Identification by association?

A few months ago, I wrote briefly about the problems of naming and identifying very small diatoms (see “Picture this?”).   It is a problem that has stayed with me over the last few months, particularly as I oversee a regular calibration test for UK diatom analysts.   The most recent sample that we used for this exercise contained a population of the diatom formerly known as “Eolimna minima”, the subject of that post.   Using the paper by Carlos Wetzel and colleagues, we provisionally re-named this “Sellaphora atomoides”.   Looking back into my records, I noticed that we had also recorded “Eolimna minima” from an earlier slide used in the ring test.   These had a slightly less elliptical outline, and might well be “Sellaphora nigri” using the criteria that Wetzel and colleagues set out.   There are slight but significant differences in valve width, and S. nigri also has denser striation (though this is hard to determine with the light microscope).   These populations came from two streams with very different characteristics, so there is perhaps no surprise that there are two different species?


A population of “Eolimna minma” / Sellaphora cf. atomoides from unnamed Welsh stream used in UK/Ireland ring test (slide #39)  (photographs: Lydia King).

The differences in ecology are what concern me here.   Wetzel and colleagues focus on taxonomy in their paper but make a few comments on ecology too.  They write: “The general acceptance is that S. atomoides … is usually found in aerial habitats (or more “pristine” conditions) while the presence of Sellaphora nigri … is more related to human-impacted conditions of eutrophication, pesticides, heavy metal pollution and organically polluted environments”.  This statement is worrying because it suggests that the ecological divide between these two species is clear-cut.   Having spent 30 pages carefully dissecting a confusing muddle of species, it strikes me as counterproductive to repeat categorical statements made by earlier scientists who they had just demonstrated to have a limited grasp of the situation.

The risk is that a combination of slight differences in morphology coupled with (apparently) clear differences in ecology leads to the correct name being assigned based on the analyst’s interpretation of the habitat, rather than the characteristics of the organism.   This is not speculation on my part, as I have seen it happen during workshops.   On two occasions, the analysts involved were highly experienced.  Nonetheless, the justification for using a particular name, in each case, was that the other diatoms present suggested a certain set of conditions, which coincided with the stated preferences for one species, rather than with those for a morphologically-similar species.

I have no problem with environmental preferences being supporting information in the designation of a species – these can suggest physiological and other properties with a genetic basis that separate a species from closely-related forms.  However, I have great concerns about these preferences being part of the identification process for an analysis that is concerned, ultimately, with determining the condition of the environment.  It is circular reasoning but, nonetheless, I fear, widespread, especially for small taxa where we may need to discern characteristics that are close to limits of the resolution of the light microscope.

Gomphonema exilissimum is a case in point.  It is widely-regarded as a good indicator of low nutrients (implying good conditions) yet there have been papers recently that have pointed out that our traditional understanding based on the morphology of this this species and close relatives is not as straightforward as we once thought.   Yet, the key in a widely-used guide to freshwater diatoms (written with ecological assessment in mind) contains the phrase “In oligotrophen, elektrolytarmen, meist schwach sauren Habitaten” (“in oligotrophic, electrolyte-poor, mostly weakly-acid habitats”) amongst the characters that distinguish it from close relatives.  The temptation to base an identification wholly or partly on an inference from the other diatoms present is great.

Including an important environmental preference in a key designed for use by people concerned with ecological assessment brings the credibility of the discipline into question.   Either a species can be clearly differentiated on the basis of morphology alone, or it has no place in evaluations that underpin enforcement of legislation.   That, however, takes us into dangerous territory: there is evidence that the limits of species determined by traditional microscopy do not always accord with other sources of evidence, in particular DNA sequence data.   These uncertainties, in turn, contribute to the vague descriptions and poor illustrations which litter identification guides, leaving the analyst (working under time pressure) to look for alternative sources of corroboration.  I suspect that many of us are guilty of “identification by association” at times.   We just don’t like to admit it.


Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011).  Diatomeen im Süßwasser-Benthos von Mitteleuropa.  A.R.G. Gantner Verlag K.G., Rugell.  [the source of the key mentioned above]

Wetzel, C., Ector, L., Van de Vijver, B., Compère, P. & Mann, D.G. (2015). Morphology, typification and critical analysis of some ecologically important small naviculoid species (Bacillariophyta).  Fottea, Olomouc 15: 203-234.

Two papers that highlight challenges facing the identification of the Gomphonema parvulum complex (to which G. exilissimum belongs) are:

Kermarrec, L., Bouchez, A., Rimet, F. & Humbert, J.-F. (2013).  First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta).   Protist 164: 686-705.

Rose, D.T. & Cox, E.J. (2014).  What constitutes Gomphonema parvulum? Long-term culture studies show that some varieties of G. parvulum belong with other Gomphonema species.  Plant Ecology and Evolution 147: 366-373.

The complicated life of simple plants …

I have a theory, which I have touched on before in these posts, that the success in conveying the wonders of nature to non-biologists is easiest when the audience can relate what they see directly to their own experiences.   You only have to watch a typical David Attenborough documentary to see this principle at work: it may feature sumptuous photography in glorious landscapes, but the events portrayed are not so different to a typical Friday evening at the Bigg Market in Newcastle.   The BBC Natural History Unit would find plenty of courtship activities, territoriality and several kinds of violence here, much of it set around watering holes.   Who needs a plane ticket to an exotic location?

As we lose that sense of empathy, so nature becomes “weird”.  A few of us find fascination in the weird but we are a minority.   Strangeness, however, brings problems, as I have commented before (see “Reflections from the trailing edge of science”) as stories cannot be conveyed using familiar metaphors drawn from our own experience.   The example I used in that earlier post was the concept of “alternation of generations” in plants and my recent encounter with the red alga Lemanea a couple of weeks ago (see “Spaghetti Carbonara con Lemanea”) reminded me of a set of wonderful photographs by Chris Carter that illustrate this concept very well.

That post contained a photograph of Lemanea from the River Ehen in Cumbria which shows some of the wiry filaments growing on the stream bed.   These filaments are, actually, hollow tubes of cells (see photograph in “The River Ehen in April”) along which there are a series of nodes.   The nodes, in this case, bear sexual cells at certain times of the year (see “Lemanea in the River Ehen”).


A cross section of a filament of Lemanea from the River Rede, Northumberland (photo: Chris Carter).

Chris’ photographs shows how the Lemanea filaments are actually composed of a hollow tube of cells with an outer cortex.  However, the centre of this tube is not completely empty, and the clusters of cells that we can see inside the tube are spore-producing organs called “carposporophytes”.   At some point during the development of the carpospores, two cells fuse so that the carpospores is diploid (2n), rather than haploid (n).   The carpospores are released when the Lemanea filament dies back in late Spring and these then germinate into a filamentous sporophyte (2n) phase, called the “chantransia”.  At some point during the winter, these chantransia undergo meiosis, and the resultant haploid cells grow, still attached to the chantransia, into the next generation of gametophytes.


Transapical view of a Lemanea filament; the arrows show the sporophytes (“carposporophytes”) inside (photo: Chris Carter).

Finally, I have included Chris’ high magnification photograph of some of the cells of this carposporophyte plant, looking very similar to simple red algal genera such as Audouinella, which prompted my original series of posts on alternation of generations.

These photographs capture my fascination with the algae: apparently simple, easily overlooked, but actually presenting sophisticated, highly-evolved solutions to survival under tough circumstances.   The constant current in rivers makes establishing and maintaining a population at one place hard enough, more so when a “population” actually consists of two discrete stages.   This has led some to suggest that the complexities of the red alga life cycle may be a form of “bet hedging”, spreading the risk of mortality between the life stages.   Having a large gametophyte phase, for example, gives the plants access to more light, making them more productive, but they are also exposed to the strong currents in the river, increasing their risk of loss due to scour.   On the other hand, the smaller sporophytes (the “chantransia”) are protected from the ravages of the current because they live close to rock surfaces, within a “boundary layer” where current velocity falls off due to drag.  It could be seen to be roughly parallel to the metamorphosis of butterflies and other insects, with phases of the life cycle optimised for different activities.

Lemanea faces a particular challenge: the gametophytes have “solved” (excuse the teleology) the challenge of living in very fast current speeds, where they have little competition from other plants and algae and, I would guess, little threat from grazing invertebrates.   This gives the genus plenty of scope to thrive in fast-flowing upland rivers.   There is normally a benefit to an organism of releasing spores and gametes into their immediate environment, as this encourages dispersal and cross-breeding. Were Lemanea to do this, the spores and gametes would be washed quickly downstream, away from their ideal habitat.  The practice of keeping the carposporophyte inside the thallus, rather than on the outside, increases the chances of some of the carpospores finding their way to the rocks in the immediate vicinity of the gametophyte and, thereby, ensuring that the chantransia are well-placed to produce a new gametophyte generation the following year.

It is all very complicated.  This is, I suspect, partly because systematic biologists have a fondness for obscure terminology that makes it hard for the non-initiate to follow the twists and turns of life cycles.  But it also, I suspect, a consequence of dealing with habits and life cycles that are unfamiliar and, more importantly, cannot be distilled down to simple, anthropomorphic metaphors.


High magnification view of carpospores of Lemanea (photo: Chris Carter).


Sheath, R.G. (1984).  The biology of freshwater red algae.  Progress in Phycological Research 3: 89-157.

Evolve or die?


Last June, I wrote a post titled “So what?”, which included a cartoon summarising all that I thought was wrong with the world of diatom specialists within which I move.   We have become, as a group, very good at naming and counting diatoms, but not very good at understanding how these fit into ecosystems.   Along with two colleagues, I included this cartoon in a paper that we wrote based on talks at the meeting that I wrote about in that post. One reviewer took umbrage at this, suggesting that “… it is really making a very bad favour to all the people working with diatoms, and to the efforts expended during many years to implement techniques related to them …” (sic).   Unfortunately, I feel that there is so much complacency amongst diatom specialists at present that we are hardly doing them a favour by writing platitudes. Inhabitants of the curious sub-discipline of diatom science seem to have drifted far from the frontline of functional ecology and some shock tactics are necessary in order to drag them back towards reality. We argued our case for including the cartoon and the editor agreed with us.

The roots of the problem are sociological and cultural rather than scientific: diatoms became established as the first choice algae for ecological assessment for a number of reasons, one of which was the absence of competition from advocates of other groups of organisms. Diatom methods behaved like an invasive species, spreading rapidly across Europe and beyond, exploiting the new “niche” created by the Water Framework Directive’s requirement that “phytobenthos” (i.e. attached algae) should be considered when Member States were evaluating the condition of their fresh waters.

What happened next was, I suspect, the natural consequence of academic specialisation. We all recognised that the first generation of methods were far from perfect but, as circumstances had selected diatom specialists (with their inclinations towards taxonomy) over those with interests in other algal groups and, more significantly, ecological processes, these people then dictated the next stages of development.   Over the past 15 years, I have watched the lists of species that analysts are expected to recognise gradually grow in length in many parts of Europe. Adherents of this approach claim greater sensitivity as a result, but there is little hard evidence to support this.   Rather, I think we are watching the natural inclination of specialists towards greater specialisation.

The line that we took in our new paper is that the “ecological status” that we are all trying to measure is a much broader concept than can be encapsulated by the composition of a single group of algae.   Importantly, it needs to consider not just what species are present but also how much biomass these create.   We recognise that measuring biomass is not an easy task but, paradoxically, diatom specialists in yet another recent paper point out that differentiating some groups of diatoms is difficult yet seem to think that this can be resolvable by greater diligence on the part of analysts, whilst every other facet of ecological status can be quietly ignored.

My inclination is to aim for much greater breadth of information in our assessments, accepting, at the same time, that this may entail less detail within the individual nuggets of information (see “The democratisation of stream ecology?”). There is, I recognise, a fine line between “streamlining” a method and “cutting corners” but it may be a price worth paying in pursuit of a wider goal. I explored this in a recent paper on redundancy in lake assessments (see “Unmasking the faceless Eurocrats …”), invoking the economic principle of “decreasing marginal utility”. Broadly speaking, the information content of any individual type of data decreases by a power law, such that the first 20% of effort (roughly) yields 80% of the answer.   The unique information content associated with the extra effort gradually tails off.   The question that no-one has satisfactorily answered is whether the “splitting” that now seems axiomatic amongst diatomists adequately balances the huge amount of information (on other algae, on biomass) that is completely ignored.

It seems straightforward if put in purely scientific terms, but the situation is complicated, again, by non-scientific, socio-cultural aspects. Specialist biologists, like all craftsmen/craftswomen, take pride in doing the best possible job. It is possible, too, that the extra data that they extract from a detailed analysis may turn out to be useful in the future, so why ignore it?   On the other hand, the creation of a cadre of specialist “diatomists” means that they see the “best possible job” exclusively in terms of their data and not in terms of the overall management of a river or lake. And finally, the widespread adoption of diatoms for assessment has created a niche for specialist contractors who work for environmental agencies and others performing the highly detailed analyses that are currently required. Any attempt to “streamline” the process threatens their livelihood.   So what starts as an impartial scientific debate is anything but, as the “Guild” of diatom analysts marshals its arguments.

Our paper forms the introduction to a series of papers arising from the Trento meeting. It may seem strange to open the proceedings with a fairly negative evaluation of the state of affairs, but I offer no apologies.   Pushing my ecosystem analogies just a little further, “specialist” organisms are vulnerable to changes in their habitat in a way that “generalists” are not.   The landscape of environmental regulation is not static and biologists, no less than the organisms they study, need to evolve in order to survive.


Kahlert, M., Ács, E., Almeida, S.F.P., Blanco, S., Dressler, M., Ector, L., Karjalainen, S.M., Liess, A., Mertens, A., van der Wal, J., Vilbaste, S. & Werner, P. (2016). Quality assurance of diatom counts in Europe: towards harmonized datasets. Hydrobiologia (in press) DOI: 10.1007/s10750-016-2651-8

Kelly, M.G., Schneider, S.C. & King. L. (2015).   Customs, habits and traditions: the role of non-scientific factors in the development of ecological assessment methods.   WIRES Water 2: 159-165.

Poikane, S., Kelly, M.G. & Cantonati, M. (2016). Benthic algal assessment of ecological status in European lakes and rivers: challenges and opportunities.   Science of the Total Environment (in press). (doi: 10.1016/j.scitotenv.2016.02.027) (The picture at the head of this post is the “Graphical Abstract” from that paper which is “open access”, thanks to the European Commission’s Joint Research Centre)

Going with the flow …


I’ve written before about my enthusiasm for Leonardo da Vinci as an exemplar of the fertility of bringing artistic sensibilities to science and vice versa (see “Imagined but not imaginary”).   A small exhibition at the Laing Gallery in Newcastle with ten of his drawings from the Royal Collection on display gave me an opportunity to indulge my passion, particularly as it included one drawing that is pertinent to the subject of this blog.

It is an intriguing story because it brings Leonardo together with some of the most notorious names in Renaissance Italy: Cesare Borgia and Niccolo Machiavelli.   It was at the court of Cesare Borgia that Leonardo crossed paths with Machiavelli, then the Florentine ambassador, and was later employed by the government of Florence on a grand engineering scheme.

The scheme – which truly deserves the adjective “Machiavellian” – involved diverting the River Arno downstream of Florence in order to deprive their rivals, the Pisans, of the water supply they needed to survive a siege.   Later in the same year, he was also commissioned to design a canal to help convey Florentine trade goods to the Mediterranean. The diagram above is one of the maps he drew as part of his preliminary survey of the river and shows the River Arno flowing from left to right.

What is interesting is his depiction of the damage caused by the river at two points on the bank below the weir. The impression from the map is of an artificial embankment on the right bank of the river which is being eroded by the force of the river as it emerges from the weir and then again a short distance downstream as the current describes an arc within the river channel. Called in to advise on “hard engineering”, he deftly points out the folly of working against nature.  Like many of Leonardo’s grand ideas, the diversion of the Arno never got passed the planning stages. Ironically, his plans to alter the Tuscan landscape were confounded by changes in the political landscape: the defeat of Pisa by conventional military means and, ultimately, the defeat of Florence and Machiavelli’s fall from power.

I would have noted this drawing and have moved on were it not for an article I had read the same morning in the Independent on Sunday, describing the UK Government’s belated conversion to the importance of soft engineering in the aftermath of the winter floods. Increased spending on flood defence is also a key feature of today’s budget and, whilst a large part of this will, I am sure, be directed towards old-fashioned hard engineering (and, indeed, this will be necessary to protect some towns), I am glad to see that, 500 years after Leonardo, its limitations are finally being recognised by politicians.

How to make an ecologist #8


During my PhD years, Brian Whitton was also running a project in Bangladesh, looking at the ecology of deepwater rice fields, and gave me the opportunity to exchange the bleak Pennine hills for the tropical lowlands of the Indian sub-continent for part of one summer.   The premise of the project was that the rice fields here typically flooded to 1.5 or even 2 metres depth. The varieties of rice that grow in these fields had been studied by traditional agronomists but the sheer quantity of water meant that the rice fields resembled shallow lakes and, perhaps, studying the rice from the perspective of a freshwater ecologist would yield better insights into their yield.

The British High Commission allocated us a house in the diplomatic suburb of Dhaka, and gave us use of a Land Rover to negotiate the noisy mêlée of bicycles, rickshaws, buses and lorries that congested the streets of the capital, before we broke free from the urban areas and drove along narrow tree-lined roads running along the ridges between rice fields.   About an hour to the south east of Dhaka, we pulled to the side of the road, close to a small village where the team had worked in previous years.   The village was on a small island about 300 metres away across the rice field, but the sight of our Land Rover arriving would prompt our boat boys to set off in their punts to join us.

Moving through the fields in their small boats, I was struck by the fecundity of the fields. Prolific growths of aquatic plants thrived amidst the rice plants. Some, such as the water lilies in the foreground of the picture above, were familiar from home, others, such as water hyacinth (Eichhornia crassipes) and water lettuce (Pistia stratiotes) I had only previously read about.   The rice plants, themselves, were intriguing: they had shallow roots in the sediments, relying on the water for support, but had clusters of “aquatic roots” growing at intervals along their long (up to two metre) stems.   The stems and leaves were also smothered, in places, with growths of nitrogen-fixing blue-green algae such as Rivularia. I wanted to illustrate this diversity with some of my photographs of this diverse ecosystem but have only managed to find a few very general shots.   Accepted wisdom was that the fertility of lowland Bangladesh was derived from silt deposited by the rivers Ganges and Brahmaputra; looking closely at a rice field and the situation looked far less straightforward.    The prolific aquatic roots, compared with the shallow true roots, suggested that the rice plants depended upon the water, and not the sediments.


One of our boat boys at Sonargon in Bangladesh. The upper photograph shows fieldwork underway in the rice fields with (from left), Motaleb, Ashit Paul and Jo Rother.

The question we were trying to answer was how the rice plants got the nutrients they needed, given this situation.   The answer came, at least partly, from extensive measurements of the water chemistry of the rice fields using a combination of dataloggers, attached to a range of instruments measuring pH, temperature and oxygen concentration in the water. These sat in metal boxes on specially-constructed platforms, guarded by the village boys who were also our boatmen.   We also moved amongst the fields collecting other measurements to complete the picture.

The water in the rice fields was very soft, with little natural buffering capacity and this, along with the warm temperature and abundant sunlight, meant that the pH fluctuated dramatically between daytime (when plants were removing carbon dioxide from the water for photosynthesis) and night-time (when the carbon dioxide they produced during respiration reacted with the water to produce dilute carbonic acid).   There was a very neat relationship, too, with the concentration of oxygen in the water – high concentrations produced during daytime and low concentrations recorded at night.   This, in turn, is key to understanding the fertility of the fields as phosphorus, in particular, is more soluble in the anerobic conditions, so the deeper, darker areas of the rice fields were rich in phosphorus released from the sediments, which was then available to the aquatic roots. As the season progressed, so the extent of the anoxic areas within the field increased.   The “fields”, in other words, were behaving in exactly the same way as shallow lakes.


Graphs from one of the Durham University reports on deepwater rice ecosystems to the Overseas Development Administration and EEC on deepwater rice fields showing the relationship between dissolved oxygen and pH in deepwater rice fields in Bangladesh, 1985 and 1986.   All measurements on a graph were made on the same afternoon, showing the wide variation in conditions even in a small area.

In between our fieldwork, we had a spacious house in the diplomatic quarter of Bangladesh with a very competent cook, Swapan, who came from Chittagong, close to the border with Burma (now Myanmar).   Our diet was mostly local food, heavily biased towards fish and prawns, which also formed part of the rice field ecosystems.   I had a particular fondness for biryanis, but also for a rice and lentil dish called khichuri. Neither, however, was washed down with beer because Bangladesh was dry. Our only source of alcohol was the British Aid Guest House, populated by characters who could have walked straight off the pages of a Graham Greene novel.   Compared to experiences a few years later in Nigeria, attitudes amongst the aid community were antediluvian, bordering on racist at times. Fortunately, perhaps, our intensive work schedule left us with little time for socialising.

At a deeper level, this experience of tropical ecology brought me closer to the world of television natural history programmes that had excited my interest in ecology in the 1970s.   The lush vegetation and exotic landscapes had piqued my interest although fate seemed to have decreed that my world would rarely overlap with the charismatic megafauna that populated Attenborough’s documentaries.   My future seemed to lie at the unfashionable end of biodiversity.

Spaghetti alla Carbonara con Lemanea


Fieldwork in March brings out the forager in me, as lush growths of the red alga Lemanea smother the beds of our upland rivers at this time of year. Considered a delicacy in some parts of the Himalayas, I started my own culinary experiments with it and, last year, had my first success (see “Freshwater algae on the menu … again”). This year, I have branched out a little further, and offer you my own variant of the classic Italian dish Spaghetti alla Carbonara, which you can find in most Italian cookbooks (interesting theory for the origin of the dish if you follow this link. The twist to my recipe is to replace the bacon or pancetta with hot smoked salmon.

Gently fry a crushed garlic clove in a little olive oil whilst the pasta is cooking, then, add the salmon, cut into chunks (about 50 g per person), and turn for a couple of minutes.   Drain the pasta and add it to the pan with the salmon and garlic. Now take it off the heat and stir in a mixture of beaten eggs (two per person) and parmesan cheese (about a tablespoon per person) plus salt and pepper.   The key to a good Carbonara is to make sure that the eggs thicken to form a creamy sauce, and do not scramble.   I added chopped filaments of Lemanea, prepared as described last year, as a garnish on top of the pasta / egg / salmon mix, and served it with a rocket and water cress salad.   The alga has a distinctive fishy taste that complements, but does not overwhelm, the salmon.   Not only delicious, but also less than 20 minutes from putting the pasta into boiling water to sitting down to eat it.


Spaghetti alla Carbonara con Lemanea.

The photograph shows Lemanea growing on a submerged stone (about 20 cm across) in the River Ehen, Cumbria in March 2016.

Identity crisis?


Plant or not? Filaments of the red algal genus Batrachospermum, with whorls of branchlets and carposporophytes (the dark patches amidst the branchlets), photographed by Chris Carter.   250 mm = a quarter of a millimetre.

When I worked in Nigeria, I used to set my students an essay with the title “Euglena: plant or animal? Discuss”. I was trying to get my students to think about what we meant by words such as “plant” and “animal”, especially when confronted with simple life forms that shared characteristics with both plants and animals” (see “A visit to Loughrigg Fell” for more about Euglena).   Over the subsequent 20 years, the question has resolved itself, insofar as most textbooks offer a resounding “neither” in response to questions about the provenance of many algae.   The old certainties were overturned first by evidence provided by the electron microscope and, more recently, by molecular biology. Now, academic scientists mostly accept that “algae” is a collective term for a disparate group of simple organisms, and that many of these groups, individually, are more closely related to protozoans and fungi than they are to each other, or to what we usually think of as “plants”.


Plant or not? An assortment of cells of various species of the desmid Micrasterias, photographed by Chris Carter.   The largest is about a quarter of a millimetre in length.

Oddly, those who study algae continue to gather, despite the increasing irrelevance of the term.   Perhaps, then, “algae” can be defined as organisms studied by algologists?   Or perhaps not, partly because the neat alliteration is inappropriate, as most of us prefer the term “phycologist” (see “It’s all Greek to me …” for an explanation; “algos” actually means “pain” in Greek … work that one out if you can.).   The fact that those who study algae still find common ground suggests that the term “algae” still has some relevance.

So I turned with interest to a new opinion piece in the journal Aquatic Botany by John Bolton, with the title “What is aquatic botany? – and why algae are plants…”. He wrote it as a reaction to the increasing pedantry of editors and reviewers who object to, for example, kelps being referred to as “plants” and he makes a very strong case for retaining algae within the popular concept of “plants”.   His point is that we should not think of terms such as “plant” simply in terms of Linnaean taxonomy (and, more particularly, through minds conditioned by Hennigan cladistics that presumes biological taxa to be monophyletic). This is because the naming of plants is not the exclusive preserve of taxonomists.   Another pertinent recollection from my time in Nigeria is that the locals referred t many spinach-type plants as “green leaf”. These plants came from many different families but were united by shared use in Nigerian cuisine. It was a functional taxonomy that trumped Linnaeus everywhere outside the botany laboratory.   And so it is with algae.


Plant or not? Cells of the diatom genus Achnanthidium, photographed by Chris Carter (25 mm = 1/40th of a millimetre)

John Bolton’s definition of plant is “those organisms which carry out chloroxygenic photosynthesis” (i.e photosynthesis using chlorophyll a and producing oxygen); his definition of “algae” is: “all plants, excluding the Embryophyta” (i.e. “higher plants”).   In other words, “algae” are what we always thought algae were, before the pedants shouldered their way in to the party.   Of course, these pedants are right in strictly evolutionary terms. However, taxonomists are biology’s janitors, tidying away all of nature’s marvels into neat categories, but not necessarily always seeing the big picture. In a Platonic sense, an alga has a “form” that transcends taxonomy and this, in turn, generates properties that algae share with each other and with other “plants”, regardless of their evolutionary pathway. Algae from different phyla often live in close proximity in similar habitats. They interact with one another, which means that to understand the ecology of one group, you really need to know about the ecology of others too. And, more practically, these common features mean that the methods we use to study them are similar.

That brings us back to my first alliterative (and etymologically clumsy) definition: “algae are what algologists study”.   The overlaps between “algae” and “plants” and between groups of algae may not be valid in the eyes of a systematist, but they reflect reality.   I started my career in a Botany department, and I am pleased that John Bolton thinks that I was not there under false pretences.   Algae are still plants. Hooray!

Plant or not?   The first two images, are of red and green algae, which are “plants” in both a strict taxonomic sense (“Plantae”) and a more widely-understood sense. Diatoms, on the other hand, are “plants” in the broader sense that John Bolton suggests, but belong to one of the parallel pathways that purists would not consider to be “true” plants.


Bolton, J.J. (2016). What is aquatic botany? – and why algae are plants: the importance of non-taxonomic terms for groups of organisms. Aquatic Botany (in press) doi:10.1016/j.aquabot.2016.02.006

See also: Raven, J.A. & Giordano, M. (2014). Algae. Current Science 24: 590-595.

How to make an ecologist #7


Casting a plankton net to collect algae, somewhere in Scotland (possibly Loch Earn), April 1985.

At some point between leaving Westfield as a rookie ecologist with an enthusiasm for Sphagnum, and finishing a PhD on mosses at Durham I started the slow metamorphosis into a phycologist.   Brian Whitton expected his PhD students to help out in undergraduate practicals and my lack of phycological training up to that point was not regarded as sufficient reason to excuse me from this duty.   It was a steep learning curve but, in turn, it opened windows onto new worlds that have kept me fascinated ever since.

Brian had an old school natural historian’s approach to undergraduate practicals.   Technicians were sent out to local ponds and came back with handfuls of vegetation which were squeezed and scraped to yield rich harvests of algae. At the start of the practical, no-one had any idea which species might be present; three hours later, with the help of a handful of books in a range of languages (we just looked at the pictures) and cajoling from Brian, the demonstrators, at least, emerged older and wiser.

Straight after Easter, the third year botany students were taken on a week-long field trip to Loch Lomond, staying at University of Glasgow’s Rowadennan Field Centre, and learning about algae at a time when most of them would really have preferred to be getting on with revision for their finals.   However, once they arrived at the field centre, set amidst the forests on the east shore of Loch Lomond in the shadow of Ben Lomond, they usually mellowed.   It was a glorious location. We went out to various lochs and streams, sampled different habitats, collected a few environmental measurements, and then spent time in the laboratory trying to name what we had found.   In the evenings most of us made the three kilometre walk to Rowardennan Hotel for a pint of beer.

On one of the days we made a long excursion, down the east shore of Loch Lomond, then up the west shore, making a short diversion at Tarbet to Loch Long, the only sea loch we visited during the week. Then it was back into the vans and up to the north end of Loch Lomond, stopping at a stream in Glen Falloch before sampling Loch Lubhair and Loch Linhe. The final leg swung south past Loch Venachar to Lake of Menteith in the Trossachs (‘the only lake in Scotland’) before returning to Rowardennan in time for dinner. In one long day we had seen marine and freshwater habitats, sampled hard and soft streams and lakes, planktonic and benthic habitats and seen seaweeds as long as our arms and microscopic algae a 100th of a millimetre in diameter.


Durham University botany undergraduatest getting to know freshwater algae at Rowardennan Field Centre, April 1985.

At this time, the Durham botany degree was strong on biochemistry and molecular biology and notoriously light on traditional botanical skills.   There was a running joke during my postgraduate years that some of our molecular biologist colleague’s plant identification skills ran no further than reading the label on a packet of seeds. Reductionism ruled, with teaching on whole plants and their interactions with the environment pushed to the edges of the course.   The honours botany students were taken on a two week field course to Austria at the end of their second year to learn about alpine plants. This week in Rowardennan dealt with the 75 per cent of UK’s plant diversity that has now dropped off most undergraduate curricula over the past couple of generations. And, once again, the demonstrators, acting as intermediaries between Brian’s extensive knowledge and the near complete ignorance of the students, were probably the principal beneficiaries.

There were other beneficial outcomes to the course. I spent long hours walking to and from the pub sharing our experiences of travelling in the Himalayas with one of the students.   This same individual (and her distinctive orange cagoule) cropped up in more of my photographs than a hypothesis concerning the random distribution of students on 35 mm film would predict.

Reader, I married her.


Durham undergraduates sampling a stream in Scotland during the algae field course, April 1985.

Unmasking the faceless Eurocrats …


My own small contribution to the campaign to keep the UK in the European Union takes the form of a scientific paper. This will probably not raise many eyebrows outside the small band of specialists amongst whom I work but it offer it as an antidote to the rhetoric of the anti-EU campaigners and their scaremongering about the Brussels bureaucracy. I have made no secret that I am pro-EU (see “What has the European Union ever done for us?”) and that I think the UK benefits from EU environmental legislation. What one person thinks to be sensible regulation can easily be portrayed by the disingenuous as excessive red tape peddled by faceless, unelected Brussels bureaucrats.

Our paper deals with about half a sentence in an annex of an 80 page Directive that deals with how EU Member States should assess the quality of lakes.   Should the suspended algae, the attached algae and the larger plants be used to assess lake condition, or can you get the same outcome by just using two of these three components? Interpretation of those few words can, however, result in considerable and recurring expense for a large Member State such as the UK.   Opinion on how they should be interpreted differed between the 28 countries of the EU.   How do you find the balance between the environmental risks associated with lax interpretation of EU law and the extra costs that a stringent reading of the Directive would entail?

I was contracted, along with two colleagues, by the European Commission’s Joint Research Centre to look into this issue by examining the datasets of those countries that had analysed all three components to see how much extra information additional types of monitoring added to a manager’s overview of lake condition.   One additional twist to the problem was that my own particular specialism, the attached algae, was the Cinderella at this particular ecological assessment Ball, with about 60% of EU states deciding that these were not necessary.   Ironically, my career as Fairy Godmother to fellow algal specialists was extremely short-lived, as the outcome of our analyses was that, if a lake had a problem, it could usually be detected using the suspended algae and higher plants (the “ugly sisters” … metaphor overload .. no more of this, I promise).   There are situations when all three are needed to understand how to manage a lake but, for strategic overviews of the condition of a country’s lakes, little was gained by including them.

So what has all this got to do with our EU referendum?   In brief, this was a matter of interpretation discussed by representatives of all Member States at meetings mediated by European Commission representatives.   Having identified a difference of opinion, they brought us in to work on an evidence-based solution which was then discussed, in depth, at another meeting of national representatives (mostly ecologists). Many agreed with our conclusion; a few made the case for continuing to use all three components.   Ecological arguments were put forward by both sides but, in essence, we were debating whether this was an issue that should be decided within or between Member States.   Most were happy that this level of detail could be determined within Member States.   Even if the outcome had been in favour of imposing a more rigorous interpretation of the Directive, it would have been the consensus of Member States enacted through the Commission, not a blanket edict from these (hypothetical) faceless bureaucrats that the right wing press constantly demonises.

An interesting coda to this story is that after our report had been circulated and discussed my colleague at JRC was contacted by people from one Member State who were slightly alarmed by the conclusion.  The point that they made was that devolving responsibility to individual countries would lead to many dropping the use of attached algae, simply on the grounds of financial expediency. I had some sympathy (one of the authors was a fellow consultant who, like me, makes part of his living from this type of work) but it also touched on something that has been exercising my mind over recent months.   Do countries use this type of monitoring because they have to (i.e. the Directive tells them to) or because they need to (i.e. it contributes valuable information to lake management)?   It shifts the onus on us, as advocates of a sub-discipline, to make a reasoned case for the continued use of attached algae, rather than simply assume that “Brussels” will guarantee our livelihood.

Note: the photograph shows Derwent Water in the English Lake District, looking south from Friar’s Crag, July 2015.


Kelly, M.G., Birk, S., Willby, N.J., Denys, L., Drakare, S., Kahlert, M., Karjalainen, S.-M., Marchetto, A., Pitt, J.-A., Urbanič, G. & Poikane, S. (2016). Redundancy in the ecological assessment of lakes: Are phytoplankton, macrophytes and phytobenthos all necessary? Science of the Total Environment

Constructing a stalk …


Shortly after I posted my piece on calcification in Chara last week (see “Everything is connected …”), I came across another paper that discussed similar processes in a very different organism.   I’ve written about the diatom Didymosphenia geminata before (see “A journey to the headwaters of the River Coquet …”) and commented on the long stalks that it produces.   I mentioned in this post that the stalks were composed of carbohydrates and that this may be part of the reason why Didymosphenia can growth in such large quantities in rivers that are naturally nutrient-poor.   As carbohydrates are composed of just carbon, hydrogen and oxygen, they can be built by the miraculous rearrangement of carbon dioxide and water that we call photosynthesis.

Although other diatoms produce stalks too, the stalks produced by Didymosphenia are intriguing because they are so much larger than those of other species.   An organism that is only a tenth of a millimetre long can produce a stalk ten times as long – enormous, by the standards of the microscopic world.   Just as a builder might need to adjust his methods when building a skyscraper, compared to a normal-sized house, so it may be that Didymosphenia has acquired some structural reinforcements to make sure that the polysaccharide stalk can support the cells amidst the rigours of a fast-flowing stream.

A paper by a large team of researchers from Germany, France, USA, Russia and Poland sheds some intriguing light on this subject.   At the heart of the story is the same inorganic chemistry that we encountered for calcification in Chara, and the same enzyme, carbonic anhydrase, to enhance the process. In the case of Didymosphenia, however, there are some intriguing differences.   The researchers suggest that the stalk of Didymosphenia is strengthened by calcite nanofibres within the polysaccharide matrix.   They pointed out that the “foot” of the Didymosphenia cell is rich in mitochondria, which provide the energy for the production of the stalk.   Carbonic anhydrase is an enzyme that can both produce bicarbonate and protons from carbon dioxide and water, and the reverse. This means that it can regulate the concentration of carbon dioxide, ensuring a constant supply for photosynthesis whilst, at the same time, preventing a build-up in those parts of the cell that are busily respiring. The same carbonic anhydrase-mediated process that we saw in Chara can take place inside the Didymosphenia cell to capture calcium to build the nanofibres for the stalk.   However, intriguingly, a parallel reaction can take place outside the cell.

A long stalk is no advantage to an organism unless it is well-anchored and the suggestion now is that the carbonic anhydrases can generate localised patches of acid conditions that erode the rock surface and allow the stalk to form rhizoid-like “holdfasts” within the substrate. About half of all the carbonic anhydrase activity seems to take place outside the cell, and so contribute to these processes.   It is an interesting hypothesis that makes sense when the substrate contains a high proportion of limestone; whether it explains the success of Didymosphenia on other rock types (such as basalt, found in Didymosphenia-rich streams of the Cheviots) remains to be seen. The researchers (who approach the topic from the perspective of materials scientists rather than ecologists) describe the outcome as “mechanically stable and simultaneously very flexible under challenging hydrodynamic conditions of rivers with especially strong flow”.

Other evidence points to stalk production being at least partially controlled by the need to acquire nutrients, so a picture is starting to emerge of a single-celled organism with a range of physiological adaptations that enable it to survive in fast-flowing nutrient-stressed environments where relatively few other organisms can survive.   Having grumbled a few times in the past about diatom scientists wanting to know the shape of everything and the meaning of nothing, it is great to see that, in a few cases at least, we are beginning to get a more rounded understanding of the ecology of these fascinating organisms.

Note: the picture at the top of the post shows Didymosphenia stalks smothered in epiphytes, based on material collected from the headwaters of the River Coquet, Northumberland, May 2011.


Bothwell, M.L. & Kilroy, C. (2011). Phosphorus limitation of the freshwater benthic diatom Didymosphenia geminata determined by the frequency of dividing cells. Freshwater Biology 56: 565-578.

Ehlich, H., Motylenko, M., Sundareshwar, P.V., Ereskovsky, A. et al. (2016). Multiphase biomineralization: enigmatic invasive siliceous diatoms produce crystalline calcite. Advanced Functional Materials DOI:10.1002/ADFM.201504891.