Damp days in search of desmids …

Seatoller, in Borrowdale, is the wettest place in England, so we should not have been surprised by the persistent drizzle that accompanied us as we set off hunting for desmids last week.  The combination of Borrowdale’s hard volcanic rocks and a damp climate combine to create ideal habitats for bog-loving desmids and I had intelligence that Dock Tarn, on the fells above Borrowdale, was a hot spot of desmid diversity.   Getting there, however, was no easy task.  Though just a couple of kilometres from Stonethwaite on the map, there were an awful lot of contour lines awfully close together between the beginning and end of our walk.   The footpath zig-zagged through ancient woodland clinging to a steep hillside until we emerged onto the moorland above.  We then made our way across a plateau covered with heather moorland until we saw the tarn stretching away into the mist in front of us.

You know you are in good desmid habitat when there is water percolating into your body from both ends: rain dripping down from the hood of your cagoule and dampness seeping in through your shoes.  They are organisms that love marshy, boggy conditions, especially in areas where the water is as soft as it is here.   The alternative to damp feet would be to either climb up from Borrowdale in Wellingtons or waders or carry them up that steep hillside in a rucksack.   However, I suspect that the mud at the bottom of the tarn was too soft and deep for Wellington boots and lugging waders up that hillside would have been hard work so damp feet was the price I had to pay.   I leaned out as far as I could from the shore to grab some of the sedge stems which had a visible coating of attached algae, and also squeezed the peaty water from a few handfuls of Sphagnum that I pulled from a boggy pool.  That would have to do on this particular morning as the rain was now soaking through my trousers and, in any case, there were places I needed to be later that morning.   I shoved the bottles containing my samples into my rucksack and followed the path back down the hillside.

Epiphytic algae growing around a sedge stem in the outflow of Dock Tarn, Cumbria, July 2017.   The width of the stem plus epiphytes is about half a centimetre.

Dock Tarn is one of a number of sites identified as an “Important Plant Area” (IPA) on the basis of the rich desmid flora, largely due to work over the years by David Williamson.   It qualifies as an IPA on four criteria: the presence of threatened species, high diversity, a long history of study and because it represents a “threatened habitat”.   David Williamson has recorded over 50 species from this location, 13 of which are candidates for a “potential Red Data List”.   A few of these are illustrated in the figures below.   One of the species in the first image, Haplotaenium minutum, belongs to a genus only recently separated from Pleurotaenium, which looks very similar to the untrained eye (the difference lies in the structure of the ridges on the chloroplast).  Looking at these long cylindrical cells serves to emphasise just how much dexterity Chris Carter needed to produce his Hilda Canter-Lund prize winning image.  Images in the second plate include two more species of the genus Xanthidium, which we met in “Desmids on the defensive …”.

Dock tarn desmids: a. Netrium digitus var. latum; b. Tetmemorus brebissonii; c. Haplotaenium minutum.  Scale bar: 25 micrometres ( = 1/40th of a millimetre). 

The desmids in the lower plate, in particular, show one of their key characteristics very clearly: their cells are divided into two distinct lobes (“semicells”) joined by an isthmus (the word desmid comes from the Greek desmos, meaning “bond”).  The image of Staurastrum manfeldtii var. productum also shows a number of bacteria growing on the cell: these are probably growing within the mucilage that desmids secrete around themselves whilst there are distinct pyrenoids in the two Xanthidium species.  Their predilection for soft water means that they need the carbon-concentrating mechanisms that these contain if they are to thrive.   Not all desmids live in water as soft as this, and some are able to use inorganic bicarbonate to fuel their photosynthetic engine, but there will be little or no bicarbonatae in a habitat such as Dock Tarn.   I wrote about these carbon concentrating mechanisms in algae from Ennerdale Water (see “Concentrating on carbon …”) and the two filamentous algae that featured in that post, Mougeotia and Spirogyra, both belong to the same class within the green algae as the desmids (Conjugatophyceae or Zygnemtetophyceae).

There will be more about desmids on this blog over the next few months in preparation for a the weekend of 15-17 September when I am organising a joint meeting of the British Phycological Society and Quekett Microscopical Club in Windermere.  We’ll be visiting some other Lake District tarns known to be rich in desmids during this weekend and have Dave Johns and Allan Pentecost on hand, amongst others, to offer expert advice on what we find.  There are still a few places left, so hurry up to book your place.  I haven’t done a great job of selling the Cumbrian climate in this post but we have the use of the Freshwater Biological Association facilities, including a laboratory and the library, so no one need get damper than they want.   See you there…

More desmids from Dock Tarn: d. Euastrum cuneatum; e. Xanthidium cristatum var. uncinatum; f. Xanthidium antilopaeum; g. Staurastrum manfeldtii var. productum.   Scale bar: 25 micrometres
( = 1/40th of a millimetre). 


Coesel, P.F.M. (1994). On the ecological significance of a cellular mucilaginous envelope in planktic desmids. Algological Studies 73: 65-74.

Kiemle, S.N., Domozych, D.S. & Gretz, M.R. (2007). The extracellular polymeric substances of desmids (Conjugatophyceae, Streptophyta): chemistry, structural analyses and implications in wetland biofilms. Phycologia 46: 617-627.

Spijkerman, E., Maberly, S.C. & Coesel, P.F.M. (2005).  Carbon acquisition mechanisms by planktonicdesmids and their link to ecological distribution. Canadian Journal of Botany 83: 850–858.


Hilda Canter-Lund competition 2017 winners

The winner of the 2017 Hilda Canter-Lund photography competition is Chris Carter for his image of the desmid Pleurotaenium coronatum var. robustum.   This is the second time that Chris has won the competition and his fifth time on the shortlist, confirming an already impressive reputation as a photographer of the algal world.   This particular image is of a specimen that was collected whilst on holiday in Newfoundland, Canada, and preserved in formalin.  This led to the loss of chloroplast colour but which, in turn, made the pore field at the end of the cell more obvious.

The technical skill behind this image is not immediately obvious unless you know the genus Pleuotaenium typically consists of cylindrical cells several times longer than wide.  This particular specimen is 45 micrometres (about 1/20th of a millimetre) in diameter but is almost half a millimetre long.  The challenge was increased because the 100x magnification oil-immersion objective which he used has a very shallow depth of field.  Chris had to suspend the cell in dilute jelly in a cavity tank not much deeper than its length.  Having done this, he agitated the cell with a length of fine wire and once it was no longer horizontal he could manipulate it by gently sliding the coverslip relative to the cell.  The photograph which won the competition is one of many attempts and, even so, Chris commented that the cell is probably a degree or so away from vertical even here but, he went on: “I thought the lighting was actually quite attractive with the bronze hue of the preserved wall contrasting with a blue tinge from the light source; even the very slight tilt perhaps suggests a monster (or a something) rising out of the deep.”

Pleurotaenium coronatum var. robustum.  The top left image is an apical view, showing the pores and the radial ring of tubercules (knobbly projections).  The lower image shows the cell in plane view.   All images by Chris Carter.

Chris Carter, Hilda Canter-Lund prize winner, 2013 and 2017.

The second prize this year was also awarded to a former winner.  Tiff Stephens won the competition last year with her photograph of Durvillaea antarctica in the intertidal zone of the sub-Antarctic Snares Islands.  This year, it was her photograph of the red alga Bonnemaisonia clavata that caught the judge’s eye.   This is a very different style of photograph to her winning entry from last year, taken using an Olympus DP20 camera on a dissecting microscope.   The row of spheres along the secondary axis (“stem”) contain female reproductive cells and the prominent branchlet in the centre right is 1.5 mm long.

“Cystocarp Central”: Tiffany Stephen’s winning entry for the 2017 Hilda Canter-Lund photography competition. 

Though the style of the picture is very different to last year’s entry, it shares with that image an encapsulation of the “decisive moment” (see “How to win the Hilda Canter-Lund competition”). Tiff comments that many of her images are “opportunistically taken while sprinting around doing fieldwork”.  In this particular case, she was on a fun dive outside of Victoria, British Columbia (Canada), collecting seaweeds to look at later, with a view to possibly making herbarium pressings.   She saw dense lumps of Bonnemaisonia clavata, a species with which she was not familiar, at depths between 5 and 10 metres on semi-exposed reefs and collected some to have a closer look later.

The two images represent the two extremes of photographing the microscopic world: Chris applied a great deal of technical skill and ingenuity to create an aesthetically-pleasing image from difficult subject matter whilst Tiff saw an elegant composition drift into view as she scanned around recently-collected field material.  Both photographers have an “eye” for a good composition and the patience and technical skill needed to capture a fine image when the occasion final presented itself.   They are also – and this is important – keen field scientists, grabbing samples out of sheer curiosity and then marvelling as new and fantastical worlds open up to them under the microscope.  Both worthy winners and, with John Huisman (winner in 2014, shortlisted five times), now form algal photography’s “superleague”: the people to beat in 2018!

Tiff Stephens surrounded by Macrocystis in Alaska earlier this year.  Follow Tiff on Twitter at @tiffanybot to see more examples of her photography.

Sticky water …

It seems strange to be writing about an alga that thrives in winter in the middle of one of Britain’s rare heatwaves but I came across two papers recently that shed some light on the ecology of Ulothrix zonata.  This is a species that has intrigued me for some time, having a very distinct preference for times of the year when our rivers are at their coldest and I have tried to unravel the reasons for this in some earlier posts (see “Bollihope Bhavacakra” and “The intricate ecology of green slime …”).

The lead authors on these papers are based at Irkutsk, beside Lake Baikal in Siberia, so are in a good position to contemplate the effects of cold conditions on algae.   Whereas I complain about plunging my hand into cold water in northern England to collect Ulothrix zonata, they had to Scuba dive under the ice of Lake Baikal in water only just above freezing point.  They have found two adaptations in the Lake Baikal populations of U. zonata to cold conditions.  The first of these is that the ratio of polyunsaturated to saturated fatty acids are higher in these populations than in those of other Ulothrix species.   This sounds as if it could be an algal equivalent of the “blubber” that insulates sea mammals but the truth is rather more mundane: it is part of a series of adaptations of the cell membrane that allows the organism to keep functioning despite the harsh conditions.

Living underwater is, in many ways, the easy option for a plant in Siberia, where the average outside temperatures in winter are less than -10 °C, and the record low is almost -50 °C.  Terrestrial plants adapt to such harsh environments simply by shutting down operations.   However, whilst the surface layers of Lake Baikal freezes, life below the ice can continue and there are several studies about the rich algal life within this enormous lake (which contains a fifth of the planet’s fresh water).   Enough sunlight can penetrate through the ice to sustain growth, albeit at a slow rate but, on the other hand, the cold water creates problems of its own.   In particular, the density of water increases as temperature drops, making it more viscous.  We might not notice that cold water is more gloopy than warm water but that is because how we experience viscosity is partly a function of our size.  What might be an insignificant change to a human can be a big deal to a microscopic alga.

The cell membrane is composed largely of lipids and, like margarine, these are soft in warm environments (such as frying pans) but hard in cold environments (such as refrigerators or Lake Baikal).  The problem for cells is that there are other molecules embedded in the lipid layers which help the cell obtain the raw materials it needs, and these will not be able to function if the lipids in the membrane are too rigid.   Molecules of saturated fats pack together more compactly than those of polyunsaturated fats which means that a membrane with lots of these is more rigid than one with a high ratio of polyunsaturates.   Consequently, if an organism is to thrive in cold environments then it is beneficial for it to have a high ratio of polyunsaturated to saturated fats in the lipid molecules.

Water is one of the molecules that submerged algae need to shift into their cells to keep their cellular machinery running as this is one of the raw materials of photosynthesis.   There is no shortage of water on the outside of the cell.  However, having a membrane composed largely of hydrophobic lipids means that this is not straightforward and one of the molecules that is embedded in the lipids belongs to a group of proteins called “aquaporins”.  These are shaped in such a way that there is a narrow channel in the centre (like the hole in a doughnut) through which water molecules can pass in single file.

Aquaporins are well known in animal, plant and bacterial cells but it is only recently that they have been found in algae too.   Aleksey Permyakov and colleagues showed that Ulothrix zonata populations from Lake Baikal and streams in the vicinity had more aquaporins in winter than the summer, which they interpreted as an adaptation that ensured a steady supply of water to the cell despite the higher viscosity of the water.  This is also the first time that algal cells have been shown to be able to regulate the amount of aquaporin in membranes in response to their environment.

These two observations together suggest how cold-tolerant algae may have to invest some of their hard-earned energy in modifying their membranes to help them thrive.  I suspect that this is part of a complex network of interactions here: survival in such extreme conditions is possible because the slow rate of growth in very cold water is offset by an even slower rate of grazing and other processes which remove algal biomass.  Diverting energy and resources to make more aquaporins, in turn, means that photosynthesis is not limited by a shortage of raw materials.   It is a fine balance but, if an organism can get this right, then there is an opportunity to thrive with relatively little competition from other organisms.  It is another reminder that ecology is a science that depends on a 365 day perspective and that we should not assume that a few fieldtrips when the weather is most clement will reveal all of its riches.


Osipova, S., Dudareva, L., Bondarenko, N., Nasarova, A., Sokolova, N., Obulinka, L., Glyzina, O. & Timoshkin, O. (2009).  Temporal variation in fatty acid composition of Ulothrix zonata (Chlorophyta) from ice and benthic communities of Lake Baikal.  Phycologia 48: 130-135.

Permyakov, A., Osipova, S., Bondarenko, N., Obolinka, L., Timoshkin, O., Boedekker, C., Geist, B. & Schäffner, A.R. (2016).  Proteins homologous to aquaporins of higher plants in the freshwater alga Ulothrix zonata (Ulotrichales, Chlorophyta).  European Journal of Phycology 51: 99-106.

The photograph at the top shows Ulothrix zonata growing on the bed of the River Wear at Wolsingham, Co. Durham in February 2009.

Hilda Canter-Lund competition shortlist 2017

The shortlist for the annual Hilda Canter-Lund competition to find the best algal photograph has just been uploaded to the British Phycological Society website and here is a quick guide to the images.  No less than three previous winners have made it to the shortlist again, along with three newcomers, so it looks like being a particularly intriguing year.

2013 winner Chris Carter has made it to the shortlist for the fifth time with an apical view of the desmid Pleurotaenium coronatum var. robustum with an image that combines aesthetics and technical ability in his own inimitable manner (above left).   The desmid genus Pleurotaenium typically has cylindrical cells several times longer than wide, so getting a good image of one end of a cylinder that is about 1/20th of a millimetre in diameter is quite an achievement.   He is joined on the shortlist by 2016 winner Tiff Stephens, who switches style this year to offer a macroscopic view of female reproductive cells of the subtidal red seaweed Bonnemaisonia clavata, collected off the coast of Vancouver Island in Canada (above right).   The prominent branchlet in the centre-right with its own side branches is 1.5 mm long.

John Huisman shares with Chris Carter the honour of being the most shortlisted photographer in the competition, with five nominations including the winning entry in 2014.   His image this year shows the green alga Ulva stenophylloides, at the centre of a diverse assemblage (above left), photographed whilst snorkelling off the coast of Western Australia.   Heather Spalding, by contrast, makes her first appearance on the shortlist, with a view of Chara zylanica beds in a brackish lagoon in Hawaïi (above right).  Note the small snail making its way across the plants in the foreground, reminding us of the important role that macroalgae play in structuring ecosystems.

We go back to Australia – the D’Entrecasteaux Channel in Tasmania actually – for the next entry: Luis Henriquez’s image of a young plant of the brown alga Carpoglossum confluens emerging from a bed of Caulerpa trifaria (above left). As well as providing a striking image, Luis’ image also tells a story of marine eutrophication as the slow growing brown algae such as Carpoglossum are struggling to compete with the fast growing green algae such as Caulerpa.   Finally, Alizée Mauffrey brings a completely different style to the competition, with a collage of images of seaweeds exhibiting different functional traits (above right).   As well as telling a story about how different morphological, phenological and physiological traits combine to equip each species to inhabit a particular niche, Alizée also creates a pleasantly abstract composition.   She is also the first person to submit an image produced using a flatbed scanner rather than a camera (for more examples of this technique, see An Ocean Garden by Josie Iselin).

This shortlist is unusual in that there is only a single true micrograph and a single freshwater alga (both represented by Chris Carter’s image).   A number – using both the light microscope and scanning electron microscope – were submitted but the judges who selected the shortlist felt that most did not quite make the grade.  It was a close call in a couple of instances (and, in at least one case, some minor adjustments to contrast might have persuaded us) but that is the sad truth.  It may simply be that taking a really good image using a high power microscope is a more technically demanding task than photographing macroalgae in situ?   If nothing else, this does show just how good a photographer Hilda Canter-Lund was.

The final step in the competition is for the council of the British Phycological Society to vote for the winning entry.  After that, a second (but equal) prize will be awarded for the best of the shortlisted entries in a contrasting style (i.e. a micrograph is a photo of a macroalga wins and vice versa).   Both winners should be announced within the next couple of weeks so keep an eye on www.brphycsoc.org for the announcements.  And, while you are there, browse through the archives of pictures that we’ve accumulated since the competition started in 2009 and enjoy some of the remarkable and beautiful organisms that they portray.

Theme and variations

Following our visit to the cities of the Silk Road (see “Daniel and his den of diatoms …”) in April we turned our eyes in the opposite direction and, within an hour of leaving Tashkent, we had left the flat plains behind and climbing into the foothills of the Tien’shan mountains.   The intensive agriculture of the lowlands gave way to pine forests and, as the road started to twist and turn up the slopes, we started to get tantalising glimpses of the snow-capped mountains which straddle Uzbekistan’s eastern border with Krygyzstan.

As ever, I looked for opportunities to combine business and pleasure, collecting one sample from a small calcareous seepage in the hills near the village of So’qoq and another from a stream running through mixed geology near the village of Kumyshkang, where we were staying in a Soviet-era dacha.   Sampling the seepage drew some curious looks from two women who were collecting water mint from further downstream, and yielded an almost pure growth of a diatom that is either Achnanthidium pyrenaicum or a close relative.   This would have been, by the way, the diatom that I would have expected to find were I to sample a remote, unpolluted calcareous stream in the UK.

Achnanthidium cf pyrenaicum from a calcareous stream near So’qoq in eastern Uzbekistan (41°18’45.6” N 69 ° 51’40” E).  a. – d.: rapheless valves; e. – g.: raphe valves; h.: girdle view.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

Later in the day, we explored a side valley of an unnamed river that flows through the village of Kumyshkang.  The steep landscape on the south side of the valley had a thin cover of scrubby vegetation (in contrast to the wooded slopes on the other side) and the stream tumbled off the hillside towards the river below.  The biofilm, partly as a result of this harsh environment and partly, I suspect, due to grazing by invertebrates, was very thin but, nonetheless, quite diverse, with Achnanthidium minutissimum predominating.  There were a lot of outcrops of pink granite in the hillsides around the stream, but there were other rocks too, including shales and slates.   The flora here, as a So’qoq, would not look out of place in samples I find in the UK although the mix of taxa is not what I would expect if granite was the predominant rock in the catchment.   I travel light, without meters to check the chemical composition of the water, so there is no way to confirm this.  Except by going back one day better prepared …

Diatoms from a stream near Kumyshkang, Uzbekistan (41°18’45.6” N 69 ° 51’40” E, approx. 1400 m above sea level).  .   i.: Ulnaria ulna; j. – l.: Achnanthidium minutissimum; m.: A. cf. pyrenaicum; n., o.: A. cf caledonicum; p.: Achnanthidium girdle view; q.: Navicula tripunctata; r. Navicula sp.; s. Gomphonema gracile; t. Gomphonema sp.; u. Surirella brebissonii var. kutzingii; v. Diatoma moniliformis; w. Nitzschia sp.; x. Planothidium lanceolatum; y. Reimeria sinuata; z.: Encyonema ventricosum; aa.: Encyonopsis sp.   Scale bar 10 micrometres (= 100th of a millimetre).

I should add a caution about names applied to Asian diatoms using identification literature written for European freshwaters, especially after my comments in “Back to the Himalayas …”.   Until the 1980s there was a widespread belief that diatom species were cosmopolitan and could be found all around the world.  This belief became self-fulfilling as, armed with this assumption, biologists set out with books written by and for Europeans and blithely applied the names to the diatoms that they found.  From the 1980s, however, papers started to appear in which people took a closer look at variation in some of these apparently cosmopolitan species and argued that there were, in fact, substantial differences between forms from different locations, and that there were, in fact, much greater numbers of diatoms than previously thought, and that many of these were restricted to particular geographic regions.   But then, in 2002 Bland Finlay and colleagues challenged this emerging view by arguing that it was not diatoms that were restricted in their distributions, it was the locations where these detailed studies had been performed that were rare.   In other words, given enough time and effort on the part of diatomists, we should expect to see these so-called endemic species cropping up in samples from all over the world.

This created a brouhaha within the diatom world which resulted in some further papers that questioned Finlay’s assertions and argued from theoretical grounds that there was no reason why diatoms should not be restricted to a limited geographical area.  As the new century progressed, diatomists added molecular barcoding to their armouries and this offered partial support for both positions: some diatoms – or at least some strains of some diatoms, Nitzschia palea and Gomphonema parvulum, for example – do appear to be genuinely cosmopolitan whilst others do not.  Of course, Finlay and colleagues always hold the trump card in this respect: it is not possible to disprove the existence of any so-called endemic species elsewhere in the biosphere until every conceivable habitat has been examined. But a truce, of sorts, does seem to be emerging.

Sampling the calcareous seepage near So’qoq, April 2017.  The picture at the top of the post shows the valley upstream of Kumyshkang.

The truth may well lie between the two extreme positions.  Maybe many diatoms really are widely distributed because random dispersal mechanisms for microscopic organisms are highly effective, as Finlay and colleagues argue.  But every time a few viable cells of a diatom species land on a suitable habitat, their small pool of genetic variability will either thrive or disappear.   When they thrive, the story of Darwin’s finches will be replayed and a combination of genetic drift and selective pressures will create variations on the original theme, just waiting for an observant biologist to come along and discover the new species.

The question that intrigues me is whether or not the bugs that crawl across the submerged stones in search of food ever notice the difference.   One of my perennial bugbears is that the careful taxonomic work that has resulted in the discovery of all this diversity within diatoms is rarely accompanied by ecological analyses of similar rigour.   In particular, do these different forms of what we once regarded as “cosmopolitan” species actually have any effect on how energy flows through the ecosystem?  Do they, in other words, taste different to the invertebrates that crawl across the stones in search of food?  Or, as Bland Finlay hinted in a subsequent review article, are these different genotypes, in effect, variations on the same basic “ecotype”?   In which case, a casual observer crouching beside a foreign stream may not know the precise name of every species he encounters but still may have a pretty good idea of how these fit into the bigger picture of aquatic diversity.


Finlay, B.J. (2002). Global Dispersal of Free-Living Microbial Eukaryote Species.  Science (New York) 296: 1061-1063.

Finlay, B.J. (2004). Protist taxonomy: an ecological perspective.  Philosophical Transactions of the Royal Society Series B 359: 599-610.

Finlay, B.J., Monaghan, E.B. & Maberly, S.C. (2002). Hypothesis: the rate and scale of dispersal of freshwater diatom species is a function of their global abundance. Protist 153: 261-273.

Kemmarec, 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.

Mann, D.G. & Droop, S.J.M. (1996).  Biodiversity, biogeography and conservation of diatoms.  Hydrobiologia 336: 19-32.

Telford, R.J., Vandvik, V. & Birks, H.J.B. (2006). Dispersal limitations matter for microbial morphospecies. Science (New York) 312: 1015.

Trobajo, R., Clavero, E., Chepurnov, V.A., Sabbe, K., Mann, D.G., Ishihara, S. & Cox, E.J. (2009). Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae). Phycologia 48: 443-459

Vyverman, W., Verleyen, E., Sabbe, K., Vanhoutte, K., Sterken, M., Hodgson, D.A., Mann, D.G., Juggins, S., van de Vijver, B., Jones, V., Flower, R., Roberts, D., Chepurnov, V., Kilroy, C., Vanormelingen, P. & de Wever, A. (2002). Historical processes constrain patterns in global diatom diversity. Ecology 88: 1924-1931.

A view of the Tien’shan mountains from near So’qoq, Uzbekistan.

What does it all mean?

Just over a quarter of a century ago, my friend and colleague Steve Juggins and a group of other palaeoecologists came up with a clever way to relate the composition of diatom samples taken from different levels of a sediment core to the environmental conditions of the lake at the time that these diatoms were alive.   At the heart of this was a set of statistical tools called “transfer functions” and the use of these has proliferated over subsequent years, spilling from diatoms to many other groups of organisms and from palaeoecological studies to contemporary investigations of man’s impact on the environment.   So pervasive have these methods become that Steve returned to the subject a few years ago and critiqued the many misuses of the method that he was seeing in the literature.

The principle behind the use of transfer functions is that each species has a characteristic response to an environmental pressure gradient (in early studies this was pH) which could be portrayed as a unimodal (approximately bell-shaped curve).   The point along the gradient where a species is most abundant represents the “optimum” condition, the level of the pressure where the species thrives best.  The average of the optima of all organisms in a sample, Steve and colleagues showed, could be then used to estimate the value of the pressure.   This unlocked the door to quantitative reconstructions of changes in acidification of lakes in the UK and Scandinavia that, in turn, ultimately shaped environmental policy. It was one of the most impressive achievements of applied ecologists in the 20th century.

A diagrammatic representation of the principle behind transfer functions: each organism has a characteristic response to the predominant pressure (nutrient/organic pollution in this case).

Part of the reason for their success in building strong predictive models was, I suspect, that the pollutant that they were focussed upon had a direct effect on the physiology of the cells which, in turn, created strong selective pressures on the community.   Another reason was that palaeoecological samples condense all the habitat variation within a lake (plankton v benthic, seasonal differences etc) into a single assemblage.   This, then, begs the question of how well we should expect transfer functions to perform when applied to assemblages which represent much narrower windows of space and time, and when the pollutants of interest exert indirect rather than direct effects on the organisms.   Or, to recast that question another way, are some of the problems we encounter interpreting diatom indices from rivers another form of the misuse of transfer functions that Steve dissects in his review?

It is easy to believe that transfer functions do work when applied to contemporary diatom assemblages from rivers.   If you evaluate datasets you will almost certainly find that the “optima” for all the species do appear to be arranged along a continuum along the pressure gradient.  The question that we need to ask is whether this represents a causal relationship or is just a statistical artefact?  I touched on this issue in “What we expect is often what we get …” but, in that post, I was mostly interested in how samples react along a gradient, not the response of individual species.  I suspect that, given the importance of alkalinity in freshwater algal ecology (see “Ecology in the Hard Rock Café”), this must influence the distribution of optima along a nutrient gradient.   This will be compounded when sample sizes are small, as the likelihood is that the sample optimum will not correspond exactly to the “true” optimum for the species in question (a question Steve has also addressed in a more recent paper – see reference list below).  Finally, this is all embedded within a larger problem: that most of the work I have discussed here involves statistical inference from datasets compiled from samples collected from a range of sites in a region, but is intended to address changes in time rather than space (so-called “space-for-time substitution – see reference by Pickett below).   There has been relatively little testing of species preferences under controlled experimental conditions.

In practice, I suspect, the physiological response of benthic algae to nutrients is less complicated than our noisy graphs suggest.   I set out a version of this in “What we expect is often what we get …”.   That post dealt primarily with communities of microalgae; this is the same basic scheme (with some slight revisions) but posed in terms of the physiological response of the organisms.  It borrows from the habitat matrix conceptual model of Barry Biggs, Jan Stevenson and Rex Lowe (which, itself, builds on earlier work on terrestrial plants by Phil Grime and colleagues).

An alternative explanation for the response of benthic algae to nutrients and organic pollution.  a., b., c. and d. are explained in the text.

  1. Low nutrients / high oxygen concentrations – the “natural state” in most cases. Biggs et al. referred to species adapted to such conditions “stress-adapted” as they can cope in situations where nutrients are scarce. Associated with TDI scores 1 and 2.  Examples: Hannaea arcus, Achnanthidium minutissimum, Tabellaria flocculosa.
  2. high nutrients / no “secondary effects” of eutrophication – these are “competitive” species in Biggs et al.’s template and can thrive when there is anthropogenic enrichment of nutrients. Ideally, this group would consist of species that have a physiological adaptation that allows them to thrive when nutrients are plentiful though, in practice, our understanding is based mostly on inference from spatial patterns. The “window” where such species can thrive is wide, and will overlap with the two states described below, in many cases.  Associated with TDI scores 3 and 4.  Examples: Amphora pediculus, Rhoicosphenia abbreviata, Cocconeis pediculus.  Cladophora glomerata would be a good example of a non-diatom that belongs to this group.
  3. high nutrients plus “secondary effects” of eutrophication – this category extends the habitat template of Biggs et al. to include organisms whose are reacting to secondary effects  of nutrient enrichment (e.g. shade and low oxygen) rather than to the elevated nutrients per se and is, consequently, difficult to differentiate from a direct response to organic pollution. Associated with TDI scores 4 and 5. Examples include several species of Nitzschia as well as Mayamaea and Fistulifera, amongst others.   Importantly, this group may co-exist with representatives from group b. – perhaps inhabiting different zones of the biofilm that typically blend together when a sample is taken.
  4. high nutrients / very low oxygen – a final category that represents extreme situations when an ability to cope with reducing conditions is beneficial, and where diatoms that are facultative heterotrophs may thrive. Associated with TDI score 5. Heterotrophic fungal and bacterial growths (“sewage fungus”) may also be abundant.  Once again, there is likely to be some overlap between this and other groups.   Technically, this group is more likely to be associated with serious organic pollution than with nutrients; however, it will be found at sites where nutrient concentrations are high and it is possible that an association with nutrients may be inferred from spatial patterns.

We are left, in other words, with a choice between deriving optima along a continuous scale based on inferences from spatial patterns within which we know that there are significant confounding variables or dividing species into a few physiologically-defined categories for which there is not very much experimental underpinning.   Neither is ideal, and some of our recent analyses suggest that, in terms of model strength, there is little to choose between them.   The former, in my view, suggests an artificially high level of precision that is unrealistic, given the current state of knowledge.   The latter, on the other hand, links the data to a conceptual model rather than simply relying upon the numbers that squirt out at the far end of a statistical process.

That does not mean that such an approach might not be appropriate for some other groups of organisms.  The reason why I urge simplicity for diatoms is largely because of the scale of the habitats that we are sampling, in relation to the wider patterns of variability.  A continuous series of optima may be appropriate in some cases too.   Macrophytes surveys, for example, encompass all visible organisms found along a 100 m stretch.   These will have a range of life history and nutrient acquisition strategies: some of these will take up nutrients from the water, some from the sediments.  Different types of sediment will vary in the supply of phosphorus and nitrogen, and so on.   There will still be issues of confounding variables and risks of inferring from correlative rather than causal relationships, but perhaps the overall patchiness experienced over the survey length will create a more complex web of interactions between nutrients and community that justifies a continuous scale.

For diatoms, however, simplicity is probably the best choice.   In the absence of definitive evidence one way or the other we apply Occam’s Razor (“entities should not be multiplied unnecessarily”) and opt for the simpler of the two hypotheses pending evidence to the contrary.   This, in turn, may address a deeper issue: that of finding robust answers to complex problems (see “Unravelling causal thickets …”).   Inference from statistical models is only as good as the conceptual models that underpin those models and, I fear, we too often are so lost in the detail of the many confounding variables that we lose sight of our goals.  Being able to understand our observations in terms of ecological process is the first step to finding robust solutions to our problems.


Bennion, H., Juggins, S. & Anderson, N.J. (1996).  Predicting epilimnetic phosphorus concentrations using an improved diatom-based transfer function and its application to lake eutrophication management. Environmental Science & Technology 30: 2004-2007.

Biggs, B.J.F., Stevenson, R.J. & Lowe, R.L. (1991). A habitat matrix conceptual model for stream periphyton. Archiv für Hydrobiologie 143: 21-56.

Birks, H.J.B.,  Line, J.M., Juggins, S., Stevenson, A.C. & ter Braak, C.J.F.  (1990). Lake surface-water chemistry reconstructions from palaeolimnological data. Diatoms and pH reconstruction. Philosophical Transactions of the Royal Society of London Series B 327: 263-278.

Juggins, S. (2013).  Quantitative reconstructions in palaeolimnology: new paradigm or sick science?  Quaternary Science Reviews 64: 20-32.

Kelly, M.G., King, L. & Ní Chatháin, B. (2009).  The conceptual basis of ecological status assessments using diatoms.  Biology and Environment: Proceedings of the Royal Irish Academy 109B: 175-189.

Pickett, S.T.A. (1988).  Space-for-time substitution as an alternative to long-term studies.  Pp. 110-135.   In: Long-term Studies in Ecology: Approaches and Alternatives (edited by G.E.. Likens).  Springer-Verlag, New York.

Reavie, E.D. & Juggins, S. (2011).  Exploration of sample size and diatom-based indicator performance in three North American phosphorus training sets.  Aquatic Ecology 45: 529-538.

Lost in detail?

In my first post of 2017, I wrote “I fear, microscopic benthic algae may be ecology’s Sirens, sitting on submerged rocks and luring the unsuspecting into a world of taxonomic detail that is too rarely accompanied by profound ecological insight” (see “Not so bleak midwinter?”).   That was a post about Ennerdale Water and the River Ehen and I return to that same remote and beautiful part of north-west England to put some flesh onto the bones of that statement.

I chose a slide Ennerdale Water for the latest “ring test” which tests the competence of the analysts involved in routine ecological assessments using diatoms.   Everyone analyses the same slide and sends their results to me and I sort through and note areas of disagreement.   In this case, there was quite a lot of disagreement even amongst the experienced analysts but, as if to prove the point in my opening paragraph, this did had only a small effect on the conclusions that people reached on the quality of the ecosystem that the sample represented.

One of the areas of disagreement was a population of Brachysira that some described as Brachysira brebissonii whilst others suggested it was B. intermedia.   My inclination, following the illustrations in Hofmann et al’s Diatomeen im Süsswassser-Benthos von Mitteleuropa, was to call it B. intermedia as the illustrations of B. brebissonii show more broadly-rounded ends than were apparent in the Ennerdale population.  However, Bryan Kennedy, a member of our scheme, has been looking into the taxonomy of this genus as part of his PhD and directed me towards a paper by Bart van der Vijver, in which he had examined the type material for B. brebissonii (as “Navicula brebissonii Brébisson).  His illustrations show a population with more acute ends than Hofmann et al.’s illustrations.  Its shape is, in fact, much closer to that of the examples of B. intermedia that they illustrate.  Yet, we were all agreed, this taxonomic ambiguity had little effect on the interpretation that an ecologist would reach.  Most Brachysira species (with the curious exception of the type species, B. aponina) are associated with circumneutral to slightly acid water and low nutrients.   The species of the genus vary in their preference for alkalinity and hardness but, generally, indicate high quality conditions.

Another of the species present in the same sample was Frustulia crassinervia, which presents an interesting counterpoint to the situation I described for Brachysira brebissonii.   In this case, there was another possible candidate, Frustulia saxonica and, in fact, the rhombic-lanceolate outline of the Ennerdale Water population did suggest this species.  However, the clearly protracted ends and the size are more characteristic of F. crassinervia which was the name that the majority of experienced analysts opted for.   Once again, however, both species have similar ecological requirements: soft, often peaty water with low levels of enrichment.

Frustulia crassinervia from the south-east end of Ennerdale Water (circa NY 127 140), July 2016, scale bar: 10 micrometres (= 1/100th of a millimetre).  The top illustration shows Brachysira brebissonii from the same location.   Photographs by Lydia King.

The difference between the situation for Brachysira and Frustulia is that, in the case of Frustulia, the traditional morphological taxonomy is underpinned by molecular studies whereas, in the case of Brachysira, we only have morphological evidence on which to base names.   The interesting point is that the molecular studies of Frustulia suggest that there is no genetic difference between F. crassinervia and F. saxonica.   This alone does not mean that they are not separate species (they did not look at the whole genome), but it does suggest that more work is needed before we have a full understanding of the limits of the species in this genus.   A similar study on Brachysira (and, indeed, on any genus with a surfeit of recently described species separated purely on morphological criteria) might emphasise that differences in shape to which traditional taxonomists assign so much importance are real or it might not.   That would, at least, give people such as myself who use diatoms to gain a wider perspective of ecological health a better insight into where we really need to put in time and effort to discriminate between species.   In the post I mentioned at the start of this article I referred to the nineteenth century scientist Alexander von Humbolt and his concern that scientists got so bogged down in detail that they missed the big picture (“naturgemälde”). Some things never change …


Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011).  Diatomeen im Süßwasser-Benthos von Mitteleuropa.  A.R.G. Gantner Verlag K.G., Rugell.

Lange-Bertalot, H. & Moser, G. (1994).  Brachysira.  Monographie der Gattung.  Bibliotheca Diatomologica 29: 1-212.

Urbánková, P., Scharfen, V. & Kulichová, J. (2016).  Molecular and automated identification of the diatom genus Frustulia in northern Europe.  Diatom Research 31: 217-229.

Van der Vijver, B. (2014).  Analysis of the type material of Navicula brachysira Brébisson with the description of Brachysira sandrae, a new raphid diatom (Bacillariophyceae) from Iles Kerguelen (TAAF, sub-Antarctica, southern Indian Ocean).  Phytotaxa 184: 139-147.

Veselá, Urbánková, P.,Černá, K. & Neustupa, J. (2012). Ecological variation within traditional diatom morphospecies: diversity of Frustulia rhomboides sensu lato (Bacillariophyceae) in European freshwater habitats.  Phycologia 51: 552-561.


In an earlier post about diatoms from this location (see “Reflections from Ennerdale’s far side …”) I showed some images of live cells of Stenopterobia sigmatella but added a comment to say that there was a very similar species, S. densestriata, that I could not rule out on the basis of observations of live cells alone.   I now have had the opportunity to have a looked at cleaned material as well and can confirm that the population in Ennerdale Water is, indeed, S. sigmatella.  S. sigmatella has less than 24 striae in 10 micrometres whilst S. densestriata, as the name suggests, has more (> 26 / 10 micrometres).   S. densestriata is also shorter (< 110 micrometres) and narrows to more acutely-rounded ends.

We also found a few valve of S. delicatissima, the other member of the genus that has been recorded from the UK.

Stenopterobia spp. from Ennerdale Water, July 2016.  i.: part of a cleaned valve of S. sigmatella; j. S. delicatissima.   Scale bar: 10 micrometres (= 100th of a millimetre).  Photographs by Lydia King.