Eye to the microscope … _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 _Chamaesiphon_ does 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 _Chamaesiphon_ creates 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. ### Share this: * Click to share on X (Opens in new window) X * Click to share on Facebook (Opens in new window) Facebook * Like Loading... ### _Related_

Love this blog; here's a beautiful mix of detailed observation and conceptual digression #SciComm #algae #dataviz #MartynKelly #LifeOnEarth
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Living rocks, gently rolling … A trope in film noir where the protagonist is seduced by a femme fatale which came to mind when I was in Ambleside earlier in June. There were signs of a surface cyanobacterial scum in Windermere when we were sampling with our students (similar to the one described in the addendum to “A hitchiker’s guide to phytoplankton …”), feeding into broader concerns about the state of England’s largest lake. Yet, a day later, I was being wooed by cyanobacteria in a very different habitat, just a few kilometres from the side of Windermere. One minute, I’m the hard-boiled algal detective, trying to make sense of a problematic situation. The next, I’m running off with a Manic Pixie Dream Alga. Followers of the blog are shouting at their computer screens: “don’t do it, Martyn, they’re cyanobacteria …. they’re baaaad”. “They’re not bad”, I reply, “just misunderstood. They need to be given another chance …”. And off I go again, chasing my latest cyanobacterial seductress … This latest tryst happened at an abandoned quarry at Whitbarrow, on the narrow belt of limestone that runs along the southern edge of the Lake District. I’ve had flings here before (the most recent is described in “Cyanobacteria inside their comfort zones …”) but on my latest trip, my eye was caught by some small pebbles on the bed of a seepage. These were not just any old pebbles, there was a distinct brownish film on their upper surfaces that suggested that there was a microbial community here and observation under the microscope revealed this to be Cyanobacteria, probably _Rivularia_ or, possibly, _Calothrix_. **Oncoids on the bed of a seepage at Whitbarrow Quarry, Cumbria, June 2025. The photograph at the top of the post shows the limestone cliffs at the edge of the quarry.** The story of oncoids goes something like this: “Teesdale’s unseen natural history …” explained how Cyanobacteria such as _Rivularia_ formed hemispherical colonies and the previous post (“A garden of sub-visual lifeforms …”) commented on how these colonies led to the precipitation of calcite (described more fully in Allan Pentecost’s publication listed below). The _Rivularia_ colonies that I described from Upper Teesdale are, in other words, miniature freshwater stromatolites. If this process continued indefinitely, these tiny hemispheres would grow into substantial structures such as those seen in Shark Bay, Western Australia. But Upper Teesdale is a very different place to the sheltered environment of Shark Bay, and periodic storms disrupt this process of stromatolite formation and the largest we see there are rarely more than a centimetre across. Now imagine a situation where there is some periodic but gentle disturbance, such that the colony is turned over but not washed away completely. The Cyanobacteria continue to grow but the light is now on the other side so the original hemispherical colony starts to become spherical. But then it is turned again, perhaps showing a different face and the process is repeated. As the colony grows, so the innermost parts of filaments are starved of light and die off, leaving behind the calcite deposited around them. Repeat these cycles over decades or even centuries and the original hemisphere, a few millimetres in diameter, becomes a round object a centimetre or more across, with a solid core and just a thin layer of actively growing filaments on the outside. It is these that we refer to as “oncoids” or “oncolites”. Think of them as mini-stromatolites, “living fossils”, if you will, that connects us with the pre-Cambrian world when Cyanobacteria ruled the world and, through their photosynthesis, created the oxygen-rich atmosphere that allowed life as we know it to evolve. That’s why I can never resist the flirtations of an attractive Cyanobacterium. **_Rivularia_ filaments from the surface of an oncoid from Whitbarrow Quarry, June 2025. Scale bar: 20 micrometres (= 1/50th of a millimetre). ** The problem with making Cyanobacteria the pantomime villains of campaigns for better water quality is that the essential roles that Cyanobacteria play (and played) in ecosystems is overlooked. I would go as far as to say that Cyanobacteria are routinely “othered” in the way that migrants are in other political contexts, as a means of distilling complex environmental problems into simplistic political messages. Cyanobacteria do what evolution has made them extremely capable of doing only because we, and the governance systems within which we function, create conditions where they can flourish. In the process (and, again, just like migrants), their positive contributions are downplayed. I dream of a day when, instead of this demonisation, the rare sighting of a Cyanobacterium such as _Anabaena_ can be celebrated, and the beauty of these ancient organisms fully appreciated. **Reference** Pentecost, A. (1981). The tufa deposits of the Malham District, North Yorkshire. Field Studies 5: 365-387. Some other highlights from last week: **Wrote this while listening to:** Alanis Morisette’s set at Glastonbury **Currently reading:** Tony Parson’s _Man and Boy_. **Cultural highlight:**_The Anatomy of Painting_ , Jenny Saville’s show at the National Portrait Gallery. **Culinary highlight:** Tasting menu at _Bamboo Mat_ , a restaurant serving Nikkei – a fusion between Japanese and Peruvian cuisines. Sharp, clean flavours, ideal for a hot summer’s evening. Enjoyable stroll back to the station through the Olympic Park, albeit set to a soundtrack of Iron Maiden playing at the nearby London Stadium. ### Share this: * Click to share on X (Opens in new window) X * Click to share on Facebook (Opens in new window) Facebook * Like Loading... ### _Related_

Lovely blog from #MartynKelly #cyanobacteria #algaedon microscopesandmonsters.wordpress.com/2025/07/01/living-rocks-...

A garden of sub-visual life-forms … _We are inclined to overlook the very small that dwell among us; yet, without them we ourselves could not exist; for every one of us is a Garden of sub-visual life forms … Think of them as God’s tiniest angels, doing His unfathomable work in their own way, for these creatures, too, reside in the Eternal Mind, and shine in the Eternal Light, and form part of the polymorphic symphony of Creation._ Margaret Atwood, _The Year of the Flood_ , 2009 I was reading Margaret Atwood’s dystopian _novel The Year of the Flood_ as I finished this painting, and her quotation seemed apposite to the message that I was trying to put across: that Cyanobacteria, far from being a “nuisance”, are one more part of the “polymorphic symphony of Creation”. To push the symphonic metaphor just a little further, Cyanobacteria would provide the dominant themes of the first, second and third movements, and those discords we hear towards the end of the fourth movement are due to the arrival of humans, not malfeasance on the part of Cyanobacteria. The painting follows on from “Teesdale’s unseen natural history …” back in May, but I had to work through several versions before I was satisfied. In the picture, you can see the hemispherical colonies of _Rivularia biasolettiana_ overgrown (on this occasion) by filaments of _Spirogyra_. Inside the _Rivularia_ colonies you can see crystal of calcite, produced as the uptake of carbon dioxide by the cells disrupts the delicate chemical balance of the water flowing over Teesdale’s sugar limestone, leading to the precipitation of calcium carbonate. The _Rivularia_ filaments, each enclosed in a sheath, have a heterocyst, for nitrogen fixation, at the base, and narrow to a terminal hair, which plays a role in acquiring phosphorus from the environment. I should have included some diatoms (_Encyonopsis, Fragilaria, Ulnaria_) but this was a complication too far. The presence of _Spirogyra_ overgrowing the Rivularia surprised me, but may have been the result of the warm spring we had this year (how I wish I could have discussed this with Brian!). **_Rivularia_ colony, pastel on paper. 2007/2008. ** One problem, when thinking about _Rivularia_ , is that Cyanobacteria are now the provenance of the scientist rather than the natural historian – a slightly different situation to a hundred years ago when microscopy was a popular hobby of the middle classes. We live in a democratic, rather than a technocratic world and therefore we should not spend money because a scientist tells us to, but because there is a consensus that a particular course of action will fulfil a broader ambition of society at large. How, then, can scientists bring the unique properties of a Cyanobacterium into the popular conversation? I ended “Teesdale’s unseen natural history …” musing on 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”, and wondering how this applies to the microscopic world. The sad truth is that the microscopic world is unknown to the vast majority of people, so Baba Dioum’s expression quickly becomes strained when applied to any organism that cannot be seen with the naked eye. Yet Margaret Atwood, through “Adam One”, the leader of God’s Gardeners, an ecologically-aware religious sect, does a good job. Her novel, written in 2009, anticipates the broadening sense that human health is dependent upon a healthy microbiome. Maybe the success of Tim Spector and others at communicating the importance of a healthy gut microbiome should be our starting point? Healthy rivers, too, are dependent upon bacteria and other microbes and organisms such as _Rivularia_ tell a story of how __ these contribute to ecosystem functioning rather than just branding all Cyanobacteria as “nuisance alga”. Cyanobacteria, as I have explained elsewhere (see “As old as the hills …”) have been here much longer than we have. They do what 350 billion years of natural selection have made them extremely efficient at doing and it is humans, who by disrupting nature’s balance, are the nuisances, not them. **Footnote:** Margaret Atwood’s phrase “God’s tiniest angels” reminded me of a line in the poem _Making a Living_ by Anne Sexton, where she refers to plankton as “God’s littlest lightbulbs”, a reference to the capability of some for luminescence. Some other highlights from last week: **Wrote this while listening to:** _The Civil Wars_ , because the music in _The Ballard of Wallis Island_ (see below) reminded me of this (and the two members of _The Civil Wars_ also went their own separate ways too soon). **Currently reading:** Margaret Atwood’s _The Year of the Flood_ **Cultural highlight:** The very wonderful _The Ballard of Wallis Island_ , my film of the year so far. A low budget story about an eccentric millionaire trying to reunite his favourite folk band for a concert. For me, Sian Clifford’s understated performance was the highlight, but the whole film (along with the soundtrack) is unmissable. **Culinary highlight:** Zefarelli’s vegetarian Italian restaurant in Ambleside, for the course meal at the end of the 2025 FBA Algae Identification Course. ### Share this: * Click to share on X (Opens in new window) X * Click to share on Facebook (Opens in new window) Facebook * Like Loading... ### _Related_

On holiday but sharing latest blog from #MartynKelly #Slimewatch
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