West Cork Palaeoecology - the natural world around us, from past to present

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Introduction to the Blog Pages

These webpages are a series of blog posts that refer principally to my work on the palaeoecology of West Cork. As time progresses my focus of study will move to various sites across West Cork.

Palaeoecology is the ecology of the past, generally the distant past, as in ancient.

In reality of course it all connects seamlessly in a long unbroken timeline, so what we see today, is yesterday’s future and tomorrow’s past.

It is the traces that environments leave that can be used to get some understanding of what environments existed and what life was in them at any particular time, and if we can extract a whole series of these traces through time, then we can maybe see how landscapes and populations interact and change, and maybe understand why.

This photo shows a beach on the shore of Bantry Bay in which we can see the traces of at least 4 different environments, from different times, all lying together. The enormous 30m mound of boulder clay deposited under the 300m thick ice sheet from maybe 18,000 years ago; a woodland floor that grew in the valley after the ice but before the sea levels reached their present state (right inset), todays beach, and the sediments of interspersed grey mud and yellow silt from 300 million years ago when this area was an arid plain being washed by periodic floods (left inset).

Beach beach on Bantry Bay south shore

Beach beach on the southern shore of Bantry Bay.

Ecology deals with the living systems, organisms and the environment they inhabit, and the chemical and energy flows into and out of the system. Ecologists study these systems in the here and now, and sometimes over a period of time, but what is lacking is a long term picture of how the system behaves over a long period.

Palaeoecology can give just that, a long term picture of the ecosystem over long periods of time - hundreds or even thousands of years. Even, using geological remains, hundreds of millions of years. But palaeoecology generally lacks the facility to understand all the organisms and all aspects of the environments, because not all of these are preserved.

Thus the methods and principles of both ecology and palaeoecology are complementary, and each can be used to expand the scope of the other.

By combining knowledge and understanding of present day ecology, with the information gleaned from the sediments and fossil remains from the past, we can put together a picture of the environment at that place at a particular time. This can be combined with knowledge of more wide reaching situations, like global climate, changes in atmospheric constituents and so on, to fill in some details and build a more complete picture.

My personal interest is in discovering what was alive at those various periods, and what the environment was like at different times, with a focus on appreciating the variety and diversity of organisms.

When I see something in the landscape, I ask myself, and want to know, what it is, why is it there, how did it come to be, how long has it been there, what was there before it. I want to create a picture of that thing, place, or feature, as it was before. A large scale background picture can be created, either through research or examination or enquiry, based on clues and discoveries. Then using knowledge, appreciation, and understanding of the natural world, we can go a long way to filling in the details.

What is Palaeoecology?

Palaeoecology, as I have already said, is the ecology of the past; most usually the distant past. But palaeoecology can involve investigation into the ecology of some geological period long gone, hundreds of millions of years ago; or it may involve investigating the relatively recent, historic past. Like the remains of a pond from the early 1900’s.

The most direct way to delve into the ecology of the past is by examining sediment, and anything deposited in that sediment, for clues left by living organisms or events. Clues left by the action of the climate on the rocks, by living things living, and dying, and clues left in the sediment themselves as to how they formed, what from, and why.

The sediments most suited to such enquiries are those rich in organic matter, and in Ireland there are plenty of those. Bogs, mires, and lakes.

A lot of palaeoecological studies have been undertaken in areas of uplands, largely because those areas have been assumed to have been interfered with least by human action in the more recent past. Which is reasonable - fewer housing developments, less intensive agriculture, and little industry has traditionally been found in upland areas. They are generally harder to get to, more exposed to the elements, the ground is less fertile and so on. But of course, they are upland areas, and what are uplands now, have been uplands for a long time, certainly for as long as most palaeoecological studies will extend back. And we all know that the climate, flora, and fauna are all different up there. So to get a picture of what life and the environment was like down here, where humans have mostly lived for most of history, in the lowlands, we need to study the palaeoecology of lowland bogs, mires, and lakes.

So, why bogs, mires, and lakes? And what is the difference between a bog and a mire?

Bogs mires and lakes are all wet places, and if sediments remain wet oxygen is largely excluded which makes the sediment anoxic, i.e. deprived of oxygen. This reduces bacterial and microbial activity and so decomposition is reduced to a minimum. There is therefore a better chance of more organic remains being preserved. Additionally, because of this anoxic state, the sediments are high in organic matter, which makes them well suited to radiocarbon dating. So lakes, mires, and bogs contain lots of macro fossils, big enough to see, potentially of both plants and animals, and also microfossils of all sorts.

These environments, as well as being wet, are often acidic, which also reduces microbial action. Siliceous rocks, high in silica, like we have in West Cork,can also give rise to acidic mires. Limestone areas are generally more alkaline, and an added complication with limestone is the effect that the carbonate can have on radiocarbon dating - but we do not have to worry about that here in West Cork.

A bog is generally considered to be both largely populated by sphagnum mosses, and the water comes mostly from the atmosphere, as rain. Mires have a somewhat different flora, not based on sphagnum moss, and the water comes from the ground as well. This means there is more of a mineral component, which affects the nutritional value of the sediment. But of course there are extremes in both cases, and there are all the possibilities in between. A raised bog is a vast community of sphagnum moss that has grown upon itself, above the water table, retaining its own water and taking nutrient and moisture only from the atmosphere, whereas a minerogenic mire is best shown by a river swamp that expands out into a large flat wet area, ground water flowing in all the time and washing in minerals. So really the difference between a bog and a mire is that a bog is low in nutrients, lacking in mineral sediments and largely populated by moss; a mire is high in mineral nutrients, lower in mosses and based on, and interspersed with, influxes of mineral sediment.

Palaeoecology in West Cork

Ireland is a country that is well suited to palaeoecology.

In West Cork we have some lovely uplands, but we also have a lot of lowlands, and there are still a lot of small bogs and lakes. In a lot of cases the bogs and mires were too small to be commercially developed and so in most cases retain their sediments. They haven’t been dug for peat or turf.

In West Cork the geology is almost entirely siliceous, that is, made up from silica based rock, and so is potentially slightly acidic; as opposed to lime based rock, like limestone, containing lime (calcium carbonate), that would be alkali. Some rocks in West Cork have a slight calcareous element to them, but really there is only one small part of West Cork that has true limestone. An added complication with limestone is the effect that the carbonate can have on radiocarbon dating. Carbon from the limestone, released as the lime reacts with the slightly acidic rainwater, can alter the proportions of isotopes that are included by living organisms in their structure. In these cases the ratios of the different carbon isotopes do not reflect the atmospheric ratios, and although minute, this can affect the calculation and calibration of dates. But we do not have to worry about that here in West Cork.

Being a rural area the effects of past glacial action can still be quite easily seen. Indeed it can in most parts of Ireland, but again West Cork is special in that there was - it is thought - a separate ice sheet covering Cork and Kerry, which means a lot of the effects of glacial erosion and deposition are quite local. And also still quite fresh and visible.

(We need to be careful with the term glacial. It gives images of glaciers, rivers of ice moving ponderously down a valley. But a more realistic image should be of an ice sheet, a layer of ice maybe 200 or 300 or even 1000 metres thick, lying on top of, and moving across, the landscape, sometimes, but not always, following the topography. Also bear in mind that the sea level was quite a bit lower, 100m or more, so most of what we know as the coast now was five or even ten miles inland then.)

As mentioned in the introduction, palaeoecological analysis can also be employed on rocks, and this has been done for the sedimentary rocks that make up the foundation of West Cork. Geologists studying the area over the past 100 years have combined knowledge of similar rocks of similar ages at other locations, and the fossils they contain. The results do not seem to be widely known - and they should be.

The geological palaeoecology of West Cork is a fascinating subject, and deserving of a separate blog entry (see here).

Algae - possibly the most important set of organisms on the planet

Most of us are familiar with the concept of algae, principally as a green growth on puddles, lakes and ponds, on a damp wall, an abandoned car, damp rock or wood. Anywhere damp really. And that is exactly right. Algae prefers to live either where it is wet or where it is damp.

Algae used to be thought of as a member of the plant kingdom, but that has been revised now, for various reasons. Once we start looking in detail at the various types of algae, we can start to understand why that is.

There are several different types, or classes, of algae, and they are an important consideration in palaeoecology. Some, the diatoms, have skeletons, or frameworks, that persist through time and endure as fossils. Some will only live under certain very specific environmental conditions. And most of them are the basis of the interlinking foodweb by which most natural organisms are sustained. Most algae are autotrophic, that is to say they produce their own food in a similar way to plants, by photosynthesis. They use the energy from the light of the sun to manufacture sugar, which is an energy store, from water and carbon dioxide, producing oxygen as a waste product.

When we combine this fact of carbon fixation, oxygen production and sugar manufacture with the almost complete global distribution of algae anywhere where it is wet or damp across the globe, the fundamental importance of these organisms to life itself becomes more understandable. It is often quoted - because it is true - that the largest single organ of the human body is the skin. This is exactly paralleled by the covering of algae across the globe, making it the most important organism which is also fundamental to life.

Because algae requires light to photosynthesise, it is found where light can penetrate. Surfaces of wet and damp areas, including the soil, bogs and mires; the surfaces of the sediment lying at the bottom of lakes, ponds, rivers, streams, and the ocean, at depths where light can reach. Other damp areas such as damp rock faces, walls, tree trunks, leaves; even on ice, snow, animal fur, and birds feathers.

Algae are generally small individuals, microscopic, measured in hundredths of a millimetre, sometimes reaching some tenths of a millimetre in size, occaisionally larger. They reproduce both asexually and sexually, over quite short time periods. Some of them can move, either with a smooth gliding motion, or by the use of whip like tails, or brush like cilia. But no matter where they are, from the tropics to the poles, from the ocean to a mountain top, they are fixing carbon from the atmosphere, producing oxygen and making sugar.

Some of the algae encountered in palaeoecology are extremely important and widely used, like diatoms, single celled photosynthesising algae with frameworks made of silica; some less so, like the dual celled desmids; and some rarely occur in the fossil record except by very subtle signs, such as the green algae.

So whenever you think of biodiversity, make sure you put the algae, those microscopically small green producers upon which most of life exists, at the very top of the list. As is so often the case in nature, it is the things we know little about, or can’t see, or even don’t know exist, that are so very important.

Algae are just one constiuent of phytoplankton, the vegetative microscopic organisms that form the basis of the oceanic food web globally. See here for a short film that demonstrates how widepread and vital such microscopic organisms are.

Desmid Algae - immortal cells, or dual aged?

Desmids are a type of algae. The Desmidiales. It reminds me of a song - but that aside, these present us, with our narrow restricted view of life forms and the way that things should be, with another interesting conundrum.

Desmids can be recognised by the fact that these single celled organisms are generally formed of two symmetrical halves, connected in the middle.

Each half is known as a semicell, and each semicell contains a very large chloroplast by which it photosynthesises. The two semicells are joined in the middle by a very narrow isthmus where the cell's nucleus is to be found. Because the chloroplasts in the semicells are so large, the general appearance of a desmid is bright green. They stand out quite prominently when seen under the microscope. Indeed, they colour the waters of ponds and puddles, water tanks, drinking trucks, and lakes.

Desmids photosynthesise and are a lovely bright green. They are also beautiful shapes with a high degree of symmetry. They used to be regarded as part of the plant kingdom. And yet some of them are capable of movement, by either the use of cilia, hair like projections that enable a sort of swimming motion; or by flagellae, one or two long whips by which they ‘whip’ their way through the water. Hardly the behaviour of a typical plant.

A montage of various desmids from Three Lakes in West Cork

A montage of various desmids from Three Lakes in West Cork. Note the two parts to each of them. The eye shaped ones are the same as the triangles, just seen from a different angle. Spot the diatom that sneaked into the picture.

When the desmid wishes to reproduce, the two semicells split, each taking a small replicated nucleus with it. So one desmid formed of two semicells joined by a nucleus, becomes two separated single semicells each with a small nucleus. Once separated, the second semicell grows anew.

What this means is that each desmid is made up of two semicells - of different ages. So how do we determine the age of the single celled desmids? One half is older than the other, and yet a semicell is not a complete desmid. Or is it?

And if reproduction continues in this fashion, one semicell continues on down through the generations. Does that make it immortal? Well, longlived anyway, until it dies.

Brook, A. J. 1958. Desmids from the plankton of some Irish loughs. Proc.R.Irish Acad.,B.59, 71-91.

West, G. S., and Carter. N. 1923 British Desmidiaceae. V. London, Royal Society.

West, W., and West, G. S. 1905 British Desmidiaceae. II. London, Royal Society.

West, W., and West, G. S. 1906 A comparative study of the plankton of some Irish Lakes. Trans. Royal Irish Acad., 33, B,77.

West, W., and West, G. S. 1908 British Desmidiaceae. III. London, Royal Society.

Jobs, with no one to fill them. That’s loss of biodiversity

In Ireland today - and probably all across Western Europe as well - there are problem situations in the job market. There are jobs that it seems no one wants to do. Farmers are crying out for milkers, for drivers, and it seems that any job that requires hard work, long hours, and getting dirty, is not popular. People have got the idea that staying indoors, in the warm and dry and in a nice clean environment, is preferable. A better way to earn a living.

Let us hope this doesn’t get worse, and also that this doesn’t continue. Because if these businesses can’t get employees to do the work, the businesses could collapse. And if too many businesses collapse, the economy collapses. And if we take the whole idea to an extreme, that bodes very ill for all of us, whether involved in the job market, living in central Dublin, or rural West Cork.

This is a perfect parallel example of the need for high levels of biodiversity. Think of each ecological niche as a job opportunity, specifically a job for a certain set of special skills. And think of each organism as possessing a certain set of unique skills.

With high biodiversity, every job is filled by a skilled worker, and the whole system - the ‘economy’ - prospers. If the odd job, or odd set of workers fail, die out, get disrupted, the effect on the economy is slight and the hiccup is taken up by the rest of the workforce.

But the fewer skilled labourers there are, the more jobs there are that remain unfilled, and so holes appear in the job market, unfilled positions, businesses that cannot operate, functions that cannot be filled, services that cannot be provided.

At a certain point, the gaps become a serious problem, and the whole economy starts to suffer. And then if there is some slight disruption to the market, like a war in some distant country affecting the flow of produce, there are few workers who can step into the gap, make up the shortfall, fix the problem; or if temperatures rise or water supply drops, there are fewer organisms that can cope with the change, and fewer that can fill the gaps that arise. Eventually we are looking at the collapse of the system, with an inability to sustain itself to a degree that is even near useful.

High biodiversity, like a population of skilled, willing and variously experienced workers, gives a highly resilient and productive system. Resilience to change and disruption, and an ability to survive and continue.

Loss of biodiversity is like a population of unwilling, uncooperative, unskilled workers - it is vulnerable at best, disruptive at worst.

So for High Biodiversity - think Resilience - think Productive - think Survival.

I don’t think that is too strong a comparison.

Next time you think about getting the weedkiller, insecticide, fungicide, or mosskiller out - think of the labour market and what you are going to do to the economy. You are about to make some vacancies that cannot be filled.

It’s all Greek and Latin

Epitheca and hypotheca, the two parts of the diatom frustule, can be remembered by the fact that the epitheca, epi meaning above or upper (think epidermis, the upper layer of the skin), sits above and over the hypotheca - hypo meaning lower or below (as in hypodermic, below the skin). These two parts fit together like a box, with the epitheca acting as an overlapping lid that sits upon the hypotheca. The water in the surface layers of a lake are called the epilimnion, the deepest layers the hypolimnion. Limnic refers to lakes - see the entry below about Three Lakes.

The use of Greek or Latin words, the classical languages, in science has been cause for complaint by many people, most often students who find the new language terms a hurdle. But it is also seen as a barrier to the non-academics, a barrier that prevents them from even trying to understand what is being said or what has been written.

This is a great shame, and a failing of our school education system. These terms are not difficult, and in fact they are very logical. Indeed there are a lot of them that are incorporated into our everyday language and which we use without a second thought.

Maybe that is the secret. We should think more about the words we use.

But why do the sciences use so many of these Latin and Greek terms? The simple answer, and the most practical answer, is because they work so well at being additive, and embrace whole concepts in one single compound word. Things that in English - and possibly in other languages too, though I know German often incorporates nice long words that convey a whole sentence of meaning - but in English certainly, a sentence is instead required. As an example think about the word palaeoecology. Palaeo has the sense of past, mostly the ancient past, as in palaeolithic (including lithos which means rock or stone - so old stone age), palaeontology (incorporating onto meaning living being or creature, and logos meaning knowledge of - the study of ancient living things). Ecology incoporates the logos element as well as eco which is from the Greek for home, oikos - the study of our home, or the natural home of living things. Thus palaeoecology is the study of the natural home of living things in ancient times.

In addition to just extracting what the words mean, when added together they take on a specific and more complex meaning. Thus ecology is widely understood and is in reality a far more complex idea than just the study of the natural home of living things - it incorporates an understanding of the flows of energy and materials, the interactions between the environment and the living organisms, between the different organisms and relationships and fluctuations of all the populations. In fact the whole ecology of an area, however small, is so complex that it defies full understanding in all aspects.

The most basic Greek and Latin terms that are widely used in the sciences are not difficult. They have to be learned, but since so many are already incorporated into words in everyday use, the task is not that great.

There is the historical fact that Latin, and to a lesser extent Greek, was the language used by scholars and therefore enabled people from different cultures and languages to be able to communicate. It is still used in some cases in scientific papers particularly in cultures that use different letter systems - Chinese or Cyrillic for example.

Knowledge of these classical language terms would expand the vocabulary of modern English that is in use, and would also improve the ability to understand so much more. In fact it would also make the romance languages of French, Spanish and Italian less alien to English speakers.

A Floral Survey, Amoebae,and Bacteria

With palaeoecology being a study of past ecology, we have to decide at what point the past becomes the present. Or do we? In the case of the study at Three Lakes, I decided that the present is just the most recent part of the long timeline, and since I am looking at the fossil pollen and spores in the sediment, and using these to determine the vegetation at the many different times over the past 16,000 years, the vegetation at Three Lakes now is just the latest in that line.

So we undertook a floral survey (Fig 1).

Fig 1 - Surveying the lake margin flora

Fig 1 - Surveying the lake margin flora

The first one was done in June, on midsummer’s day in fact. But because different plants flower, seed, live, and die at different times throughout the year, we will probably do a similar survey every month of the year. Added to which there are so many habitat types it just isn’t possible to cover the area without an army of people. A small army. More about the floral survey will be forthcoming later.

I am also taking monthly diatom samples for the same reason - diatom populations rise and fall at different times of the year, and to compare my samples of fossils, that represent what got left behind and preserved, I need a full representative sample from today.

I was surprised, when I paddled in my canoe around to the south eastern wing of the lake, to find blobs of black slime floating like little black jelly icebergs, hanging down in the water. There was an accompanying petrol like sheen and a vile sulphurous smell (Fig 2). The water was warm to the touch following a very warm spring.

Fig 2 - Nasty stinky black effluent

Fig 2 - Nasty stinky black effluent

Under the microscope this black slime was not, as I had hoped, a diatom bloom, and all I found were a large number of large amoebae, between 50 and 800 microns across, which it seems are of the genus Pelomyxa (Fig 3) Also see here. Was it these amoebae causing some sort of anaerobic respiration? After contacting two experts in their fields, Wim van Egmond and Ferry Siemensma, both in Holland it seems that this phenomenon is not uncommon in freshwater lakes and ditches of the Netherlands. It was suggested by Ferry that a bloom of cyanobacteria (blue-green algae - but actually bacteria) on the bottom of the lake, amongst the low oxygen environment that Pelomyxa prefers, caused a generation of ?sulphurous? gas that caused rafts of sediment to float to the top; carrying poor oldPelomyxa with it.

Fig 3 - A selection of Pelomyxa amoebae

Fig 3 - A selection of Pelomyxa amoebae

But after a couple of days, when I looked at the sample again, it was infused by hundreds if not thousands of spirochaete bacteria, all wiggling like little corkscrews (Fig 3). At least, that is what I think they are. But they may be Spirilla bacteria, which are ‘helically curved rod-shaped cells’ (Brock Biology of Microorganisms 16th edition). I do not have the time to go down the bacteria route.

Fig 4 - ?Spirochaete bacteria?

Fig 4 - ?Spirochaete bacteria? Scale bar is 10 microns

Just to top it all off, it was just that part of the lake where I took a sample the previous month (May) of some shoreline sediment. Amongst the diatom community I found some strangely shaped diatoms that defied identification. Experts at the diatom group forum suggested they were teratological forms, that is, diatoms that have grown in deformed shapes (Fig 4). They are most likely of the genus Eunotia. Interestingly, what makes them deformed is likely some condition within the environment that results in aberrant growth. Might this be the action of blue-green algae proliferating? Or was the bloom caused by the same condition that caused Eunotia to deform?

Fig 5 - Various Teratological forms of Eunotia

Fig 5 - Various Teratological forms of Eunotia

We are inclined to immediately think of human causes for this 'pollution', but it might equally well be natural causes. There is only one inlet stream to the lake, running through a small number of pasture fields, as well as an inflowing connection from the western lake. These lakes are high up in the watershed and surrounded by either forestry with minimal disturbance, or non-intensively managed pasture. Natural events can have similar effects to human pollution, but it generally fits in with the ecology of the area. An example is just these anoxic and sulphic conditions that occur when large amounts of organic matter accumulate in a wet environment. In extreme, this is known as a euxinic environment, taking the name from the Black Sea, where such an environment occurs at depth, resulting in black mud rich in iron and sulphur. Temperature plays a big part as well, and interestingly when I visited 8 days later, after the weather had turned cool and it had rained, the black slimy rafts had all gone.

A lifetime of study on the occurrence of iron sulphide, also known, when crystalline, as pyrites, has been the work of David Rickard and his book “Pyrite: A Natural History of Fool's Gold” is full of surprises. Not least the fact that pyrites occurs almost everywhere where anoxic and sulphic respiration occurs, resulting in it being one of the most widely occurring minerals, albeit in microscopically small grains, on the planet - and often created by organic action.

Finally, a very in-depth study which yielded fascinating results was undertaken on Lake Vechten in Holland. The resulting paper detailed the variation in 10 different environmental parameters at different depths throughout a full year; temperature, pH, dissolved oxygen, dissolved organic carbon, sulphides, nitrates, sulphates, phosphates, ammonium, and chlorophyll A. The lack of inflow into Lake Vechten is similar to the Middle Lake which has only a small stream flowing in, but Vechten is up to 10m depth, whereas Middle Lake appears to be a constant 2.5 to 3m depth, so possibly the waters of Middle Lake do not get stratified to the same degree. There is room here for some fascinating studies.

See Diao M, Sinnige R, Kalbitz K, Huisman J and Muyzer G (2017) Succession of Bacterial Communities in a Seasonally Stratified Lake with an Anoxic and Sulfidic Hypolimnion. Frontiers in Microbiology. 8:2511. doi: 10.3389/fmicb.2017.02511

The Floral Survey at Three Lakes

Wet Willow Woodland with Royal Ferns

A very special lakeside wet willow woodland habitat with Royal fern understorey

The reasons for taking a floral survey as part of a palaeoecological study are three fold.

At the present time there are major concerns, world wide, but also specifically in Ireland, that biodiversity is being lost. This is happening at an alarming rate, and as described in other posts, there are several reasons for this. But a major part of understanding what has been, and is being, lost, is to find out what is there now, so biodiversity surveys are all the rage at the moment. Ireland has a specific organisation and website for understanding this - The National Biodiversity Data Centre - and data is being accepted from any genuine source - citizen science is coming into it’s own at last. The floral survey at Three Lakes will add in to this.

As a postscript to that first point there is also a scheme to register habitats across Ireland, and the original habitats defined by Fossitt (see here - pdf file) have since been replaced by a national vegetation classification ( see here - NBDC) which is managed by the National Biodiversity Data Centre. As well as determining the degree of biodiversity by surveying the vegetation, we will also be able to help define specific habitat types as we find them, and any variations that may be found.

Small selection of special plants

A small selection of plants from the various habitats within the Three lakes area

More specifically related to palaeoecology is the fact that having determined the vegetation that exists at this place today, we can make use of this to understand the vegetation of the past.

We shall be examining the pollen record from the top layers of the core, and we can make the assumption that the vegetation growing today is not so very different - because we believe the habitat types have not changed - from what grew here a hundred or two hundred years ago. So we can then relate the pollen preserved in the bog or lake sediment with the vegetation that was producing the pollen. Not all plants produce the same amount of pollen, and not all pollen is preserved, so looking at pollen does not give a complete picture. But maybe we can fill in the gaps by understanding what plants grow together, so finding pollen of one plant can indicate that another set of plants were probably also present. This will help to interpret the fossil record and build a picture of the vegetation from that time. An added implication of this aspect is that we shall also have to survey the vegetation of the surrounding area, the valley sides, back west towards the watershed, and eastward into the gorge. That way we can gain an understanding of how pollen from further afield ends up in the sediment we are examining.

The third use of the vegetation survey is simply to provide a final stage in the historical record of the changing plant communities over time. At Three Lakes the sediment covers the last 16,000 years, approximately, providing a record that goes back to the end of the Ice Age. In the intervening time the vegetation communities have built up through various changes in climate - a warming after the ice, a severe cooling for a thousand years or more at the Nahanagan Stadial (otherwise known as the Younger Dryas), and then, in the Holocene, a warming to above what used to be normal, then slight cooling. And of course we are now going into a rapidly warming period.

The record will continue into the future and we can assume there will be some quite severe changes. The past record may help us to understand these changes, not because they have happened before, but as part of a continuing process.

Floral Surveys, Mobile Phones and the Internet

While we are on the subject of floral or vegetation surveys, it might be worth mentioning the method that was used. Technology has many benefits, some of which are stunningly simple in concept - if not in implementation - like Google Maps and the facility whereby we can never get lost any more…

A central database of plant images - leaves, flowers, seeds and fruits, bark, and so on, for each species, along with botanical and local names as identifiers, is accessible via a smart phone. This application is called PlantNet, and is freely downloadable. By taking a photograph of the particular part of the particular plant the app checks the image taken with those on the database and suggests possible matches. Not only that but the GPS location of the particular point where the photo was taken is also recorded. Once a satisfactory identification has been made it can be shared onto the database, with the rest of the PlantNet community, where it will be checked and either verified or rejected.

PlantNet does not do all the work - the onus is on the user to verify the plant identification given the likely options that PlantNet offers. A book is still essential, and for Ireland Webbs Irish Flora is irreplaceable; or for a well illustrated book Collins Guide to the Wild Flowers of Britain and Ireland.

The location used by PlantNet appears to be based on mobile phone masts, and in Ireland this can mean the locations are a bit inaccurate. So it is not a bad idea to run another application while recording flora. A good one is the modern version of MyTracks, which is quite different to the original - and somewhat better. This app can run in the background and record every place the plant spotter goes.

Back at the office, or home, or lab, PlantNet can be accessed online and the identifications verified, and the dataset, complete with locations, downloaded in a format that can be imported to a mapping software.

Likewise, the route tracked by MyTracks and saved whilst out in the field can be downloaded from the phone, and also loaded into the mapping software.

You now have a graphically mapped set of data that shows the route taken and the plants identified.


Human Achievement

It does seem at times that the human race gets a bit of a bashing for all the doom laden destruction, industrialisation, money making schemes and greed that is going on.

We must not lose sight of the fact that so much that is not damaging, nor destructive, nor fuelled by greed or hatred, has been created by humans. It just seems right to acknowledge this occasionally.

The greatest achievement of the human race is artistic, and I have to mention this particular piece. A pinnacle of musical composition and orchestration. This performance is superb, showing the joy and companionship that can be generated by people playing great music, beautifully, together.

In addition, this piece demostrates the amazing technological simplicity achieved by the designers, creators, and builders of the violin family.

It all comes together in this performance. Even if the music is not to your taste, such incredible achievement cannot be denied.

Watch, listen, marvel

Spatial Analysis of Raths - or - Why Are They Where They Are?

One of the benefits of digital mapping is the ability to analyse the geographical distribution of features. This can apply to the combining of different layers in the maps, such as topography, geology and sediments, to get an idea of how they are related. And it can be used to great effect on man made features. In this regard an analysis of archaeological monuments in the countryside might throw up some interesting and otherwise hard to detect relationships. Such an exercise is being undertaken for the Raths in West Cork. The results will be presented on the Ringforts page of the WestCorkPalaeo website.

Raths on Drumlins south of Bantry Bay

A screen grab from a digital map of raths on drumlins on the southern shore of Bantry Bay

Analysis of elevation, aspect (which way the hillslope they are on is facing), and angle of the slope can all be quite simply considered. Also the distribution of Raths within townlands, the size of the townlands and the number of raths in them, and the intervisibility of the raths. All of these aspects can only make use of the information we have, so in the case of intervisibility - which rath is within view of which other raths - this will be on the basis of topography. Whether forestry or hedgerows at some time obstructed the view we cannot know. We also cannot know what degree of visibility, if indeed any, was required. In assessing intervisibility we have to make assumptions about the height of the observer (you can see further standing up that you can sitting down) and also the height of the feature being observed (how high was a rath? well, it wasn’t flat). A column of smoke will make a rath visible by rising 20 , 30, 40 metres into the sky above - is this a relevant consideration to hold?

We also do not know, and can only guess, at the considerations that are given to where raths were sited. Was the nearness of water a factor? Or the closeness to a relative in their rath? Did the quality of the ground - deep soil for the souterrain underneath the rath, rocky subcrops for a firm and non muddy base - make a difference? There are many possible factors.

So there are obvious problems in making these assessments, and many pitfalls that could be fallen into, all of which need to be borne in mind when undertaking spatial analyses. Giving consideration to raths of West Cork requires validation as well. The county boundary probably wasn’t in existence at the time, so when looking at regional groupings of raths, we need to try to understand the geographical groupings. Was it by peninsula, different ranges of hills and valleys, specific river drainage areas, areas of rock type or sediment type - like the difference between limestone and sandstone, or boulder clay and peat? There is an assumption that townlands probably date from the same period as raths, so is it relevant to assess the number of raths in each townland? We know that some townlands have been split, or newly created, as a result of relatively recent changes in land ownership, certainly long since the rath period.

Digital mapping does at least allow the examination of the landscape and it’s features to a level of detail not normally afforded by conventional maps, with the possibility of including calculated layers (such as an intervisibility network), and layers of data of disparate sources - geology, archaeology, environment, hydrology etc. Various ways of portraying the topography can be explored, such as contours at various intervals, and hillshading. The image above shows a group of raths on the southern shore of Bantry Bay just south of Whiddy Island. This is an area of drumlin hills - two drumlins can be seen ‘sliced open’ by coastal erosion on this part of the shore, at the western facing beaches. The red dots are raths, the white are souterrains (within the raths); red lines are roads and tracks, black lines are townland boundaries, contours are at 1m intervals. The yellow lines are the rath’s intervisibility network - by which one rath has line of sight to another, or not, according to the topography. Black patches are rock outcrops. An image of a larger area at smaller scale, with 5m contours, is shown below.

Raths on Drumlins south of Bantry Bay

A smaller scale screen grab from a digital map of raths on drumlins on the southern shore of Bantry Bay

Seeing this representation can raise all sorts of questions - why were the raths built on these drumlins? Why so close together? Did they therefore have smaller parcels of land? Were they even farmsteads?

I have yet to visit these raths to see them in the flesh which is, of course, the best and ultimate way to understand a feature within the context of the landscape.

Finally, while experimenting with visibility networks, what was visible from these raths situated on the drumlin tops? This third image shows the viewsheds of the drumlin raths; these raths are red, all other raths are purple. The shades of green signify visibility - to all intents and purposes we can say that the dark green areas are those that were not visible from our raths on the drumlin tops, all other shades are areas that were (and presumably still are) visible. The yellow lines are the lines of vision between raths, from the drumlin raths outwards. Visibility range has been extended to 10km.

Raths on Drumlins south of Bantry Bay

The areas of visibility of the drumlin raths on the southern shore of Bantry Bay

Visualising the The Tree of Life

Whilst talking about the wonders of Human Achievement in the arts and in technology, we do well to consider that so much that has been achieved is of such vastness in concept it is hard to visualise. Biodiversity is a very big thing to take in, despite the fact that the word is bandied around in the media these days with such freedom. I have tried to engender an appreciation of what biodiversity loss actually means to the world, and to us in the blog  Jobs, with no one to fill them. That’s loss of biodiversity. But what is biodiversity? How diverse is biodiversity? How deep does it go, how far, how complex is the web that life encompasses?

It is only now, within the last ten or fifteen years that we are really starting to appreciate how all-encompassing the concept is, and although some of the older generation were deeply worried at the levels of pollution, destruction and blindness that was being practised across the globe - from our own streets and hedgerows, to forests and fields, plains and deserts across the globe - that was damaging the very life that we rely on to keep the nature that we evolved with running smoothly, nobody listened and nothing was fixed. So now, in the wake of the climate crisis, these concerns are, at last, being brought to the fore, even though they often detract from the focus and urgency of the climate crisis itself and the immediate main causes. The fact remains that these are issues that should have been sorted decades ago. But it is only now they are being considered seriously. We could say better late than never...

Consider the achievements of such figures as Darwin and Wallace, swimming against the tide of religious belief, stepping outside the accepted norms of scientific thinking, and embracing concepts that were so vast in extent. They must have been truly staggered when the realisation hit them of what later became the theories of evolution and natural selection, and the vastness of time that was represented, the vastness and breadth of the development of species. Not just those in existence today, but all of those that evolved, developed, specialised, flourished, receded and then died out along the way. The ones that only remain to us as fossils, often as dismembered pieces of the whole organisms, sometimes microscopic remains petrified inside rocks, or maybe even just traces of their passage over or through wet sediment.

Thankfully technology can help us grasp some of these concepts in their depth, breadth, extent, and age. Consider a journey, starting from the very base - or top - of the evolutionary tree, the tree that we have constructed to help us see the interrelationships between organisms. How one developed from another, or how one evolved alongside another; how some developed down a side branch that became more predominant than the main branch it came from. It was not a simple linear process, and there were and are lots of dead ends. But think of the journey from the basic start to the eventual emergence of a complex organism like.... a dandelion. Do you have any idea how that journey would proceed?

Well, go to this website and in the search box type 'dandelion' and select the top one that is shown Tree of Life (opens in a separate tab). Notice that every leaf you pass is a separate species alive today (the vastness of extinct organisms is only just beginning to get incorporated into this software). Branches are where development, evolution, caused a split down two different routes.

When you arrive at your destination, you are looking down into the vastness of the diversity of dandelions. Just dandelions. Not all flowers, not just daisy types. Just dandelions. The global spread of dandelions.

Now type into the search box 'Taraxacum borovezum', select the one listed, and watch. The rest of this journey is through the many dandelions that have diversified to fill the many environmental niches they have encountered, and adjusted to, evolved to cope with, across the globe. When you get to the end, breathlessly, scroll back, retrace your steps, and see where the route took you, which plants, proto plants and prior organisms you visited along the way. Alternatively click on the compass icon in the bottom left, the top icon. You will be shown a list of the main classifications, and you can click on each one, and go there. If you do this, notice how the occurrence of 'Land Plants', 'Vascular Plants', 'Seed Plants' and 'Flowering Plants' occur close to each other. These were evolutionary developments that occurred relatively close together in time, and resulted in the spread of plants across the land which changed just about everything in the world at that time. From then on the diversification of green, vascular, seed plants on the land has been enormous. Just look at how many branches, twigs, shoots and finally, leaves, you pass through from 'Flowering Plants' onward. This is biodiversity.

Try some other species - try a moss, a non vascular plant, like Ectropothecium ichnotocladum. Yes. It doesn't roll off the tongue. Then come back to 'True Mosses' using the compass icon. About 17 thousand species, which hardly compares with the 400 thousand of flowering plants. Ferns (Polypodiopsida) and Clubmosses (Lycopodiopsida) likewise. And yet ferns and mosses, of primitive types, dominated the world until the vascular plants, the plants we are familiar with around us, evolved explosively. Then the world changed, And it is only for the good fortune that they did evolve, that we can live today. I will explore what that meant in my next blog - it is crucial to understanding how West Cork developed.

OneZoom is a fantastic piece of software for visualisation. Play with it. But remember. This was created by voluntary work, so there are some out there who wish to disseminate knowledge and understanding without the need for monetary payment in return. This is just an example of how technology can be of such enormous use and facility.

Soil 1 - The Failure to Understand Soil

The fifth IPCC report dated to 2013 includes a chapter that discusses biogeochemical carbon, that is, carbon that is involved in the processes in the soil, whether associated with plants, animals, fungi, and microbes, or with rocks, sediments, and ground water.

In other words, the soil and all that is in it, what it does, and how it behaves.

Scientific understanding of the organic content of soils since the late the 18th century, and so it is ill defined - there is no clear definition of what humus, or humic acids, or the process of humification, actually is. Which is a little bit shocking, since the global human population relies on the soil to grow our food, and to grow he food for the animals that provide us with food.

In palaeoecology when we examine organic sediment, like peat, or lakebed sediment, we have to process it to be able to get at the fossils, micro fossils, like pollen, spores, diatoms and so on. We can get rid of humus, in the form of humic acid and fulvic acid, by cancelling them out chemically with an alkali, sodium hydroxide or potassium hydroxide, and the humin fraction, the left over dark brown solid organic material that we don't want, then has to be dissolved using an oxidising agent, like a strong acid. That's about as close as we get to humus.

Humus, as an organic product, is essential for radiocarbon dating of sediments. Although we are now learning that humus is a constantly changing and dynamic set of chemicals, containing a lot of carbon, the original carbon held within these chemicals remains the same, for the purposes of dating, even though the compounds they are part of change. So radiocarbon dating is still valid, even though our understanding of humus is changing.

And it desperately needs to change.

We are told that it is essential to increase the humus content of the soil, beyond knowing that this means adding in organic matter that is in a process of active aerobic decomposition, it is not possible to define exactly what humus is, chemically. But your farm advisor, unless you are an organic farmer, won't advise increasing humus content of the soil, for one very good reason. The original concept of humus, how it forms - the process of humification - and what happens to it, defined it as a substance derived from organic matter that is a dark brown colour and remains in the soil. So on that basis there is clearly no point in adding more, and that is why the agricultural industry applies fertiliser, to add to the beneficial effect of the existing humus.

Except humus does not persist in the soil.

This of course is of great importance to all of us. The fertility of the soil is what grows our food, and although it all seems to have been working fine up to now, the failure to add organic matter to the soil is having several long term, global effects. So much so that the United Nations is concerned over the increasing Fertility Crisis that is creeping across the globe. See the report here. The decline of soil organic matter is the second most concerning threat to soil biodiversity; the first is human intensive exploitation. The organic matter in the soil is not just a chemical hotch-potch that helps crops grow, it is a complex mixture of organic materials at various stages of decomposition, and also mineral matter, which is part of a complex interaction between the microbes and organisms in the soil, the water in the ground, the gases in the air, the plants that grow, die, and decay, fungi, worms, bacteria... Global Soil Biodiversity Initiative. In fact the mass of microbial organisms in an acre of good topsoil is equivalent to the mass of two cows. For every acre. All year round. That is somewhere between 2 and 3 tonnes of microbes per acre. (If that seems hard to conceive, then just consider that every time 1 mm of rain falls on 1 acre, that is about 1/2 tonne of water falling from out of the sky.).

And so we come back to biodiversity and the benefits of a healthy soil. A soil with a thriving and diverse population of organisms has structure. It has drainage and aeration channels. It has roots of plants, rhizobia of fungi, burrows of worms and insects. Drainage is aided because of the many pathways into the soil that the water can take. Water retenetion is greater because of the many gaps and holes and inter particle gaps where it can reside. (Although those two statements appear contradictory, they are actually a good example of how the natural world creates systems that serve several, sometimes opposing, functions at the same time - see Ben-Noah, I. (2023), Air flow dynamics in wet soils: challenges and knowledge gaps, Eos, 104, . Published on 6 July 2023.). Stability of the soil against erosion is greater because of the organic molecules and ill defined substances that stick soil particles together, and the extensive root systems of healthy plants that bind the topsoil. And we can learn a lot about the benefits of these properties of a healthy high organic matter soil by looking at the environment when West Cork was forming.

About 380 million years ago the sediment that is now the bedrock in West Cork was being deposited in a vast sandy, muddy, silty, subsiding basin in a dry and sometimes arid and hot plain, between mountains to the north and the coast to the south. There were few plants, and those that there were, were small, rootless, stemless and leafless - they were like mosses and liverworts that we see today. And the amount of erosion and flooding that went on was enormous - West Cork lies over a sedimentary basin where over 6 km depth of sediment was deposited, the land surface sinking as the sediment washed in. Periodic floods saturated the land surface, swept in vast loads of sediment, silt and sand, and then it all slowly soaked away or dried out in the hot sun. Carbon dioxide levels were considerably higher than now. And this was all because there were no plants.

There was also no soil.

Soil 2 - How the Evolution of Plants Changed the World

Our world was created 4,500,000,000 years ago. Roughly. Four and a half billion, or four thousand and five hundred millions of years ago. An easy number to say but almost impossible to appreciate and understand. It is a mind bogglingly big number.

Equally staggering is the fact that as far as can be gathered from the fossil record, plants only really moved onto the land in a serious way just 350 million years ago. Which does seem like a long time ago. But if we consider that it was only from that point that soil bearing organic matter started to form across the globe, then we can appreciate that prior to that time, for 4,150 million years, the surface of the land was bare rock, bare sediment, scree slopes - rather like a moonscape. It was grey or yellow of brown, it was not green. The land surface was very much subject to being washed away by rainfall, moved to some other place where the sediment lay as it dried out, until the next downpour, or washed into the sea, or into rivers. Rivers eroded extremely fast, especially in higher lands, carrying enormous amounts of sediment, dislodging rocks and stone, causing collapses of the river banks and other slopes. Slopes were often unstable and very likely to be changed significantly by rainfall, frost, snow and wind. In short, the land surface was constantly changing as the weather affected it. This helps us to appreciate perhaps, the enormous amounts of sediment being moved around, the rapid rates of erosion and weathering, and the constantly changing face of the landscapes in all that early life of the Earth.

Possibly the most significant change that came about when plants moved onto the land properly and colonised the highground, lowlands, dry areas and wet areas, was the stabilisation of the land surface, an enormous reduction in erosion and a slowing down of the movemennt of sediment across the face of the land, from rocky mountainsides, through river channels, unstable hillsides, into estuaries and floodplains and then into the sea. It all slowed down and became much more stable.

Another very significant change that came about as a result of the global colonisation of the land surface by plants, was climate change.

In the absence of plants and their ability to use carbon dioxide to make sugars, a process which we know as photosynthesis, carbon dioxide gathered in the atmosphere. This CO2 came from various sources: from weathering of limestones, which released carbon from the carbonate; from gaseous outpourings from volcanoes and lava rifts;

From fossilised remains we know that the first plants colonised land back in the Silurian, or maybe even the late Ordovician period, but the ability of these plants to survive was determined by their degree of evolution. If we follow through the development of plants, then we can see how they became better and better adapted to colonising land surfaces.

The earliest colonisers of the land were probably bacteria and algae, lichens and fungi. They were very restricted as to where they could survive, requiring shelter from ultra violet radiation, or from heat, from dessication, or from wind or freezing.

Initially the earliest land plants were like the liverworts and mosses. These are non-vascuar - meaning they have no circulation system - and these plants are not organised into different organs, such as leaf, root, stem etc. A moss does not have roots, just some fibrous strands that help it hold onto rock or whatever surface it is on. Moss does not take up water from the ground; it relies on being in a damp situation to keep the plant from drying out. Each part of the moss needs to be in a damp situation.Some can cope with some drying out and then burst into life when dampness returns.

Such environmental requirements were obviously very restricting as to where mosses could grow - shaded, damp, not subject to great heat or drying, but with access to light to enable photosynthesis. And not too exposed to wind or water - with no great root system mosses can be dislodged and moved quite easily.

The next step in the evolution of plants brings us towards the ferns. Ferns are vascular - that is they have a system by which water taken up by the roots can be circulated to the rest of the plant, and sugars created during photosynthesis in the chloroplast containing cells distributed to the plants; ferns also developed a sytem of fibrous roots and rhizomes by which the hold onto the earth was rather better. But they were still pretty restricted as to the habitat they could colonise.

One development that greatly aided the spread of these early plants was their production and distribution of spores. Spores are extremely light and dusty and easily spread by wind currents and thermals of warm air. They are minute and so can be produced in large numbers. And although they are often compared to pollen, they are more like seeds. When they settle, and if the conditions are right, they will grow into new plants - see the later blog on the "Alternation of Generations". The plant that they develop into then goes on to reproduce sexually, externally, and so conditions must be just right for this to happen. The production of spores in profusion, and easily facilitated wide distribution of them is presumably an adaptation to try to ensure that some at least manage to find the right place to settle.

The big change came when plants developed extensive rooting systems, profuse leaf growth, and a vascular system. These didn't all happen at once, but they appear to have happened in fairly quick succession. It is very difficult to be sure since what is found as a fossil from 350 million years ago will in most cases just be a bit of a plant - a portion of stem, or root, or leaf, or twig or seed, and it is not possible to match a seed to a leaf and be sure they came from the same plant. In fact a lot of fossils were , and are, given names as seperate entities when eventually it is found they are just different parts of the same plant. The fossil evidence tells us though that plants soon colonised vast areas and grew in great profusion. The enormously thick coal deposits from the late Devonian and into the Carboniferous were plants similar to horsetails that we have today, but they grew to the size of big tall trees. Every year. It seems they were annual. The speed of growth was phenomenal, the amount of water, oxygen and carbon dioxide consumed was enormous, the amount of plant tissue stored away in rapidly accumulating beds of rotting (or not rotting) vegetation was incredible. These mostly occurred in swampy areas where water was avilable constantly and in large amounts. But other plants colonised and spread across dry land. They anchored the sediment with root systems, they stabilised land surfaces, slopes, and hillsides. The vegetation that was deposited in annual cycles of shedding, or lifetime cycles of death and regeneration, accumulated on the ground surface and a new substance was born. Soil, layers of decomposing organic matter, full of moisture, sugars, gases; an ideal habitat for microbes, insects, and even higher forms of animal life.

The change in global climate was extensive. The hot, arid, burning land surfaces of the Devonian developed into a coller more temperate Carboniferous period. The atmosphere changed as carbon dioxide was extracted by plants photosyntesising, producing new growth by using the sun's energy. Oxygen levels rose, carbon dioxide levels dropped, greenhouse effect reduced.

Isn't it amazing how very relevant, but opposite, this is to today's situation.

Soil 3 - How do we know that a diverse and thriving soil ecosystem benefits us?

This is just the obvious way to conclude this series of blogs on soil. Agriculture, horticulture and amateur gardening are all thriving perfectly well using conventional practices, with mineral fertilisers, dairy slurry, pesticides, fungicides and so on. So how can we prove to ourselves that the whole soil biodiversity thing is not just a green and organic option? As a committed gardener for many years, I can personally verify that the only time my garden has produced good quality vegetables with minimal pest or disease issues, with minimal 'bolting' plant responses to climate stress, and fast growth with fully functioning fertilisation and fruiting and plant development, was when the soil organic matter was at a maximum and - this is crucial - the soil is not disturbed by extensive and deep digging.

The application of high humus content compost to the surface of the soil as a mulch, and the allowing of that compost to be assimilated into the soil by the soil biota is all highly conducive to encouraging and aiding a full, thriving and complete soil ecosystem.

The natural predators of slugs, and slug eggs and larvae, are beetles and beetle larvae. I see fewer slugs and slug damage when I see more ground beetles.

Drainage of the soil is best with minimal waterlogging in wet weather where a liberal humus content occurs. This is caused by active macro biota in the soil, like beetles, worms, slugs etc. making channels and burrows, creating pathways that aid drainage. But by allowing water to permeate throughout the soil structure, films are formed around all the many different sizes of particles, increasing the water holding ability of the soil but still allowing the passage of gases. Oxygen is as crucial to the survival of plant roots and soil biota as water is. With optimum amounts of organic matter roots develop profuse growth to access both the water films and the nutirents within the particles. The root systems of such plants are far more extensive and constitute an enormous capacity for retention between the land and the plant, with great resistance to direct and easy, and damaging, flow of water, which has to permeate, as well as presenting a more complex surface of resiustance to erosion and weathering.

Compaction is minimal in similar situations, with high organic matter in the soil, root systems grow to be more extensive, more stabilising, but also, paradoxically but true, better able to be plucked from the ground - the deep tap roots of pernicious weeds can be withdrawn relatively easily, despite their obvious size and health.

Mossy areas of lawn are eradicated by surface application of compost which changes the soil biota and structure, enhancing drainage, relieving compaction, encouraging drought resistance, improving aeration, and allowing extensive root growth. The grass thus outgrows the moss in a soil that is damp, aerated, and not waterlogged or compacted.

Not turning the soil allows biotic populations in the soil to establish themselves in a suitable and stable environment, in some cases forming complex but very delicate weblike structures - like fungal mycelial networks - within the right conditions of dampness, light, aeration. Microbiota are specific in their requirements of water, gases, light, and turning the spoil over buries those at the surface and exposes those from depth. a few inches may not seem much to us, but it can spell death to microbes.

The burial of weed seeds, as layers of compost are added to the soil, means that they are not exposed to light and air. This prevents them from germinating, thus minimising weed growth. But burial of surface living microbes is not complete and does not result in the same disruption as turning the soil does.

Here we come up against some of the very real obstacles to understanding how the soil behaves, and how it needs to be managed. The microbiota is so small we cannot watch it or monitor how changing conditions affect it. It is, of course, possible to take samples of soil from different depths or different conditions, but then the microbes, of many different types, of minute size, and enormous numbers, need to be found, identified, counted. It is an impossible task, especially for the smaller microbes, like bacteria. The only possibility, which is just now starting to be utilised, is DNA analysis.

In an approach called shotgun sequencing, which takes its name from the wide spread of target organisms, DNA can be extracted from samples of soil. The strands of DNA are recorded, as a sequence of bases, or base pairs, resulting in long chains of the four letters that represent the amino acids used in DNA encoding - A, G, T, and C. These lines of code can then be matched against known sequences that have previously been obtained from organisms and stored in a reference database. If the code sequence is in the reference database, the strands match, and the organism was present in the sample. If it doesn't match, then the likelihood is that the organisms DNA is not stored int he reference database. As time goes on, of course, the reference databases are actuively added to by researchers, and the percentage of successful matches increases. What the results of such analyses are, and will be, remains to be seen, but currently this is an exciting and rapidly developing revolution in our understanding of microbial ecosystems.

Coming back to the more everyday issues of management, the main problem that requires some careful management, is the production and creation of ample amounts of compost such that liberal applications can be made to wider areas of land - such as in horticulture and commercial vegetable production, and most particularly farms. The comments - findings - above are all well and good in a single household garden. The larger the farm, in land extent, the greater the problem in that greater quantities of compost are required, greater areas need an applcation, and greater time is required. It is tempting to suggest that smaller sized farms can, in this respect, be better managed.

Better managed for soil quality, that is.

Atlantic Rain Forests

I visited a rainforest recently, but close to home. A temperate rainforest. They have been known as Temperate Rainforests since the beginning of the 20th century, but the term has been used more often more recently, probably to enable us to connect better with the most exotic of forests, the Tropical Rainforest. They were previously known as High Latitude Rainforest, Atlantic wildwood, Quercus... well, see below . Rodwell's British Plant Communities does not contain the word rainforest but W17- Quercus petraea-Betula pubescens-Dicranum majus woodland refers to these woodlands, while Fossit's WN1 Oak - birch - holly woodland comes close, and it is hard to see which of the new Irish Vegetation Classification classes would apply.

Leaving aside issues of classification of floral associations, the mixture of oak, birch and holly is common enough along the Atlantic western coasts of UK and Ireland. These woodlands, although relatively sparely distributed these days, also support a variety of other trees and plants, not to mention fungi, insects, birds, mammals, and a host of other living things. What makes a rainforest is a combination of a small temperature range across the year, between a max of c. 16 degrees and a min of c.4 degrees, on average, a rainfall of over 1 metre each year, at least 10% of annual rainfall occurring during the summer, and, most crucially, a lack of human disturbance.

Rodwell defines this woodland in the key as "Well-defined tree canopy or thicket-like tree/ shrub layer or coppice regrowth with Quercus petraea (rarely Q. robur) and/or Betula pubescens constant, and dominant and Sorbus aucuparia, Corylus avellana and Ilex aquifolium the most frequent associates; field layer sometimes sparse but with Deschampsia flexuosa constant and Pteridium aquilinum, Vaccinium myrtillus and Oxalis acetosella frequent; ground layer always well-developed with six or more of the following present: Rhytidiadelphus loreus, Polytrichum formosum, Dicranum majus, Hylocomium splendens, Pleurozium schreberi, Plagiothecium undulatum, Dicranum scoparium, Thuidium tamariscinum". This is named as "W17 Quercus petraea-Betula pubescens-Dicranum majus woodland".

In Ireland we have two systems of Floral Habitat classification. The earlier one was compiled by Fossitt and does not mention rainforest at all. However, it does contain a couple of woodland types that could be applicable.

Fossitt's classification has now been superceded by the Irish Vegetation Classification that has been compiled by the National Biodiversity Centre in Waterford.


These classification systems are intuitive in that we can see the sense in identifying a community of plants with an environment; and environment that suits the plant communities that grow in them. This idea of course is what biodiversity is all about; plants - and other organisms - moving into and occupying niches that are suited to that organism's specific needs and requirements. And research is starting to show that it is not just the environment that matters, but the organisms that are in it, that has an influence on which other organisms move in and survive. There are intimate relationships between organisms that can make the difference between survival in, and extinction from, an environment. The obvious example is the fungal mycorrhizal connections between plants, even between utterly unrelated plant types. And a predator-prey relationship both in the animal world, but also in the plant-predator relationship.

In the 19th century and continuing to the present day, particularly in Europe, such communities and relationships have been used as a basis for Phytosociological community definitions - the defining of societies of plants; and also Phytogeographical classifications. Each of these has inspired a great deal of work and a profusion of terminology - but there is still something missing.

I suspect we are getting to the stage where the "phyto" will come out of phytosociology and instead attention will focus on a more diverse range of organisms - "biosociology" perhaps?

Rising Sea Levels

I took a visit during last summer, to the beach at Bunaneer, just west of Sneem on the south Kerry coast. The trip was guided and arranged by the participants in the LIVE project, a collaboration between the Iveragh peninsula in Kerry and the Lleyn peninsula in Wales. Bunaneer beach is a site where the remains of an ancient forest are now lying exposed, containing stumps of trees that have been dated to between 4000 and 5000 years ago. It would appear that these tree stumps, principally it is thought of Scots Pine (Pinus sylvatica), were exposed by storms in 2013. The fact remains that the stumps are below the high tide mark and therefore not in the same position relative to sea level as when they were alive. So sea level has risen since 2,000 or 3,000 BC.

The view from Bunaneer beach south to the north side of Beara

The view from Bunaneer beach south to the north side of Beara.

A large pine stump high up on Bunaneer beach

A large and ancient pine stump high up on Bunaneer beach.

The Bunaneer ancient woodland exposed at low tide.

The stumps of the Bunaneer ancient woodland, exposed at low tide.

This is in fact not very unusual, there are quite a few places around the coastline of south and west Ireland and also southern England and south Wales where relict land surfaces have been covered by rising sea levels. On the coast of South Wales at Goldcliff there have been extraordinary finds of human footprints from a family group, and the skeleton of a wild boar, lodged beneath a large piece of tree, with a flint arrow or spear head lodged in it's shoulder. All of this covered by sediment and then inundated by rising sea levels, and now exposed by some quirk of fate, maybe storm or tidal removal of some sediment, and then exposed at low tide. There are several other sites along both the northern (Welsh) shore and the southern (English) shore of the Bristol Channel (Severn Estuary) where tree stumps, branches, leaves, and dark brown organic woodland floor can be seen at low tide.

In West Cork we have Tralong Bay, on the coast beneath Drombeg stone circle, where tree stumps, both in situ and also fallen and dismembered, as well as the organic woodland floor that grew up beneath the trees, can be seen at low tide. The degree of preservation in such places is sometimes quite staggering, with even whole leaves pressed flat into the compressed mud, and seeds, and small plant remains. There are quite a few other sites along the south coast of Cork and Waterford - see the Intertidal peat deposits between Toe Head and Red Strand, West Cork (IQUA 2017 research award) by Tony Beese

At Beach beach on the southern shore of Bantry Bay at the far end of the beach from the airstrip, is a flooded woodland floor, clearly visible at low tide. Sticks and branches can be seen, and initial examination of the sediment - although it is not thick here, just 40 cm, the top layers probably having been eroded away by the action of the waves and tides - suggests this was a damp alder woodland with some hazel and willow trees growing in and around the woodland, and plenty of ferns. Presumably this woodland grew up after the drumlin had been deposited by the ice and the ice had melted as the climate improved. So maybe this woodland dates to between 10,000 and 12,000 years ago. See here for the westcorkpalaeo.com webpage for Beach beach.

On the foreshore of Ringaroigy Island in the mouth of the Ilen estuary is a passage tomb (CO150-057----) which gets inundated at high tide.

At Ballyrisode on the southern shore of the Mizen peninsula west of Schull, again on the foreshore and covered at high tide, is the remains of what may be a burial cist, and also flagstones arranged upright in what appears to be the form of a tank for holding water, as we find with fulachta fia CO147-091----. This was reported by Finola Finlay and Robert Harris in their Roaringwater Journal. It may have been an intertidal fulacht fia, but more likely a dryland site that has been inundated by the rising sea level.

The Ballyrisode fulacht fia at low tide.

The Ballyrisode fulacht fia, exposed at low tide.

So we have woodland dating back to between 4,000 and 5,000 years ago, or more judging by the depth of organic sediment under the tree stumps at Bunaneer; a passage grave probably dating back to between 2,500 to 3,500 BC; a fulacht fia which may be Bronze Age c. 2,000 BC; all of which are now below high water mark. So the sea level has risen significantly since just 4,000 years ago.

The likely cause for this continuing sea level rise is the adjustment of sea level following the warming of the earth's climate that signified the end of the last glacial period. This isostatic adjustment has been investigated quite intensely over the years, and a study of Bantry Bay in particular, in 2015, resulted in a graph that suggests how sea level in SW Ireland has changed over the last 20,000 years.

Glacial Isostatic Adjustment - Relative Sea Level.

A graph showing post glacial isostatic adjustment to relative sea level in the Bantry Bay area. This has been taken from Plets et al 2015.

The graph shows how pulses of quite rapid sea level rise occurred at times, and these largely relate to injections of significant amounts of meltwater as ice sheets collapsed - the ending of a glacial period is not a smooth and steady melting of ice and addition of water back to the oceans, but occurs at different rates. Meltwater in many cases was held back on land - like the large Lake Agassiz that was held on the North American continent, and then seems to have been released into the Atlantic in a massive outpouring. This caused a serious downturn in climate, affecting at least those lands bordering the North Atlantic, by bringing the circulating currents in the Atlantic to an end. The graph above implies that the sea level adjustment has now possibly more or less finished.

However, sea level rise has a different cause now, but maybe we can be reassured that the earth has managed to adjust to these changes in the past, and will continue to do so in the future, even though we as a species are threatened with rapidly rising sea levels today, caused by the human induced climate change that is so prominent in the news.

Meyssignac, B.,Cazenave, A. 2012. "Sea level: A review of present-day and recent-past changes and variability". Journal of Geodynamics. 58. 96–109.

Plets R.M.K. et al. 2015. Late Quaternary evolution and sea-level history of a glaciated marine embayment, Bantry Bay, SW Ireland. Marine Geology 369 (2015) 251–272

Finlay. 2019. Ballyrisode Fulacht Fia: A New Bronze Age Site on The Mizen. Skibbereen Historical Journal

Dog Vomit - Fuligo septica

As with so many things in nature, the indigenous or common name is based on appearance. And so it is with this slime mould. (It is also called 'scrambled egg slime mould').

IMPORTANT UPDATE. The blog below entitled 'More on Slime Moulds' refers and corrects this blog.

Dog Vomit slime mould - Fuligo septica

Dog vomit slime mould (Fuligo septica) on moss in a larch plantation in West Cork, July 2023

Despite the common name, and the general name of 'slime mould', this is a fascinating organism that is well worth applying some consideration to.

The slime mould pictured here is just one process in a chain, or cycle, of events that leads to propagation of the species. The organism starts off as separate cells, single cells, living in an amoeba form in their environment. In the case of Fuligo septica the environment is one of rotten wood, or moss, or leaf mould on a woodland floor; or a damp rotting piece of wood. At a certain time, when conditions become either stressful for survival or conducive to propagation - researchers seem divided on what prompts the change - the amoebae, all those individual cells living individual lives - move in a certain direction and start congregating. How these single celled organisms know where to go, and when, is not known by us. But they congregate and form a body of living cells called a 'slug'. Which apparently is similar in appearance to a slug, but without the things slugs have. As a slug, some of the amoeba-like cells act as foragers, some as protectors, and the whole body behaves more like a bee or wasp or ant colony, each individual helping and supporting others. Somehow.

As the process progresses the slug, at an appropriate time, starts to separate into different functional forms. Some form spore producing amoebae, some stem amoebae, and also basal amoebae. And probably other functional types as well. The long and the short of it is that the amoebae that give themselves up to becoming spore producing bodies, are elevated up onto the ends of those that become stems. And after an appropriate time, or at an appropriate time, the spore bodies burst and the spores are distributed out into the environment, where each one will eventually become an individual amoeba.

A closer view of Fuligo septica

A closer view of Fuligo septica, Dog Vomit plasmodial slime mould.

In the case of Fuligo, which is a plasmodial slime mould, the individual amoebae, once they have consumed all the bacteria within reach, during which time the amoebae grow and divide and increase in number, they start to coalesce into one large cell incorporating all the nuclei. Eventually, each one of these nuclei will form a spore body and be released.

Plasmodial Slime Mould life cycle

Starting with the individual amoebae at lower left, we follow the cycle clockwise. Following increase in numbers, fusion of cytoplasm (6 - plasmogamy) and of nuclei (7 - karyogamy), the plasmodium forms by accumulation of the many individuals, and under the right conditions, sporangia form (1), finally releasing spores into the environment (bottom right - 3).

To see the original caption to this diagram, click here.

How do these widely scattered, independently living amobae communicate so that they come together at a single place? Smell? Chemical signals? Sixth sense? They are single cells, they don't have noses, vocal chords, or brains. As is so often the case while studying microscopic organisms, one is left wondering how on earth such small things can communicate, change function, work together, and even appear to make decisions. All in a microscopic world of single celled organisms that we so poorly understand.

It would appear to possibly be something called quorum sensing, which is a bit like pheromones being released into the environment by each individual, and other indviduals sensing thise chemicals. Molecules. But quorum sensing is a bit more complex than pheromones, and is only now being accepted and investigated. For a start the process involves evolved systems of specific signals, with a linked recognition of chemicals upon which to act, so both the sending and receiving of such messages is a specific evolved system. Additionally the concentration of the signal indicates the need to act; so for example if enough amoebae produce the signal, concentration levels in the environment reach a point where the indiduals all start acting, as one. And presumably the signal is also directional, enabling the amoebae can congregate.

It is early days for exploration of quorum sensing, so more will be revealed in time. But just keep hold of the idea that this is something that the (supposedly) simplest of organisms, single celled bacteria, protists, and even viruses, engage in. For us to detect a smell we need to employ our multicellular noses, nervous systems, and brain...

Fuligo septica spore bodies

Spore bodies, on stalks, of Fuligo septica - a collage (x100 magnification).

Back to the Dog Vomit. As the sample I took dried out - and presumably came under stress, or entered a state conducive to sporulating - spore bodies formed, small spherical translucent balls on the ends of long, fine stalks.

Fuligo septica spore body

A spore body of Fuligo septica (x100 magnification).

In this image (a series of photos a different focal points that have been stacked to make a composite image with greater depth than we can actually see through a microscope) we can see some (out of focus) yellow plasmodium, and also some that has darkened as it dries out, and connecting the two, the slime that gives slime mould it's name. The plasmodia are not usually all together in one lump, but are usually more or less scattered, but linked by the slime.

Ripening Fuligo septica

Fuligo septica ripening prior to releasing spores (x40 magnification).

The dried out brown parts eventually split open to release the spores with which they are filled.

Ripe Fuligo septica spore body

A spore body of Fuligo septica split open and showing the spores packed inside (x40 magnification).

At the same time, despite overnight rain, the patch in the woods degenerated into a less colourful, less easily seen, mess. And two further patches appeared nearby. We can visualise thousands of microscopic amoebae sliding together across the woodland floor, in response to molecular signals released by them all, coming together and congregating, combining cytoplasm and forming large plasmodium of free flowing cytoplasm containing many thousands of nuclei, all in the silence and darkness on the moss of the woodland floor.

A closer view of Fuligo septica

The new patch of Fuligo septica plasmodial slime mould.

As the days passed, with wet nights, cooler weather, wet days, and then back into warmer and drier days and nights - all in mid to late July - different patches of Fuligo septica appeared. Within a day, or at most two, they melted away, sometimes leaving blackened moss stems, sometimes leaving no trace; to be replaced by another patch elsewhere. Sometimes it was hard to see if the patches of yellow growth could count as two, close together, or one vaguely connected, or even many different patches, distributed on separate fronds of moss or stems of grass. Under the microscope it appears that even if the yellow blobs are not continuous, they are connected by a clear slime. Clearly this little area of larch woodland, open to the sky, with quite high light levels, sheltered and damp, has an active and thriving population of Fuligo septica amoebae. But exactly why, we do not know. Or maybe not thriving, and that is why they keep forming these plasmodia on the way to spore production. Maybe these populations are under stress. But because of the minute size of the amoebae it would be very hard to find out exactly what is going on.

We are only aware of the things that we see around us because they are of a size that we can see - obviously. But how often or how much, do we consider the vastness of what we can't see? We need to, because the world that we can't see is far more numerous, omnipresent, influential, dominant, resilient, and, in short, crucial, to life on earth, than us humans ever suspected.

Figure - and highlighted text - is shared under a CC BY-NC 4.0 license and was authored, remixed, and/or curated by Melissa Ha, Maria Morrow, & Kammy Algiers (ASCCC Open Educational Resources Initiative). No changes have been made.


  • Moulds - their isolation, cultivation and identification. David Malloch.
  • Book - The Social Amoebae; the biology of cellular slime moulds - John Tyler Bonner. Princetown University Press, 2009.
  • Book - Progress in and promise of bacterial quorum sensing research. Whiteley M., Diggle S.P., Greenberg P. Nature Review. doi:10.1038/nature24624
  • The Eumycetozoan Project
  • Book - Myxomycetes : A Handbook of Slime Molds. Steven Stephenson, Henry Stempen. Timber Press. 2000
  • Book - Myxomycetes: Biology, Systematics, Biogeography, and Ecology. Eds Steven Stephenson, Carlos Rojas. Elsevier. 2017.

Glandart - the Lake on the top of a Hill

A long blog.

Lakes are not usually on top of hills, principally because they form in depressions where water drains into them from higher ground. But in this case, things are different.

A view of Glandart Lake looking west, over the edge

A view of Glandart Lake looking west, over the edge.

Glandart Lake lies at a height of between 330 m and 340 m above sea level, with a total surface area of about 0.4 hectares, and a circumference of 230 metres. It is largely circular. The most significant characteristics about this lake are the facts that it lies at the top of a steep slope, with only a very small amount of land to the east at a higher level. Surrounding high ground to the north and south are separated from the land the lake lies on by valleys that extend deeper than the lake level and that drain to the west. In addition, the water of the lake is retained from flowing down the slope to the west by a narrow bund of land that extends just 2.5 m above the lake level and is only some 5 or 6 m wide. Glandart Lake is thus perched right on the edge of a steep slope that descends 100 metres within 435 metres, a slope gradient averaging a 1m drop for every 4.35m – 1 in 4. A stream emerges from the slope below Glandart Lough at a height of 260 m, that is 80 metres below the lake level.

A 3D (rotatable and zoomable - use a mouse) virtual model can be seen here. This was constructed using QGIS mapping software, with the 3DJS plugin, and data purchased from BlueSky surveys. The data was not freely avaiulable because of the fine definition - based on a grid of 25 cm, 100 times more detailed than satellite imagery. In the case of this topography, it was necessary - satellite images at a resolution of 30m miss the essential nooks and crannys of this landscape, the ones that effectively isolate the lake.

Glandart Lake lies within a band of the Castlehaven Formation which with the older Gun Point formation outcropping further to the east north east, lies within the core of a faulted anticline, flanked by the younger Toe Head and then the Old Head Formations. These Late Devonian sediments are all essentially a very similar series of sedimentary rocks, principally sandstone, siltstone and mudstone. They are generally not massive, but very heavily cleaved by folding and faulting, and relatively easily shattered and split. Although the siliceous sediments, with a hard siliceous cement, can create an impermeable surface, the degree of faulting and cleavage means that the bedrock is very often free draining.

The bank holding the water back from rushing down the slope into the valley is only 5 or 6 metres thick, and yet clearly impervious. The formation of this depression, so close to the edge of the hillslope, but separate, is as yet unknown. Possibly a kettle hole, from the last ice age, formed when a buried block of ice melts, leaving a 'hole' in the ground. Or possibly the ground here is till, impervious boulder clay left on the hillside by the retreating ice at the end of the ice age. However, probing the land around the lake, including the bank, suggests bedrock lies not far beneath the surface.

The westcorkpalaeo.com webpage for Glandart is here.

The water in the lake would appear to be principally ground water, topped up with whatever rain might fall. As a consequence, the lake having no surface drainage flowing in, has an unusual and seemingly fairly limited biota. In addition the vegetation around the lake and in the immediate locality is also very limited, and does not provide a lot of organic matter into the lake. It is not known how deep the lake is, nor how deep any lakebed sediment might be. Scooping from the edge of the lake has yielded only thin organic sediment with a very high silt content and seemingly a low oxygen (anoxic) content. No living algae or diatoms have been found in the bottom sediment, only some live testate amoebae, but many tests of testate amoebae as well as cast off Cladocera (water flea) carapaces, pollen grains, and spores.

Testate amoebae tests from the anoxic bottom sediment of the lake

A testate amoeba test from the anoxic bottom sediment of the lake (x200). There are many nore examples on the Glandart Lake webpage here

An extremely interesting find from the bottom sediment was a Suctorian, attached to a Cladocera carapace. These predatory, sessile, non-ciliated forms of a group of ciliates, are not widely studied, nor widely known. This one has not been named, yet, but unlike others has a lovely regular shape as a seven pointed star. Take note of the 'tentacle' like structures coming from the star points - these are for sensing, and catching, and ingesting - by 'sucking' - the prey, any passing protist that touches a tentacle. No other suctorians have yet been found.


A suctorian from Glandart Lake (mag x600). It is about 30 microns across (3 hundredths of a millimetre).

Around the edge in shallower water the principal algae found is Paludicola turfosa, a dense algae formed in whorls around a central 'stem'. Despite being a lovely deep green colour, it is in fact classified as one of the red algae (Rhodophyta). This algae produces large amounts of mucilagenous strings, presumably to deter browsers - it's sticky, slimy and tangling. These can just be seen in the photo below as fine transparent strings emanating out from the main greenery (click on the image and zoom right in). Like the suctorian mentioned above, Paludicola has a complex and interesting life cycle.

Paludicola turfosa

Paludicola turfosa - note the transparent strands of slime secreted by this algae, just visible in this photo (mag x200).

The Paludicola provides both anchorage and shelter for a selection of diatoms, a separate family of algae which are distinctive for their silica skeletons, or frameworks. Although still single celled organisms, diatom species can be recognised by the intricate and distinctive shapes and patterns of these silica frameworks. These only become visible once the surrounding cytoplasm is removed, and the lakebed is littered with these skeletons of diatoms past. Surirella and Pinnularia, two large (relatively) and motile ('raphid' - bearing raphes by which they exude a substance enabling a gliding motion across a surface) diatoms, living on the sediment surface (epipelic). I haven't yet found these species alive, just their remains in the bottom sediment. They probably browse the deeper edges of the lake, but the lake edge overhangs the water, and the one thing nearly all diatoms neeed, is light. They photosynthesise, like green plants. But they are motile and can move to places where conditions are better; lighter, cooler, warmer...

So to add to the strange behaviours of predatory non- ciliate ciliates, Paludicola life cycle, and single celled amoeba making a shell to live in, we have photosynthesising algae... that moves.

Surirella and Pinnularia

Surirella (left, x400) and Pinnularia (right, x200) from the lakebed sediment at Glandart.

But on, and in, the Paludicola we can see other, smaller diatoms, hiding, or making use of the protecting lines of sugary slime. Some of these motile diatoms dwell within their own tubes of jelly, or slime, for protection possibly. And they commune within these tubes.

Dangling off the ends of the Paludicola 'fronds' are the curvy Eunotia exigua, in their thousands.

Eunotia on Paludicola

Eunotia exigua on Paludicola, and (inset) Eunotia, from the lakebed sediment at Glandart.

The Paludicola is the main surface to which these diatoms can attach, the lake edge descends abruptly to a depth at which light is poor, not good for photosynthesising organisms; and the actual lake edge is overhung by vegetation and peat outgrowth, largely mosses. This is a common situation in many lakes, so there is no gradual deepening of the water with a slowly descending shoreline, but instead an abrupt depth overshadowed by peat and moss and vegetative detritus.

However, some diatoms are freely floating - planktonic - amongst the Paludicola - round ('centric') Cyclotella, strings of colonies of attached Tabellaria flocculosa, and the larger boat shaped Frustulia saxonica. Less common here are Eunotia tetraodon, with the crescent shape bearing four (tetra-) humps (-odon) along the dorsal side.

Planktonic Diatoms amongst Paludicola

Cyclotella sp.- the circular diatom centre right (x1000), Tabellaria flocculosa - individual at centre left (x1000), attached colony at bottom right (x1000), Frustulia saxonica individual (x200) bottom left, four communing in a mucus tube top right (x1000), and Eunotia tetraodon bottom centre (x1000), from the lake at Glandart. Anything else is Eunotia exigua (x1000)

Recent research on lake bodies and the behavior of microbes in them has thrown up some interesting issues relevant to the changing climate. One study showed that the amount of CO2 released by microbes in a lake is greater both at higher temperatures, and also more the closer to the shore they are. Another study suggests that the ability of microbes to either photosynthesise, or act as predators on other microbes, might change as temperature within the lake water rises. This latter study found this was more the case in high nutrient waters.

The first finding might well be simply linked to the amount of light penetrating the shallower water and allowing a greater concentration of microbes - both CO2 using photosynthesisers, and their CO2 producing predators. How the dynamics might change as temperature rises, as in the second finding, is uncertain. Even more so in lakes such as Glandart, which appear to have a low biodiversity, and a low nutrient status.


More on Slime Moulds

This entry adds to, and corrects, the entry above that describes Fuligo septica, the Dog Vomit slime mould.

The excitement at finding the slime mould - believe it or not I recognised it as such straight away - was added to by my identifying it as having a great name - Dog Vomit slime mould. I monitored the occurrence of clumps of this slime mould as described above, and this is ongoing as of August 2023. There are between one and six new clumps every day, but, noticeably, not when it is actually raining.

However, having brought some home to examine under the microscope as it matures, and produces spores, I realised that this is not Fuligo septica, the Dog Vomit (or Scambled Egg) slime mould, but is in fact a myxomycete slime mould named Physarum virescens.

In my own defence I was reassured to find that the two I have named are very similar in general appearance and occurrence and not only do they belong to the same family, but there have been suggestions that for various reasons they should combine into one genus. But they are different enough to stay separate.

Well. Whatever.

To be continued

The Alternation of Generations

The differences in the shape and mode of life of liverworts, hornworts, mosses (all of which are called bryophytes, but actually only true mosses belong to the Bryophyta); and ferns (which are generally grouped together as pteridophytes - ferns - but clearly include some non-ferny type plants);, and the flowering plants; is a close reflection, and helps to explain, the progressive process by which plants gradually moved onto the land during the Silurian and Devonian periods. The final colonisation of land was rather explosive and had enormous consequences for the environment on earth as a whole.

The relevance to us in West Cork, and to this blog, is that this move happened just at the time that the West Cork bedrock was being deposited as sediment.

In reading the rest of this blog entry, there are two things to remember:-

Mitosis is cell division in which the number of chromosomes is reduced from the full double set - diploid - to just a single set - haploid. Meiosis is just cell replication that occurs with haploid cells. They start with single chromosome sets, and end up with single chrmosome sets.

(There is also a cell division which will reproduce a full diploid cell, and this is vegetative reproduction, using a bit of the existing organisms to create a new organism, a clone. Mammals don't do it, some plants can.)

The second thing is that the generations that alternate are haploid (one set of chromosomes) and diploid (double set of chromosomes, the 'normal' state of affairs). This switching between the two is really just a different way of looking at sexual reproduction, and provides a good way to relate one thing to another. The essetial requirement is to halve the number of chromosomes, so that when two (haploid) sex cells meet, they combine and form a diploid cell. In humans, and mammals generally, the haploid generations exist internally and do not form an apparently different generational organism. But other orgaisms are very different, but dominant in numbers, so make us the odd ones out, no matter how strange the other behviours might seem to us. So the Alternation of Generations may seem a bit strange to humans since we consider just our own selves and our diploid bodies as the only generation, each one succeeding the diploid body (or bodies) that formed it. We do not consider those haploid cells - the sperm and egg - as an other generation.

Also remember that spores are not like pollen - pollen is the male sex cell, haploid, one set of chromosomes - whereas spores are diploid, ready to grow, more like seeds. But as small and easily dispersed as pollen.

True Mosses (Bryophyta) Life Cycle.

The mosses that we generally see are the single chromosome bearing plants, the haploid gametophyte. This means that all the cells within the plant have only one set of chromosomes. There are male plants and female plants, and each of these produce haploid sex cells. Wet conditions are required for the male sex cell to swim, externally, from where the male sex is produced (the antheridium - think 'anthers') to the place where the female sex cell resides (the archegonium). (The planetary symbol for Mars, the 'male' planet, is the same as the symbol for male, a circle with an arrow, signifying that the male goes off in search of a female. Or hunting, I suppose. Or fighting. Or to the pub. The female symbol - that for Venus, is a circle with a cross underneath, suggesting planted, or static, or stable.)

When these two haploid cells meet and join, they form a cell with double set of chromosomes - diploid - and this then germinates and grows into another generation, but remains fixed within the archegonium. So in effect, the new plant grows on top of and out of the originating plants. These are the spore capsules you might see on the end of a stalk. The spores are produced by cell division and are single chromosome sets, haploid. When the capsule bursts the spores are released, into the wind, and eventually will grow into new gametophyte plants.

The release mechanism can be quite sophisticated. Some sphagnum mosses, that grow on bogs, rely on the capsule drying and constricting such that the air pressure builds up inside. Then, suddenly, pop! The cap pops off and the spores are propelled out significant distances - up to 16 cm. Considering each spore is just about 2 or 3 hundredths of a millimetre in size, they are flung between 5 and 6 thousand times their diameter. See The Secretly Speedy Life of Plants.

Liverwort (Marchantiophyte) Life Cycle.

Liverworts are similar to Mosses in that the main plant we see is the gametophyte haploid plant. On each plant there grows either a female cell bearing organ - archegonium - or a male bearing organ - antheridium. Just like mosses. Or there may be both male and female on the same plant. Either way, the male sex cell has to reach, by swimming through a moist external environment, a female cell inside an archegonium. Some liverworts propel their male sex cells in a sort of 'liverwort sperm ejection' - or ejaculation I suppose. Researchers have not yet identified quite how, but some liverworts squirt out a stream of sperm laden water from the antheidium such that female liverworts up to 1 metre away are fertilised.

When the male cell meets the female cell, they join and form a new diploid generation. The new plants forms in three parts, a basal 'plate' that anchors itseld inside the female capsule, a stem, and a spore bearing capsule. The cells inside the capsule divide by meiosis and form haploid spores. The stem grows longer, the capsule is hoisted aloft and bursts open, spreading spores that will then grow into new liverworts. This sporophyte generation, the spore bearing capsule that arises from the junction of male and female cells in the archgonium, is very short lived.

Hornwort (Anthocerotophyte) Life Cycle.

In Hornworts, as in both Mosses and liverworts, the main plant occurs as the gametophyte haploid plant. The gametophyte plant grows to have the appearance of a leathery wrinkled leaf, up to 5 cm in diameter and several cells thick. Once each plant has grown to maturity there grows a female cell bearing organ - archegonium - and a male bearing organ - antheridium, both male and female, on the same plant. In some species there may only be either male or female on each plant. The male sex cell has to reach, by swimming through a moist external environment, a female cell inside an archegonium, and to achive this they swim when the environment is wet enough. These sperm cells have two tails, they are biflagellate.

As with both mosses and liverworts, when the male cell meets the female cell, they join and form a new diploid generation. However, unlike liverworts, the new plants that form are horn shaped, very long lasting and capable of photosynthesis. But they also form in three parts, a basal 'plate' that anchors itseld inside the female capsule, a stem, and a spore bearing capsule. The cells inside the capsule divide by meiosis and form haploid spores. The stem grows longer, the capsule is hoisted aloft and bursts open, spreading spores that will then grow into new hornworts.

So the cycle is very similar for mosses, liverworts, and hornworts.

Ferns (Pteridophyte) life cycle.

Let's finish with the ferns. The ferns - pteridophytes - 'ptera' means feather and suggests the shape of the fronds - are generally visible to us as sporophytes, that is, the diploid generation. These fronds of the sporophytes have the spore bearing bodies on their undersides, but some ferns bear the spores on seperate structures, like the royal fern (Osmunda regalis)which has what could almost be termed a flower spike. When the spore germinates and grows it produces a seperate, independent living gametophyte haploid generation, as a plant. These are generally small and insignificant and go unnoticed. But it is they that bear the haploid producing cells, the male and female cells, that then have to meet to produce a diploid generation. As with the bryophytes, the process of fertilisation has to take place in the environment and thus required the right conditions.

Back to Three Lakes

Back to University as well

So I took the plunge and returned to UCC realising that there was no way I was going to channel my interests sufficiently well to produce something meaningful from my studies of palaeoecology and palaeoenvironment in West Cork, without some management, some tuition, and some focussing.

I'll cut to the chase - the first couple of months has seen me focussing on testate amoebae in the modern environment - to get a grip on identifying them - and then latterly in the core samples.

The initial identification exercises gave me an opportunity to go and collect some surface samples from lakes and bogs I (and you, if you have read other blog entries) know well. They are great places.

Glandart Lake (which now turns out to be called Loch Agower (or Loach a Gabhar)), Driminidy Lake, and Three Lakes middle lake.

I have to say here, that some of these places can be pretty dangerous. These lowland lakes (even though Loch Agower is at 320m ) have plenty of plant growth around the edge which often turns out to be a floating mat. Extreme caution is needed. Sinking through the floating mat would be akin to a quicksand - extremely difficult to get out of, and ultimately deadly. One does not take ANY risks.

The reason for examining the sediment for testate amoebae is that the different taxa have been found to be quite specific as to the wetness of their habitat. So by identifying the different taxa of testate amoebae that are present, and then looking at - and performing some statistical analysis on the figures - it is possible to ascertain the 'depth to water table' (DWT) that they represent. And we can then build up a picture as to how the DWT changed over time, and postulate why that might have changed. And the reason may be increased or decreased rainfall, episodic flooding or drying, changes in drainage patterns, changes in the catchment area from which the bog or lake water comes, and so on.

But most of these studies have been undertaken at bogs, and, more specifically, ombrotrophic bogs; that is, sphagnum moss dominated raised bogs, which are supplied by water from rainfall only, have low levels of nutrition, and generally have a low acidity of pH 5 or 4 or 3. Some studies have been undertaken on lake sediment, but they represent a different picture. The testate amoebae that occur in lakes are more indicative of the trophic level of the lake, that is, what sort of nutrition level is there. And an added complication is that the tests (shells) of the testate amoebae once the organism dies, are deposited and sink to the bottom, but then, depending on water circulation currents, they may get swept together in a congregation on the bed of the lake. This may include tests from those that lived on plants on the edge of the lake, those that lived in the depths (profundal), or on the shallow beach like (littoral) habitats. All mixed up. Which gives us a bit of sorting out to do, but overall this can all be dealt with by numerical and statistical analysis of the numbers of different taxa.

I have run into a different problem at Three Lakes.

The 'bog' surrounding the lakes at Three Lakes is mineratrophic, that is, they get their water supply from the ground water as well as from rainfall, so the plants and mosses growing there have the input of minerals.

Not many studies of testate amoebae have been undertaken in mineratrophic mires, which means that the taxa I can expect to find might not fit in too well with the data obtained by studies of either bogs or lakes.

But there is an added complication. Studies generally indicate a lessening in number of tests further down the core (deeper into the sediment and therefore the older the sediment). Is the change in number because there were fewer living there, or because the environment has changed, or because the tests do not survive the time spent in the sediment, or the pressure of several metres of sediment on top of them? There have been experiments to ascertain how the different types of tests survive different conditions. And there have been statistical explorations into how a reduction in different types of tests will affect the final determination of DWT. The experimenting with conditions came up with a certain number of conclusions, but overall it seems that the problem is how to mimic in an experiment, the gradual burial over hundreds or thousands of years, and the possible changes in environment as that happened. The statistical explorations concluded that changed numbers of tests do have a certain effect, but generally not a dramatic one.

But what happens when we look at the sediment down core and don't find any testate amoebae tests? What then?

This is what I am finding at the moment, and although this is going to impact the project quite seriously, it is a fact of nature and presents a challenge. We need to find out why.

Where have all the tests gone?