Entrances and exits …

Having shown in two recent posts how the presence of one alga influences the quantity of many others in the River Irt, I thought I should see if this relationship holds in other streams in the region.   As Gomphonema exilissimum was the “ecosystem engineer” in the River Irt, I started with Croasdale Beck because I knew that this, too, had abundant populations of Gomphonema at certain times of the year.   Whereas the River Irt flows out of Wastwater, Croasdale Beck tumbles straight off the west Cumbrian fells.  It is, as a result, a much flashier stream than the Irt, and this has a big effect on the stream’s algae.

Gomphonema in Croasdale Beck shows the same general annual pattern as it does in the River Irt but without the coupling to diatom biomass that I showed in “High-rise habitats” (there are weak relationships, but these are not statistically-significant).  The most abundant Gomphonema is different at the two sites I visit on Croasdale Beck: G. parvulum at the upper site and G. calcifugum at the lower one.  Neither grows on long stalks in Croasdale Beck although I have certainly seen relatives of G. calcifugum form long stalks elsewhere in northern England (see: “And the Oscar for the best alga in a supporting role goes to …”).  I suspect that the harsher conditions compared to the River Irt would mean that “high-rise” growth forms would get scoured away too frequently and that, in turn, means that there is less opportunity for other algae to exploit the habitat that a cushion of stalk-forming Gomphonema creates.   

Gomphonema parvulum (top row) and Gomphonema calcifugum (bottom row), the two most common species of Gomphonema in Croasdale Beck (seen in the photograph at the top of the post)

Both Gomphonema species in Croasdale are at their most abundant about now (just as in the River Irt).   As March passes to April so a different diatom, Odontidium mesodon will become abundant and then, during the summer, it will be Fragilaria that dominates (at least two species – F. gracilis and F. novadensis) before, towards the end of the year, Meridion constrictum will become abundant.   Platessa (P. saxonica and P. oblongella) show a weaker trend, with dropping to minima in mid-summer before rising again, whilst Achnanthidium shows no annual trend at all.  

Annual trends in relative proportions of six common diatom genera in Croasdale Beck.   Vertical lines divide the year into 12 months.  

The diatoms are, in other words, behaving just as the terrestrial vegetation.  Outside my window I can see crocuses where, a few weeks ago, I would have seen snowdrops.  Daffodils are also beginning to appear.   In nearby woodlands, I can see celandine, but this will soon be replaced by wood anenomes, bluebells and then wild garlic.  The processes that drive these changes in higher plants are hard-wired into the genomes.  We know much less about the reasons for changes in stream diatoms.  Maria Snell made a convincing case for seasonal changes in diatoms in a stream on the other side of Cumbria being the result of changes in nutrient supply.  However, I think it unlikely that Croasdale Beck experiences the same scale of nutrient flux.   We know that the rise and fall of Asterionella formosa (another late winter/spring diatom) in Cumbrian lakes is a much more nuanced story, with temperature playing a key role and there is no reason to assume that the same does not apply to stream diatoms too.   Nutrients will certainly be part of this tale, but there is a richer cast of characters than this simplistic interpretation allows. 

Cobbles from Croasdale Beck in February 2023, their upper surfaces glistening with a thick film of diatoms.

Why is seasonality in stream diatoms overlooked?   One possible reason is that most sampling frequencies are too low to detect patterns within individual streams.  Another, however, is that diatomists are not primed to look for this type of pattern.   The Freshwater Benthic Diatoms of Central Europe, the one-volume handbook that many of us use, describes over 800 common species, and includes ecological and habitat notes for all of these.   However, there is not a single comment on seasonality.  By contrast, preferences for chemical water quality are described in detail.   A benign explanation may be that seasonal preferences vary around Europe, but it is also possible that seasonality in diatoms is widely overlooked.   The two reasons – not being told to expect seasonal patterns and not sampling consistently at the same sites with sufficient frequency – are intertwined.

It is the inverse of Newton’s famous statement, “if I have seen further it is by standing on the shoulders of giants”.  What if those we thought of as “giants” were actually, themselves, only dwarves?   Maybe there are more patterns under our noses that earlier generations of diatomists had overlooked but which are ripe for a new generation to discover?   Wouldn’t science be boring if everything the “giants” of earlier generations told us turned out to be true and there was nothing left for us to discover? 


Maberly, S. C., Hurley, M. A., Butterwick, C., Corry, J. E., Heaney, S. I., Irish, A. E., … & Roscoe, J. V. (1994). The rise and fall of Asterionella formosa in the South Basin of Windermere: analysis of a 45‐year series of data. Freshwater Biology 31: 19-34.

Snell, M. A., Barker, P. A., Surridge, B. W. J., Benskin, C. M. H., Barber, N., Reaney, S. M., … & Haygarth, P. M. (2019). Strong and recurring seasonality revealed within stream diatom assemblages. Scientific Reports 9: 3313.

* All the world’s a stage,
And all the men and women merely Players,
They have their exits and their entrances ….
                        William Shakespeare, As You Like It Act 2 Scene 7

Some other highlights from this week: 

Wrote this whilst listening toLynyrd Skynyrd (pronounced ‘lēh-‘nērd ‘skin-‘nērd) following the death of their guitarist Gary Rossington. I’ve long been uncomfortable about a band that performed with the Confederate flag as a backdrop.  It raises similar issues for me as the film Tár, about the extent to which it is possible to separate an artist’s views from their work.  This week, however, I’ll give them the benefit of the doubt …

Currently reading: Lessons, by Ian McKewen

Cultural highlight:  Fergus McCreadie Trio at the Sage, Gateshead although, to be honest, I’m still on a high after the Vermeer exhibition at the Rijksmuseum 

Culinary highlight:   Slightly belated shout-out for Gertrude’s Restaurant and Bar in Amsterdam where we ate and drank last week.   “Small plates” and a bottle of an Alsatian Orange Gewürztraminer.  

And finally, two sketches made on my iPad after the Vermeer show.   My disappointment is that Vermeer’s “The Art of Painting” was too fragile to travel from Vienna.  Otherwise, I could have drawn someone photographing a painting of someone painting someone.  I had to make do with drawing someone photographing a painting of someone.


The man who stares at algae …

At the risk of writing a post that leads to every reader silently screaming “get a life …”, Lemanea, the subject of my previous post, was not the only alga growing on the stones on the bed of the River Irt.   Alongside the dark brown tufts of Lemanea there are also patches of green algae.   And when you look closely at these, you see that they often arise from dark brown and also that these are a different shade of dark brown from the Lemanea patches on the rock surface itself.  

Unfortunately, you cannot see this clearly in my photographs.  We visited Cinderdale Bridge at the end of a long day, the water was 6 oC and the screen on my camera is not very good for assessing the quality of images of small green and brown blobs moving in the current in real time.  You’ll just have to trust me when I tell you this.   

I might not be able to take perfect underwater macro photographs, but I can recognise an excellent stream phycologist from some distance.  So can you.   They have three hands: one to hold the bathyscope that lets them see the stream bed, one to manipulate a pair of forceps underwater and one to hold the sample vial into which a small portion of the algal community will be dropped.  Two-handed people cope by using their knees to support a bathyscope held by the same hand that is gripping a sample vial.  Somehow, I managed to transfer a small piece of this green/brown floc into a vial and get the lid screwed on without disaster.

Mougeotia (green) and Microcoleus autmnalis (brown) from the River Irt in a Petri Dish (approx. 9 cm diameter).   The photograph at the top of the post show filaments of Mougeotia growing out of mats of Microcoleus autumnalis in the River Irt at Cinderdale Bridge, February 2023.   Scale bar: 20 micrometres (= 1/50th of a millimetre).

Back at home, in my study (rather warmer than the River Irt in February), I emptied the vial into a Petri dish,  teased out a small portion roughly at the border between the brown and green parts and put this under my microscope.  The green growths were filaments of Mougeotia, an unbranched, typically slimy, alga that is common in lakes and streams in this part of the world whilst the brown sections were dense mats of the cyanobacterium Microcoleus autumnalis, also often common in these streams (see “Fieldwork notes, August 2021”.  In this and all earlier posts it was referred to as “Phormidium autumnale”).

Microcoleus autumnalis often lives in habitats where the water level fluctuates and, when exposed, dries into thin, papery layers (“in nuda terra autumno” in the original description – “in the bare earth in autumn”).   That would not be a situation that Mougeotia would enjoy.   However, here in the River Irt, the mats of Phormidiumwere permanently submerged and the Mougeiotia filaments seemed to be growing out from these, their basal sections tangled amongst the interwoven strands of Microcoleus.    I described something similar in the River Liza where Stigonema mamillosum was the host (see “Ever changing worlds …”) and I’ve touched on the idea of cyanobacteria as “ecosystem engineers” on several occasions (see “Landscape architects”).   However, there is nothing in the formal scientific literature about their role in supporting filamentous green algae in streams.   

In fact, the literature devotes very little time to the basic conundrum of how filamentous algae (which don’t have roots) stick to submerged rocks (that are too hard for roots to penetrate anyway).   Old taxonomic works often refer to filaments having “basal cells” or “holdfasts” or, in some genera, putting out rhizoids, but these are never described in great detail, and have not been followed-up in recent years.   We accept the presence of filamentous algae in streams without ever challenging their right to be there in the first place. 

Could it be that cyanobacteria, rather than facilitating colonisation by green algae occasionally, actually play this role quite often but their presence is usually camouflaged by the green algae above them or is simply overlooked by most field biologists?   The interwoven filaments of cynaobacterial mats hug the contours of rocks much more tightly than green algae, meaning that they live in the “boundary layer” where they are protected from the rough and tumble of the stream.   A green algal propagule, or a fragment of a filament, that becomes trapped within this mat, therefore, has a better chance of success than one outside the mat.   I offer this as a hypothesis rather than as a fact.  It might just help us understand why some rivers are greener than others.


The paper explaining why Phormidium autumnale had to be transferred to Microcoleus is: 

Strunecký, O., Komárek, J., Johansen, J., Lukešová, A., & Elster, J. (2013). Molecular and morphological criteria for revision of the genus Microcoleus (Oscillatoriales, Cyanobacteria). Journal of phycology 49: 1167-1180.

Some other highlights from this week: 

Wrote this whilst listening toThe Art of the Fugue by J.S. Bach

Currently reading:   Girl With a Pearl Earring, by Tracy Chevalier.   Getting me in the mood for …

Cultural highlight: Vermeer exhibition at the Rijksmuseum, Amsterdam.   28 of the 37 paintings known to have been painted by Vermeer gathered in one place.  An experience of a lifetime.

Culinary highlight:   Iranian meal kit supplied by Modern Persian Kitchen which started out in Durham but now delivers nationwide.

Looking after their own …

Much has changed in the two months since I was last at the River Irt.  The conspicuous yellow-brown patches of diatoms that attracted my attention in Cold Comforts have gone, but other algae have appeared: clusters of dark brown filaments, each a couple of centimetres long, on the upper surface of boulders.   These tufts are the red alga Lemanea fluviatilis, which I’ve written about before (see“Lemanea in the River Ehen”).   Interestingly, I did not see Lemanea at Lund Bridge, the focus of the posts about winter diatoms, but at Cinderdale Bridge, a few kilometres further downstream.  Lemanea is also not found in the River Ehen close to the outfall of Ennerdale Water but becomes abundant a few kilometres further downstream.  There must be something about proximity to a lake that does not favour this genus.  

Young shoots of Lemanea fluviatilis along with green algae on a boulder in the River Irt at Cinderdale Bridge, February 2023.   The boulder is about 40 centimetres long.    The photograph at the top of the post shows the River Irt at Cinderdale Bridge.

These filaments (which are actually hollow tubes of cells) had some growths which looked remarkably like another red alga common in streams hereabouts, Audouinella hermainii.  But we could also turn that argument around and say that Audouinella looks remarkably like juvenile stages of several red algae (see “The complicated life of simple plants …”).  Unravelling the identities of these simple filaments has kept taxonomists busy for over a century and molecular analyses are still presenting us with surprises.   I’m going to assume that these are young gametophytes of Lemanea until someone convinces me otherwise, simply because of their proximity to so many other young shoots of Lemanea.  

A filament of Lemanea fluviatilis with young epiphytic gametophytes.  Scale bar: 100 micrometres (= 1/10th of a millimetre).  

Close-up of young gametophytes on a filament of Lemanea fluviatilis in the River Irt, February 2023. 

These were not the only residents on Lemanea.   There were also some thin, unbranched filaments belonging to a cyanobacterial genus Chamaesiphon.   This is a genus with two very distinct habits: some species form dark brown/black crusts on rocks (see “A bigger splash …”) whilst other species live as epiphytes.    I last wrote about the epiphytic forms in “Whatever doesn’t kill you …”.  In that post, I was circumspect about naming the species because I could only see a single “exospore” at the end of filaments.   The population in the River Irt, however, has several filaments with a very characteristic stack of exospores so I can use the name C. confervicola with more confidence.  

A young filament of Lemanea fluviatilis with epiphytic Chamaesiphon confervicola. A stack of exospores is visible on the filament to the left of centre.  Scale bar: 20 micrometres (= 1/50th of a millimetre).  

The last image in this post is a graph showing the changes in the cover of Lemanea fluviatilis in rivers in West Cumbria over the course of a year.   This shows very clearly that Lemanea is most prolific in winter and spring, becoming very sparse in summer through to autumn.  It is a similar pattern to that shown by Gomphonema.   There are algae that have pronounced summer peaks but we tend not to see these in the very nutrient-poor streams of the Lake Disrict.   My theory is that these small streams tend to be shaded and to have healthy populations of (hungry) invertebrates which are most active in the warm waters of summer.   Consequently, winter offers the best opportunity for an alga to grow relatively unmolested.   And, just as I showed how Gomphonema created a “housing estate” for other diatoms to inhabit, so Lemanea might well be determining the fluxes of the tiny Chamaesiphon confervicola filaments too.  

Seasonal changes in the cover of Lemanea fluviatilis in rivers in West Cumbria, 2019 – 2023.   Cover is expressed on the 9-point scale used for macrophyte surveys in the UK.   Vertical lines separate the twelve months.

Some other highlights from this week: 

Wrote this whilst listening toIn a Silent Way, by Miles Davies.   My favourite of his many records. 

Currently reading:   Animal, Vegetable, Miracle: Our Year of Seasonal Eating by Barbara Kingsolver.  

Cultural highlight: finally got around to seeing BAFTA-winning and Oscar nominated film Aftersun, starring Paul Mescal.  

Culinary highlight:   homemade prawn, crab and fennel cannelloni.   

High-rise habitats …

In the previous post I said that I had looked at one patch of algae in the River Irt from four different perspectives.  I’ve actually looked at this patch from five perspectives, because I forgot to count the graphs that I included in Cold Comforts.   Graphs are visual representations of the algae but they are not figurative in the sense that the photographs I’ve used are.   They are abstract in the sense that they convey an essence of the subject matter whilst being independent of visual references.   In the case of these graphs, I was able to convey a sense of changes over time that would have been impossible without sophisticated time-lapse photography.

The genus Gomphonema has featured prominently in the two earlier posts, so we’ll start with a closer look at how this changes over the course of the year.   This is mostly G. exilissimum but, as we saw in the previous post, other species are also present.   This graph shows a similar trend to the one showing chlorophyll concentrations on the riverbed over the course of a year, with the lowest values in the summer and higher values at the beginning and end of the year.   

The percent of total diatom valves belonging to the genus Gomphonema in the River Irt downstream of Wastwater (2019 – 2022).  The y axis is presented on a square-root transformed axis.   The photograph at the top of the post shows Cinderdale Bridge on the River Irt.

The question that arises is whether the Gomphonema is following a general trend in diatom biomass or whether it could actually be responsible for the annual fluctuations that we can see in biomass.   Over the course of the year, it rarely accounts for more than ten percent of all diatoms although, as we saw in the previous post, this equates to a larger proportion of total biovolume.   When we add in the stalks, then Gomphonema is by far the most abundant diatom.   The stalks do not contribute to the amount of chlorophyll that we measure, but they do create surfaces on and around which other algae can grow.   

The next step, therefore, was to look for relationships between the amount of Gomphonema and the amount of chlorophyll.   As you’ll see below, there is a positive relationship – more Gomphonema is associated with more chlorophyll.   If this was just a correlation with the annual trend in chlorophyll then we might expect to see this type of pattern in other common alga.  In fact, as the other three graphs below show, these do not show any relationship with biomass.   This is not conclusive, but it does hint to a role for Gomphonema in this particular stream as a creator of ephemeral habitats that other taxa can then exploit.   

Relationships between diatom biomass and Gomphonema (a.), Brachysira (b.), Achnanthidium (c.) and Fragilaria (d.) in the River Irt downstream of Wastwater (2019-2022).  Only the regression for Gomphonema is significant (adjusted r2 = 0.44).

My interpretation is that many of the diatoms that I find in the River Irt are not particularly fussy about the substratum on which they grow, so I find them throughout the year, regardless of the biomass.   However, when Gomphonema exilissimum proliferates, the surface area available for other diatoms to colonise increases, leading to an increase in diatom biomass.   G. exilissimum has created opportunities for “high-density housing” – algal equivalents of tower blocks (“housing projects”, for North American readers).  

I suspect, too, that these Gomphonema-dominated communities make perfect meals for grazers once they get active in the spring.  The combination of crunchy protein-rich diatoms and lots of carbohydrates in the stalks creates a nutritious salad which, in turn, means that they do not last for very long.  These habitats are ephemeral, shifting in space and time.  That is probably one reason why diatoms are rarely considered to be “foundation species” in the generally adopted sense.  But in the brief window of opportunity when Gomphonema can thrive, they are every much as essential for the health of the overall community as the oak trees in an ancient woodland.

Some other highlights from this week: 

Wrote this whilst listening to: Hothouse Flowers and My Bloody Valentine: two very different bands sharing a common origin in Dublin in the early 1980s.  

Currently reading:   The Origins of Virtue by Matt Ridley.  

Cultural highlight: Transatlantic Sessions at the Sage, Gateshead, a coming together of Celtic and North American (mainly Appalachian) musicians exploring their common heritage.  Musicians included Liam Ó Maonlaí, leading me to explore Hothouse Flowers.

Culinary highlight:   Dinner at Khai Khai in Newcastle before heading to the Sage for Transatlantic Sessions.  Khai Khai is fast becoming our Indian restaurant of choice in Newcastle.

Ways of seeing …

I’m back at the River Irt, in the shadow of the Wastwater Screes, for this post.   I wrote about my visit in early December in “Cold Comforts”, then followed this up with “Temporary Foundations” in early January.   Together, these offer three “views” of the algae in the River Irt: first, as seen with the naked eye, then as observed through a microscope.   The third view was an imagined microscopic view had the catastrophic interventions required to transfer field growths to a microscope not been required.  Today, I offer a fourth view: that of the diatoms following standard cleaning procedures.   This is the approach adopted by most diatomists, prioritising the structure of the silica frustule (cell wall).  

In the earlier posts, I explained how the stalks of Gomphonema exilissimum formed a matrix within and around which other diatoms existed.   It is not always easy to see all the details needed for a confident identification when looking at fresh material, and a close look at cleaned material showed that, whilst this was the certainly the most abundant Gomphonema species, there were also several cells of two other species.  G. cymbelliclinumlooks very similar to G. exilissimum but there is a pronounced asymmetry along the long axis and the striae are also more radiate.   There were also a very small number of cells of G. hebridense

Gomphonema species from the River Irt, December 2022.   a. – f.: G. exilissimum; g., h. G. cymbelliclinum; i. G. hebridense.   Scale bar: 10 micrometres (= 100th of a millimetre).   The photograph at the top of the post shows the River Irt at Lund Bridge, just downstream from the outflow of Wastwater.

However, although playing an important role as a “foundation species” in the biofilms of the River Irt, Gomphonema was not the most abundant genus in the sample.  That honour went to Achnanthidium, which accounted for 63 per cent of all the cells.  I spotted at least six species, five of which are illustrated below.  Two were common (A. minutissimum and A. siemenskae), two less so (A. caledonicum and A. neomicrocephalum) and two were scarce (A. “eutrophium”, A. lineare).   A. siemenskae has only recently been recognised in the UK.  Previously, it was “lumped” with A. caledonicum but some astute detective work by Ingrid Jüttner finally showed that it was distinct.   

Achnanthidium from the River Irt, December 2022.  a. – g. & k. – o.: A. siemenskae; h. – j.: A. minutissimum; p. A. eutrophilum; q., r. A. lineare; s., t. A. caledonicum.  Scale bar: 10 micrometres (= 100th of a millimetre).  

Simply counting the number of individuals can be misleading, however.  Achnanthidium cells are smaller than Gomphonema exilissimum cells, and if we convert the number of cells to their volume, then Achnanthidiumdrops from representing 63 per cent of the total, to just 32 per cent.   G. exilissimum, by contrast, leaps from 13 per cent to 36 per cent.  The biovolume calculation is probably a better representation of how the two genera contribute to the primary productivity of the community but this is just based on the cell and excludes the stalk.  If we could include the stalks in the calculation, G. exilissimum would be even more dominant. 

The next most abundant species, assessed by numbers was Brachysira microcephala.  This is a curiosity for another reason: I calculate that it has changed names four times since I started looking at diatoms.  First, it was included in Anomoensis vitrea.  Next, freshwater species of Anomoensis were moved to a resurrected genus (originally created by Kützing in 1836) and it became Brachysira vitrea.  Then B. vitrea was split and forms found in soft water were placed in B. neoexilis.  Some people thought that there was no need to create this new species as a previously described species, B. microcephala, took priority.  Last year, however, Bart van der Vijver and colleagues showed that B. neoexilis and B. microcephala were two distinct species.   I think of this species as being more typical of lakes than rivers but this part of the River Irt is very close to the outfall of Wastwater, which may explain its frequency here.   We met this and some relatives from nearby Ennerdale Water in “Baffling Brachysira”.

Brachysira microcephala from the River Irt, December 2022.  Scale bar: 10 micrometres (= 100th of a millimetre).  

Finally, I have included a plate of the long, needle-like cells of Fragilaria tenera, a common species that has cropped up in many posts.   This was the fifth most abundant taxon when I just counted numbers of cells, but the long, thin cells each pack a lot of biovolume.   In Cold Comforts you can see it living as an epiphyte on the stalks of Gomphonema exilissimum, and I’ve also seen it growing on green algal filaments in rivers near here.   If Fragilaria tenera was a houseplant, the instructions would read “place in a well-lit environment and keep well-watered”.

This view of the diatoms of the River Irt is neater than the views I showed in Cold Comforts.   The photographs offer two-dimensional representations of three-dimensional objects which is fine if we want to peer at their fine details and try to match what we see with pictures in the scientific literature.   It is difficult, for example, to be aware of the full variety of forms of Achnanthidium (and, to a lesser extent, Gomphonema) in the earlier photographs but this extra information comes at a cost.   Nature is not as tidy as the plates I’ve presented in this post suggest.  The very untidiness, in fact, is an important part of the story.   I alluded to that in Cold Comforts and I’ll come back to this message again in the next post.

Fragilaria tenera from the River Irt, December 2022.  Scale bar: 10 micrometres (= 100th of a millimetre).  


Jüttner, I., Hamilton, P. B., Wetzel, C. E., Van De Vijver, B., King, L., Kelly, M. G., … & Ector, L. (2022). A study of the morphology and distribution of four Achnanthidium Kütz. species (Bacillariophyta), implications for ecological status assessment, and description of two new European species. Cryptogamie, Algologie43(10), 147-176.

Van de Vijver, B., Schuster, T. M., Kusber, W. H., Hamilton, P. B., Wetzel, C. E., & Ector, L. (2021). Revision of European Brachysira species (Brachysiraceae, Bacillariophyta): I. The Brachysira microcephala-B. neoexilis enigma. Botany Letters168(4), 467-484.

Some other highlights from this week: 

Wrote this whilst listening to: Martha Wainwright and her father Loudon Wainwright’s songs about their dysfunctional relationship, ahead of a trip to see Martha Wainwright at the Sage, Gateshead next week.

Currently reading:   Kingdom of Characters by Jing Tsu, about the evolution and adaptation of Chinese writing to fit the needs of the modern world.

Cultural highlight: Cezanne exhibition at the Tate Modern  

Culinary highlight:   Haggis, neaps, and swede.  Belated Burns Night shorn of the ridiculous oratory.

Pesticide-induced myopia …

The previous post ended with a reflection on how algal communities in rivers changed.   This one picks up that theme and takes it forward, looking at a very different reason.   First, we need to move from the shadow of the Wastwater screes to a chalk stream flowing through Dorset, an altogether more gentle landscape.    It was beside this stream that Helen Rosenkranz, a PhD student I co-supervised, ran some experiments on what happens to stream algae when they are exposed to herbicides.  

The graph below  summarises the situation.   The bars represent  (from left to right): the control treatment (water from the River Frome), samples treated with the herbicide chlorotoluron, samples treated with glyphosate and samples treated with both herbicides.   The two herbicides were applied at quite high concentrations for 12 hours, simulating the situation if the spray had accidentally drifted to the water course or if the herbicide had washed off the plants and soil following rainfall.   Helen measured a number of characteristics of the algae, but I have just shown one of her measurements.   

Ratio between total number of cells of diatoms and green algae in control (CON) and herbicide-treated biofilms (CLT = chlorotoluron, GBH = glyphosate, GHBC = chlorotoluron and glyphosate combined.   Bars show mean values; vertical lines show standard errors.   See Rosenkranz et al. (2023) for more details.   The photograph at the top of the post shows the upper reaches of the River Wylye in Wiltshire, an example of a southern English chalk stream. 

Because a lot of stream monitoring around Europe uses diatoms, we know less about how pollutants affects other groups of algae.   In this case, we did see an effect of the herbicides (particularly glyphosate) on the diatom species but more interesting was an overall shift in the proportions of green algae and diatoms.  The glyphosate seems to have encouraged the green algae but suppressed the diatoms whilst not affecting the overall quantity of algae at all.  Helen also showed that the changes to the diatom assemblage affected the Trophic Diatom Index (TDI), the basis for UK’s assessments of the health of benthic algae. This is important because the TDI is used primarily to assess the impact of nutrients from rivers, so another pollutant that affects the TDI potentially influences the decisions that the Environment Agency make about how a river should be managed.  

The problem is that pesticides have always been a blind spot in the UK’s river management strategy.   Everyone knows that they are there, but measuring their effect is difficult.  Our knowledge of the chemical composition of river water is based on a network of sites sampled four times a year.   They used to be sampled monthly, but that was trimmed back a few years ago.  Let’s say it takes ten seconds to dip a bottle into a river to collect a sample.   Four samples spread through the year means that we have an accurate idea of conditions for 0.001 per cent of the year.   That’s not a problem if we can assume that those four brief moments are representative of the year as a whole.   The effluent from a sewage works, for example, runs continuously, so there is no particular reason to presume that one sample is wildly different from another.   

However, we know that pesticides are only applied at certain times of year, and also that rainfall events around those peak spraying periods are when the risk to river ecology is greatest.   That means we really need to focus our sampling on those brief periods.  That’s the ecologist in me speaking, but try scheduling that into the work programmes of a team of public sector workers.   The result is a very imperfect understanding of the extent to which pesticides affect stream biology.  

Two recent German studies tried to overcome this by using automatic samplers that switched on when it started to rain.   These measured substantially more pesticides in the water than a conventional sampling programme, and they found that pesticide concentrations in the water were probably the most important source of stress on aquatic invertebrate communities.   If that is the situation in Germany, then there is no reason why this is not also the case in the UK.   

It’s a question that’s easy to ask but which will be difficult to answer.   As in many situations with environmental health, the issue is not the technology itself but finding the resources and the willingness to deploy it.   The importance of agriculture to the UK economy and food security means that pesticides in rivers s a subject that the government would prefer to kick into the long grass.  It is a manifestation of what philosophers call the “trolley problem”: there are losers whatever they do and that does not make for easy political messaging.   


Liess, M., Liebmann, L., Vormeier, P., Weisner, O., Altenburger, R., Borchardt, D., … & Reemtsma, T. (2021). Pesticides are the dominant stressors for vulnerable insects in lowland streams. Water Research, 201, 117262.

Rosenkranz, H., Kelly, M. G., Anesio, A. M., & Yallop, M. L. (2023). A Multi-Faceted Approach to Quantifying Recovery of Stream Phytobenthos Following Acute Herbicide Incidents. Phycology, 3(1), 25-46.

Weisner, O., Arle, J., Liebmann, L., Link, M., Schäfer, R. B., Schneeweiss, A., … & Liess, M. (2022). Three reasons why the Water Framework Directive (WFD) fails to identify pesticide risks. Water Research, 208, 117848.

Some other highlights from this week: 

Wrote this whilst listening to: Elderly vinyl copy of Elgar’s Cello Concerto with Jacqueline du Pre and Daniel Barenboin which has a scratch on the final bars.   It does mean that a piece of music that you wish could last forever literally does, so long as you don’t mind listening to endless repetitions of half a crescendo.

Currently reading:   The Wonderful Adventures of Mrs Seacole in Many Lands: the autobiography of a pioneer nurse working during the Crimean War.  Realised, amidst all the grim news from Ukraine that the Crimean War (1853-1856) was also a confrontation between Russia and the West fought out in Ukraine, and that I knew very little about it.

Cultural highlight: Tár, film starring Cate Blanchett exploring the question of whether a monster can make great art.  The plot centres on rehearsals for performances of Mahler’s 5th Symphony and Elgar’s Cello Concerto (see above).  

Culinary highlight:   Vegan ragu, made to recipe by Felicity Cloake in The Guardian, with homemade tagliatelle 

Temporary foundations …

I spent the quiet period between Christmas and New Year converting my comments on the structure of diatom communities in the River Irt (see “Cold comforts …”) into a picture, as a way of illustrating how Gomphonema exilissimum acts as a “foundation species”.  Gomphonema exilissimum grows on long branched stalks which create a matrix upon which other species can attach.   The most abundant of these epiphytes were Achnanthidium and Fragilaria tenera, both of which I’ve included in the picture.   There were also a few ribbons of Tabellaria flocculosa and occasional green cells (top left corner of the final illustration in “Cold Comforts …”) but I have not included them in this image.   Neither the photos nor the painting really conveys the patchiness of the actual colonies.   Some fields of view were dominated by Gomphonema cells, others had as many Fragilaria or Achnanthidium cells as Gomphonema.  Any illustration is, necessarily, a simplification.   As is a conventional “name and count” analysis.  You may be able to produce a longer list of species and, because the samples are better homogenized during the preparation steps, better estimates of the relative abundance of each, but you lose the sense of their interrelatedness.   

Interrelatedness is the key here.   Remove Fragilaria tenera from the mix, and another Fragilaria species will come in and replace it.  I’ve found several other Fragilaria species in samples from these streams over the years, often growing as epiphytes, and there is no obvious reason why they would not also thrive on the stalk of a Gomphonema.   However, remove Gomphonema exilissimum, however, and there would be nowhere for Fragilaria tenera to gain a foothold.  This distinctive diatom-dominated assemblage, visible with the naked eye, would disappear.  Fragilaria tenera might not disappear from the reach as a whole, as it also grows as an epiphyte on some of the green algae that grow in these streams (e.g. Oedogonium).   However, that would be a different community.   The old habitat is demolished and a new one built in its place.   From the coarse perspective of a biologist interested in a list of species from a location, Fragilaria tenera is still there.  From a more focussed perspective, however, it has been “rehoused” in a different suburb, a community built around a different foundation species.   

The Gomphonema community viewed down the microscope.  The image at the top is the result of scanning multiple fields of view such as this.

It is not always easy to get an impression of interrelatedness from simply peering through a microscope.   Gomphonema exilissimum was neither the most abundant species in the sample nor the largest, at least based on cell size.  Diatom stalks are extracellular structures which disappear when samples are prepared by the standard cleaning procedures.  It might well be that G. exilissimum plus stalks constituted more biomass than the other species present, but I have not measured that.   However, it does not need to be the case because the stalks are, themselves, supported by the water and by each other.  We cannot simply extrapolate from terrestrial habitats where a plant needs to invest in structural tissues in order to stand up straight.   The tangled mass of stalks creates a matrix that is greater than the sum of its parts.  

My experience is that it is the stalk-forming species that are the most obvious diatoms to fit the term “foundation species”.   In freshwaters these tend to be in the order Cymbellales.   Examples covered in this blog include Didymosphenia geminata (see “A journey to the headwaters of the River Coquet …” and Gomphosinica (see “Subaquatic landscapes in Pangong Tso”).   It is important to distinguish between a “foundation species”, which shapes a community, and a “dominant species” which is the most abundant species (number, biomass, whatever) but which is replaceable, in terms of their control of population and community dynamics.  But that opens up another problem: this community is not always present.  It waxes and wanes (see graph in “Cold comforts …”).   A terminology that was developed by biologists concerned with the visible world sometimes struggles when fitted to the microscopic domain.   Describing Gomphonema exilissimum as a foundation species works right here right now, but not when applied across the whole year.   Algal communities in lakes and rivers are often transient, with an ever-shifting patchwork of growth forms.  In  essence, however, the same processes govern these and the forests which extend up the hillside beside the river.   We just need to recalibrate our minds in order to understand what we are seeing.    


Record, S., McCabe, T., Baiser, B., & Ellison, A. M. (2018). Identifying foundation species in North American forests using long‐term data on ant assemblage structure. Ecosphere, 9(3), e02139.

Some other highlights from this week: 

Wrote this whilst listening to: Simon and Garfunkel Live in Central Park.  

Currently reading:   A Ballet of Lepers by Leonard Cohen.   A short novel and stories published posthumously.  Just finished Takeaway by Angela Hui, a memoir of growing up in a Chinese Takeaway in the valleys of South Wales. 

Cultural highlight: Catherine Called Birdy, 2022 film by Lena Dunham.  

Culinary highlight:   Old-school Chinese takeaway, inspired by reading Angela Hui’s memoir.   We’ve had plenty of Chinese food since our visits to China but have gravitated towards Sichuan restaurants and this meal reignited my love of Cantonese cooking.

Memories of last time …

This boulder is to me what madeleines were to Marcel Proust: it stirs memories.   You’ve already read about it in Hunger Games and in some older posts.   When I looked at it on my most recent visit in early December, I not only remembered, but I noticed that it was different.  It is time to take a closer look.   

The first thing to notice is that more of it is exposed than back in October.   The lake must be about twenty centimetres lower.   Second, the zonation of algae is back.   When I visited in August, I commented on the clear distinction between bands of cyanobacteria and green algae (see “More from the splash zone …”).    In October, the green algae had disappeared.  Now, in December, they are back again.   Microscopic examination showed these to be mostly Spirogyra, as in August, along with smaller quantities of Mougeotia, Oedgonium and Klebsormidium.

Third, the growths of Tolypothrix on the side of the boulder are less conspicuous.   I’m guessing that it has been outcompeted by the green algae.  I’m also guessing that it is present, and possibly even serving as a “rooting medium” for the green algae.   It is another example of the “patchiness” in space and time of aquatic algal assemblages (see previous post for more about this).   

Algae below the waterline on the littoral boulder in Wastwater in December 2022.   The photo captures about 20 centimetres depth and cyanobacteria and green algae are both visible.   The photograph at the top of the post shows the boulder with Great Gable in the background.

This drop in lake levels meant that a flat “plateau” of rock on the right-hand side which had been submerged was now largely exposed.   In my earlier post, I had commented on how this had been dotted with Tolypothrix colonies.   Tolypothrix was, on this trip, still conspicuous in depressions on this surface – miniature “rock pools”, as it were, that were rewetted at regular intervals by waves breaking against the boulder.  

I’ll keep this post brief.   It is just an update on a ever-changing situation.  Having made a comparison with Marcel Proust, I need to be mindful of length.   À la Recherche du Temps Perdu spills over into seven volumes and over 3000 pages.   Most of us have heard about it, but almost none of us have read it.   I don’t want that to be my fate too.

The “rock pool” on the right-hand end of the boulder.  It is about 30 centimetres across, and growths of Tolypothrix (up to about a centimetre in diameter) are just visible.

Wrote this whilst listening to:   Phoebe Bridger’s EP of Christmas songs, including her exquisite cover of Merle Haggard’s If We Make It Through December

Currently reading:   How to Feed a Dictator by Witild Szabłowski.   Interviews with the personal chefs of Idi Amin, Saddam Hussein and others.  

Cultural highlight: Standing on the Sky’s Edge, new musical set in a brutalist high-rise development in Sheffield.   Features songs by Richard Hawley. 

Culinary highlight:  Christmas dinner, cooked by my daughter at her home in Sheffield.

Cold comforts …

Clouds were low enough to obscure the views that I used to illustrate my last post about Wastwater and Wasdale (see “Hunger games …”), so I have started this post with a photograph of the underwater landscape of the River Irt, rather than the distant mountains.  You should be able to see three distinct algal lineages here: diatoms forming the yellow-brown patches in the foreground and left-centre, cyanobacteria along with mosses forming black patches on the centre-right boulder and green algae in the right foreground and growing amidst the black cyanobacteria/moss patches.  The underwater landscape is verdant at the same time as the surrounding fields and fells are at their most depleted.

Is ”verdant” even the right word?  It comes from the French word for “green” yet green is just one of a number of hues on display.   All these, however, are the outcome of mixtures of green chlorophyll and other pigments, so we may have strayed from a literal definition of verdant whilst still being within the popular meaning of lush vegetation.  But, before we get lost in etymology, let’s think about why some rivers in the Lake District present this counterintuitive burst of colour in the depths of winter.

We do not yet have a definitive answer but suspect that the temperature of the water plays an important role.  The lushest algal growths are found in rivers immediately downstream of lakes which act, as it were, as huge “water-source heat pumps” – warming up gradually during the spring then cooling slowly throughout the rest of the year (see graph below).   The difference between the River Irt and nearby River Calder (which does not have a lake upstream) is small when measured as absolute temperature but nonetheless means that there is a third more heat energy in the River Irt every day at this time of year compared with the Calder.   It all adds up.

Water temperature (2021 & 2022) and benthic chlorophyll (2019-2022) trends in the River Irt downstream of Wastwater.

That’s not the whole story.   The flow regime in rivers downstream of lakes is not as harsh as it is in rivers without lakes upstream, and there must be differences in the intensity of grazing by invertebrates.   But small differences in temperature have effects on a wide range of processes in rivers, and there is no reason why it should not be an important factor in determining algal dynamics in Lake District streams either.

Gomphonema exilissimum in the River Irt (Lund Bridge), December 2022.   Scale bar: 20 micrometres (= 1/50th of a millimetre).  

Do not misinterpret all this talk of the relative warmth of the River Irt in December.  Plunging an arm into a northern English river in December is not for the faint-hearted.  But you’ve got no other option if you want to know what organisms are responsible for those vivid yellow-brown patches on the stream bed.   Back in the relative warmth of my study, I examined these with my microscope and saw that the bulk of the diatoms belonged to a single species – Gomphonema exilissimum. – growing on long branched stalks.   Sometimes there were patches where other diatoms were prominent – Fragilaria tenera, Tabellaria flocculosa and Achnanthidium species.    But these were growing on and around the matrix of Gomphonema stalks.   Gomphonema, in this setting, is a “foundation species”, shaping the habitat in ways that let other organisms thrive.   We think of the trees of a forest as foundation species but these “bushes” of Gomphonema play similar roles in streams, albeit on much smaller scales.  

Gomphonema cf. exilissimum and Fragilaria cf. tenera in the River Irt (Lund Bridge), December 2022.  Scale bar: 20 micrometres (= 1/50th of a millimetre).  

We could, perhaps, argue that the mosses and cyanobacteria play similar roles.  I’ve written about these before (see “As old as the hills …”) and also described how cyanobacteria can create conditions within which green algae can thrive in another stream in the western Lakes (see “Ever changing worlds …”).   These relationships all help to create the patchworks visible with the naked eye (see also “The multiple dimensions of aquatic biofilms”).   We need to think of the patterns not just in terms of variation across the stream bed, but also over time.  One big spate could roll the stones on which the algae grow or rip the filaments from the surfaces, leaving spaces for new species to invade.   It’s the ecological equivalent of Heisenberg’s Uncertainty Principle: we can predict that certain algae will live under certain conditions, but there is a limit to the accuracy of these predictions.   It is not that our measurements are necessarily flawed, just that this patchiness – across space, through time and at multiple scales – is an inherent property of the system that needs to be respected.   

I’ll end where I started: this is all happening in the midst of a northern English winter.  The trees are bare and the water is cold.  We watch the weather forecasts closely, and plan our fieldwork for the short gaps when water levels are low enough to permit safe wading.  When we get to the rivers, though, we find richer growths – both in quantity and diversity – than we see at any other point in the year.   We can only wonder …

Some other highlights from this week: 

Wrote this whilst listening to:   The Specials, following the untimely death of Terry Hall.  In particular, their most recent album, Protest Songs:1924 – 2012

Currently reading:   Henning Mankell’s The Pyramid, short stories featuring the Swedish detective Kurt Wallander.

Cultural highlight: non-existent.  A combination of winter lurgies and too much work to finish before the Christmas break

Culinary highlight:  homemade mince pies.   

The diatoms of Lago Trasimeno

Back in October I wrote, somewhat apologetically, about my inability to switch off completely whilst on holiday (see “Reflections from Lago Trasimeno”).  The flip side of that condition is that I can continue to revisit a holiday two months after I have packed my flip-flops and sunhat away for the year.   On a damp, cold winter afternoon I can travel, virtually, back to warmer climes simply by peering through a microscope.   Somehow, the presence of particular assemblages of diatoms synergises with the memory of being there to take me to a flow state, where time melts away and space ceases to have any relevance.  For a couple of hours, at least, I can feel the Umbrian sun on my face again. 

Looking at the diatoms of Trasimeno not only took me back to the summer, it also linked Trasimeno to some other places I have visited and written about here.  It recalls Cassop Pond and Croft Kettle in my own neighbourhood (see “The diatoms of Cassop Pond” and “More about Croft Kettle”), but also turloughs in the west of Ireland (see “Famous for 15 minutes …”), small lochs in the Shetland Islands and shallow lakes in Greece that I have been studying.   Genera such as Epithemia, Rhopalodia and Mastogloia all crop up together in these hard water habitats, irrespective of geography.   

Diatoms from Lago Trasimeno.  a., b. Diatoma moniliformis; c. Tabularia fasiculata; d. Cocconeis placentula.  Scale bar: 10 micrometres (= 1/100th of a millimetre).   The photograph at the top of the post shows Lago Trasimeno from Passignano sul Trasimeno, September 2022.

I found 32 species in the sample I collected on the shore of Isola de Maggiore, and could have found more had I been inclined to spend more time.   I always prefer to spread my effort over several samples from different locations or collected on different dates rather than to “mine” a single sample to exhaustion.   32 is a respectable haul for a single sample: not especially species rich but, at the same time, not depauperate either.  

About ten percent of these belong to the genera Epithemia and Rhopalodia which are capable of nitrogen fixation.   These are relatively large diatoms, so they will represent a greater proportion of the biomass and biovolume than a simple count of individuals suggests.  No great surprise, perhaps, that Lago Trasimeno in September, is short of nitrogen as these are also ideal conditions for the bacteria which break down the nitrogen compounds that run off the surrounding farmland and release it back to the atmosphere.   My earlier post on the algae of this lake pointed out the abundance of the cyanobacterium Gloeotrichia, another nitrogen-fixing organism, again emphasising the nitrogen-limited state of the lake at this time of year. 

More diatoms from Lago Trasimeno.  a. Navicula crptotenelloides; b. Navicula cryptotenella; c. Navicula cf. microdigitoradiata; d. Navicula duerrenbergiana; e. & f. Mastogloia baltica (two focal planes); g. Haslea spicula; h. Cymbella neocistula; i. Encyonema caespitosum; j. Seminavis strigosa; k. & l. Amphora sp.; m. & n. Amphora pediculus.   Scale bar: 10 micrometres (= 1/100th of a millimetre). 

About a third of the diatoms belonged to genera such as Navicula and Nitzschia that are capable of movement.   Large numbers of these can often be signs of human disturbance, but not always.  In this case, I suspect that the naturally hard water leads to the precipitation of calcium carbonate, which smothers surfaces and challenging any organism living there.  Being able to constantly adjust position means that a motile diatom has an advantage over its sessile cousins.   A further twist to the story is that 20% of the diatoms are tolerant of saline conditions, which ties in with some evidence that the concentration of ions in the lake is increasing (see references in earlier post).   The two most likely reasons are abstraction of water from the lake for irrigation and climate change so this, too, is a potential sign of human disturbance.   Greater evaporation also makes it more likely that calcium carbonate will precipitate at the same time as the lake water gets more salty.   My interpretation of conditions, based on a single sample, is that the water is getting close to being “brackish” rather than strictly “fresh”.  If trends for global warming continue, then shallow lakes in warm regions such as this will become more salty, with implications for the ecosystem services that they provide to the region.  

Diploneis cf. elliptica, photographed at three focal planes.   Scale bar: 10 micrometress (= 1/100th of a millimetre)

I’ve found at least one of the motile diatoms – a small Nitzschia – in brackish lakes in Greece too.  It does not correspond to any Nitzschia I’ve seen described (“e.” in the plate of Nitzschia and Tryblionella below), so one challenge for the next few months is to try and find out some more about this, comparing Italian and Greek populations and digging a little deeper into the literature. 

More diatoms from Lago Trasimeno.  a. Epithemia sorex; b., c. Epithemia adnata; d., E. frickeri; e., E. turgida.  Scale bar: 10 micrometress (= 1/100th of a millimetre).

This slide is my “souvenir” from Trasimeno.  We associate the word souvenir with knickknacks and trinkets, but the word has its roots in the French word meaning “remember”.  Peering through a microscope on a cold winter day in northern England is enough to transport me back to sunny days in Umbria.  At the same time, the diatoms that I see bring me back to my own locale because I can find several of them in a pond that is walking distance from my house.   At the same time, finding salt-tolerant diatoms so far from the sea is a reminder of the encroaching reality of global warming.   All these pictures combine to tell a story … happy memories, certainly, but no guarantee of a happy ending.

More diatoms from Lago Trasimeno: a. Nitzschia acicularis; b. Nitzschia filiformis var. conferta; c. Nitzschia cf. palea; d. N. palea var. tenuirostris; e. Nitzschia sp.; f. Tryblionella sp.   Scale bar: 10 micrometress (= 1/100th of a millimetre)

Some other highlights from this week: 

Wrote this whilst listening to:   Low’s Christmas and Sufjan Stevens’ Songs for Christmas.  Two very leftfield Christmas albums. 

Currently reading:   more Nadime Gordimer.  This time it is Livingstone’s Companions, a book of short stories.

Cultural highlight:   A recreation of local artist Norman Cornish’s house and studio at Beamish Museum in County Durham.

Culinary highlight:  “dirty broccoli” – broccoli roasted with a peanut and chilli marinade.