The Hidden World of Diatoms

A character in Rose Tremain’s latest novel, set in Victorian Britain, finds solace in his microscope:  “… it soothed Ross to think that he could find ‘wonder’ in the detritus swept from his hearth or from a sliver of matter tugged out from his eyelid”.   “The microscope,” he announced …. “reminds us that we’re born blind to the intimate secrets of everything in the world”.   

That could be the leitmotif for this blog: there are more wonders on our doorstep than most of us realise.  The question is how do bring these to the attention of a wider audience?

This week’s post is a little different.  Rather than me writing, I am going to direct you all to a short video I made last week, in which I talk to Emanuela Samaritani.   She has written a book for children, The Hidden World of Diatoms, in which she tries to capture this wonder in an accessible form.   Watch the video, then visit her website and maybe buy this book or its companion, The Hidden World of Testate Amoebae

Some other highlights from this week:

Wrote this whilst listening to:  Julian Baker’s new single, Hardline followed by Mumford and Son, the latter being the result of unexpected connections with the next item on the list: Sutton Hoo is in Suffolk, the location for the Latitude festival.  Carey Mulligan, who stars in The Dig, is married to Marcus Mumford, who we saw performing in Suffolk with Mumford and Sons at the Latitude Festival in 2017.

Cultural highlights:  The Dig, new film about the discovery of the Sutton Hoo, an Anglo-Saxon burial site in Suffolk.  Available on Netflix.

Currently reading:  Islands of Mercy, by Rose Tremain.

Culinary highlight:  Goan Fish Curry.   

Baffling Brachysira …

I should have been in the Lake District last week on a sampling trip.  It was not lockdown that stopped me but the weather.   There was rain at the weekend and the river levels went up.  I then watched the hydrographs slowly sink back but not quite to a safe level for wading before Storm Christoph blew through and the river levels went up steeply.   After two days of almost constant rain, the temperature dropped, then the rain turned to snow which is great news for me because snow on the fells means that the river levels start dropping, even if it is fiendishly cold.  As I write (Sunday) the levels are just about back to conditions that permit safe wading, albeit with air temperatures below freezing.  We should get out early next week.  Meanwhile, I am left thinking about the lakes and streams rather than actually experiencing their chilly reality.

My ruminations took me back to Ennerdale Water and along themes that I explored in a post from 2017 (“Lost in detail?”).  Once again, we are looking at the genus Brachysira in this lake but this time, rather than pick up on the identity of a single species, I want to reflect on just how many different species of Brachysira seem to inhabit the littoral habitat of one lake.  This also links with two other recent posts: The stream eats itself … and Curried diatoms?.

As was the case for the 2017 post, the slide was used in the UK/Ireland diatom ring test, which means that it was scrutinised by more analysts than just myself.  All of us, however, agreed that several species of Brachysira were present with, in one case, eight different species being recorded by a single analyst.   I’ve included illustrations of all of them and the first comment that anyone who is not familiar with diatom taxonomy will make is, almost certainly, that they don’t look particularly different from one another.   There are differences but these mostly lie just at the edge of the resolution of the light microscope.  More pertinently, those analysts who do not have light microscopes with the very highest specification will be unlikely to discern these differences.   Whereas 25 years ago, you could probably do a perfectly adequate analysis of a sample such as this with a microscope equipped with a 100x achromatic objective with a numerical objective of 1.4, now you need a plan achromatic objective with a numerical objective of 1.25 and a differential interference contrast condenser and you will still struggle to differentiate some of these species.   

Brachysira intermedia, Ennerdale Water, June 2020. Similar to B. brebissonii (pictured at the top of the post) but slightly drawn-out ends and with undulating longitudinal lines dividing the striae into two, rather than three, areolae.  Scale bar: 10 micrometres (= 1/100th of a millimetre).  Photos: Bryan Kennedy.

Several questions arise.  One is that if there is so much diversity discernible (albeit only just) with a light microscope (i.e. “semi-cryptic variation”), how much more are we missing because it is not discernible with a light microscope (“cryptic variation”)?   For some freshwater diatom genera we have been able to walk away from taxonomy’s traditional reliance on morphology and approach the problem from a different perspective.  Mostly, in this age, this different perspective comes from molecular genetics and in some cases (e.g. Fragilaria, Nitzschia, Sellaphora) it suggests that there really is variation beyond that readily discernible with light microscopes.  In others (e.g. Gomphonema) the evidence is less clear cut and it is even possible that taxonomist’s enthusiasm may have run ahead of the actuality.  Unfortunately, we don’t have any detailed molecular studies of Brachysira with which to test the ideas of species limits developed with morphological approaches.  

A second question is whether we need all this information in order to draw the ecological insights that catchment managers need in order to decide what measures, if any, are needed to keep the water body in a healthy state.   The autecological information that we have suggests that Brachysira species are mostly associated with healthy, low nutrient, circumneutral water bodies.  Where there are differences, it is primarily due to the hardness of the water rather than to the levels of human-derived pressures.   The very fact that we see several species in one lake is evidence that their preferences for these conditions, in any case, overlap.   So there is little evidence that different species of Brachysira “indicate” starkly different environments.

Brachysira microcephala (formerly B. neoexilis and, further back still, Anomoensis exilis), Ennerdale Water, June 2020. Scale bar: 10 micrometres (= 1/100th of a millimetre).  Photos: Bryan Kennedy.

As I suggested in Curried diatoms?, however, there may be some value in knowing that there are several species present but for reasons that are not associated with rather naïve associations between species and chemical measurements.  As the present generation of methods for assessing lake or river health are tied to these tired notions of indicator values there is probably not a lot of extra “signal” to be squeezed from splitting Brachysira further.  

Brachysira procera, Ennerdale Water, June 2020. Generally longer and broader than B. microcephala.  Scale bar: 10 micrometres (= 1/100th of a millimetre).  Photos: Bryan Kennedy.

Having said that water hardness plays a greater role in determining the distribution of Brachysira species than water quality, one of the oddities of this sample was that there were small numbers of two species associated with hard water (B. neglectissima and B. vitrea).  There is absolutely no limestone or any other rocks that might create hard water conditions within the Ennerdale catchment, so why are these species here?   I have found B. vitrea, especially, in small numbers in other soft water areas so these are not isolated occurrences.   Do they represent genuine viable populations hanging on at the extreme edge of their range (and, one assumes, competing for resources with physiologically “fitter” Brachysira species) or are they “noise”, carried into the catchment by wind or on the feet of mammalian vectors such as, er…, myself?   The latter has implications: firstly, it lends support to the controversial “everything is everywhere, environment selects” hypothesis (that I’ve mentioned in the past but never fully explained … I’ll do so in a post in the near future) and it also casts doubt on some of the claims of metabarcoding enthusiasts that they can extract more ecological information because the sequencing depth that is now possible exceeds that of traditional ecological analyses.  If what we hope is “signal” is, in fact, “noise”, then that depth is as likely to confuse or even mislead as it is to inform better decision making. 

Brachysira garrensis, Ennerdale Water, June 2020. Similar to B. microcephala but with denser striae (very difficult to see without very good optics).  Scale bar: 10 micrometres (= 1/100th of a millimetre).  Photos: Bryan Kennedy.

Studies of the microscopic world are only ever as good as the technology available.  But, equally important, studies of microbial diversity are also complicated by the observer’s expectations.  How different do two cells have to be before you treat them as separate species?   Not only did Hustedt not have such good microscopes as are now available when he wrote his Flora in 1930, but he also assumed that diatom species concepts were much broader than we now know to be the case.  And the final twist is that the ability of anyone to match what s/he sees with the images in the literature.  Hustedt used a single drawing to illustrate “Anomoensis exilis” (what we would now call Brachysira microcephala) in his Flora whereas Bryan Kennedy used 96 photographs, taken with differential interference contrast lighting, along with 31 scanning electron micrographs in his 2017 paper highlighting, in the process, four different morphotypes. Whether these represent different species is yet to be determined.  My point is that “seeing” depends partly on how light stimulates the optical nerve (which depends on the quality of equipment we have), but more on how that raw signal is processed by our brains.  

Brachysira neglectissima, Ennerdale Water, June 2020. Like B. garrensis, this has denser striae than B. microcephala.  Note, too, the undulating pattern of areolae.  Scale bar: 10 micrometres (= 1/100th of a millimetre).  Photos: Bryan Kennedy.

Postscript: we finally got out into the field on Monday, catching a gap in the weather when the rivers were low but the snow did not impede travel.  We had some spectacular views of snow-covered Pennines, High Street, Blencathra and Skiddaw on the way over, but the western Lakes were virtually snow free.   We even found time for a short walk around Loweswater on the way back, making the most of a rare opportunity to travel during Lockdown 3.0. 

Brachysira vitrea, Ennerdale Water, June 2020. Generally broader (>5.5 micrometres) than B. microcephala.  Scale bar: 10 micrometres (= 1/100th of a millimetre).  Photos: Bryan Kennedy.


Hustedt, F. (1930).  Susswasserflora von Mitteleuropa 10: Bacillariophyceae.  Gustav Fischer, Jena.

Kennedy, B. & Allott, N. (2017).  A review of the genus Brachysira in Ireland with the description of Brachysira prageriand Brachysira conamarae, new raphid diatoms (Bacillariophyceae) from high status waterbodies.  Phytotaxa 326: 1-27.

Some other highlights from this week:

Wrote this whilst listening to: Brandon Marsalis’ soundtrack album for the film Ma Rainey’s Black Bottom and Arvo Pärt’s Spiegel im Spiegel.

Cultural highlights:  White Tiger, new film set in India.   

Currently reading:  Still reading The Science Delusion by Rupert Sheldrake

Culinary highlight:  Homemade piccalilli pickle.   Too soon to give a definitive opinion on flavour (it needs three weeks to mature) but I’m fantasising about piling it into a thick ham sandwich already.

A winter’s tale

Inspired by Anne Jungblut’s public lecture at this year’s British Phycological Society meeting, where she talked about the algal life that thrives in Antarctica (available here), I decided that a mere thirty centimetres of snow was not going to deter me from some pond dipping at a local lake.   “I’m going out, I may be some time” I muttered to no-one in particular as I pulled on my boots, filled my pockets with energy bars, and headed into the snow-blasted waste that was County Durham.  

Fortunately, my companion on this expedition has a heritage that embraces the nationalities of both Scott and Amundsen, so I knew that I had a 100% chance of getting there and at least 50% chance of returning home. Undaunted, we made our way across snow-covered fields, through a Narnia-esque woodland and finally emerged at the edge of a Cassop Pond which was, perhaps unsurprisingly, frozen over, foiling my efforts to gain a sample by usual means.   We tracked cautiously around the margin, never quite sure where solid land was replaced by thin ice, until we found the outflow where there was an exposed channel and some dead read stems.   This would have to do as a sampling location so I dug out a sample bottle and plastic bag and pulled on a veterinarian’s disposable glove, designed to be shoved up into the warmth of a cow’s rectum but also a way of keeping your arm dry whilst sampling cold water in the middle of the winter.

A frozen Cassop Pond, January 2021.  

This was the moment, of course, when two acquaintances passed by and, recognising us, wanted to know why I was crouched beside a stream of freezing cold water wearing a bright orange veterinarian’s glove and fumbling around amongst decaying reed stems.   This, I am fairly sure, does not happen to real Polar explorers.   Amidst all the trials and tribulations of life in Antarctica, feeling a bit of a plonker is the least of your worries.

An effective way of collecting the algae off submerged plant leaves and stems is to place them in a plastic bag with a little stream or pond water and give them a vigorous shake.   This is what I did with a couple of handfuls of reed stems and the result was a brownish suspension in the bag which I poured into a sample bottle before allowing our inner Amundsen to guide us home.  Our return route passed a field of Highland cattle all of whom gazed placidly at me in a way that they almost certainly would not have done had they known that I had a veterinarian’s glove in my bag.   

Back home and warmed up, it was time to look at the murky suspension and see what it contained.  I’ve visited Cassop a lot over the years (the very first post on this blog, for example, described a visit, also in January) and had a good idea of what algae I might find.  Whether the unprepossessing substratum of dead reed leaves or the time of year or a combination, there was not quite the rich diversity I was expecting, but there were a lot of cells of Fragilaira (probably F. tenera) and a few other species too.   There were also plenty of tiny Lemna minor plants floating around at this time of year and, as my first ever post showed, these host a number of epiphytic diatoms.  

Algae and protozoa from Cassop Pond, January 2021: a. – e.: Fragilaria cf. tenera; f. Ulnaria ulna; g., h. valve and girdle views of Gomphonema acuminatum; i. possibly Tetrastrum; j. unidentified protozoan.  Scale bar: 20 micrometres (= 1/50th of a millimetre).   

This will be the first of several visits to Cassop pond this year.  Last year was the first time in several years that I did not have a regular focus for my posts (see “Reflections from Castle Eden Burn” for an overview of my 2019 explorations).  I had originally planned a series of visits to a location which, though easily reachable by car, would fall foul of the current lockdown restrictions.  Instead I’m looking at a pond that is walking distance from my house.   Maybe that is not such a problem: not everyone is lucky enough to have a National Nature Reserve on their doorstep and I have, in all honesty, not given this pond the attention it deserves over the years.

The richness of aquatic microscopic life in winter has been a recurring theme in this blog over the years but should that richness surprise us?   We approach the world of algae with mindsets that could be described as “Angiosperm Supremacists”, basing our assumptions on the entire plant kingdom on how we expect higher plants to respond.  Yet, in evolutionary terms, angiosperms are relative newcomers forced to exploit dry land because the best aquatic habitats had already been monopolised by algae.   Away from the protection that water’s high specific heat capacity offers a plant, survival in winter depends on being able to divert energy into a range of protective strategies in order to prevent damage due to freezing (see reference below).   There are algae that live in and on ice but, for most, the environment beneath the ice offers fewer challenges.  Indeed, as most of their grazers are poikilotherms, winter (all other things being equal) is not a bad time to be an alga.   


Knight, M.R. & Knight, P.H. (2012).  Low temperature perception leading to gene expression and cold tolerance in higher plants.  New Phytologist 195: 737-751.

Some other highlights from this week:

Wrote this whilst listening to: John Martyn and, in particular, a 1978 Rock Goes To College set on YouTube that I remember watching when it was first aired. []

Cultural highlights:  A great new film called Sylvie’s Love, set in jazz-era New York.

Currently reading:  The Science Delusion by Rupert Sheldrake

Culinary highlight:  Recipe from The Guardian last weekend: a chocolate and marmalade tart.

The Hidden World of Algae

The British Phycological Society meets this week at the University of Nottingham where I’m an honorary professor so, unsurprisingly, I found myself on the organising committee.   “Let’s have an exhibition of Hilda Canter-Lund photographs as part of this” I said, rashly, at an early meeting.   “Good idea” came back the reply, followed, a couple of weeks later by “there isn’t a room at Lakeside Arts that would fit our needs, but they suggested putting the exhibition on boards around Highfield Lake instead”.   That piqued our interest as Highfield Park gets a lot of visitors from the surrounding suburbs so our pictures would get a large audience.   Then came Covid 19 and, overnight, our second-best option became the only show in town.   

If you live in Nottingham, then get along to Highfield Park to look at the exhibition.  We’ve focussed on the Hilda Canter-Lund competition but Hannah Kemp, who is doing a PhD on nuisance green algae, sent some samples of the unsightly green flocs that float in the lake during the summer to Chris Carter and we’ve also been able to show people what these look like when highly magnified.   

If you don’t live in Nottingham, then don’t worry: there is also an online version of the exhibition, created by Hannah using the Artsteps platform.  Use the navigation bar at the bottom of the screen to stroll through the exhibition and enjoy the pictures without the inconvenience of the January weather.   

The display board showing the condition of the lake at Highfield Park during the summer.  The photo at the top of the post was taken by Hannah Kemp.

Under Chris’ microscope the unsightly surface scums on the lake are transformed into objects of great beauty.  Look at the image below of Spirogyra, with its characteristic helical chloroplast.   These filaments are each only about a fortieth of a millimetre across, so the casual observer has no idea of how beautiful these can be unless they have access to a microscope.   Other flocs consisted of Cladophora glomerata, a broader (though still less than a tenth of a millimetre across) branched filament.  Cladophora, unlike Spirogyra, is rough to the touch and the absence of superficial slime means that other algae, such as yellow-brown diatom cells are able to piggy-back on its filaments to absorb some sunlight.  

The green alga Spirogyra, from surface scums growing in the lake at Highfield Park, Nottingham.  Photograph: Chris Carter. 
Filaments of the green alga Cladophora glomerata from flocs in the lake at Highfield’s Park, Nottingham.  Photograph: Chris Carter.
The diatom Rhoicosphenia abbreviata growing on a filament of Cladophora glomerata, from a floc growing in the lake at Highfields Park, Nottingham.  Photograph: Chris Carter.

These unsightly flocs are becoming increasingly common around the UK and Hannah is attempting to understand why this is the case during her PhD.  The literature on this topic is surprisingly thin: many words have been devoted to understanding how shallow lakes can swing from having diverse assemblages of macrophytes to being dominated by “pea soups” of suspended phytoplankton but, somehow, the reasons why flocs of filamentous algae can develop instead of phytoplankton has not been addressed.   Like many PhD students, Hannah’s plans have been thrown off course by the pandemic but sampling is, at least, underway now, so maybe we will have some hypotheses ready over the coming months.

Some other highlights from this week:

Wrote this whilst listening to: cellist-songwriter Lucinda Chua and, for nostalgia, Sade’s Diamond Life from 1984.

Cultural highlights:  Soul, the new Pixar film and the 2017 film Phantom Thread.  You may have heard of “Chekhov’s Gun”: this film features Chekhov’s Mushroom.  That might be a spoiler.  Sorry.

Currently reading:  G.K. Chesterton’s Napoleon of Notting Hill.  For a book group.  Otherwise I would probably have given up and reached for something a little less dated.

Culinary highlight:  a Sinhalese cook-at-home meal provided by Hoppers restaurant in London (“Cash and Kari”).  A Christmas present from our daughter.