Shifting states …

The backdrop for this post is the spectacular scenery of the Greater Caucasus mountains, extending to over 5000 metres in height (Mont Blanc, by comparison, is 4807 metres) but with an added frisson of geopolitical tension as Russia lies just beyond the peaks at the back of the picture and the foreground itself, though in Georgia, lies within the contested region of South Ossetia.  The Georgian Orthodox nun who serves drinks to weary travellers at the head of the valley is, at least in part, a defiant territorial statement to Georgia’s powerful neighbour to the north.

The river in the foreground is the Terek, which rises a few kilometres above this point, at the head of the Truso valley, and then swings round to flow north to the Russian border and thence east to the Caspian Sea.  The valley forms the major trade artery in the region, the Georgian Military Highway, which was busy with trucks bearing Turkish and Armenian, as well as Georgian plates.  But before this heads over the Jvari pass our taxi driver swung off and headed along a rough track for a few kilometres to the point where common sense says that 4WDs only should proceed, leaving us to follow the track into the hills.  

It is, however, the light-coloured area to the left centre of the image, 90 minutes or so from our drop-off point, which interests me on this occasion.  From a distance it looked like some kind of construction activity was taking place but, close up, it revealed itself to be an extensive area of cream-coloured travertine with, for the most part, a thin trickle of water flowing across it.  Parts have a distinctly pinkish-red tinge, suggesting the Cyanobacterium Schizothrix, and some of the wetter areas have soft brown growths that, again, I suspect are Cyanobacteria though I cannot confirm their identities until I have them under my microscope. Technically, travertine is a deposit formed mostly by physical and chemical processes without, as is the case for tufa, any help from biology (see: “Living rocks, gently rolling …”).  But I suspect that Cyanobacteria are cutting in on the action when they can in this particular situation.

The Truso valley travertines.  The lower image shows a view across the calcareous deposits.  Top left shows part of a pinkish-red mat from a small pond whilst top right shows the dark brown growths in a rivulet running across the travertine bed.  The image at the top of the post shows the view up the Truso valley just before reaching the travertines. 

The geology of this area is complicated, both in the diversity of rock types and their layering and folding, so what follows is an approximate interpretation of what is happening, with some help from Claude.  There are extensive beds of permeable Upper Jurassic limestone in the Great Caucasus overlying relatively impermeable Lower to Middle Jurassic shales.  When water percolating through the limestone reaches the shale beds it emerges as calcium-carbonate-rich springs.  As the supersaturated calcium carbonate-rich water equilibrates with the atmosphere, the calcium is deposited creating the layers of travertine that we could see.

We continued up the valley to the Convent of the Blessed Virgin Mary where we rested and ate our lunch before heading back along the other side of the river.  Along the way we encountered more springs, this time without obvious travertine, with a distinctly sulphurous smell and with red deposits characteristic of iron precipitation.  Most prominent amongst these was the Abano mineral lake (a pond, really) with streams of bubbles rising through the turquoise water.  There were mats of Cyanobacteria mixed in with other vegetation, especially towards the edges but, again, the identities of the organisms will have to remain a mystery until I am back home.

The Abano mineral lake in the Truso valley, September 2026.  Note the bubbles of carbon dioxide-rich water coming to the surface and the red colour of the outfall, associated with the precipitation of iron compounds.

Floating mat of Cyanobacteria and associated vegetation at the edge of Albano mineral lake in the Truso valley.  The largest growth is about 10 cm across.

I was on Google Scholar almost as soon as I got back, trying to understand more about the geochemistry – and microbial ecology – of this intriguing valley, but no combination of search terms revealed anything of relevance.  It may be that there are publications in Georgian or Russian that were not turned up by this search but even the apparently comprehensive Physical Geography of Georgia is very vague on details. I am now  intrigued to see what the samples I collected contained (assuming they survive for the next ten days in my luggage), but those will just scratch my own personal itch,  A fascinating adventure into microbial ecology and environmental geochemistry awaits anyone who fancies some fieldwork in one of the most spectacular landscapes in Europe.

Reference

Kharadze, K., & Salukvadze, E. (2022). Protected areas and remarkable features of  inorganic nature. pp. 181-218 In: The Physical Geography of Georgia (edited by N. Bolsshivili & Neidze, V.), Springer International Publishing.

Mount Kazbegi (5054 metres): the early-morning view from our hotel balcony during our stay in the Caucasus mountains.  

Some other highlights from this week:

Wrote this while listening to: a backdrop of Georgian music. 

Currently reading: Peter Naysmith’s travelogue, Georgia: in the Mountains of Poetry.

Cultural highlight: icons and frescos inside the Georgian Orthodox churches we’ve visited.  

Culinary highlight: many good Georgian meals, but the highlight is probably one in “Cozy Corner” on the edge of Stepantsminda, where we were staying: ostri (a rich meat and tomato stew), lobio (a bean stew), mushroom ojakhuri and very fresh flat bread along with a bottle of Georgia’s distinctive qveri-fermented wine.

The periphyton mess …

The previous post contained my most recent painting of the microscopic world, encapsulating my “imagined but not imaginary” approach to painting.  This one also has paintings of the microscopic world, this time by Daniel Zamorano of the Universidad Austral in Valdivia, Chile.  They address similar themes to my own work but are painted in a very different style: brighter and more expressionistic.  

Daniel writes of the painting at the top of the post, “In this painting, I am trying to give you a glimpse into the private life of periphyton, thousands of microscopic algae living attached to streambeds.  In these mini-forests, algae clump together, interact, disperse, and coexist, going through all the well-known ecological processes and others that we may never fully understand.  Here, the river represents an omniscient presence that flows endlessly over them, bringing nutrients but also the storm”.

Another of his pictures, “Tiny – Biggy” captures the  range of scales that stream ecologists deal with in their work.  In the foreground are microscopic algae, measured in micrometres (a thousandth of a millimetre).  The diatom in the lower central foreground looks like Rhoicosphenia which is typically 20-30 micrometres long (30 – 50 placed end to end would measure a millimetre) but then Daniel plays with perspective, with this close-up of the periphyton giving way to the stream bed which, itself, becomes part of a landscape measured in kilometres rather than micrometres.   Nine orders of magnitude separate the scale of the hills that make up the catchment in the background and the algae that live on the stream bed in the foreground.  

The final one of Daniel’s pictures that I’m including is from a 3M Tech Talk and is called “Tiny Mountain”. Daniel says, “I like to say that under the river water, there are tiny mountains with tiny forest of microalgae.  I noted that with that analogy it was way easier to explain periphyton”.  

These types of visualisation is an important connection between “dry” data and a sense of the living community that this represents.  The modern ecologist is more likely to go down the road of “abstraction”, drawing on multivariate statistics to gain insights, rather than “representation”, but the two approaches are complementary, not alternatives.  I’ve written many times about how one organism can create or modify a habitat that another can then use (see “Eye to the microscope …” and “High rise habitats …”): both started as observations and sketches and suggest interactions that could not have been deduced from ordination plots or metabarcoding data.  Sometimes, old-fashioned skills are what works best, both as a scientist trying to untangle the complexities of life on a stream bed and as a communicator, trying to interest the next generation in these fascinating worlds. 

References

Some of Daniel’s academic publications are listed below:

Zamorano, D., Ingram, T., Labra, F. A., & Matthaei, C. D. (2025). Assessing how biofilms modulate stream periphyton metacommunity assemblage: A translocation experiment. Ecology 106: e70207.

Zamorano, D., Ingram, T., & Matthaei, C. D. (2025). The role of local and upstream colonisation in determining stream periphyton metacommunity assemblages. Ecology and evolution 15: e70850.

Zamorano, D., Labra, F. A., Matthaei, C. D., & Romero, Ú. (2024). Biogeographical patterns of species richness in stream diatoms from southwestern South America. Ecology and evolution 14: e11156.

Zamorano, D., Peredo-Parada, M., Lillo, D. J., Parodi, J., & Díaz, C. A. (2019). Mat thickness associated with Didymosphenia geminata and Cymbella spp. in the southern rivers of Chile. PeerJ 7: e6481.

Tangled tapestries …

I’ve turned the cyanobacterial mat I described in “Vertically challenged …” into a picture to try to understand how the different elements interact with each other.  The abundant branched Scytonema filaments are, I think, key to understanding this, as they create a dense network within and upon which other algae can exist.  As such, it serves as a “foundation species” and dominates the image.  I’ve included a few filaments of Dichothrixon the left hand side, and also some Mougeotia towards the top, as well as a number of diatoms (see “In the family …”).

Several factors combine to create this mini-ecosystem: the basalt of the Whin Sill is overlain by Carboniferous limestone and blanket bog, the latter ensuring that there is a constant trickle of water down the rock face to enable the algae to grow.  The dense entangled filaments of Scytonema have a sponge-like effect, soaking up the water and releasing it only slowly, a stately dance between gravity and capillarity.   This favours motile diatoms such as Delicatophytus and Encyonopsis, which were very abundant in the sample.  People who study diatom motility tend to follow their horizontal movement on glass slides whereas the reality of the natural world is that diatoms move within three-dimensional matrices.   A diatom on a glass slide only needs to engage one of its two raphes; a diatom in a Scytonema mat acts more like a climber in a narrow chimney, using first one, and then the other raphe to connect with surfaces.  I suspect, too, that the abundant scytonemin, the natural sunscreen which imparts the brown colour to Scytonema’s sheath, plays a role too.  The mat was on a south-facing cliff on Falcon Clints, so the diatoms are partially protected from the ultraviolet radiation by the host’s coloration.  

I’ve also included a few cells of Achnanthidium in the image.  These were attached to the Scytonema sheaths, as were a few cells of Cymbella.  One Cyanobacterium can, it seems, create a number of micro-niches if only we care to look closely enough.  Maybe, too, the diatoms are benefiting the Cyanobacteria, but I have no idea how this might be happening.

In “In the family …” I asked whether Cyanobacteria and Cymbellaceae (the family to which Cymbella, Cymatophleura, Delicatophytus and Encyonopsis belong) thrived here because they share the same preferences, or was the success of the Cymbellaceae conditional on the presence of Cyanobacteria?  I’m inclined to think that both factors are invoked: Scytonema and Cynbellaceae tend to favour the clean, well-oxygenated waters of the uplands and neither needs the other.  But within this broad habitat template, a Scytonema mat offers many opportunities for Cymbellaceae that are denied to it on bare rock surfaces.  Motile genera are relatively unusual in these types of streams, so there must be a reason why Delicatophytus and Encyonopsis are sometimes able to thrive.  Does the answer lie in company they keep rather than any innate capability?  Or it could be a combination of the two?  I used the term “foundation species” at the top of this post; perhaps it is better to think of Scytonema as an “ecosystem engineer” because there very presence creates a habitat that did not previously exist.  They are, in their own way, the microscopic equivalents of beavers in the places where they thrive.

Some other highlights from this week:

Wrote this while listening to:  Lost Weekend, new album by Phoebe Bridgers.

Currently reading:  still Georgia In the Mountains of Poetry by Peter Naysmith.

Cultural highlight: The Lady, low budget mocumentary starring Sian Clifford

Culinary highlight: apple auflauf: partly a response to a surfeit of apples in our garden and partly nostalgia for childhood holidays in the Rhine valley.

The natural history of nitrogen (I) …

I’m back in the Lake District but, this time, looking at it through the eyes of a four-year old boy equipped with his first “I Spy” books.  Natural history, in his eyes, is mostly observational, tipping into the experimental only when a slug needs to be gently poked in order to watch its antennae retract.   We’re trying to instil the patience necessary to see the red squirrels that inhabit the surrounding woods, but this may be a losing battle.   Where I hope we are winning is getting him to appreciate nature as something tangible and explorable rather than simply as a topic confined to the pages of a book (shortly after writing this sentence, he stepped on a wasp nest, which was something rather more brutally tangible than any of us were anticipating).

And that leads me to think about my own interactions with nature.  This blog, of course, makes the point that there is a world of wonder beyond the obvious subjects of natural history – flowers, birds, butterflies, trees and so on.  There are organisms too small to be seen with the naked eye and, just as we use lenses to make out the features of distant birds, so  – configured differently – we can also use lenses to uncover hidden natural histories.  But there are also aspects of the natural world that are even more hidden than the microscopic world yet which have significant implications for those aspects that we can see.

Microscopy is experiential but one step-removed from a direct visual encounter.  I may see an interesting growth when out on a walk but I cannot fully appreciate this until I am back home and have teased the growth out and put it on a slide to observe.  However, if viewing microscopic organisms is a skiddle that most natural historians don’t want to bother with, then the equipment and concoctions necessary to measure the concentrations of chemicals in soils and water is going to be step beyond how most natural historians want to spend their time.

Looking towards Rosthwaite in Borrowdale from near Castle Crag, August 2026.   The image at the top of the post shows the view along Newlands Valley towards Bassenthwaite from Catbells, also in August 2026.

But knowing something of the chemistry of the landscape can help explain why particular organisms are favoured or not in any particular place.  More importantly, chemistry often provides the link between human actions and the consequences for nature.  The problem for the natural historian is that what we know about the chemistry of a place comes largely from what we have been told.   It is not like hearing the hooting of an owl or catching a glimpse of a weasel.  Environmental chemistry needs teams of people working in laboratories and a high degree of coordination with correspondingly high costs.  But overcome these problems and stories can emerge, as this new series of posts will show.

The picture at the top of this post shows the Newlands Valley in the Lake District as the starting place for one such story.  The valley bottom has a mosaic of fields of different shades of green, representing different approaches to management.  The sapphire-green fields that make up about half the total have probably had an application of fertiliser, albeit low by the standards of most of the country.  It is mid-August and the farmers are thinking about harvesting their hay or (more likely these days) silage.  When I worked on a Devon hill farm during a university vacation, the rationale was that we needed to replace the nutrients that we took away from the field in the form of silage or milk.  Armchair ecologists might shake their heads sadly and mutter about organic or regenerative farming but the farms of the Newlands Valley are, like my farm in west Devon, mostly small and struggling to make ends meet (their situation is explained well in James Rebank’s book Pastoral).

This is the first of a series of posts about the natural history of one of these nutrients, nitrogen, in which I want to write about how it influences and changes those aspects of the natural world that we can see and, from here, to think about how it could and should be managed.  I offer myself as a sympathetic guide to this interface between the worlds of chemistry and biology because I struggled with the subject at school, dropped it as soon as I could, and have spent the subsequent four decades trying to make up for this lack of formal training.  

One fact, which I do vaguely recall from school days, is key to understanding much of what follows: all nitrogen salts – inorganic compounds in which nitrogen is a core component – are soluble.  The first consequence of this is that the nitrogen fertiliser that the farmers of the Newlands Valley spread on their fields dissolves quickly, especially in such a notoriously wet corner of the country.  That, in turn, means that it washes out of the soil following rainfall, so is not available to do what the farmers put it there to do: sustain the lush grasslands that would produce the fodder for cows and sheep.  The second consequence is that concentrations in the streams of the Newlands Valley are higher than they should be if natural processes alone governed their chemical composition.  The implications in an area such as the Lake District are quite subtle, only bothering a hardcore nerd such as myself but, in areas draining intensively farmed land, nitrogen concentrations can be high, causing significant problems in the coastal waters into which they drain.  

This, then, is an introduction to a series of posts in which we will explore nitrogen through the eyes of a natural historian, thinking about the roles it plays in organisms and ecosystems and also about the effects that human activities have on the amounts of nitrogen in freshwaters, and the consequences for nature.  Along the way, we will go back to the Precambrian era to learn about the role nitrogen played in the evolution of life itself, and also dip into the fraught world of global geopolitics, to understand why farmers across Europe are protesting about proposals for better management of Europe and why the closure of the Straits of Hormuz precipitated a crisis for world agriculture.  But a fellside overlooking the Newlands Valley is a good place to start because the mosaic of habitats below us offer us glimpses into several aspects of this story.   We’ll be returning here later in the series but our next stop is, curiously, a kitchen…

The view across Derwent Water towards the Newlands Valley in August 2026.

Some other highlights from this week:

Wrote this while listening to:  Punching the Clown, new album by Lambchop

Currently reading:  Georgia In the Mountains of Poetry by Peter Naysmith: a travel book ahead of our trip to the Caucasus region in a couple of weeks.

Cultural highlight: watching the 1974 film of Swallows and Amazons with my four-year old grandson (who now runs around shouting “chump-headed galoot” at everyone)

Culinary highlight: Barua, rather good Indian “street-food” restaurant in Keswick. 

Dog days of summer …

Whilst much of the country is wilting under the unprecedented summer heat and praying for rain, I was hoping for the dry weather to persist for just long enough for me to complete my August field surveys in Cumbria.  It would have been ironic in the extreme if, after all this dry weather, my fieldwork had to be postponed because of high flows.  Having argued in this blog that algal proliferations in rivers are as much due to the weather as to nutrients (see: “The greening of our rivers (2) …”, “Understanding verdant rivers (V)” and “Green days …”), I saw this period as an extended natural experiment and last week was my opportunity to harvest this year’s data. 

The streams and lakes of western Cumbia offer a good template for reflecting on the role that the weather plays in boosting algal growth because they are all located in a region without significant urban centres and agriculture is relatively unintensive, meaning that nutrient concentrations are generally low and we have to look to other factors to explain patterns in algal growth.    

What did I find?   First, the three lakes that I visit – Crummock Water, Ennerdale Water and Wastwater – all had low biomasses of benthic algae (those attached to surfaces).   Primary production in these habitats is dominated by phytoplankton which are extremely efficient at hoovering up the scant nutrients, leaving little for the attached algae to utilise.  The larger stones at the margins often have a fine “stubble” of filamentous algae (typically Spirogyra) but the overall quantities are quite low.

Boulders at the margin of Wastwater showing the typical “stubble” of green algae.   The photograph at the top of the post shows the River Irt about 5 km below the outfall from Wastwater.  

The situation, however, changes almost immediately below the lake outfalls, where filamentous green algae covered much of the river bed at six of the seven sites I visited.  The picture at the top of the post, from the River Irt, is typical of what I saw across the region.  Those rivers and streams that are not downstream of lakes showed a variation on this theme.   Superficially, the river beds looked to be in good condition, without the conspicuous growths of green algae that I had seen elsewhere.  However, the rocks were slimy to the touch and measurements suggested that prolific diatom and Cyanobacteria growths were responsible.  There were patches of green algae in some of these rivers and streams, but these generally covered relatively little of the stream bed. 

The difference between the lakes and their outfalls is most likely due to the switch to circumstances where the supply of nutrients, though low, is constantly replenished and the suspended algae that thrive in the lake are washed downstream and out of contention.  Add to this the perfect growing conditions – warm water and plenty of sunlight – and the algae on the stream bed can easily outstrip the best efforts of invertebrates to graze on this largesse.  The difference between rivers downstream of lakes and those not connected to lakes is a little harder to explain.  It is not a difference in quantity so much as in the types of algae that predominate.  The smaller streams tend to be more shaded, but I don’t think that this, alone, can explain the difference.   I suspect that it may be something to do with the composition of the grazers, but I have no evidence at this stage. 

The bed of Croasdale Beck in August 2026.   Just a few kilometres from the location where the photo at the top of the post was taken but, in this case, the algae are better camouflaged and, as a result, more likely to be overlooked.  

A quick scan back through my data suggests that there has been a steady upward trend in the quantities of algal biomass that we measure since we started these observations in 2013.  It is a noisy trend, because riverbeds are patchy and the British summer is unpredictable (we recorded less in the wet summer of 2024, for example), but it is significant.  Adapting the terminology I introduced in “Understanding verdant rivers (V) …”, these streams are showing “meteorology-induced summer euphytic condition” (“meterology” rather than “climate” because this is a response to a particular local manifestation of the climate) and I suspect that it is very widespread this year.  In many parts of the country (though not in this part of the Lake District), it will exacerbate the effect of nutrients, so maybe it is better to think in terms of a broad “syndrome” rather than sticking to the metaphor of disease too strictly.   

We are still only in early August, so there is still time for the weather to break and enough rain to fall to flush most of these algae downstream.   Shorter days might start to limit the amount of sunlight available to fuel photosynthesis, but the lakes act as huge heat pumps, keeping the rivers they feed a few degrees warmer than other streams during the autumn.  It means that I’m already curious to see what will be growing at these locations in October, when I next visit.  After visiting this group of lakes and streams regularly for over a decade, I’ve got a good idea of what to expect but also know to expect to be surprised.   

Training up the next generation …

Some other highlights from this week:

Wrote this while listening to:  Janis Ian, whose music featured in Chuck Chuck Baby (see below).  

Currently reading:  a collection of John Mortimer’s Rumpole short stories

Cultural highlight: Brilliant 2024 low budget romcom Chuck Chuck Baby, available on the iPlayer.. 

Culinary highlight: … or highlights (plural) due to the steady flow of Sichuan home cooking from our kitchen whilst our daughter-in-law is staying with us.

In the family …

Back in May, I wrote about some algae I had encountered in Upper Teesdale (see: “Vertically-challenged …”).  I commented on the range of diatoms that I saw living in and around the Cyanobacterial growth, but only gave broad details because identification can be difficult without cleaned samples and high magnification.   I’ve now had a chance to look at a cleaned sample, so can offer some more detailed insights into what I found on that warm spring day.  

My analysis revealed about 30 diatom species, several of which I could not immediately recognise.  I think I know the streams and rivers of northern England reasonably well, so finding so many unfamiliar diatoms in a single sample was intriguing.  A second curiosity was that about two thirds of all the diatoms belonged to a single family, the Cymbellaceae which, whilst not rare, does not often form such a significant part of either the total number of cells or the overall diversity within a sample.  

Four genera of the Cymbellaceae were represented, of which the most abundant was the genus Delicatophycus (formerly Delicata), with three representatives (D. delicatulus, D. alpestris, D. minuta).  Next came Cymbopleura, represented by C. incerta, then Cymbella (C. affinis, C. exicisiformis) and finally a few valves of Encyonopsis, probably representing at least three genera but none sufficiently abundant to get a secure determination.   I’ve written about a similar phenomenon for a different family before (see: “When is a diatom like a London bus?”): why do some habitats seem to attract particular families?

Delicatophycus and Encyonopsis from Falcon Clints, May 2026.  a.,b.: Delictophycus delicatulus; c.,d: D. alpestris; e. – i.: D. minuta; j. – l.: Encyonopsis spp.   The photograph at the top of the post shows Cymatopleura incerta.  The scale bars are 10 micrometres (= 1/100^th of a millimetre).

I have a hunch that the presence of visible Cyanobacterial growths is part of the story, because this is not the first time I have seen Cymbellaceae in the vicinity of these.  But is it an association, because both Cymbellaceae and Cyanobacteria share the same preferences, or is the success of the Cymbellaceae conditional on the presence of Cyanobacteria?  Or is it a bit of both?  I lean towards this idea: both Cymbellaceae and the Cyanobacteria that I saw in this sample have a preference for environments with relatively low nutrient concentrations but the dense tangle of Cyanobacterial filaments then creates a microhabitat within which the Cymbellaceae can thrive.  

But microhabitat preferences within the Cymbellaceae are not straightforward to disentangle.  The genus Cymbella typically lives on stalks, so would be looking for points of attachment, on the Scytonema sheaths, perhaps.  Delicatophycus and Encyonopsis, by contrast, are unattached and highly motile, gliding around the filaments.  Little seems to be known, by contrast, about the preferences of Cymbopleura in this respect: it is one of those genera that is better known as cleaned valves than as living entities.  We know that it does not form stalks (it lacks apical pore fields, a prerequisite) but beyond this, it is guesswork.  I suspect that it moves around in the Cyanobacterial mats, as Delicatophycus and Encyonopsis do, but cannot be sure.  When I had the living sample under my microscope three months ago, I was not looking at it with a prepared mind.  Now I know what I should have been looking for.  However,  the sample comes from a relatively remote location, about five kilometres from the nearest road and with some rough scree beside the River Tees to be negotiated before I can get back to collect another sample.  

I’ll add this to my to-do list, but life this summer is dominated by small people for whom five kilometre treks over rough ground are not a realistic option.  Meanwhile, I will reflect on how, whilst five kilometres barely counts as a major expedition by the standards of most adventurers, the really journey involves rearranging synapses in my own mind and coming up with a small suggestion that somehow seems to have passed by every other curious person from the past two hundred years.  That’s the magic of the microscopic world: the weird and wonderful, the unknown and the unsuspected, are never quite as far away as we might think. 

Some other highlights from this week:

Wrote this while listening to:  Knat’s A Great Day in Newcastle. 

Currently reading:  I Deliver Parcels in Beijing, by Hu Anyan, a revealing memoir of the underside of the rise of Chinese capitalism.

Cultural highlight: Christopher Nolan’s The Odyssey. Not perfect but some fine moments, with the encounter with the witch Circe standing out for me. 

Culinary highlight: home-made katsu curry

Nitzschia and Denticula species from Falcon Clints, May 2026.  a. – c.: Nitzschia denticula; d., e.: Denticula tenuis.  Scale bar: 10 micrometres (= 1/100^th of a millimetre). 

Tales of the unexpected …

I’ve written about the benefits of returning to the same site over and over again in order to catch it in all its moods.  There is a danger in this, in that you can become blasé and approach the site with expectations already fixed in your mind.  This is a particular danger towards the end of a long day, and when weather is inclement.  Or, in the case of my most recent visit to Wastwater, both of these conditions occurring simultaneously.  

There is a boulder on the south western shore that I have written about on a few occasions (see: “Hunger games …” and  “Memories of last time …”).  There is a small depression at one end where water is trapped when the boulder is exposed and where I often find growths of Tolypothrix distorta var. penicillatus.  I always scratch at the surface here with my forceps to confirm that this is, indeed, the case.  Added motivation on this occasion was that I wanted to have some examples to take with me to the FBA course on algal identification the following week.  So I pushed myself, despite being tired and the weather being less than ideal, and dropped a vial into my cool box for the journey home.   

Colodesmium wrangelii from Wastwater, showing bundled sheaths with epiphytes (smaller Cyanobacteria and diatoms).  Scale bar: 20 micrometres (= 1/50^th of a millimetre). The photo at the top of the post is a low-power image of C. wrangelii with single false branches evident (scale bar: 50 micrometres, 1/20^th of a millimetre).  

Under the microscope, however, the organism that I had collected did not look quite like Tolypothrix distortavar. penicillatus.  It was similar in some respects, including the brown epiphyte-laden sheaths and single false branches, but the filaments were bundled together rather than spreading to give the distinctive “plant-like” appearance of T. distorta var. penicillatus.  It was closer to a Scytonema, but those bundled filaments confounded me.

I showed this to Allan Pentecost when we were together at the FBA algae identification course and, after some thought, and consultation of images in Fritsch he suggested Colodesmium wrangelii, a species described as “rare” in the Freshwater Algal Flora of Britain and Ireland.  Rarity, as I have mentioned before (see: “Studies in brown …”), is the intersection between the actual distribution of a species and the distribution of people able to recognise it.   In the case of Cyanobacteria, there is a very small pool of potential observers, and that probably influences the number of records as much as the availability of suitable habitat.  On the other hand, Allan does know the Cyanobacteria of northern England better than anyone else I know, and when he raises his eyebrows, I know that this is something out of the ordinary, even for him.

This, I guess, is what should drive us on.  Academic ecology is increasingly deductive in nature, with research questions being derived from theory; there is less and less scope for inductive ecology, that starts with observations.   And by “observations”, I mean actually observing nature, ideally in remote locations where human influence is minimal.  Deductions may start with observations on existing data, but such observations will have all the limitations that new science needs to challenge embedded within it.  Being in the position to be curious about why the Tolypothrix I expected to see is not Tolypothrix after all is a privilege that I must never take for granted.

Colodesmium wrangelii (as Desmonena wrangelii) from F.E. Fritsch’s Structure and Reproduction of the Algae Volume II (1945, Cambridge University Press).

Some other highlights from this week:

Wrote this while listening to:  Alex Kassian x Mad Proffessor E2-E4: a reference to E2-E4 by Manuel Göttsching.  Dance music inspired by the first computer-derived music.

Currently reading:  Suzanne Simard’s When the Forest Breathes: Renewal and Resiliance in the Natural World, about commercial and indigenous approaches to forestry in British Columbia and their implications for climate and biodiversity.

Cultural highlight: Durham Miner’s Gala, local gathering of mining communities, accompanied by their banners and brass bands

Culinary highlight: my daughter-in-law’s home-cooked Sichuan food. 

Achnanthidium: microscopic “grass” …

In my career as a freelance consultant, I have analysed over 6500 diatom samples and I thought that the next of my occasional essays on diatom genera should probably focus on the genus that I have found most frequently in those samples.  A quick query on my Access database showed this to be Achnanthidium, more specifically Achnanthidium minutissimum which, with just over five million valves, accounted for about two thirds of all the diatoms I have ever recorded.  That, in turn, says something about the types of streams that I have studied rather than being a comment on the distribution and abundance of this species (I’ll come back to this later).  It is, however, a very common genus, so definitely deserves a closer examination.

As is the case for many of the genera that I record now, names have changed over the years.  When I started, I would record “Achnanthes minutissima”; the shift to “Achnanthidium minutissimum” occurred in the mid to late 1990s prompted, I recall, by the work of Frank Round.  However, this was actually a resurrection of an older name that had fallen into disuse in the twentieth century.  Hustedt, for example, regarded it as a subgenus within Achnanthes.  It was only when it was possible to look at diatoms with a Scanning Electron Microscope (SEM) that the similarities that seemed to be so important when using a light microscope were overridden by fundamental differences in the fine structure.  Within a few years, a slew of new genera had arisen to accommodate the extraordinary diversity within Achnanthes.  The true Achnanthes is now largely a marine genus, rarely recorded in inland waters except when salt levels are elevated.

Achnanthidium rivulare from Fahaduff, County Kerry, Ireland, June 2024.  Scale bar: 10 micrometres (= 1/100^th of a millmetre).  The picture at the top of the post shows Achnanthidium species from Costa Beck, North Yorkshire, June 2023.   1-10: A. minutissimum; 11 – 15: A. atomoides; 16 – 20: A. cf. lineare; 21 – 23: A. sieminskae; 24 – 27: girdle views.  Scale bar: 10 micrometres (= 1/100^th of a millimetre.   

Recognising that “Achnanthes minutissima” was, in fact, “Achnanthidium minutissimum” was, in fact, only the start of the story.  Krammer and Lange-Bertalot’s revision of Hustedt’s Süsswasser Flora von Mitteleuropa described 12 varieties and forms within Achnanthes minutissima but did not recognise these as formal species (in some cases, they had adopted a more conservative approach than Hustedt).  From this point on, however, diatomists armed with SEMs started to rigorously dissect the variation within the genus and split off a huge number of new species.

The problem is that, whilst there is little doubt that there is extraordinary diversity within this genus, converting the insights from SEM studies into practice when using a light microscope is challenging.  These species are small, and key attributes, such as striae arrangements, lie at the limit of resolution of light microscope.  What is more, Achnanthidium species have a tendency to lie on their sides – girdle view – when these diagnostic characteristics are not visible.  Achnanthidium, in other words, encapsulates many of the challenges I describe in “Call me by my name …”  

Achnanthidium subhudsonis var. kraeuselii, generally regarded as a non-native species (see “Achnanthidium subhudsonis invades Britain?“), from Afon Seiont, North Wales, September 2016. Scale bar: 10 micrometres (= 1/100^th of a millimetre.   

Not only do we have the problem of naming species whose diagnostic characteristics are close to the limit of resolution of the optical microscope and which often do not present themselves in an optimal manner for seeing these characteristics anyway, but the ecological requirements of these species are often also imperfectly known.  The graphs below show the distribution of Achnanthidium minutissimum which encapsulates much of what we do know for the genus: it is most abundant at the cleaner end of the water quality gradient, where it very often dominates assemblages, but it is also often found when nutrient levels are elevated.  Whether this demonstrates a genuinely broad ecological spectrum, or cryptic species displaying different ecological tendencies, or just the consequences of dislodgement and downstream drift of A. minutissimum cells from their preferred habitat is not clear. I suspect the latter plays a large role.

Distribution of “Achnanthidium minutissimum” (broadly defined) in in UK streams and rivers.  Vertical lines indicate average positions of ecological status class boundaries (blue = high, green = good, orange = moderate; red = poor/bad).  There are no status class boundaries for alkalinity; the vertical lines divide the scale into “very low”, “low”, “moderate” and “high”.  A longer explanation of how the boundaries for nitrate-N and reactive P is given here [https://microscopesandmonsters.wordpress.com/2026/01/21/rhoicosphenia-the-hitchhiking-diatom/].  

These graphs also show a general preference for circumneutral water and for lower alkalinity, though this particular graph may be misleading, as the geologies that create high alkalinity also creates good farmland, with the associated enrichment which Achnanthidium species generally do not like.  Achnanthidium is also one of the few diatom genera that can withstand intense heavy metal pollution, probably through gradual acquisition of tolerance when populations are exposed to this stress rather than to innate characteristics of the genus.  

But this focus on water chemistry, I think, misses the point.  A better way of thinking about Achanthidium was suggested by Barry Biggs and colleagues for their conceptual habitat matrix for stream periphyton.  They suggested that Achnanthidium was a typical “ruderal” species – a “weed” in common parlance – able to colonise disturbed surfaces rapidly.   This explains its proliferation in turbulent Lake District streams where cobbles are prone to roll around, scouring away any attached algae.  But this also means that it is able to withstand grazing by mayflies and other invertebrates foraging on the stream bed.  It is, in effect, the “grass” of submerged microscopic communities. That means we could look at Achnanthidium – the whole panoply of species – as indicating healthy linkages between trophic levels, rather than simply as a genus that indicates (mostly) an absence of chemical pollution.  That’s a very simplified hypothesis (see “Curried diatoms …” for a potential complication) but then so is the idea that water chemistry alone holds the key to understanding the distribution of Achnanthidium species.

Achnanthidium, in other words, encapsulates the “yin” and the “yang” of diatom studies.  The “yin” is that we know a lot more than we did thirty years ago about the diversity of the genus, and have a respectable body of both morphological and genetic evidence to underpin this (even if the morphological evidence is often at the edge of resolution of light microscopes).  The “yang”, though, is that we are barely beyond first base in understanding how this diversity translates into ecological function.  As is often the case with diatoms, we know the shape of everything, but the meaning of nothing.

More information

The Freshwater Diatom Flora of Britain and Ireland

Diatoms.org

References

Biggs, B. J., Stevenson, R. J., & Lowe, R. L. (1998). A habitat matrix conceptual model for stream periphyton. Archiv fur Hydrobiologie 143: 21-56.

Round, F.E. & Bukhtiyarova, L. (1996).  Four new genera based on Achnanthes (Achnanthidium) together with a re-defintion of Achnanthidium.  Diatom Research 11: 345-361.

Some other highlights from this week:

Wrote this while listening to:  The Band’s eponymous second album and The Last Waltz, as a soundtrack to …

Currently reading:  Across the Great Divide by Barney Hoskins, the story of The Band and their place in popular American music.

Cultural highlight: still vaguely on the same subject, I watched The King of Comedy, directed by Martin Scorcese (who also directed The Last Waltz) and with some music by Robbie Robertson of The Band. 

Culinary highlight: too many pub meals over the last couple of weeks, but potted Morecambe Bay shrimps eaten in a pub near Grange overlooking Morecambe Bay were noteworthy.  

Studies in brown …

The headlines screamed “hottest May ever!” last week, and whilst the south of England sweltered under record temperatures, the Borders, where Bill Brierley and I were teaching a course on rapid algal assessment, became the perfect outdoor classroom, with the cool waters of the River Tweed to keep us from overheating.   This is, I feel, payback for the fieldwork in brutally-cold conditions I described in “Cold cases …”

For once, it is pleasurable to linger in the channel and examine the vegetation at my leisure.  There is some blanket weed, but not too much, plenty of Lemanea fluviatilis and Hildenbrandia rivularis and, close to the banks especially, extensive beds of Ranunculus.  But what catches my eye are the small round brown patches on many of the larger cobbles and boulders.   These are Heribaudiella fluviatilis, the freshwater brown alga that I have written about before (see: “Spotting spots …” and “Depths of imagination …”).  There are over 1800 species of brown algae – including the conspicuous kelps and wracks of our coasts – but only about thirteen of these are found in freshwaters, and just three have been recorded from Britain and Ireland.  One of these is a single record from 1959.  

Heribaudiella fluviatilis on a submerged boulder in the River Tweed at Mertoun Bridge.  Most patches are about a centimetre across.  The picture at the top of the post shows the River Tweed at Mertoun Bridge.

Heribaudiella is a good example of the challenges of biological recording because the question we want to ask (“where is it found?”) is confounded by a second question, “where are the people who can recognise it looking?”.   In the case of an alga that forms insignificant brown dots on submerged rocks, the biggest problem is noticing it, and recognising that it is worth recording, in the first place.

One of the people who could do this was the late Nigel Holmes, an exceptionally alert and observant macrophyte ecologist, who did his PhD on the River Tweed in the early 1970s.  He was a student of Brian Whitton in Durham a decade or so before I arrived, and he took Brian’s early experiments on how to survey the macrophyte flora of rivers and developed this in his PhD.  The fieldwork on which his thesis is based involved wading the entire length of the River Tweed (about 150 km from source to tidal limit) and most major tributaries, recording all the vegetation he could see, using a standard 0.5 km length as his recording unit.  This method then became the standard survey method for the Nature Conservancy Council, where Nigel worked after graduating, and then evolved into the macrophyte survey method still used by the Environment Agency and SEPA today.   

Nigel’s observations of Heribaudiella fluviatilis in the Tweed show just how widespread it was, with records from almost every 0.5 km length between 25 and 140 km from the source.  Unfortunately, few people apart from Nigel went on to record it systematically subsequently.  It never went away but it is not a particularly prepossessing alga so the “intangible cultural heritage”, if you like, of one biologist pointing it out to another could not be sustained.   Heribaudiella became a species we read about in dry academic tomes rather than part of the lived experience of river ecology.

The distribution of Heribaudiella fluviatilis in the River Tweed in the early 1970s: a graph from Nigel Holme’s PhD thesis.  Each bar shows the number of 0.5 km lengths where H. fluviatilis was recorded for each 10 km length of the river.  

This changed a few years ago when David Mann was re-examining the metabaracoding data produced from our diatom studies.  The brown algae are reasonably closely related to the diatoms (see: “Unlikely bedfellows …”) which means that the primers we used for diatoms also picked up any Heribaudiella or relatives that were in the same sample.  Not only was Heribaudiella fluviatilis quite widespread, but he also found many records of Pleurocladia .. and of Bodanella lauterbornii, previously thought to be restricted to alpine lakes (see: “Depths of imagination …”, which also links to a paper questioning the taxonomic status of Bodanella).  

Heribaudiella fluviatilis on a small boulder from the River Tweed at Mertoun Bridge, May 2026.

We were also able to link several of our Heribaudiella records to water chemistry, showing that it was a species that preferred circumneutral, well-buffered water with low phosphorus concentrations, though it was tolerant of slightly elevated nitrogen concentrations (probably because phosphorus is the limiting nutrient in most of these places).  Based on my own observations, I would add that it prefers stable substrata (large cobbles and boulders) in well-lit stretches of the river.  In many aspects, it overlaps with the red alga Hildenbrandia rivularis, but the latter is more conspicuously shade-tolerant and can tolerate more nutrient enrichment. 

Arguably, metabarcoding has helped us to “rediscover” Heribaudiella but in a different, more abstract manner to Nigel Holmes’ encounters with this species in the 1970s.  It is no longer part of the “lived experience” of standing in a river examining the vegetation; instead, it is one more entry in a spreadsheet.  I read Pope Leo XIV’s Encyclical Magnifica Humanitas, on the challenges presented by AI, this week, in which he refers to “the dignity of work” insofar as it is a “requirement of the human condition, a normal path towards maturity, development and personal fulfilment”.  Our metabarcoding data give us some insights into this small alga that would have been much harder to glean by traditional means but I still wonder if ecologists also need to think about the “dignity of fieldwork”, where traditional skills still provide an essential connection to the reality of the stream bed and the necessary abstractions required to understand this.  

References

Holmes, N.T.H. (1975).  The vegetation of the River Tweed.  PhD thesis, University of Durham. 

Holmes, N. T. H., & Whitton, B. A. (1975). Macrophytes of the River Tweed. Transactions of the Botanical Society of Edinburgh 42: 369-381. 

Kelly, M. G., Mann, D. G., Taylor, J. D., Juggins, S., Walsh, K., Pitt, J. A., & Read, D. S. (2024). Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers. Science of The Total Environment 914: 169445. [the paper that describes the metabarcoding dataset which we used to explore the distribution of Heribaudiella)

Pope Leo XIV (2026). Magnifica Humanitas.  https://www.vatican.va/content/leo-xiv/en/encyclicals/documents/20260515-magnifica-humanitas.html

Some other highlights from this week:

Wrote this while listening to:  Jason Isbell, in preparation for his concert at the Glasshouse

Currently reading:  Elif Shafak’s There Are Rivers in the Sky.  A novel in which the Rivers Thames and Tigris are central characters.

Cultural highlight: A busy weekend: Jason Isbell’s southern rock on Saturday followed by stand-up comedy from James Acaster, whose improvisations around an unexpected heckle added at least 20 minutes to the length of the set.

Culinary highlight: scallop cerviche and lemon sole, cooked by my daughter, and served with a Georgian orange wine, in anticipation of our trip to the Caucasus region later in the summer.

Vertically-challenged …

There was a heatwave forecast across northern England on the Whitsun holiday, so we set off early to avoid the worst of it and, when we arrived in Upper Teesdale, the growing heat of the morning sunshine was abated by a refreshing breeze.  Curlews, oyster catchers and red shanks circled and called in the sky above us, and there were birds eye primrose, marsh marigold, a few orchids and extensive growths of globe flowers in the grasslands beside the path.  Towards the end, on Widdybank Fell, we found a single sapphire-blue flower of a late spring gentian to round off our day.

Before we reached Widdybank Fell, we had to scramble along the rocky section where the Whin Sill cliffs of Falcon Clints rose up above the River Tees and, as I did so, I noticed multicoloured seepages on the vertical faces above me.  All had a somewhat spongy texture and the range of hues suggested a diversity of organisms present – darker browns indicating Cyanobacteria, yellow-browns suggesting diatoms and occasional patches suggesting filamentous green algae.  I’m always at my happiest when the more obvious natural wonders are balanced by some of nature’s shyer faces.   

Some of the seepages on Falcon Clints, where my samples were collected.  The picture at the top shows Falcon Clints on the walk towards Cauldron Snout and Cow Green Reservoir.

When I teased apart some of the soft dark brown cushion and put it under my microscope, I saw a mat of interwoven yellow-brown branched filaments.  This change in colour as you put a specimen under a microscope is common phenomenon: when we look at the mats growing on the Whin Sill in Teesdale, our eyes rely on reflected light and the filaments sit on a dark surface.  When they are under the microscope, however, we shine a bright light from underneath and this transmitted light reveals their true colour.  In this case, the filaments belong to Scytonema alatum and the yellow-brown pigment is scytonemin, a natural sun-screen produced by many Cyanobacteria but first isolated from this genus.  

A short while later, I see greener filaments of a related genus, Tolypothrix, which typically has less scytonemin than Scytonema so displays the more typical blue-green coloration we expect of Cyanobacteria.  This alone is not a reliable criterion for differentiating the two genera, as some Tolypothrix species can produce scytonemin under the right circumstances.  Scytonema, however, has branches arising singly and in pairs, whereas Tolypothrix only has single branches, and the heterocysts (specialised cells used for nitrogen-fixation) are at the ends of filaments in Tolypothrix but not in Scytonema.  I also found a colony of another cyanobacterium, Dichothrix, similar to the Rivularia that is common elsewhere in Upper Teesdale (see “Teesdale’s unseen natural history …”).  But it was the Scytonema that dominated the algal cushion. 

Scytonema cf. alatum from a vertical face of Falcon Clints in May 2026.  Scale bar: 50 micrometres (= 1/20^th of a millimetre).

Tolypothrix tenuis (possibly var. calcarta) from the vertical face of Falcon Clints, May 2026. Scale bar: 20 micrometres (= 1/50^th of a millimetre).  

Teasing out some of the other patches revealed some green algae – Zygnema and Mougeotia – which, I suspect, were anchored in the Scytonema in much the same way as I have described for similar algae in Lake District streams (see: “Ever-changing worlds …” and “Something, somewhere, just for a moment …”).  But there were also yellow-brown patches of diatoms, amongst which Encyonopsis and related genera were most abundant, along with some Achnanthidium and a few other species.  I’ll need to examine these at high magnification to be sure of identities of particular species so this post will stick to generalisations. 

I had seen diatoms, particularly Delicatophycus (or is it Encyonopsis?), in all the samples I collected, but there were yellow-brown patches where it seemed to dominate.  I suspect, from this, that the Scytonema creates a matrix on the rock surface, exploiting the trickle of water from the seepage, and that the green algae and diatoms then use the shelter that this generates.  When conditions are right, the mobile diatoms move to the light and form a separate layer on the outer side of the Scytonema.  It evokes the communities I wrote about from Deptford Creek (see: “Commuting to work …”) but in a very different context.  

Diatoms from the vertical face of Whin Sill at Falcon Clints, May 2026.  Delicatophycus is abundant, along with Fragilaria and Achnanthidium.  Scale bar: 20 micrometres (= 1/50^th of a millimetre).  

I’ve written about vertical communities before (see “Fifth columnists …”) but this Whin Sill habitat got me thinking again. A south-facing rock face beneath a seepage is a perfect environment for algae, in many ways, so long as they can counteract the forces of gravity.  Quite how Scytonema adheres to the rock is a mystery  There is evidence that Cyanobacteria and other bacteria can exploit and, over time, enlarge, tiny cracks in the surface of even hard rocks such as basalt, and they also produce mucilage that help with adhesion.  Having established a network of filaments close to a rock surface.  The green algae, as I have noted before, benefit from being tangled amongst Cyanobacterial filaments (see: “Something, somewhere, just for a moment …”) and both they and the diatoms also produce mucilage that will further assist this process.  Finally, there are physical forces such as surface tension that mean that the liquid that we know as water is a stickier, more viscous fluid when considered from the perspective of a microorganism.

All these factors combined mean that a community on a vertical rock face in Upper Teesdale is not such a precarious proposition as we might first think.   Yes, there will be the occasional catastrophic failure when the whole film might shear off, but for most of the time, there is a space that is theirs for the taking, bathed in the warmth of the Teesdale sun, when it deigns to shine, and soused in a steady trickle of water and associated nutrients.  That both sunshine and nutrients are in relatively short supply in this environment is actually a positive sign, nature generally being at its best when hungry.  Nearly all the problems we associate with algae and Cyanobacteria arise when we make their environments unnaturally nourishing.  Those negative associations make it hard, sometimes, to persuade people that Cyanobacteria are an expected part of the diversity in a National Nature Reserve yet, here they are, sitting quietly by the Pennine Way minding their own business in the May sunshine … 

References

Herrera, A., Cockell, C. S., Self, S., Blaxter, M., Reitner, J., Thorsteinsson, T., Arp, G., Dröse, W. & Tindle, A. G. (2009). A cryptoendolithic community in volcanic glass. Astrobiology 9: 369-381.

Robins, R. J., Hall, D. O., Shi, D. J., Turner, R. J., & Rhodes, M. J. C. (1986). Mucilage acts to adhere cyanobacteria and cultured plant cells to biological and inert surfaces. FEMS Microbiology Letters 34: 155-160.

Staudigel, H., Furnes, H., McLoughlin, N., Banerjee, N. R., Connell, L. B., & Templeton, A. (2008). 3.5 billion years of glass bioalteration: volcanic rocks as a basis for microbial life?. Earth-Science Reviews 89: 156-176.

Some other highlights from this week:

Wrote this while listening to:  Bruce Springsteen’s Darkness at the Edge of Town

Currently reading:  City of Djinns by William Dalyrymple

Cultural highlight: the 2024 dark comedy A Real Pain, written and directed by Jesse Eisenberg.

Culinary highlight: Paccheri di Mamma Carmela, a spicy tomato and pasta dish at Monte Cassino, a rather good Italian trattoria in Melrose in the Scottish Borders