Desmids on the defensive …

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I made a short diversion back to the car after sampling at Ennerdale’s south-eastern end (see “Reflections from Ennerdale’s Far Side …”) crossing the boggy land behind the gravel spit and dipping into one of the pools to pull out a handful of submerged Sphagnum in the hope of finding some desmids, a group of algae that I have not looked at for some time (see “Swimming with desmids …” for my most recent post on this group).

Squeezing the water from a handful of Sphagnum from a bog pool into a vial and allowing the contents of this water to settle is usually a reliable way of collecting desmids; however, on this occasion the haul was rather meagre.  There were plenty of diatoms, but desmids were sparse and limited to a few Pleurotaenium and Euastrum species and some rather impressive cells of Xanthidium armatum.

The distinctive feature of the genus Xanthidium is the bristling armoury of spines around the margins.  The arrangement of spines varies between species and X. armatum has one of the most impressive collections, with bundles of three or four short spines at each angle.   The photograph below does not really capture the depth of the cell, and it is also not possible to see that there are two “decks” of marginal spines, but also bundles of spines on the top surfaces as well as at the margins.   This is truly a man-of-war amongst desmids.

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Xanthidium armatum from a boggy pool at the south east end of Ennerdale Water, January 2017.  Scale bar: 10 micrometres (= 1/100th of a millimetre).  The photographs at the top of this post show the pool from which the sample was collected.

I’m intrigued by desmids but do not claim great competence with the group, so this is a good place to advertise a field meeting organised jointly by the British Phycological Society and the Quekett Microscopical Society.   We will be using the Freshwater Biological Association beside Windermere as our base but heading out to various desmid-rich locations in the Lake District over the course of the weekend.  There will be opportunities to look at other groups of algae too, but desmids will be the main focus of our weekend.  David John of the Natural History Museum will be helping with this group, but there will be experts on other groups available too.  If you are interested in coming, let me know and I will keep you informed as the programme evolves.

A simple twist of fate …

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Amidst the dreary nothingness of the sample that prompted the previous post, I stumbled across the diatom in the photograph above.  This image gives a misleading impression as it is a relative large diatom with considerable variation in three dimensions and my first thought was that I was looking at a fragment of vaguely diatom-like structures amidst a unfocussed blur.   Careful use of the fine focus control revealed the twisted nature of the structure and I was able to create this semi-focussed image from a “stack” of images of the individual focal planes using Helicon Focus software.   The scale bar is 10 micrometres (= 1/100th of a millimetre).  As there are relatively few diatoms with a frustule with such a contorted form, it was relatively easy to identify it as Surirella spiralis Kützing 1844.

Surirella spiralis is one of a small number of diatoms whose outline is twisted.   There are diatoms that show considerable curvature within a single plane (see Stenopterobia sigmatella in “Reflections from Ennerdale’s Far Side”) but few where this curvature occurs between planes.   The only other diatom with this feature that I have written about in this blog are Entomoneis (see “A typical Geordie alga …”) and Cylindrotheca (see “Back to Druridge Bay”).   These twisted diatoms, like sigmoid diatoms such as Stenopterobia, typically have motile habits.  In my post on Stenopterobia I wondered what advantage a sigmoid outline conferred on a diatom and we really need to ask the same questions when thinking about twisted diatoms.  I have the germ of an idea, but want to think it over some more before unleashing it onto the world.

Surirella, Stenopterobia and Entomoneis are all members of an order of diatoms, the Surirellales, that are the subject of a recent paper by Elizabeth Ruck, from the University of Arkansas, and colleagues.  They compared morphology and genetic differences amongst members of this order, along with a related order, the Rhopalodiales, two of whose members are Epithemia and Rhopalodia, both of which I have also written about in this blog.   Their conclusion is that current generic limits need an extensive shake up with long-established genera that seemed to be based on sensible criteria when viewed with the light microscope split apart and reassembled, based on ultrastructural and genetic characteristcs.

The main changes relevant to a freshwater ecologist are as follows:

  • Campylodiscus: some freshwater species retained in Campylodiscus, some moved to Iconella; marine species moved to Coronia. The Fastuosae group of Surirella are now included in Campylodiscus;
  • Cymatopleura: now included in Surirella
  • Entomoneis: no change
  • Epithemia: all species now merged into Rhopalodia;
  • Rhopalodia: now includes Epithemia;
  • Stenopterobia: now included in Iconella;
  • Surirella: now limited to the Pinnatae group of Surirella, plus former Cymatopleura species;
  • The genus Iconella has been re-established for a group of former Surirella species (section Robusta) along with some freshwater Campylodiscus species and Stenopterobia. Of particular relevance to this post, Surirella spiralis is now Iconella spiralis (Kützing) Ruck & Nakov in Ruck et al. 2016; and,
  • The order Rhopalodiales has been subsumed into Suriellales.

It will be interesting to see whether or not, and how quickly, these names diffuse through the community of scientists who study diatoms.   Taxonomy has a dual nature: on the one hand, specialists are driven by a desire to understand how evolutionary forces have shaped and differentiated a group of organisms; on the other hand, taxonomists act as biology’s janitors, sorting and organising information about species so that other biologists can use this for their own purposes.   I am the editor and co-translator of a guide to European diatoms that was being finalised just as this paper was published and which, as a result, uses the “old” names.   These books often have a ten or twenty year shelf life which will prolong the use of these names, and slow the uptake of new ones.   I also know, from many years training people to analyse diatoms, that taxonomic changes, however well justified, sow confusion among beginners.   On the other hand, we are entering a new era, when molecular barcoding will be used more widely for routine identification of diatoms and, for this, a correct understanding of the phylogenetic relationships amongst a group of organisms improves the accuracy of the bioinformatics routines that assign names to the diatoms.

For most practical purposes, in other words, Surirella spiralis will remain S. spiralis for some time (and Stenopterobia sigmataella will remain S. sigmatella too), if only because of the innate conservatism of most of the people who work with diatoms.   My use of the old name in this post means that the part of my readership who know at least a little about diatoms could place the diatom within a familiar framework, even if Iconella spiralis is the correct name.   The term “post-truth” has entered our political vocabulary over recent months; in diatom taxonomy and identification, however, we sometimes have to accommodate “pre-truth” as well.

References

Ruck, E.C., Nakov, T.., Alverson, A. & Theriot, E.C. (2016).  Phylogeny, ecology, morphological evolution, and reclassification of the diatom orders Surirellales and Rhopalodiales.  Molecular Phylogenetics and Evolution 103: 155-171.

Ruck, E.C., Nakov, T.., Alverson, A. & Theriot, E.C. (2016).  Nomenclatural transfers associated with the phylogenetic reclassification of the Surirellales and Rhopalodiales.  Notulae algarum 10: 1-4.

 

When is a sample not a sample?

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If you have followed this blog over the years, you will probably have worked out that the only inevitable outcome of a close study of diatoms is that you are older at the end than you were at the start. Whether you are also wiser is, alas, not guaranteed.   The older : wiser ratio can vary quite a lot, depending on what, exactly, you are studying and a further factor to stir into the mix is that a freelance ecologist such as myself needs to be prepared to forego the pursuit of wisdom if the price is right.

And so it is that I have spent a fair part of my time since Christmas staring down my microscope at a batch of samples that I have been sent whilst, at the same time, cursing my pecuniary instincts.   These samples are one part of a large survey and, I know, are not collected by people with any experience of freshwater algae.  Judging by the muddy sludge that I get in some of the sample tubes, I am not wholly sure that all can be trusted to distinguish a stream from a field, let alone find stones likely to yield a representative crop of diatoms.   But when, I wondered, after an hour hunting around a slide for fragments of diatoms to identify, do I throw up my hands and say “enough”?

The two photographs in this post are from one of these irksome slides.  In both cases, there is a single diatom but, also, quite a lot of mineral matter.   I would expect maybe five to ten diatoms in a field of view on a well-prepared slide from a good sample,.  In this one, there were more fields of view without diatoms than there were with (typically, I had to scroll past two empty fields between each identifiable diatom, but there could be as many as four or five empty fields between diatoms).   In theory, my first action when confronted with a slide such as this is to make another, more concentrated slide but this will also concentrate all that mineral matter.

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A field of view with a single valve of Achnanthidium minutissimum (top right) from a sample from an unnamed stream.   The image at the top of the post shows a different field view, this time with a single valve of Cocconeis euglypta.  Note the large quantity of inorganic matter in the sample.

Here then, are a few questions to ask when you encounter a very sparse slide.

  • Who collected the sample? Do you trust them or not?   A lot of samples these days are collected by people who have little understanding of the ecology of benthic algae and who will not know when a sample is unlikely to yield enough diatoms for analysis;
  • Is there a lot of particulate matter that has resisted oxidation during the preparation stages? These might be telling you something about the habitat itself: mineral particles suggest a depositional, rather than an erosional, habitat.  Some organic materials, particularly from peaty habitats, are also resistant, and can obscure diatoms, unless a dilute preparation is made;
  • What is the state of the diatoms that are present on the slide? If a large proportion are broken, this may suggest that there was not a viable community of algae at the time the sample was collected and you are, in fact, counting diatoms that have been washed in from elsewhere in the catchment;
  • Do the diatoms that you do find in a sample tell a consistent story? Sometimes the diatoms I find in a sparse sample have ecological profiles which, when combined, suggests a particular interpretation but, on other occasions, I see samples that are both very sparse and very diverse, with species representative of several different environments.  When the ecological profiles are not broadly consistent then, again, it is a warning that you may be dealing with washed-in diatoms and fragments, and not an assemblage that is telling you much about the site in question.

I believe that you should be able to count at least 100 valves and have answered the second, third and fourth questions after no more than an hour’s analysis.  This is a good point at which to decide whether it is worth pushing on to complete the analysis or abandon the count.   I try to make this clear in my terms and conditions, emphasising that it takes about as long to decide that a sample cannot be analysed as it does to perform an analysis on a “normal” sample.   I should also emphasise that these suggestions apply to samples from rivers and lake littoral zones and different criteria may need to be applied when dealing with other types of samples (e.g. for palaeoecological or forensic work).

The judgements that you need to make are easier if you have direct knowledge of the site from which the sample was collected; however, this is often not possible.   As “streamcraft” is undervalued by managers (see “Primed for the unexpected” for my most recent moan on this topic), the natural habitat of the diatom analyst is the laboratory not the field and sample collection is often delegated to less-highly trained individuals.   The determination of my fellow analysts to wring every last mote of knowledge from empty silica frustules has also contributed to a greater focus on the laboratory, rather than the field.   Most of the time, to be fair, sample quality is not a factor.  We produced some PowerPoint presentations a few years ago to help people collect diatom samples (see “A cautionary tale…” for the whole story) and, let’s be honest, collecting a decent diatom sample should not be rocket science.   The question underlying all of these is whether or not the diatoms you have on a slide are an accurate representation of the assemblage of living diatoms present at a particular point in space and time.   If you cannot say “yes” with confidence, then you will certainly be older, but no-one will be any wiser.

Reflections from Ennerdale’s Far Side …

ennerdale_far_end_170105

Ennerdale Water is, as I have described in earlier posts, is a lake of two halves, with a south eastern end influenced by granite and the north western end by softer mudstones and sandstones.  That has a big effect on the algae that we find in the littoral zone, with Cyanobacteria (blue-green algae) abundant in the south-east end and Chlorophyta (green algae) more conspicuous at the other end.   Diatoms are conspicuous in the littoral zone all around the lake, although there are some differences in the types of species encountered.  That is a story for another day, but I did find one species in some of the samples I collected from the south-eastern end that point to one other influence on the ecology of Ennerdale’s littoral zone.

Look at the photograph at the start of this post.  It was taken as I walked up to the south-eastern end (circa NY 127 140) and shows the view up the lake, with Angler’s Crag visible on the left hand shore in the distance.   The River Liza enters the lake on the right hand side (just out of the frame) and the low lying area between the River Liza and the raised ground where I was standing is an area of wet heath with a range of Sphagnum species and several boggy pools.   The shoreline of the lake itself is formed by a shingle spit which acts as a barrier between the wet heath and the lake itself.

ennerdale_gravel_bar_170105

The shingle spit separating the wet heath at the south-east end of Ennerdale from the lake itself.   Photographed in January 2017.

Several of the diatoms that I found at this end of the lake were species that I associate with acid conditions although, curiously, the limited chemical data that we have does not show a lower pH here than elsewhere in the lake.   I suspect that the proximity to the acid Sphagnum heath may lead to occasional pulses of acid water entering this area and exerting a subtle effect on the attached algae before being diluted by the water of the lake as a whole.   Of the species that I found, the most intriguing was Stenopterobia sigmatella, a long, sigmoid diatom with a single plate-like chloroplast.

The genus Stenopterobia fulfils most of my criteria for a genuinely rare diatom (see “A “red list” of endangered British diatoms”).   I only have 11 records in my dataset of 6500 samples, and in only one case did Stenopterobia constitute more than one percent of the diatoms in the sample.   These samples are all from acid habitats (mean pH: 6.1), with low nutrient concentrations (never more than 2 mg L-1 reactive phosphorus).  Those for which we have location information are plotted below.   The record in East Anglia needs further investigation (meaning: “I don’t believe it … but I haven’t had a chance to track down the slide for a closer look”). If we ignore this, the distribution is confined to mountainous regions of western Britain, and these Ennerdale samples also fit this trend, although the lake has soft water and is circumneutral rather than acid.

Stenopterobia sigmatella is another diatom with a sigmoid outline, and this brings me back to a question that I have posed before (see “Nitzschia and a friend …”): what advantages does a sigmoid outline confer on a diatom?  I cannot think of any other genera of algae that has species with a sigmoid outline, which only adds to the mystery. All of the diatoms that are sigmoid are motile, so I guess that the explanation may be linked to movement, but I don’t know for sure what the reason may be.   For all of the rich diversity that we see in diatoms, there is still, to pick up on a phrase from my biography of Humboldt, a “poverty of meaning” …

stenopterobia_sigmatella_en

Stenopterobia cf sigmatella from Ennerdale Water, October 2016 and January 2017.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

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A distribution map of records of Stenopterobia in Great Britain.   S. curvula is a synonym for S. sigmatella (see taxonomic note below).  Map prepared by Susannah Collings (see “Why do you look for the living among the dead?” for more details of how this was done)

stenopterobia_densestriata_

A valve of Stenopterobia densestriata.  Photograph from the ADIAC database (photographer: Micha Bayer).  Scale bar: 10 micrometres (= 1/100th of a millimetre).

Taxonomic note

I have used the name “Stenopterobia sigmatella” in this post, but this still needs confirmation as there is a closely-related species, S. densestriata (Hustedt) Krammer 1987 (see image above).  S. sigmatella has < 24 striae in 10 micrometres whilst S. densestriata has > 26 striae in 10 micrometres.  S. densestriata also has slightly smaller overall dimensions.

David Mann made the following comment about Stenopterobia sigmatella on the website Common Freshwater Diatoms of Britain and Ireland (predecessor to the new Diatom Flora of Britain and Ireland: “A nomenclatural mess. For most of the 20th century, this species was referred to (wrongly) as S. intermedia. Ross (in Hartley, 1986) stated that there is an earlier name, sigmatella, that could be applied to this species and made a new combination S. sigmatella. Unfortunately, this was wholly ignored by Krammer (in Lange-Bertalot & Krammer, 1987; and see Krammer & Lange-Bertalot, 1988) who made the new combination S. curvula. However, Nitzschia curvula of W. Smith is preceded by N. sigmatella of Gregory (1856, 1854, respectively).”   The references can all be found on the Common Freshwater Diatoms website.

 

Not so Bleak Midwinter?

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Occasionally – just occasionally – the gods smile on us when we least expect it.  And Wednesday was one of those days: fieldwork on a glorious winter day in the Lake District without a cloud in the sky and barely a breath of wind.  The pleasure of being outside on such a day was offset slightly by the necessity of plunging my arm into freezing cold water at intervals, but the views of the mountains beyond Ennerdale Water more than compensated for these temporary discomforts.

The coldness of the water, today, offers me a link to a book I am reading, about the 19th century German scientist Alexander von Humboldt, a polymath who was ahead of his time in many ways, and whose writing pre-empted ecological thinking of the twentieth century.   One of his strongly held beliefs was that scientists could not really understand nature from a laboratory: they had to be outside, experiencing nature first hand.   That seems to be a fine New Year message in a world where ecologists seem to spend more and more time staring at screens, and their managers are increasingly reluctant to let them spend time in the field.

The ecology of lakes and rivers in this area in winter continues to fascinate me.   Look at the picture below: a stream bed at the coldest time of year that is covered with lush growths of algae in a range of hues, most strikingly the pink-red of the Rhodophyta Audouinella, complemented by the green and blue-green algae around it.  The first young olive-green filaments shoots of Lemanea, another Rhodophyta, were also apparent at a couple of the sites that I visited, and there were thick brown diatom blooms smothering many of the stones too.   These are all thriving at a time of year when either most nature has shut down for the winter or most natural historians have plonked themselves onto the sofa to watch Living World II rather than challenging the first clause in this sentence.  You decide.

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A riot of colour on the stony substrata of the River Ehen, a few kilometres downstream of Ennerdale Water, Cumbria, January 2017. 

One of Humboldt’s big concerns was that scientists saw the big picture (“naturgemälde”) rather than getting bogged down with details.   He was someone whose mind had been formed by the Enlightenment, when the necessity of cataloguing and classifying the diversity of nature was a primary concern.  However, he saw that this was not enough, and that one had to understand the connections between these different life forms, and between each of these and their environment.  He saw the natural world as a web of interdependencies, and humans as potential disruptors of the delicate balances that existed.

The problem we have in the modern age is balancing the need to see the big picture in focus without losing site of important details.  Or, as Ed Tipping said during a meeting at CEH last year: “we stick to the principle of simplifying to just short of the point of naivety”.   He had his tongue in his cheek but there is an important point here: the complexity of the natural world means that its secrets will only be yielded to those scientists who can keep their natural proclivity to get lost in detail in check.   At the same time, if we forget that those details are out there we may reach erroneous conclusions.  And, I fear, microscopic benthic algae may be ecology’s Sirens, sitting on submerged rocks and luring the unsuspecting into a world of taxonomic detail that is too rarely accompanied by profound ecological insight.

William Wordsworth, born in Cockermouth, just a few miles away from Ennerdale, was one of Humboldt’s readers.  He recognised the need to be outside experiencing nature applied as much to a poet as to a scientist and reacting against the dry, dissected knowledge that the Enlightenment encouraged.  His words offer a succinct conclusion for this first post of 2017, and encapsulate my resolution to be as holistic as possible in my thinking during the year ahead:

For was it meant
That we should pore, and dwindle as we pore,
For every dimly pore on things minute,
On solitary objects, still beheld
In disconnection dead and spiritless,
And still dividing and dividing still
Break down all grandeur …

William Wordsworth, The Excursion, 1814

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