Thursday, December 30, 2010

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!

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

Thursday, December 23, 2010

A fungus gnat , Sciarida (possibly Bradysia)

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

Buoyed up by my successful (?!) identification of a fly to species level in my previous posting, today I'm taking on a related, though tougher challenge: the little gnat in photo 1 (click on photo's to enlarge). This one was around in my garden mid-May last.

As I've discovered through writing this blog, to stand any real chance of identifying the smaller insects it's pretty much essential to have a microscope. This needn't cost the earth. Photo 1 was taken by holding a 'point and click' digital camera up to the eyepiece of a sub-£100 'DM2' stereo microscope. With 10x and 20x eyepieces this would probably suffice for a fair range of the needs of many amatuer naturalists though if you want to study the more minute structures such as mushroom spores, or the smaller pondlife, a microscope capable of 1000x magnification is needed. I have a (sub-£200) Westbury SP2 microscope which I've found to be thoroughly adequate for all my needs (the only minor drawback, for those in-the-know about such things, is I'm not certain this particular scope has the option to be equipped for 'dark field' operation, though this is a 'luxury' rather than a 'staple'). For anyone considering making a purchase, I have always been very satisfied with the service from Brunel Microscopes Ltd (I am unconnected with the company, and have received no payments for plugging them here!).

To set about identifying my fly I turned first to "A Key to the families of British Diptera" by D.M.. Unwin, available free here. This is designed specifically with the amateur in mind, being copiously illustrated to explain any technical terms. There are more than 80 families of British fly. The fact that my fly has long, thread-like, multi-segmented antennae immediately rules out more than 5o of these however, and places my fly in the nematocera, a sub-order of around 30 families. To distinguish between these its necessary, in part, to carefully examine your fly's wing. In my last posting on a crane fly I discussed the prehistoric origins of fly wings and the so-called 'Comstock-Needham' code for labelling up their veins. I'll not repeat this here and simply point out that I've labelled up the wing veins in photo 1.

With the wings of my fly in view, the key above pretty quickly bought me to a choice of my gnat being in one of two families: the Sciaridae or the Mycetophilidae. The 'decider' was the eyes. Photo 2 (taken from above looking directly down onto the antennae) shows my fly's 'left' and 'right' eyes, though this is a rather arbitrary choice of words since in fact the eyes are joined together to form one continuous band above the antennae. If ever you wanted an example of how 'alien' is the world of insects' senses, surely having eyes that join on top of you're head is one! Anyway, this 'eye bridge' decides against my fly being in the Mycetophildae and makes it a member of the Sciaridae. In searching for information on sciarid flies I came across two useful websites, the first dedicated to Sciariod flies, and the second, a list of free, online keys to different diptera.

The Sciarid flies are sometimes called 'fungus gnats', mushrooms being the larval food for some species. Mushrooms are not the only food however, and species have been reported emerging from a wide variety of substances from dead animals to birds' nests. Perhaps the most amazing thing I learnt about Sciarids in a short time searching is that the larvae of some occasionally undergo mass movements, thousands of them marching in columns several centimetres wide and metres long. I found an online paper reporting one such movement here [1]. It seems no one knows why they do this.

So far so good! Unfortunately, whilst identifying a fly to family level (Sciaridae in this case) is generally tractable, getting much further can be decidedly tricky. The first problem is that there are a lot of families of fly and finding a text-book or key that deals with yours can be difficult or indeed impossible. As luck would have it however, having become interested in flies and having something of a passion for natural history books, last summer I treated myself to some of the Handbooks for the Identification of British Insects from the Royal Entomological Society, amongst them Sciarid Flies by P. Freeman.

The book starts a little ominously:

[Sciard] taxonomy has always presented problems [...] the student has always been faced with a mass of similar looking species which he has been unable to group adequately.

Fortunately Freeman's book provides a detailed guide to identification, covering about half (according to this paper [2], as of 2005 there were 263 species of British Sciaridae in total) the British species across 18 genera.

So how did I get on sifting through the 18 genera of Sciaridae in Dr. Freeman's key? Well, On the basis of wing-vein shape and length, I was able to rule out 4 of the 18 genera; There was no sign of largish hairs ('macrotrichia') on my fly's wing veins, though there were tiny, downy hairs ( 'microtrichia'). This rules out another 5 genera; My fly has tiny spurs on its leg tibia (see photo 1). These are not 'distrinctly longer than the width of the tibia', ruling out the genus Corynoptera. After a little further work I was down to a choice between the genus Bradysia and the genus Lycoriella...and...I dropped my fly on the floor and lost it!!! On the basis of a couple of half-examined features, and the fact that Bradysia is the larger, more common genus, I'm going for Bradysia. But it all goes to show - you can't win 'em all!

[1] C. T. Brues,
A Migrating Army of Sciarid Larvae in the Philippines, Psyche 58:73-76, 1951.

[2] Zoological Journal of the Linnean Society, 2006,146, 1–147. The sciarid fauna of the British Isles (Diptera: Sciaridae), including descriptions of six new species Frank Menzel, Jane E. Smith and Peter J. Chandler

Monday, December 20, 2010

A crane fly Limonia nebeculosa

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

My garden, along with the rest of the UK, is currently buried beneath a thick blanket of snow. Aside from a collection of tits on my bird feeder there's little sign of life. For this posting therefore, I'm falling back to a photo of a crane fly I took in summer (photo 1. Click on photo's to enlarge). Dozens of them swarmed out from amongst some garden ivy I happened to disturb at the time.

I know almost nothing about flies (diptera). Along with beetles, ichneumon wasps and various other orders of insect however, they strike me as offering rather "good value" to any amateur naturalist keen to make a genuine contribution to science since a) there are very large numbers of them (15,000 species of fly in Europe alone) b) they can display a rich and complex behaviour (see my posting on P. nobilitatus for example) and c) for countless species almost nothing is known. Take hoverflies for example. After hundreds of years of intense study by armies of naturalists there can be few countries in the world whose natural history has been so well catalogued as Britain's. Further, there are few flies as conspicuous as hoverflies. Yet even for these, a staggering 40% of the larvae of the 265 British hoverfly species of are simply unknown. In the U.S. its 93%. (This, at least, was the situation persisting in 1993 when my copy of 'Colour Guide to Hoverfly Larvae' (G.E.Rotheray) was published). Anyway, we're not here to discuss hoverflies. On to the star of today's show...

What makes a crane fly a crane fly? Well, firstly flies (=the order diptera) are separated from other insects by the presence of two vestigial wings called halteres. I've ringed these in photo 2. Next, the order diptera is separated into two sub-orders of flies called the nematocera and the brachycera. The split is based on the structure of the antennae - the nematocera all have long, thread-like antennae with more than five segments. You can see this in photo 3. The sub-order nematocera gets further subdivided into more than 70 families of fly, the crane flies amongst them. If you want a fuller flavour of how these families are separated, the redoubtable Field Studies Council has made a key to the families of fly by D.M. Unwin freely available here.

It used to be that all crane flies were clumped together in one family called the Tipulidae. At some point however it was decided to split this family into four, the Tipulidae, Pediciidae, Limoniidae and the Cylindrotomidae. I read on the (searchable) Catalog of the Craneflies of the World that worldwide there are more than 10,000 species of Limoniidae, 4000 Tipulidae nearly 500 Pediciidea and 70-odd Cylindrotomidae. Separating these families is a tricky job. To complicate matters further, recent DNA studies [2] are casting doubt on the very existence of the Limoniidae as a family.

The whole thing is rather confusing for the amateur (=me!) and for a long time whilst preparing this posting I despaired of being able to identify my crane fly. Fortunately, rescue was at hand in the form of an excellent set of test keys from Alan Stubbs I found on the Dipterists Forum website.

Before discussing these keys I need say something about how dipterists characterise the wings of flies: An influential theory, originally due to Comstock and Needham in the 1890's, is that way back in prehistory, a first primeval insect wing evolved. Exactly how this first wing appeared is still uncertain but a current theory [1] is that it evolved from the multi-branched external gills seen on the larvae of some aquatic insects such as mayflies. The veins in insect wings are hypothesised to be modifications of these gill 'tubes' (trachea). Anyway, assuming the existence of this ancestral wing, Comstock and Needham named the veins in it the Costa (C), the Radius (R), the Media (M), the Cubitus (Cu) and the Anal veins (A). As these veins fanned out through the ancestral wing they forked. So, for example, the radius vein, R, is supposed to have forked into five sub-veins called (logically enough) R1 to R5. No modern fly has retained all the veins of the ancestral wing, over millenia evolution has caused different families of fly to lose different veins. Which veins a fly has retained however is a very important clue to its identification.

Photo 4 shows the wing of my crane fly labelled up with the help of Alan Stubbs' keys above according to the Comstock Needham system.

There was one more piece of information I needed, namely whether my crane fly's palps (=little facial apendages) were long or short. Photo 5 shows they're short.

Armed with this information I was finally able to identify my cranefly as Limonia nebeculosa. Final 'clinchers' were the presence of 3-coloured bands on my fly's femurs (enlarge to see these in photo 1) and the sort of smudgy 'hoop' on the wing I've delineated with the dashed white line in photo 4.

Today's posting was a bit technical in places but I am pleased to have identified my first fly to species level. Only another 250,000 to go!


[1] Averof M., Cohen S.M., Nature 385, 627-630, 1997 Evolutionary origin of insect wings from ancestral gills.

[2] Matthew J., Phylogenetic synthesis of morphological and molecular data reveals new insights into the higher-level classification of Tipuloidea (Diptera), Systematic Entomology (2010), DOI: 10.1111/j.1365-3113.2010.00524.x

Saturday, December 11, 2010

A lichen Malanelia subaurifera

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

Photo 1 shows a lichen growing, amongst a number of similar patches, on a wooden bird table in my garden.

I am very far from being an expert on lichen identification but in the course of doing this blog over several years I have picked up a few tricks. One is to examine your lichen through a hand lens for any characteristic surface lumps on bumps. Some lichen species become decorated with powdery granules called soralia. Others with tiny sausage shaped protuberances called isidia. For my lichen, the latter are present in abundance as can be seen in the close-up Photo 2 (click on photos to enlarge).

Another trick to help with lichen identification is to check the under surface. In photo 2 I have peeled back a small section to reveal a black underside with a covering of tiny, root-like hairs. In the jargon, these are known as rhizines. Not all lichens have them. They are not roots in the traditional sense, since they do not function to suck-up water as do the roots of plants. Rather their job seems to be to help anchor lichens to surfaces.

Armed with the features above and my trusty copy of Lichens (Dobson, Richmond Publishing) I'm confident to identify my lichen as Melanelia (Parmelia) subaurifera. The book suggests a final test: gently rubbing the surface should leave a pale yellow-white abrasion. Photo 4 shows this.

I am fond of lichens and so was very pleased when someone recently made me a present of the new edition of Lichen Biology (Ed. Thomas H Nash III, publ. Cambridge). This book is primarily aimed at professionals and I don't pretend to have followed some of the very detailed sections on e.g. lichen biochemistry, but I was able to follow others and came away with a new respect for the intricacy with which nature adapts these little creatures to their environment. Take for example the construction of the little air-filled spaces often found inside the bodies of lichens:

Under a microscope a lichen is revealed to be a mass of long, spaghetti-like fungal cells ('hyphae'), mixed-through with a sprinkling of green, single-celled algae or sometimes cyanobacteria. (The fungus carries out various tasks such as water storage. The algae or cyanbacteria do what no fungus can: photosynthesise food from sunlight). In considering this description however it would be wrong to picture things as a random tangle of fungal threads and algal cells. Photo 5 shows a lichen cross section I made and discussed some time ago (here) and reveals that things are far from random. Of particular relevance for today's posting is the layer known as the medulla that contains a lot of air-filled voids (see the region of the box in photo 5 for example). What is the purpose of these voids? The answer of course is that algae, like all plants, 'feed' (via photosynthesis) on a diet of sunlight and gaseous carbon dioxide. This is the key to understanding the voids: they are present to allow the flow of gaseous CO2 gas to the algae.

So far so good, but possibly it might occur to you to wonder what happens when it rains?! Do these voids fill up with water and in so-doing stifle CO2 flow, and hence photosynthesis, in the lichen? As I learnt from the book above Nature, of course, has an answer. In one chapter, a remarkable photograph taken by Rosmarie Honeggar with an electron microscope reveals how the fungal threads in the medulla carefully coat themselves and their precious cargo of algal cells in a minuscule layer of water-repellent proteins. This remarkable water repellent 'jacket' prevents the medulla from becoming saturated with water and so maintains the algae in a gaseous environment conducive to photosynthesis.

The water-repelling proteins the fungal hyphae secrete are known as hydrophobins and their discussion would make a lengthy posting in its own right. They were unknown to science until the 1990's when they were discovered by Wessel and co-workers in a fungus called Schizophyllum commune. Since their discovery these remarkable molecules have turned out to be widespread amongst fungi, with fungi using them in a variety of ingenious ways to 'manipulate' the surface tension of watery environments. For example, in order to help their spores get airborne, some plant-infecting fungi coat their spores in hydrophobins so as to prevent them becoming trapped or stuck together by thin films of water. Hydrophobins also help the infectious spores stick to the waxy, water-repellent leaves of targeted host plants. You can find a short introduction and further references on hydrophobins in lichens here ( P.S. Dyer, New Phytologist (2002) 154 : 1–4).

So there you have it! Minuscule, air-filled voids in a wafer-thin lichen...but take a closer look and as so often in natural history, one finds a hitherto unimagined world of subtlety and sophistication.

Saturday, December 4, 2010

Greater Plantain Plantago major

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

Taken in August, photo 1 shows a specimen of the weed Greater Plantain (Plantago major) growing on my lawn. This plant is very common in the UK and likely to be encountered on any patch of rough wasteland (= my lawn!).

For such a common plant I have found relatively few freely available papers dealing with Greater Plantain on the web. There are a number (such as here and here) that deal with its medicinal properties. Plantago major appears to have a long list of antibacterial, antifungal and antitumeral properties and has even been recommended to treat the bites of rapid dogs! Amongst the interesting snippets I picked up from skimming the paper by Velaso-Lezama [1] is that Greater Plantain is today used as a medicinal tonic in Mexico having been originally introduced there by the Spanish conquistadors.

A number of species of Plantain grow in the UK including Ribwort- and Buck's Horn- , both of which have narrower ('lanceolate') leaves than Greater Plantain. Also Hoary Plantain (Plantago media) which as the name implies differs from Greater Plantain in having greyish down on the leaves. That at least is how things are set out in my copy of The Wild Flower Key (F. Rose, publ. Warne). If however, the Plantago media above is one and the same as the Plantago intermedia described in this paper [2] by El-Bakatoucshi, then these authors cast doubt on whether major and intermedia are sufficiently distinct to be regarded as separate (sub) species.

In skimming the paper above by El-Bakatoucshi , a word I came across that was new for me was protogynous (in context: "Plantago major is protogynous"). A little research and I now understand what this means. I'll share it here for interested readers: Firstly one has to recall that for many plants, the flower is typically neither male nor female. Rather the same flower combines male pollen producing parts (the anthers) and a female reproductive part (the stigma). This gives plants an issue of how to avoid self-fertilisation (i.e. self pollination). Plants have come up with a variety of solutions including i) Ignore the problem (= allow self pollination) ii) Separate your line into two, so that some plants carry only male and others only female parts (these are the so-called dioescious plants - from the Greek "two houses" . Our old friend the stinging nettle is an example) iii) Develop some "chemical / structural" approach that avoids self pollination. I wrote about a classic example when I discussed the two types of primrose, 'pin' and 'thrum' iv) Separate the time at which the male and female parts of a flower are active / receptive. This latter method ('iv') is protogyny and is the technique adopted by Greater Plantain. The female stigmas of Greater Plantain flower are protruded 1-3 days before pollen is produced and in this way the chances of self pollination are reduced. Another of those small but elegant behaviours Mother Nature has carrying on all around us.

[1] Effect of Plantago major on cell proliferation in vitro R. Velasco-Lezama, Journal of Ethnopharmacology 103 (2006) 36–42

[2] Introgression between Plantago major L. subspecies major and
subspecies intermedia (Gilib.) Lange. in a British population, R. El-Bakatoushi , Watsonia 26: 373-379 (2007)