Wednesday, October 29, 2014

Almost This Or Almost That? Must Be The Other

Biology concepts – Protista, taxonomy, phylum, kingdom, monophyletic, paraphyletic, cladistics, algae, diatom, dinoflagellate

Euglena gracilis is an organism in the Kingdom Protista. It has
one long flagellar undulipodium, but it can also move by
amoeboid movement. It has chloroplasts and can do
photosynthesis, but it also can eat other organisms. Is it any
wonder that classifying protists is so hard?
Classifying living organisms is self-perpetuating job. Imagine if the dentist sold candy in his/her office, “Here’s your root canal and your Laffy Taffy.” Scientists try their best, but whenever you start sorting things out, you always have that pile left over that doesn’t seem to fit anywhere. So you have to rethink your categories and try again.

The best example of the inanity of classification is Kingdom Protista. The word means, “the very first,” probably because it is supposed that these were the first eukaryotes. How do we define the organisms of this Kingdom? The best we can manage is to say that they are the eukaryotes that aren't animals, plants, or fungi. Really, is that the best we can do?

In a perfect system, all the organisms of one kingdom would be descended from a single common ancestor (be monophyletic, mono = one, and phulon = tribe). But it don’t work like that. And this is where Kingdom Protista serves as a good example.

There are protists that look a lot like animals, those that resemble plants, and those that share features of fungi. No way did they all come from a single ancestor. Protista is a paraphyletic (para = near) kingdom, the group may exclude a member with a common ancestor. As such, the protists are a catch-all, those that don’t fit in some other kingdom. Protists are like pornography – hard to define, but you know it when you see it.

Classification isn’t perfect, some groups come from
different ancestors. A shows a group (in yellow) that
is monophyletic, they all come from one ancestor.
The paraphyletic group (B) shows that some groups
can’t include all descendents of a common ancestor.
And if a group is made from descendents of different
ancestors, it is called polyphyletic (C).
We already said that some behave like animals, plants, or fungi. Some are unicellular, some are multicellular, and some can be either. Some do photosynthesis, while some eat other organisms. How can you break these up into phyla, classes, orders, families, genera, and species when they are all so different?

You might do it by common ancestor; let their genes do the talking. We are learning more and more about who begot who – this is the study of cladistics. But if you break down protists into their clades – they don’t seem to make sense. Organisms that look or act similar might be in different clades, with wildly different organisms linked close together.

Alternatively, you might divide them up based on the characteristics, as Linneaus did - the animal-like protists in one phylum, the plant-like protozoans in another. But this may separate genetically related organisms into very different phyla. Same problem. How about by the way they get around? Some use flagella-like undulipodia, some use undulipodia called cilia, some use cytoplasmic crawling called pseudopodia, and others are immotile. Again, disparate organisms may be lumped together just based on their preferred mode of travel.

The idea of the "phylum" is to place the organisms in categories so that they are “more related to each other than they are to any other group.” Wow, that sounds scientific. Related based on what? We just discussed motility, genetics, and physical characteristics or behaviors.

The Kingdom Protista sits between the modern plants,
animals, and fungi, and the ancient prokaryotes. As such,
they end up being a catch all group. The right image
shows how some people group the protists based on
undulipodia characteristics, not ancestry.
And this assumes that we even know how related they are to each other and to organisms outside each phylum. Genome studies haven’t even begun to get close to establishing the ancestral relationships between all the organisms.

So we guess. And then we change things as new information becomes available. The work never ends, and the students never get to just memorize the categories.

As of today, some scientists classify protists based on a combination of the characteristics above. In the system I like best, there are 15 phyla, and we can roughly divide them as we show below. But there are six different phyla just for the protists that perform photosynthesis! The reason I like this system best -it roughly mimics the way they use undulipodia. And this is what we’re interested in today.

Kingdom Protista contains the organisms that seem to have made the most obvious uses of undulipodia. Eukaryotic flagella and cilia abound, some protists have both, and some have them only part of the time. There are six phylums of plant-like protists. Many have flagella, none that I could find have cilia. Here are some examples:

Pyrrophyta organisms will bloom and then bioluminesce
in order to scare predators away. Movement in the water
causes vesicles in the dinoflagellate to rupture via action
potential and release the reagents to make light. It’s exactly
the same system that fireflies use.
Phylum Pyrrhophyta The dinoflagellates are in this phylum; they have two flagella, one from that side that beats and one on the posterior that whips more traditionally. Some species of this protist are responsible for the red tides that poison fish and can (and have) killed humans who eat the fish. Other dinoflagellates are bioluminescent and make the water appear to be on fire (hence the phylum pyrro = fire).
Phylum Euglenophyta This phylum includes the Euglena gracilis organism shown in the animation at the beginning of the post. These protists also have two flagella, but one of them is reduced and doesn’t stick out. They have an eyespot, perhaps the genesis of our own eye. The eyespot helps them to move away from strong light sources, sources that would overheat them.

Euglena are common model organisms, on this world and in (near) space. They traveled on the parabolic flights to have their flagellar motions studied in zero gravity. The 2010 publication that resulted from the experiments showed that the process of beating is regulated and physiologic, as the change from hypergravity to microgravity stopped the flagellum from moving. The opposite change in gravity reoriented the cells and they started swimming to the bottom of their tank again.

The remaining phyla of plant-like protists can be included in a supergroup called the Chromista (colored organisms).  In terms of their undulipodia, the chromists tend to have two flagella, one on each end. The forward flagellum is usually longer and has lateral growths called mastigonemes. The best description for this type of flagellum is that it looks like Christmas tinsel.  The back flagellum is shorter and smooth.

These are the phyla of the Chromista; the colored protists.
Problem is, not all of them are colored and some colored
protists aren’t included in this group. Top right and bottom
left are the chlorophyta, the green algae. These are the most
recognizable algae. The bottom right is the diatoms, they have
the most interesting shapes. Look them up.
The Chrysophyta are the golden algae and diatoms. The diatoms are only flagellated when undergoing sexual reproduction, and is just the male gametes that have the flagella, sounds like male gametes in mammals doesn’t it?
Green algae are the ones we recognize; they belong to the Chlorophyta phylum. These are the ancestors of the land plants, and some have flagella in all stages, while others only have flagellated gametes.  We will see soon how some land plants still have flagellated gametes.

Brown algae belong to the Phaeophyta phylum. They are exceptional amongst the protists because every organism in this phylum is multicellular. No brown algae live as individual cells. Kelp is an example of brown algae. Kelp forests are multicellular example of brown algae thalli, growing to 40-60 m (130-200 ft) in height! Kelp forests are some of the most productive ecosystems on earth.      
The gametes of the brown algae are flagellated like in most of the other chromists. A 2014 study has started to look at the flagella of the chromists, using brown algae as the model organism. The study found that the flagella have functions in motility, signal transduction, and even metabolic activities.  The two different types of flagella had common proteins and proteins specific to each form, for a total of 495 different proteins associated with flagellar function and structure. For instance, only the posterior flagellum has a protein that senses blue light, and may be used for steering the organism. 

The Rhodophyta are where we get food stuffs. On the left
represents agar that can be used to make things that are like
Jello, it fills the role of the gelatin. In the middle, agar is also
used as a polysaccharide source of nutrition for growing
bacteria in the lab. On the right, nori is a rhodophyta
seaweed used in sushi.
Finally, Phylum Rhodophyta is the last of the Chromists. They are known as red algae, but you may know this protist better as seaweed. We saved them for last because they are the biggest exception in the plant-like protists.

If you’ve eaten Japanese sushi rolls, then you’ve eaten red algae in the nori that the rice and fish are wrapped in. Nori is made from several species of red algae of the genus Porphyra. Not a sushi fan? How about ice cream? Carageenans that make ice cream smooth also come from red algae.

Ice cream is reason enough to love the red algae, but there’s more. A 2014 study indicates that one compound found in the Porphyra is a strong antibiotic. Studies of 1,8-dihydroxy-anthraquinone from this red algae genus can disrupt the cell wall of Staphylococcus aureus. This is hugely important, since many strains of S. aureus (like MRSA and VRSA) are now resistant to most existing antibiotics.

Rhodophyta algae are red because although they use some chlorophylls for photosynthesis, they also use phycoerythrins and phycocyanins. Interestingly, these are the same pigments that are present in the cyanobacteria. This suggests that there is an ancestral link. The link is supported by one other factoid. Both cyanobacteria and red algae lack undulipodia!

The seaweed Rhodophyta organisms often live in the tidal
pools. The spongy material in the stalks and “leaves” is the
agar and is related to the mucin product that attaches to the
male gametes as they are released. I couldn’t find a picture of
the gametes with their mucin tails, so this will have to do.
The male gametes of red algae are at a deficit; they don’t have flagella to swim toward the female eggs. They must relay on water movement to disperse them. An older study showed that when the male spermatia are released by the discharge from vesicles, the vesicle contents can hang on to the gametes and form mucin appendages. These are then more likely to be moved around by the water.

Whatever it is, the system seems to work. A 2014 study found that fertilization success was dependent on male organism biomass, but neared 100% when there were relatively few male gametes present. This was hypothesized to be possible because low tides in the tidal pools where the organisms live greatly increase the chances of male/female interaction and fertilization. Seaweed takes advantage of the moon’s effect on the tides to ensure reproductive success – who needs flagella!?

So far we have met protists that use flagella at some point in their life cycle (except for the red algae). Notice that none of them have used cilia. Next week, how about the animal-like protists? I bet there are some exceptions there as well.

Fu G, Nagasato C, Oka S, Cock JM, & Motomura T (2014). Proteomics Analysis of Heterogeneous Flagella in Brown Algae (Stramenopiles). Protist, 165 (5), 662-675 PMID: 25150613

Wei Y, Liu Q, Yu J, Feng Q, Zhao L, Song H, & Wang W (2014). Antibacterial mode of action of 1,8-dihydroxy-anthraquinone from Porphyra haitanensis against Staphylococcus aureus. Natural product research, 1-4 PMID: 25259418

Maggs CA, Fletcher HL, Fewer D, Loade L, Mineur F, & Johnson MP (2011). Speciation in red algae: members of the Ceramiales as model organisms. Integrative and comparative biology, 51 (3), 492-504 PMID: 21742776

Strauch SM, Richter P, Schuster M, & Häder DP (2010). The beating pattern of the flagellum of Euglena gracilis under altered gravity during parabolic flights. Journal of plant physiology, 167 (1), 41-6 PMID: 19679374

For more information or classroom activities, see:

Kingdom Protista –

Euglena –

Red tide –

Pyrrophyta –

Kelp –