Let's go on an introductory tour of the protist world – a micro-dive if you will – led by our ocelloid-bearing submersible: let's take Nematodinium out for a ride today. A seeing eye dinoflagellate. In fact, a seeing eye dino armed with nematocysts, a microscopic analogue of harpoons – just in case we see something yummy or get harassed by one of those pesky ciliates. This tour will be somewhat rapid and disorganised – the point is to give a feel of protist diversity and what they tend to do. Later on we'll explore many of these abridged stories in greater detail, with proper scientific detail. For now, I'll link to my past posts on the topics where applicable, and abuse Wikipedia links elsewhere. The locations of the organisms may or may not involve some poetic licensing (since there's relatively little known about microbial community ecology), but the biology and behaviours should be fairly accurate.

[caption id="" align="alignnone" width="555" caption="Nematodinium, a Warnowiid dinoflagellate with an ocelloid (left, double arrowhead) - the subcellular camera eye structure this blog is named after. Note the nematocysts (micro 'harpoons') indicated in the right image. (Hoppenrath et al. 2009 BMC Evol Biol)"][/caption]

We'll start off in the shallow seas, amongst the kelp forests – I'd like to point out that not all protists are microscopic, and some, like the multicellular brown alga Macrocystis (Giant Kelp) can reach ~50m in length. These enormous protists provide a unique habitat for fishes, invertebrates and fellow protists alike. The sleek blades of the seaweed are covered in tiny houses of the bryozoans, which themselves likely host a microcosm of unique microbial diversity. An occasional labyrinthulid – a distant member of the same supergroup as the kelp – may form an elaborate network of amoebal traffic jams. Upon closer examination, the kelp forest is much like the Amazon rainforest, teeming with epiphytes and various attached animal, protist and bacterial communities and an entire ecosystem built upon them.


[caption id="" align="alignleft" width="298" caption="Gromia, a filose amoeba notable for being large enough to leave tracks on the ocean floor. (Burki et al. 2002 Protist)"][/caption]

We look towards the powerful holdfast ('root') of a nearby kelp giant. On it crawls a fine-footed amoeba with a colourful test – Gromia, who made it into the news a couple years ago for being large and heavy enough to leave tracks in fine sediments, an ability previously thought to be restricted to bilaterian animals. Gromia's test ('shell') has an elaborate opening that can close shut upon retracting the pseudopodia ('feet'). One interesting feature of these organisms is that they store their waste products inside their test. Upon reaching full maturity, the organism reproduces and forms multitudes of swarmers and abandons the test anyway, so lack of waste secretion is not too much of a problem. In fact, in somewhat close-ish relatives, the foraminiferan Xenophyophores, the stercomata serve a structural role. In other words, storing waste can also provide support and allow cells to grow very big – I'd imagine in some cases, pathological hoarding in humans may also lead to strengthening their houses, but probably very rarely.


As we look down on the ocean floor, we see more filose ("thin-footed") amoebae: this time carrying enormous elaborate shell structures full of chambers, windows and canals connecting them. You see buried in the sand the abandoned ruins of these architectural marvels – thousands of empty foraminiferan shells strewn across the ocean depths, many fated to persist through eons in limestone. Foraminiferan size and preservation potential led to them being arguably the first protists mentioned in human history – enormous fossil numulites, centimetres in diameter, are embedded in the limestone used in ancient Egyptian pyramids, taking on a second life as part of enormous and everlasting structures of the human realm. You can take a look at some photos of Egyptian nummulites in situ (site in French). Here's a mini-blog of a paleontology trip (in English) to Egypt starring loads of adorable foram disks. Keep in mind that these are all single-celled organisms (probably with a single nucleus), so reaching sizes in centimetres is quite impressive for these guys!


Large forams are far from extinct, however, and the living UFO-shaped condos we see in these shallow waters are actually tropical Marginopora - I'm calling them condominiums because they house multitudes of symbiotic algal tenants – more dinoflagellates. While the motive beyond hosting algae is far from altruistic and is perhaps more closely analogous to farming,  it's difficult not to fall for some anthropomorphising when the forams feature window-like openings for the captive algae. In some forams, the tests also possess little alcoves for the algae – whether these alcoves are there specifically for the algae or the latter just happen to like hanging out there remains to be properly investigated, but the architectural complexity of these creatures is remarkable nevertheless. For more images and descriptions of some of the foraminiferan structural marvels you can check out this illustrated glossary site featuring Hottinger's amazing SEMs and diagrams.

[caption id="" align="alignnone" width="640" caption="Numerous live Marginopora forams. Each is probably about a centimeter in diameter, for an approximation of scale. (Source)"][/caption]

We could get stuck poking at forams for many hours, but we need to move on. We will definitely come back to these awesome amoebae, partly because they're one of my favourite protist groups. Up next we'll take a look at the close relatives of some foram symbionts – the dinoflagellates. Dinoflagellates, or dinos for short, are a diverse group of whirling single-celled organisms carrying a characteristic flagellum wrapped around their waists. They can be predatory, photosynthetic or both, and some groups feature incredible parasites. Some dinos have a habit of gobbling up toxic bacteria and inadvertently concentrating them (and their toxins) as they bloom. The seafood industry has a less-than-amicable outlook on these creatures for that reason. Dinos, among some other algae, are often responsible for bans on shellfish gathering you may see in coastal areas. But they're not all evil to us – our seeing eye dino, Nematodinium, is a high level predator that is relatively rare – so rare that none have yet been cultured, and very few people have ever seen these remarkable organisms. One must sift through cubic metres(!) of seawater using a microscope in order to spot just one or two. Unfortunately, this poses a great barrier to understanding what the ocelloid actually does and how it works.

[caption id="" align="alignright" width="313" caption="Karenia, a photosynthetic dinoflagellate with a tertiary endosymbiont (Andersen & Patterson via ToLWeb)"][/caption]


If you look at the first image in this blog, you may wonder whether the nucleus, indicated by 'n', can really be that big. Oh, it is. Dinos have some of the largest eukaryotic genomes, and that's just the beginning of their strangeness. You may notice something chromosome-like about the nuclear texture – dinoflagellates have massive condensed chromosomes visible without staining. They also lack a few histones – proteins used for wrapping DNA around them in sane eukaryotic nuclei. The massive genomes are full of junk, some of which may perhaps now have taken on a secondary structural role. Furthermore, every gene transcript made by the nucleus has a special starter "splice leader" sequence attached to the beginning of it. The nuclear genomes aren't the only messed up compartment – mitochondria contain short linear gene fragments with only three coding genes and ribosomal DNA (which is responsible the RNA part of ribosomes), the later fragmented all over the place. The plastid genomes, on the other hand, are full of small circles containing a single gene each, and get transcribed into repeating linear sequences much like a cylindrical stamp works.

On the topic of weird doughnut-shaped DNA genomes, there's an ever-ubiquitous Bodonid swirling about in the distance. Let's head over there. We see a small flagellate crawling about with a flagellum trailing along the surface of a decaying seaweed, nibbling on bacteria here and there. Since our eyes don't work on that scale, we can ignore physics and pretend we can sort of see through the cell (you probably would be able to, hypothetically-speaking, but I'm not sure...). Beside the nucleus you see another visible clump of DNA in a thick 'hockey puck' shape, and may be surprised to learn that's a mitochondrial genome ?– one of the easiest to see with light microscopy.

But that's just the beginning of the weirdness: the path of genetic information from DNA to protein involves an unusually high intensity of RNA-editing, or sequence modification in messenger RNAs after being transcribed from DNA. The templates for sequence correction come from multitudes of small circles of DNA. When researchers first started sequencing mitochondrial DNA from these bugs, they were shocked to see total nonsense where highly-conserved genes were supposed to be. Later it was revealed that an elaborate process involving a few hundred proteins was required to fix those nonsense sequences to code properly. This topic deserves a post of its own, but for now here's a final neat tidbit: this bodonid's close relatives, Trypanosomes – some responsible for African Sleeping Sickness, Chaga's disease and nagana,  a major reason raising cattle is so damn difficult in Africa – have elaborate meshes of interlinked DNA circles in their mitochondrial genomes, woven together much like chainmail. Oh, and this clump of DNA somehow manages to rotate during replication, because it's just not weird enough otherwise. (I have some ramblings on these weird mitochondrial genomes towards the end of this post here.)

[caption id="" align="aligncenter" width="577" caption="Perkinsella endosymbiont in Neoparamoeba. n - nucleus; k - kinetoplast (disk of mitochondrial DNA); NN - host (amoeba) nucleus. Transmission electron microscopy. (Dykova et al. 2003 Eur J Protistol)"][/caption]

One such critter with a messed up mitochondrial DNA disk, Perkinsella, has found a home in an amoeba (Neoparamoeba), and the relationship is so intimate that the endosymbiont was initially thought to be a full-fledged organelle. Its role there is far from understood, but neither the host nor the endosymbiont can live without each other. Which leads us to the next point: intimate relationships between different species, symbioses (this includes everything from parasitism to mutualism), occur fairly frequently in the microbial world and feature some outright bizarre associations. Particularly common are associations between bacteria and protists, where we will begin in Part II.

In the next few 'microdives' into the protist world, I would like to systematically destroy as much as possible of what you may have learned about how organisms are supposed to function. Not only are attempts to depict a 'typical' eukaryotic cell crude at best, the 'typical' cell most often depicted is quite derived and a poor representation for eukaryotes as large. Animal cells have undergone a loss of functions per cell (as there are more cells and cell types), and can hardly live independently. Cells of multicellular organisms are degenerate and fail to capture the true wonder of cell biology. In a similar way, ecology is in some ways more exciting on the microbial, and while many principles are preserved, many new and unusual interactions are introduced at that level.