A lichen Aspicilia contorta

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

Returning to the iron manhole cover I discussed in my last posting, photo 1 shows yet another lichen eking out a living on the metal surface. From my copy of Lichens (F. Dobson, Richmond Publishing) I'm fairly confident the lichen here is Aspicilia contorta.

The little 'volcanoes' I've marked in the picture are the lichen's spore producing fruits (apothecia). If you're trying to identify a species of a lichen it's worth knowing that apothecia come in different 'flavours', in particular lecideine and lecanorine apothecia. This is well covered in the text books, but I wasn't able to readily locate a picture on the web so I've drawn one myself (I'm no botanical illustrator as you can see!). The difference is in the margin of the fruit body: The margins of lecanorine lichen apothecia tend to be the same colour as the main underlying lichen body (thallus) and contain algae. By contrst, the margins of fruits of lecideine lichens tend to appear distinct from the thallus and do not contain algae. The latter are often black (the books sometimes refer to the margin being 'carbonised'. I don't know whether this is just poor terminology or whether the lichen really does manufacture something akin to raw carbon in the margin. Anyone?).

From the description above it will be clear Aspicilia contorta is a lecanorine lichen.

Actually, my efforts to track down a description of all this on web led me to encounter a fair amount of technical jargon surrounding apothecia that had me quite confused at first. To save any fellow interested amateurs out there the trouble of going through the same, drawing two and the description below summarises the understanding I managed to pick up.

As I'd understood from my previous experiments slicing up apothecia, lichen fuits comprise an array of asci (= little tubes filled with spores). Photo 2 shows a single ascus I managed to separate from an apothecium I took from my garden A. contorta. As shown in drawing 2, the asci come sandwiched amidts a mass of upright fungal threads ('hyphae') known as paraphyses. The specialist textbooks often include pictures of these paraphyses, as they too can help in identifying the species of a lichen.

The fact that the asci are neatly arranged in an upright position is of course, no accident. It's important to the reproductive success of the lichen that when spores exit an ascus, they do so into the open air. There would clearly be no point in having the asci oriented haphardly and liberting a substantial proportion of their spores into back into the walls of the apothecium from where they've arisen in the first place. Of course, this only explains why the asci stand upright, it doesn't explain how they know which way is 'up'. I was fascinated to learn recently however (from a copy of the classic Spore Discharge in Landplants (Ingold) that I was lucky enough to find in a secondhand bookshop) that many cup fungi are phototropic (= sensitive to the direction of daylight), and use this to beneficially orient themselves. The book describes this for various cup-fungi, and I assume it is also the mechanism used by lichens, though strictly, I haven't come across a reference to confirm this (anyone?).

The asci + paraphyses are arranged on a thin layer known as the hypothecium. This comprises a mass of dikaryotic fungal cells, each containing two DNA nuclei. By a complex process of chromosome divison (mitosis) these cells eventually form (single nucleus-) spores. The whole business of sexual reproduction in lichens is complex and there is probably a lot left to discover. The pdf document here has some details.

The outer part of the fruit (technically termed the excipulum) comprises a mass of single-DNA-nucleus (haploid) fungal cells.

So now you know!

Today's has been a rather technical posting and perhaps marks a suitable point to leave my garden's lichens for a while (though I have yet to exhaust them). Outside the first signs of Spring are here: The volume of birdsong is increasing as the breeding season approaches and today on a country walk I spotted my first ladybird of the year (despite Oxfordshire still suffering regular frosts at night), all of which suggests I will not have to look too hard for new signs of life in my garden. Until next time...

A lichen Lecanora dispersa

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

I have a manhole cover in my garden. (Try to contain your excitement at hearing this news dear reader!) This may seem an unpromising place to search for life, but a closer look reveals a host of those most enterprising (in terms of the habitats they are willing to conquer) of creatures - the lichens.

Zooming in, photo 1 (click on photos to enlarge) reveals at least two species: The yellow lichen (which looks like our old friend Caloplaca citrina - though I've not taken time to carefully check this) and a second species with numerous white, frosted fruits ('apothecia').

A little time spent with my trusty copy of Lichens (Frank Dobson, Richmond Publishing) and browsing some similar images on the internet, and I'm tolerably confident the latter is the lichen Lecanora dispersa.

There are at least 20 British species of Lecanora lichen. Dobson describes L.dispersa as 'very common and found even in the centres of cities'. It will grow on a variety of basic substrates including bark, stone, iron and leather.

Photo 3 shows a magnified view of the apothecia, with their white, wrinkled rims.

For photo 4 I took one apothecium and made a squash between a microscope slide and a coverslip. As I've discussed previously, lichens are a partnership between fungi and algae. The small green, algal cells are clearly seen in photo 4. That algae can be present throughout a lichen's cup-shaped apothecia was a new discovery for me - I'd hitherto only associated them with the non-fruit parts of a lichen.

The main purpose of a lichen's apothecia is to act as surfaces from which to liberate numerous reproductive spores. I've talked about this before, but I was not previously in a position to complement my descriptions with photographs. Recently however, I've been lucky enough to come into possession of a Cambridge rocking microtome. For those unfamiliar, this is a device for taking extremely thin (~few microns) slices of a specimen, which can then be viewed under a microscope. Actually things are not entirely straightforward, since, in order to avoid said slice ripping and disintegrating as it's cut, it's necessary to first provide support to the cellular structure of the sample by embedding the whole thing in a block of wax. The recipe for doing this is a little involved: Starting from pure water, you pass the sample through half-a- dozen water+alcohol baths. The baths are arranged so that the alcohol concentration steadily increases until finally your sample is left sitting in pure alcohol, the water in the sample's cells having, by then, been replaced with alcohol. Next, you substitute the alcohol for the solvent toluene (a solvent of wax) before dropping it into a bath of molten paraffin wax and leaving for several hours. Finally, you pour the wax+sample into a mould and leave to cool. (In fact, there are still futher steps that finesse this process - but you get the general idea! Should you wish to try it yourself the best guide I've found is the booklet Practical Microscopy (Eric Marson, Northern Biological Supplies) and/or you could join one of the hobbyist microscopical societies such as the redoubtable Postal Microscopical Society.)

Photos 5 and 6 show my rocking microtome. The blue handled blade is the extremely sharp sectioning razor. The white object is the wax-block-embedded sample. Pulling the lever at the rear of the microtome (photo 5) raises the sample and releasing (photo 6) forces it down onto the blade shaving off a wafer thin slice and simultaneously ratcheting the sample forward ready to take the next.

And the consequence of all this labor?... Photo 7 shows a cross section through a lichen apothecium. Strictly, for this posting it ought to be that of L.dispersa, but working on the principle 'walk before you can run!' I instead sectioned a sample of our old friend X.parietina from my apple tree, since the latter has large apoethecia and a robust surrounding thallus (= 'body'). I've labelled up photo 7 (click to enlarge) and you can clearly see that the apothecium surface (technically termed the hymenium) comprises an assemblage of sausage-shaped 'asci' packed full of spores.

One thing puzzles me: I have not seen the granular bodies I see here labelled up in the handful of books I have on lichen. Possibly these are air bubbles. They turned up very frequently in my samples however and I don't believe they are. Can anyone comment?

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!

Comma butterfly Polygonia c-album

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

January is seeing heavy snow falls in the UK and as I write there is more than a foot of snow in my garden. To remind us of those balmy summer afternoons during these dark winter days therefore, a picture of a butterfly on the buddleia bush I've blogged previously.

The unusual shape of my butterfly - unique amongst British species - leaves no room for mistaking it as anything other than The Comma (Polygonia c-album).

The species name c-album was a new one for me (I'd not come across a hyphenated Latin name before). The Latin album or alba generally means you should look for some white feature on your animal or plant. All is revealed when you learn that the butterfly carries two distinctive white letter-c's (or white "commas" - if you prefer the English common name) on the lower face of its wings. Unfortunately I don't have a photo but you can find one here.

I read here that male Commas are territorial. They take up residence on a particular leaf or somesuch, ready to chase after anything that flutters-by in the hope it may be a passing female, returning afterwards to the same leaf. I've written previously about the inspirational studies of the great naturalist Niko Tinbergen into the subtle behaviour of butterflies in such circumstances.

In the early 19th century Commas were rare in Britain (see here) possibly for reasons connected with an increase in the practise of burning of hops (a foodstuff of the caterpillars) at the time (see here). Since then however, numbers have grown to the point where the Comma is today relatively common throughout Britain. The caterpillars are striking (see photo here), with markings that camouflage them as birds droppings.

I have frequently remarked (to the point at which I fear I may be becoming a bore on the subject!) that amongst my greatest pleasures in writing this blog has been the discovery that almost any life form I come across, no matter how seemingly commonplace, will turn out to have some unusual and fascinating facet to its lifestyle or behaviour. Take the ability of the Peacock butterfly to emit sounds to startle predators, or the high latitude melanism exhibited by Hebrew Character moths. The Comma is no exception, possessing as it does a somewhat unusual breeding cycle: Adult Comma's emerge from hibernation in March. Eggs are laid, and caterpillars appear from the end of April through to mid-June. It turns out that Comma caterpillars show a peculiar sensitivity to day length. Firstly, it will be obvious that caterpillars appearing early in the season will experience a day-length that is increasing from day-to-day whilst those hatching later experience a decreasing day-length. After a period of growth the caterpillars pupate. When the adult butterflies emerge, it's found that those emerging from the pupae of 'decreasing day-length' caterpillars have dark undersides. These enter hibernation shortly afterwards, to re-emerge in Spring and repeat the cycle. By contrast, adult butteflies from earlier (=increasing-day length) caterpillars are lighter-underwinged and, rather than entering hibernation, go on to breed a second generation of adults before winter arrives. By tracking day-length in this fasion, the species gives itself an improved chance of arriving at winter with a good sized population of adult Commas.

All of this was first worked out by one Emma Hutchinson (1820-1906), who sounds to have been a remarakable lady, being a Herefordshire vicar's wife and 'renowned breeder' of butterflies and moths. There's a nice article about her by D. Jackson in this online edition of the magazine (entitled, appropriately enough, The Comma) of the West Midlands branch of Butterfly Conservation.

Along with hops, British Comma caterpillars will eat nettles. Interestingly, Swedish Commas are far less fussy, being known to feed on plants from seven different plant families. To the professionals this raises intruiging questions about how such dietary variation might be encoded within a species DNA, how it is inherited down the generations, and the evolutionary impacts of such a variation within the one species. P. c-album has been much studied in this regard. A paper by Nylin et.al. (Biol. J. Linnean Soc. 2005, 84, 755) available online here is an example, and explains that dietary prefence in the Comma is encoded on the X-chromosome of the male butterflies.

Finally, my searches led me to an intriguing comment in a paper by Vanhoutte et.al. (J. of. Neuroscience Methods, 2003, 131, p195). The paper is rather technical and I haven't taken the time to follow the details, but roughly the authors set out to study the optical properties of the eyes of various butterflies. As everyone knows, insects have compound eyes made up of hundreds of identical ommatidia (the little hexagonal facets that tile together to form the eye)...

... "identical" that is, until you read in the introduction to the paper above that "recent research has shown that the ommatidia of butterfly eyes can be highly heterogeneous " (=variable)...

...except that P. c-album itself has rather homogeous (=non-variable) ommatidia!

All of which suggests there is more to butterfly eyes than meets the eye. Anticipating future butterfly postings, I've not gone much further into exploring this topic at present, but the few quick searches I've done suggest this is very much the case, with butterflies appearing to have a superiority and variety to their 'apparatus' for colour vision unique amongst insects (there's a review article by Frientiu et.al. here).

And amidst all this talk of fluttering butterflies in summer gardens, what of my garden right now? Answer: -5'C and falling!

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.

Fieldfare Turdus pilaris

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

Happy Christmas!

And what better way to enjoy the day than with a photo of one of my favourite visitors to the British garden: the Fieldfare (Turdus pilaris). Photos 1 and 2 show rear and front views (captured using my home-made camera trap incidentally).

I have an apple tree in my garden, which, besides providing a home for various lichens and mosses (not to mention a resting post for beeflies!) yields a bumper crop of cooking apples. So many in fact that that I have given up trying to collect them all and lots are left to lie on my lawn where they fall. They may look a bit untidy but this is more than made up for by the large numbers of Blackbirds, Fieldfares, Song Thrushes and other birds they attract come winter. In my garden, it is not unusual to find fifty birds at a time feeding upon them .

At 26cm in length and 100g, Fieldfares are a little larger and stockier than Song Thrushes (the BTO site has a host of biometric data). They eat invertebrates and berries (and apples!).
Fieldfares are not really resident in Britain. I say 'not really' since, as I learn from my copy of the RSPB Handbook (Holden and Cleeves) in fact a first British breeding pair was recorded here in the Orkney Isles in 1967. Over subsequent decades the number climbed to a peak of 13, but has since fallen back to less than five pairs a year. Of the population of one million individuals in Britain and Ireland, the overwhelming number are winter migrants, arriving here from late October from Scandinavia and Northern Russia.

Attempting to learn something further about Fieldfares I did a quick internet search and came across an interesting online paper by O. Hogstadt Nest Defence Strategies in the Fieldfare (Ardea 92(1), 79-84) in which the author reports studies of the response of nesting Fieldfares to effigies of crows and stoats - common egg predators of the Fieldfare. The Fieldfare's under study showed a distinct and rather well optimised reaction to these two predators. With crows, the reaction was to try to deter the attackers by defecating on them. This makes sense as fecal matter would certainly be detrimental to the performance of a crow's feathers. With stoats however, the reaction of the Fieldfares was to silently slip away from the nest and delay their return - eminently sensible when faced with a predator that hunts mainly by smell and is an equal danger to eggs and adults alike.

To end why not a few lines of poetry. These from the Cornthwaite by the British poet, Norman Nicholson (1914-1987):

Granite and black pines, where the migrant fieldfare breeds
And the ungregarious, one-flowered cloudberry
Is commoner than the crowding bramble.

A mushroom Psathyrella lutensis

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

Photo 1 shows a small troop of mushrooms I found growing in some damp grass beneath my garden hedge.
From its general appearance my first thought was that these were a type of ink cap mushroom (see my previous posting here), but after watching them for a week there was no sign of any of the caps dissolving into an inky mess and it was clear further investigation would be needed.

The first thing to do when seeking to identify a mushroom is to take a spore print. This is extremely easy: place a cap, gills down, on any suitable surface, wait twenty minutes, remove, and hey presto - a spore print. That of my mushroom is shown in photo 2. Knowing spore colour (here, black) will typically allow you to rule out at least half the species in the average mushroom guide.

If you have a microscope it can also be valuable to ascertain spore shape and size. Mine were ovoid and around 12x6micron (photo 3).

Other features I noted for my mushroom were the the grooved (the technical term being striate) mostly brown cap, fading to white at the edge, and the 'flakey stem' (a.k.a. floccose stipe) in photo 1.

With these features in mind it was time to turn to the guide books. Unfortunately, such is the number of species of mushroom in Britain (more than 3000, with others, new to these shores, being recorded regularly) that no single guide book can cover them all. This proved the case for my mushroom. I failed to find it in the first three books I tried, the floccose stipe proving a rather troublesome feature, ruling out a number of otherwise similar small brown mushrooms in the books. It wasn't until I turned to my copy of Mushrooms and Toadstools (Cortecuisse and Duhem) that I found a picture of Psathyrella lutesnsis. All the features were there and I'm fairly confident in this indentification.

Cortecuisse describes P. lutensis as growing on damp ground (a fit with my location) and being scare-to-rare.

I have learnt in the course of writing this blog that almost any life form I come across will have some unique and curious aspect to its lifestyle (for example, its relationships with other creatures, its chemistry, or its means of reproduction). No doubt this is true of P.lutensis. Unfortunately my searches have failed to turn up any information about it whatsoever. Perhaps I have merely looked in the wrong places. On the other hand, so sporadic and fleeting may be its appearance that perhaps no one has ever studied my enigmatic little mushroom. If anyone knows more any more about it than merely its name, do please leave a comment.