Remembering John Carter

I wondered, as I re-read the previous post, what my late mentor and friend John Carter would have called the diatom I was writing about.   When I first started looking seriously at diatoms in the early 1990s, there was no-one in my laboratory in Durham with any experience from whom I could learn, and Brian Whitton suggested I went up to visit John at his home near Hawick, in the Scottish Borders.   I rung to arrange a date and, a couple of weeks later, made the two hour drive up through Northumberland and across the border to his house in the small village of Denholm.   Stepping into John’s study was like stepping back in time fifty years: it was dark and dusty, with piles of books and file boxes lining the walls and stacked on tables, along with boxes of microscope slides.  In the fireplace there was some of the equipment that he used to digest his diatom samples – apparatus that really belonged in a laboratory fume cupboard.   And, on a narrow desk against one wall, an old brass microscope equipped with a tilting mirror rather than its own light source.

John_Carter

John Carter in his study at Denholm, in Scotland.  An uncredited photograph from his obituary in Diatom Research

We spent the day in this study, John peering down his microscope and calling out the names of the diatoms he saw along with a commentary on the diatomists he had known (Hustedt, I remember him telling me, was a member of the Nazi party, which made it difficult for him to re-integrate with the scientific community after the war).  I perched on a chair beside him taking notes and occasionally squinting down the microscope to see for myself what he was describing.  I often, too, got a pithy assessment of the state of the slides that I had brought with me.   After a couple of hours of this, we would be summoned by his wife into the dining room for a hearty casserole, and while we ate they would quiz me about my children and talk about their years in the Borders.

Later, back in Durham, I would go back through the slides and try to reconcile my notes with what I could see under the laboratory’s much more modern microscope, ever marvelling at just how much detail John had been able to see with his old equipment.   It was a steep learning curve but, after half a dozen visits to John, it all began to make sense, and I gradually gained the confidence I needed to identify diatoms on my own.   Not long after that we had a telephone call in the laboratory to say that John Carter had died.  I felt that a door onto an older, more civilised, way of doing science had closed.

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First record of Platessa bahlsii in the UK?

I have spent the past two or three weeks looking at diatoms from an almost unique perspective.   Rather than trying to name them by looking down a microscope and observing their physical properties, I have been looking at their barcodes (see “When a picture is worth a thousand base pairs …”).   We have over 100 different known diatoms in a “library” of barcodes, each of which has been grown in the laboratory, named from photographs and then had its DNA extracted and sequenced.  However, we also, now, have results from some mixed samples collected from rivers and analysed by a new approach called “Next Generation Sequencing”.   The challenge is trying to match the sequences found in the field samples with the diatom species that they match.  Sometimes there is clear agreement, but in some cases I had to go back to my microscope slides to check the names of things that should, in theory, have matched something in our library.

The diatom in the illustration below is one such example of a “near miss”, which made me scratch my head and have another look.   As it did not appear to match any of the illustrations in my books, I also sent photographs off to a colleague, Luc Ector, in Luxembourg.  He pointed me towards some pictures in a recent paper from the USA, leading to a provisional identification of Platessa bahlsii Potapova 2012.

   Image

 

Platessa cf bahlsii Potapova 2012 from the River Teise at Caddingford, Kent (TQ 691 488), 29 September 2011.

Though I call this a “new record” I am fairly sure that I have seen it before and suspect that it is probably easy to misidentify.  These diatoms are less than 10 micrometres (1/100th of a millimetre) long and, mostly, occur in relatively small numbers only sporadically, so this is the taxonomic equivalent of a “perfect storm”.   It is only in the relatively rare instances when a larger population is encountered along with good facilities and enough time that it is possible to track down the true identity.  

Indeed, is Platessa bahlsii the “true identity” of this organism?  Here we stray into deep water.   P. bahlsii was first described from the USA and there is a vigorous debate on the extent to which diatoms are cosmopolitan or have restricted geographical distributions.   Another problem is that the genus Platessa is, itself, only 10 years old and not everyone would agree with the decision to create this genus.  A colleague once pointed out that whilst a species is a rigorous and objective biological concept, all higher levels of taxonomy are, to some extent, negotiable.   Twenty years ago, this species would have been placed in the genus Achnanthes.   Since then, freshwater species of Achnanthes have been split into ten separate genera, two of which have quietly fallen out of favour already.  Looking at the results from our barcode study, I suspect that another shake-up may be necessary before we reach a classification of this group of diatoms that is biologically realistic.   That will mean more names changing and more confusion in the meantime. Hey ho …

More about mosses

In 1795, the explorer Mungo Park set off from what we now know as The Gambia to try to discover the course of the River Niger.   He describes his many adventures vividly in Travels into the Interior of Africa including, at one point, being robbed of absolutely everything he possessed, including his clothes.   He sat, naked, in the bush, and contemplated his situation.  “Whichever way I turned,” he wrote, “nothing appeared but danger and difficulty.  I saw myself in the midst of a vast wilderness in the depth of the rainy season, naked and alone; surrounded by savage animals, and men still more savage.”    Then, he wrote an extraordinary passage: “At this moment, painful as my recollections were, the extraordinary beauty of a small moss in fructification, irresistibly caught my eye. I mention this to show from what trifling circumstances the mind will sometimes derive consolation; for though the whole plant was not larger than the top of one of my fingers, I could not contemplate the delicate conformation of its roots, leaves, and capsula, without admiration.   Can that Being (thought I) who planted, watered, and brought to perfection, in this obscure part of the world, a thing which appears of so small importance, look with unconcern upon the situation and sufferings of creatures formed after His own image? – surely not!”

I was thinking of this passage this afternoon, as I walked passed a wall and noticed several hemispherical cushions of a moss, Grimmia pulvinata.  This is one of the more distinctive of the mosses of wall-tops.    Just as for Bryum capillare (“Wonders in my own backyard …”), the leaves gradually taper to long, fine hair-points, creating the fine, downy “cloud” around the cushion .  If you look closely, you’ll also see the capsules, which contain the spores, buried inside the cushion, although it will rise above the cushion later on.  Mosses such as these are easy to overlook but, when you adjust your focus and pay attention to them, you can start to appreciate their beauty, and understand Park’s rhapsody.

Grimmia_pulvinata

Cushions of Grimmia pulvinata on a wall-top in Durham, March 2014.   Both cushions are about two centimetres across.

Incidentally, Mungo Park was wrong in one respect, as mosses do not have roots.  It is an easy mistake to make when sitting naked in the bush.  Most modern bryologists work fully clothed, which has the additional advantage of providing pockets for storing specimens, notebooks, hand lenses and cameras.   This, actually, raises an interesting question: the moss that Park observed, a species of Fissidens, is now in the herbarium of the Natural History Museum in London (registration number: BM000871833).   How on earth did he get it back?  

The meaning of … nothing

I had to dig out some old papers today as background reading for a report I am writing.  In the process, I came across one by Horst Lange-Bertalot written in 1979 which implied that, with a knowledge of the ecological requirements of 50 – 100 species of diatom, the condition of almost any river in Europe could be assessed.   About a decade later, Frank Round made a similar assertion, going on to suggest that, for a group of organisms to be useful as environmental indicators “… the species should be easily identifiable (modern floras must be available), quantifiable (preferably without time consuming labour and preferably by workers who can be trained to perform the analyses without the need for detailed knowledge of the biology of the organisms”.

How times change.  Both Lange-Bertalot and Round played a major role in the paradigm shift that has overwhelmed diatom taxonomy over the past three decades.   My own view is that Round’s statement is broadly correct, as I have tried to illustrate in earlier posts (“Lago di Maggiore under the microscope”, “Subsidiarity in action”, “’Speed dating’ with diatoms”).  Many of my colleagues around Europe would contest this, and a veritable flood of books and papers describing new species has pushed the process of accurate identification of diatom species out of the reach of the generalist biologists Round was envisaging, to highly-specialised individuals with very expensive microscopes.

However, here is a problem: assume that the community of European diatom analysts is a finite resource, and that effort is disproportionately directed towards taxonomy.  Something else has to sacrificed, doesn’t it?   To test this idea, I scanned the abstract booklet for the most recent International Diatom Symposium and made a rough classification of the subject matter for the oral presentations.  49 papers dealt with freshwater diatoms.  Of these, 20 (41%) were concerned with taxonomy and a further 26% dealt with the spatial or temporal distribution of diatoms with no reference to other groups of organisms.   Only two papers dealt with physiology and none at all with functional ecology.   Lots of people are interested in the microscopic structure of the diatom cell wall yet almost no-one seems to care about the role that these actually play in freshwater ecosystems.

So we have two problems: the first is that the use of diatoms for ecological assessment has got much more complicated than when Lange-Bertalot and Round were writing their pioneer papers.   This has pushed the work into the realm of “experts” who take longer (and cost more) whilst, at the same time, producing outputs that are harder for lay people to digest.  The second problem is that the work on which this is based is barely, now, connected to the ecosystem functioning that we claim to want to preserve.   Diatomists, it seems, may end up knowing the shape of everything yet the meaning of nothing.

References

Lange-Bertalot, H. (1979).  Pollution tolerance of diatoms as a criterion of water quality estimation.  Nova Hedwigia 64: 285-304.

Round, F.E. (1991).  Use of diatoms for monitoring rivers.  pp. 25-32.  In: Whitton, B.A., Rott, E. & Friedrich, G. (editors) Use of Algae for Monitoring Rivers.  E. Rott, Institut für Botanik, Universität Innsbruck, Austria.

 

Wonders in my own backyard …

One of my many half-worked out and not-fully-proven theories is that the golden age of Victorian microscopy coincided with an era when many educated British men were heading off to the colonies and sending back reports of weird and wonderful flora and fauna that they encountered.   The microscope was, for those left behind, a similar portal into hitherto unexplored worlds; one that, furthermore, could be found without leaving your own grounds.

A case in point: here is a photograph of some moss on my driveway.  I have walked past these mosses thousands of times without giving it a second thought.   Today, however, I have a point to prove.   The second photograph is a close up of the same moss, taken with the extreme macro lens on my new Olympus TG2 compact camera.   This reveals the colonies to consist of tongue-shaped leaves, each terminating in a long hair-like projection.   My somewhat dated guide to mosses tells me that these are plants of Bryum capillare.   Even at barely a millimetre across, these leaves are enormous compared to the algae I normally write about here.

Bowburn_driveway_mosses

A row of bright green colonies of Bryum capillare beside my driveway in County Durham, with a lens cap (five cm across) as an indication of scale.

The next step is to strip a few of the leaves off the plants using a pair of forceps and blade and mount these in a drop of water to examine under my high power microscope.   Ironically, the lowest magnification lens I have on this microscope (10x) is too powerful and I cannot get all the leaf into a single image, but we can see the hair point as an extension of the “nerve” that extends the length of the leaf.   Just visible, too, are the long, narrow cells which form a border around the leaf edge.  The cells, themselves, are just a single cell thick, each parallelogram-shaped, about 50 micrometres long and containing a number of small chloroplasts.

I wrote about the tops of boulders being like miniature deserts last year (“Upper Teesdale In March”) and the same applies to man-made habitats such as paths and driveways.  The cushion-like growth forms contains networks of tiny spaces which turn the whole plant into a miniature sponge, soaking up and retaining water, enabling it to continue to grow long after the ground around it has dried up.   In the past, I presume, mosses such as Bryum capillare would have been rare but, with our modifications to the landscape, including building walls and driveways, we have greatly expanded the habitat available to this species.   As a result, our sedentary Victorian naturalist had just as many opportunities to explore deserts as Richard Burton, Charles Montagu Doughty and Wilfred Thesiger.

Tortula_muralis_140302

Bryum capillare.  The left hand image is taken with a macro lens; the right hand image was taken under a microscope; the scale bar is 100 micrometres (1/10th of a millimetre).   The hair is roughly double the length of the portion included in the image.