Two species of cyanobacteria (possibly Nostoc commune and Anabaena cylindrica)

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

Some of you may recall that in a recent posting I bought a puddle into my house (it was in a plastic fishtank!). Well, I've hung on to my puddle. Indeed I've been periodically topping it up with fresh puddle-water and inspecting its inhabitants under my microscope. Photos 1 and 2 show two such 'denizens of the deeps'. No, not frog or toad spawn. The scale is all wrong for that. Twenty of the larger spheres in photo 2 for example, would sit side-by-side in 1mm. In fact these are of colonies of blue-green algae (cyanobacteria).

Cyanobacteria are some of the most ancient lifeforms of all. Their microfossil record goes back 2.7 billion years. What I have learnt about them has been mostly through reading a new book - Phycology (=the study of algae) by R.E.Lee (CambridgeUni. Press) - which Santa very kindly delivered to me recently.

Like plants, cyanobacteria carry out photosynthesis. In fact, it is believed that photosynthesis evolved first in cyanobacteria and at some point in the ancient past a cell that was to become the first plant 'swallowed' (co-opted) a cyanobacterium. Chloroplasts, the green organelles responsible for photosynthesis found inside all plant cells are the remnants of these 'swallowed' cyanobacteria.

Today such photosynthetic 'slavery' still persists in the lichens. About 10% of lichens use cyanobacteria to do their photosynthesis (the other 90% use algae).

Photosynthesisis is not the only chemical magic that cyanobacteria have mastered. They are also able to 'fix' nitrogen - that is take nitrogen gas from the air and turn it into an amino acid (glutamate). No higher plants or animals can do this, and a range of plants have formed symbiotic relationships with cyanobacteria to take advantage of this ability. Some plants have special nodules on their roots to house colonies of cyanobacteria. The water fern Azolla has cavities in the leaves. According to the book above, nitrogen fixation by cyanobacteria also plays a fundamental role in keeping the world's 100million square km of paddy fields fertile in areas where otherwise farmers would be too poor to nitrogen-fertilise the soil.

The twin ability of cyanobacteria to remove nitrogen and carbon dioxide from the atmosphere had a profound affect on the earth's early climate. Over eons, cyanobacteria, as the dominant lifeform at the time, transformed an ancient atmosphere rich in CO2 and almost devoid of oxygen into the one we breathe today. A glimpse of what the ancient earth might have looked like can be seen today at Shark's Bay in Australia where warm and salty waters limit other forms of life and allow cyanobacteria to dominate and grow into large, rocky (actually calcium carbonate) colonies called stromatolites - see photo 3 which I'm using under the terms of the Wikimedia free licence. Stromatolites grow slowly and exhibit 'growth ring' like features. Analysis of these has allowed scientists to determine that for example, 1-billion years ago the earth's year comprised 435 days [1].

So, how do you set about identifying the species of a cyanobacterium? The answer is: with difficulty! Like so many areas of biology at present, DNA analysis is over-turning a lot of old species definitions. Things are further complicated by the fact that the appearance (morphology) of a specimen of a cyanobacterium can depend strongly on the conditions in which it has grown. Nevertheless with a little patience it's possible for the amateur (me!) to make a little progress. I've also been fortunate in having been able to borrow a copy of the hefty The Freshwater Algal Flora of the British Isles (Whitton and Brook). Firstly you need to know you're looking at a cyanobacterium. If the cells you're examining show any significant internal structure (especially a nucleus) then it's not a cyanobacterium, and is instead a true algae. Next one needs to take careful note of the detailed shape of the colony. For example, if your cyanobacteria exhibit chain-like growth its important to note whether the filaments branch, whether or not they taper towards the ends and whether or not the cells are encased in any sort of slimy envelope (as they are in photo 2). These features help separate the main genuses. Finally, it's important to note the presence and form of any heterocysts and akinetes. I've labelled these in photo 4. Heterocysts are specialised, largely colourless cells that carry out nitrogen fixation. My impression from the textbooks is that the role of akinetes is a bit of mystery. They have reduced photosynthetic ability and seem to be involved in food storage. Anyway based on these features and Whitton and Brook's book above I'm tentatively identifying my cyanobacteria as Anabaena cylindrica and Nostoc commune. As always I'm happy for anyone out there to correct me.

Finally, one of the most amazing things I learnt about cyanobacteria is the way in which some of them achieve movement. Some species develop tiny gas bubbles (vacuoles) inside the cells that help them float upwards in water to receive more sunlight. More fantastically some species can undertake a form of movement known as gliding. Here the surface of the cells is sculptured in a series of grooves. The grooves may spiral around along a chain of cells. The cell pumps slime into the grooves through tiny pores. If a chain of cells is close to a surface, the flow of slime pushes against the surface and causes the whole filament to glide along over the surface at up to half a mm per second. Hooray for slime power!

Reference
[1] J.P. VANYO, S.M. AWRAMIK Precambrian Research, 29 ( 1985 ) 121-142, STROMATOLITES AND EARTH-SUN-MOON DYNAMICS,

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!

Jurassic sea creatures

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

Hello, and welcome to my 100th creature posting!

I started my blog three years ago almost to the day. My motivation then as now, was simple curiosity. When I began I was almost completely ignorant of the identity of many of the insects, plants, mosses and lichens in my garden.I wanted to learn a little more. I am still learning! It has been a revelation to come to realise just how rich a diversity of life there is on my doorstep, and to discover the incredible variety and subtlety of form, function and behaviour that exists just outside my window. I have encountered flies with larvae that invade the nests of bees, cup-shaped fungi that close the 'roof' in the dry weather, hoverflies that can regulate their body temperature and spiderlings whose first meal is their own mother. It has been a further revelation for me to learn what an enormously detailed body of knowledge exists regarding the natural world (sixty years' worth of data on a Scarlet Tiger moth population in a woodland in Oxfordshire; a study of the behaviour of the Greyling butterflies taking in a staggering 50,000 experimental tests; an online database of 125,000 species of algae...) and yet at the same time, what a mass of unanswered questions exist that that any sufficiently motivated amateur could answer, thereby make a lasting contribution to human knowledge. I find it an inspiration to keep looking and learning about the countryside when I read that of 265 British species of hoverfly, a staggering 40% of larvae are simply unknown (that at least was the status in 1993 according to the Colour Guide to Hoverfly Lavae, G.E.Rotheray) ; or that there are 235 sub-species of British dandelion whose distribution and ecology in the UK in only sketchily understood; or that with changing climate patterns, the amateur has every chance of spotting some immigrant creature (a ladybird, say) new to their environment.

On to today's posting. This being my centennial posting it seemed appropriate to pick something a little different, and what better than to discuss the rarest of all the creatures in my garden, so rare in fact that they have been extinct hereabouts for around 150 million years, when my garden was last a submerged mass of Jurassic oyster beds and coral reefs.

What I know about the geology of my garden I have got from reading the splendid The Geology of Oxfordshire (Philip Powell, 2005, The Dovecote Press):

For those unfamiliar with the UK, Oxfordshire is a county located towards the centre of England. Layers of strata have built up over the eons and at some point the stack of layers has been tilted, so that as you travel across the county from North to South the layer exposed at the surface beneath your feet changes from a youngest (~100 MY-old) chalk layer in the South to an oldest (~200MY-old) ironstone and clay 'lias' layer in the North. Some of these layers are softer than others and have eroded more over time, given Oxfordshire its gently undulating landscape of hills and valleys. (These are the surface-exposed rocks, were you to drill down you would hit much older rocks; 490MY-old rocks from the 'Ordovician' period are known in the neighbouring county of Buckinghamshire). The splendid people at the British Geological Survey have recently put their maps online for free viewing so you can see some of this for yourself.

The rocks in photo 1 are known as 'Wheatley Coral Rag' limestone, Wheatley being a town in Oxfordshire where they're common, although outcrops of the rocks are also found at other locations in the county including Headington (where it was extensively quarried from the 14th to the 19th century), Cowley (where, apropos of nothing, the BMW 'Mini' car is manufactured) and the hill-top village of Beckley. Probably the most magnificent example of the use of Wheatley limestone in Oxfordshire is my garden wall...although I suppose the Radcliffe Camera building (built in the 1740's) in central Oxford isn't bad either! (Photo 2 - was taken by Tom MurphyVII and I understand I can use it here under the terms of the GNU free licence). The lower 3rd of the building is the Wheatley limestone.

The material that went into making Wheatly rag was laid down in shallow seas in the Upper Jurassic period (145-161 MY-ago) when my garden would have been at a latitude of 35-40 deg. North (the latitude of Southern Spain today). The rocks are composed of masses of shards of mollusc shells, bits of sea urchin and fragments of coral. In photo 2 I've zoomed in on the rock at the rear of photo 1. I'm not a skilled photographer but I hope you get an impression of this.

I have not attempted to identify the species of my fossils. Indeed I would hardly know where to start. If one finds a fossilised Jurassic mollusc shell, is it a relatively simple matter of keying out the find from amongst a handful of known and easily distinguished species, or is exhaustive analysis needed to separate it from hundreds or even thousands of candidate Jurassic molluscs? (Can anyone comment?). Part of me would love to throw myself into a study of this, but logic tells me that with limited time to devote to my hobby, and around 750 UK species of moss, 800 larger moths, 3500 larger fungi, a similar number of lichens, 4000 species of beetle, 7000 flies, heaven only knows how many mites and nematodes...I have more than enough living species to occupy my time without embarking on a study of the extinct ones.

I am left with one lead as to species. In discussing locally discovered Corallian fossials, the book above shows images of fossil oysters of the species Nanogyra nana, corals of the species Isastrea explanata and Thecosmilia annularis and sea urchins of the species Nucleolites scutatus. Whether any of these were truely present in my garden I do not know, and even if they were they're not living there now and so strictly I shouldn't count them in my species tally. Since this is 'my party' however, I am going to flagrantly break the rules, assume at least one of them did once live in my garden, and chalk up one more species to my blog count. Complaints should be addressed to my lawyer!

A freshwater ciliate

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

Some time ago I wrote about the Haematococcus algae I discovered in a puddle in my garden. At the time I enthused about the book Freshwater Microscopy by W.J. Garnett, a guide from another era for the amateur to culturing and identifying pond life. Inspired by the book I recently revisited my puddle and was well rewarded with a number of tiny critters new for me. Photo 1 (click to enlarge) shows three : a) A ciliate (more below) b) what I think may be a cyanobacterium and c) another ciliate that I think may be a paramecium. (As always my identifications come with a health warning. I'm happy to have them corrected).

Photo 2 shows a closeup of 'a' taken at 1000x magnification using my microscope's oil-immersion lens. Features to note about my organism are its large nucleus and the numerous swimming hairs (cilia) covering its body.

Those interested in such arcane matters (those not may like to skip this paragraph) may like to know the specimen here was stained with ~0.01% aqueous Eosin dye then mounted in a mix of water and glycerin with a little added disinfectant (to prevent future growth of mould). In an attempt to render the slide permanent I adopted the 'double cover slip method' . There's a detailed explanation of this here but briefly it involves sandwiching the specimen in its aqueous mountant between two differently sized coverslips, then mounting this sandwich in turn in a solvent based mountant (Permount in my case) thereby sealing in the aqueous mountant against evaporation and hopefully rendering the whole arrangement permanent. (Since acquiring my hobbyists microscope a couple of years ago I've developed a growing passion for making up microscope slides!)

Returning to my specimen itself, I have a couple of basic photoguides to pondlife and from images in these, and the general size (~40um) and form of my ciliate, I was tempted to identify it as a species in the genus Colpidium. You can find some stunning photo's of this and other protozoa here. From the volume of images on the web this seems to be a not uncommon find in pondwater. Unfortunately however, having looked at the equally splendid Protist Images website I'm no longer so confident. The problem is that the phylum Ciliphora (=little organisms like mine with cilia) is broken down into such a large number of superficially similar genera that it's hard for the amateur like me to know that my wee beastie is definitely a Colpidium and not say, a member of the catchily entitled Trithigmostoma, or the Drepanomonas, or the Cinetochilium...or for that matter the Tetrahymena I hear you cry! The Protist Database does give some guidelines for discriminating amongst these genera - typically discrimination involves carefully noting the position of mouth parts, the presence/absence of any stiffer bristles amongst the more whiskery cilia, or the absence of cilia on some parts of the body - but I confess I've not attempted to apply these to my organism since, firstly, the time commitment, my limited number of specimens and my comparatively humble microscope setup would, I'm sure, limit my chances of a successful identification. Secondly, there exists a nagging worry at the back of my mind that the taxonomy ('family tree') of the protozoa may not in fact be correctly established at this time. Certainly, the arrival of DNA sequencing technology is requiring that large amounts of what was assumed to be true about the inter-relationships of different species in other fields of biology is having to be drastically revised. The problem is that what two species look like is not necessarily a guide to how closely related they really are. DNA testing is revealing that superficially similar organisms can sometimes be only distantly related. The opposite is also true. I wrote about this in detail in my previous posting on the Glistening Inkcap Coprinus mushroom. I have no knowledge of the true status for microscopic cilates but I would not be at all surprised to learn that their taxonomy is also undergoing something of an upheaval amongst the professionals. For this reason also I've not attempted a more detailed identification of my ciliate. Of course, my thinking on all this may be entirely wrong. Perhaps someone looking at my photo's can tell immediately what species I have. If so, and you're that person, do please leave a comment.

A microscopic Peritrichia Cillate (Vorticella?)

I am an amateur naturalist trying to discover what lives in my garden.

Readers of my blog may recall that some time ago I decided to investigate the microscopic inhabitants of some rainwater that had collected in my garden. I was delighted at the time to discover some mobile little Haematoccus algae. Spurred on by this success I recently decided to revisit a similar puddle.

This time the water was in shade and contained quantities of decaying leaf-matter. Placing a few drops under my micro- scope I saw nothing at first, but then began to notice numerous small, semi-transparent, stalked objects, such as those above the number '3' in the microscope photo 1 (click to enlarge). My first guess was that these were some sort of fungal spores. Then one moved!

Zooming in (Photo 2) revealed an ovoid creature with a fringe of hairlike cilia at the front end. You can just about make out one poking out above '2.7' on the scale bar. These cilia were in constant motion and set up eddy currents in the water, drawing in small food particles as I watched.

The move- ments made by my creature were highly charac- teristic. Any small distur- bance (such as a tapping the micro- scope slide) caused the stalk supporting the 'head' to rapidly contract, jerking the head backwards in the blink of an eye and at the same time changing the head-shape from ovoid to compact and spherical. Gradually over a period of perhaps half-a-minute the stalk would re-extend and the head return to its original shape.

My creature had one further surprise in store: I was amusing myself tapping the slide and watching the response, when, as if grown tried of my irritating presence, one of my little creatures suddenly detached itself from it's stalk and swam away!

I'm in possession of a nice introductory, colour Guide to Microlife (Rainis and Russell, Grolier Publishing) and I was relatively quickly able to identify my lifeform as a ciliate, the cilophora being a large collection ('phylum') of microscopic animals belonging to the even larger collection of microscopic animals, the protists (to get an idea of just how large you might like to peruse the 81,000 (!) images on the Protist database.)

Fortunately, the structure and habits of my creature allowed for some further progress: the presence of a contractile stalk, the cilia around the mouth and the fact that my little critter was able to swim free of its stalk all point to it being a member of the smaller (though still sizeable) subclass of organisms the peritrichia (which I read is from the Greek, peri=near, trichia=hair).

Now, had I observed any 'stalks' with more than one 'head', that might have narrowed things down to my creature being in the genus Epistylis. I didn't (though of course absence of evidence isn't evidence of absence), which finally brings me to the (somewhat tentative) conclusion that my little creature is a member of the genus Vorticella. Unfortunatly that's as far as I've got. There are a more than a dozen species in this genus and which mine is I can't tell. I'll be happy if anyone out there can tell me.

Naturally, I'm not the first microscopist to observe Vorticella and a little web browsing led me to two very nice articles (here and here) for the amateur. The latter includes some excellent photos including some of Vorticella reproducing by asexual budding. From these and other sites I also learn that a free swimming Vorticella 'head' is termed a telotroch and the stalk is able to contract by virtue of a contractile bundle of threads within termed a moneme. A paper by Sotelo and Trujillo-Cenoz (available to download here) has some ultra-high magnification electron-microscope photos of this and also reveals that the moneme is responsible for the shape-change the head suffers when the stalk contracts.

On the subject of cilia a quick web search turned up numerous papers and articles. My intention was talk about some here, but since I've already gone on for some length in this posting, and since I'm certain to have another opportunity to discuss cilia in the future (so many microscopic creature have them), I'll leave the topic for now.

Instead I'll end with a photo of a free-swimming little animal I encoun- tered in the same sample of water. The ident- ification of this one defeated me. Am I looking at a free swimming Vorticella or is this something else? If you know do please leave a comment.