A pinch of salt …

Five weeks have elapsed since my last post – the longest gap since I have started this blog.  I think of it as a brief sabbatical and am returning revitalised and reenergised, I hope, just as the country starts to emerge from what seems like a long, damp and dreary winter.   I got in the car, turned on a podcast and set off in search of a different type of river to any that I have previously described in Microscopes and Monsters.

My destination is a village called Darton, just north of Barnsley, in South Yorkshire, once the heart of the South Yorkshire coalfield, though evidence of this former industrial heritage is hard to find.  In the past, many of the men in this village worked at Wooley Colliery, as did, at one point, Barnsley-born Arthur Scargill, leader of the National Mineworkers Union during the 1984-85 Miner’s Strike.   But the colliery closed in 1987 and the surface structures have since been demolished.   

Underground, however, there are still hundreds of kilometres of abandoned workings.  When the mine was active, water that found its way into these workings had to be pumped to the surface to keep the mines from flooding.  As it flowed over the exposed coal seams, it became contaminated and the pumped minewater created major pollution problems in local rivers.   Pumping had to continue after the mines closed otherwise the water would build up and eventually burst out of one of the abandoned shafts, with devastating consequences for the rivers downstream, as happened at Wheal Jane Mine in Cornwall in 1992.   So the River Dearne, the stream that flows through Darton, continued to receive pumped minewater long after Whalley Mine itself had closed down. 

I last encountered the Dearne about ten years ago, when I was looking for an example of a saline river for another project.  The salinity occurs when minewater comes into contact with minerals deep underground, which then, due to the absence of oxygen and (often) low pH, dissolve resulting in brines that can be more saline than seawater.   After treatment and dilution, the Dearne’s water was not as salty as seawater, but there was at this time still a detectable “brackish” effect.  I thought it might be interesting to return to this location as a contrast to my recent excursions to Deptford Creek but, as the graph below shows, recent improvements in treatment mean that the salinity (as measured by conductivity) is now below the level where any effects are likely to be seen.   The conductivity on the day that I visited was, however, 1856 mS cm^-1, which is higher than these recent measurements, and in the range where some ecological impact might be expected. I should point out that the Environment Agency does not include salinity as part of its formal status assessment of rivers, so high conductivity will not, by itself, influence their classification results.

Conductivity in the River Dearne at Darton from 2013 to 2020.   The dashed lines are approximate levels where chronic (lower) and acute (upper) effects of salinity are likely to be experienced.  They are based on analyses in Kelly et al. (2024).   The photograph at the top of the post shows the River Dearne at Darton, photographed in May 2024.

That’s not the end of the story because this just means that the Dearne is yet another polluted lowland polluted river, receiving inputs from small sewage works as well as the pumped minewater and agricultural runoff.  The Environment Agency classifies the biology here as “poor” and I am not going to disagree based on what I could see.  The river bed was smothered with Cladophora glomerata and most of the diatoms that I saw through my microscope belonged to species that could tolerate elevated nutrient concentrations.  Several of them also thrived at Deptford Creek, interestingly – Navicula lanceolata and Rhoicosphenia abbreviata, for example (see “Floundering around in Deptford Creek”).  They are freshwater species that can tolerate some salinity, rather than brackish species that can tolerate freshwater.  I’m guessing that the conductivity here fluctuates a lot, depending on the relative balance of minewater and surface water and, on my visit, treated minewater formed a greater part of the total flow, leading to the high conductivity I measured.   

Cladophora glomerata smothering a boulder in the River Dearne at Darton, May 2024.

In my first paragraph, I said that I had set off in search of a different type of river to any that I have previously described in Microscopes and Monsters.   I found, instead, a river rather similar to many in my own area (also a former coal mining area).  That was partly because the reason that the Dearne was special in the past was a pollution source whose treatment had been improved in recent years.  I cannot complain: an interest in the impact of pollution usually comes from a desire to remove its effects. The conundrum is that this in turn makes it harder to understand the effects the more esoteric forms of pollution have on our landscapes.  I failed in my objective but only, I guess, because a wider goal had been achieved.

Diatoms from the River Dearne, May 2024.   a. Diatoma vulgaris; b. Navicula lanceolata; c. Melosira varians; d. Rhoicosphenia abbreviata; e. Gyrosigma cf. acuminatum.  Scale bar: 20 micrometres (= 1/50^th of a millimetre).  

In my first paragraph, I said that I had set off in search of a different type of river to any that I have previously described in Microscopes and Monsters.   I found, instead, a river rather similar to many in my own area (also a former coal mining area).  That was partly because the reason that the Dearne was special was a pollution source whose treatment had been improved in recent years.  I cannot complain: an interest in the impact of pollution usually comes from a desire to remove its effects. The conundrum is that this in turn makes it harder to understand the effects the more esoteric forms of pollution have on our landscapes.  I failed in my objective but only, I guess, because a wider goal had been achieved.

References

Kelly, M.G., Teixeira, H., Lyche Solheim, A., Free, G., Phillips, G., Salas Herrero, M.F., Kolada, A., Varbiro, G. & Poikane, S. (2024).  Physico-chemical criteria to support Good Ecological Status in Europe.  Publications Office of the European Union, Luxembourg. [https://publications.jrc.ec.europa.eu/repository/handle/JRC136407#:~:text=Physico%2Dchemical%20criteria%20to%20support%20Good%20Ecological%20Status%20in%20Europe,-2024Technical%20reports&text=This%20report%20summarises%20approaches%20to,%2C%20temperature%2C%20salinity%20and%20acidification.]

Laine, D. M. (1999). The treatment of pumped minewater at Woolley Colliery, West Yorkshire. Water and Environment Journal 13: 127-130.

Younger, P.L. (2000). The adoption and adaptation of passive treatment technologies for mine waters in the United Kingdom.  Mine Water and the Environment 19: 84-97.

Some other highlights from this week:

Wrote this whilst listening to:  Bop Til You Drop by Ry Cooder

Currently reading:  Lamentation by C.J. Sansom who, sadly, died last week.

Cultural highlight:  A performance by the Daniel Martinez Flamenco Company at Northern Stage in Newcastle.

Culinary highlight:  some great memories of recent meals in Chengdu 

Paradigm shift …

When I’m teaching people to identify diatoms, I start by telling them that there are two groups: the centric diatoms, characterised by at least one plane of radial symmetry, and the pennate diatoms, which have only longitudinal symmetry.  This is a good place for a beginner to start but reality is, inevitably, more complicated.  The two diatoms I describe in the previous post are, for example, both centric diatoms but it is difficult to discern this from the photograph, because their side views do not suggest any radial symmetry.  But, as I’ve said many times before, taxonomy and identification require very different approaches.

The basic centric/pennate dichotomy, however, is not just about outline, however convenient this is as a teaching aid for beginners.  Centric diatoms have a different mode of reproduction (oogamous) compared to pennates (isogamous) and also typically have many discoid plastids rather than a few plate-like ones.   I’ve illustrated one of the diatoms we saw at Deptford – Hydrosera triquetra – in the illustration at the top of the post, in order to delve deeper into this topic of shape as an identification aid.

The first thing we notice is that the valve face is not circular.  The literature describes it as “triangular” but, in reality, the shape is closer in shape to a star-of-David.  You could, however, take a pair of compasses and draw a circle that connected all of the valve angles, so you can see how this may be related to the more obviously circular diatoms.  The valve face is covered with a seemingly random array of coarse pores apart from the ends of three of the valve angles (termed “pseudocelli”) which appear to be plain, but which are, in reality, a mesh of very fine pores through which mucilage is secreted. This allows the cells to join together to form chains, or to attach to surfaces.  

Hydrosera triquetra is related to the other diatom I illustrated in the previous post – Biddulphia pulchella but whilst I can just about persuade you that Hydrosera is related to centric diatoms, it is harder to do this for Biddulphia, which is more obviously lanceolate in outline.  It also has psedocelli, which hints at a relationship with Hydrosera, and also has many small discoid chloroplasts (hinting at a relationship with the wider centric diatoms) but it sure ain’t round, by anyone’s definition.

The efforts of many taxonomists to shoehorn Biddulphia into the centric diatoms recalls Thomas Kuhn’s observations in The Structure of Scientific Revolutions – scientists approach data with strong preconceptions and outliers to the prevailing wisdom require ever more elaborate justifications to fit the pattern, something Kuhn described as “puzzle solving”.  Eventually, someone recognises that “normal science” is no longer viable, and proposes a new theory – a so-called “paradigm shift” (a phrase first used by Kuhn). 

In the case of Biddulphia and Hydrosera, the paradigm shift came in a 2004 paper by Linda Medlin and Irena Kaczmarscka who proposed a new class, Mediophyceae, for these “multipolar centrics” based on molecular sequence data, and that has now become the established classification (see “Who do you think you are?”).  Or, to use the language of Kuhn, we have re-entered a phase of “normal science”, at least until the next revolutionary biologist comes along with a better idea …

My picture was supposed to show Hydrosera triquetra growing on a vertical wall in Deptford Creek (with the bridge carrying the Dockland Light Railway over the river just visible in the background).  There are eight orders of magnitude difference between the Hydrosera cells (which are relatively chunky by the standards of diatoms) and the DLR bridge – which is a depth of field way beyond any camera could achieve.  Less impressive, from my point of view, is the appearance of a few mutant Hydrosera cells with five, rather than six, poles.  I finished the picture in rather a hurry as I wanted to post this before we headed off on holiday.  Sorry.

References

Ashworth, M. P., Nakov, T., & Theriot, E. C. (2013). Revisiting Ross and Sims (1971): toward a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae). Journal of Phycology 49: 1207-1222.

Kuhn, T. (1962).  The Structure of Scientific Revolutions.  University of Chicago Press.

Medlin, L. K., & Kaczmarska, I. (2004). Evolution of the diatoms: V. Morphological and cytological support for the major clades and a taxonomic revision. Phycologia 43: 245-270.

Some other highlights from this week:

Wrote this whilst listening to:  Marika Hackman, following her gig at the Cluny in Newcastle.

Currently reading:  The Story of Art Without Men by Katy Hessel.  My daughter thought I needed educating.

Cultural highlight:  Marika Hackman in a packed Cluny.  Can’t help wondering why she’s not better known.  

Culinary highlight:  immediately prior to the gig, we ate at the Ship Inn, just across the road, which has all the attributes of a traditional Newcastle pub with football on big screens and “pub grub” on the menu, only the whole menu is vegan.  We ate their take on fish and chips – tofu wrapped in seaweed and then battered and deep fried – which rather proved my point that fish is algae-flavoured protein.

Dispatches from the city of migrants …

The journey to the location for this post started at the foot of the first “s” in the East Enders title sequence and ended beside the little blue squiggle at the bottom of the television screen, directly under the “a”.  I got off the Elizabeth Line at Stratford with no other plan other than that I had some time on my hands and headed roughly south, triangulating on glimpses of the O2 Arena and Canary Wharf as best I could.  I passed the splendid Italian Gothic edifice at Abbey Mills that houses the pumping station built as part of Bazelgette’s great sewer, walked alongside the muddy lower reaches of the River Lea, skirted numerous industrial estates and finally arrived, some two hours and nine kilometres later, at Island Gardens, a small area of green amidst the docklands sprawl, with a splendid view across the Thames to Wren’s Royal Navel College.  After crossing the river via the Greenwich foot tunnel, I emerged beside the Cutty Sark from where a short walk brought me to the blue squiggle that was my destination. 

That blue squiggle is Deptford Creek, scene of some posts at the end of last year (see “Floundering around in Deptford Creek” and “Throwing shapes …”) and I had come back to see how the project was progressing as well as finding some time to poke and scrape at more patches whose golden-yellow hue promised interesting diatoms.  The mudflats themselves looked much greener than I remembered, but it is hard to know if this is a genuine biological phenomenon or is just the random chance of two observations being different.  Today, however, I was more interested in what was growing around on the training walls at the edge of the creek rather than on the mud itself.  

My eye was caught straight away by bright green growths on the shelf on the wall beside the slipway.  Their distinctly felty texture made it easy to recognise the genus as Vaucheria although naming the species is a more difficult job.  We’ve met Vaucheria several times in freshwater (see “the pros and cons of cell walls …”) but it is also commonly found in brackish habitats.  My interest today was not in what species was growing, but in the way that it was helping to build a habitat within which a clump of moss and the shoot of a flowering plant were able to grow.  We saw this with happening with Rhizoclonium riparian during my previous visit (see “If only we looked …”); this time it is an alga from a different phylum, but we are looking at essentially the same phenomenon.

A patch of Vaucheria growing on the wooden training wall beside Deptford Creek, March 2024.  Note the moss (back right) and the shoot that have established themselves in the algal patch.  The patch is about 30 cm across.   The photo at the top of the post shows the training wall beside the slipway at Deptford Creek. 

Underneath this shelf, there was a distinct yellow-brown patch on the wall whose dominant constituent was Hydrosera triquetra.  I commented on its absence in a previous post (see “Deptford’s Heart of Darkness …”) but, in truth, the mudflat is not where I would most expect to find it.  It is a chain-forming diatom that seems to be associated with vertical surfaces and which can tolerate exposure. When individual cells are seen end-on (“valve view”), they are very distinctive, resembling a Star of David, with two overlapping triangles; however, the cells attach at these faces and the characteristic shape is not immediately apparent when seen in fresh material.  You need to focus carefully to understand the third dimension (see “Seeing with my fingers …”).  

Hydrosera triequetra in Deptford Creek, March 2024.  The left-hand image shows a patch growing on a wooden support (the central one visible in the image at the top of the post). The right-hand image shows a magnified view. The scale bar is 20 micrometres (= 1/50^th of a millimetre) long.  

Hydrosera triquetra was first observed in the Thames in the early 1970s, and is widely-assumed to have been accidentally introduced, perhaps by a ship discharging ballast water.  Now it is widely-established.  I’m often sceptical of claims about “alien” species  but H. triquetra is sufficiently large and distinctive that it seems unlikely that it would not have been seen by earlier generations of microscopists at least occasionally.  Whether it justifies the term “invasive” is a moot point (see “Pens are too light …”).   That would require some evidence of wholesale changes in both the composition of the microscopic flora, and the way it functioned.  Personally, I love the diversity of modern London and am prepared to embrace a migrant diatom or two without feeling the need to apply pejorative adjectives.  

On the opposite side of the slipway, I noticed a seepage that, again, had a golden-brown hue suggestive of diatoms.  However, I could not see any Hydrosera growing amidst this assemblage, instead, there was a mix of Melosira varians and Biddulphia pulchella, a relative of Hydrosera, which lives in brackish water and forms zigzag colonies.  Motile diatoms such as Nitzschia sigma glided in and around these filaments.  The presence of Melosira varians is interesting.  I am fairly sure, based on examination of living cells, that these filaments are not one of the related species of Melosira that are more tolerant of salinity. That a freshwater species with only mild affinity for salt is thriving here supports some observations of higher plants on the slipway made by Nick and Andy from Creekside Discovery Centre. They noticed that these, too, are mostly not especially salt-tolerant plants, leading them to think that the upper slipway represents a freshwater tidal marsh, rather than a salt marsh, and that it is the result of fresh water from the Ravensbourne being lifted above the denser salt water that pushes into Deptford Creek on each tidal cycle.  A freshwater species tolerant of some salt rubbing along beside a brackish species that can cope with an occasional dose of freshwater seems like a good metaphor for this part of London where people from every part of the world live side-by-side.

Another seepage beside the slipway at Deptford Creek, this time with a mix of Melosira varians (right) and Biddulphia pulchella (left). The scale bar is 20 micrometres (= 1/50^th of a millimetre) long.

Some other highlights from this week:

Wrote this whilst listening to:  vintage Jefferson Airplane and, for contrast, Kendrick Lamar’s To Pimp A Butterfly.

Currently reading:  The Secret Diaries of Charles Ignatius Sancho by Patterson Joseph, a novel that is, by coincidence, about 18^th century migrants in London.

Cultural highlight:  Lines, a play at the Crucible in Sheffield exploring injustice in Palestine and Uganda.  Rather challenging.

Culinary highlight:  Seven course tasting menu at Prashad, an Indian vegetarian restaurant  in Drighlington, just south of Leeds

What lurks beneath The Skating Minister?

My reason for visiting Duddingston Loch (see “Paddling in January”) was to contrast the way that a location is perceived in an art gallery with the way that it is seen by a scientist.  Duddingston Loch is familiar as the location for Henry Raeburn’s The Skating Minister. A few years ago this was voted “Scotland’s favourite painting” and it is one of the biggest attractions at the National Gallery of Scotland.  But how many of the people who gaze at the image hanging on the gallery wall know that it represents a location within walking distance of the gallery itself, and how many of that subset know anything about this particular loch other than that it is the setting for this rather famous painting?  This is a theme I’ve circled around for most of the time I’ve been writing this blog.  We “see” a place differently, depending on what we are looking for.   For the casual visitor to the National Gallery of Scotland, Duddingston Loch is no more than a setting for a painting, and the character of the loch itself was never part of Raeburn’s vision for his painting.   For Edinburgh’s citizens, the loch is somewhere to enjoy fresh air and nice views without the need to travel beyond the city limits.  Keener naturalists might take binoculars and watch the waterfowl.  I’m pushing that “natural history” angle one stage further today by exploring the world that only becomes apparent when you peer through a microscope.  

Even then, there is not one single world that becomes apparent.  In my January post I wrote about the algae that I saw in the fresh sample that I had brought back.  Since then, I have prepared the sample for examination at high magnification, and the results of that are presented in this post.  I found a total of 37 different species of diatom in my examination, of which 17 are illustrated below.  Of particular note, given where the sample was collected, are the variety of species of Navicula and Nitzschia.   I referred to these in my earlier post as “gliding around” because, when you observe them on a microscope slide, they move as gracefully and serenely as the Reverend Robert Walker appears to do in Raeburn’s painting.  In Duddingston Loch, however, their habitat is not an ice-smooth microscope slide, but a tumble of tiny silt and sand particles. Their movement is more like that of the algae I described from Deptford Creek (see “Commuting to work …” and links) but without the strong tidal rhythms.  Just as the swans who glided across to me in the expectation that I was going to toss them some bread, so the diatoms here are savvy enough to adjust their position when they think that there is some benefit.  In their case, as “plants”, rather than “animals”, they are more interested in light than bread.   

Diatoms from Duddingston Loch I: Fragilariophyceae: a., b. Fragilaria radians; c.,d.,e.: Pseudostaurosira brevistriata; f.,g. Staurosira construens; h., i. Staurosira binodis; j. Staurosirella pinnata; k.,l. Pseudostaurosira elliptica.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).  This post is about the range of encounters we have with nature.  Many people come to Duddingston Loch simply for the pleasure of being in a being in the countryside, albeit in the midst of a large city.  Many others experience it vicariously via Henry Raeburn’s picture, either in the National Gallery of Scotland or in reproduction.  But others encounter it as more active observers, whether of the birds and other wildlife or, in my case, looking at the microscopic life that inhabits the loch.  There is a direct pleasure that we obtain from this observation – another form of the type of encounter that casual visitors are experiencing.  However, we can take the observer’s experience one step further.  When we pass from purely observing to recording what we see, another opportunity arises.  We can look at Duddingston Loch not in isolation but as one of many small lochs in Scotland.  I can, for example, compare the records I have made at Duddingston with those myself and others have made at other lochs and ponds around the UK.  Is there anything unique about Duddingston Loch and, more importantly, is there anything that should concern those involved with its management?   

My day job involves performing “health checks” on lakes and rivers and I could not resist applying one of these tests to the data I collected from Duddingston Loch.  Unfortunately, the result was not encouraging: Duddingston Loch would not, I am afraid, meet the criteria for “good ecological status” based on the sample I collected.  The standard test is based on two, rather than a single sample so we should not leap to a hasty conclusion. However, to take a footballing analogy, Duddingston Loch is going into the second leg of this fixture at a distinct disadvantage.  

Diatoms from Duddingston Loch II: other groups.  a., b.,c.,d. Amphora pediculus; e. Rhoicosphenia abbreviata; f.,g. Navicula caterva; h., Platessa conspicua; i., Sellaphora atomoides; j. Encyonema leibleinii; k. Epithemia adnata; l. Nitzschia amphibia; m., Nitzschia fonticola; n. Nitzschia solgensis; o.,p.,q.,r. Nitzschia soratensis.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).  

The most likely reason is, I suspect, the wildfowl themselves.  Duddingston Loch has a very small catchment area, mostly draining the south and west side of Arthur’s Seat, and unlikely to be a major source of nutrients.  As well as the ducks and swans greedily feeding on bread brought by visitors, there is also a heronry at the west end of the Loch.  Birds such as herons which scout around quite large areas but then return to the same location each night are going to transfer nutrients from other ponds and streams into Duddingston Loch via their faeces.  There is quite a large literature on the impact that birds can have on water quality in small shallow lochs.  Of course, birds also have a positive impact, drawing naturalists to locations such as this and it is also possible that it is the loss of good habitats more widely that ends up in birds congregating in numbers in the places where conditions are favourable.  I certainly don’t want to end this post by annoying the ornithological lobby.  Not least because if I want to play out the “second leg” of this particular fixture, then I will need to keep on the right side of the wardens!  

References

Gremillion, P. T., & Malone, R. F. (1986). Waterfowl waste as a source of nutrient enrichment in two urban hypereutrophic lakes. Lake and Reservoir Management 2: 319-322.

Scherer, N. M., Gibbons, H. L., Stoops, K. B., & Muller, M. (1995). Phosphorus loading of an urban lake by bird droppings. Lake and Reservoir Management 11: 317-327.

Tobiessen, P., & Wheat, E. (2000). Long and short term effects of waterfowl on Collins Lake, an urban lake in upstate New York. Lake and Reservoir Management 16: 340-344.

Some other highlights from this week:

Wrote this whilst listening to:  Laufrey, lush jazz-pop from Iceland.

Currently reading:  To the River, by Olivier Lang, a travel book following the Sussex Ouse from source to sea, with reflections on the life of Virginia Wolff.  And I have just finished The Fraud by Zadie Smith.

Cultural highlight:  Zone of Interest, a remarkable film about Auschwitz that perfectly captures the meaning of the phrase “banality of evil”.

Culinary highlight:  A home-cooked Ghormeh Sabzi (Iranian lamb, kidney bean and herb stew) wins over an enjoyable but somewhat lacklustre meal at The Ivy in York.

Deptford’s Heart of Darkness …

Joseph Conrad set the opening passage of Heart of Darkness on a boat on the Thames, waiting for the tide to turn so that it could set off, carrying Marlowe, Conrad’s protagonist to Africa.  Conrad starts his story with a river that would have been familiar to many of his readers before taking them to the Congo, which would have been alien and exotic.  Only the hardiest and most intrepid of souls would have been able to face the challenges that the tropical climate – and the plants, animals and diseases that thrived there – presented.  Marlowe and his companions were, most likely, just a few kilometres from Deptford Creek, the urban intertidal habitat whose diatoms I described in two posts towards the end of last year (see “Floundering around in Deptford Creek …” and “Commuting to work …”).  They were, ironically, surrounded by organisms that were, then as now, just as exotic and unbelievable as the inhabitants of the African rain forests, if only they had cared to look. 

In my earlier posts, I covered the macroscopic and live microscopic views of the diatoms.  In this one, I am taking the “classical” approach of examining cleaned valves at high magnification, in which the information about chloroplasts and motility that we lose is offset, to some extent, by the close detail of surface ornamentation that is revealed.  There is also an element of circular reasoning here: the traditional taxonomists who write the essential identification guides all assume that their readers are viewing a cleaned valve at high magnification, which puts anyone observing a living cell at an instant disadvantage.

Overall, I found 53 species in the two samples that I collected back in November, of which 32 are illustrated here.   Both samples were dominated by motile diatoms (63 and 66 percent respectively), reflecting the silty nature of the habitats here.  The first plate shows the diatoms from the stones in the centre of the creek, many of which I also find in lowland fresh water habitats.  The second is a scraping of the diatom film growing on the mud surface, and most of these diatoms are genuinely brackish or marine.  I did, however, find a surprising number of valves that I associate with good ecological status – Tabellaria flocculosa, Achannthidium spp. and Brachysira microcephala.  It is not unusual to find a few cells of these that have drifted into samples from habitats further upstream, but 8.5 percent of the cells in this sample had this preference, which is more than I would have expected.  I see no plausible habitats for these species in the densely-urban catchment of Deptford Creek so this is something of a mystery.  Missing from the list is Hydrosera triquetra, a tropical diatom that has become common in the lower Thames over the past 50 years.  I did see one girdle band but have not yet found an intact cell or frustule.

I’m a Londoner, born less than 10 kilometres from Deptford Creek and, in some ways, the diatoms in these samples remind me of the city itself.  They are diverse, some are immigrants that have chosen to settle here, others are indigenes, adapted to intertidal muds.  The mudflats, themselves, are forever changing.  What I see in November 2023 might not be what I will see a few months later just as the London I remember from the 1960s and early 1970s is very different to London in 2024.  Indeed, the docklands skyline, which we can see from the Creek, was not there in my childhood, nor were many of the skyscrapers in the city, a short distance upstream.  Watching nature ebb and flow in the shadow of these apparently substantial structures helps to remind us that change is the only constant.  Even in a city with a history as rich as London’s.   Looking at diatoms in mudflats reminds us that we do not have to get on a boat and travel vast distances to get to unknown and unexplored places, as Marlowe was doing in Conrad’s tale.  It only takes a short journey on the Dockland Light Railway to find worlds still waiting to be explored.  

Deptford Creek diatoms, plate 1.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).

a., b.	Nitzschia filiformis var. conforta	c.	Nitzschia dissipata
d., e., f.	Nitzschia sociabilis	g.	Nitzschia amphibia
h.	Nitzschia inconspicua	i.	Nitzschia sigma
j.	Tryblionella angustatula	h.	Gyrosigma acuminatum
l., m.,n.,o.	Rhoicosphenia abbreviata	p.	Amphora pediculus
q.	Delphineis surirelloides	r., s., t.u., v.	Navicula gregaria

Deptford Creek diatoms, plate 2: centric diatoms.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).

a., b.

Actinoptychus sp(p)

c.

Actinocyclussp.

Deptford Creek diatoms, plate 3: Nitzschia and Tryblionella.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).

a. – d.	Nitzschia sigma	e.	Nitzschia cf. capitellata
f.	Nitzschia pusilla	g.	Nitzschia …
h.	Nitzschia inconspicua	i., j.	Tryblionella apiculata
k.	Tryblionella littoralis

Deptford Creek diatoms, plate 4.  Scale bar: 10 micrometres (= 1/100^th of a millimetre).

a.	Raphoneis amphiceros	b.,c.	Frustulia vulgaris
d., e.	Achnanthes brevipes	f.	Tabellaria flocculosa
g.,h.,i.	Achnanthidium spp.	j.	Brachysira microcephala
k.	Cocconeis pediculus	l.	Cocconeis euglypta
m.,n.	Navicula gregaria	o.	Navicula sp.
p.	Fallacia subpygmaea	q.	Luticola mutica
r.	Surirella sp.

Reference

Hartley, B., Barber, H.G. & Carter, J.R. (1996).  An Atlas of British Diatoms.  Biopress, Bristol.

Tittley, I. (2014).  Non-native marine algae in southeastern England. Bulletin of the Porcupine Marine Natural History Society 1: 28-32.

Witkowski, A., Lange-Bertalot, H. & Metzeltin, D. (2000).  Iconographica Diatomologica 7: Diatom Flora of Marine Coasts 1.  Koeltz Scientific Books.

Some other highlights from this week:

Wrote this whilst listening to:  Dire Straits first album.  Mainly because, whilst Googling “Deptford Creek”, I learned that Dire Straits first got together in this part of London in the mid-1970s 

Currently reading:  A Gentleman in Moscow by Amor Towles.  

Cultural highlight:  Small exhibition of charcoal portraits by Frank Auerbach at the Courtauld Gallery.  Intense records of encounters with a few close friends worked and reworked in classic Auerbach style.  Emerging from the exhibition into the room holding the Courtauld’s collection of classic Impressionist paintings seemed almost anticlimactic.

Culinary highlight:  Dhosa in Chutneys in Drummond Street near Euston Station in London following the first British Diatom Meeting since lockdown.  Mostly for the sheer pleasure of spending a day and sharing a meal with friends I had not seen for a long time.

Hiding in plain sight …

My final post of 2023 (“Call me by my name …”) looked at the fraught business of putting names onto microscopic organisms, dividing the problem into limitations of knowledge and practical challenges.  Limitations of knowledge mean that there is no single definitive work to which we can refer.  Practical challenges include limitations of our equipment but also our capacity to access an increasingly diffuse literature, some of which sits behind internet paywalls.  At the intersection of these two challenges sit “cryptic species”: those that we know exist, but which cannot reasonably be differentiated with light microscopy.   

In many parts of the world, diatoms are used as part of statutory assessments of freshwater health so it is worth asking ourselves just how much extra sensitivity we may unlock by accessing all this unknown and hidden information about diatom species.  How might we do that?   The dominant approach to naming diatoms uses characteristic shapes and structures to differentiate species so we need to find a way of differentiating all the variety within diatoms that does not rely upon our ability to see and describe this variation.  The answer lies in molecular genetics where, rather than using morphology, we differentiate using sequences of DNA.  Until now, though, people have mostly tried to link these sequences to traditional names defined by (you’ve guessed it …) our inherently-flawed system of shape- and character-based taxonomy.  Suppose that, instead of this, we did all steps required of DNA-based identification except for that final one where we fitted the outputs to traditional names.  How would that change the situation?

About 2800 diatoms have been recorded from the UK and Ireland, based on traditional shape-based species concepts.  Our study, based on a dataset of 1220 samples from rivers all around the UK, we found 4036 distinct entities.  Not all of these will be “species” in the traditional sense but, on the other hand, some of the sequences we identified may encompass more than one species.  Metabarcoding uses relatively short fragments of DNA from a single gene whereas taxonomists would work with longer lengths of two or more genes as well as morphology.  However, this does at least offer us a ballpark figure for how many diatom species we are yet to find.  Very roughly, for every two diatom species we already know about, there is one more waiting to be described.  As our dataset comes from rivers, we are probably missing some of the diversity in lakes and soil, so the true figure may be even higher. 

Our primary purpose in doing these analyses was to see if we could improve the models we use for statutory assessments.   Way back in 1995 when I put together the first version of the Trophic Diatom Index (TDI), it explained 63 percent of the variation in the river phosphorus gradient.  Since then, the TDI has gone through several iterations as species have been added and coefficients have been tweaked but, until this study, we always used traditional diatom species names (even when using molecular genetics to generate our data). Now, almost 30 years since the first version of the TDI, we generated a model that bypassed traditional names (and all the limitations this introduces) and produced a model which explained 72 percent of the variation in the nutrient gradient.   

Results of weighted-average (WA) predictive models, showing relationship between observed and ASV-inferred nutrient pressure for diatoms and non-diatoms, and both (combined) (left). Upper plots show relationship for model fits, lower plots show results after 2-fold leave-out cross validation.  See Kelly et al. (2024) for more details.  The figure at the top is the graphical abstract from this paper.

This is not a perfect statistical comparison, but it reflects the reality of the situation.  We captured most of the diatom v nutrient signal with our relatively crude approach back in the early 1990s and have spent the last 30 years crawling slowly towards the asymptote.  We calculated that the strongest model we could compute with the (imperfect) chemical data we are given is, in theory, 86 per cent.  However, that assumes no other factors are influencing the diatoms and we know that is not the case.  Whilst strong models should allow regulators to better predict the ecological benefits of reducing phosphorus, there is also a danger that we become blind to the complexity of river systems in the process of developing these.  

Our result suggests that, however hard taxonomists work to track down the 1200 or so “missing” species, this will add relatively little functionality to our current mode of assessment.  Of course, having a better idea of the diversity of the algae of Britain and Ireland is a worthwhile end in its own right, although some of this diversity will be “cryptic”, impossible to unlock with conventional microscopy.  The answer is to find new ways to use this rich source of information rather than refining existing approaches. 

The problem, as we attempt to unravel this diversity and explain it in terms that can be used when identifying diatoms using a microscope is that we are encountering many of these 1200 “missing” species all the time.  They are hiding in plain sight, but we are not recognising them as discrete species because no-one has told us how to differentiate them from their near-neighbours.  The challenge for taxonomists is to capture the characteristics of these unambiguously using words and pictures, when many of the characters visible with the light microscope will overlap with those of near neighbours.  Otherwise, the sensitivity gained by extra knowledge will be cancelled out by error introduced by mis-identifications resulting from ambiguous and diffuse literature.  We are almost back where we started, still channelling the spirit of van Leuwenhoek four hundred years ago, struggling to make sense of realms that sit at the borders of our awareness … 

References

Kelly, M. G., & Whitton, B. A. (1995). The trophic diatom index: a new index for monitoring eutrophication in rivers. Journal of applied phycology 7: 433-444.

Kelly, M. G., Mann, D. G., Taylor, J. D., Juggins, S., Walsh, K., Pitt, J. A., & Read, D. (2023). Maximising environmental pressure-response relationship signals from diatom-based metabarcoding in rivers. Science of The Total Environment 914: 169445.

Some other highlights from this week:

Wrote this whilst listening to:  music referred to in Do Not Say We Have Nothing (see below).  In particular, Pink Floyd’s Set the Controls to the Heart of the Sun and Mahler’s Das Liede von der Erde, both of which have words derived from ancient Chinese poetry.  

Currently reading:  Do Not Say We Have Nothing by Madeleine Thien, a novel that spans Chinese history from the Sino-Japanese war to Tiananmen Square in 1989.  

Cultural highlight:  Mercury-prize nominated Irish band Lankum at the Boiler Shop in Newcastle.  Traditional folk instrumentation but with enough of a nod to My Bloody Valentine to make me want to gaze at my shoes at times.

Culinary highlight: fillets of sea bass roasted and served over a bed of pan-fried fennel. A recipe from a book of Venetian recipes that we had forgotten we had.

Paddling in January …

There was a brief break in the dreary, wet weather that has beset Britain this winter last weekend, and I was fortunate enough to be well-placed to take advantage.  I was in Edinburgh, walking from Waverley station, past St Leonard’s police station (made famous by Ian Rankin’s Rebus novels) and then following the perimeter of Holyrood Park until an open expanse of water appeared before me.  The view at the top of the post does not look like I was in the centre of a capital city, but that rocky expanse rising from the side of the loch is Arthur’s Seat, the other side of which lies the Royal Mile and the Scottish Parliament.

Why Duddingston Loch?  I wrote last year about a trip to Borrowdale, to link a landscape painting by Turner to the microscopic landscapes that existed in the stream he depicted.  Duddingston Loch is also the location for a famous painting, Henry Raeburn’s picture popularly known as the Skating Minister (c. 1795).  This depicts a black-clad clergyman skating on the frozen loch with the slope of Arthur’s Seat just visible in the misty backdrop.  A visit in January seemed appropriate, even if the loch was not frozen.   

Travelling to Edinburgh by train limited the amount of equipment I could bring and this created a problem as the loch did not provide any suitable surfaces for me to sample within an arm’s length of the shore.   A further problem then presented itself, as a group of curious swans came across to investigate my presence.   I sat on a bench and reviewed options until they got bored and swam away then, resigned to my fate, took off my boots and socks, rolled my trousers to the knee and waded into the water.  The lake bed in this area was silty but firm, with a few protruding pebbles and one or two small cobbles for me to collect into my tray.  The water was, I measured, about 5.5 degrees Celsius and I emerged a couple of minutes later with a renewed admiration for cold water swimmers.  I brushed the silty diatom-rich film off the stones with my toothbrush whilst I sat on a bench letting the sun dry my feet and chatting to passers-by who were curious to know what I was doing.

A group of swans investigating my presence beside Duddingston Loch in January 2024.  The picture at the top shows a view looking west across the loch.

That was as much as I was able to do on this first visit.  I could see some promising reedbeds on the far side of the loch, but I would need to get a key from the Scottish Wildlife Trust to visit there.  I put my socks and boots back on, then followed an old railway line along the southern edge back to St Leonards and then to the city centre where I went into the Scottish National Gallery to look at Raeburn’s painting and browse around some other Scottish landscapes before heading back to the station.  

I looked at the sample under my microscope the following day, and found a dozen or so species very easily.  Most suggest that the loch is nutrient rich, which is not a big surprise given its urban surroundings.  There were at least three species of Navicula gliding around, as well as Nitzschia dissipata.  There were also a couple of species of Encyonema, one free-living and the other inside a tube, plus some cells of Fragilaria, Amphora pediculus and Rhoicosphenia abbreviata.   Alongside these diatoms I found filaments of the green algae Mougeotia and Oedogonium plus a narrow Oscillatoria.   I was rather relieved, I have to say, to find so many algae, as my first impression of the rather silty sample was not encouraging and I thought that my excursion into the freezing waters of the loch may have been in vain.  There was, however, no obvious focal point for a picture, so that will have to wait for another visit.   As I said earlier, those reedbeds on the far side look more promising, though I suspect I am going to annoy some birdwatchers if I spend too long splashing around close to their hide.

Some diatoms from Duddingston Loch, January 2024: a. – e. Navicula spp (likely N. radiosa, N. tripunctata and N. gregaria); f. Nitzschia dissipata; g. Amphora pediculus; h., i.:Encyonema cf. silesiacum; j. k., Rhoicosphenia abbreviata; l., m. Fragilaria cf. tenera; n. Encyonema leibleinii.  Scale bar: 20 micrometres (= 1/50^th of a millimetre).  

Some other highlights from this week:

Wrote this whilst listening to:  Art School Girlfriend

Currently reading:  The House of Doors by Tan Twan Eng, which cleverly weaves real-life characters and events into a novel set in Malaysia in the first half of the 20^th century.  

Cultural highlight:  Rye Lane, 2023 film set in Brixham and Peckham in south London which had good reviews when it came out but we were unable to see in the cinema.

Culinary highlight: enough fruit puree harvested from our allotment accumulates in our freezer that we are able to enjoy the pleasure of a summer pudding in the middle of the winter.

Duddingston Loch looking east

Call me by my name …

One of my very earliest posts addressed a very basic problem in the study of microscopic organisms: knowing the identify of whatever you are looking at (see “All exact science is dominated by the idea of approximation …”).  The germ for this post came from a quotation from Bertrand Russell that said that, when you counted anything, you had a good idea of what constituted whatever it was you were counting.   If you were counting oranges, you knew to exclude apples, obviously, but also tangerines and satsumas, which may look similar but are genetically-distinct.  That’s not always so straightforward for microscopic algae, as I’ve discussed in many posts, but it is a core, largely unspoken, assumption.   I’ve also emphasised the distinction between the sciences of taxonomy and systematics, and the craft of identification (see “Disagreeable distinctions …” and, more recently, “How to identify diatoms from their girdle views …”).  As an ecologist, I need to use the outputs from taxonomy but, at the same time, I am constrained by time, equipment and, indeed, by the knowledge that I can readily access, in my ability to do this.  

I’ve tried to encapsulate this as two overlapping triangles in the diagram below.  The reason why we cannot name a specimen distils into one of two reasons: limitations of knowledge (represented by the blue triangle) or practical limitations such as the quality of the microscope or the way that the specimen presents on the microscope slide.   So every identification challenge sits somewhere on the gradient from left to right: we are either limited by available knowledge or practicalities.

The challenges involved in identifying diatoms (and other microscopic organisms) fall into two types: the quality of the knowledge that we have available, and our ability to link this knowledge to the specimen we see under our microscope.  

Knowledge limitations encapsulates everything that is known at the time that the specimen is being analysed, and will include the following: 

• The species within a genus may have not yet been fully discriminated and described for the region you are studying;  
  
•  There are limitations associated with light microscopy which means that the full range of genetic variation within a complex of species cannot be resolved (“crypticity”).
  
• The literature for that genus is dispersed in numerous journal articles rather than gathered in a single accessible volume.  In theory, we can access these via Google Scholar or Web of Science, but some will be behind paywalls.  Sometimes, knowing where to look is, itself, the problem.
  
• The keys in taxonomic works are often poor (which inhibits identification by logical reasoning) and/or there may be insufficient images (inhibiting pattern recognition) and there is often insufficient focus on critical differentiating characteristics.  

Next, there are problems that relate to the practicalities of identification, irrespective of the knowledge that is available:

• Individual cells do not present in an optimal manner (e.g. as girdle views in the case of diatoms) or key diagnostic criteria are absent (reproductive organs are necessary to identify species of filamentous algae such as Spirogyra and Oedogonium) or the taxon is sufficiently sparse in the sample that the full range of morphological and diagnostic characteristics cannot be discerned.
  
• Equipment available is not sufficiently sensitive.   A common problem when instructing students is that microscopes used in university teaching laboratories have a lower specification than those used for research, so the students often cannot see the same level of detail that the textbooks assume.  A twist on this general theme is that the camera on a microscope used for routine analyses cannot capture the level of detail required to allow someone else to identify a specimen when you email them an image. 
  
• The observer is unaware of recent literature or is working under time constraints that prevent a full literature search.   This is similar to the third point in the “knowledge” section, reflecting a second facet: problems arise not only because specialists are no longer prepared to write detailed monographs that gather together the literature on a genus in a region, but also because time and budget limitations mean that the alternative – thorough interrogation of a very diffuse literature  – is not always possible. 
  
• Faulty memory links a particular set of morphological properties to the wrong name.  Mistakes, in other words.  There is a danger that our recollection of the properties associated with a particular name drifts over time, and needs regular calibration.

In reality, I often have to make a judgement about the value of any extra information that I can glean from a sample, relative to the effort I will need to in order to unlock this information.   There is a basic scientific curiosity in me that wants to know the identity of an alga I’ve never seen before, and to understand the diversity within a habitat better, but I’m also often working under pressure and spending time trying to name a single cell whose identity eludes me will add very little to the interpretation based on the other 299 cells I’ve already examined and named.  On the other hand, if there was a single volume work on the Fragilaria of Europe (for example), the marginal effort required to make that extra determination might be reduced so that I can pluck the book from my shelf, flick through the pages, name it and move on.  The danger of this lies in the first point I made – about incompleteness in our basic understanding of the variety within most genera – and means that a monograph may, itself, not be sufficiently comprehensive.  “Hard cases” will be force fitted to available descriptions, perpetuating the longer term problem of fitting morphology-based descriptions to the biological species concept. 

There was a time, not so long ago, when there was a general belief that there was a finite number of cosmopolitan species of freshwater diatoms, and an unspoken assumption that all could be differentiated with light microscopy.  Over the last thirty years, those ideas have been superseded as forms once regarded as a single species have been fragmented into a multitude of distinct entities.   No-one seriously doubts that there are many more species than diatomists a generation older than us had contemplated, but one side-effect is that the capacity of Linnaean taxonomy to serve as helpful “tags” that ensure consistency in identification between scientists is close to breaking-point.   The craft of identification depends to a large extent on the willingness of taxonomists to invest time not just in expanding our knowledge but also in gathering this together into practical resources.  That’s now become such a Sisyphean task that few seem to want to take it on.  Yet, not having such resource creates problems of its own, not least in contributing to a sense amongst bureaucrats that diatomists are better at talking the talk than walking the walk, in terms of their ability to contribute to answering the pressing environmental challenges of our day. 

Some other highlights from this week:

Wrote this whilst listening to:  New Energy by Four Tet.

Currently reading:  Still on Amy-Jane Beer’s Flow.   Her explorations of British rivers includes a snorkalling trip in West Beck / River Hull which I wrote about in “Past Glories …”.

Cultural highlight:  A World in Common: Contemporary African Photography – an exhibition at the Tate Modern in London. 

Culinary highlight:  When I first started this post, I was in Belgrade, eating traditional Serbian food in the Tri Seseria restaurant in Belgrade’s old town.  That was in an unseasonably warm October, and the unfinished post has sat on my laptop for almost three months awaiting completion.   

Commuting to work …

I’ve written about the different colours of the mud in Deptford Creek; yellow-brown in areas where the diatoms are thriving and green where Euglena is predominant.   In between, there are areas of plain, unprepossessing brown mud.  Take a few steps in any direction and the colours of mud will change.  Alternatively, imagine standing still for a period of time.  You’ll see the colours on a single patch of mud changing.  Admittedly, you’ll get rather damp and cold in the process because the tide will come and go, and your legs will be tired, as you really need to stay in one place for an entire tidal cycle (that’s 12 hours).   But you’ll learn that these coloured patches are a phenomenon that occurs on exposed mud.  As the water level rises, so the colours fade back to a uniform muddy brown. 

The scientific literature refers to this as “migration” but “commuting” is probably a better term (and more appropriate, given our proximity to London’s financial centre).  A commuter lives in one place and moves daily to and from work.  Our algae all “live” in Deptford, and they have a short commute (about a millimetre) to contribute to the “carbon economy”.  During the summer, they work long days, sometimes (depending on the tide cycles) taking a prolonged “siesta” in the middle of the day when the tide comes in, and then working long into the evening.  On days like the one when I visited, however, their working hours are similar to those of the humans around them, with the start time changing each day to keep pace with the monthly cycle between neap and spring tides.

The picture at the top of the post shows the Euglena and Nitzschia cells as they reach the surface, ready to start their day’s work.  As I painted it, I was thinking of Jason’s penultimate challenge before he was given the golden fleece: he had to sow the teeth of a bull into a field, which then sprouted into an army of well-armed soldiers.  I’ve captured the moment when the algae start to “sprout” at the surface.  The green and golden-brown patches that I described in earlier posts will have been exposed for longer and be composed of many layers of cells, each jostling for position (“survival of the fittest” rules on Deptford’s mudflats, just as in the financial institutions that inhabit Canary Wharf’s skyscrapers).  

The lower picture shows how the images relate to the tidal cycle (represented as a sine wave in the upper image).  When the tide is high, the algae are below the surface (a.) but when it is low, they are at the surface (b.), so long as it is daylight).  Light seems to be the most important factor, but tidal cycles and temperature also play a role.  Algal cells start to move away from the surface before the mud is submerged, suggesting that movement is controlled by more than just external cues.  Very roughly, diatoms seem to move about a millimetre an hour (i.e. about ten times their own body length).  The depth of their daily commute is quite variable – very little light penetrates beyond the first half millimetre of sediment but a deep migration will soon encounter a black layer with no oxygen and potentially toxic sulphides.  The depth also depends on the type of sediments, and the local habitat, but think in terms of a couple of millimetres as a rule of thumb.   It is a tiny distance by human standards, but enough to take them away from the physical forces that may batter them as the tide comes in, whilst still being one that can be ascended relatively rapidly as the tide goes out.

Diatom movements in relation to tidal cycles in Deptford Creek.   The sine wave showing the tidal cycle and the black/grey bars showing nighttime are roughly coincident with conditions on the day of my visit.  The lower images show the algae below the sediment surface at high tide (a.) and at the surface at low tide (b.).   The Euglena cells are about a 10^th of a millimetre long.  The image at the top is a representation of the view at the mud surface at low tide.

What’s the point of it all?  Remember that photograph of a flounder that I included in my first post from Deptford Creek?   That fish eats smaller fish and invertebrates – worms and small crustaceans for example. Most of these are opportunistic scavengers and omnivores, and these algal films will represent one of many possible items in their diet.  So a flounder is, at least in part, reformulated algae (in the same way that humans are reformulated wheat, rice and, at this time of year, turkey and chocolate).  It has been estimated that up to about a third of all the carbon fixed in estuaries comes from these biofilms, so they are the intertidal equivalent of the Tesco Local that I passed on my way from Cutty Sark station to theDeptford Discovery Centre.   

Reference

Consalvey, M., Paterson, D.M. & Underwood, J.R.C. (2004).  The ups and downs of life in a benthic biofilm: migration of benthic diatoms.  Diatom Research 19: 181-202.

Some other highlights from this week:

Wrote this whilst listening to:  The Tide is High by Blondie, obviously, plus Sufjan Steven’s Songs forChristmas and RM Hubbert and Aiden Moffat’s Ghost Stories for Christmas. 

Currently reading:Amy-Jane Beer’s The Flow, an exploration of rivers and their place in English culture.  

Cultural highlight:  Bradley Cooper’s film Maestro, about the life of Leonard Bernstein.  Not as good as Tár but asks similar questions (can a monster produce great art?)

Culinary highlight: vegetarian mezé at Bubala in Spitalfields, London, washed down by an Pfälzer orange wine.

Floundering around in Deptford Creek …

“Fieldwork” usually involves pointing the car towards the countryside and leaving all the travails of urban living behind for a day or two.  I like to stand amidst glorious scenery sucking pure air into my lungs and reflecting on how lucky I am to do the work I do.  But all that changed earlier this week.   My destination was not the Pennines or the Lake District but a muddy creek in Deptford surrounded by blocks of flats, old industrial premises and a viaduct that carried the Docklands Light Railway into the badlands of south London.  

Just out of sight on  the right of the picture at the top of the post is the low wooden building of the Creekside Discovery Centre, a charity that promotes urban wildlife.  My involvement here is part of a citizen science project that will help the staff at Creekside raise awareness of the microscopic algae that inhabit Deptford Creek.  It is co-ordinated by Susi Arnott, a filmmaker, whose film Moon, Mud and Microbes I took to Green Man in 2021 (see “Cover versions …”).   I

The visit had to be closely-calibrated to coincide with low tide, so that we had as much time as possible wallowing on the mud looking for algae.  I’m somewhat out of my comfort zone, but we soon spotted a rich chocolatey-brown patch on the mud surface that looked extremely promising.  This would have been submerged at high tide, and had probably been exposed for five or six hours by the time we visited.   I scraped off some of the growth to look at later, although we also tried a variant of the “lens tissue” method for sampling (see “Eyes wide open in Cassop’s muddy fringe …”).   My sample turned out to be full of a large sigmoid Nitzschia, cells of which glided to and fro across the field of view as I peered down my microscope.   I’m going to be circumspect about naming the species because I’m not familiar with brackish water diatoms and there are a number of possible candidates, but the genus is unmistakable.  

The patch of diatoms growing on a low shelf on the embankment at the right hand side of the image at the top of the post.

I felt more at home standing in the middle of the creek itself.   The bed here is rocky rather than muddy and the water, at low tide at least, is fresh.   There are some distinct diatom patches on some of the stones here too, and I picked some up using a toothbrush to look at later.  Again, I’m tempted to name them but, with the exception of Rhoicosphenia abbreviata (which is both distinctive and can tolerate brackish conditions), I’m reluctant to do so without having looked at cleaned frustules.   There are species of Navicula, in particular, which have similar outlines and dimensions to common freshwater species but which, on close inspection are something else altogether (see: “More diatoms that like cold weather …”).

The sigmoid Nitzschia growing on mud surfaces in Deptford Creek, November 2023.   Scale bar: 20 micrometres (= 1/50^th of a millimetre).  

More diatoms from Deptford Creek.  a. – d. Nitzschia spp.; e. Tryblionella sp.; f.g. Rhoicosphenia abbreviata; h., i. Gyrosigma; j. – o. Navicula spp.   Scale bar: 20 micrometres (= 1/50^th of a millimetre).  

There was another diatom with a sigmoid outline in this second sample.  I wish I knew what advantages this curved outline confers on an organism because this is the not the first time that I have seen two sigmoid genera, quite distantly related, living so close together.  This particular organism is Gyrosigma.  Whilst I need cleaned material to be sure of what species of Gyrosigma I’ve got, it is easier, ironically, to differentiate the genus from Pleurosigma when looking at live material because the plastids (chloroplasts) have different structures (see “Microscopic monsters in mud …”).   Pleurosigma has two or four ribbon like plastids which have a convoluted form whereas the two plastids of Gyrosigma hug the valve outline.  Despite outward appearances, these two genera belong to different families.

Both samples were dominated by diatoms that can move around, reflecting the shifting, unstable nature of the habitat within which they live.   When viewed under a microscope we see this as horizontal movement but, out on the mud of Deptford Creek, this will be in three-dimensions, including a daily “commute” from the deeper parts of the mud to the surface in phase with the tides.   We see them gliding serenely across a glass slide but the process is more like a climber ascending a tight “chimney” on a rock face – first one, then another of the diatom’s two raphes will be engaged, and sometimes both together.  Talking of commuting, the sun was starting to descend on Deptford Creek and I had a train to catch.   I emerged from the tiny oasis that the Creekside Discovery Centre nutures and joined the stream of people heading towards Deptford Station to start the journey back home.

If you are wondering why the word “floundering” appears in the title, look at the picture below.  We were walking up the creek when we noticed this fellow who seemed to have got stuck in the shallow water of the creek.   He didn’t seem too alarmed by our presence (or maybe he just didn’t have too many options for escape – flounder body language is not something I know much about), allowing me to get my camera into the water to take some pictures.   

Some other highlights from this week:

Wrote this whilst listening to:  Patti Smith’s Horses and west coast cool jazz on Chet Baker and Art Pepper’s 1956 album Playboys

Currently reading: Colm Tóbín’s Homage to Barcelona

Cultural highlight: Installation by Céline Condorelli, Artist-in-Residence at the National Gallery in London, featuring a rug whose abstract patterns were based on the patterns of pigments on pictures from the gallery’s collection viewed under a microscope.  The title Pentimenti (the corections) comes from the use of imaging technologies to discern the changes artists make during the process of composition. 

Culinary highlight: nut roast and trimmings: Sunday lunch cooked by our daughter, followed by a rather good vegan sticky toffee pudding.

Part of Pentimenti (the Corrections) by Céline Contorelli in the National Gallery, November 2023.