Wednesday, October 13, 2010

Smooth Hawks-beard Crepis capillaris

I am an amateur naturalist trying to learn something about everything living in my garden.

I have mentioned previously that the pleasure for me in maintaining this blog is that some previously unnoticed (by me at least) plant or insect, once researched, takes on a whole new aspect. So it is with today's posting. A scattering of facts about the genetics of an inauspicious weed may seem obscure to some, but for me, a weed on my lawn catches my eye with a new interest these days. Photos 1,2 and 3 shows said weed. It pops up frequently in my garden.

For the unskilled amateur botanist (=me!) identifying yellow flowered weeds isn't altogether trivial as the guide books contain a long lists of yellow-flowered ragworts, fleabanes, marigolds, colts-foots, dandelions, sowthistles, cats'-ears and hawkbits. After a little work however I'm fairly confident my plant is none of these and is instead Smooth Hawks-beard (Crepis capillaris). A characteristic feature of the Hawks-beards are 'involucre bracts' (=the little leaves around the base of the flower head - best seem in photo 2) organised in distinct inner and outer rows.

Surprisingly, although it is a common UK weed, I've been able to find almost no detailed online information on Smooth Hawksbeard. One exception is the bioimages site that lists a handful of fungal rusts (including some Puccinia species - see my post here) and a gall fly known to parasitise Hawksbeard. The other exception was an online paper by Oud [1] that describes the chromosomes of C. capillaris. With my comments of the opening paragraph above in mind, its this I'll discuss.

As most people know, the DNA inside cells is packaged into structure called chromosomes. When new cells are needed by a body, the existing cells set about creating copies of themselves by dividing into two, in a process known as meitosis. (Cells destined to become specialist structures such as sperm or eggs do something slightly different called meiosis, but never mind that here). To create two cells from one its clearly necessary to replicate the DNA. To do this the chromosomes perform a complex little 'dance' inside the cell in which they double in number (in a process called interphase), pair up and line up along of the middle of the cell ('prophase' and 'metaphase' respectively) and finally split apart ('anaphase') as the cell separates into two ('telophase').

I got the hang of this terminology recently using my colouring crayons! (I've a copy of the very clever - 'The Botany Colouring Book', Young - in which you learn by doing). You can find any number of explanations on the web however (here for example).

It's perfectly possible to watch the whole miraculous 'chromosomal dance' down a hobbyists microscope. The classic place to look is at the growing tip of a young plant root where new cells are being feverishly created to grow the root. Indeed, I've tried looking for it myself a few times. I've yet to succeed in getting any really good results, but rest assured when I do there'll be a posting...

I can't resist a small digression at this point to mention microtubules. When it comes to pulling chromosomes apart (i.e. during anaphase), cells do this by strapping tiny cables (microtubules) to chromosomes in a process akin to hauling logs out a log pile by pulling on ropes. These microtubules are tiny (around 25nm across where a 'nm' is a millionanth of a millimetre) and hollow. So tiny are they that some physicists (notably the famous blackhole physicist Roger Penrose) have even speculated that inside microtubules, reality ought to be dominated by the small and weird world of quantum physics (cats being both alive-and-dead; particles being in two places at once - that sort of thing) and that signals propagating inside microtubules in the brain might have something to do with the mystery of human consciousness (you can listen to Penrose give a lecture on it here). Anyway, this is a highly contentious claim and a long way from today's discussion. To return to more certain issues:

In their paper above Oud set out to study the three-dimensional arrangement of chromosomes inside replicating cells during prophase. It turns out if you want to study chromosome arrangements inside a cell without being mired in complexity, you can do worse than make use of Smooth Hawks-beard since it has a mere 6 chromosomes (strictly one should write '2n=6' - see my previous explanation here). Compare that with humans with (2n=) 46, or some ferns with around a thousand! (I have no idea why there is such variation in nature. Generally, there is no relationship between the number of chromosomes and the complexity of an organism. Anyone?).

Trying to image the three-dimensional arrangement of tiny objects is not simple when you remember that looking down a conventional microscope all you see is a flat, two-dimensional view of an object. To achieve a 3D visualisation of chromosomes Oud used a special type of microscope known as a confocal scanning laser microscope. As anyone who has a normal microscope knows, images suffer from a limited 'depth of field': only a portion of your object appears in focus. Other parts of an object, at different depths, appear blurred. Often this is a nuisance, but confocal microscopes cleverly use it to advantage. They physically block out light from anywhere other than the one extremely thin section of a sample that happens to be in focus. The advantage of this may not be immediately clear, but the point is that by slowly varying the point of focus, one can build up a stack of images where each image contains only light coming from that single, selected slice through the sample. By taking a bunch of such images from different depths, and stacking them all together (using a computer) one arrives at a three dimensional image.

Using this method Oud arrived at the wonderful picture of the three dimensional arrangement of chromosomes in a Smooth Hawks-beard root cell in their paper. Of course, their study was not about making 'pretty pictures'. They were interested in adding to biologists' long-standing interest in knowing how chromosomes are arranged in space inside the nuclei of cells; In particular whether the arrangement is random or not. Their conclusion (as I understand it) was that although a range of differing arrangements were observed across cells, overall the chromosomes seemed to arrange themselves in space in a finite number of non-random ways.

So there we have it! A week ago, for me, an unknown weed. Now, a named plant with a intriguing inner life. Bye for now.

I have begun to think that my habit of normally giving only a link to articles isn't the best, as articles may disappear online in future. From now on therefore, I'm going to make an effort to selectively include proper references at the end of postings. To that end:
[1] Oud JL, Mans A, Brakenhoff GJ, van Der Voort HT, van Spronsen EA, Nanninga N. Three-dimensional chromosome arrangement of Crepis capillaris in mitotic prophase and anaphase as studied by confocal scanning laser microscopy. J Cell Sci. 1989 Mar;92:329–339

Sunday, October 10, 2010

A Rotifer, Genus Mniobia

I am an amateur naturalist trying to discover everything living in my garden.

Autumn has arrived in the UK. The leaves are dropping from the trees and the wet weather has created puddles of rain water and detritus in my garden. Hoping to investigate the life therein, and having a cheap plastic fish tank to hand, rather than stand outside getting wet I decided to bring a puddle inside. It makes rather an attractive room feature don't you think?! (Photo 1).

Photo 1 shows one of the inhabitants: a rotifer.

Rotifers have long been a favorite of amateur naturalists. Under the microscope they have instant appeal. Take a drop of pondwater and you'll find smaller creatures swimming around (algae, protozoa, fungal spores...) but all tend towards the 'minimalist', typically a single, roughly spherical cell. Rotifers by comparison have a true multicellular body. The amateur gets to search for eye spots, 'buccal tubes', kidneys, ovaries... add to this the wonderful, whirling 'wheel organs' at the front of the head, setting up eddies in the water and dragging hapless prey into the mouth and onwards to the tiny but perpetually snapping jaws ('trophi'), and you have a recipe for many hours of fascinating microscope viewing. In photo 1 I didn't manage to capture the 'wheel organs'. There are some virtuosic photos by Charles Krebs here. Ultimately however there's no beating moving images, these being a fine example.

When it comes to identifying my rotifer I don't have any dedicated books. I did find a basic key in my copy of Microscopic Life in Sphagnum (Marjorie Hingley, Richmond Publishing) however. Some of the features of importance for rotifer identification include the presence of any hard shell ('lorica') and the presence of any eye spots. Mine has neither. The foot is another important feature. My rotifer crawled around 'inch worm' fashion beneath a microscope cover slip and obligingly gave me the views in photo 2. The labelled features point to my rotifer being in the genus Mniobia. As always, I'm happy to have any reader correct me.

The professionals too have given their attention to rotifers. One feature that has provoked serious study has been rotifer sexual reproduction. For many rotifer species, males are very rare. For some, no male has ever been found. How and why rotifers accomplish this, when almost everywhere else in the animal kingdom evolution has rendered reproduction reliant on two sexes, has been actively researched. I considered making this the topic for today's posting. I decided instead however to talk about some experiments into rotifer populations by a Professor Gregor Fussman and colleagues (very helpfully Prof. Fussman has made his all papers available online here).

Biologists have long been interested in trying to model the dynamics of populations. Suppose an isolated island starts out supporting a population of, say, a hundred rabbits and ten foxes. Biologists would like to be able to predict how many foxes might exist on the island a certain number of years into the future. The non-mathematically-minded amongst you (the others might want to skip this bit) might be puzzled by the meaning of the word "model" in the sentence before. Basically it means this: Take a pen and paper. In the middle of your page write an equals sign ('='). On one side of the equals-sign write a letter ('f' say) to represent the thing you're trying the predict (here, the rate at which the fox population is changing). On the other, write all the stuff you guess 'f' depends on - for instance, one might guess the size of the fox population would depend on the size of the rabbit population, the breeding rate of foxes, the old-age-limit of foxes etc. Finally, take the equation you've by now written down, and stuff it into a computer (i.e. tell the computer to plot a graph of the fox population over time using your equation). Of course there are many subtleties and details in order to do this sort of thing well, but in principal at least that is how population models are done.

Rather than 'foxes', Fussman and colleagues set out to model a population of rotifers (Brachionus calyciflorus). The rotifers were feeding on algae ('the rabbits') called Chlorella vulgaris not unlike the alga I blogged here. Rather than an 'isolated island', the environment was a 'chemostat' which is basically a fancy fishtank with tubes in and out in order to controllably input and extract nutrients for the algae to feed on ('grass for the rabbits'). Fussan and team wrote down a set of equations they presumed took account of all the factors that would influence the population growth of their rotifers and fed their euqation into a computer. When the computer results were compared with real life however, they got a surprise: The predictions of their model were in gross disagreement with experiment.

In a textbook example of the scientific method the investigators set out to track down the 'missing ingredient' from their equations. The answer, when it was found, was sufficiently surprising and profound to ensure its publication in the prestigious journal 'Nature'.

The hidden factor influencing their population experiments could be summed up in a word: Evolution. This was a great surprise. After all, the effects of evolution are only 'supposed' to show themselves only over millenia. Evolution doesn't go around dominating the behaviour of fishtanks over a period of a fortnight, right!? What was going on? The answer was subtle: It turned out that the algae in the chemostat occurred in two subtly different forms - the species existed as two clones (I'll call them 'A' and 'B' here). Although only a little different, it transpired that rotifers were unable to 'go forth and multiply' when feeding on one of the clones, 'A', but could happily do so when feeding on the other ('B'). When a population of predatory rotifers was introduced to a population of algae, at first there would be plenty of both types of clone. The hungry rotifers would start to feed on the B's and the rotifer population would grow. Simulataneously, the population of 'A' algae would also grow as they carried on reproducing, free from predation. By contrast, alga B's population would fall, not only because they were being eaten up by rotifers, but also because the bugeoning population of 'inedible' A's was using up an inreasing amount of the tank's nutriants. Eventually the population of 'B' could crash to zero...

...And there it was: Darwin's famous "survival of the fittest" acting on a small difference between two sub-species so as to drive one to extinction in mere weeks!

Actually, my explanation above is oversimplified. In fact the B's didn't always disappear. Sometimes, it was the rotifers whose population would crash as they ran short of food as the B-algae became scarce. The disappearance of predators would then give the 'B' algae the chance to recover. Rather than complete extinctions, the experimenters often observed more complicated oscillations in population sizes in their tank therefore. Nevertheless, once suitably analysed, the conclusion was the same: Evolution was a powerful force at work in their system.

The implications of this discovery for biologists seeking to model important systems may be very large. If evolution is a driving force for the dynamics of algae in a fishtank on short timescales, is it also an important, fast-acting player in such vast and critical eco-systems as the oceans' plankton food chains?

I don't know the status of this last suggestion. I do know however that these days a humble puddle in my back garden evokes a new fascination. Hoorah for natural history!

Saturday, October 2, 2010

A lichenicolous fungus Illosporiopsis (syn. Hobsonia) christiansenii

I am an amateur naturalist trying to learn something about everything living in my garden.

No, not another lichen posting! Instead, the star of today's posting - the pink blobs in photo 1 - is a fungus. Specifically a lichenicolous fungus (from the Latin colous = living amongst [lichen]).

The lichen being infested here is our old friend Physcia tenella.

Photo 2 shows the rather lumpy, 'coralloid' texture of the fungal blobs close up.

I first noticed pink blobs of this type some years ago on a country walk. I struggled to identify them for a long time but an acquaintance suggested the fungus Marchandiomyces. Searching the internet for more information led me to the very nice website of Alan Silverside. There I found pictures of two species: the rich-pink blobs of M. corallinus and the orangey-pink blobs of M. aurantiacus. I was ready to settle for one of these, but then I noticed a comment alluding to yet another pink-blob species called Illosporiopsis christianesnii. (There is yet another called Hobsonia christiansenii - but as far as I can tell this and Illosporiopsis are the same).

Distinguishing between these various blobs seemed a forlorn hope. As it said in a paper by Sikaroodi (Mycological Reserach, April 2001) I came across during my searches

"These [species] are frequently misidentified because of a paucity of morphological characters"

I was about to quit, but then I caught sight (here and in a paper by Lowen Mycologica 78(5), p.842) of a mention that the 'conidia' (= asexual spores) of I. christiansenii had a characteristic 'spiral' appearance. I took a tiny part of my fungus in a drop of water, squashed it between a slide and cover slip and viewed it with my trusty student microscope. The result is shown in photo 3 (click to enlarge).

I'm not expert enough to be confident of what I'm really looking at here. Furthermore, working at x1000 magnification is a tricky and frustrating business - there's hardly any depth of focus and the slightest knock sends things scudding out of the field of view. Nevertheless I was left pretty confident there were indeed some spiral 'objects' in my sample (the object in the photo inset for example, and another in the main image above the number '3'). On that basis I'm identifying my fungus as Illosporiopsis (syn. Hobsonia) christiansenii.

Searching more generally for information about lichenicolous fungi I was rewarded by finding the splendid review article by Lawry and Diederich here. From this I learn that the whole research topic of lichenicolous fungi is enjoying a purple (pink?!) patch. From a single illustrated species (a gall on the lichen 'Usnea') in 1792, the number of known species grew steadily to reach around 686 in 1989. Over the past 10-years however, as scientists around the world have started look in earnest for such lichen-loving fungi, the number of known species has more than doubled.

With this explosion in species-count is coming a growing appreciation of just how rich a field-of-enquiry the lichenicolous fungi represent. Take the task of unravelling and understanding the interactions between the attacking fungus and its target lichen. Some fungi are very unfussy, being adaptable to a wide range of lichens. Others have a very intimate and specific relationship with only one or two hosts. Some invaders aggressively attack and kill their target lichen. Others are parasitic, insinuating their hyphae (=the long tube-like cells that make up a fungus) into the cells of their host to suck the juices, vampire-like, from their cells. Some lichenicolous fungi even stage a 'take-over' bid: A lichen is basically a fungus that is 'farming' a crop of algae (see my post here). The game plan of some lichenicolous fungi is to kill the 'farmer'-fungus' in order to acquire his algae.

There are more questions over how lichenicolous propogate and spread themselves. It's hypothesised that some may hitch a lift with roving, lichen-feeding mites. But generally not much seems to be known. There are unanswered questions about the sensitivity of lichenicolous fungi to air quality. Certainly some lichens are incredibly sensitive to impure air, unable to survive even trace amounts of pollution. Whether this holds for their attackers isn't known.

There are further questions about how lichenicolous fungi affect the ecology of a region. It's been argued by biologists that having a lot of parasites in some eco-system ought to encourage a lot of species diversity. Whether this is born out in regions where parasitic lichenicolous fungi are prevalent however is not well studied however.

These topics (and a lot more) are discussed in the review above. All in all, I suspect that any amateur naturalist hoping to make some genuine and lasting contribution to scientific understanding could do worse than to cultivate an interest in lichenicolous fungi!

To return to the pink blob species M. corallinus and I. christiansenii, and the paper I mentioned above by Sikaroodi, a remarkable thing to learn was that these two nominally identical blobby fungi in fact represent two entirely separate fungal kingdoms. There are millions of species of fungi, but (crudely) they can be split into two huge groups. There is a huge group of fungi that grow their spores inside little sausage-shaped bags called asci (see photo 4 on my posting here). Such fungi are termed ascomycetes. The other group grow their spores, not inside asci, but on the ends of sausage-shaped protruberences called basdia. Such fungi are termed basidiomycetes. From everything I've read this is a very deep and ancient division, the ascomycota and basidiomycota representing an ancient 'parting on the ways' in the evolution of fungi. What's surprises me therefore, is that whilst M. corallinus and I. christiansenii seem almost indentical in every regard (both are small pink blobs, and both grow on the same types of lichens), whilst the former is a basidiomycete the latter is an ascomycete. Now, sometimes, entirely different lifeforms can end up evolving very similar bodies simply because these are the best bodies for the life they're trying to live ('convergent evolution'): Think 'whales' and 'fishes' or 'birds' and 'bats'. Have two very distant fungal cousins independently evolved the conclusion that if you want to survive on lichen, being a small pink blob is a good way to go? The plot only thickens when you learn that although DNA testing shows the species above to be members of the basidiomycota and ascomycota respectively (and therefore that they should grow their (sexual) spores in quite different ways) in fact for neither species has this (sexual) fruiting stage ever actually been seen! (Though it should be remarked that the same was true of the blob M. aurantiacus until recently when a fruit body ('teleomorph') was discovered by Diederich and co workers).

So there we have it. A tiny inconspicuous fungus occupying the (to our human eyes) minute and obscure niche of subsisting in the crevices of a lichen. And yet what a rich and unexplored natural history awaits.

"Great fleas have little fleas upon their backs to bite 'em,
And little fleas have lesser fleas, and so ad infinitum"
( Augustus de Morgan, 1806-1871)