A day out in Wasdale


A few days after my trip to Weardale I found myself beside the River Irt, a few hundred metres below the point where it flows out of Wastwater, in the western part of the Lake District.   Whereas the River Wear drains a catchment underlain by Carboniferous rocks, including a high proportion of limestone (see “Co. Durham’s secret Karst landscape”), the Irt’s catchment is largely underlain by ancient volcanic rocks, resulting in much softer water.   I was curious to see how different the algae were here compared to those in the Wear.

The river bed at this point is dominated by boulders of granite, which host a patchwork of mosses, filamentous algae and discrete growths of diatoms (visible on the right-hand side of the figure below).  Between these there were areas of pebbles and gravels, suggesting good habitat for freshwater mussels.   The patches of filamentous algae (mostly no more than a couple of centimetres in length) were a mixture of Mougeotiaand Zygnema, similar to the forms that I find in the River Ehen, a 30 minute drive to the north.   These two species differ in the form of their chloroplasts (Mougeotiahas a flat plate whilst Zygnemahas two star-shaped chloroplasts, attached by thin cytoplasmic strands to resemble an animal skin stretched on a frame) but are closely-related, both belonging to the family Zygnemtaceae.


An underwater photograph of the substratum of the River Irt in November 2018 showing patches of filamentous green algae, mosses and (on the right-hand side) diatoms growing on granite boulders.


Filamentous green algae from the River Irt, November 2018.   The upper photograph shows cells from a filament of Mougeotiawhilst the lower image shows two filaments of Zygnema. Scale bar: 20 micrometres (= 1/50thof a millimetre).

In between the tufts of filamentous algae were apparently bare patches of rock (they almost certainly had a very thin biofilm that would be hard to sample in isolation from the lusher algal growths that shared their habitat) and some conspicuous orange-brown growths of colonial diatoms.  These turned out to be almost pure growths ofGomphonema hebridense, or a close relative (I can’t give a definitive answer until I have examined cleaned material), growing on long mucilaginous, sometimes branched, stalks to create a veritable “bush” of diatoms.  There were a few other species of diatom growing within this bush, most notably some cells of Achnanthidium (cf.) caledonicumthat seemed to be growing on short stalks attached to the Gomphonemastalks, but also a few cells of Gomphonema capitatum(which also grows on long stalks) and some chains of Tabellaria flocculosa.

Gomphonema hebridenseis a diatom that I have written about several times before, as it is also common in the River Ehen, and also presents a number of interesting challenges to taxonomists (see “Diatoms and dinosaurs”). Whatever future studies reveal, however, the presence of colonies of this (or these) species that are visible with the naked eye is something I associate with only the cleanest rivers in the country during the cooler times of year.  It should not have been a great surprise to me to find it flowing out of one of the most pristine lakes in England (see “The Power of Rock …”).


A close up of cells within a colony of Gomphonemacf hebridense.  Several mucilaginous stalks are also visible as well as (top left) a cell of Achnanthidiumcf caledonicum.   Scale bar: 10 micrometres (= 100th of a millimetre).

The predominance of boulders over smaller, more easily moved stones, suggests a river that has more energy than the River Ehen, one of my regular Lake District haunts.   Both flow out of lakes whose catchments include some of the wildest and most mountainous terrain in the country.   Lakes tend to act as shock absorbers in catchments, slowing down the water that pours off the fells after heavy rain.   Streams in this part of the world that have no such impediments to flow tend to have rocky, mobile beds and relatively sparse algal communities.   By contrast, the Irt and Ehen just below their respective lakes have relatively lush growths of algae.   The substrates of the two rivers, however, are very different: the Ehen having very few boulders in comparison to the Irt, due to the presence of a weir at the outfall. This allows Ennerdale Water to be used as a water supply for the towns of north west Cumbria but, at the same time, turns the lake into an even more effective hydrological shock absorber.  Yet more of the energy that should be washing smaller stones down the river is no longer available except after the most exceptional storms.

That’s my working hypothesis, then: the Irt is a river that is subject to just enough high energy events to move the rocky substrates around yet no so many that rich algal communities cannot develop between these.  The Ehen, by contrast, has fewer events, leading to fewer opportunities for the algae to be scoured away, whilst unregulated streams such as Croasdale Beck (see “What a difference a storm makes …”) have such regular scouring spates that the algal communities are usually sparse.   I might be wrong, of course and I might be back in a years time with a better hypothesis.  Until then …




The River Wear in November


I was back at the River Wear last week for my final visit of the year.   The heatwave that dominated the summer seems like an aeon ago as I plunged my arm into the cold water to find some stones and take some photographs.  I’m curious to see what is here, though.   The river has surprised me several times already this year.  Has it reverted to type as the British climate has regained a semblance of normality, or will the changes that we saw in the summer (see “Summertime blues …” and “Talking about the weather …”) still have consequences for the algae growing on the river bed?

The river bed itself had many patches of green filamentous algae which, on closer examination, turned out to be my old friend Ulothrix zonata, an alga that is common in these parts and which has a distinct preference for early spring conditions (see “Bollihope Bavakakra” and references therein).   A closer look showed two types of filament present: the normal vegetative ones with a single chloroplast encircling the cell but also some where the cell contents have divided to produce zoospores which are released and which, if they land on a suitable surface, will produce new vegetative filaments.   The “parent” filaments, themselves, are produced as zygotes, produced back in the spring, germinate.  The zygotes are the product of sexual reproduction, triggered by lengthening days (see reference in earlier post) and are dormant through the summer, only germinating once day length shortens and temperatures start falling.


The river bed of the River Wear at Wolsingham, November 2018, showing conspicuous growths of Ulothrix zonata.


Magnified views of Ulothrix zonatafilaments from the River Wear at Wolsingham.  The upper image shows a vegetative filament and the lower image shows filaments where the cell contents have divided up prior to the release of zoospores.  Scale bar: 20 micrometres (= 1/50thof a millimetre).

The areas between the patches of Ulothrix zonatawere covered with a thick film, composed primarily of diatoms, in contrast to the situation on my last two visits when non-filamentous green algae predominated.  This time, it was Achnanthidium minutissimumdominated my count (about 70% of cells) although, because they are relatively small, they comprised just under half of the total volume of algae present.   Other diatoms bumped this up to about 70 per cent of the total volume, with motile cells of Navicula and Nitzschia, which were so abundant at the start of the year, beginning to appear in numbers again.   The green cells that dominated my counts in July and September now only constitute about five per cent of the total.   The River Wear, in other words, has shaken off the effects of the summer, just as a healthy human gets over a winter cold, and is now back to its old self.


A view down my microscope whilst examining samples from the River Wear at Wolsingham showing the predominance of Achnanthidium minutissimum with (on the right-hand side) a filament of a narrow Ulothrix (not U. zonata).  

Entomoneis in three dimensions

I’ve written about the genus Entomoneison a few occasions in the past (see “A typical Geordie alga …”).   It is a challenging species to understand partly because the cells often do not survive digestion in the strong oxidizing agents that we routinely use to understand the structure of diatom cell walls, and partly because of its unusual three-dimensional architecture.   I’ve commented on this before, using some of Chris Carter’s photos to illustrate this (see “The really rare diatom show”).  Now, thanks to yet more careful work from Chris, we have a new set of photos with which to understand this species.

The underlying problem of a complicated geometry (the frustule [cell wall] is actually twisted in two planes) is compounded by the shallow depth of field that is available when viewing organisms at high magnifications. The first of Chris’ images shows how most diatomists will encounter Entomoneis: as a cleaned cell mounted on a slide and shows how the girdle bands bands (the silica “spacers” between the two valves) seem to present a particular problem.  Look, in particular, at the arrangement of these in the left-hand image, focused on the top of the cell, and note how they appear to cross over one another.  Compare this to image that is focused on the bottom of the cell.  By contrast, a cell that has not been subjected to the strong oxidising agents that we use to “clean” diatoms prior to observation presents quite a different view, as seen in the second set of three photographs.   The contrast is poorer here, as the cell is not mounted in a high-resolution mountant (the reason diatomists “clean” their samples in the first place) but we can, nonetheless, see the girdle bands.   When Chris focuses on the top of the cell. the girdle bands are clearly visible, not criss-crossed, and diagonal across the cell. At the other extreme (focus on bottom of cell) the bands are still just visible, sloped the other way somewhat obscured by the cell contents but, most importantly, not presenting a gaping hole.

B Entomoneis naphrax mount.jpg

A cell of Entomoneisthat has been cleaned and mounted in Naphrax before being photographed at three focus levels using simple brightfield microscopy.  The left-hand image is focussed on the top of the cell and shows how the girdle bands appear to cross one another whilst the right hand image is focussed on the bottom of the cell and shows a chasm in the centre of the cell where the girdle bands have collapsed. The middle image shows an intermediate focal plane where the apices are in focus: this is where the girdle bands are attached.

C Entomoneis alcohol mount.jpg

A cell of Entomoneisthat has been mounted in alcohol before being photographed at three focus levels. The contrast is much poorer here but at one extreme (focus on top of cell ie towards observer) the bands are clearly visible, not criss-crossed, and diagonal across the cell. At the other extreme (focus on bottom of cell) the bands are still just visible, sloped the other way but somewhat obscured by the cell contents.

What we think is happening is that the girdle bands are so weak that they collapse as soon as the frustule is dried or hits hot Naphrax; this collapse can be either towards the observer or away from the observer, creating a slightly different optical effect in each case.   Most of the time, however, the bands detach completely leaving isolated valves – sometimes with some straggly bits attached.  Chris thinks that almost all the published images of this taxon are misleading: usually flattened either optically or by software in order to give a sharp image for presentation and, in the process, disguising this detail.

These images all show us what Entomoneis looks like in girdle-view, the way we are most likely to encounter an intact cell when looking down a light microscope.  The next two plates show it from above (“valve view”) and in apical view (i.e. looking at the cell from one end), both of which are not often seen during routine observation.    The pair of valve views show the outline at different focal levels, and we can see how the thin wing (keel) is twisted towards the viewer; this twist is also present in the main (cylindrical) part of the cell but is not visible in these photographs.   The series of photographs in the next plate takes this further: the sequence along the top shows an apical view at several points of focus.  Some particulate matter is caught within the open structure of the frustule and acts as a reference point when comparing the two views. The thin keel with its thickened edge (containing the raphe) shows clearly. The body of the cell is not symmetrical because of the twist; the girdle band section is at the bottom of the inverted U section and is demarcated by ridges associated with each band: the number of bands can be estimated as shown on the enlarged fourth section. The other valve must have detached without holding onto any girdle bands.

A Entomoneis valve view in alcohol.jpg

Valve view of an alcohol mounted celul of Entomoneisat two focus levels.

D Entomoneis semicell in apical view in alcohol.jpg

An alcohol mounted semicell of Entomoneis caught in both apical (top row, showing several points of focus) and girdle views (bottom right).  The image at the bottom left shows a slightly magnified version of the fourth apical view indicating the location of the girdle bands on the opposite sides of the valve (indicated by the vertical red lines).

Entomoneis highlights the limitations of using two-dimensions to portray algae.  The answer, Chris and I agree, would be a three-dimensional model (see “Taking desmids to the next dimension …”) that we could pick up and view from all angles.  Another option is to use a scanning electron micrograph (SEM), and the two references at the end of this article contain several useful images.   However, most of us are still going to encounter Entomoneisprimarily via the light microscope.  Having a sense of the three-dimensional form of an alga lodged in your mind makes it much easier to interpret the flattened two-dimensional images that we routinely encounter.  Prior to the era of SEMs, the three-dimensional form of Entomoneis, and, indeed, its true taxonomic position, was very difficult to appreciate.   Both the 1930 and 1990s editions of the Süsswassflora von Mitteleuropaplaced it with Naviculawhereas we now understand enough about the form of the raphe to know that Entomoneis is more closely related to Surirella(see Round et al.,referenced below).  It is a good reminder that the study of diatoms has always been limited by the technology available.   Our toys may have changed enormously over the past hundred years but the gaps in our understanding remain …


Round, F.E., Crawford, R.M. & Mann, D.G. (1990).  The Diatoms: Biology and Morphology of the Genera.  Cambridge University Press, Cambridge.

Dalu, T., Taylor, J.C., Richoux, N.B. & Froneman, P.W. (2015).  A re–examination of the type material of Entomoneis paludosa(W Smith) Reimer and its morphology and distribution in African waters.  Fottea15: 11-25.

The Imitation Game

About a year ago, I made a dire prediction about the future of diatom taxonomy in the new molecular age (see “Murder on the barcode express …“).   A year on, I thought I would return to this topic from a different angle, using the “Turing Test” in Artificial Intelligence as a metaphor.   The Turing Test (or “Imitation Game”) was derived by Alan Turing in 1950 as a test of a machine’s ability to exhibit intelligent behaviour, indistinguishable from that of a human (encapsulated as “can machines do what we [as thinking entities] can do?”).

My primary focus over the past few years has not been the role of molecular biology in taxonomy, but rather the application of taxonomic information to decision-making by catchment managers.   So my own Imitation Game is not going to ask whether computers will ever identify microscopic algae as well as humans, but rather can they give the catchment manager the information they need to make a rational judgement about the condition of a river and the steps needed to improve or maintain that condition as well as a human biologist?

One of the points that I made in the earlier post is that current approaches based on light microscopy are already highly reductionist: a human analyst makes a list of species and their relative abundances which are processed using standardised metrics to assign a site to a status class. In theory, there is the potential for the human analysts to then add value to that assignment through their interpretations.  The extent to which that happens will vary from country to country but there two big limitations: first, our knowledge of the ecology of diatoms is meagre (see earlier post) and, in any case, diatoms represent only a small part of the total diversity of microscopic algae and protists present in any river.   That latter point, in particular, is spurring some of us to start exploring the potential of molecular methods to capture this lost information but, at the same time, we expect to encounter even larger gaps in existing taxonomic knowledge than is the case for diatoms.

One very relevant question is whether this will even be perceived as a problem by the high-ups.  There is a very steep fall-off in technical understanding as one moves up through the management tiers of environmental regulators.   That’s inevitable (see “The human ecosystem of environmental management…“) but a consequence is that their version of the Imitation Game will be played to different rules to that of the Environment Agency’s Poor Bloody Infantry whose game, in turn, will not be the same as that of academic taxonomists and ecologists.  So we’ll have to consider each of these versions separately.

Let’s start with the two extreme positions: the traditional biologist’s desire to retain a firm grip on Linnaean taxonomy versus the regulator’s desire for molecular methods to imitate (if not better) the condensed nuggets of information that are the stock-in-trade of ecological assessment.   If the former’s Imitation Game consists of using molecular methods to capture the diversity of microalgae at least as well as human specialists, then we run immediately into a new conundrum: humans are, actually, not very good at doing this, and molecular taxonomy is one of the reasons we know this to be true.  Paper after paper has shown us the limitations of taxonomic concepts developed during the era of morphology-based taxonomy.  In the case of diatoms we are now in the relatively healthy position of a synergy between molecular and morphological taxonomy but the outcomes usually indicate far more diversity than we are likely to be able to catalogue using formal Linnaean taxonomy to make this a plausible option in the short to medium-term.

If we play to a set of views that is interested primarily in the end-product, and is less interested in how this is achieved, then it is possible that taxonomy-free approaches such as those advocated by Jan Pawlowski and colleagues, would be as effective as methods that use traditional taxonomy.   As no particular expertise is required to collect a phytobenthos sample, and the molecular and computing skills required are generic rather than specific to microalgae, the entire process could by-pass anyone with specialist understanding altogether.  The big advantages are that it overcomes the limitations of a dependence on libraries of barcodes of known species and, as a result, that it does not need to be limited to particular algal groups.  It also has the greatest potential to be streamlined and, so, is likely to be the cheapest way to generate usable information.   However, two big assumptions are built into this version of the Imitation Game: first, there is absolutely no added value from knowing what species are present in a sample and, second, that it is, actually, legal. The second point relates to the requirement in the Water Framework Directive to assess “taxonomic composition” so we also need to ask whether a list of “operational taxonomic units” (OTUs) meets this requirement.

In between these two extremes, we have a range of options whereby there is some attempt to align molecular barcode data with taxonomy, but stopping short of trying to catalogue every species present.  Maybe the OTUs are aggregated to division, class, order or family rather than to genus or species?   That should be enough to give some insights into the structure of the microbial world (and be enough to stay legal!) and would also bring some advantages. Several of my posts from this summer have been about the strange behavior of rivers during a heatwave and, having commented on the prominence and diversity of green algae during this period, it would be foolish to ignore a method that would pick up fluctuations between algal groups better than our present methods.   On the other hand, I’m concerned that an approach that only requires a match to a high-level taxonomic group will enable bioinformaticians and statisticians to go fishing for correlations with environmental variables without needing a strong conceptual behind their explorations.

My final version of the Imitation Game is the one played by the biologists in the laboratories around the country who are simultaneously generating the data used for national assessments and providing guidance on specific problems in their own local areas.   Molecular techniques may be able to generate the data but can it explain the consequences?  Let’s assume that method in the near future aggregates algal barcodes into broad groups – greens, blue-greens, diatoms and so on, and that some metrics derived from these offer correlations with environmental pressures as strong or stronger than those that are currently obtained.   The green algae are instructive in this regard: they encompass an enormous range of diversity from microscopic single cells such as Chlamydomonas and Ankistrodesmus through colonial forms (Pediastrum) and filaments, up to large thalli such as Ulva.   Even amongst the filamentous forms, some are signs of a healthy river whilst others can be a nuisance, smothering the stream bed with knock-on consequences for other organisms.   A biologist, surely, wants to know whether the OTUs represent single cells or filaments, and that will require discrimination of orders at least but in some cases this level of taxonomic detail will not be enough.   The net alga, Hydrodictyon(discussed in my previous post) is in the same family as Pediastrumso we will need to be able to discriminate separate genera in this case to offer the same level of insight as a traditional biologist can provide.   We’ll also need to discriminate blue-green algae (Cyanobacteria) at least to order if we want to know whether we are dealing with forms that are capable of nitrogen fixation – a key attribute for anyone offering guidance on their management.

The primary practical role of Linnaean taxonomy, for an ecologist, is to organize data about the organisms present at a site and to create links to accumulated knowledge about the taxa present.    For many species of microscopic algae, as I stressed in “Murder on the barcode express …”, that accumulated knowledge does not amount to very much; but there are exceptions.  There are 8790 records on Google Scholar for Cladophora glomerata, for example, and 2160 for Hydrodictyon reticulatum.  That’s a lot of wisdom to ignore, especially for someone who has to answer the “so what” questions that follow any preliminary assessment of the taxa present at a site.  But, equally, there is a lot that we don’t know and molecular methods might well help us to understand this.   There will be both gains and losses as we move into this new era but, somehow, blithely casting aside hard-won knowledge seems to be a retrograde step.

Let’s end on a subversive note: I started out by asking whether “machines” (as a shorthand for molecular technology) can do the same as humans but the drive for efficiency over the last decade has seen a “production line” ethos creeping into ecological assessment.   In the UK this has been particularly noticeable since about 2010, when public sector finances were squeezed.   From that point on, the “value added” elements of informed biologists interpreting data from catchments they knew intimately started to be eroded away.   I’ve described three versions of the Imitation Game and suggested three different outcomes.  The reality is that the winners and losers will depend upon who makes the rules.  It brings me back to another point that I have made before (see “Ecology’s Brave New World …”): that problems will arise not because molecular technologies are being used in ecology, but due to how they are used.   It is, in the final analysis, a question about the structure and values of the organisations involved.


Apothéloz-Perret-Gentil, L., Cordonier, A., Straub, F., Iseili, J., Esling, P. & Pawlowksi, J. (2017).  Taxonomy-free molecular diatom index for high-throughput eDNA monitoring.   Molecular Ecology Resources17: 1231-1242.

Turing, A. (1950).  Computing machinery and intelligence.  Mind59: 433-460.

Casting the net wide …

A  month or so ago I wrote a couple of posts about the green algae that were thriving in the River Wear this summer (see “Keeping the cogs turning …” and “More green algae from the River Wear”).  In one of those, I promised to write a post about a related genus, Hydrodictyon.   I did try to find some recent populations but ran out of time so have fallen back on some old pictures along with more of Chris Carter’s spectacular photography.

Hydrodictyon reticulatum is commonly called the “water net” and can form extensive, and sometimes nuisance, growths, either floating in a lake or a slow-flowing river, or as a mat at the edge (see photos below).   The cylindrical cells are arranged in pentagons or hexagons which can be visible with the naked eye (hence the net-like appearance).   These have a mode of asexual reproduction that results in tiny zoospores being formed inside each cell.  Each of these develops into a small daughter cell whilst still inside the mother cell, and the ends of these daughters then join together to form mini-nets.  You can see this happening in Chris’ image at the top of the post: there are some young cells in the foreground with a mature “mother” cell full of “daughter” cells forming their own nets inside.  Eventually, the wall of the mother-cell disintegrates and the daughter net is released.

A mat of Hydrodictyon reticulatum from the lower River Tweed; b. macro, and, c. microscopic views of coenobia of H. reticulatum from Thrapston Lake, Northampton (b. and c. by Chris Carter).

This is an extremely effective way of enabling Hydrodictyon reticulatum to spread quickly when conditions favour its growth and the image below shows just how extensive these mats can be.   It is a species that is more common in the warmer parts of the world but it does occur in the UK as far north as Scotland and Brian Whitton has predicted that it is a species that is likely to be favoured in some climate warning scenarios.   Some authors have suggested that Hydrodictyon favours nutrient-rich water, but some of the locations where I have found it (the River Tweed in Scotland, Sunbiggin Tarn in Cumbria) do not meet this criterion.  Rather, I suggest that well-lit, relatively undisturbed summer conditions are the key factor and that this is more likely to be the case in lowland areas that are, in many cases, also rich in nutrients.  It is more likely to be a correlation than a cause, in other words.   Whatever the cause, there is a huge dichotomy between the beauty of the organism under the microscope and the nuisance that it can cause.

A huge growth of Hydrodictyon reticulatum at Manor Farm Weir on the Jubilee River (a flood alleviation channel of the River Thames near Maidenhead).  Photo: Environment Agency.

This mode of asexual reproduction – in which the zoospores aggregate inside the parent – is also a feature of Pediastrum.  Even though the shapes and dimensions of the organisms are very different, they share some fundamental properties.   Molecular phylogenetic studies have also shown that there is a close affinity between Hydrodictyon, Pediastrum and the other genera I mentioned in “Keeping the cogs turning …”.   However, their habits and ecology are very different and that raises some interesting questions about a different matter entirely … the subject of my next post.


John, D.M., Pentecost, A. & Whitton B.A. (2001).  Terrestrial and freshwater eukaryotic algae.   pp. 148-149.  In: The Changing Wildlife of Great Britain and Ireland (edited by D.L. Hawksworth).   Taylor & Francis, London.

Krienitz, L. & Bock, C. (2012).  Present state of the systematics of planktonic coccoid green algae of inland waters.   Hydrobiologia 698: 295-326.


Algae from the Alto Duoro …

From the highlands of Serra da Estrela w headed north-west towards the vineyards of the Duoro Valley from which the grapes that make port are picked.  I’m supposed to be on holiday but, as the narrow road twists and turns down a steep hillside, with vineyards on both sides, I see a case study in how humans alter rivers and their catchments to suit their needs.  I wonder if the passengers on the cruise ships that move sedately through this beautiful landscape have any idea of just how difficult this same journey would have been just fifty years ago.   Now there are 51 large dams within the watershed, regulating the flow and, at the same time, generating much-needed hydroelectricity.   Before these were in place, the only way to get the port from the quintas in the Alto Duoro to Porto was to load the barrels onto a “barco rabelo”, and then to plot a perilous path through the rapids before using a combination of sail, oars and oxen to make the slow journey back upstream (you can see videos of these journeys on YouTube).

A replica of a barco rabelo moored in the Rio Duoro at Porto, September 2018.

The Rio Douro is a type of river that is rare in the UK but very common throughout the rest of Europe in that it crosses (and, for part of its course, forms) national boundaries.  There are a few rivers in Ireland which straddle borders (the Foyle is one, and some of the headwaters of the Shannon can be found in County Fermanagh) but, mostly, this is a complication that our river managers do not have to face.  By contrast, eighty per cent of the Rio Douro’s catchment lies in Spain (where it is called the Duero) and it is actually the largest watershed on the Iberian Peninsula.   The whole European project, and its environmental policy in particular, makes so much more sense when you are looking at a well-travelled river.

Our immediate objective was the Quinta do Bomfin at Pinhão, which produces grapes for Cockburns’, Dow’s and Taylor’s ports.  However, after a morning walking through the vineyards and following a tour of the winery (the robot that has replaced human grape treaders has, we learned, been carefully calibrated to match the pressure that a human foot exerts, lest the grape seeds are crushed, imparting bitterness to the resulting wine) plus some port tasting, the lure of the river was too strong.

A view across the Douro Valley from Quinta do Bomfin at Pinhão.   This, and the previous two photographs, were taken by Heather Kelly.

The river bank at Pinhão is lined with rip rap (loose stones) enclosed in mesh cages to protect it from erosion from the waves created by the many cruise ships that make their way up the river with tourists.   This, along with the floating jetties at which they embark and disembark, meant that it was not easy to get access to the river; however, I eventually found a small slipway close to the point where a small tributary joins.  There were a few loose stones with a green film in shallow water that I could just reach, plus some algal mats coating the concrete of the slipway at water level.   I managed to get small samples of each to bring back for closer examination, attracting the usual curious stares from passers-by in the process.

The mats on the slipway were composed of an alga (technically, a cyanobacterium) that has featured in this blog on several occasions in the past: Phormidium autumnale (see “In which the spirit of Jeremy Clarkson is evoked”).   This is the time of year when the Douro is at its lowest so living at this point on the slipway means that it spends a small part of the year exposed to the air, but most of it submerged.

Phormidium cf autumnale on a slipway beside the Rio Douro at Pinhão, September 2018.  The left hand image shows the mats on the lower part of the slipway; the right hand image shows individual filaments.  Scale bar: 20 micrometres (= 1/50th of a millimetre).

The stones beside the slipway had a thick greenish film which, when I looked at it under a microscope, turned out to consist largely of bundles of thin cyanobacterial filaments belonging to a relative of Phormidium: Homoeothrix janthina (kindly identified for me by Brian Whitton).   Homoeothrix differs from Phormidium in that the filament are often slightly tapered, rather than straight-sided and usually aggregated into colonies, often growing vertically towards the light rather than intertwined to form mats.   It is a genus that I see in the UK (including, sometimes, in the River Wear) but which I have not previously written about on this blog.   The photos below show tufts of filaments but it would be quite easy to imagine several of these clumps joined together to form a hemispherical colony, before I disrupted them with my vigorous sampling technique.

Left: the rip rap at the edge of the Douro at Pinhão from which I sampled algae in September 2018; right: the stone after vigorous brushing with a toothbrush.

Bundles of filaments of Homoethrix janthina from the River Douro at Pinhão. Scale bar: 20 micrometres (= 1/50th of a millimetre).

Many of my posts try to make the link between the algae that I find in lakes and rivers and physical and human factors in those water bodies and their surroundings.  That is not an easy task in a large river basin such as that of the Douro as there is so much more of a hinterland including large towns in Spain such as Valladolid.   The river, to some extent, integrates all of these influences and, whereas the vines around Pinhão have their roots in nutrient-poor granite and schist soils, the river’s journey to this point has covered a range of different rock types, including chalky clay soils in the Spanish part of the catchment and the water reflect this.   This cocktail of physical alteration and pollution, shaken up with a dash of international relations, recurs in the largest rivers throughout Europe and is either a fascinating challenge for an ecologist or a complete pain in the backside, depending on your point of view.

I’ll come back to the Douro in a few weeks, once I’ve had a chance to have a closer look at the diatoms.  Meanwhile, I have one more stop on my travels along the Rio Douro, at the port lodges of Vila Nova de Gaia to try some vintage port …


Bordalo, A.A., Teixeira, R. & Wiebe, W.J. (2006).  A water quality index applied to an international shared river basin: the case of the Douro River.  Environmental Management 38: 910-920.

The end of the journey: port maturing in barrels at Cockburn’s lodge in Vila Nova de Gaia.


Notes from the Serra de Estrela

At the end of my last post I suggested that the next time I wrote it may be from Portugal.   In reality, tiredness and, to be frank, a steady consumption of Vino Verde intervened and this post may be about Portugal but is not, alas, written from that country.   Our travels took us from Lisbon northwards to Covilhã, a town on the edge of the Serra da Estrela mountain range, then onwards to the Duoro valley and Porto, and finally back to Lisbon.   The lower part of the Duoro is the home to many of the Vino Verde vineyards, although our focus was mostly on the vineyards further upstream from which the grapes for port are grown.  I’ll write more about the Duoro in a later post but, first, I want to take you on a journey to the Serra da Estrela.

These are the highest mountains in mainland Portugal (there is a higher point in the Azores) but summit with a summit at 1993 metres at Torre.  Unusually, for the highest peak in a mountain range, there is a road all the way to the top, along with a couple of shops and a small bar/restaurant.   On the day we visited, a couple of hardy cyclists had toiled their way up from the plains but most of the visitors had driven up.   We had stopped on our route up from Covilhã to explore the granite landscape and botanise so felt that we had earned our bica and Pastéis de Nata by the time we got to the very top.

Much as I appreciate a summit that satisfies a caffeine addiction, the real interest lies elsewhere, with the road up from Covilhã passing through some dramatically-eroded granite outcrops, composed of huge boulders apparently perched precariously on top of each other.  These resemble the granite “tors” we find in Dartmoor in south-west England, and have a similar origin.   The area around the tors had distinctive vegetation that will, no doubt, be described in greater length in a post on Heather’s blog before too long.   The free-draining sandy soils that the granite landscape creates mean that there was not a lot of surface water for me to indulge my own passions, so I will have to take you to another part of the Serra da Estrela for the remainder of this post.

Granite landscapes near Torre in the Serra da Estrela Natural Park in northern Portugal, September 2018.  

We found an inviting stream as we were walking near Unhais de Serra, at the southern end of the Natural Park.  The first plants to catch our eye were a submerged Ranunculus species with finely-divided leaves and five-petelled white flowers sitting at the water surface.   As well as these, we could see shoots of patches of water dropwort (Oenanthe sp.) and, looking more closely, several of these appeared to be growing out of dark coloured patches which turned out to be a submerged moss overgrown with algae (more about which a little later).   I am guessing that, once the rains come, much of these mini-ecosystems will be washed downstream leaving just a few moss stems to be colonised again next year.

Submerged vegetation in the stream at Unhais de Serra in September 2018 (40°15’44” N 7°37’21” W).  The top photograph shows a Ranunculus species and the lower photograph shows mosses overgrown with algae (a mixture of Cyanobacterial filaments, diatoms and coccoid green algae), within which young plants of Oenanthe sp. have taken root (top photograph: Heather Kelly).

Somewhat to my surprise there were also some patches of Lemanea.   This is a red algal genus that I usually associate with late winter and spring in my own part of the world, so I had not expected to find such prolific growths at this time of year at lower latitudes.   Maybe Iberian species of Lemanea behave differently to those with which I am familiar?

The Lemanea species found in the stream at Unhais de Serra in September 2018.  The top photograph shows it growing in situ and the lower photograph is a close-up.  The filaments are about a millimetre wide.

The dark film itself contained a variety of algae, some of which I have put in a plate below.   There were some cyanobacterial filaments which looked like Oscillatoria to me but which were not moving (their life between collection and examination was less than ideal).  There were also a large number of diatoms, mostly Navicula and Surirella.  Again, both would have been moving around in a healthy sample but were static when I got around to examining them; the chloroplasts in the Surirella, in particular, were not in very good condition).  I also saw some chains of Fragilaria species and several small green algae (especially Monoraphidium, discussed in the previous post).  I’ll return to the diatoms in a future post, once I have been able to get permanent slides prepared and examined but first impression is that I am looking at a community from a low nutrient, circumneutral environment.

Some of the algae living in the dark films overgrowing mosses in the stream at Unhais de Serra in September 2018.   a. – c.: Navicula angusta; d. –g. Surirella cf. roba; h. – i. two different chain-forming Fragilaria sp.; j. – k.: Navicula cf cryptocephala; l. – m.: Oscillatoria sp.    Scale bar: 20 micrometres (= 1/50th of a millimetre). 

The diatoms, in particular, reiterate the important point that notwithstanding the huge number of new species that have been described in recent years, it is possible to peer through a microscope at a sample from anywhere in Europe and see a familiar set of outlines that, for the most part, give a consistent interpretation of environmental conditions wherever you are (see, for example, “Lago di Maggiore under the microscope”).   That same rationale applies, to some extent to other organism groups too: we have recently shown this for macrophytes in shallow lakes for example.   Likewise, the geology here was shaped by the same broad forces that created the landscape of south-west England even if local climate means that the flora surrounding the tors in the Serra da Estrela is adapted to more arid conditions than that on Dartmoor.    It is important that, when we travel, we see the differences but, perhaps even more important in this fractured age, that we see the similarities too.


Chapuis, I.S., Sánchez-Castillo, P.M. & Aboal Sanchero, M. (2014).  Checklist of freshwater red algae in the Iberian Penisula and the Balearic Islands.   Nova Hedwigia 98: 213-232.

Poikane, S., Portielje, R., Deny, L., Elferts, D., Kelly, M., Kolada, A., Mäemets, H., Phillips, G., Søndergaard, M., Willby, N. & van den Berg, M. (2018).   Macrophyte assessment in European lakes: Diverse approaches but convergent views of ‘good’ ecological status.  Ecological Indicators 94: 185-197.