgi bodies, maturing side facing outwards — since generally you’re trying to get secreted products to or near the surface. While seemingly perfectly shaped for this exact arrangement, the centrohelid cell is essentially inside-out, with the finished products delivered to the centre of the cell. But it makes sense — at the centre, the secretion products hitch on to the axopod microtubules, and ride them outwards, to the edge of the cell body proper and beyond.

For the morbidly curious, most of these structures can be seen in the electron micrograph below from Bardele 1975 Cell Tiss Res, sectioned through the centre of the cell:

All this is surrounded by the ectoplasm, in this case a bubbly vacuolated layer where prey gets digested and savoured. And the cell body proper itself is usually covered by a myriad of spicules and plates, which can be seen in pictures here. This layer of surface decoration serves as a valuable feature for identifying species, to a certain extent. Of course, it may well be that what appear to be ‘species’ to our bloated macroscopic eyes may be genetically equivalent to entire families or phyla in the animal kingdom.

The axopods themselves carry kinetosomes, or little sticky-stabby organelles that act in catching prey. The long, fine axopods extend quite far beyond the cell, and wait until a hapless flagellate comes swimming by. Once triggered, the kinetosomes stick to and stun the victim, and other axopods are recruited to help hold it down. Typically, as one images, these flagellates are small, but it’s not uncommon to see centrohelids with prey larger than themselves. In some species, the individuals even join forces (ie, fuse) with their neighbours to catch large beasts! (Sakaguchi et al. 2002 Eur J Protistol) The victim is then delivered towards the cell body proper, where pseudopods extend and engulf the food for a gradual digestion ritual.  The waste is delivered outwards by the same axopods, which essentially make the cell functionally bigger without having to sustain all the material in-between that clogs up valuable gas exchange surface.

Centrohelids do move about, and in plenty of different ways: many float, some seem to use their axopods to glide along the surface, some attach to the surface with one end and slide like amoebae, some others apparently roll around like balls (Zlatogursky pers. comm.). They reproduce by cell division, like most things, but the complete life cycle remains unknown. To my knowledge, no flagellate stages have been found, but that does not mean they don’t exist. To this day we keep on discovering new life cycle stages, even of well-known organisms, and quite often the two stages were long thought to be completely unrelated things. (a notorious case of this is in fungal taxonomy, of moulds, where the sexual and asexual fruiting bodies still carry separate genus and species names, primarily to deter taxonomically-challenged undergrads from pursuing mycology any further). I had the fortune to come across one in the midst of division, which you can see below:

Not much is known about how centrohelids live (let alone their potential molecular peculiarities), and the entire centrohelid research community at the moment constitutes two or three people. The field is so tiny that it was struck badly by an unfortunate unexpected death of their recent expert, Kiril Mikrjukov. With his passing, centrohelid research essentially stopped, and much valuable insight was lost. I know of at least one person currently trying to revive the centrohelids (to our eyes; they’re doing quite fine without being noticed by us, of course), but that’s it. I’m bringing this up to point out how tiny some areas of research are, and how easily they can be devastated by the loss (or stalled by the retirement) of one or two people. And since the old apprenticeship model where a student follows their advisor’s footsteps is largely gone (in large part due to the horrid job market, rather than being replaced by something better), it’s painful to think about the wealth of knowledge and insight that gets lost without ever seeing the light of publication. Many tantalising observations never make it to publication, sometimes due to experimental difficulties, but usually due to the limits of how much one individual can really do (not much, in science…), oh, and, of course, lack of funding. This is just one example, but the world of protistology is full of fascinating organisms left obscure and untended by human curiosity.

They’re kind of addicting to photograph. Evidently, Haeckel (1904) thought similarly about engraving them (figure 10 in Plate 15)

Bicosoecids aren’t the only protists who build loricas — in fact, house- or cup-like structures are fairly popular throughout the eukaryotic world. Take this choanoflagellate (Diploeca sp.), for example, sitting in a flask as it waves its flagellum to draw in bacteria to meet their doom.

Or the Jakobids (excavates, notable for having the most complete mitochondrial genomes — ie, seemingly having retained the most genes from the original bacterial symbiont mitochondria come from): Histiona sp., and — I’m not making this name up — Reclinomonas americana, genus aptly named for the flagellate’s appearance of reclining in its lorica as it ‘lazily’ waves about its flagella. Reclinomonas went an extra step and covered its lorica with nail-like scales — facing outwards, of course — which are marginally noticeable in its photo below.

Some ciliates build themselves flasks and bottles too; for example, folliculinids, which I have written about on my other blog. Lagynion is an obscure chrysophyte alga also sitting in a bottle, though a much more common relative, Dinobryon, builds massive tree-like colonies  similar to those of the bicosoecids above. This is by no means a comprehensive survey of bottle-dwelling protists!

These structures provide some protection from predators as well as general mechanical events (eg. you stepping on their microhabitat — yes, we’re all continuously guilty of that!). When in danger, or when tired, perhaps, the protists withdraw themselves into their respective vessels, and wait. Once again, our size as animals might be worth appreciating a little — imagine walking around in the woods with menacing critters and their flagella jumping out of cryptic pots!

How many different types of bacteria do you think you can see here? Just for fun — of course one can’t identify such small microorganisms particularly well using morphology!

Bicosoecids are non-photosynthetic relatives of brown algae. Usually nestled in a delicate lorica (but sometimes devoid of one), bicosoecids sit attached to a substrate with one flagellum, and wave around the other to bring in bacterial prey to devour. At the base of the flagella is a lip-like structure where the unfortunate prey get engulfed after travelling down the current. When startled, they rapidly withdraw their flagellum into a characteristic spiral, which you can see in the bottom specimen of the group. Most tend to be solitary, but this species forms loricate tree-like colonies, like wineglasses stacked upon each other. Despite their small size and timid appearance, their cell structure is fairly complicated and –hoping you’d agree with me — quite elegant.

For this Friday, let’s do mushrooms. I’ve collected a few photos of these things while going out hiking, and spend way too much time staring at the ground and rotten tree trunks for my own good. Despite having a slight extracurricular obsession with mushrooms, I’m not very good at identifying them — can do genus if I’m lucky (ie, it’s obvious). But they’re alien and pretty to look at nevertheless, so I hope you enjoy! Remember, just as in the previous Frivolous Photo Friday where we witnessed a killing machine devouring a roach, these guys are not any more docile. Beneath the passive-looking fruiting bodies, the mycelium is busy exuding digestive substances into its surroundings, and soaking in the tasty remnants. Basically, the stomach of a fungus is its outside — and we’re all part of it, sooner or later…

First, some Jack-o-Lanterns. Apparently, they bioluminesce, but I haven’t yet seen that.

A couple thinly stalked Mycena sp.. This is a particularly understudied genus of tiny, yet elegant, finely-stalked mushrooms — some quite colourful, but most fairly pale. They still look cute close up though.

And here is something yellow with a seriously slimy cap. This is a young specimen, as the veil is still intact and hiding the gills. If this veil is finely net-like, these might be a Cortinarius sp., but I think the veil might be too densely fibrillar for that. Not that I really know what I’m talking about or anything, especially without half-functional internet.

If you have some ID or general cool mushroom stories to tell — comment away!

The euglenid’s surface is covered by proteinaceous strips making up its pellicle — in many species, they slide against each other and enable metaboly, a pattern of movement that makes the euglenid feel ‘squishy’. This genus, on the other hand, lacks the sliding ability of its pellicle strips, and sits rigidly in one shape. Inside are a big clear doughnut-shaped starch globule, a red eyespot used for seeking light, and numerous green plastids that were once inherited through secondary endosymbiosis of a green alga. Only a single clade of euglenids is photosynthetic — the rest have never seen a plastid as anything other than a food item.

(a wallpaper version can be found here, hopefully big enough to crop or shrink as necessary)

Around the edge is the nuclear envelope and, potentially, a periphery of fibres called lamina. The internal blob is presumably heterochromatin and potentially nucleolar in nature — but one can’t tell without using electron microscopy as we run into the light resolution barrier here. A true nucleolus (and there can be several, contrary to what some textbooks suggest!) should be full of ribosomal material under construction. Thus, the term ‘endosome’ (inner body) is often used to avoid jumping to conclusions about the nature of those bodies. (a neat page on amoebae and their nuclei (among other things, like ID) can be found here: amoeba.ifmo.ru). Lastly, note the small granules just beneath the periphery of the nucleus. I have no idea what they are, and would probably have to go to electron microscopy to really have a clue, but they look sorta cool anyway. While the nucleus is sometimes treated as just a bag of DNA or “genome”, that DNA is in a highly organised arrangement with various regions of it existing in different states, bound to different proteins… even turned ‘on’ and ‘off’, depending on conditions or what the cell is doing.

Here, we get just a passing glimpse of that complexity… but still, I think it may serve as a nice intuitive reminder.

Here’s the view from which it came. Note the border between the clear ectoplasm at the edge of the cell, and the endoplasm where all the ‘stuff’ is. This cell is a bit squished, so you don’t get to see why it has an ectoplasm just yet…

The cytoplasm is full of refractile crystals, at least some of which may be related to urea in composition, and perhaps used to accumulate (and later dispose of) waste products. They may also be and do other things, of course.

And a general view of the amoeba. This looks like Polychaos sp., an amoebozoan amoeba with multiple pseudopods poking out in different directions (pseudopod motility is an important character for amoeba ID). Upon extending the pseudopod by laying down the ectoplasm we mentioned before, the ‘pod is soon filled with endoplasm, streaming rapidly through its centre. This is no slow amoeba. However, the nucleus is strange for a Polychaos sp., so it may well be something else, or a poorly documented Polychaos. One would probably have to resort to sequence data to figure it out, or a Russian amoeba expert (there’s a bit of a team there, and they’re really good).

Around the middle of September, my buddies and I found a giant female Chinese Mantis clinging to the window of a local watering hole. Given that cold days were coming (or so we thought…), I really wanted to keep her — with the extra excuse that she’s invasive. Of course, people don’t seem to mind invasive species that actually look cool, resenting only the ‘ugly’ or ‘annoying’ critters. Anyway, we kept her, in a big fish tank (not filled with water, of course), and finally discovered the one time one can actually appreciate the vigorous abundance of sizeable roaches on our campus. And I mean ROACHES. They’re huge — some have bodies ~5cm long! And they fly too…

Watching a squirming giant roach get devoured by a freakish killing machine is among the more satisfying activities one can do in a lab, perhaps closely following naptime. When you introduce a roach to the mantid’s lair, you witness a stark juxtaposition of representatives of r- and k-selected species of the insect world, respectively. The roach — a master of stealthy survival and rapid, proliferous reproduction; the mantis — a rare yet powerful predator who takes much of an entire year to reproduce. Curiously — both in the same order, Dictyoptera. Mantids and roaches (including termites, cladistically-speaking) are sister taxa. Not that family really matters much when the swaying behaviour kicks in and the mantis lunges towards her juicy prey, catching the roach in one strike of her forearms.

She neither cooks nor kills her prey. She eats it, alive, ripping chunks of flesh out with eerily mechanical-moving mandibles.

The roach meat kind of looks like chicken… almost appetising, somehow — if we put aside for a moment its actual identity.

She devours everything except for the rather lean final leg segments, and the hard wings. The first prey I fed her was a cricket, and upon returning the next day to see if she had eaten, there was hardly any evidence of either the cricket’s survival or the mantid’s feast — save for a pair of antennae lying on the bottom of the tank. Yet the ferocious carnivory was somehow fully compensated for by the elegance of her movement — mantids are beautiful, and quite charismatic. They almost seem to interact with you — and probably could if they wanted to (like cats). And they’re big — who can say no to an oversized arthropod?

She lived, prayed, and preyed with us for a couple of months until the endpoint of her life cycle was truck. Sadly, as elaborate and remarkable as mantids are, they only live about a year. We probably extended her life by a month or so thanks to captivity, but even being k-selected does not grant you a long life in insect world. She was gorgeous and fascinating, especially for a non-protist.