Back to the bog


The microscopic world of an Upper Teesdale Sphagnum bog revisited, with diatoms and desmids living on and in the spaces between Sphagnum leaves and diatoms The chlorophyllose cells are about ten micrometres in diameter (1/100th of a millimetre) whilst the desmid in the foreground (Cosmarium ralfsii) is about 100 micrometres (1/10th of a millimetre) across.

I showed my first attempt at portrayal of the microscopic life of a Sphagnum bog a few weeks ago (see “Swimming with desmids …“) but, at the same time, I felt that there were a few elements that could be improved, so here is my second effort. The first time I tackle a new subject, there are usually technical issues to address and, perhaps, the outcome was not quite as naturalistic as I would have liked. Not that I, or anyone else, really has a great insight into “natural” in this particular context, but then none of us have seen dinosaurs hunting in Jurassic forests, but that hasn’t stopped people producing “naturalistic” illustrations.   In my first picture, just capturing the underside of a Sphagnum leaf in something approaching linear perspective and including two desmids seemed like progress. This time, there are two Sphagnum leaves plus a couple of diatoms – a single cell of Eunotia implicata on the underside of one leaf, plus a couple of cells of Tabellaria flocculosa on the other leaf. Both of these specimens were present when I made my initial observations of the Sphagnum leaves back in December.

One additional issue that the composition of this picture raised, is that the morphology of the upper surface of a Sphagnum leaf differs from that of the lower surface. This relates to the relative size of the chlorophyllose and hyaline cells (see the schematic diagram in Swimming with desmids ...). There were moments, I promise you, when I interrupted my meditations on Sphagnum morphology to wonder if I should go and get a life.

My justification, if any is needed, is that peering down a microscope and compiling data about the species present without sometimes contemplating the organisms in their natural state seems like an equally bizarre way of spending one’s life. I write this post having peer-reviewed a paper for the journal Limnology and Oceanography this afternoon. The work was quite interesting but, at the same time, I felt that it was a very sterile, technical study that had abstracted the real world into long lists of diatom species and then processed these using complicated statistical methods, without giving much sense of a real understanding of the ecosystems that they were studying.

County Durham’s tropical seashore?


The Magnesian limestone escarpment, looking north from Bowburn.

The village where I live is overlooked by the Magnesian limestone escarpment formed from a coral reef dating from the Permian era.   On cold winter days I get a perverse pleasure from contemplating this escarpment and mentally transporting myself to a balmy tropical beach beside the Zechstein Sea, 250 million years ago, watching the trilobites scuttle around in the shallows.

The Magnesian limestone extends about 20 kilometres east from here, ending at the Durham coast where there is some classic limestone coastal scenery You may have encountered this coastline before as Easington, a few kilometres to the north, was the setting for the film Billy Elliot and the closing sequence of the 60s thriller Get Carter were also filmed here. Both of these films refer back to Durham’s mining heritage. Now, however, the pits have all closed and the area’s natural beauty is able to flourish once again. There are some unique limestone grassland communities associated with the Durham coast, with orchids and primroses abundant in the spring.

It was, however, far from spring-like when I visited last week, with a biting wind blowing in from the North Sea. The clear skies, however, gave some spectacular views. Looking north, I could see almost the entire Permian coastline, as far as the headland at Souter, just south of South Shields whereas in the other direction I could see the industrial sprawl of Teeside and, beyond it, the North York Moors south to Whitby. About 80 kilometres of coastland were on display from the beach at Blackhall.


Looking north along the coast at Blackhall Rocks on a cold February day.

My interest in Blackhall lies in the particular type of limestone that is found here.   The technical term is the “Hesleden Dene biostrome” and, looking closely, I can see within it some finely laminated horizontal layers within the rock, each no more than a millimetre thick, that are formed from layers of filamentous blue-green algae, such as those we have seen in the River Ehen and elsewhere, albeit marine rather than freshwater, that gradually accumulated on the shallow bed of the tropical sea that I fondly dream about.   They are often flat, as in the picture below, but sometimes form mounds and hummocks reminiscent of the stromatolites that I wrote about recently (see “The origins of life …”). The twenty kilometres I travelled from my home to Blackhall is also a journey back 250 million years, well before the age of the dinosaurs. Yet it is also a reminder of a yet more ancient world, that of the Precambrian where the earliest fossils of stromatolites have been found. That requires us to repeat the 250 million year journey to the Permian about six more times to take us back 1.5 billion years to the middle of the Precambrian.


Laminated strata of fossilised algae in the Hesleden Dene biostrome at Blackhall Rocks.  

I’ve known about the fossil algae at Blackhall for a long time and they were even the subject matter for a piece of video art I produced whilst doing my Fine Art degree (fear not .. the file is far too large to consider uploading).   Whilst searching the internet for information to refresh my memory I happened upon a resurrected online edition of The Vasculum. This was a local natural history journal produced by the Northern Naturalists Union, which thrived on contributions by both amateur and professional ecologists. During my time as a postgraduate student, Tom Dunn, the editor (and an enthusiastic lepidopterist) would prowl the corridors of the Botany and Zoology Departments at Durham making sure that we had all paid our subscriptions.   I had thought that The Vasculum was one more victim of our gradual slide towards a culture of armchair naturalists so I was delighted to see that it is now thriving in a new, online format. Long may it last.


Birtle, M. (2012). The Permian landscape of the north-east coast in 2012. The Vasculum 97: 1-32.

See also: Blackhall Rocks (GCR ID: 3016) In: Volume 8: Marine Permian of England, Chapter 3: North-east England (Durham Province), Geological Conservation Review, JNCC

First record of Navicula supergregaria in the UK?

I encountered a diatom in a sample yesterday that I had not seen before and, after checking some books, am fairly confident that this is Navicula supergregaria Rumrich & Lange-Bertalot 2000 and that this is the first record of the species from the U.K. I found this in a sample collected from the River Alver, close to Kingfisher Caravan Park in Gosport, Hampshire from April 2014.   It was a gritty sample that did not make for easy counting and contained several taxa that suggested that the river at this point is brackish.

As the name suggests, Navicula supergregaria is similar to Navicula gregaria, albeit larger (> 6.5 mm breadth) and the pores in the striae are just about visible with the light microscope (24-28/10 mm).   My previous post mentioned three distinct forms of Navicula gregaria recognised by Eileen Cox; N. supergregaria is an additional form, previously recorded in similar habitats in the Netherlands and Germany as well as in the USA.   In this sample, it mingled with “true” Navicula gregaria and a distinctive population of Navicula salinarum too.


Navicula supergregaria from the River Alver, Gosport, Hampshire, April 2014. Scale bar: 10 micrometres (1/100th of a millimetre).


Navicula salinarum from the River Alver, Gosport, Hampshire, April 2014. Scale bar: 10 micrometres (1/100th of a millimetre).

The ecology of cold days …

It is counter-intuitive but algal communities in rivers are often at their most diverse and abundant during the coldest months of the year.   Three months ago, the upper surfaces of stones at a site I visited last week were rough to the touch but, today, they are covered with a thick, chocolaty- brown film.   The explanation may lie in the absence of the small snails that were so abundant on my previous visit (see “The Complex Ecology of a Submerged Stone”) though this is probably only part of the story.   Were you to lift up the bonnet and poke around in the engines of these algae, you might find some clever adaptations to the cold that the bugs that graze them lack, though there are only a few tantalising hints in the scientific literature. More about this in a future post …


Thick biofilms from Smallhope Burn, February 2015.   Left hand image: a submerged brick removed from the water at Knitsley Bridge; right hand image: a cobble photographed in situ at Low Meadows.  

The dark-brown layer is usually very thin and underlain by a thicker, lighter layer (think of the stone as a slice of toast, topped with butter and marmite).   Under the microscope, this dark-brown layer resolves into a mass of motile diatoms that have congregated at the top of a mixture of organic and inorganic particles and other microorganisms, many of which will be fungi and bacteria involved in the breakdown of organic matter.   The most common diatom in these films, in my experience is Navicula lanceolata, but you rarely find pure growths, and other Navicula species, particularly N. gregaria and N. tripunctata are often intermixed and sometimes dominate.

Navicula lanceolata has very characteristic kayak-shaped cells which contain two parallel chloroplasts.   Navicula gregaria is generally smaller but has a similar shape, except that the ends are drawn out to a short “beak”.   Once again, there are two chloroplasts but these are slightly offset from one another.   Navicula tripunctata is has parallel sides, reminiscent of a Canadian canoe and, again, two parallel chloroplasts.   All three move around constantly under the microscope slide, making it hard it measure them accurately.


Navicula lanceolata from Smallhope Burn, County Durham, February 2015.   Scale bar: 10 micrometres (1/100th of a millimetre).


Navicula gregaria from Smallhope Burn, County Durham, February 2015.   Scale bar: 10 micrometres (1/100th of a millimetre).


Navicula tripunctata from Smallhope Burn, County Durham, February 2015.   Scale bar: 10 micrometres (1/100th of a millimetre).

All three of these species are both taxonomically well-defined and very widely distributed. Many Floras refer to them as having preferences for enriched water but my data contradicts this, as they are common across the pollution gradient. I have also found them in numbers at many sites almost free from human influence.   They seem to grow well on the top surface of stones in almost any type of water so long as it is well-buffered and close to neutral pH,. The seasonal preference is easier to demonstrate: the graph below shows how much more likely it is to encounter Navicula lanceolata in abundance in late Winter and Spring compared to other months.   N. gregaria and N. tripunctata show similar (though not identical) trends and I suspect that the ecology of all three species is defined more by physical than chemical conditions: give them cool, well-lit conditions and they will thrive. Indeed, for a river-dwelling organism, “cool” and “well-lit” often go hand-in-hand as there is less marginal vegetation at this time of year, compared to in the summer.

At this point, hard evidence to support my comments dries up. We know a lot about how the distribution of diatoms varies in relation to chemical variables that are fairly straightforward to sample and/or measure in the field – pH, conductivity, nutrient concentrations etc – but far less about the detailed interactions of these organisms with other organisms and, indeed, with less straightforward parameters.   To paraphrase Donald Rumsfeld, there are far more “known unknowns” than there are “known knowns”, and I have no idea (obviously) about the “unknown unknowns”. Except that I suspect that there are some very interesting stories yet to be revealed.


Distribution of records of Navicula lanceolata by month. The line represents sampling effort (percent ofamples collected in a given month) and vertical bars represent samples where N. gregaria forms >16% of all diatoms (90th percentile of all samples where N. lanceolata is present, ranked by relative abundance).

Note: my comments about these three species being taxonomically well-defined are partly based on extensive analyses of the RbcL genes of these species in a study that I have written about previously (see “When a picture is worth a thousand base pairs …”) though which is still unpublished.   There are some nuances in the case of Navicula gregaria, as there are at least three distinct forms, though one is largely brackish and the other mostly found in more oligotrophic (low nutrient) habitats. Our study has probably focussed mostly on the third type (“Navicula gregaria B” in Cox, 1987).  More about Navicula gregaria in “On the trail of Arthur Scott Donkin”.


Cox, E.J. (1987).   Studies on the diatom genus Navicula Bory. VI. The identity, structure and ecology of some freshwater species. Diatom Research 2: 159-160.

Kelly, M.G., Juggins, S., Guthrie, R., Pritchard, S., Jamieson, J., Rippey, B, Hirst, H. and Yallop, M (2008). Assessment of ecological status in U.K. rivers using diatoms. Freshwater Biology 53: 403-422.

The madness that is “British values”


This post is a slight diversion from the core business of my blog, but bear with me because some of the themes will resonate with issues that I have been writing about over the past couple of years.

Recently, a local school, Durham Free School, made national headlines after an excoriating Ofsted report.   The Ofsted inspection was one of a number of inspections called at short notice on faith schools in the region and there seemed to have been a particular focus on determining whether or not the school taught “British values”.   The inspectors commented that the school was “…failing to prepare students for life in modern Britain. Some students hold discriminatory views of other people who have different faiths, values or beliefs from themselves”.   If true, it would be damning but as my job for the past 20 years has involved developing objective measures to determine the success of policy (albeit for the environment rather than education), I was curious to see just how OFSTED inspectors arrived at this conclusion.

The report itself is not very illuminating on methods: the inspectors “…spoke to students in lessons, at break and during lunchtimes. They also spoke formally to two groups of students on the first day of the inspection.”   What, in particular, I wondered, did they ask before arriving at their conclusion about these “discriminatory values”?   I’ve read the whole report, I’ve searched the OFSTED website and I’ve looked at OFSTED’s publication Inspecting Schools: A Handbook for Inspectors.     The Handbook explains that Inspectors should consider how well management and leadership ensure that the curriculum “… promotes tolerance and respect for people of all faiths, genders, ages, disability and sexual orientation…” but there is nothing that explains how such an evaluation should be performed.   The Inspectors, I conclude, simply reported their opinion based on the conversations they had with this small sample of pupils.

Let’s look at this process from a statistical perspective: the Inspector’s opinion is, in effect, a test of the hypothesis that “students hold discriminatory views”, which could be re-cast as a null hypothesis: “students do not hold discriminatory views”.   The Inspectors reach their opinion via the conversations mentioned above (no mention of whether there was a set form of questions, whether students were interviewed as a group or individually or whether closed or open questions were used).   The outcome is cited in the report in absolute terms but, in reality, is a probability based on the outcomes of the interviews.   And, because they only interviewed a sample of students, there will be uncertainties associated with this outcome.   The Inspectors might have reached the wrong conclusion. In statistical terms this means that they rejected the null hypothesis based on their sample because most of the students, in fact, hold non-discriminatory views – a “Type 1 error”.

That the Inspectors concluded that “some students” held these views is, perhaps worrying in itself. We could argue, in support of the inspectors, that there should be zero tolerance of discrimination of any kind. Yet this then raises the question of whether the limited sampling program deployed by the inspectors is sufficiently sensitive to detect discrimination in every school where it occurs (i.e. to retain the null hypothesis when it should have been rejected – a “Type2 error”).   On the other hand, if Ofsted published detailed guidelines on how such evaluations were to be performed (guidance on sample size, types of questions and so on), and the Inspectors at Durham Free School had given more details of the sample size on which they based their judgements, then perhaps we would be in a better position to evaluate the credibility of their judgements. The reality, I suspect, is that the risk of a wrong outcome will be high because the sample size was small. The two inspectors had just two days to evaluate all aspects of the teaching and governance of the school. Some topics that deserved detailed scrutiny were, inevitably, evaluated in a superficial manner as a result.

The core of the problem was summarised neatly in an editorial in The Independent today which places the blame squarely on Michael Gove, the previous Education Secretary, for putting “British values” onto the list of criteria that Ofsted were required to inspect.   The problem, The Independent comments “is that no one can say exactly what it means, which gives inspectors enormous leeway to decide whether or not a school is teaching the said value correctly.”   Political ideology, at some point, has to be translated to practical action and the success or otherwise of policy depends on being able to make judgements consistently across the entire country.   If Ofsted are unable to convert Michael Gove’s rhetoric into transparent and fair measures, then they should resist being drawn into an arena where objectivity comes second to political grandstanding.

Ecological assessment in the fast lane …

Fifteen months ago, I reported on a new approach to rapid assessment of streams and rivers that I was developing with some colleagues (see “A RAPPER in da Lake District …”). Since then, we’ve continued developing and testing the method and, I am pleased to say, the results are very encouraging.

The idea behind RAPPER (“Rapid Assessment of PeriPhyton Ecology in Rivers”) is that a biologist can make a quick examination of the composition of larger algae which can then be used to assess the ecological status of the stream.   This involves recording the presence of different types of algae and, if necessary, checking the identity under a microscope. At the moment, this check needs to be done back in the laboratory, but it should also be possible to do this with a field microscope, which means that results will be available almost immediately.   The method allows sites to be classified as “high or good status” (which are both acceptable conditions according to the Water Framework Directive) or “moderate, poor or bad status” (which means that their condition needs to be improved). The former category is defined by the presence of algae which we know to be sensitive to pollution; the latter by high abundances of algae that we know are tolerant to pollution.

We managed to achieve agreement between RAPPER results and outcomes from more labour-intensive assessments in 72% of cases, which compares favourably with other situations where I have compared different types of algal-based assessments.   Of the remaining sites, 17% either had no appropriate indicator species or low abundances of tolerant species, whilst the remaining 11% had both sensitive and tolerant species present.   After some more analyses, we decided that these sites were probably in an intermediate state of risk.

The sensitivity of the RAPPER classification is highlighted by the charts below. The first shows the relationship between the three classes identified by RAPPER and the accompanying Trophic Diatom Index (TDI) value.   The first three classes show a nice clear separation, with low TDI values associated with the high and good status sites and higher TDI values associated with the more impacted sites. The final class (4_no_data), those for which we had no reliable indication of status, spanned a wide range of TDI values.   There are a number of possible reasons why these sites could not be classified, including a lack of suitable substrata for the algae to grow or heavy shade.  Maybe some extra refinements to RAPPER will mean that we can obtain more reliable classifications but it is important that we do no lose sight of the principle of “rapid assessment” in the process.   Better, perhaps, to reliably classify most sites, in order to free resources to look at those sites that are problematic in more detail?


Box-and-whisker plot showing difference in average TDI values for sites classified by RAPPER as high or good status (“1_HG”), maybe at risk of eutrophication (“2_both”) or moderate, poor or bad status (“3_MPB”) along with sites that could not be classified (“4_no_data”)

The second graph shows the relationship between the RAPPER classifications and soluble phosphorus and a similar pattern emerges, with sites classified as high or good status associated with low phosphorus concentrations, and those classified as impacted (3_MPB) associated with higher values.   Results for total phosphorus, total oxidised nitrogen and ammonia-nitrogen show similar trends, all of which suggest that the method is classifying sites correctly.


Box-and-whisker plot showing difference in median for soluble P for sites classified by RAPPER as high or good status (“1_HG”), maybe at risk of eutrophication (“2_both”) or moderate, poor or bad status (“3_MPB”) along with sites that could not be classified (“4_no_data”).

I’m particularly enthusiastic about RAPPER because it the outcome of convergent thinking between myself and colleagues in two separate agencies dealing with variants of the same need to cover a lot of ground with limited resources. The cost of full-scale ecological assessments is such that the sampling network is relatively thin.   This means that a diagnosis of a problem needs to be followed up by an investigation of the source of that problem in order to develop an appropriate programme of measures to address this. The idea of RAPPER and other rapid assessment approaches is not to replace the official methods, but to enable the operational biologists to collect information from a number of sites in a catchment that would then allow them to use resources more intensively.   RAPPER is, in other words, is part of an ecological “triage”.   And, with the public spending squeeze set to continue, being able to prioritise resources effectively continues to be one of our biggest challenges.

Swimming with desmids …

My sampling trip to Upper Teesdale in search of desmids (see “Hunting for desmids in Upper Teesdale”) has now yielded another picture, this time figurative rather than semi-abstract.   I have tried to depict the world inside a Sphagnum bog so have shown two desmids underneath a canopy of Sphagnum leaves.   The Sphagnum leaves have a characteristic structure, with chlorophyllose cells alongside water-filled “hyaline” cells. The desmids live, in effect, inside a glass-roofed conservatory although I have probably conveyed an overly bright impression of the subaquatic world of the bog.   The reality is that the slow decay of Sphagnum yields brown humic materials that create an altogether murkier environment.


The microscopic world of an Upper Teesdale Sphagnum bog, with desmids living in the space underneath Sphagnum leaves.   The chlorophyllose cells are about ten micrometres in diameter (1/100th of a millimetre) whilst the desmid in the foreground (Cosmarium ralfsii) is about 100 micrometres (1/10th of a millimetre) across.

I’ve tried to illustrate the structure of a Sphagnum leaf in the diagram below.   Compare this with the photograph in “More from Upper Teesdale” (showing the view from above) the leaf to get an idea of how the leaf is constructed.   It also demonstrates why Sphagnum moss is capable of absorbing so much water: two-thirds or more of the leaf is composed of empty space and there is even a convenient pore to let the water in.


A schematic cross-section through a leaf of Sphagnum showing the arrangement of hyaline and chlorophyllose cells.   The chloropyllose cells are about 10 micrometres (1/100th of a millimetre) across.

My illustration of the microscopic world of a Sphagnum bog is a step outside my comfort zone, as I tried to combine the various elements together from separate microscopic images.   Microscopy tends to flatten perspective, partly because specimens are squashed onto microscope slides but also because of the focal length of the lenses involved.   Added to this was the problem of depicting the sinuous chlorophyllose cells in an approximation of single-point perspective.   Almost as soon as I had finished the picture, I was thinking about how I could be improving the next version. Striving towards realism is, itself, an ongoing mind experiment that offers tantalising glimpses of an otherwise hidden world.

The origins of life …

I have been reading Richard Fortey’s book “Survivors” (see “”They don’t do much, do they?””) which is a rare and precious thing in the world of natural history writing as he devotes two whole chapters to the algae.   The first of these describes his encounters with living stromatolites in Shark Bay, in Western Australia.   The point he is making as he writes is that he did not just make an extraordinarily long journey to get there (first, get to Perth, then travel a further 800 km north …) but that he is also making a similarly long journey back in time, as stromatolites are survivors from the Precambrian era and, indeed, may have played a vital role in creating the oxygen-rich atmosphere that we take for granted.

I have a polished specimen of a stromatolite, purchased from a fossil shop in Durham, which shows the characteristic fine laminations. Each of these represents a layer of Cyanobacteria (blue-green algae) filaments which have, in turn, trapped sediment particles.   The laminations are, in turn, formed into dome-like structures, reflecting the vertical growth of the filaments in search of sunlight.   This stromatolite is from the Ordovician era (I think), which dates it to between 443 and 485 million years ago.


A stromatolite from Argentina, possibly from the Ordovician era. The specimen is 10 cm long.

Not only were stromatolites extremely abundant in the Precambrian (approx. 4.6 billion to 540 million years ago) but the organisms from which they were formed appear to be very similar to Cyanobacteria that can still be found today.   They are extremely delicate structures that thrived, at least in part, because there were few other organisms in the Precambrian that could compete with them or graze them and, consequently, had shallow marine habitats to themselves for an extremely long time. During this period, they were busily photosynthesising away, taking carbon dioxide and water and converting it to simple sugars (which they needed to grow) and oxygen (which was, as far as the Cyanobacteria was concerned, a waste product). This oxygen was released as tiny bubbles (see “Ecological yin and yang…”) which, ever so slowly, accumulated in the atmosphere.   Maybe it is no surprise that the Precambrian, the era before fossils of multicellular organisms are common, lasts for about four fifths of the entire lifespan of the earth: it took this long for all those tiny bubbles to add up to enough oxygen to allow more complicated organisms to survive.

And what did those multicellular organisms feed upon?   That’s right: the Cyanobacteria had sown the seeds of their own destruction.   There is evidence not just of a gradual decline of stromatolites through the later Precambrian and into the Cambrian and Ordovician eras, but also of a resurgence of stromatolites after the mass extinction at the end of the Ordovician (which would have removed the multicellular grazers and left our tough little Cyanobacteria behind).   Stromatolites are found sporadically throughout the fossil record and in a small number of locations in the present day, but their heyday lies far in the past.


Bengston, S. (2002). The early worm catches the – what?   Pp. 289-317. In: The Fossil Record of Predation (edited by Kowalewski, M., and Kelley, P.H.). The Paleontological Society Papers 8, The Paleontological Society, Boulder, Colorado.

Fortey, R. (2011).   Survivors: the Animals and Plants that Time Has Left Behind.   Harper Press, London.

Sheehan, P.M. & Harris, M.T. (2004). Microbialite resurgence after the Late Ordovician extinction. Nature (London) 430: 75-78.