Sunday Protist – Gromia: beautiful predatory grapes of the sea

And we're back. The protists and I, that is. Well, the protists never quite went anywhere but you know what I mean...

You may have heard of Gromia a couple years ago when it hit the news by leaving tracks on the ocean floor resembling Ediacaran trace fossils (tracks). Or perhaps not; I tend to get overly excited the one time a year some protist makes the news. The giant (3cm) track-leaving Gromia in question sounded even cooler as it came from the great deep sea; other species of Gromia are in fact quite content with the more familiar shallow waters as well, crawling on the holdfasts of kelp in addition to thriving in the ice cold polar waters of McMurdo Sound (Antarctica), where the vibrantly colourful first specimen below comes from:

Gromia, from various locales including Antarctica (A), Madeira in the Atlantic (B) and Guam (C). Big and colourful, what's not to like there? Scalebars: A - 1mm; B - 0.5mm; C - 0.1mm (Burki et al. 2002 Protist)

For some time, there has been considerable confusion between Gromia and the cruelly similarly-named foraminiferan Allogromia, bad enough to warrant a Nature paper (Hedley 1958). At first glance, they do appear somewhat similar: a sizeable grape-like blob of a test surrounded by a mass of fine pseudopodia. While foram pseudopodia form a rather elaborate and extensive network of doom and terror for anything they come in contact with, Gromia uses more modest non-fusing alternative of pseudopodia. Thus, prior to molecular data, it was often considered a sort of a precursor to the more grown-up real forams, and assumed to have a rather simple test. They could hardly be more wrong, both with the assumed relation to forams and the simplicity of its test.

Typically (using that word rather loosely), a protist test consists of the plasma membrane covered by some sort of an organic matrix (often sugary proteins and protein-y sugars), followed by the deposited structural material, be it agglutinated bits of rock from the environment (often carefully and specifically selected) or secreted calcium carbonate, siliceous scales or something else entirely. To my knowledge, the process of selecting material for the test in agglutinating species, and formation of the test in general, is still quite poorly understood. There is some understanding of how diatoms and some coccolithophorids build their extracellular wonders, but most amoebae have been largely ignored, even the more 'famous' representatives like the forams, euglyphids and arcellinids. The Allogromia mentioned earlier has the organic (non-calcified, non-agglutinated) test characteristic of Allogromiids at large, who form a vast paraphyletic sea of diversity from which the more popular lineages arise – the Protista of the foram world, if you will.

Gromia also carries an organic test, hence the confusion with Allogromiids. But its test turns out to be a bit more elaborate, with an inner lining consisting of up to ten layers of odd honeycomb membranes, the whole thickness of the structure penetrated by multitudes of pores. The test surface is sometimes covered by attached bacteria (Aranda da Silva & Gooday 2009 DSR II). Furthermore, rather than simply a hole in the wall, its opening is surrounded by a complicated oral capsule which acts as a valve or a trap door: when the pseudopodia are withdrawn, the opening closes. One seldom thinks of movable structural parts on the microscopic level, but here you go:

The structure of Gromia's test and oral capsule, in that order. The figure on the right shows a pseudopodium gradually protruding through the closed aperture. (Hedley & Bertaud 1962 J Protozool; Mazei & Tsiganov 2006 in Presnovodniye Rakoviye Amyobi (in Rus.))

The pores make the test surface look quite pretty in reflected light:

The giant deep sea Gromia sphaerica; note the complex test surface structure with prominent perforations. (Matz et al. 2008 Curr Biol)

To make these mysterious 'grapes' of the sea even sexier, they are known to have sex. Upon conjugation, flagellated gametes are exchanged between the parents, producing amoeboid diploid swarmers that ultimately form a new test and complete the cycle. The parental shell and all the work that went into building one is abandoned in this process. Both forams and gromiids are 'mortal' in our sense – they spend a period of time building a body that eventually becomes abandoned by the next generation. Organisms like many flagellates, for example, are somewhat 'immortal' in that the cell is never abandoned between generations, but rather split up and shared by mostly clonal offspring. Extra structural complexity often bears the curse of losing 'immortality'.

Gromia's life cycle. (Arnold 1966 J Protozool)

Gromia shares some strangeness with giant deep sea Xenophyophores (forams): they like to live in their own excrement. This may sound disturbing, but they're still fairly microscopic, so their shit is of a rather more chemical character. Curiously, both Xenophyophores and Gromia tend to lean toward the upper end of the protist size range, perhaps partly aided by their inability or lack of desire to part with their faeces – these faecal pellets, so-called stercomata, appear to play a structural role in the Xenophyophores, and may well contribute to structure in Gromiids as well. Waste accumulation is not too grave a problem for these organisms due to their habit of generating clouds of swarmers that ditch the parental shell forever.

As alluded to earlier, gromiids are fairly distantly related to forams, and definitely evolved their elaborate test independently. For some time, gromiids were thought to be closely related to filose amoebae with shells, ie cercozoan euglyphids and such. Turns out, while not too close to the euglyphids, Gromia is a cercozoan (Burki et al. 2002 Protist), and tends towards the endomyxean side with the plant parasite phytomyxids, vicious vampyrellid amoebae and the ornate haplosporidia. In other words, things that look little like them, aside from a tendency to form thin pseudopodia.

Gromiids probably have a bigger story to tell, as environmental sequence data reveal swaths of cryptic diversity, and new species are still being described from the deep sea as well as polar waters (eg. Rothe et al. 2009 Zool J Linn Soc; Gooday & Bowser 2004 Protist; Rothe et al. 2011 Polar Biol; and Aranda da Silva et al. 2006 Mar Biol for diversity porn). As for their ecological niche, the gromiids seem to play a similar role to allogromiids and other forams – versatile predators preying on algae and anything else that gets caught in their feet.

Aww, they even grow on trees! Gromia schmoozing with a tree-shaped foram, Pelosina, possibly in some sort of a symbiotic relationship. (Gooday & Bowser 2004 Protist)

Hopefully back to more regular blogging now. Quality of writing is at the mercy of my irritating writer's block, you have been warned...

References
Aranda da Silva, A., & Gooday, A. (2009). Large organic-walled Protista (Gromia) in the Arabian Sea: Density, diversity, distribution and ecology Deep Sea Research Part II: Topical Studies in Oceanography, 56 (6-7), 422-433 DOI: 10.1016/j.dsr2.2008.12.027

Silva, A., Pawlowski, J., & Gooday, A. (2005). High diversity of deep-sea Gromia from the Arabian Sea revealed by small subunit rDNA sequence analysis Marine Biology, 148 (4), 769-777 DOI: 10.1007/s00227-005-0071-9

ARNOLD, Z. (1966). Observations on the Sexual Generation of Gromia oviformis Dujardin The Journal of Eukaryotic Microbiology, 13 (1), 23-27 DOI: 10.1111/j.1550-7408.1966.tb01863.x

Zach M. Arnold (1952). Structure and Paleontological Significance of the Oral Apparatus of the Foraminiferoid Gromia oviformis Dujardin Journal of Paleontology, 26 (5), 829-831

BURKI, F. (2002). Phylogenetic Position of Dujardin inferred from Nuclear-Encoded Small Subunit Ribosomal DNA Protist, 153 (3), 251-260 DOI: 10.1078/1434-4610-00102

[Fuck this, the browser crashed TWICE and I'm not finding all the links again. Not tonight anyway. URLs are in the post.]

Eight supergroups on a table

Back, after a bit of a distraction and an irritating bout of writer's block (how do you get rid of those things, seriously?). While I go write up a post for the long-interrupted Sunday Protist series, have a protisty doodle. My friends have this makeshift coffee table from two pieces of wood, which serves as a canvas for procrastination painting and such; anyway, if you supply me with permission to doodle on something, it invariably ends up protisty (or anime characters, or a frightening mix of the two), so here are eight supergroups on a table: (flash gets a a sharper image but the colours get screwed up)

Watercolour, pencil and [lab] marker on painted wood. Really fun to do watercolours on top of paint – you're not sneered at by warped wet paper, and it's very easy to wash off mistakes.

The cast:
Archaeplastida – Acetabularia
Alveolata – dinoflagellate (eg. Protoperidinium)
Stramenopila – Chaetoceros
Rhizaria – Gromia
"Hacrobia" – centrohelid "heliozoan"
Amoebozoa – tubulinid amoeba
Opisthokonta – choanoflagellate with a chitinous basket
Excavata – photosynthetic euglenid

(Accuracy not guaranteed as I was too lazy to use references)

Deciphering protist shapes

A while ago, while rigorously procrastinating, I came across a slightly odd tiny freshwater flagellate that was sufficiently morphologically non-straightforward it lent itself well to 3D reconstruction/sketching practice. Figuring out cell shape from micrographs isn't as easy as it looks – for one thing, the bloody cell is three dimensional, while the images are flat and further complicated by DIC optics – and thus a very fun exercise! And then, once you've got a cell shape in your head, you have to figure out a way to draw it out for others to see. I still suck, but the sketches at the end looked kinda pretty together with the micrographs, so here they are:

I still have no idea what this thing is. Acts vaguely ancyromonad-like, but may well be a glissomonad or something else entirely. Pretty positive it's biflagellated. Probably nothing too earth-shattering (and may well be well-known by everyone but me), but if anyone has some sort of research interest in this thing, let me know – don't have time to deal with it myself. Not that I'm likely to find it again... Here's the pics and videos:

Science Online 2011 ramblings

By now, about every aspect of Science Online has been thoroughly blogged and overblogged, so for a comprehensive review, see the Science Online 2011 website, namely the Blog and Media Coverage page. I don't think I have much to add, but I'll ramble anyway. After all, this is why I have a blog, right? Plagued by an epic writer's block lately though, so lower your expectations accordingly. Even more so than you should normally when approaching this place. In fact, since this has been sitting in my drafts folder for about four five six days, I'm just going to hit random parts of the keyboard and hope the result resembles English somehow, while torturing you with a sequence of cumbersome, poorly linked clauses, so I can get back to regular blogging, ideally with readable sentences that time.


Cheesy as it sounds, the highlight of the conference was definitely the people. In a way, it's more of a 'reunion' than a conference sensu stricto, as some put it. A major aim of the conference is to humanise the blogosphere, as knowing each other personally should make the environment more pleasant and less aggressive, and I think it works. Without knowing the physical entity behind an online alias, it is sometimes easy to find yourself carried away with something they wrote, as opposed to evaluating the person as a whole. We all have our quirky opinions, and we all write stuff from time to time that can piss off someone, somewhere. Sometimes it's too easy to get fixated on a single idea you find personally irritating, and forget that there is more to the poster than that one comment. Knowing each other in a more personal manner could diffuse some of those conflicts.

I was pleasantly surprised by how little of the general blogosphere drama carried over into the physical conference. People generally seem more chill offline. Maybe I was just oblivious to the real picture, as I usually am (drama usually passes by me without even acknowledging my existence – I guess that has its own perks), but everyone was really friendly and full of energy. Combine that with Deep Sea partying and North Carolinean hospitality*, and great times were had!

*I'll ramble about 'surprising' non-homogeneity of North American cultures in a later post...

The group of attendees was surprisingly diverse in the professional/occupational sense, including a range from students and scientists to full-time writers and journalists to PIOs and librarians and some people behind things like PLoS and Mendeley. There were those with various artistic talents, from science illustration (eg @flyingtrilobite/Glendon Mellow) to music (eg. Adrian and Kevin's GFAJ-1 Arsenic Blues – though that recording does not do it justice) and comedy (@sciencecomedian/Brian Malow). Being somewhat locked up in the ivory tower by this point, it was great to meet people with real jobs who actually talk to people outside academia. Science Online is also unusual in that everyone was on a fairly even level, regardless of professional rank. Your professional hierarchy and reputation were irrelevant since there was hardly anyone from your own field. Thus, faculty, students, librarians, writers, postdocs, etc all spoke on equal ground, which was a wonderful experience in itself. As much as some try to suppress hierarchy at traditional academic conferences, it's still clearly there, and your rank in the field does matter. At Science Online, your online presence was more important, but that hierarchy is, thankfully, less rigid, and still rather nebulous in concept.

The use of Twitter at the conference was rather surreal...it's as if between all the smaller discussions and conversations in the physical realm was a broader conversation in the electromagnetic waves of Twitterland. The badges had a place for one's Twitter handle, along with a QR code for the website. It's as if we had multiple identities, and I did for sure. I went by my blogger alias (shocking plot twist: Psi Wavefunction is not my legal name ;p) since that's how people know me online. Given that, I still preferred by real name in offline conversations. Which made it even more awkward. Some people insisted on calling me Psi – I don't mind at all, but it was odd to be called by something other than my real name!


I won't even try to go over all the highlights regarding people and events, but I'll just casually mention some snippets, in a totally random manner and order. Mostly my own reactions to them, since others have already discussed the topics in greater detail (and insight).

First off, our keynote was Robert Krulwich, a journalist and co-host of Radiolab. In attempting to attract an audience who typically think they don't care about science, they have a very interesting approach to explaining complicated topics: acting stupid. Stupider than their listeners. We like feeling smarter than others, so it often works better when the teacher (sensu lato) speaks the language of a novice rather than an expert, and asks such questions of the guest experts that the audience would never 'stoop' to. Ie, very basic questions, prodding for very basic answers in return. That way, the audience doesn't feel like material is dumbed down for them (which may feel somewhat insulting, and definitely distanced), but rather for the host, ie Krulwich. Of course, there is also much humour involved, and the programmes are, as a result, entertaining. It's amazing what these people can do, as it is incredibly difficult to convince someone a topic is interesting once they've made up their mind it's not. Making it relevant is not enough – making it relevant and fun, without the feeling of distance (and definitely not lecturing!) is an art, and one we really need more of.

* This happened around hour 56** since I last had sleep, so I shamefully admit to not processing much information at that point

**let's see, got up around 9ish on Tuesday, hung out + packed all night, went to Seattle on Wed, hung out, flew out Wed night, horribly packed flight with stopover at Washington DC, too short to sleep much, arrived at RDU on Thu around 9am, couldn't check in or sleep, keynote around 8pm...yeah. Must've been a zombie by that point.

Went to the history of science panel, where we underlined the importance of understanding the context of scientific discoveries, and the richness that the extra dimension (time) adds to scientific stories overall. And historical context provided properly, not crudely mocking the past thinkers for coming up with such "ridiculous" hypotheses. Probably most of the stuff we think today will be laughed at in a couple centuries or so, if we as a species make it that far. The historical aspect includes not only the history of one's field, but also the sociopolitical context of the time, since science is not this purely 'objective' holy thing independent of human thought; science is a human process, and thus carries with it the stamps of every generation's worldviews. It can only make more sense that way. Where possible, good science writing should happen in four dimensions.

With John Logsdon and Julie we directed a discussion on improving public outreach for small and/or obscure "micro"-disciplines, with emphasis on internet presence. I'll make a separate post on this topic later.

I was also on a panel my awesome co-moderators on beginning blogging and issues like the impostor syndrome, which was a great lot of fun. Others have blogged about it already, and I'll add the links once I find them (soooo many #scio11 posts to catch up on...!).


There is currently some talk about compromised diversity in the blogosphere, but we must keep in mind that we are biased by being an anglophone blogsphere, and the conference was in North Carolina, which was difficult to get to even for those of us on the other coast, let alone from overseas. I personally doubt pushing labels could help much, and think the problem, where it truly exists, lies deeper than online presence. Yes, some races/ethnicities/groups are underrepresented in the English-speaking blogosphere, but that may have something to do with the same races/ethnicities/groups being underrepresented in the educational system in general, and not with the internet or the community.

When I read blog posts, I pay very little attention to the background of who writes them, aside from their field of expertise/activity. If I find the stories interesting, I'll read them regardless of the gender of the author, and I don't feel particularly obliged to read a story I wouldn't otherwise touch simply due to their background. On the internet, it is especially easy to be truly 'colourblind' (in the metaphorical sense too), since you don't even see the author unless you look. So the issues with diversity online are probably a direct result of the problems offline, which are much harder to fix with online means. Maybe instead of focusing on the skewed diversity of bloggers, we should first look at how blogging can help the problem closer to its root. Eg, are underprivileged groups even reading any of our stuff in the first place, and if so, what can we do to be more useful to them, etc.

But I'm not sure it's entirely helpful to start shelving ourselves into categories like "female blogger" or "white blogger" or whatever. I don't particularly care for being read as a "female immigrant Russian atheist blogger". I would prefer to be read as some person whose writing people occasionally find interesting. My background would be a digression, perhaps interesting for my regular readership, but far from necessary for the main goal. But then again, maybe as a scientist I underestimate the average reader's desire to understand the blogger's character – would love for my readership to chime in on this!

Anyway, those were my [somewhat obligatory] two cents on the diversity issue, and I'll probably leave the discussion there. It's not that I don't care, but rather that such topics are not my forte, so I prefer to lurk quietly. But, by all means, feel free to discuss here!


And lastly, before I forget, some nebulous panel ideas for #scio12:
- Online presence of non-English languages
- Issues/specifics of niche blogging
- Dealing with "writer's block" (successfully, unlike Upper 1974 J Appl Behav Anal)
- Making the most of course blogs

Next up, eventually I'll put up some pictures from the overall east coast journey. And post some fucking protists, at last! =D

Mystery Micrograph #26

And we're back with a fresh batch of Mystery Micrographs! I'm sure you missed the frustration that goes along with attempting to ID an obscure microorganism no one cares about from a limited set of grainy photos. I understand. Today, labmate and I discovered this 3D maze puzzle thing our supervisor oddly (and cruelly) left in the lab, and spent a good 4h cursing at it. I expect my Mystery Micrographs to have a similar effect, if only to make up for all the emotional suffering we experienced today trying to solve a children's game, to no avail yet. At least my micrographs aren't aimed at 5-year-olds. Anyway, I assume you've all taken advantage of my absense to go off into the faraway mountains* and undergo rigorous daily training in the high art of protist taxonomy. So here's a slightly evil one. I want the genus. Enjoy!

Fig 13 is x400 (To be referenced later)

* Ironically, rigorous training in protist taxonomy with a black-belt master would currently entail going to places with rather unimpressive/lacking mountains...

Back from Science Online 2011 and the east coast

*brushes off a layer of dust* Long time no see! Done travels for the time being, am here to stay in one place for a while. ScienceOnline 2011 was absolutely fantabulous, as was my little trip up the eastern states to Massachusetts (look, I even learned how to spell that!). Never been to eastern or southern US before, which is embarrassing for someone who's lived on this continent for two decades. Well, I guess the North Carolina Research Triangle barely passes for 'south', but it was definitely different already, enough to pique my interest in further exploring the southern US someday. Passed by New York City on my train ride north, and was a very obvious hick, glued to the window in total awe – so big! I really don't get out much these days, and seeing a little bit more of the world, of only briefly, was quite necessary at this point. Hell, it was my first time in Seattle since passing through there c.10 years ago, even that was worth the effort of flying out from there (well, that and the substantially cheaper tickets, of course).

Apparently people don't mind us bloggers revealing random oddments of our personal lives, like travel. At least a couple people found the preceding snow camping post interesting, so I'll do something with my east coast photos too. The ones without people in them, since we don't want any careers terminated prematurely due to the context of those photos and the ethanol-rich atmosphere ;-) (for some idea, look up the hashtags #DSNsuite and #TheGam, at your own risk). You can also read the potentially incriminating records of the #scio11 tweets here, sorted by days of the conference. And yes, that hashtag is still alive and well because we just can't stop, and #scio12 is up and running already too...

So I intend to have two posts, one summarising the conference and my thoughts on things, and another on my rapid 'tour' past 8 states (and Washington DC) in 24h. Behold, I even have blurry photos of the Washington Monument in the distance, at night!

Before embarking on attempting to write something marginally passing for coherent and maybe even intelligent about Scio11, I must point out that the organisers of the conference, Bora Zivkovic and Anton Zuiker, are fucking awesome, and we in the science blogging community are really lucky to have them around!

To be continued.

Why I did not blog this weekend...

Happy New Year, everyone! (hey, it's still January...) While I did only get back a week ago, with plenty of urgent offline matters to attend to, I was totally going to dust off the blog this past weekend. But I didn't. As much as I enjoy protists and writing for you, I just had to take the liberty to sneak off from the internet and enjoy THIS:

That's right, I actually went outside and explored those pointy things outside my lab window up close and personal. (have I mentioned being able to see snow-capped mountains from the lab pretty much year-round, except for maybe late August-early September? ;p) Tried out backcountry skiing (telemark) for the first time, though that didn't work out too well due to a combination of an impressive sheet of ice, steepness, busy trail with ruts and holes everywhere and bindings that didn't want to fit properly...so the skis were mostly carried. Uphill and downhill. Ah well, will actually check snow conditions next time (some seasoned skiers also resorted to carrying them so we didn't feel so bad).

Went with a pretty large group (university-affiliated), the point was actually winter camping. In snow caves. Igloos too, but those are freaking impossible to build, it turns out. If Canadians really did all live in igloos, we'd all be structural engineering geniuses up here. My friend and I resorted to a simple cave to start with:

Yes, you really do wake up to that shade of blue. Does the ceiling look thin? There's a good half a metre of snow up there. Amazing how much light it lets in. It had pretty good insulating properties, kept things warm - at around 0˚C. The other option was -12-15˚C outside...oh yes it was freaking cold. Meanwhile, in the distance lay the city with it's non-freezing temperatures and sane people who got to sleep without worrying about hypothermia and frostbite. Without their hair freezing to snowy walls even!

Sure they had the warmth and luxurious comfort, but did they have this to surround them when they woke up?

Did they get harassed by these rather bold birds as they tried to eat breakfast? Seriously, that little grey bird (apparently a jay) would approach you to about 20cm away and not care. Even the ravens were a little more cautious...

And where there is ice, there are ice sculptures. Natural or man-made. (neither of them are mine)

One of the wonderful things about camping is that you get a rush of euphoria from the simplest things. Like hot tea. Or getting home with all your toes still intact. Somehow, those things become much harder to appreciate back in the city.

Apologies for total off-topic-ness and protist-less-ness (was going to sample but it was waaay too cold), but it's kinda fun to step back and look at a different scale from time to time, especially for a microscopist. And I'm ashamed for not having taken much advantage at all of living in such a beautiful place. Anyway, protist blogging shall return later, after I get back from ScienceOnline 2011, which should be after the 19th. Also, there may or may not be some exciting announcements to make. Watch this space...

Happy holidays to all, back in January!

I totally meant to do a kick-ass end-0f-the-year post, but that'll have to wait until January... was swamped with everything. Promise to return to regular, proper blogging in the new year! (after ScienceOnline2011!) Mostly away from internet until 05 Jan.

Almost late for my flight... so a happy and relaxing whatever-you-celebrate (protistmas? =P) to everyone!

Walsby's Square Archaea! Haloquadratum walsbyi

Procrastination and overwhelming itch to get back to blogging win over the more pressing obligations tonight. Fuck'em, it's Friday night, I can write about protists if I feel like it. Moreover, I can even write about non-protists, especially those I've been meaning to write about for a month now. Square Archaea!

Despite their awesome morphological diversity, seldom do cells take the shape of a flat square. Or any other flat geometric shape. In fact, there are reasons for this – the cell cytoplasm is generally hypertonic relative to its surroundings (the cell contains more solute), so there is considerable osmotic pressure against the cell membrane, kind of like an inflated balloon. The optimal favoured geometry in this situation is a perfect sphere, so without cytoskeletal or cell membrane alterations, the cell swells up into a ball. Plant mutants deficient in wall cellulose tend to have very bubbly cells, as do plants treated with cellulose-inhibiting drugs, due to turgor pressure from within. Thus, it would take a lot of structural effort for a cell to take on a very flat shape, with a high length x width : height ratio.

Normally. Except when they do just that: brought to us from a very salty pool on the Sinai Peninsula is Walsby's square archaeon, a thin rectangular sheet of cell:

Left: Walsby's square archaeon, Haloquadratum walsbyi. A – phase contrast of archaean with conspicuous gas vesicles; B – TEM detail of gas vesicle; C – darkfield micrograph of large cell – their unusual flexibility means they're seldom found unfolded. (Bolhuis et al. 2004 Env Microbiol) Right: Original images of the square archaean, from Walsby 1980 (Walsby 2005 Tr Microbiol).

These flat ~1.5 x 1.5 µm cells are only 0.1µm thick at most. The cell periphery is lined with conspicuous gas vesicles of undetermined function; they were previously thought to be involved in buoyancy, but experimental data cast doubt on that idea. Instead, they may participate in positioning cells parallel to the surface in order to optimise light exposure for their photoactive pigments (Oren et al. 2006 Saline Syst, OA). They may also play a role in buffering changes in turgor pressure (Walsby 2005). Some cells are unbelievably square, but most tend to be rectangular, due to growth. One can't really divide into squares unless some weird four-way cell division process is employed, so the non-square delinquents have a reason for their geometric imperfections.

Left: Cryo TEM of H.walsbyi, showing prominent gas vesicle in the corner. The scalebar is 1µm. (Burns et al. 2007 IJSEM) Right: Electron tomography of a single H.walsbyi cell. Gas vesicles (GV) line the cell periphery, while electron-dense blobs of acidic polymers fill the inside of the cell. (Bolhuis et al. 2006 BMC Genomics, OA)

Unlike protistologists, bacteriologists are blessed with small genomes, and can thus sequence whatever they like with little pain (relatively). This means they get to sequence all the cool things they want, which is a little unfair. Haloquadratum has been sequenced (Bolhuis et al. 2006 BMC Genomics); there is also unusually high amounts of polymorphisms in ribosomal DNA both within species and within the genomes themselves, thought to be an adaptation to their extreme environments (López-López et al. 2007 J Mol Evol), although the adaptation aspect is to be taken with a grain of salt as it is difficult to distinguish from consequence.

Haloquadratum belongs to a large group of extreme halophilic archae, the Halobacteriales. Obligatory latest tree (note the taxonomic mess, and the swaths of poorly-understood organisms in need of attention):

Phylogeny of salty extremophilic Halobacteriales; as with anything microbial, taxonomic chaos is inevitable. Unusually high rDNA polymorphism within single species doesn't help much either. (Modified from Minegishi et al. 2010 IJSEM (abbreviations deciphered in red))

The salty waters Haloquadratum inhabits are no regular salty waters – the salinity exceeds that of typical seawater by a factor of ten. In other words, really salty. Not only that, but Haloquadratum thrives in Mg-rich waters just below the lethal concentration (past which nothing lives). This extreme salinity means the cells are no longer hypertonic relative to the medium, and in fact may be hypotonic – recall classic experiments involving dipping onion cells in saltwater to show shrinkage. In fact, despite living in aqueous environments, these organisms have very little access to water, and the extremely saline muck is also highly anoxic (low in oxygen). In other words, not the ideal vacation spot for most life.

Presumably, there is considerable selective pressure to optimise for a very different surface-area-to-volume ratio, particularly to enhance gas exchange (otherwise severely hampered by salinity). Thus, not only does the non-hypotonic environment with respect to the cell enable it to easily deviate from its spherical tendencies due to lack of turgor (Walsby 2005), but in fact favours it to expand its surface area by being a flat sheet.

There are also triangular hypersaline Archaea, Haloarcula japonica:

Left: Triangular Haloarcula japonica cells under normal conditions. Right: H.japonica after lowering magnesium concentrations – the cells become rounded "spheroplasts". (Horikoshi et al. 1993 Cell Mol Life Sci, modified therein from Nakamura et al. 1992)

Quite fascinatingly, the decrease of magnesium concentrations in H.japonica cultures results in the cells becoming spherical! A specific glycoprotein appears to be responsible for maintaining H.japonica's triangular shape, and is released upon lowering magnesium levels, allowing the cells to spring back to their natural rounded selves (Horikoshi et al. 1993 Cell Mol Life Sci). This is also a cool case of membrane morphology being predominantly regulated by a single protein, which is not so common. There's a whole area of research based around the shaping of membranes with various proteins...really cool stuff too. Interestingly, the triangular H.japonica divides asymmetrically (Hamamoto et al. 1988 FEMS Microbiol Let), resembling the division of triangular stomatal lineage meristemoids in Arabidopsis...

Extreme environments can provide opportunity for some extreme geometric experimentation, as shown by a couple flat square and triangular archaeans here. While prokaryotes are notoriously dismissed for being morphologically 'plain', many are far from it, and even have elaborate cell structures within, but that's for another day. But zoologists and botanists take note: the little awesome that is left outside the protist kingdom is hoarded by prokaryotes, ha!

References:

Bolhuis, H., Poele, E., & Rodriguez-Valera, F. (2004). Isolation and cultivation of Walsby's square archaeon Environmental Microbiology, 6 (12), 1287-1291 DOI: 10.1111/j.1462-2920.2004.00692.x

Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeiffer, F., & Oesterhelt, D. (2006). The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity

BMC Genomics, 7 (1) DOI: 10.1186/1471-2164-7-169

Burns, D., Janssen, P., Itoh, T., Kamekura, M., Li, Z., Jensen, G., Rodriguez-Valera, F., Bolhuis, H., & Dyall-Smith, M. (2007). Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 57 (2), 387-392 DOI: 10.1099/ijs.0.64690-0

Hamamoto, T., Takashina, T., Grant, W., & Horikoshi, K. (1988). Asymmetric cell division of a triangular halophilic archaebacterium FEMS Microbiology Letters, 56 (2), 221-224 DOI: 10.1111/j.1574-6968.1988.tb03181.x

Horikoshi, K., Aono, R., & Nakamura, S. (1993). The triangular halophilic archaebacteriumHaloarcula japonica strain TR-1 Experientia, 49 (6-7), 497-502 DOI: 10.1007/BF01955151

López-López, A., Benlloch, S., Bonfá, M., Rodríguez-Valera, F., & Mira, A. (2007). Intragenomic 16S rDNA Divergence in Haloarcula marismortui Is an Adaptation to Different Temperatures Journal of Molecular Evolution, 65 (6), 687-696 DOI: 10.1007/s00239-007-9047-3

Minegishi, H., Kamekura, M., Itoh, T., Echigo, A., Usami, R., & Hashimoto, T. (2009). Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 60 (10), 2398-2408 DOI: 10.1099/ijs.0.017160-0

Oren, A., Pri-El, N., Shapiro, O., & Siboni, N. (2006). Buoyancy studies in natural communities of square gas-vacuolate archaea in saltern crystallizer ponds Saline Systems, 2 (1) DOI: 10.1186/1746-1448-2-4

Walsby, A. (2005). Archaea with square cells Trends in Microbiology, 13 (5), 193-195 DOI: 10.1016/j.tim.2005.03.002

(h/t Opisthokont, who owes my boss few hours of my productive work time)

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?!