Shuffling the pack

Microcystis-Ladybower_CCarter

The next group of algae I’m going to consider in my review of higher taxonomy and systematics, the Cyanobacteria, or “blue-green algae”, present some significant challenges.  Not least of these is a shift over the past forty years from being classified according to the rules of botanical nomenclature to being classified according to the International Code of Nomenclature of Bacteria.  The former assumed species could be defined from field material on the basis of morphology, with “type specimens” preserved in herbaria; the latter uses axenic (i.e. pure) cultures as the basic taxonomic unit, and allows a wider range of attributes than just morphology.   In recent years, as those who follow this blog will know, properties such as gene sequences have also been used to define species although the Code of Botanical (now Biological) Nomenclature still requires a description of the any new species that are described, with an expectation that the morphology will take a prominent role in that description.  As this post will show, morphology is no longer such a reliable indication of how Cyanobacteria are organised as it was in the past.

For practical purposes, many Cyanobacteria fall into the same size range as other algae, live in communities that include many protist groups and can be identified using similar techniques as would be employed to identify other algae.  They also have a form of photosynthesis that produces oxygen as an exhaust gas, in contrast to other bacteria which are capable of photosynthesis. This means that a default view of the Cyanobacteria as “algae” is a reasonable starting point for a field ecologist.   However, at an intercellular scale, the Cyanobacteria are very different to other algae, and we should never lose sight of the fact that they actually belong to a different Domain to other algae.

The problems are clear when I compare the morphology-based classification that I used when I first taught classes on algae in 1990 with the classifications that are accepted now.  Then, Cyanobacteria were divided into three or four orders, typically:

  • Chroococcales – single cells or cells loosely-bound into irregular gelatinous colonies
  • Oscillatoriales – filamentous forms lacking heterocysts
  • Nostocales – filamentous forms with heterocysts

The high-level classification, in other words, was based solely on whether or not the organism formed filaments and, if so, whether or not it possessed heterocysts (specialised cells responsible for nitrogen fixation).  This made logical sense when your primary source of insight is morphology.  Unfortunately, more recent studies have shown that it bears little relationship to the genetic relationships amongst the organisms that have been revealed over the past thirty years or so.   A more recent organisation is given in the diagram below.

First, note that this shows subclasses, rather than orders, within the class “Cyanophyceae” (the only class in the division Cyanophyta).   There is rarely unanimity amongst experts on the appropriate organisation of high-level classifications so just bear with me on this one.   Of the four sub-classes, one, Nostocophycidae, contains a single order (Nostocales) which includes all the heterocyst-bearing forms.  No change there.   However, the other two classes diverge very much from the older classifications in that they both contain a mixture of filamentous and non-filamentous forms.

Cyanobacteria_subclasses

The organisation of the Cyanobacteria (blue-green algae) division into four sub-classes.  Filled boxes indicates the classes that are represented in UK and Irish freshwaters.   Organisation follows Algaebase.   The image at the top of this post shows a Microcystis bloom at Ladybower Reservoir (photo: Chris Carter)

The Oscillatoriophycidae is a good example, with five sub-classes, four of which are represented in the UK and Ireland.  Two of these have featured in several posts (see Appendix) so you can see for yourself just how different they are in appearance.  The Oscillatoriales includes filamentous forms without heterocysts whilst the Chrococcales has taxa that either exist as single cells or in masses loosely-bound within gelatinous colonies.    A similar situation exists within the Synechococcophycidae; indeed, some genera that would formerly have been considered to be relatives of taxa within Oscillatoriales (e.g. Schizothrix and Heteroleibiana) are now included in families in this group.   There is, however, still more work to be done to unravel all the relationships within this sub-class.   The current understanding is that there is a single order (“Synechococcales”) but a great number of families.  Similarly, all the heterocystous forms are grouped into a single order, the Nostocales, within the Nostocophycidae, also divided into a large number of families.

Oscillatoriophycidae_orders

Organisation of the Oscillatoriophycidae showing the orders that include genera found in UK and Irish freshwaters.  

I always stress that taxonomy and identification are two distinct crafts: the taxonomist calls on a wide range of tools to find natural groupings of species at different levels whilst an ecologist only needs a parsimonious route to an unambiguous identification.  For the purposes of identification, recognising whether an organism is filamentous or not is a logical early step, even though both options will contain representatives of both Oscillatoriophycidae and Synecchococcophycidae.   We need to recognise that some of the characteristics that contribute to our taxonomic understanding (gene sequences, arrangement of thylakoids) are useless from the point of view of someone trying to name an organism encountered in a field sample but, at the same time, the taxonomist’s standpoint will not necessarily capture all of the features that explain how an organism contributes to energy and nutrient flow within ecosystems.

Calothrix-stagnalis_CCarter

Calothrix stagnalis: a member of the Nostocales.  Note the heterocysts at the base of the filaments (photo: Chris Carter)

References

Mai, T., Johansen, J.R., Pietrasiak, N., Bohunciká, M. & Martin, M.P. (2018).  Revision of the Synechococcales (Cyanobacteria) through recognition of four families including Oculatellaceae fam. nov. and Trichocoleraceae fam. nov. and six new genera containing 14 species.  Phytotaxa 365: 1-59.

Palinska, K.A. & Surosz, W. (2014).  Taxonomy of cyanobacteria: a contribution to consensus approach.  Hydrobiologia 740: 1-11.

Appendix

Links to posts describing representatives of the major groups of Cyanobacteria found in freshwaters.  Only the most recent posts are included, but these should contain links to older posts (you can also use the WordPress search engine to find older posts).

Group Link
Synechococcophycidae  
Synechococcales Chamaesiphon: A bigger splash

Heteroleibleinia: River Ehen … again

Oscillatoriophycidae  
Chrococcales Aphanothece: No excuse for not swimming …

Gloeocapsa: The mysteries of Clapham Junction …

Oscillatoriales Microcoleus: How to make an ecosystem

Oscillatoria: Transitory phenomena …

Phormidium: In which the spirit of Jeremy Clarkson is evoked …

Pleurocapsales Watch this space …
Spirulinales Watch this space …
Nostocophycidae  
Nostocales Nostoc: How to make an ecosystem (2)

Rivularia: Both sides now

Scytonema, Stigonema, Tolypothrix: Tales from the splash zone

   

Some other highlights from this week:

Wrote this whilst listening to: Leonard Cohen’s posthumous album Thanks for the Dance.   And, as I used it to name a post, Joni Mitchell’s Both Sides Now.

Cultural highlights:  David Hockney: Drawing from Life at the National Portrait Gallery.   Great examination of the importance of drawing and observation to artistic practice.   By coincidence, another post I’ve cited is named after one of Hockney’s paintings

Currently reading: Robin Wall Kimmerer: Gathering Moss (Oregon State University Press).  A collection of essays on the natural and cultural history of mosses.

Culinary highlight: dinner at The Sichuan on City Road in London.

Hockney_drawings

Rhapsody in red

Audouinella_Oxbow_Dec19

On an overcast winter day with just a sprinkling of snow on the fells the Lake District can appear very monochrome.  Look closely at the bed of some rivers, however, and you are confronted by a much more vibrant palette with browns, greens and reds vying for your attention.  Somehow, paradoxically, the stream algae are at their most prolific and vigorous when the rest of Cumbria’s biological diversity has hunkered down to wait for the onset of Spring.

One of the most conspicuous groups at this time of the year are the red algae.  The green algae, diatoms and cyanobacteria are there all year round, even if winter is the time when they are most abundant.  The red algae, however, are barely evident – and certainly not to the naked eye – during the summer months.   It is only when autumn is well underway that the first blushes of pinkish red appear on the stones lining the beds of rivers.   This is in contrast to the red seaweeds which can be found on our coasts all year round, and indeed, to the many red algae that inhabit warm tropical seas.  What is so different about red algae in streams that leads them to favour the colder periods of the year?   What is it about streams, too, as I rarely see red algae in lakes (Batrachospermum is the exception: see “More algae from Shetland lochs”)?

This post will not answer those questions, but will give a quick overview of the red algae we find in freshwaters, in the manner of an earlier post about green algae (see “The big pictures …”).   The table below shows the systematics of the red algae, following a molecular phylogeny study by Hwan Su Yoon and colleagues from 2006.   There are two sub-phyla, of which one, Cyanidophytina, has no representatives recorded from the UK or Ireland.   There are just eight species in this group of primitive red algae, associated mostly with extreme environments.

The other subphylum, by contrast, has over 7000 species, divided between six classes, but 94 per cent of these are marine.   There are just thirteen genera of red algae recorded from freshwaters in the UK and Ireland, but spread amongst five of these six classes.   This seems to suggest that an ability to thrive in freshwaters has evolved several times during the evolution of this group.

Rhodophyta_classes

The organisation of the red algae (Rhodophyta) showing division into two subphyla and seven classes.  Pink fill indicates the classes that are represented in UK and Irish freshwaters.   Organisation follows Algaebase and Yoon et al. (2006).    The photo at the top of this post shows Audouinella hermainii in the River Ehen, Cumbria, in December 2019.

Of the five classes that do have freshwater representatives, well over half of the genera and species recorded from the UK and Ireland are found in the Floridiophyceae.   This class has over 6900 species (95% of all red algae) split between 34 orders, of which five contain genera found in UK and Irish freshwaters.   Of these, the Batrachospermales, one of the few red algal orders that is exclusively freshwater, contains five genera and eleven species, whilst the other four contain just one genus each.

The Batrachospermales contain two morphologically-distinct groups of genera: Batrachospermum, Sheathia and Sirodotia form one of these, whilst Lemanea and Paralemanea form the other (see links below for more details and images).   Whilst we have molecular evidence that suggests that the Batrachospermales are a natural group, it is hard to point to a single characteristic that helps someone more interested in identification than taxonomy.   In fact, it is the life-cycle that is most distinctive (“… diplohaplontic … heteromorphic and contains a reduced tetrasporophyte”) but few of us are as well-schooled in algal life-cycles now as our predecessors were (see “Reflections from the Trailing Edge of Science”).   A hundred years ago, we would have had to rely upon the same limited set of morphological characters for both identification and taxonomy; now the taxonomist’s toolkit has expanded considerably whilst identification is still mostly reliant on features we can see with the naked eye or a light microscope.  For the red algae, this is still mostly enough to answer questions about what species we have found but unravelling the logic behind a classification may need a broader perspective.

Florideophyceae_orders

Organisation of the Florideophycae showing the orders that include genera found in UK and Irish freshwaters.  

 

References

Entwisle, T.J., Vis, M.L., Chiasson, W.B., Necchi, O. & Sherwood, A.R. (2009).  Systematics of the Batrachospermales (Rhodophyta) – a synthesis.   Journal of Phycology 45: 704-715.

Yoon, H.S., Müller, K.M., Sheath, R.G., Ott, F.D. & Bhattacharya, D. (2006).  Defining the major lineages of red algae (Rhodophyta).  Journal of Phycology 42: 482-492.

van den Hoek, C., Mann, D.G. & Jahns, H.M. (1995).  Algae: an Introduction to Phycology.  Cambridge University Press, Cambridge.

 

And some other cultural highlights from the week:

Wrote this whilst listening to: Dave’s Psychodrama,

Cultural highlights:  Dave’s performance of Black (from Psychodrama) at the Brits Award Show.  I would not normally have watched this but was stuck in a hotel room with no wifi reception and was totally blown away by the power of his performance.

Currently reading: Bill Bryson’s The Body

Culinary highlight: I’m trying to cook one meal each month using only UK-sourced ingredients, in order to help me focus on seasonal cycles.  My February effort was a beer and cheese fondue: very easy to cook, using beer from about 500 metres from my house (Durham Brewery’s Evensong) and a mixture of Cheddar and Lancashire cheeses from Durham Indoor Market.

 

Appendix

Links to posts describing representatives of the major groups of red algae found in freshwaters.  Only the most recent posts are included, but these should contain links to older posts (you can also use the WordPress search engine to find older posts).

Group Link
Bangiophyceae Watch this space …
Bangiophyceae Watch this space …
Compsopogonophyceae Watch this space …
Florideophyceae  
Achrochaetiales Something else we forgot to remember
Balbianiales The Hilda Canter-Lund prize
Batrachospermales Lemanea: The complicated life of simple plants

Batrachospermum: More algae from Shetland lochs

Hildenbrandiales More about red algae
Thoreales Watch this space
Porphyridiophyceae Watch this space …
Stylonematophyceae More pleasures in my own backyard

My name is Legion …

I promised to write a little more about Gomphonema subclavatum, one of the diatoms we encountered in the previous post.   I picked this one out for more attention because it is one of many diatoms that have changed names in recent years and it is sometimes interesting to scratch around to understand why this has happened.

Had I seen this particular species fifteen years ago I would have called it Gomphonema clavatum without hesitation.  Although G. subclavatum was recognised as a distinct species back in the nineteenth century, for most of the twentieth century it was treated as a variety of G. longiceps, which Krammer and Lange-Bertalot then subsumed into G. clavatum.  If you look at their plate of G. clavatum, you will see a huge range of sizes and shapes so it is perhaps no surprise that people subsequently realised that there was more than one species lurking under this name.

Gomphonema subclavatum from Cregduff spring, Co. Mayo, Ireland, September 2017.  Photographs: Bryan Kennedy.  Scale bar: 10 micrometres ( = 100th of a millimetre).

When this happens, taxonomists ask which of the various contenders was the Gomphonema clavatum seen by the person who originally described the species.  This involves going back to the museum collection where that person deposited the material that they examined and taking another look.  This process of “typification” helps determine which of the forms is the rightful inheritor of the name.   Erwin Reichardt decided to have a go at this process for G. clavatum and went to examine the samples, now in the Museum für Naturkunde in Berlin, on which Christian Gottfreid Ehrenberg had based his original description.  However, he could find nothing that resembled G. clavatum, with the closest match being G. olivaceum.

I’m reading a biography at the moment that contains the warning that “history is always a matter of trying to think into the minds of people who think differently from ourselves”.  That serves as a useful reminder that Ehrenberg knew far less about the biology of diatoms than we do today, but was also limited by the technology available.  Not only were his microscopes far less sophisticated than ours but also capturing the essence of the organisms he saw in print was far from straightforward (see “Picture this?”).  The idea of Gomphonema clavatum that we had until Reichardt re-examined the type material was the result of a 180-year game of “Chinese whispers”: each generation matching their specimens to inadequate images and descriptions, then making their own images which, in turn, became the basis for their successor’s identifications.  By the time Krammer and Lange-Bertalot wrote their Flora, it was finally possible to reproduce high quality micrographs, rather than line drawings but over a century of taxonomic drift meant that their images are no longer connected to the right name.  Their plate actually shows two species: the larger forms with undulate margins belong to G. longiceps Ehrenberg 1854) whilst the smaller specimens are G. subclavatum.   That assumes, of course, that there are no further twists to come.  As I alluded in my previous post, morphology might not be telling us the whole story for this genus.

The unfortunate twist, also mentioned in my previous post, is that the taxonomic confusion in the past means that we don’t actually get any sharper ecological insights in the present as a result of unravelling these names.   Anyone looking at ecological data associated with “Gomphonema clavatum” from twenty years ago needs to know that this could represent either G. longiceps or G. subclavatum or one of a number of other species that have been split away in recent years.  There is always a hope that this better understanding of taxonomy will yield fruits as we go forward but I’m always suspicious that someone else might come along and rearrange things yet again…

Reference

Krammer, K. & Lange-Bertalot, H. (1986).  Süsswasserflora von Mitteleuropa. 2/1 Bacillariophyceae 1: Naviculaceae. Spektrum Akademischer Verlag, Heidelberg.

Reichardt, E. (2015). The identity of Gomphonema clavatum Ehrenberg (Bacillariophyceae) and typification of five species of the genus Gomphonema described by C.G. Ehrenberg.  Diatom Research 30: 141-149.

The biography to which I refer is Tom Wright’s new book on Paul (SPCK, 2018).

 

Tales of Hofmann …

freshwater_benthic_diatoms_

For the past five years or so the constant companion on my desk whilst I stare down my microscope has been a thick tome (2.8 kg) entitled Diatomeen im Süßwasser-Benthos von Mitteleuropa by Gabi Hofmann and colleagues.  It serves as my aide-mémoire when I am analysing freshwater diatoms, jogging my memory when I see a diatom that I recognise but whose name I have forgotten.  Before this was published, I used a French publication Guide Méthodologique pour la mise en oeuvre de l’Indice Biologique Diatomées which was free to download (I cannot find a link on the web any longer, unfortunately).   Neither of these is the last word in diatom taxonomy, but that was not the point: a lot of the time, I just need a gentle reminder of the right name for the species I am looking at, and I don’t want to have to pore through a pile of books in order to find this.

One of the strong points of both books is that they are copiously illustrated, and the plates are arranged very logically so that similar-shaped diatoms are together, making it easy to pick out differences.   For most routine identification, this is exactly what is needed: we may pretend that we are logical people but, in truth, pattern matching beats using a key nine times out of ten.   The 133 plates in Diatomeen im Süßwasser … act as a visual index and, to make life even easier, the species descriptions are arranged alphabetically and cross-referenced in the plates.  Having found an image that resembles the diatom I am trying to identify, it is straightforward to flick to the description to check the details.

There is just one problem: Diatomeen im Süßwasser-Benthos von Mitteleuropa is in German, and quite technical German at that.   I tell people not to worry because all the images are in English but, in truth, I worry that I may lose some of the nuances due to my linguistic limitations.   I was delighted, then, to be asked by Marco Cantonati to help produce an English version of the book.  Marco is half-German so reads and speaks the language fluently, and I was able to work on his first drafts in English to produce the final text.   Conscious that translating a German book into English is only a partial solution for the almost 70% of the EU who have neither as their first language, we also unpicked the prose in order to put the information about each species into a series of “bullet points” so that it was more accessible and we also took the opportunity to update some of the taxonomy.   A large part of last weekend was spent poring over the proofs so it should not be long now before it is available to purchase.

The great irony for me is that I am putting the finishing touches to this book at the same time as I am helping the Environment Agency to move away from using the light microscope to identify diatoms altogether.   I am just finalising the last of the regular competency tests that I organise in which, Environment Agency staff will participate, after which routine samples will be sent off for Next Generation Sequencing rather than being analysed by light microscope.  I’ve written about the pros and cons of this before (see “Primed for the unexpected …”) but there is a funny side.   After over a decade of struggling with identification literature in a language that almost none of them spoke my dedicated band of Environment Agency analysts get the book they dreamed about two months after their last diatom slide is packed away.   My sense of timing is, as ever, impeccable …

Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011).   Diatomeen im Süßwasser-Benthos von Mitteleuropa. A.R.G. Gantner Verlag K.G., Rugell.

Prygiel, J.  & Coste, M. (2000).   Guide Méthodologique pour la mise en oeuvre de l’Indice Biologique Diatomées.   NF T 90-354.  Cemagref, Bordeaux.

A simple twist of fate …

surirella_spiralis_117024

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.

 

Identification by association?

A few months ago, I wrote briefly about the problems of naming and identifying very small diatoms (see “Picture this?”).   It is a problem that has stayed with me over the last few months, particularly as I oversee a regular calibration test for UK diatom analysts.   The most recent sample that we used for this exercise contained a population of the diatom formerly known as “Eolimna minima”, the subject of that post.   Using the paper by Carlos Wetzel and colleagues, we provisionally re-named this “Sellaphora atomoides”.   Looking back into my records, I noticed that we had also recorded “Eolimna minima” from an earlier slide used in the ring test.   These had a slightly less elliptical outline, and might well be “Sellaphora nigri” using the criteria that Wetzel and colleagues set out.   There are slight but significant differences in valve width, and S. nigri also has denser striation (though this is hard to determine with the light microscope).   These populations came from two streams with very different characteristics, so there is perhaps no surprise that there are two different species?

Eolimna_minima_GMEP37111

A population of “Eolimna minma” / Sellaphora cf. atomoides from unnamed Welsh stream used in UK/Ireland ring test (slide #39)  (photographs: Lydia King).

The differences in ecology are what concern me here.   Wetzel and colleagues focus on taxonomy in their paper but make a few comments on ecology too.  They write: “The general acceptance is that S. atomoides … is usually found in aerial habitats (or more “pristine” conditions) while the presence of Sellaphora nigri … is more related to human-impacted conditions of eutrophication, pesticides, heavy metal pollution and organically polluted environments”.  This statement is worrying because it suggests that the ecological divide between these two species is clear-cut.   Having spent 30 pages carefully dissecting a confusing muddle of species, it strikes me as counterproductive to repeat categorical statements made by earlier scientists who they had just demonstrated to have a limited grasp of the situation.

The risk is that a combination of slight differences in morphology coupled with (apparently) clear differences in ecology leads to the correct name being assigned based on the analyst’s interpretation of the habitat, rather than the characteristics of the organism.   This is not speculation on my part, as I have seen it happen during workshops.   On two occasions, the analysts involved were highly experienced.  Nonetheless, the justification for using a particular name, in each case, was that the other diatoms present suggested a certain set of conditions, which coincided with the stated preferences for one species, rather than with those for a morphologically-similar species.

I have no problem with environmental preferences being supporting information in the designation of a species – these can suggest physiological and other properties with a genetic basis that separate a species from closely-related forms.  However, I have great concerns about these preferences being part of the identification process for an analysis that is concerned, ultimately, with determining the condition of the environment.  It is circular reasoning but, nonetheless, I fear, widespread, especially for small taxa where we may need to discern characteristics that are close to limits of the resolution of the light microscope.

Gomphonema exilissimum is a case in point.  It is widely-regarded as a good indicator of low nutrients (implying good conditions) yet there have been papers recently that have pointed out that our traditional understanding based on the morphology of this this species and close relatives is not as straightforward as we once thought.   Yet, the key in a widely-used guide to freshwater diatoms (written with ecological assessment in mind) contains the phrase “In oligotrophen, elektrolytarmen, meist schwach sauren Habitaten” (“in oligotrophic, electrolyte-poor, mostly weakly-acid habitats”) amongst the characters that distinguish it from close relatives.  The temptation to base an identification wholly or partly on an inference from the other diatoms present is great.

Including an important environmental preference in a key designed for use by people concerned with ecological assessment brings the credibility of the discipline into question.   Either a species can be clearly differentiated on the basis of morphology alone, or it has no place in evaluations that underpin enforcement of legislation.   That, however, takes us into dangerous territory: there is evidence that the limits of species determined by traditional microscopy do not always accord with other sources of evidence, in particular DNA sequence data.   These uncertainties, in turn, contribute to the vague descriptions and poor illustrations which litter identification guides, leaving the analyst (working under time pressure) to look for alternative sources of corroboration.  I suspect that many of us are guilty of “identification by association” at times.   We just don’t like to admit it.

References

Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011).  Diatomeen im Süßwasser-Benthos von Mitteleuropa.  A.R.G. Gantner Verlag K.G., Rugell.  [the source of the key mentioned above]

Wetzel, C., Ector, L., Van de Vijver, B., Compère, P. & Mann, D.G. (2015). Morphology, typification and critical analysis of some ecologically important small naviculoid species (Bacillariophyta).  Fottea, Olomouc 15: 203-234.

Two papers that highlight challenges facing the identification of the Gomphonema parvulum complex (to which G. exilissimum belongs) are:

Kermarrec, L., Bouchez, A., Rimet, F. & Humbert, J.-F. (2013).  First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta).   Protist 164: 686-705.

Rose, D.T. & Cox, E.J. (2014).  What constitutes Gomphonema parvulum? Long-term culture studies show that some varieties of G. parvulum belong with other Gomphonema species.  Plant Ecology and Evolution 147: 366-373.

Picture this?

Teesdale_desmids_linocut

A curious moment of serendipity saw me stuffing a new scientific paper into my bag to read on the train as I travelled to a workshop on reduction linocut printing. A second instance of serendipity occurred when I walked close to the site of Thomas Bewick’s studio in Newcastle as I contemplated the contents of this paper whilst walking from Newcastle Station to Northern Print‘s workshop in the Ouseburn Valley. I was, clearly, destined to write a post on natural history illustration, and the problems of reproducing images.

The paper I was reading related the efforts of Carlos Wetzel and colleagues to understand the taxonomy and nomenclature of a group of very small diatoms, historically placed in the genus Navicula but more recently spread between Sellaphora and Eolimna. The problem they address is essentially one of calibration: do the names we use for modern diatoms correspond to the organism to which the name was first applied, or has our understanding of that species gradually ‘drifted’ over time so that we now use it either for a different species altogether, or for a number of species that match the original description?

The plate below puts the problem into perspective. It shows a number of specimens corresponding to the description of what we thought was Eolimna minima at the time, though should now probably be called Sellaphora nigri. These cells are mostly less than a hundredth of a millimetre in length, have a linear-elliptical outline and few surface features that can be resolved easily with the light microscope.    Small variations in the valve outline and the density of striae had encouraged diatomists to establish new species and varieties until there were a large number of names in circulation and it was not always easy to separate the wheat from the chaff.   Wetzel and his colleagues had tracked down the original descriptions and the “type material” (the specimens that formed the basis of these original descriptions) in an effort to sort out the mess.

Eolimna_minima_StMawgams

Sellaphora nigri / Eolimna minima from Menahyl River, St Mawgan Bridge, Cornwall, September 2009. The scale bar is approximately 10 micrometres (= 1/100th of a millimetre) long.   Specimens are arranged into two “morphotypes”: “narrow” and “blunt”.   Photographs: David Mann.

Our understanding of diatoms is driven in large part by the technology available to scientists at any point in history. Not surprisingly, the first diatoms to be described tended to be the larger species, relatively speaking, and it is no surprise that the earliest descriptions of the very small forms that are the subject of this post are rather basic.   These date back to Kützing in 1849, Rabenhorst in the 1850s and Grunow in the 1860s, all of whom would have had relatively basic microscopes by modern standards, and who worked without electric light with which to illuminate their specimens. They also did not have access to high resolution mountants, which only became available in the middle of the twentieth century. Nor were they able to photograph their specimens and, indeed, any drawings that they made would have had to be passed to a specialist engraver, who would have transferred the image either to a woodblock (using the ends of hard woods such as box and cherry rather than cutting into the grain) or a metal plate.   So there would have been at least two steps between the observer’s initial view of the diatom and the published illustration which, in the case of diatoms such as these, was working right at the edge of the resolution of the light microscopes of the day. It is no surprise, then, that the organism that Kützing described as “Synedra minutissima” and which later workers considered to be a small Navicula has subsequently bounced through several genera (and families), before Wetzel and colleagues decided on the basis of light and electron microscopical observations of Kützing’s original material that it probably belonged to Halamphora.

Image reproduction is, I suspect, almost as significant as optical technology in determining the rate of advances in understanding of diatoms. You only have to look back at papers in Diatom Research published only 20 years ago, and compare both the quality and quantity of images to understand this. Photo-editing packages such as Photoshop and CoralDraw are the unsung heroes of modern diatom taxonomy, enabling images to be edited and rearranged in multiple combinations.   We can now do in a couple of hours what would have taken weeks of time for an engraver in the 19th century, capturing images of a quality that would have been beyond Kützing’s wildest dreams.   Having done this, we can then discuss the results via email and Skype with people in other countries, or even different continents.

Yet there is one final twist to this tale: the plate of Sellaphora nigri / Eolimna minima is one of a series of plates that David Mann put together last year whilst he and I were pondering some RbcL sequences from field populations.   The genetic information seemed to be telling us that there were several distinct genotypes within complexes that we were identifying, with the light microscope, as Eolimna minima.   The scale of difference was such as to suggest that these genotypes may well be distinct species, albeit barely discernible even with the very best light microscopes available. We put that work aside, distracted by other, more pressing tasks, but I dug out the plates when thinking around the issues I’ve discussed in this post.   So it is quite possible that we have still not solved all the mysteries of this group of tiny, but very common, diatoms.

Reference

Wetzel, C.E., Ector, L., van de Vijver, B., Compère, P. & Mann, D.G. (2015). Morphology, typification and critical analysis of some ecologically important small naviculoid species (Bacillariophyta).   Fottea, Olomouc 15: 203-234.

More about the life and work of Thomas Bewick in:

Uglow, J. (2006). Nature’s Engraver: A Life of Thomas Bewick.   Faber and Faber, London.

The picture at the top of the post is the result of my labours at Northern Print. It is a reduction linocut (also known as a “kamikaze linocut”, as the plate is destroyed during the production of the image) showing desmids from Upper Teesdale (see “Abstraction and Reality in Upper Teesdale”)