microscopesandmonsters

My comments on diatoms and topophilia (see: “Hannaea: springing into life …”) also apply to the subject of this post, but with a few variations.  The genus Eunotia is, like Hannaea, a species of remote, often upland habitats, but the landscapes it conjures in my imagination are likely to be boggy places where my boot might, at any moment, disappear into a damp, peaty tussock of Sphagnum.   The majestic sweep of moorland might well be broken by the angular outlines of coniferous plantations and, if there are outcrops, they are likely to made of granite or a similarly tough impenetrable rock that refuses to absorb the rainfall that is all too common.    

Scrape up a sample from a rock or a plant in one of the streams that traverse these peatlands, or from one of the pools, and look at it under the microscope.  The first organisms you notice might well be the desmids, which are common in aquatic habitats in these landscapes, particularly the boggy. Pools (see: “Invisible worlds at Malham Tarn” and “Desmids from Moss Dub”).  They are large, half a millimetre or more in length, and thus an order of magnitude larger than most of the diatoms.  But you will start to see other organisms too, including diatoms with their yellow-brown chloroplasts.  Some will have boat shapes and be gliding around but others will be boxy or have curved outlines, and it is these that we will be thinking about today, as they are the two most common views of members of the genus Eunotia.   When you peer straight down at a cell, it will have a rectangular appearance but when you look at it from the side, you will see that it is asymmetric in the sense that the top half has a different outline to the bottom half, but symmetric in that the left-hand side is usually a mirror image of the right-hand side (though there are exceptions, as the diagram below shows – but bear in mind that these are presented at right angles to their natural way of sitting on flat surfaces).   

The diversity of Eunotia in a single sample from Lamba Water, a small loch on Mainland, Shetland Isles (October 2021).  a. Eunotia faba; b. Eunotia tetraedon; c. Eunotia botuliformis; d. E. incisa; e. Eunotia rhomboidea.  Scale bars: 10 micrometres (= 100th of a millimetre).  Photographs: Lydia King.

That basic theme lends itself to a multitude of variations: cells might be linked so that you see a ribbon of “boxes” and the asymmetric side view may be subtle or pronounced or even, in some cases, with a crenelated appearance (see: “Seeing with my fingers …”).  The lower surface is often flat but can be concave.  We usually see two chloroplasts but, occasionally, there are many (see: “The mystery of the atypical diatom …”).  There’s also a raphe, but it is small and indistinct so often difficult to see in live material. Many species in the genus are relatively large so it is not a surprise that it was established as a distinct genus relatively early, by Ehrenberg in 1837.  West and Fritsch wrote in 1927 that, “there are about ten Brit. sp.” (sic) but they were woefully underestimating the situation.  Hustedt, in 1930, reported 33 species in central Europe in 1930 whilst Lange-Bertalot et al.’s 2011 monograph reports over 2000 taxa although the majority of these are tropical.   

The most remarkable feature of the genus Eunotia, however, is its consistent preference for soft, often acidic water.   It is common to find Eunotia in circumneutral water in small numbers but, once the pH drops below 7.0 it is often the most abundant genus in a sample, and a few species can tolerate extremely high acidity, with many records of the most tolerant species (such as E. exigua) from pH < 3.0.  Because the regions that have soft, acidic water are often remote and poor for agriculture, Eunotia is also often associated with low nutrient concentrations.  

Environmental preferences of Eunotia 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.

The different tolerances of Eunotia species to pH mean that the genus played an important role in elucidating the causes of acid rain during the 1980s, because changes in the types of Eunotia and other soft-water diatoms through the different layers of sediment could be dated and linked to historical events.   In the case of the Galloway lochs I wrote about in “Acid trip …”, the shift in composition towards acid-tolerant species of Eunotia sp. roughly coincided with the onset of the industrial revolution. This strengthened the case for acidification being caused by atmospheric transformation of sulphur dioxide and, ultimately, led to strengthened legislation to control emissions.  I like to say that diatoms helped to change Margaret Thatcher’s mind.  

Eunotia exigua from the Glennamong River, Co. Mayo, Ireland, 12 December 2007.  Scale bar: 10 micrometres.

Eunotia minor from the Glennamong River, Co. Mayo, Ireland, 12 December 2007.  Scale bar: 10 micrometres.

More information: 

Reference

Battarbee, R. W. (1990). The causes of lake acidification, with special reference to the role of acid deposition. Philosophical Transactions of the Royal Society of London. B, Biological Sciences 327: 339-347.

Flower, R. J., & Battarbee, R. W. (1983). Diatom evidence for recent acidification of two Scottish lochs. Nature(London) 305: 130-133.

Hargreaves, J. W., Lloyd, E. J. H., & Whitton, B. A. (1975). Chemistry and vegetation of highly acidic streams. Freshwater Biology 5: 563-576.

Lange-Bertalot, H., Bak, M. & Witkowski, A. (2011).  Eunotia and Some Related Genera.  A.R.G. Gantner Verlag K.G., Ruggell. 

Wrote this while listening to:  Avalon Emerson and the Charm.

Currently reading:  Ali and Nina by Kurban Said.  A love story set in the Caucasus before, during and after the first world war.

Culinary highlight: family lunch to celebrate my sister’s birthday at Coarse [https://www.coarse.restaurant] in Durham

I’m back from my annual fortnight sojourn in western China and spending a day standing in cold streams in West Cumbria pondering the condition of their algae and the state of the world.  And how the state of the world impacts the condition of the algae and what the condition of the algae tells us about the state of the world.  Just another day at the office, in other words …

More specifically, I’m standing in the River Irt in western Cumbria looking at the bright yellow-brown patches of diatoms on the stream bed and trying to compare these with what I saw the last time I was here.  Were there more of these patches on that occasion, or fewer?  And what of the green algae?  My memory is that there was substantially less this time.  When I get back, I can check my notebooks but, if my hunch is correct, what might be the reason for this?  

The River Irt has been the subject of many posts over the years, including the post preceding this one, “cold comforts …” and “cold cases …” (a theme seems to be emerging, because the River Irt is at its most intriguing when it is least tempting to plunge hands in to gather samples).   But I have not, previously, looked at the annual trends, and tried to piece together what might be happening.  

The photo at the top of the post shows the type of diatom growth that confronted me when I was peering at the bed of the River Irt.  This, I know from previous visits, is composed of a matrix created by the diatom Gomphonema exilissimum, subsequently colonised by a range of Achnanthidium and Fragilaria species (see: “High-rise habitats …”).   We’ve been visiting the Irt regularly since 2018, so have accumulated a dataset that now lets us put this one-off visual experience into perspective.  

The graphs below shows annual trends in green algae and diatoms, as measured with a BenthoTorch, based on the aggregated data from all our visits, and the trend lines show quantile GAMs (General Additive Models) for the 50th, 90th and 95th percentiles of the data.  Both algal groups show pronounced trends of high winter biomass and low summer biomass that is typical for rivers downstream of lakes in this region.   Two other points stand out: first, is that whilst both peak in November, the decline in green algae is faster than that of diatoms, dropping away by the end of February, whilst the diatoms persist for another month or more.  The second point of note is that the green algal data is much more “noisy” than that for diatoms, with many more outliers throughout the year above the fitted 95th percentile.  What is going on here?

Annual trends in diatoms and green algae (expressed as chlorophyll concentration) on cobbles in the River Irt, Cumbria, 2018-2026.   The trend lines show quantile GAMs fitted to the 50th (red), 90th (green) and 95th (blue) percentiles of the data.  The photo at the top of the post shows diatoms growing on the bed of the Irt in April 2026.  

My hunch is that the green algae are boosted by the relative warmth of the water emerging from Wastwater in late summer and autumn (I don’t have figures for this lake, but the River Ehen below Ennerdale Water is four degrees warmer than the River Liza which is that lake’s main inflow).  The diatoms, in turn, thrive from the habitat opportunities that the green algae create for them (see: “Friends with benefits …”) but, as this heat subsidy fades away in early winter, the diatom’s natural proclivity for cold weather and the meagre winter light takes over.  At about this time of year, the phytoplankton of Windermere is dominated by the diatoms Aulacoseira and Asterionella formosa, an ecological phenomenon studied extensively by John Lund and his successors at the Freshwater Biological Association.  And I’m fairly sure that something broadly similar also happens in the rivers of the region 

The ”noise” I refer to in the data for green algae is a consequence of the patchiness of green algae compared to the diatoms.  We find a lush diatom carpet on most of the stones, but wefts of green algae only on, perhaps, one in five, and that translates into widely-different biomass measurements, particularly as the lushest growths are often on the boulders whereas we target cobbles for our sampling.  This, in turn, relates back to themes discussed in “The greening of our rivers (1)…”.  It is important for us as ecologists to recognise that “noise” is often an intrinsic feature of the systems we are studying, not an irritant to be expunged from our models.  

Reference

Reynolds, C.S. & Irish, A.E. (2000).  The Phytoplankton of Windermere (English Lake District).  Freshwater Biological Association, Ambleside.

Wrote this while listening to:  The Low Anthem’s albums Oh My God, Charlie Darwin (2008) and Smart Flesh (2010).

Currently reading:  Rana Mitter’s China’s War with Japan, 1937-1945, a fascinating account of the role China played (at an enormous cost in lives) in defeating the Axis powers. 

Cultural highlight:  just before we set off for China we went to see Project Hail Mary, which is a great film, so long as you avert your eyes during the scene when Ryan Gosling uses a centrifuge.  The title of the film in China, incidentally, is the more-literal “Rescue Plan”.

Culinary highlight: Lots of wonderful food during our visit to Chengdu, and it is difficult to single out a highlight.   If I had to name a favourite, maybe it was the spicy, umami hit of a bowl of dan dan noodles, served with copious green tea, in a tea house in Renmin Park in the centre of the city.  The noodles cost just over a pound.

I was asked during my recent Diatom Web Academy talk about how I produced my paintings of the microscopic world so this post is a diary of the journey, from idea to finished image, for a picture that I have produced in the aftermath of that talk.   The germ of the idea for this particular picture came on 11 March, because preparation of this talk had sent me back to some old posts where I had been musing on the interactions between Cyanobacteria and green algae.  I “fixed” the painting with a final, decisive burst of hair spray on Monday 23 March, two weeks later and I’ve put it at the top of the post for reference.

The starting point was the post “Something, somewhere, just for a moment …” which describes how I often see filamentous green algae growing out of Cyanobacterial growths in Lake District streams.  It is an association that has intrigued me for some time, but this post is more about, and I have suggested that this association may be part of the reason why the Irt, and similar rivers in the Lake District, often have prominent filamentous green algal growths (see: “The man who stares at algae …”).  But that’s not the point of this post except to say that the image in the older post showed Mougeotia growing from Microcoleus autumnaliswhereas I more often see Tolypothrix distorta var. penicillatus as the “foundation species” for this association, and I thought it would be interesting to capture this in a painting.  

The first stage was to put down some ideas in my sketch book.  These are based on my observations and photographs but I’m trying to arrange the different elements into a more coherent composition, and bring in the depth of field that is lost in microscopic photography.  You can see that I was also experimenting with the helical chloroplast of Spirogyra (which is often part of these associations) but I eventually decided to focus on Mougeotia.  The big question I was asking in my mind during this period was whether to go for a “portrait” or “landscape” format.  I did not fully decide to go with the “portrait” format until the very last minute, deciding that it would be a better way of presenting the tree-like growth form of the Tolypothrix.

Two pages from my sketchbook, as I worked out the composition.  The photograph at the top shows the finished image.

I laid down some light washes of Payne’s Grey onto 40 x 50 cm watercolour paper to start the composition, with just a suggestion of “hills” (the jumble of distant cobbles).  This is the nerve-wracking time because three separate washes, each drying at room temperature, takes plenty of time for doubt about the composition to creep in.  Later, as the image starts to come together, this drying time becomes more meditative, offering space to think through what comes next.  

With the background in place, I am ready to start on the foreground, sketching the arrangement in light pencil, because I want to capture the tangle of Cyanobacterial and algal filaments and this requires planning as watercolour is a very unforgiving medium.  Working from the foreground to the background necessitates a cautious approach, trying to think one or two steps ahead in order to allow the composition to evolve with a plausible measure of entanglement.   

First washes in place, and the position of the two most prominent filaments marked out.

The Cyanobacteria start as a series of washes of a mixture of Hooker’s Green and Ultramarine (allowing me to differentiate the heterocysts from the vegetative cells), whilst the green algae are washes of Hooker’s Green, Yellow Ochre with a touch Cadmium Yellow.  I also wanted to show how diatoms colonised the Cyanobacterial sheaths, so I used Raw Sienna, straight from the pan, to place the chloroplasts into the composition. I move to coloured pencils to add depth to the filaments and to define the cell walls. 

With the foreground in place, I can now add a layer of filaments behind the foreground and repeat the process of building up flat colour with paint and then adding detail with pencil.  When this is in place, I do the same again a third time, by which time the composition is beginning to look suitably crowded with filaments.  I’ve also added in the distinctive sheaths of the Tolypothrix which, in this river at least, are generally not heavily stained with orange-brown scytonemin.  I can also finish off the diatoms now, adding in their frustules with pencil and, for Achnanthidium, adding short stalks attached to the Cyanobacterial sheaths.  Healthy cells of Mougeotianever have epiphytes.  

Two stages in the creation of my image of entangled Tolypothrix and Mougeotia from the River Irt.

The final stage is to leave it somewhere where I can see it several times during the day, so that I can think about how it can be improved. I might make a few minor changes here or there, or I might (in extreme cases) start again with a new composition.  This, and all my other paintings of algae, are acts of imagination.  The algae I see living on stream beds are too small to make out details either of their structure or their interactions.  I have to put them under a microscope to understand this, but that involves disrupting their integrity and living with the distortions that the microscope introduces (see: “Do we see through a microscope?”).  So then I have to take a further step to reassemble the components into a plausible arrangement with the constraints of two types of reality as my benchmarks (what I see with the naked eye and what I see with the microscope).  It means that the compositions are more like fugues or sonnets than truly free-form pieces of art (something that was always a source of tension with my tutors on my art degree).

I use the phrase “imagined but not imaginary” to describe how the actuality of life on the river bed has to be pieced together from individual components because it is impossible to view them in situ at an appropriate scale. Any picture, as a result, is not a definitive statement of ecological truth, but a waymark of my own journey towards a better understanding.  I’ll be out at the River Irt in three weeks time and looking hard at the algae both in situ and under my microscope.  Maybe I will see it from a different perspective as a result, and that will lead to an idea for a new painting.  As I have said before, the river is my muse …

Some other highlights from the past week:

Wrote this while listening to:  Raye’s This Album May Contain Hope.

Currently reading:  Arabia Through the Looking Glass by Jonathan Raban.  With the Gulf very much in the news, it is intriguing to read this account from 1979 and reflect on how much – and how little – has changed.

Cultural highlight:  Peter Grimes, by Opera North, at the Theatre Royal, Newcastle. 

Culinary highlight: Inspiring tasting menu at Pine, a Michelin-starred restaurant in the Tyne Valley that grows most of its own vegetables on site and creates some rather wonderful dishes.

Sometimes, the sight of a diatom generates associations in mind, and I am momentarily transported to the time and place where I collected the sample.  My optic nerve triggers other nerves and, all of a sudden, memories are welling up, if not of an actual place (I know that from the slide or sample label) but of the topophilia – a strong sense of connection – with the landscape through which the river flows.  Hannaea arcus, the topic of this post, is a diatom that does that for me.   Seeing a cell under my microscope carries me off to the moorlands of the Northern Pennines on a spring day when the wind is flattening the moorland grasses and, in sheltered nooks beside the stream, I am blessed with a glimpse of birds-eye primrose or cowslip and the calls of curlews and oystercatchers.  

Hannaea arcus is, to all intents and purposes, the only species of this genus that we find in the UK and has a distinctive curved outline with a small protrusion at the middle on the concave side.  It has two chloroplasts but lacks the raphe that helps many diatoms to move around.   Mostly, the cells are solitary, living in the biofilms that coat submerged surfaces, though occasionally you see a couple of cells stuck to one another.  It may attach itself to surfaces via the apical pore field that is visible under the electron microscope, but this attachment is, I suspect, quite weak.

It was one of the first diatoms I learnt to identify, but it had a different name in those days. The older literature refers to it as Ceratoneis arcus but that was problematic as the original representatives of that genus were subsequently transferred to Nitzschia and Cylindrotheca, meaning that Ceratoneis arcus was an orphan in a genus that no longer made any sense.   In the sixties, Ruth Patrick and Charles Reimer transferred it to a new genus, named after G Dallas Hanna, an eminent US diatomist (apparently, his first name was, literally, “G”!).  Now, with better microscopes than were available to the nineteenth century pioneers, it was easier to see how Hannaea arcus related to other diatoms, and it was placed in a family alongside Fragilaria and Synedra.

The similarities amongst Fragilaria, Synedra and Hannaea, however, were so strong that Kurt Krammer and Horst Lange-Bertalot, in their revised edition of the Süsswasserflora von Mitteleuropa, decided that the three genera should all be combined into a single genus, Fragilaria.  So Hannaea arcus got a third name, Fragilaria arcus.  There was, in the early 1990s, a vigorous debate amongst taxonomists around the topics of genus limits, with David Williams and Frank Round staunchly defending the “splitter” camp against the continental “lumpers”.  The dust, now, has settled, with Hannaea arcus being the most widely-used name, although “Fragilaria arcus” still pops up from time to time in the literature.   Now that we have molecular data, we can see Hannaea standing a little apart from Fragilaria but genus distinctions are always, to some extent, judgement calls.

All of this is a deviation from my opening paragraph describing the topophilia that Hannaea arcus indues in me.  Generally, Hannaea arcus is a species of unpolluted streams – hence my association with landscapes in regions of low population density.  More interesting, though, is Hannaea arcus’ distinct preference for spring conditions, shown in the second figure.  The highest abundances are recorded in April and May, after which the relative proportions I record fall away.   

Environmental preferences of Hannaea arcus in UK streams and rivers.  Vertical lines indicate average positions of ecological status class boundaries (blue = high, green = good, orange = moderate; red = poor/bad).  Arrows indicate the optimum for each variable.  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/].  The photograph at the top of the post shows Hannaea arcus from Harwood Beck in Upper Teesdale.  Scale bar: 20 micrometres (= 1/50th of a millimetre)

I’ve written about this propensity of some diatoms to thrive in rivers in late winter and early spring before (see … “Golden brown …”) but there is not a lot in the literature to explain this.  Very few Floras – old or new – address seasonality amongst benthic diatoms at all, but it is certainly happens, and the lack of reference in benthic and stream settings is in contrast to the well-known “spring bloom” phenomenon in lakes.  My speculation is that these diatoms are able to exploit the combination of low temperatures and relative short days in a way that most other algae cannot and, therefore, thrive when grazers are least active.  What’s interesting is that Hannaea arcus is not prolific in January or February, suggesting that there may be a physiological “trigger” stimulating a burst of growth as the year crawls towards spring.  There really is not much in the literature to back this up, but I did find an old paper by Dick Castenholz that related the seasonality of littoral diatoms off the Oregon and Norwegian coasts to differences in their sensitivity to daylength and light intensity.  

Distribution of records of Hannaea arcus through the year.  The lines represent Generalised Additive Models fitted at the 0.5th, 0.9th and 0.95th quantiles on all records of the species in my database (~6500 records in total, of which 456 contain H. arcus).

Relevant posts”

Diminishing with age

More information at:

Diatom Flora of Britain and Ireland

Diatoms. org

References

Castenholz, R. W. (1964). The Effect of Daylength and Light Intensity on the Growth of Littoral Marine Diatoms in Culture. Physiologia Plantarum 17: 951.

Castenholz, R. W. (1967). Seasonal ecology of non-planktonig marine diatoms on the western coast of Norway. Sarsia, 29(1), 237-256.

Jahn, R. & Kusber, W.-H. (2005).  Reinstatement of the genus Ceratoneis Ehrenberg and leptotypification of its type specimen: C. closterium Ehrenberg.  Diatom Research 20: 295-304.  

Round, F.E. & Williams, D.M. (1992).  The generic status of some diatom genera with special reference to the araphid group – a reply.  Nova Hedwigia 55: 485-500.

Some other highlights from the past couple of weeks:

Wrote this while listening to:  Tim Buckley and Jeff Buckley

Currently reading:  Fintan O’Toole’s Heroic Failure: Brexit and the Politics of Pain – an Irish perspective on Brexit.

Cultural highlight:  a rather wonderful exhibition of Gwen John’s paintings at the National Museum of Wales in Cardiff, which have a quiet intensity that, on occasion, reminded me of Vermeer.

Culinary highlight: good South Indian food at Arusuvai in Kirkstall, on the outskirts of Leeds.

This post is about the genus Amphora and, more specifically, about the most common representative of that genus in UK rivers, Amphora pediculus. The photograph at the top shows citizen scientists peering at a rich population of this diatom, though they almost certainly do not realise this. They are peering at the pebbly/gravel bed of the River Wensum, which just happens to be an almost perfect habitat for this, the most common representative in UK freshwaters: hard water, an easily-disturbed, mostly filamentous-algae free substrate and, if our citizen scientists were to stand up and look around, a rich agricultural landscape to provide a steady feed of nutrients.   Amphora pediculus exemplifies Britian’s “green and pleasant land”, feasting on the generosity of our farmers.

The genus Amphora exemplifies one of the philosophical problems that beset the study of diatoms because the question “what does it look like?” elicits very different responses depending on how you are observing it.  The cells of Amphora pediculus that live on the bed of the River Wensum are wedge-shaped, resembling a couple of segments of an orange but the two valves that comprise the cell wall usually come apart during the preparation of permanent slides, so we see, instead, slightly truncated hemispheres (“dorsiventral” in diatomspeak).   In the complete cell, both of the raphes are on the same side, which has implications for how these cells move around.  

Amphora species from the River Wensum at Hellesden Mill, July 2025. a. – j.: Amphora copulata; k.: Amphora ovalis; l. – m.:  Amphora indistincta; o. – ee.: Amphora pediculus; Scale bar: :10 micrometres (= 1/100th of a millimetre).   Photographs: Lydia King.  The photograph at the top of the post was taken on the day the sample was collected.

Amphora was quite a large genus, found in both fresh and saline waters but, in 2009, Zlatko Levkov recommended splitting off a group of species into a new genus, Halamphora. As the name suggests, this genus was more common in saline waters but we do still find representatives in freshwaters.  The split is quite interesting as, from the point of view of someone peering down an average-quality microscope, the visible rationale is quite esoteric – the presence or not of girdle bands (“copulae”).   However, molecular studies have not only supported this division but also indicated that the two genera actually belong to two distinct lineages and are not closely-related at all.   Amphora is in the same family as Surirella and Epithemia whilst Halamphora is more closely related to Brachysira and Frustulia.  Meanwhile, those of us who still rely on pattern recognition to name our diatoms will probably continue to present Amphora alongside Cymbella, Encyonema and relatives, as these are the diatoms that a beginner to light microscopy is most likely to confuse it with.  

Amphora pediculus is the most commonly-encountered member of the genus in the UK, but others can also be found, and differentiation of the smaller members of the genus can be difficult with a light microscope.  The sample from the River Wensum, for example, included at least four species, two of which were represented by cells less than 10 micrometres (=1/100th of a millimetre) in length.

The graphs below show how it responds to water chemistry in the UK.  These graphs look similar to those I presented for Rhoicosphenia but there is an important difference: Rhoicosphenia benefits from the presence of filamentous algae; Amphora pediculus, by contrast, prefers these to be absent.  A. pediculus is one of the early colonisers of small stones, the “grass”, if you like, of submerged ecosystems; Rhoicosphenia is more like ivy or mistletoe, growing on and over the filamentous algae that are able to out-compete the low-growing algae for light.  We often find both in a sample but that simply reflects the diverse nature of stones in a stream, some with and some without filamentous algae.

Environmental preferences of Amphora pediculus  in UK streams and rivers.  Vertical lines indicate average positions of ecological status class boundaries (blue = high, green = good, orange = moderate; red = poor/bad). Arrows indicate the optimum for each variable.  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.  

Another species that can squeeze Amphora pediculus for space is Achnanthidium minutissimum, a different form of microscopic “grass”.  This tends to prefer low, rather than elevated, nutrients but, in small headwater streams where rainfall is high, there can be swings between the dominance of these two species, depending on the amounts of nutrients washed off from the land.  Amphora pediculus is a clear “goldilocks” diatom: there are times when nutrients are too low (Achnanthidium steals in and grabs the habitat) and there are times when the community is overgrown by filamentous algae (Rhoicosphenia is able to thrive here) but there are also times when neither of these conditions are fulfilled, and that is where Amphora pediculus thrives best.  Having a propensity for pushing metaphors too far, I should add that catchment managers fulfil the role of the “Three Bears” in this story, as our nutrient-rich waters mean that this particular aquatic Goldilocks is too pervasive, and really needs to be chased away.  

Relevant posts

More information at:

https://diatoms.org/species/45430/amphora_pediculus

https://naturalhistory.museumwales.ac.uk/diatoms/browsespecies.php?-recid=2528

References

Snell, M. A., Barker, P. A., Surridge, B. W. J., Large, A. R. G., Jonczyk, J., Benskin, C. M. H., Reaney, S., Perks, M.T., Owen, G.J., Cleasby, W., Deasy, C., Burke, S. & Haygarth, P. M. (2014). High frequency variability of environmental drivers determining benthic community dynamics in headwater streams. Environmental Science: Processes & Impacts 16:  1629-1636.

Stepanek, J. G., & Kociolek, J. P. (2014). Molecular phylogeny of Amphora sensu lato (Bacillariophyta): an investigation into the monophyly and classification of the amphoroid diatoms. Protist 165: 177-195.

Stepanek, J. G., & Patrick Kociolek, J. (2019). Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution. Journal of phycology 55: 442-456.

Some other highlights from the past week:

Wrote this while listening to:  Shaker hymns (see below)

Currently reading:  Amy Tan’s Saving Fish from Drowning.

Cultural highlight:  The Testament of Ann Lee, about the rise of the Shakers in north-west England and their journey to North America.  Wonderful music.

Culinary highlight: a recipe from the Guardian for hispi cabbage with white beans and parmesan 

I am anxiously watching weather forecasts and hydrographs this weekend because I am due to go out to do some winter fieldwork next week and want to be sure that river levels are low enough to permit this.  As I sort out the logistics and prepare my kit, I’m also preparing myself mentally for a day when I have to plunge my hand repeatedly into cold rivers.  The reward is a glimpse of an underwater world that flourishes whilst the terrestrial vegetation is at its most bleak but there is, for sure, a psychological barrier that needs to be crossed if I am to get out and get intimate with nature at this time of year.  

I am, however, committed to the principle that fieldwork is an essential part of being an ecologist.  That might seem self-evident but in these days of big data, ecologists seem to spend more of their time staring at screens and writing R code to decipher data collected by other people.  This post draws together some posts I have written over the past few years in order to make the case for getting outside, getting wet and getting cold.  

In  “The fieldwork experience …” I wrote that fieldwork lies slightly outside the formal scientific method because it is immersive, and your senses can be overwhelmed.  We go out with a clear sense of what we need to record but, when we arrive, we start to notice things that, though not necessarily within the narrow objectives for our study, are germane to the hypothesis we are testing.  We need to adhere strictly to protocols to make sure that differences we observe are due to variation in the environment rather than to our carelessness. But there also needs to be space in our schedules to savour and assimilate these experiences.  I’ve also written some other posts that expand on this theme.

A day of fieldwork in rivers when the air temperature does not rise above zero puts this into context.  I felt my capacity for observation was not quite what it might be on a warm summer day, because I have to stand in a cold river and submerged my hands in order to collect the specimens I need.  There is a temptation to rush, to get back to the warmth of my car, rather than look around, as soon as I have ticked off all my necessary measurements, photographs and samples.  I console myself that at least I am able to get out in winter, and worry that freshwater ecology in this country is increasingly becoming a fair weather and desk-based occupation.

Young shoots of Lemanea fluviatilis growing amidst a meadow of Spirogyra on a submerged boulder in the River Irt, Cumbria, January 2026.  The image at the top of the post shows the view downstream from the location where this image was taken, highlighting the contrast between terrestrial and submerged vegetation at this time of year. 

The experience of looking closely at a small cluster of lakes and streams in the Lake District has reinforced, for me, the importance of returning to a location not just in different seasons but across years too.  Getting to know a stream or lake involves more than just accumulating data.  It is about developing a sense of how it behaves, and what factors are shaping it.  Looking at how December’s storms had reshaped river channels was not part of our core objective, but it will inform data interpretation later.  We needed the five years of prior data to be able to appreciate what had changed on this visit.  Robert McFarlane’s book Is A River Alive? talks about the river as a “person” and his sometimes mystical language is not always compatible with objective science, but my Lake District streams certainly each have a “character” that I’m slowly uncovering. 

So here are the posts:

“The Fieldwork experience …” reflects on the relationship between fieldwork and the scientific method.

“On Fieldwork …” explores the boundary between “natural history” and the science of ecology, and the tension that arises between the dispassionate mindset necessary for a scientist testing an idea and the open mind necessary to develop those same ideas to the point where they can be tested.

“Fieldwork notes, August 2021” is a stream-of-consciousness about the accumulation of observations during a day of fieldwork in an area that I thought I knew well.

“The river is my muse …” continues this theme, stressing the importance of returning to the same locations over time to develop a sense of the scale of natural variation, and how they change over time.

Finally, “Slow science and streamcraft” pulls these ideas together.   “Slow science” defines the process I have been advocating – the gradual accumulation of data and knowledge in tandem from a few sites that you get to know intimately, and “streamcraft” being an attitude that helps you look beyond a narrow specialism and “read” the messages that a stream is telling you.  It may be no more than innate curiosity but it includes an element of humility.  It’s as much about what we don’t know as what we do.  Maybe we should redefine an ”expert” to be someone who has a good understanding of how their narrow specialism fits into the bigger picture?  Otherwise, people like myself are at risk of becoming “stamp collectors”, amassing knowledge for the sake of amassing knowledge, rather than constantly striving to apply the fruits of that knowledge.  

A second reflection, on re-reading these posts, is the role of fieldwork and reflections in its immediate aftermath, play in shaping ideas about how ecosystems work.  The discipline of “ecology” rests on a foundation of good “natural history” which needs us to be outside and immersed in the natural world.  Having two very different degrees is insightful here, my fine art tutors placed a premium on generating ideas whereas a modern science training is more about testing ideas.  Science education needs to think about how we train people to generate ideas and, in the case of ecology, that is going to involve getting students into the field regularly, and encouraging them to be observant.  

A final twist, which I haven’t previously written about, is how this field-based observational biology applies to someone whose focus is on studying the microscopic world.  That is probably a topic I should address in a future post …

Some other highlights from the past week:

Wrote this while listening to: Frankie Archer who we saw at Pop Recs in Sunderland last weekend.  A rising talent who combines traditional folk song with electronica.  Check out her performance on Later here [https://www.youtube.com/watch?v=d0s18RBg85Q]

Currently reading:  For the Love of Wine by Alice Fierling, a travel book about Georgia and its ancient wine culture.  We’ve just booked flights to Tiblisi for a holiday later in the year, so this is the first step towards immersing myself in the history and culture of the region.

Cultural highlight:  Crown of Blood, a retelling of Macbeth set in 19th century Yorubalandby Oladipo Agboluje at the Crucible Theatre, Sheffield.

Culinary highlight: Gormeh Sabzi at Shandiz, a Persian restaurant in Sunderland, ahead of our trip to Pop Recs.  

My account of Navicula focussed on the challenges of life inside a biofilm – the slimy layer on submerged stones – pointing out that though it may appear thin to us, from the perspective of a microscopic organism, it could be as high – and as busy – as a downtown skyscraper.  Navicula’s superpower in the face of this was the capacity to move up and down through the biofilm but this post describes a diatom with an alternative strategy.   Rather than huffing and puffing up and down the biofilm, Rhoicosphenia takes the elevator.  

Take a handful of blanket weed from a rock in a lowland river, separate out a few filaments and look at these under medium magnification and you will most likely see the branched filaments of Cladophora, often with a number of smaller organisms attached to the filaments.   Many of these will be wedge-shaped cells with a distinct flex in its outline.  These belong to the genus Rhoicosphenia.  It is not just found on Cladophora, but this is the most common filamentous algae in. lowland rivers.  Rhoicosphenia does not seem to be too picky about its hosts, at least amongst the more robust freshwater filamentous genera. 

Rhoicosphenia is a relatively small genus, at least in terms of freshwater species.  Zlatko Levkov and colleagues recorded seven species from Europe, along with eight from brackish and marine environments.  Of the seven freshwater forms, only Rhoicosphenia abbreviata is common in the UK, though the assumption that there is a single species can become self-fulfilling, as we don’t necessarily notice the fine differences that might differentiate other species as a result.

It has a distinctive shape: from above and below it is club-shaped but, viewed from the side, it is wedge-shaped, but with a kink about half-way along.  Look closely at the valves at high magnification and you will see that one on the concave side has an obvious raphe extending along most of the length, with a gap in the centre, whilst the other has just a short (easily-overlooked) raphe at the narrow end.   When seen in the live state, the narrow end is attached to the host alga, allowing the cell to sit erect.   There is a single chloroplast, wrapped around the cell interior.  

This distinctive structure means that Rhoicosphenia has been difficult to place within the evolutionary tree.  The club-shaped cells suggest an affinity with Gomphonema and relatives, the reduced raphe system on one valve suggest an affinity to Achnanthes and Achnanthidium.  Recent molecular analyses place it closer to Achnanthes and Achnanthidiumand other monoraphid diatoms, than to Gomphonema, but it is not particularly close to any of these.  It is a “Facebook friend” of these monoraphid diatoms; but they would not invite it to join their WhatsApp group, if I might gently reinterpret Linnaean systematics for our modern times.

Environmental preferences of Rhoicosphenia abbreviata 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 at the end of the post.  The images at the top of the post show valves of Rhoicosphenia abbreviata from strains isolated for the compilation of the UK’s diatom reference barcode library (photos: Shinya Sato).  

One of the distinctive features of Rhoicosphenia ecology is its preference for growing as an epiphyte on other algae and submerged plants (see illustration in “A pinch of salt …”).  It probably does grow opportunistically on other surfaces, but it is most strongly associated with filamentous algae.  No-one has ever studied the nature of this preference, so what follows is largely speculative. 

The graphs above show the occurrence of Rhoicosphenia abbreviata in response to four key environmental variables.  We see that it likes circumneutral water, is found across the alkalinity gradient, but with a preference for moderately hard to hard water and, though there are plenty of exceptions, it is most abundant when inorganic nutrients are elevated.   This means that it prefers enriched systems when there is intense competition for resources.  However, without a raphe system on both valves, it is at a disadvantage in a thick biofilm because it cannot move up and down in the way that Navicula, for example, can.  A sessile alga needs some help if it is to survive, and living on the back of filamentous algae is one way it can achieve this.  

The next graph shows the times in the year when Rhoicosphenia is most abundant.  It has a clear preference for the summer, which is also the time when filamentous algae are most abundant.   I would not go further than suggesting an association between filamentous algae and Rhoicosphenia.  We cannot say that Rhoicosphenia depends on filamentous algae in order to thrive and there is no evidence of a genetic adaptation for the epiphytic habit (never been investigated, as far as I know) or of the filamentous alga benefiting from the association. But Rhoicosphenia is one of the most common epiphytes that I see on Cladophora and other filamentous algae in lowland rivers (the others are Cocconeis spp. and the Cyanobacterium Chamaesiphon incrustans).  Maybe, if it is just a case of the filamentous algae being in the right place at the right time?    

Distribution of records of Rhoicosphenia abbreviata by month.  The line represents sampling effort (proportion of total samples collected that month) and vertical bars represent records where R. abbreviata formed > 13% (90thpercentile of all records, ranked by relative abundance).

That raises an intriguing question, that will recur in these posts about diatom genera: to what extent can their ecology be reduced to a preferences for water chemistry variables such as pH, hardness and phosphorus, along with a component of random noise, and to what extent are higher level factors, such as preferences for particular substrata or hydrological regimes, playing a role?   My instinct is that Rhoicosphenia is a good example of the latter scenario: if its niche was defined purely in chemical terms, it would have to battle with 20 or 30 other types of diatoms.   Stir in one or two of these higher-level factors (substratum, in particular, in this case) and there are situations where Rhoicosphenia has a competitive edge.  It just so happens that human activities have helped ensure that the situations where Rhoicosphenia thrives are now extremely common in the UK.    

More information at:

Diatom Flora of Britain and Ireland

Diatoms of North America

Key references:

Levkov, Z., Caput Mihalić, K., & Ector, L. (2010). A taxonomical study of Rhoicosphenia Grunow (Bacillariophyceae) with a key for identification of selected taxa. Fottea, 10(2), 145-200.

Thomas, E. W., Stepanek, J. G., & Kociolek, J. P. (2016). Historical and current perspectives on the systematics of the ‘enigmatic’diatom genus Rhoicosphenia (Bacillariophyta), with single and multi-molecular marker and morphological analyses and discussion on the monophyly of ‘monoraphid’diatoms. PLoS One, 11(4), e0152797.

Notes on species-environment plots 

These are based on interrogation of a database of 6500 river samples collected as part of DARES project.  Vertical lines show UK environmental standards for conditions necessary to support good ecological status: blue = high status; green = good status, orange = moderate status and red = poor status.  Note that there are, at present, no environmental standards for alkalinity, conductivity or nitrate-N.  With the exception of P, standards were derived from analysis of invertebrate responses rather than responses of diatoms.  Standards differ between water body types and thresholds for lowland high alkalinity rivers have been plotted here.  These indicate the maximum thresholds for particular ecological status classes for each variable and tighter standards will apply in many waters. 

Note, too, that P standards are based on the Environment Agency’s standard measure, which is unfiltered molybdate reactive P.  This approximates to “soluble reactive P” or “orthophosphate-P” in most circumstances but the reagents will react with P attached to particles that would have been removed by membrane filtration. The current UK P standards that are used here are site specific, using altitude and alkalinity as predictors.  This means that a range of thresholds applies, depending upon the geological preferences of the species in question.  The plots here show boundaries based on the average alkalinity (50 mg L-1 CaCO3) and altitude (75 m) in the whole dataset.   

There are no UK standards for nitrate-N; thresholds in this report are based on values derived using the same principles as those used to derive the P standards and give an indication of the tolerance of the species to elevated nitrogen concentrations.  However, they have no regulatory significance. 

Some other highlights from the past week:

Wrote this while listening to: Courtney Barnett’s A Sea of Split Peas.

Currently reading:  Lower than the Angels: a History of Sex and Christianity by Diarmaid MacCulloch. I should have worked this out for myself before I handed over my money but, for a book with “sex” in the title, it has a lot to say about chastity.  

Cultural highlight:  Turner and Constable: Rivals & Originals at Tate Britain, in London.  Quite an intense experience but revealing about their similarities and differences.

Culinary highlight: lunch at Lilibets [https://www.lilibetsrestaurant.com], a seafood restaurant in London’s Mayfair, subject of an ecstatic review by Grace Dent in the Guardian. It sets a high bar for all other culinary experiences during 2026.

December was an exasperating month for a stream ecologist.  I needed to make one of my regular visits to my Lake District sites but river levels were unremittingly high for the first three weeks and every date I hoped to go had to be pushed back, and hotel bookings adjusted, as another weather front moved in and heavy rain pushed river levels to some of their highest levels since Storm Desmond in December 2015.  Finally, the rains abated and river levels dropped but, by this stage, the Christmas holidays were starting.  Christmas Day and Boxing Day were, ironically, almost perfect for fieldwork but I was otherwise engaged.  

By the turn of the year, another weather system had established, with cold winds blowing in from the north sending temperatures plummeting.  There was little rain or snow, at least in the region where I lived, but it was brutally cold.  Fieldwork was now possible, but it required a mental effort to pull myself from the warm cocoon of my home to the chilly riverbank.  The incentive was an intense curiosity about what such a prolonged period of high flows had done to the rivers (see: “And the waters prevailed on the earth …”).  The same paradox looms: catastrophic events help to shape ecosystems, but their very nature makes studying them difficult.   By definition, they don’t occur to any predictable schedule, and certainly not one that fits the funding cycle for conventional research.  Then, because of their extreme nature, they complicate the very fieldwork that was intended to understand them.  

But that’s not what this post is really about.  It is about the view that sits at the top of the post – a splendid panorama taken from the south west end of Wastwater looking towards Great Gable and Scafell Pike – which makes fieldwork on a freezing cold day worthwhile, and on two other views, both taken in the warmth of my study after I had returned, showing the secret world of the River Irt which flows out of Wastwater.  I had arrived at my regular sites on the River Irt curious to see how the green algae that typically flourish at these locations had responded to the battering that they had received from the high flows in December.   What we saw was a river bed composed mostly of clean cobbles, with visible algal growths limited to the well-bedded boulders where they seemed to be thriving, despite the cold weather.

The bed of the River Irt about 500 metres below the outfall from Wastwater.   The picture at the top shows the view towards Great Gable from the south-west end of Wastwater in early January 2026.

The green algae that I saw were mostly Spirogyra and Mougeotia but with a few filaments of other genera including Oedogonium.  Unlike Spirogyra and Mougeotia, Oedogonium often carries a payload of epiphytes, typically diatoms but, on this occasion, there was a colony of very narrow cylindrical cells, each topped with a series of small round “exocytes”.  This was Chamaesiphon confervicolus (see also: “Looking after their own …”) which sparked my interest, because of recent posts about a different Chamaesiphon species (see: “Eye to the microscope …”).  Most species in Chamaesiphon belong to one of two subgenera, Chamaesiphon (which mostly grow on plants) and Godlewskia (which are mostly found on rocks).  Molecular studies have shown that these two subgenera are not particularly closely-related and could each be considered as separate genera.  The distinct habitat preferences of each suggests some clear differences in physiology such that one wonders why they are still lumped together in the same genus.

Chamaesiphon confervicolus growing around a filament of Oedogonium from the River Irt, just below the outfall from Wastwater.   Scale bar: 20 micrometres (= 1/50th of a millimetre). 

It’s a relevant question because, a couple of kilometres downstream, I saw the same broad pattern of green algae restricted to boulders but, here, they were intermingled with clusters of young filaments of the red alga Lemanea fluviatilis and these had a different cyanobacterial epiphyte, Heteroleibleinia rigidula (see: “River Ehen … again”).  It looks similar on first lok, but lacks the exocytes and, if you look closely, each filament is composed of many small cells whereas filaments of Chamaesiphon confervicolus were a single long cell topped by exocytes.  The genus Heteroleibleinia, which are predominately epiphytic, was split from Lyngbya(which has a much broader range of habitat preferences) in 1985 by Lucien Hofmann, so offers an interesting contrast to Chamaesiphon.  In one case, differences within an established genus justify a split; in the other, they do not.  As these are fiddly little devils to manipulate and isolate, and are not “problematic” in the way that many of the planktonic Cyanobacteria are, I guess they fall through the cracks and have never had the thorough molecular studies that they deserve. 

But let’s end on a positive note.  Winter fieldwork, so long as you are appropriately dressed, is a rewarding occupation because, even when the world outside the stream or lake is frozen and silent, there is a diverse and intriguing world humming away on the rocks and in the crevices of stream beds.   It takes some mental resolve to pull yourself away from the warmth of your study and the temptation to spend the cold months reflecting on all the wonderful nature you saw when the weather was more clement.  But ecosystems run to a 365 day schedule and seeing them in the depths of winter is a necessary step on the road to a better understanding of how we should be looking after them.

Heteroleibleina rigidula growing on a young filament of Lemanea fluviatilis in the River Irt at Cinderdale Bridge.   Scale bar: 20 micrometres (= 1/50th of a millimetre). 

References

Kurmayer, R., Christiansen, G., Holzinger, A., & Rott, E. (2018). Single colony genetic analysis of epilithic stream algae of the genus Chamaesiphon spp. Hydrobiologia, 811(1), 61-75.

Strunecký, O., Ivanova, A. P., & Mareš, J. (2023). An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis. Journal of Phycology, 59(1), 12-51.

Some other highlights from the past week:

Wrote this while listening to: Dark Star.  Because David Bowie died 10 years ago this week.

Currently reading:  just about to start Alisdair Gray’s Poor Things, the novel on which the 2023 film was based.

Cultural highlight:  The Coen brothers’ dark comedy Fargo whose snowclad landscapes seemed appropriate for this week.

Culinary highlight: fieldwork and a trip to London has meant a week of pub grub, leftovers and fast food, so there hasn’t really been any culinary experiences of note, unfortunately.

The modus operandi of this blog from the start has been to write in a “natural history” style about aspects of the natural world that are otherwise only discussed using the opaque language of hard science.  My rationale is that the state of our water is now highly politicised, but most of the organisms that inhabit our rivers and lakes – and whose presence and abundance determine their condition –  cannot be seen with the naked eye.  We feel an emotional attachment to our rivers and lakes, but have little comprehension of the biodiversity that they contain.  There is, as a result, a disconnect, which recalls Baba Dioum’s quotation, “In the end we will only conserve what we love, we will love only what we understand, and we will understand only what we are taught”.  My posts during 2026 therefore will try to correct this, with overviews of some of the most common types of microscopic diatoms, one of the most abundant groups of microscopic organisms (see: “Diatoms 101 …” for background information).

In the middle of the 17th century, a Dutch draper called Anton van Leeuwenhoek walked a few kilometres from his home in Delft to a pond, took a sample of water from this pond and looked at it under one of the primitive microscopes that he had constructed.  The Dutch at this time were at the forefront of exploration, and he may well have encountered sailors would have been arriving at Delft with tales of the exotic lands that they had visited. Yet what van Leuwenhoek saw under his microscope was stranger by some orders of magnitude than any of these tales.  His gift to humankind was awareness of a hitherto hidden aspect of nature: exotica right on our own doorsteps.

You can reconstruct van Leuwenhoek’s journey by visiting a stream or pond close to your own home.  Pick up a submerged stone and run your finger across the surface.  The likelihood is that it is slimy to the touch.  Now take a toothbrush (not available in van Leuwenhoek’s day!) and brush some of this slimy layer into a bottle or jar.  Add some stream water and take it home.  You have, in your hands, a veritable zoo of exotic organisms, the only limitation being that most are too small to be seen with the naked eye.  The next step, then, is to put a drop of this suspension of slime and stream water under a microscope and have a look at it when magnified at least 100 times. 

Navicula antonii from the River Teme at Powick Bridge, July 2025.  Scale bar: 10 µm (photos: Lydia King).   The photograph at the top of the post shows the skyline of Chengdu in China, a city (and country) where modern life is lived in three-dimensions,  

My guess is that you will see at least a few boat-shaped cells containing yellow-brown structures gliding around.  These are diatoms from the genus Navicula.  To see them properly you will need to magnify them to 1000x but lower magnifications will let you see enough to be intrigued.  My rationale for telling you the name of an organism in a sample that I have not examined is simply that Navicula is one of the most common genera of diatoms in streams and ponds and that their boat-shaped outline is one of their characteristic features, along with their capacity to move around.  

The genus Navicula was formally described in 1822, as befits a genus with some relatively large* members that would have been conspicuous with the relatively primitive microscopes available at the time.  It was, for a long time, used as a catch-all for all diatoms that were approximately boat-shaped but 19th century microscopists were quick to see differences amongst these and to separate these as species in their own right.   Navicula quickly grew intio a large, sprawling genus found across both freshwater and marine environments.

Navicula capitatoradiata from the River Teme at Powick Bridge, July 2025.  Scale bar: 10 µm (photos: Lydia King).

The rise of the Navicula supergenus was aided by the practice of identifying diatoms using just the characteristics of empty silica cases (“frustules”).  This meant that some important features such as the number and shape of chloroplasts was lost as samples were oxidised to remove organic matter before they were examined.  Identification was also limited by the capacity of optical microscopy, which meant that some of the very fine features of the diatom frustule were not revealed until scientists turned to electron microscopy in the 1960s.   By 1986, the genus sprawled across 152 pages and 57 plates of the Süsswasserflora von Mitteleuropa but the publication of this book also coincided with the implications of studies with electron microscopes bearing fruit.  In the four decades that followed, many of the species recognised as “Navicula” in this book were hived off into separate genera (sometimes resurrected genera created in the 19th century but subsequently subsumed into Navicula). The slimmed down descriptions of “true” Navicula occupies just 38 pages and 14 plates of the Süsswasserflora.

Navicula cryptotenella from the River Teme at Powick Bridge, July 2025.  Scale bar: 10 µm (photos: Lydia King).

Even after this balkanization, Navicula remains a large and widespread genus, so there is a strong possibility of finding at least a few specimens on a slide (especially if the sample comes from a lowland area).  Under the right conditions, they can be the most abundant diatom in a sample and some species form patches that are visible with the naked eye (see “The ecology of cold days …”).   These patches are most common in late winter and early spring, but other species thrive in summer and autumn, and there can be a succession of species even at a single site.

A summary of the ecology of Navicula might be that it is a genus of lowland, well-buffered moderately-enriched streams and rivers, and littoral zones of ponds and lakes.  However, Navicula is such a large genus that, whilst generalisations are possible, there are always exceptions.  A few species have a distinct preference for low nutrients (e.g. Navicula angusta, Navicula notha) and for very soft water (e.g. Navicula leptostriata) and there are several species that are associated with brackish conditions (e.g. Navicula bottnica: see: “An excuse for a crab sandwich, really …”).  Moreover, “true” Navicula are not abundant in water where there is very heavy organic pollution.  However, between these extremes, this still leaves a wide range of freshwater habitats where Navicula can thrive, often with several species occurring simultaneously. 

Navicua radiosa from a shallow calcareous pond near York. Scale bar: 10 µm 

Though the traditional approach to diatom ecology has been to define species and genera in terms of their preferences for a chemical environment, the genus as a whole is, I suspect, defined by the ability to adjust its position within the slime layer that coats stones.  A film that is a millimetre thick is equivalent, from the perspective of a typical Navicula, to a 25-story building crowded with other microorganisms all competing for a limited oxygen supply whilst pumping out their own waste products.  Being able to move upwards allows Navicula to access the sunlight it needs for photosynthesis as well as to avoid the fetid conditions lower down.

Classic ecological theory (the “competitive exclusion principle”) would suggest that two closely-related species should not thrive in the same habitat.  The reason why we often find several diatoms from the same genus in a sample is most likely not that they are, strictly, “sharing” the habitat, but that they have preferences for microhabitats but that our routine sampling methods are too crude to enable us to separate these.  This separation may be in time as well as in space, as the turbulent world of a streambed will mean that adjacent stones are turned over and algae attached to them are scoured or grazed off in different ways, such that each has a slightly different “history”, allowing different diatoms to thrive on each.  

There is, in short, a lot more that we don’t know about Navicula than that we currently do. It offers a fertile field for informed research into functional ecology rather than just matching forms to simplistic measures of water chemistry.

* “large”, in this context, means at least a 20th of a millimetre long.

More information at:

Diatom Flora of Britan and Ireland

Diatoms of North America.

Key reference:

Lange-Bertalot, H. (2001).  Diatoms of Europe 2: Navicula sensu stricto.  10 Genera Separated from Navicula sensu lato.  Frustulia.  A.R.G. Gantner Verlag K.G., Ruggell.

Some other highlights from the past week:

Wrote this while listening to: Rub-a-Dub Soul, Beatles classics reinterpreted as Dub Reggae.

Currently reading:  Trust, by Hernan Diaz, multiple accounts of the same events by a series of unreliable narrators.

Cultural highlight:  Goodbye, June, an emotionally-intense film directed by Kate Winslet.  This film comes with a health warning as it may be a harrowing watch for anyone currently caring for an elderly relative.   Available on Netflix.

Culinary highlight: Roast venison on Christmas Day.

The eye always knows more than it sees.  Kenneth Clark

I have been watching the weather forecast and the river levels closely for the past three weeks, trying to find a window of opportunity when I can get back to the Lake District for some fieldwork.  Each pulse of heavy rain over this period has sent river levels to a point where entering the river would be foolhardy then, just as levels drop towards a workable point, the next weather front arrives, and the rivers are in spate again.  The longer this cycle of wet weather and high flows persists, the more curious I become about the effects this is having on the algal communities in rivers and streams in this area, which just adds to the frustration.

Meanwhile, I am busy rearranging schedules to make the most of the time when I should have been out on fieldwork, and also taking the opportunity to reflect on some of the patterns that I have recorded from these sites in the past. I have just been reading about how Anton van Leeuwenhoek pioneered new ways of “seeing” in the 17th century through his use of microscopes to explore a hitherto completely unknown and invisible world in his local ponds.  Yet another way of “seeing” emerged just over a century later when William Playfair started using graphs as ways of presenting information.  The microscope, by itself, is a fine way of exploring the here and now but graphs, in their many and varied forms, let us take those immediate sensations and compare them with observations at other locations, or at the same place over preceding months and years.

Whether Van Leeuwenhoek would have embraced graphs is a moot point.  The impression I get from his biographies is that he was extremely curious but had a relatively short attention span and was forever flitting between subjects that caught his imagination (see: “The invention of microscopy …”).  He was curious in the same way as the explorers of his age who were travelling to the far-flung corners of the world, rather than in the theory-driven sense of science emerging at the same time through he work of Descartes and Bacon.  In a way, graphs brings these two approaches together because you can not only marvel at the world the microscope reveals, you can also wonder at the changes you see in these observations in space and time and speculate about causes and consequences.

We live in an age where Cartesian hypothesis-driven science prevails but sometimes there is a place for doodling in R Studio and seeing where your curiosity takes you.  So, confined to base by the vagaries of the weather, I made a mental journey back to Croasdale Beck (see “Sick note …” and links therein).  Many of the stones on the bed of this turbulent stream have dark brown or black patches of a Cyanobacterium Chamaesiphon fuscus (see: “Spotting spots …”) and we have often noticed, whilst out in the field, that our BenthoTorch (portable fluorimeter) records more diatoms on stones with obvious Cyanobacterial crusts than it does on those that are bare.

This observation is largely substantiated by the patterns we have recorded over the past decade.  First, the quantity of Chamaesiphon in Croasdale Beck shows a distinct seasonal trend with more biomass recorded in the summer.  This is interesting because our estimates of the cover of Cyanobacterial crusts do not tend to fluctuate, so  they must be  getting thicker and thinner as seasons change.  Second, the quantity of diatoms seems to show a dependency on the amount of Cyanobacteria measured on the same stone.   

Left hand graph: annual trends in the abundance of Cyanobacteria (measured as chlorophyll concentration) in Croasdale Beck between 2015 and 2025; right hand graph: relationship between abundance of Cyanbacteria and diatoms in Croasdale Beck.  Diagonal line indicates 1:1 slope (i.e. equivalent concentrations of both groups). The photograph at the top of the post shows Croasdale Beck in April 2025.

What we may be seeing is diatoms taking advantage of the way that the Chamaesiphon alters the substrate.  One possibility is that, by creating texture across an otherwise flat cobble, Chamaesiphon creates opportunities for the diatoms to escape the constant mechanical stress exerted by the current.  A second possibility is that the habitat they create is less conducive to the marauding invertebrate grazers that we know are abundant in this stream (see: “Curried diatoms …” and “Mayfly mayhem …”).  Maybe Chamaesiphon is producing toxins that serve as deterrents (there are a few hints in the literature suggesting  that Chamaesiphondoes produce such toxins, but no unambiguous evidence.  However, this capacity is widespread within the Cyanobacteria so it must be a possibility).

This interaction between diatoms and Chamaesiphon may explain some of the patterns that I described in “Entrances and Exits …” where diatoms with a high-profile habitat were more abundant in the summer, which is counterintuitive in a stream where we often see grazing invertebrates.  It is possible  that the Chamaesiphoncreates patchiness in the habitat at a finer scale than most biologists typically sample stream algae.  The next two diagrams, then, show what I think may be happening; first, inside a Chamaesiphon patch where Fragilara gracilis and Meridion constriction are nestled amongst the cells and, then, a wider view showing low-profile diatoms (Achnanthidium spp. and Cocconeis lineata) growing alongside the Chamaesiphon crust.

A schematic diagram showing how Chamaesiphon fuscus  may create microenvironments for diatoms (Fragilaria gracilis and Meridion constrictum) to thrive in turbulent stream habitats.

There is quite a lot of conjecture in this because it is difficult to recreate the higher level structure of the algal community on a stream bed from what we see under a microscope (see: “Imagined but not imaginary”).  The Chamaesiphon species that live as crusts are particularly difficult to observe to the point where the three “standard works” that I consulted (Desikachery ‘s Cyanophyta from 1959; Brian Whitton’s chapter in the Freshwater Algal Flora of the British Isles, 2011, and Komárek & Anagnostidis’s revision of the Süsswasserflora von Mitteleuropa from 1999) all rely on the same drawings in Lothar Geitler’s first edition of the Susswasserflora dating from 1925. 

Playfair’s inventions ushered in a new era for science, one that meant that we were no longer constrained by the forms of the organisms we are studying.  At the same time, though, he introduced abstraction to scientific thought process, with reality described by patterns on graphs rather than by tangible phenomena.  This unlocked a whole range of possibilities, many of which I use in my work.  It does mean, however, that we sometimes forget to “see” in the way that van Leeuwenhoek understood, at all.

An alternative visualisation of the relationship between Chamaesiphon fuscus and diatoms in a turbulent stream such as Croasdale Beck.  The Chamaesiphon on the right hand side creates physical shelter and, possibly, an unfavourable habitat for grazing invertebrates.  On the left-hand side, an assemblage of diatoms typical of grazed habitats (Achnanthidium spp and Cocconeis lineata) develops.

Some other highlights from the past week (or so):

Wrote this while listening to:. Rosalia’s El Mal Querer and Lux.  Flamenco (hint of Fado, too, perhaps?) meets electronica meets rap meets …

Currently reading:  NoViolet Bulawayo’s Glory.  An Animal Farm-type allegory of recent Zimbabwean history.

Cultural highlight:  the film Manchester By The Sea on Netflix.

Culinary highlight: trial runs for Christmas week cooking.  

The previous posts explained how algae changed over time in rivers, and how natural factors influenced this.  In this post, we’ll try to relate these changes to seasonal patterns in rivers to explain how filamentous algal cover can change over the course of the year.

The photograph at the top of the post shows the bed of the River Ehen in Cumbria in August and October 2025.  Typically, during the summer biomass is low and filamentous algae are rarely conspicuous from the bank. This is probably due to invertebrates enthusiastically grazing the algae during this period.  The very prolific algal cover we saw in August was unusual and was, we suspect, the result of the long period from Spring to late Summer when there was little rain and plenty of sunshine, creating perfect conditions for algae to grow, despite the low concentrations of nutrients in this river.  This is shown in the diagram below.

Why, you may ask, did the invertebrates not feast on all this abundance?  Two reasons: first, filamentous algae have simpler growth-strategies than invertebrates and, as a result, can capitalise on favourable conditions more quickly.  They by-pass all the complexities that come with sexual reproduction and simply keep dividing for as long as resources are available.  The invertebrates that graze on them, by contrast, have longer and, often, more complex life-cycles involving several instars, where they shed their exoskeleton, and the adult, sexually-mature stages, take place out of the water.  In the hard scrabble world of stream beds, mitosis wins out over meiosis every time.  

Schematic view of algal dynamics over the course of a long, rain-free period, as experienced in UK rivers in spring/summer 2024. The photos at the top of the post show the state of the bed of the River Ehen in Cumbria in August 2025 (sunlight and warmth predominate) and in October 2025 (following several spates).

The second reason is that this advantage then converts into the pronounced oxygen fluctuations mentioned in the previous post, making it harder for the invertebrates to cope (the warm water, which has lower capacity to store dissolved oxygen, will also contribute).  This is, we stress, conjecture, as we were not able to look at the invertebrates in the Ehen during this period, but there are other studies that support this.  

This long, warm dry period was then followed by a wetter than average September, leading to high flows and the scouring of the visible algae so that, when we went back in October, the stones on the stream bed looked clean (see photographs at the top of the post).  Actually, there was a distinct brown film on most of these, composed mostly of diatoms.  The “succession” was truncated by the high flows, but this just opened space for other, smaller algae to move in and take advantage of the still-warm water and early Autumn sunlight.   

Schematic view of algal dynamics showing how visible algal growths change when a long, period of low flow is followed by a period of high rainfall and associated spates.   

The British summer is nothing if not unpredictable, so our explanation for 2025 could serve as a template for other years, simply by sliding the period of spates backwards and forwards.   Let us suppose that, rather than having a wet September, there was a lot of rain in July.  In that case, the algae would have been scoured away before we arrived for our August visit.  Or imagine a year in which April and May were cool and rainy, delaying the start of the period when algae could proliferate. 

That framework paints a broad-brush picture of how filamentous algae change across the course of a year in a river.  As well as varying the timing of spates, we could think about what happens if we vary the location.  We might expect the upper stretches of mountainous streams to be more turbulent, as well being located in generally cooler and rainier places.   Further down the catchment, by contrast, the river will be wider and deeper, with beds composed largely of silt.  In such cases, filamentous algae may only be able to colonise the edges.   Geology, too, may contribute to this complexity.  Chalk and limestone streams, for example, are associated with porous rocks that absorb rainwater (“aquifers”) and so tend to be less prone to spates.  Hard rocks such as granite create mountainous terrains where streams have steeper gradients and, as a result, more turbulent flow (“flashier”).

This brings us neatly back to the point where we started: we wanted to make the point that, whilst nutrients contribute to the mass growth of filamentous algae in our rivers, there are a number of other factors that interact with nutrients and which, on occasions, can override the effect of nutrients.  Part of our motive with the citizen science work we did this summer was to encourage good observational science in order to both be aware of the changing nature of algal growths in rivers, and also to engage in some simple detective work in order to consider all the possible reasons, rather than just blaming the usual suspects.   

You can also read about an example of how RAPPER can feed into catchment-level decision-making here

Some other highlights from the past week (or so):

Wrote this while listening to: Nick Cave and the Bad Seed’s Murder Ballards. 

Currently reading:  Laura Synder’s Eye of the Beholder, about how Johannes Vermeer and Anton van Leeuwenhoek reinvented “seeing” in 17th century Delft.

Cultural highlight:  Radiohead at the O2 Arena in London.

Culinary highlight:  “modern British” meal at Dobson and Parnell in Queen Street, Newcastle (a few doors down from Khai Khai, our favourite Indian restaurant)