An excuse for a crab sandwich, really …

My curiosity about the habits of Navicula bottnica led me to the fishing village of Staithes, on the North Yorkshire coast, at the weekend, in search of a sample from the location I visited in 2012 (see “More diatoms that like cold weather …”).   Staithes, the birthplace of local hero, Captain Cook, also has the added attraction of a pub in the harbour that sells wonderful crab sandwiches.


Staithes: left, a view of the village from the south and, right, sampling Staithes Beck.

I collected my samples in 2012 from a set of stepping stones across Staithes Beck, which flows through the village.   At low tide, the stream here is virtually freshwater, but the diatoms that live on the stones have to be adapted to higher salinities when the tide is high.   Even through the brown films looked identical to those that I see in rivers far from the sea (see “The ecology of cold days”), many of the diatoms are different.   I did, however, see a number of cells of Navicula gregaria gliding around.   The most abundant diatom was, however, larger than these and a subtly different shape to Navicula lanceolata, which tends to dominate these habitats in freshwaters. At very high magnification, I could just make out the dense radiate striae that characterise N. bottnica.

But no mucilage tubes.   The Navicula cells were gliding around unencumbered by any such superstructures.   They clearly have not read the literature: Andrej Witkowski’s Diatom Flora of Marine Coasts describes it as “probably cosmopolitan” (another way of saying “I don’t know where it isn’t found”), then “… tube dwelling species distributed along the coasts of the cooler seas of the northern hemisphere, more common in the brackish waters of the Baltic Sea.”   I do often find diatoms that are described as “tube dwelling” that are free-living. I suspect that this is because I mostly look at habitats where a tube would be an impediment rather than an advantage. On these submerged stones, for example, I suspect that being able to constantly adjust their position relative to the light is more important than the benefits conferred by the relatively-static tube.   On the other hand, Eileen Cox noted that tube-dwelling diatoms preferred hard to soft substrata in the Severn Estuary.


Navicula cf bottnica collected from upper surfaces of stones in the tidal section of Staithes Beck, Staithes, North Yorkshire, March 2015. The right hand view is a girdle view of a recently divided cell.   Scale bar: 10 micrometres (=1/100th of a millimetre).

In case you have not seen a tube-dwelling diatom before, I have included a couple of Chris Carter’s photos of Encyonema (caespitosum?).   The ability to form tubes seems to have evolved in several genera, although not necessarily in all representatives of a genus and not necessarily all the time. I have written about the tube-dwelling diatom Berkeleya rutilans (see “Diatoms from Pangong Tso”) and tubes are also common in the genus Frustulia as well as in several marine and intertidal genera.

Why produce tubes?   I have never read any detailed accounts of the pros and cons of tube-formation, though I imagine that the mucilage must offer some protection against desiccation, high light and grazers and I have also heard speculation that the mucilage might act as a substrate for some extracellular enzymes.   As I have grumbled before, diatomists are generally more interested in the minutiae of the silica frustule than the Meaning of Life.


Two photos of Encyonema (caespitosum?) growing in mucilage tubes.   Both by Chris Carter.


Cox, E.J. (1977). The distribution of tube-dwelling diatom species in the Severn Estuary.   Journal of the Marine Biological Association of the UK 57: 19-27.

Witkowski A. (2000). Diatom Flora of Marine Coasts I.   Iconographica Diatomologica: Annotated Diatom Monographs (edited by H. Lange-Bertalot).   Koeltz Scientific Books, Koenigstein.

John Walter Guerrier Lund (1912-2015)

I was sorry to hear that John Lund died a few days ago.   I first encountered him in a second year undergraduate lecture on succession, when his pioneering work on seasonality in lake phytoplankton was used as an example.   He was appointed to the Freshwater Biological Association in 1944 and produced a series of important papers on the ecology of the phytoplankton based on his observations in Windermere and nearby lakes over the next decades.   I also remember a paper he wrote for the now sadly defunct journal Field Studies, which demonstrated a broader interest in the natural history of freshwater algae. And, in 1996, along with his wife, he published a marvellous book, Algae: their Microscopic World Explored.   She provided the pictures, he wrote the text, drawing on his extensive experience of all algal groups.   You can find more details of his life at the Fritsch Collection website.

Others will write full obituaries in due course. I only met John on a few occasions but the last visit was very memorable.   I was searching for a freshwater Chrysophyte called Phaeodermatium, a relative of Hydrurus foetidus (see “A brief excursion to Norway”).   In their book, John Lund had explained that it thrives in the colder months of the year and usually disappears in summer.   He also commented that it was found in the stream that flowed through his garden.   As it happened, I was going to a meeting in Windermere at about this time and I thought that I could take this opportunity to visit John Lund and collect a sample from his garden.   I called ahead, arranged a time to visit and, at the appointed time, my colleague who had driven me over from Durham dropped me off at his old slate cottage, Ellerbeck, on the north side of Ambleside.   My colleague was going to wait in Ambleside for half an hour or so until I joined him with my sample.

John, at this time, was in his late 90s, physically frail and almost blind, though his mind was still sharp and he was as courteous as ever.   He not only welcomed me to his house but also announced that he would join me on the excursion through his extensive garden to find the alga.   We made our way very slowly along the paths towards the stream, talking about mutual acquaintances.   At one point he stopped, lifted his head and asked me: “are we close to the Magnolia tree?”   I said that we were.  Then, rather wistfully, “it’s very beautiful at this time of year isn’t it?”   And then we moved on again towards the stream.   I was due to be at a meeting in the very near future and took advantage of John’s lack of sight to discretely text my colleague to tell him to go on without me.

We reached the stream eventually, and I stepped in to collect my samples. He had mentioned that Phaeodermatium formed crusts on rocks and stones that could become so thick that the rocks were slippery to walk on. The rocks were certainly slippery but, when I looked at my haul under my microscope a day or two later, the sample was dominated by Diatoma mesodon not Phaeodermatium. We then made the slow journey back through the garden to his house, where I said goodbye and walked into Ambleside where, in the absence of any local taxis, I had to wait for the next bus to Windermere, eventually arriving at my meeting about an hour after it had started.

His house, Ellerbeck, incidentally, gave its name to the monotypic diatom genus Ellerbeckia.   John Lund was married to Hilda Canter-Lund, in whose memory the Hilda Canter-Lund photography prize was established (see “Hilda Canter-Lund photography award 2013 winner”.


Canter-Lund, H. & Lund, J.W.G. (1995). Freshwater Algae: Their Microscopic World Explored. Biopress, Bristol.

Lund, J.W.G. (1961). The algae of the Malham Tarn district. Field Studies 1: 85-115.

Anselm Kiefer and the art of algae …

My quest for algae in fine art took an unexpected turn at the weekend when I visited the Anselm Kiefer show at Tullie House Museum and Art Gallery in Carlisle.   I have already written about Kiefer following my visit to the major retrospective at the Royal Academy last year (see “The fine art of asking big questions”).   The Tullie House show is much smaller but amongst the exhibits was one vitrine (display cabinet) that immediately caught my eye.

The vitrine contained six clay casts of internal body parts (including heart, spleen and kidney) each covered in gold leaf, along with a frond of dried seaweed.   All the objects are arranged on a lead-covered board; lead is a recurring theme in Kiefer’s work, as he regards it as the only material heavy enough to carry the weight of human history.

Clay casts of internal body parts invokes Biblical metaphors of creation (Isaiah 64: 8: “… We are the clay, you are the potter; we are all the work of your hand.”), reflecting Kiefer’s long standing interest in identity.   Covering rough clay casts with gold leaf echoes mankind’s own exalted view of its place in the world.

But what of the alga? It is a brown alga (Phaeophyta), possibly Undaria pinnatifida (Juliet Brodie of the Natural History Museum suggested this, based on the photograph below). Placed alongside casts of human organs, it evokes a spine and rib cage.   More symbolically, perhaps, we see a juxtaposition of a very early form of life with the highest (in our anthropocentric view).   Kiefer has a long-standing interest in alchemical symbolism, imagery that suggests change and progress.   He has chosen objects here whose symbolism resonates with one another to create a larger story.   I could be pedantic and point out that brown algae and humans represent two distinct branches of the tree of life but perhaps I should just accept this as a visual metaphor for a deeper truth and move on.  Stand in front of any of Kiefer’s art and you find yourself asking questions that go far beyond the nature of the materials that he uses.


Anselm Kiefer’s Untitled (1988): a vitrine containing six gold-plated clay objects along with a frond of dried seaweed, on display at Tullie House, Carlisle, March 2015.


Royal Academy of Arts (2014) Anselm Kiefer. Exhibition Catalogue, Royal Academy of Arts, London.

Is algal gloop on the increase?

This post summarises a series of emails that piqued my interest last week.   The first was from Paul Brazier of Natural Resources Wales, asking for information about terrestrial algae. Behind the query lay a concern amongst some bryologists that the quantities of gelatinous algae in some habitats in the west of Britain was increasing and threatening rare mosses and liverworts found in these places.   He quoted bryophyte expert Nick Hodgetts who has recorded less of the rare moss Sematophyllum (Hageniella) micens who had also noted that the sites where he once found it now have a great deal of algal slime.   Other experts had confirmed this trend, and expressed concerns that it was out-competing small oceanic mosses and liverworts. Des Callaghan, another bryophyte specialist noted that a “gelatinous gloop” (which turned out to be the green alga Gloeocystis polydermatica) had overwhelmed the rare liverwort Lejeunea patens at Glen Trool in Galloway, south-west Scotland.

Des also gave me the photograph below, showing the gelatinous algae Coccomyxa confluens on Betula pubescens, competing for space with the neighbouring oceanic liverwort Scapania gracilis. He commented that at this site (Gallwyd, near Dolgellau, in North Wales), the algae is most abundant in the most humid locations, notably in the mist zone of the main waterfall. It appears that, at least here, it is a normal part of the flora and isn’t so abundant that it is something to worry about. At other sites, though, these terrestrial gelatinous species can be much more abundant.


Coccomyxa confluens growing on Betula pubescens at Gallwyd, near Dolgellau, Wales (photo: Des Callaghan)

The other photograph Des sent shows another green alga, Klebsormidium growing on heather (Calluna vulgaris) at Wybunbury Moss in Cheshire. I described Klebsormidium in one of my posts about the River Ehen (see “The River Ehen in November”) noting how it was often found in habitats that were not fully submerged although I had not previously seen it competing for epiphytes on terrestrial plants, as Des’ image shows.   Des directed me to some circumstantial evidence that Klebsormidium may benefit from high N-deposition.

Interestingly, Glen Trool, mentioned above, is close to Round Loch of Glenhead, the subject of intensive studies on the causes and consequences of acid deposition by Rick Battarbee and colleagues at University College London.   These studies have shown a gradual recovery from the worst effects of acid deposition since the 1980s but the decline in sulphur-containing compounds has been more significant than the decline in nitrogen-containing compounds. They suggested that one result is that Galloway lochs such as Round Loch of Glenhead may, as a result, be slightly more nitrate-rich now than in the far past. Until very recently, the effects of this extra nitrogen was masked by the generally negative consequences of the acidity but now the sulphur deposition has reduced, it is possible that the algae are able to benefit from this nitrogen and thrive at the expense of other plants.   Whether the same may hold true for the terrestrial and semi-terrestrial vegetation in the surrounding woods must remain speculation for a little longer but it may help to explain why bryologists are seeing more algae at locations where they hoped to find rare bryophytes.


The green alga Klebsormidium growing on Calluna vulgaris (heather) at Wybunbury Moss, Cheshire, March 2015 (photo: Des Callaghan).


Battarbee, R.W., Simpson, G., Shilland, E., Flower, R.W., Kreiser, A., Hong, Y. & Clarke, Gina (2012). Recovery of UK lakes from acidification: an assessment using combined palaeoecological and contemporary diatom assemblage data. Ecological Indicators 37: 1-16.

I also discuss the ecology of Round Loch of Glenhead in:

Kelly, M. (2012). The semiotics of slime: visual representation of phytobenthos as an aid to understanding ecological status.   Freshwater Reviews 5: 105-119.

Eclipsed … in Luxembourg City

You cannot fail to love a country whose Ministry of the Environment is to be found in Avenue du Rock’n’Roll. Nor can you fail to love a country where a mid-morning amble brings you upon a crowd of a hundred or so people staring through lens and visibly excited.   This blog is, after all, all about the wonders that you see when you stare through a lens.


Avenue du Rock’N’Roll, Esch–sur-Alzette, Luxembourg.

I’m in Luxembourg. I arrived yesterday for a meeting and today I had some time before my flight to explore the delights of Luxembourg City. The hundred or so people that I encountered were in the courtyard of the Musée National d’Histoire Naturelle and they were looking at the solar eclipse.   It was telescopes, not microscopes, that were the source of the excitement. There is something embedded deep in our natures, I guess, that makes the enormous so much more fascinating than the tiny, even though the minuscule, un-noticed bugs that fill our planet have far greater – and mostly beneficial – effects on us than you could imagine if you subsist on a diet of television natural history programmes.


Left: eclipse spotters in Luxembourg City, 20 March 2015; right: the eclipse, observed through a pinhole camera.

Perhaps we should see Brian Cox and Dara O’Brien as the latest in a long line of sun priests that extend right back to the Ancient Egyptians, and probably long before.   The Egyptians did not need high-powered science to work out that the sun was the origin of all life on our planet. Science, perhaps, only adds to this sense of wonder.   Pause for a moment before you next marvel at astronomical wonders: were it not for the sun and that wonderful molecule chlorophyll, we would all be no more than a bottle of carbonated mineral water.

The biblical King David got it. He sat on dark hillsides and contemplated the night sky and Psalm 19 is his response to what he saw (“The heavens declare the glory of God, the sky proclaims the work of his hands …”). If this is what a man writes staring up at the cosmos with his naked eyes writes, what would he have written, had he had a telescope?   And what would he have written if he had been able to stare down a microscope, too? Forty percent of all primary production on earth, plus all of the decomposition and nutrient recycling that bacteria and fungi provide, not to mention the creation of the oxygen-rich atmosphere that enabled life on earth to flourish in so many extraordinary ways?   That, surely, deserves a psalm.

Two posts in a day? Sorry about that. It will not happen again for some time, I promise.

More diatoms that like cold weather …

One of the benefits of studying diatoms is that we can produce permanent slides from our samples, which means that we can go back at any time to have another look at samples we collected in the past.   As I was writing my previous post, I recalled some other brown films that I had seen in a tidal section of a river and it did not take long to find the slide and put it under my microscope again.

The sample comes from Staithes Beck, a short stream that flows into the North Sea at the old fishing village of Staithes, on the edge of the North York Moors in Yorkshire.   I had visited this stream in February 2012 as part of a project and had wondered about the composition of the films. I did not have time to look at them in their fresh state but, instead, viewed them a month or so later when the slides were prepared. Some of the diatoms that I wrote about in The Ecology of Cold Days were here, obviously able to cope with the more saline conditions less than a kilometre from the mouth of the stream.   However, the most abundant diatom was a species that I had never encountered in freshwaters: Navicula bottnica.   It has the same symmetrical boat-shaped outline as Navicula lanceolata but the arrangement of the striae – the lines on the frustule – were very different. In N. bottnica these were both denser and much more strongly radiate, especially towards the centre.   On the other hand, apart from the difference in salinity, it seemed to have a very similar habitat – forming distinctive brown films on the tops of submerged stones in fast-flowing sections of the river in the winter and early Spring.

I did find one reference on the internet to Navicula bottnica living in mucilage-tubes, which is intriguing and makes me wish that I had checked this myself in the Staithes community.   I have found that most of the species described as living in tubes are also often found free-living too. The study that recorded N. bottnica in tubes was on the physiology of diatoms in intertidal zones on rocky shores whereas my communities in Staithes Beck were permanently submerged. I suspect that a rocky shore presents a rather more severe challenge to diatoms, with periodic exposure to the air and higher levels of radiation. This would mean that a form of extracellular protection would confer some protection to the diatoms that, perhaps, is not needed in a permanently submerged community.


Navicula bottnica from Staithes Beck, Staithes, February 2012.


Ginnever, N.E. (2014). The photophysiology of rocky intertidal microphytobenthic biofilms.   PhD thesis, University of Cardiff, Cardiff.

A typical Geordie alga …

If the photograph below looks vaguely familiar it may be because you are old enough to remember the 1970s as this scene of the Ouseburn valley in Newcastle is part of the opening sequence of Whatever Happened To The Likely Lads? Were they to revisit now, Terry would be appalled, but proto-bourgeois Bob delighted, to see the first stages of gentrification creeping through the area.


Lime Street, Ouseburn valley, Newcastle, March 2015, looking upstream towards Jesmond Dene. The entrance to Seven Stories, the National Centre for Children’s Books, is just visible on the right of the picture.

Follow the road off to the right and you pass the Cluny, a pub with a good range of real ale and a strong reputation as a live music venue, then past a warehouse (now converted to artist’s studios) to an old ford across the Ouseburn. I wrote about the Ouseburn back in October, when I made my annual visit with a group of undergraduates but the section I have brought you to today is close to the point where the stream joins the Tyne, and is tidal. I had seen some interesting growths of diatoms here in the past so had come back at low tide to add a brackish dimension to the story I was telling in The Ecology of Cold Days.

I was looking for the chocolaty-brown film on the tops of rocks, similar to those that I described in my earlier post but these were not obvious today. Instead, I found some intriguing diatom growths on the vertical wall of the old warehouse just above the water level. I scraped up some of this film and took it home for a closer look.

These samples were, as I expected, teeming with diatoms, though the assortment of diatoms that I could see was quite different to those I had seen before.   I have written about estuarine diatoms in a couple of posts (see “In the shadow of the Venerable Bede”) but do not pretend to any great expertise. However, most of the genera are familiar to me from freshwaters, even if I cannot name the species.   I could see Navicula and Nitzschia, both common in the river samples that I wrote about in The Ecology of Cold Days; however, the most abundant genera were a species of Surirella (also common in freshwaters) and, in particular, Entomoneis; a genus that is relatively rare in freshwater (see “The Really Rare Diatom Show“).


The view down the Ouseburn; the former warehouse (now artist studios) is on the right foreground; beyond is the back of Seven Stories.   The right hand image shows the diatom film just above the waterline on the side of the warehouse.

Entomoneis is a diatom whose structure is difficult to capture in a photograph as the cells are twisted around the apical axis (see Chris Carter’s photographs in The Really Rare Diatom Show). The right hand image below is an empty frustule lying in girdle view; the other four images are live cells. The constant motility of the living cells was an additional complication as I was trying to photograph them.

Common features about all these biofilms that I’ve written about over the past year is that they are dominated by diatoms that are capable of movement and they seem to be especially luxuriant in the cooler times of the year.   Being able to adjust their position is, obviously, an advantage in an unstable environment where there is a chance that particles will shift or new ones be deposited, robbing the cell of the light it needs for photosynthesis.   Luxuriance in the winter and early spring may reflect the absence of grazers at these times of the year, but there are also hints in the literature that some algae are particularly well adapted to growing at low temperatures. It is natural selection in action: having a physiology that functions in cold water lessens the chances of the fruits of their photosynthesis being turned into another organism’s roughage.

Entomoneis’ fondness for the cold extends far beyond north-east England: a recent paper recorded it as the most abundant alga growing on the underside of sea ice in the Antarctic. It is, in other words, a typical Geordie alga, swaggering through the Ouseburn’s biofilms dressed in a tee-shirt, regardless of the weather. Terry would have approved.


Entomoneis sp. from the tidal section of the Ouseburn, March 2015.   The right hand image is an empty frustule.   Scale bar: 10 micrometres (= 100th of a millimetre).


Archer, S.D., Leakey, R.J.G., Burkill, P.H., Sleigh, M.A. & Appleby, C.J. (1996). Microbial ecology of sea ice at a coastal Antarctic site: community composition, biomass and temporal change. Marine Ecology Progress Series 135: 179-195.

Freshwater algae on the menu … again

The return of Masterchef to our screens at the same time that Lemanea is at its most abundant in our streams is too much of a coincidence for me.   I have already written about my culinary experiments with the red alga Lemanea (which is eaten in parts of northeast India) and have been wondering for some time how best to use it in British cooking (see “Trout with sorrel, watercress and … algae”).   This year, I followed my instincts, in the wake of my experiments with Welshman’s Caviar after the Green Man festival last summer (see “Gastronomy in the Welsh hills”) and found that it can really enhance the flavour of scrambled eggs.

This is how to do it: collect a few handfuls of young Lemanea from a stream.   It is only common in streams that are relatively unpolluted, though it is tolerant of heavy metal pollution, so it pays to avoid areas where you know there is a history of mining. Wash the filaments in cold water to remove any particles, shake it dry and then spread it out on a plate and leave it at room temperature overnight to dry.   Chop it roughly so that the fragments are about a centimetre in length. Finally, make your scrambled eggs in the usual way, but stir a generous handful of the dried Lemanea filaments into the mixture just as it starts to thicken. Cook whilst stirring for a couple of minutes, then serve on buttered toast.   The algae gives the scrambled eggs a nice, fishy flavour without overwhelming the dish.


Scrambled eggs with Lemanea.

By coincidence, I also found myself eating algae later in the day. I watched a small bowl filled with a tangle of narrow bright green strips trundled past on the conveyor belt whilst I was having a quick pre-cinema meal in YO! Sushi in Newcastle.   This was Kaiso salad, made from seaweed (Undaria, I think) marinated with sesame.   It looked too good to resist. Algae on the menu twice in one day … if I’m not careful, you’ll be thinking I’m obsessed …


Kaiso salad at YO! Sushi

Replaced by a robot?

The two research projects that occupy most of my time at the moment could not be more different except that the motivation in each case is to make applied ecologists more efficient.   The first of these, RAPPER (see “Ecological assessment in the fast lane …”) is old-school natural history, which involves ecologists standing in streams and making observations that can give an insight into stream condition almost straight away (especially if you have a field microscope).   The second is exploring the prospects for using molecular barcodes (see “When a picture is worth a thousand base pairs …”).   Someone still needs to stand in a stream to collect a sample but that is where the similarity ends. I have been collecting samples for molecular barcode analysis for about a year now but I have been sending my samples to the laboratories of the Food and Environment Research Agency at Sand Hutton in York for analysis.

Two pieces of equipment in FERA’s laboratories emphasise the difference between the ecology with which I am familiar and the Brave New World.   The first is the BioRobot that is performs the DNA extractions although it is a disappointment to anyone who expects their robots to resemble R2D2.   The second is the Illumina MiSeq next generation sequencing machine which is the heart of the operation, producing the sequences from the genes that we use as barcodes.   We have been able to deduce the sequence of DNA bases in genes since the 1970s; however, it was a slow and laborious process. When I was doing my PhD, harassed-looking molecular biology students used to stalk the corridors holding the gels that they used to laboriously construct the DNA sequences, base by base.   The Illumina MiSeq produces more sequences in an afternoon than they produced for their entire thesis.   And, with the automation that the BioRobot brings to the process, the economics shift to such an extent that producing these sequences could well be faster and cheaper than paying myself and others to count diatoms under the microscope.


DNA preparation and sequencing equipment at FERA’s laboratories in York. Left: the BioRobot used for DNA extraction; right: the Illumina MiSeq next generation sequencing machine.

But the day after I visited FERA I was back in the River Ehen (see “A winter wonderland in the River Ehen”).   I’ve sent several samples from here off to be sequenced as part of our present project, and am waiting to see what they reveal, particularly as my colleagues and I have struggled to name all of the diatoms using our traditional microscopic approach.   This visit to the Ehen, however, threw up a surprise in the shape of an alga that had appeared at a site where we had not previously seen it.   And here is the challenge: the nature of molecular biology is that you need very specific “primers” – molecules that can target precisely the gene of interest.   It means that molecular biology is very good for finding what you are looking for, but not so good at noticing the unexpected.   That, to me, raises the biggest challenge of the work that we are doing at the moment: how can we couple the undoubted potential of next generation sequencing to the observational skills that field biologists hone over the course of their careers (see “Slow science and streamcraft …”)?

More enormous diatoms

Follow the north-east coast about 40 kilometres south from Seaham (see “Tripping over diatoms”) and you arrive at Saltburn, home to Andrew McKeown’s other diatom sculpture, once again on a clifftop, overlooking the North Sea.   This sculpture, Organism, is of a chain of the marine diatom Amphitetras.   Like Jewels of the Sea, it is made from cast iron, though this time it has a bronze patina. At two metres tall, I suspect that this may be the world’s the largest depiction of a diatom, though you are welcome to prove me wrong.


Andrew McKeown: Organism, 2007, 200 x 120 cm, cast iron with bronze patina, Saltburn