Adorable velvet worm composite

Too busy to write a proper post these days, but just happened across a cool Current Biology quick guide to onychophorans(=velvet worms), with a pretty picture showing their diversity (and really pretty textile-like patterns):

Australian onychophorans (Blaxter & Sunnucks 2011 Curr Biol)

The guide itself is quite interesting, recommend reading it if you have time. To entice you, they talk about the diversity of breeding behaviours found in onychophorans:

"Some are fully live-bearing (viviparous), with well-developed placenta-like, extra-embryonic structures that attach to the mother's uterine wall and nourishes growing embryos until the birth of sequences of self-reliant, mini velvet worms."

Onychophorans are way cooler than arthropods ;p

And they can be social with dominant/submissive behaviours, which I talked about in an earlier post (which happens to be one of my most visited, probably because it's not about protists =( ).

And with that, there may or may not be a surprise while I'm away, so stay tuned. In any case, I should engage in some form of proper blogging sometime after the 20th... (finals, shoot me)

October Mushroom Foray

Felt a little guilty not posting, especially considering I'm mentioning the blog on applications and such. So have a low-maintenance post for now! It barely even features any protists, but rather some mushroom walk pictures I had lying about since October. Also, this should put me in the right mood to start possibly considering contemplating studying for that mycology lab final next week *shudder*. The rusts are on there, and perhaps some of you might now what that means: that's right, life cycle hell. And structures that vaguely look all the same but aren't.

Most of the fungi one can easily see with unarmed eye in the forest are basidiomycetes, with a few ascomycetes if you're attentive enough. Many more fungal phyla exist, of course. In case you care, the basic layout roughly looks like this: Chytrid-y things (paraphyletic mess at the "base" of the fungal tree; characterised by having retained flagellate zoospores; though apparently a lineage in the Zygomycetes also has flagellates spores – odd...); Zygomycetes (fast-growing fungi, you'd know them if you've ever let food go bad – some of them are the scary tall molds with black-ish heads on bread and fruit); Glomeromycetes (Vesicular Arbuscular Mycorrhizae) – form internal associations with roots; have cool multinucleate spores at one stage; Ascomycetes (moldy things and tiny cuppy things, generally) and Basidiomycetes (your garden variety mushrooms, and other things). Microsporidia – really cool single-celled intracellular parasites with tiny genomes and mitochondrial remains that import ATP, are somewhere in there too, either basal among the chytrids or somewhere around Zygomycetes.

I have only two of the phyla here; but someday, I'll go hunting for chytrid zoospores – parts of fungi that actually move and appear sentient! (partial to motile things here. Which is why I worked on plants for three years. Yeah...) So we begin with a wet log – the Northwest/West coast (depending on which side of the border) has lots of wet logs in the winter. And wet weather. And wet residents. On the left are tiny ascomycete cup fungi; on the right are also ascomycetes with perithecia – flask-like spore containers – (thus Sordariomycetes) or something else. Saw it with ID once before, completely forgot the genus...
(btw you should check out Haeckel's Ascomycota plate – some elaborate pretty cleistothecia there!)

Mushroom-like ascomycete Helvella lacunosa. I love these things – ascomycetes seldom get so conveniently large and common.

A mushroom expert of some sort already beat us to it, as suggested by the carefully trimmed stem of the Helvella to reveal a distinctive structure:

Jelly fungi – contrary to their non-mushroomy appearance, they are, in fact, basidiomycetes:

These are your conventional garden-variety basidiomycete mushrooms. I forget what these are, but there may be something cortina-like (a type of veil) on the second midground mushroom (left of the heavily springtail-infested one) – if that's what it really is, then these would be aCortinarius sp. EDIT: It's Hypholoma fasiculare, or Sulfur Tuft; thanks Emma!

A reishi mushroom – those are apparently prized for medicinal qualities in East Asia, particularly Japan. They're also quite pretty, this isn't the best specimen.

Who can walk by a puffball without feeling a dire obligation to poke it? Puffballs, earthballs et al. are pretty interesting – they're basically degenerate gill fungi where the gill structures become an enclosed mass of basidia and hyphae called a gleba. These 'degraded' mushrooms have arisen multiple times independently, often in dry regions – presumably, since forced basidiospore ejection requires water to work, the selective pressure to keep the gills parallel and well-organised disappears and the mushroom is quickly allowed to lose the structures. Furthermore, dispersal the way of most puffballs – being being hit with something or stepped on – is more effective in those conditions. But the first step was likely the loss of selective pressure driving the maintenance of well-formed gills...

A tick. It was very tiny. And removed and thrown very far away promptly after photo. Ticks are scary...

A big, pretty mollusc for Aydin at Snail's Tales: (anyone got the ID?)

Finally, we return to protist – a slime mould! A Physarum-like thing, still in plasmodial stage but preparing to fruit soon:

And now I must return to procrastinating with life tackling the intimidating pile of duties for the next couple of weeks. Finals are trivial in comparison. That says something. Something terrifying...

If anyone else would like to organise a magical time warp by next week where we get an extra few days of time, I'm in! Can't we just stop the bloody calendar for a couple days?!

Of random rotifers and vicious amoebae

Still procrastinating with the Heterolobosea posts (no, I haven't forgotten). Real protistologists give me sorry looks when I mention being stuck writing about that rather obscure and messy group. I don't want to just do a taxonomic overview - I like to mention odds and ends about their cell biology as well. Sadly, the cell biology of most of those things is a sorry neglected mess. Even the eruptive pseudopodia that are quite characteristic of this group (although present in some amoebozoans as well) seem to not have been examined on a molecular level - I cannot find a single paper describing the cytoskeletal dynamics behind this peculiar mode of motility, and my sources point out a severe shortage of attention in that area. But I'm still scraping things together, so eventually something will appear...

Now for something completely different...since someone just sent me scouring piles of archaic metazoan 'mesozoan' literature to identify that damn bug (an orthonectid of some sort), I have a random metazoan of my own to show off a bit, from the latest pond microforay:

Rotifer. (Mine =P 40x* DIC) Note the contractile vacuole-like structure (actually its bladder, but appears to function in a very similar way. Another case of ultimate convergence?).

I can't quite key this one out, especially since this damn sucker is on its side. Probably the only reason I was able to capture a photo of it, since they tend to be quite hyperactive normally. This one appears to be immobilised by the cover glass. Perhaps it may be Aspelta or something from the Lepadellidae. Or might it be a Bdelloid? Perhaps a certain taxonomist could help out. Especially the one who made me browse orthonectids for the past few hours. ^^

*40x here, and onwards, refers to objective rather than magnification. We don't actually care about mag, it's the other properties of the optical system that matter much more when dealing with professional instruments. (Such as numerical aperture and field of view, focal length, focal depth, which type of immersion medium its calibrated for, etc) Technically, I should be writing down the NA and such, but we're not that meticulous crazy around here.
**Randomly found out there's a rotifer that lives inside colonies of Volvox, as a parasite...

Much of my resentment towards metazoa simply comes from them being overstudied and overemphasised, to the neglect of other phyla. That said, they are still interesting and still poorly understood lifeforms, especially among the spineless things. While representing but a mere sliver of life's overall diversity -- contrary to what our senses tell us -- metazoa are nevertheless, like all life, fascinating and weird. Metazoan multicellularity, as mundane and ubiquitous as it may seem to our rather biased eyes, is about as weird and insane as kinetoplastid kDNA editing, or the convoluted ciliate nuclear genomes, or the breathtakingly massive, and seemingly pointlessly so, nuclear genomes of dinoflagellates and some amoebozoa. I'm quite disappointed at the absense of the 'perspective of strangeness', if you will, that seems to dominate many animal-oriented classes (especially those catering to pre-meds. Must. not. rant.)

Interestingly, off all taxonomic and phylogenetic literature, I find metazoan papers to be the most difficult to follow* - we actually have common names to refer to quite a few animals metazoa. Furthermore, the obsession with ranked hierarchy is driving me insane - you DO NOT have to name every single possible grouping you can come up with, seriously! That makes searching for stuff an absolute disaster, as you have to look for the relevant subfamily, family, superfamily, suborder, order, superorder, hypersuperorder, subclass... etc. All named differently enough to not fit into one convenient Google (or PubMed, or WebofScience) search. And you have to find all of them. And they change. And your life becomes a living hell. Please stop, seriously! WHYYYYY!? Did TC-S write their taxonomies or something?! And they listened to ALL of it?! [/rant]

Another fascinating facet of biodiversity that seems to be thoroughly ignored is the interface between kindoms: the breathtaking diversity and strangeness of the possible relationships between the many corners of life. Of course we get the 'animals eat plants' story**, occasionally hear of animal-earing plants. Then we hear of fungi and bacteria as decomposers. If you hang out on the botany side of the Great Divide, you also hear of algae as the aquatic producers and fungi as mycorrhyzal symbionts (plant-fungal relationships are a fascinating world of awesome, by the way). But that's pretty much all ecology you ever get (outside of ecology programs anyways. I hope!), and frankly, it's pretty boring.

What about the vast 'multicultural' realm of the customs and ways of the parasites? What about the unexpected mutual endosymbioses, both of multicellular and unicellular things, on both multicellular and unicellular levels? What about multicellular predators, and parasites(!) of unicellular organisms? Or unicellular predators(!) of multicellular organisms? For a case of the latter, let's turn back to our rotifers. By the way, if you're desperate for a tree, or sexy SEMs of rotifer morphological features, this paper could come in handy(free access).

*Well, that and any prokaryotic literature. Bacteria are...complicated. Unlike Eukaryotes. ^_^
**A while ago while writing a biochem exam, I came across a question starting off with plant lipid synthesis. I got excited (OMG they're mentioning PLANTS!!!). Then I read on: "...which is then consumed by a herbivore." and wanted to throw something at whoever wrote that question. That pretty much sums up the biochemists' and zoologists' view of plants.

Quick aside: the border between parasite and predator is quite fuzzy and arbitrary, especially once you venture outside familiar grounds. Generally, people tend to call something a parasite when it feeds of something bigger than itself, and a predator when it feeds off something smaller.

Rotifers, like anything else out there, have no choice but to participate in the great web of things eating things. As is the case for many small pond organisms, their predators are plentiful. In fact, there's some rather embarassing ones. Including a relative of this slow thing:

(Mine again. Having my own photo stock would save me so much search and citation time. Of course, making my own stock might kind of negate that.)

Yeah, rotifers can get chomped on by Difflugia, of all things.

NOT mine this time. Han et al. 2008 Hydrobiologia. I wish I could see this live! See text for description.

The [planktonic thecate(!)] amoeba senses the thecate rotifer, quickly extends its pseudopodium along its length as if to 'measure' it, positions itself with its 'mouth' towards the rotifer's foot, somehow makes a hole in its protective jelly, and slurps in the rotifer's contents, while grasping the shell of its prey with the pseudopodia. All within 20min. Amazingly, this amoeba is not a rotifer specialist - it only eats them upon a rare chance encounter. Thus, the amoeba actually has complex behavioural patterns, enabling it to detect the type of prey, sense its shape and decide on an attack strategy.

Many protist predators are actually quite picky, sifting through the various detritus they come across and deciding on what to engulf. Combine that with eyespots and ocelli (Warnowiid dino camera eyes!), along with other oddities of the unicellular world, and we've got ourselves a whole field of Protist Behavioural Biology.

As we look more and more carefully at the unicellular world, it becomes increasingly more apparent that cells can 'think' -- not in the woo-ey "OMG feelings and consciousness!!1!" kind of way (in fact, I HATE that shit) -- but in terms of processing information from their environment in a rather complex way. Doesn't seem like much is known about cellular 'molecular intelligence' (or 'molecular instinct' - the line between canonical behaviour and genetic/biochemical pathways is quite blurry, it seems), and the field is dominated by junk thinking at the moment. And computer scientists, who don't seem to be bothered by biological reality. But hopefully as more and more results pile up suggesting some sort of 'cellular intelligence*', some fundamentally interesting stuff may come out of that research.

*I feel I may end up hating myself for using that term, but I can't think of anything better at the moment...sadly, too many good words get hijacked by sloppy thinking.

If you ever find yourself randly shrinked to the micron scale some day: Stay the fuck AWAY from amoebae. They may look slow and stupid and oozy, but they're out to fucking get you. They vicious. They don't care what unicellular or multicellular phylum you happen to be a proud member of: if they can hug you, they WILL squish you with nasty enzymes. Or make holes in you. They're freaking SCARY! o_O

Same goes for forams and "radiolaria", by the way. Actually, on the micron scale, if something doesn't eat you from the outside, chances are, it's patiently waiting to devour you from the inside. The microbial world tends to be quite innovative. And we haven't even gotten to the lethal veil of pallium...

Starting to feel good about your size yet?

As much as I'm obsessed with the microscopic world, it feels much safer to be a mere observer, rather than a participant. There's some truly terrifying monsters in those waters!

References
Han, B., Wang, T., Lin, Q., & Dumont, H. (2007). Carnivory and active hunting by the planktonic testate amoeba Difflugia tuberspinifera Hydrobiologia, 596 (1), 197-201 DOI: 10.1007/s10750-007-9096-z

Riemann, O., Kieneke, A., & Ahlrichs, W. (2009). Phylogeny of Dicranophoridae (Rotifera: Monogononta) - a maximum parsimony analysis based on morphological characters Journal of Zoological Systematics and Evolutionary Research, 47 (1), 61-76 DOI: 10.1111/j.1439-0469.2008.00482.x

Sunday Protist - Nucleariids

While exploring the various corners of the protistan world, I've been neglecting our close relatives - the Opisthokonts. Let's quickly remedy the situation.

A couple weekends ago I had some pond water on hand, and it turned out to be quite productive. I was on a bit of a heliozoan and amoeba spree when I encountered these things:

At first it seemed like a 'heliozoan'*, but wasn't quite round enough. Then I noticed filopodia. Heliozoa with filopodia? Nah. But it didn't quite qualify for your typical amoebozoan either, so I was rather confused. To make it even more fun, some of them had spicules sticking out (see the optical section through the top in the rightmost image above). Then I started seeing similar things without spicules, and they seemed to be related:

So I spent an hour or so trying to figure this one out**. They turned out to be Nucleariids, a group of filose amoebae basal to fungi. The top one appears to be Rabdiophrys, which has been, in fact, confused with or considred as heliozoa; the bottom one may well be Nuclearia itself - some mixed images of Nuclearia and Rabdiophrys can be found here.

Nucleariids are filose amoebae, meaning they produce long thin thread-like pseudopodia without internal microtubule bundles (which would be axopodia, like those of 'heliozoa'). They are on the fungal side of the great cauldron of Miscellaneous Opisthokonts sometimes called 'Choanozoa' by TC-S. Other times, he seems to reserve Choanozoa for those on the animal side of opisthokonts. Yet other times, he seems to fail to piss off cladists and actually use monophyletic terms. Which one of those is 'in season' likely depends on the monsoon patterns in Bangladesh. Or the temperature fluctuations on one of Jupiter's moons. Further research needs to be done. Materials include ethanol and acid, if I recall. Anyway, here's a damn tree already:

(Ruiz-Trillo et al. 2007 Trends Genet; Opisthokonta - our fellow ass-tailed relatives)

The Choanozoa/Misc Opisthokonts actually tend to be insignificant-looking amoeboid things most of the time, except for Choanoflagellates, which are these really cute lorica-building flagellates with a cone of microvili surrounding the flagellum on their asses. Speaking of which, opisthokont means 'posterior flagellum', or, less pretentiously, ass-tail. Some fungi (chytrids) have flagellated motile spores, and their flagellum happens to be on the posterior relative to the cell's swimming direction. As mentioned earlier, in most eukaryotes the flagellum performs a pulling action, whereas the opisthokont flagellum pushes the cell. This actually poses some problems for filter-feeding organisms, which use flagella for propelling food particles towards their 'mouth', and may be part of the reason some Choanoflagellates started aggregating into colonies - to stop themselves from moving away from their prey when using flagella.

Here's another specimen of putative Rabdiophrys:

And yet another:

I can keep going:

Seriously, I've got A LOT of those guys!

Switching to Nuclearia now:

Note the absense of spicules:

Hey, it could be worse: I also have a freaking pile of non-descript random amoeboid things. SMALL non-descript random amoebae.

There's a 'cellular' slime mould that turns out to be among the nucleariids: Fonticula (Brown et al. 2009 MBE; advance publication). The poor thing has been lumped with everything from Acrasids to cellular slime moulds, and subsequently neglected for a couple decades. This is the first documented case of slime mould aggregation in opisthokonts, which may contribute a thing or two to the evolution of fungal and metazoan multicellularity. (off topic note: ciliates can aggregate too!)

So now we've finally covered an opisthokont. Phew. That was bugging me.

* Just FYI, heliozoa are not a real group - they're united by their sun-like morphology, axopodia and nothing else...
** Being too impatient to use dichotomous keys (which also simply fail to exist for some organisms), I use a combination of papers, websites and Google image search to find stuff. Basically, you find something that lists a bunch of organisms in the vicinity of what you think it might be, and then look to see if any of the pictures might match. If it's something so obscure that even Google is unaware of its existence, you have to sift through ancient forlorn journal articles sometimes, but usually it doesn't take that long to cross another name off the list.

If completely stumped, I'll just start googling random morphological descriptions in both scholar and image search, until hitting something familiar. As random and haphazard and unprofessional as this method is, it's actually much more effective than figuring out dichotomous keys, in my opinion. Especially when you're unfamiliar with the structural terminology. And especially when such a thing doesn't even exist for your group of organisms, as is too often the case for protists... [/hint for Mystery Micrographs]

Brown, M., Spiegel, F., & Silberman, J. (2009). Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta Molecular Biology and Evolution DOI: 10.1093/molbev/msp185

RUIZTRILLO, I., BURGER, G., HOLLAND, P., KING, N., LANG, B., ROGER, A., & GRAY, M. (2007). The origins of multicellularity: a multi-taxon genome initiative Trends in Genetics, 23 (3), 113-118 DOI: 10.1016/j.tig.2007.01.005

Which opisthokont amoeboflagellate is this!?

While looking through the developmental biol lecture notes yesterday, I came across this image:

(Developmental Biology 8th ed. Gilbert fig 7.2)
So I sit there, staring at it, thinking: "Ok, so it's an amoeboflagellate opisthokont capable of transforming between the two. Shit, what kind of protist is this!? Not a Heterolobosean (those famously form flagella+centrioles de novo) due to its posterior flagellum and continuously present centrioles. Can't be a nucleariid or ichthyosporid or anything..." for a good 5min, getting frustrating that I couldn't recognise this protist... (also wondering why there were protists in a classical developmental biol class)

...and then I read 'sperm head'.

I'm so gonna fail this class in 3...2...1...

Well, actually I was right: this -is- an amoeboflagellate opisthokont with de novo flagellar formation. To a cladist, we'd be protists too!