So that was 2017 …

As is now traditional, I end the year with a word cloud based on the posts I’ve written over the past 12 months.  Comparing it to 2016’s word cloud I see that “see” is still prominent but that the word “diatoms” is now larger than “algae” whilst “desmid” also makes an appearance on the left-hand side.  “Brexit”, despite occupying much of my thoughts, does not merit an appearance.

I am no more optimistic as 2017 closes than I was at the end of 2016.  The Government still has no clear vision for life outside the European Union and the impact on the economy is still uncertain (see note at the end).   There are a few shafts of light: I was pleased to see, for example, that Michael Gove was prepared to consider a new environmental regulator wholly independent of government (“OfEnv”, as some have termed it), responding to genuine concerns raised by Caroline Lucas and others (see “(In)competent authority”).  We will, however, have to wait to see how these fine words are translated into action, bearing in mind Michael Gove’s track record in other ministerial roles.

An “OfEnv” will have its work cut out.   I suspect that one of the unintended consequences of Brexit is going to be a yet greater squeeze on public finances.   This is because many issues whose budgets were, to some extent, ring-fenced in order to meet UK’s obligations to the EU will be less protected in our post-EU economy.   Bearing in mind the huge political significance of health care and education and, in the case of the former, the increasing care needs of an aging population, every other sphere of government spending is going to be under intense scrutiny.   At best, the environment is a mid-table concern in the eyes of politicians, which makes Government funding crucially dependent upon the state of the economy.

That’s ironic in the extreme because one of the most thought-provoking books I read this year was Doughnut Economics by Kate Raworth (Random House).   Her core argument is that an economic system focussed on growth is unsustainable for many reasons, one of which is the likely consequences for the environment.   Yet environmental regulation is, at present, dependent upon tax revenues arising from the tired economic system that Kate Raworth decries.   And the hiccups in economic growth from 2010 onwards have put enormous strains on the Environment Agency and other environmental regulators, though management is reluctant to admit this publicly.  I suspect that the BBC’s self-satire “W1A” is very close to the mark for much of the public sector.   Its catchphrase “more of less”* catches the dilemma faced by middle-managers who have bought into an illusion that a leaner, more efficient organisation has arisen from the self-examination that cuts have precipitated.

There are no easy answers.   Long-term, I suspect that neither the EU nor a post-Brexit UK government will deliver a truly green future, for as long as both depend upon politicians needing to meet the material aspirations of their electorates.   Wanting less is a good first step for each of us, as individuals, but such lines of thought are too far from the core business of this blog for me to venture.  I’ll leave that with you as my personal New Year’s resolution and see you all in 2018.

* “To identify what the BBC does best and find more ways of doing less of it better”


A summary of Kate Raworth’s economic thinking can be found here:

Raworth K. (2017).   A doughnut for the Anthropocene: humanity’s compass in the 21st century. 1: e48-e49.


I was pulled up by one reader for my pessimistic view of the economic prospects post-Brexit.  I have, consequently, changed the wording to emphasise the uncertainty in all economic predictions. Three reports from responsible sources that offer perspectives on the post-Brxit economy are: Brexit and the economy one year on, Brexit: is the UK economy growing or slowing?  and: UK economy in 2018: steady growth tempered by Brexit politics.  My primary point – about the vulnerability of the budgets of environmental regulators – remains.


The multiple dimensions of submerged biofilms …

My recent dabbling and speculation in the world of molecular biology and biochemistry (see “Concentrating on carbon …” and “As if through a glass darkly …”) reawakened deep memories of lectures on protein structure as an undergraduate and, in particular, the different levels at which we understand this.   These are:

  • Primary structure: the sequence of amino acids in the polypeptide chain;
  • Secondary structure: coils and folds along the polypeptide chain caused by hydrogen bonds between peptide groups;
  • Tertiary structure: three-dimensional organisation of protein molecules driven by hydrophobic interactions and disulphide bridges; and,
  • Quaternary structure: the agglomeration of two or more polypeptide groups to form a single functional unit.

This framework describes journey from the basic understanding of the nature of a protein achieved by Frederick Sanger in the early 1950s, to the modern, ore sophisticated awareness of how the structure determines their mode of action. I remember being particularly taken by a description of how sickle cell anaemia was caused by a change of a single amino acid in the haemoglobin molecule, altering the structure of the protein and, in the process, reducing its capacity to carry oxygen.

There is a metaphor for those of us who study biofilms here. To borrow the analogy of protein structure, the basic list of taxa and their relative abundance is the “primary structure” of a biofilm. Within this basic “name-and-count” we have various “flavours”, from diehard diatomists who ignore all other types of organisms through to those who go beyond counting to consider absolute abundance and cell size in their analyses. Whatever their predilection, however, they share a belief that raw taxonomic information, weighted in some way by quantity, yields enough information to make valid ecological inferences. And, indeed, there are strong precedents for this, especially when the primary goal is to understand broad-scale interactions between biofilms and their chemical environment.

But does this good understanding of the relationship between biofilm “primary structure” and chemistry comes at the expense of a better understanding of the inter-relationships within the biofilm. And, turning that around, might these inter-relationships, in turn, inform a more nuanced interpretation of the relationship between the biofilm and its environment? So let’s push the metaphor with protein structure a little further and see where that leads us.

The “tertiary structure” of a submerged biofilm: this one shows the inter-relationships of diatoms within a Didymosphenia geminata colony.  Note how the long stalks of Didymosphenia provide substrates for Achnanthidium cells (on shorter stalks) and needle-like cells of Fragilaria and Ulnaria.   You can read more about this here.  The image at the top of the post shows a biofilm from the River Wyle, described in more detail here.

We could think of the “secondary structure” of a biofilm as the organisation of cellular units into functional groups. This would differentiate, for example, filaments from single cells, flagellates from non-flagellates and diatoms that live on long stalks from those that live adpressed to surfaces. It could also differentiate cells on the basis of physiology, distinguishing nitrogen-fixers from non-nitrogen fixers, for example. We might see some broad phylogenetic groupings emerging here (motility of diatoms, for example, being quite different from that of flagellated green algae) but also some examples of convergence, where functional groups span more than one algal division.

Quite a few people have explored this, particularly for diatoms, though results are not particularly conclusive. That might be because we cannot really understand the subtleties of biofilm functioning when information on every group except diatoms has been discarded, and it might be because people have largely been searching for broad-scale patterns when the forces that shape these properties work at a finer scale. General trends that have been observed include an increase in the proportion of motile diatoms to increase along enrichment gradients. However, this has never really been converted into a “take-home message” that might inform the decisions that a catchment manager might take, and so rarely form part of routine assessment methods.

Next, there is a “tertiary structure”, the outcome of direct relationships between organisms and environment, interdependencies amongst those organisms to form a three-dimensional matrix, and time. This is the most elusive aspect of biofilm structure, largely because it is invariably destroyed or, at best, greatly distorted during the sample collection and analysis phases. This has been little exploited in ecological studies, perhaps because it is less amenable to the reductive approach that characterises most studies of biofilms. But I think that there is potential here, at the very least, to place the outcomes of quantitative analyses into context.  We could, in particular, start to think about the “foundation species” – i.e. those that define the structure of the community by creating locally stable conditions (see the paper by Paul Dayton below).   This, in turn, gives us a link to a rich vein of ecological thinking, and helps us to understand not just how communities have changed but also why.

The tertiary structure of a Cladophora-dominated biofilm from the River Team, Co. Durham.  Cladophora, in this case, functions as a “foundation species”, creating a habitat within which other algae and microorganisms exist.   You can read more about this in “A return to the River Team”.

Finally, if we were looking for a biofilm “quaternary structure” we could, perhaps, think about how the composition at any single point in space and time grades and changes to mould the community to favour fine-scale “patchiness” in the habitat and also to reflect seasonal trends in factors that shape the community (such as grazing).   Biofilms, in reality, represent a constantly shifting set of “metacommunities” whose true complexity is almost impossible to capture with current sampling techniques.

Some of this thinking ties in with posts from earlier in the year (see, for example, “Certainly uncertain”, which draws on an understanding of tertiary structure to explain variability in assessments based on phytobenthos communities).  But there is more that could be done and I hope to use some of my posts in 2018 to unpick this story in a little more detail.

That’s enough from me for now.  Enjoy the rest of the festive season.

Selected references

Foundation species:

Dayton, P. K. (1972). Toward an understanding of community resilience and the potential effects of enrichments to the benthos at McMurdo Sound, Antarctica. pp. 81–96 in Proceedings of the Colloquium on Conservation Problems Allen Press, Lawrence, Kansas.

“secondary structure” of biofilms

Gottschalk, S. & Kahlert, M. (2012). Shifts in taxonomical and guild composition of littoral diatom assemblages along environmental gradients.  Hydrobiologia 694: 41-56.

Law, R., Elliott, J.A., & Thackeray, S.J. (2014).  Do functional or morphological classifications explain stream phytobenthic community assemblages?  Diatom Research 29: 309-324.

Molloy, J.M. (1992).  Diatom communities along stream longitudinal gradients.  Freshwater Biology, 28: 56-69.

Steinman, A.D., Mulholland, P.J. & Hill, W.R. (1992).  Functional responses associated with growth form in stream algae.  Journal of the North American Benthological Society 11: 229-243.

Tapolczai, K., Bouchez, A., Stenger-Kovács, C., Padisák, J. & Rimet, F. (2016).  Trait-based ecological classifications for benthic algae: review and perspectives.  Hydrobiologia 776: 1-17.

“tertiary structure” of biofilms

Bergey, E.A., Boettiger, C.A. & Resh, V.H. (1995).  Effects of water velocity on the architecture and epiphytes of Cladophora glomerata (Chlorophyta).  Journal of Phycology 31: 264-271.

Blenkinsopp, S.A. & Lock, M.A. (1994).  The impact of storm-flow on river biofilm architecture.   Journal of Phycology 30: 807-818.

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

The kindness of strangers …

A matter of days after we arrived in Nigeria (see “How to make an ecologist #11”) a battered old Peugeot 504 station wagon pulled up alongside us as we walked from our hotel to get a bush taxi across Jos to the university campus. A North American voice called through the open window (we were later to discover that it never closed properly) and asked if we wanted a lift. We clambered in gratefully, the vehicle crunched into gear and pulled out into the traffic again. As the car lurched forward a whisky bottle rolled across the foot well and the driver, a lean man in his fifties, introduced himself as Alvin, a worker with CUSO, the Canadian equivalent of the Peace Corps or VSO. The whisky bottle, he explained, contained local honey (invariably sold with honeycomb and a few dead bees included). By the time we had made the mile or so journey to the centre of town where our routes diverged, he had invited us back to his house for dinner the following evening.

A week at the Plateau Hotel had been enough to exhaust our enthusiasm for their rather limited menu so we accepted with alacrity and, the following evening, his Peugeot grumbled up the driveway to the Plateau Hotel to collect us for the short drive to his house on the edge of the town where we met his wife Sylvia and ate her home-cooked food. They had had a furniture business in Kenora, Western Ontario, we learned, but had sold up to take a career break teaching in a technical college. Officially, Alvin taught woodwork (which he wryly summarised as showing students how to make long pieces of wood shorter) but he had an unofficial sideline in demonstrating how random acts of kindness made the world a better place. They and we bonded despite the age difference and, at weekends, we joined them in their elderly Peugeot to explore the region.

Fishermen on the River Benue, early 1990.   The photograph at the top of the post shows rock formations near Riyom, south of Jos (but taken some months later, during the wet season).

A few days ago  we heard news that Alvin had died after a long battle with cancer. Once our initial sadness had passed, we found ourselves smiling again as memories that had faded with time reasserted themselves. One trip, in particular, summed-up Alvin’s indomitable attitude, taking us south off the Jos Plateau into the heat of the northern Nigerian plain. I can’t remember the motivation for this trip, only that we spent the night in a guest house belonging to a mission, but only after a hair-raising crossing of the Benue River. Our first approach to the river was presaged by a sudden improvement in the road surface as we drove up an incline towards a very modern-looking bridge before Alvin stood on the brakes to bring us to a halt just before the road ended abruptly with just a few traffic cones between us and a vertical drop.

From this narrow escape we made our way on smaller roads to the ferry, where a narrow barge barely wider than the car itself was tied up with some planks bridging the gap to the steeply-sloping riverbank. At this point, the rest of us climbed out declaring our intention of recording the occasion on film, leaving Alvin to line-up the car at the top of the slope and then to slither down, across the rickety planks and onto the barge.  We followed him onto the barge and were shown into the open boat lashed to the side, from which the ferryman started up the outboard motor and pointed the ferry towards the line of trees that marked the opposite shore.

Boarding the ferry across River Benue, Nigeria, 1990.

We shared the broad river channel with a few small boats carrying foot passengers and a skiff from which a local fisherman and his son were casting seine nets.  There are reports of manatee and hippopotami from the river, though we did not see any, and there are almost certainly crocodiles too, though they kept out of sight.  Our ferry moved slowly diagonally upstream across the broad river channel towards the southern shore where the exercise was repeated (the river bank on this side was far less intimidating) and we were in Benue State.  This was the heartland of the Tiv ethnic group whose distinctive round huts were the subject of one of my very first watercolours.   The Tiv are the fourth largest ethnic group in Nigeria, a farming people, proud of their yams.  Inside the round huts it is easy to imagine the scenes related by the anthropologist Laura Bohannan in her fascinating article Shakespeare in the Bush.

Having got to Tiv country on the Saturday evening we had to turn our eyes back towards Jos if we were to be back in time for work on Monday.   We took a more circuitous, albeit faster, route this time, crossing the river by the modern bridge and heading back along roads lined with mahogany plantations.   We stopped at a roadside stall beside one of these and haggled for a small pestle and mortar, which our Nigerian friends dismissed as hilariously inadequate and which imparted a tinge of brown boot polish to our first few batches of pounded yam.   And then Alvin was changing down the gears so that the Peugeot could haul itself back up to the milder climate of the Jos Plateau and we were passing familiar landmarks again.

A reconstruction of the Tiv village at the Museum of Traditional Nigerian Architecture in Jos, circa 1990. 

Recalling Alvin and Sylvia at this time of year is apt, as hospitality to strangers is an integral part of the Christmas story.  They helped us find our feet and we, in due course (I hope) followed their example with other new arrivals.   After leaving Nigeria they moved to Minnesota, to be close to their children, where we visited them in November 2012 (I watched Bill Clinton’s first election victory from their front room).  Distances were too great to see them regularly but we kept in touch by letter and email.   Though I had not seen him for over twenty years, I felt the bonds we forged in Nigeria were strong and knowing that he is no longer here to share his dry humour and practicality is enough to give me pause for thought.

More about Gomphonema vibrio

Gomphonema vibrio is part of a complex of species that has only begun to be unravelled in the past few years.   In the first edition of the Süsswasserflora von Mitteleuropa in 1930, Hustedt included it as one of three varieties of G. intricatum, along with G. pumilum and G. dichotum.  By the time of the second edition (1986), however, Krammer and Lange-Bertalot had subsumed G. intricatum into G. angustum, creating a single species that spanned an enormous range of size (see their Plate 164 if you don’t believe me).   A few years later they revised this opinion, and unpicked the G. angustum complex, reinstating several of the taxa that they had originally subsumed and also recognising some more recently described species (many by Erin Reichardt).   There may well be more changes to come as this group has not yet been subjected to critical study by molecular geneticists.

One of the other species in this melange is Gomphonema pumilum, a much smaller diatom that is common in both running and standing waters (Hustedt’s comment on the species complex only referred to a preference for “stagnant waters”).   We have met it a few times previously (see, for example, “Pleasures in my own backyard”) and I also found it in a 1999 sample from Croft Kettle whilst searching for G. vibrio.   However, I then turned to an older slide, based on a sample collected in 1872 and given to me by John Carter (see “Remembering John Carter”).   This had some cells of G. pumilum but also some that exceeded the quoted dimensions for G. pumilum (length: 12 – 36 mm; width: 3.5 – 5.5 mm) and which fell within the size range for G. vibrio.   I suspect that we are, in fact, dealing with a mixture of the two species and if this is a common situation then it may explain why Hustedt had difficulties unpicking the two species.   When I arranged the images of G. vibrio and G. pumilum that I found in this sample in order of diminishing size, there is a continuum between the two forms.  We now know that width is a better discriminator than length and, armed with this, we can see a difference between the two species. But that is one of the benefits of hindsight.

Gomphonema pumilum from Croft Kettle, May 1999.  a. – e.: valve views; f., g.: girdle views.   Scale bar: 10 micrometres (= 100th of a millimetre).

Gomphonema vibrio (h. – k.) and G. pumilum (l. – m. [and n.?]) from “Hell Kettles”, 1872.  Scale bar: 10 micrometres (= 100th of a millimetre).

This raises a question about the reliability of the size ranges quoted in the literature   A couple of the smaller valves of G. vibrio were less than 7 mm wide.  Yet, in other respects, they were more similar to the “true” G. vibrio valves than to those of G. pumilum.  The answer will vary from species to species but, as a general rule, we should not be too bothered if the extremes of a population stray a little beyond the values quoted in the literature.   These are usually based on the largest and smallest cells found in a thorough scan of one or more populations, but not necessarily on observations of an initial cell (the largest in a population) or of cells at the point immediately before sexual reproduction is initiated (the smallest).  We simply don’t have that information for most species so, as a result, should be prepared to accept larger and smaller valves into a species if they are qualitatively similar to, and quantitatively part of a continuum with, the rest of the population.  My post “Diatoms and the Space-Time Continuum”, also on Gomphonema, offers some further insights into this story.


Hustedt, F. (1930).  Susswasserflora von Mitteleuropa 10: Bacillariophyceae.  Gustav Fischer, Jena.

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

Krammer, K. & Lange-Bertalot, H. (1991). Susswasserflora von Mitteleuropa 2: Bacillariophyceae. 4 Teil: Achnanthaceae. Kritische Ergänzungen zu Achnanthes s.l., Navicula s.str., Gomphonema. Spektrum Akademischer Verlag, Heidelberg.

Reichardt, E. (1997).  Taxonomische revision des Artencomplexes um Gomphonema pumilum (Bacillariophyceae).  Nova Hedwigia 65: 99-129.

Reichardt, E. & Lange-Bertalot, H. (1991).  Taxonomische revision des Artencomplexes um Gomphonema angustum – G. intricatum – G. vibrio und ähnliche taxa (Bacillariophyceae).  Nova Hedwigia 53: 519-544.


In my post on Gomphonema rhombicum, I mentioned that the location on the type slide is given as “Appleby”, which was not very precise.   My 1872 slide is labelled “Hell Kettles, Durham”.  “Hell Kettles” is the name for the pair of ponds, of which Croft Kettle, which I described in my earlier post, is the larger.   However, the location “Durham” is not very illuminating.   The closest town to Croft Kettle is Darlington, whilst Durham City is 40 km to the north.   “Durham”, in this context, could refer to the county, which covers 2721 square kilometres and habitats from calcareous ponds such as these to moorland pools.   A slide label offers very little space to give precise details of location but, in both these cases, a little more information would be useful.   The likelihood is that Firth had more detailed notes elsewhere but these have been lost over time, so we are left with these scant words.   There is a lesson here for all of us in how we record the meta-data that accompanies our samples.

Meetings with remarkable Gomphonema …

Having written about Gomphonema rhombicum in my previous post, I thought it would be worth staying with Gomphonema and showing some images of G. vibrio.   This is a diatom that I had rarely encountered previously but which cropped up in separate email conversations with Chris Carter and Geoff Phillips in the space of a couple of months.  Chris’ samples come from a small man-made pond at Yardley Chase, an SSSI in Northamptonshire (photographed above), whilst Geoff’s was from Phragmites stems in a Norfolk marsh dyke.  Both have hard water (Geoff’s location: pH: 7.6; alkalinity: 275 mg L-1 CaCO3; conductivity: 700 mS cm-1) and good water quality (TP: 60 mg L-1; TN: 1.5 mg L-1).   This set of conditions prompted me to dig out some samples from Croft Kettle, a location I wrote about a couple of years ago (see “The desert shall rejoice and blossom …”) where I had a vague memory of having seen something similar.

Valves of Gomphonema vibrio are relatively large (30 – 95 x 7 – 10 mm, according to Hofmann et al., 2017) and club-shaped with a slight swelling at the centre.  Overall, the valves are more slender than was the case for G. rhombicum (see illustrations in the previous post).   The striae are coarse (7 – 10 in 10 mm) and mostly radiate, but there is a distinct central area where there is a single stria on each side more distantly spaced from the adjacent striae than in the rest of the valve.  On one side, this stria is very short (sometimes it can be hard to see); on the other side, it is longer and ends with a distinct stigmoid (an isolated pore).    The central endings of the raphe are often turned to the same side.

Cleaned valves of Gomphonema vibrio from a pond at Yardley Chase, Northamptonshire.  Yardley Chase is shown in the image at the top of the post.   Images are in pairs, each at a slightly different focus plane.   All photos by Chris Carter.

Chris also sent me some photographs of the living cells, showing a clear stalk protruding from the narrower “foot” pole, as well as a beautifully-clear H-shaped chloroplast.  The presence of a stalk in this species just doubles my annoyance at not having checked for the same in G. rhombicum before cleaning the valves.

There are, it seems, remarkably few records of Gomphonema vibrio from the UK.  I can find no other records from rivers and Helen Bennion found just two other records of recent samples in the UCL database, both from Scotland: Loch Levan and Loch Davan.  Three of the five records are from ponds, which may be significant, and two of these were epiphytes, though there are not enough records here to make any firm pronouncements about habitat preferences.  However, the picture that is emerging is of a species that definitely has a preference for moderately hard to hard water with relatively low nutrients. If that is the case, then it could well be a species that used to be more common that it is now, as many habitats such as these will have deteriorated in recent decades due to agricultural enrichment.   It is certainly a very different habitat from the soft water, fast-flowing stream from which I recorded G. rhombicum in Bulgaria.

Live cells of Gomphonema vibrio from a pond at Yardley Chase, Northamptonshire.  Photos by Chris Carter. 

That makes a total of five records from the UK which, even allowing for the muddled taxonomy (which I’ll talk about in the next post) and the fact that the diatoms of small ponds are rarely studied, suggests that this may be a genuinely rare. It is listed as an “endangered species with persistent risk factors” on the German red list, with a forecast of further decline over the next ten years.   I’ve voiced my concerns about “rarity” and red lists before (see “A red list of endangered British diatoms?”) but will stick my neck out on this one and suggest that Gomphonema vibrio might be a candidate.


Lange-Bertalot, H., Hofmann, G., Werum, M. & Cantonati, M. (2017).   Freshwater Benthic Diatoms of Central Europe: Over 800 Common Species Used In Ecological Assessment (edited by M. Cantonati, M.G. Kelly & H. Lange-Bertalot).   Koeltz Botanical Books, Schmitten-Oberreifenberg.