The River Wear in January

The series of events that eventually gave birth to this blog started with a visit to the River Wear at Wolsingham on the first day of 2009.  I had visited on a whim, intending to blow away the cobwebs after lunch on New Year’s Day, but with no real plan.  But I thought it would be interesting to pull on my waders and have a look at the river bed and, while I was there, I may as well collect a sample too.   Those observations and that sample must have triggered something in my mind, because I returned every month after that and, on each occasion, the samples and observations generated sketches which, in turn, made me curious about the factors that drove the algal communities in our rivers.

I thought it would be interesting to repeat that exercise during 2018 as my thinking has moved on over the past nine years.  I’m essentially visiting the same site and making the same observations but, this time, filtering them through deeper beds of experience.   The River Wear at this point is about 30 metres wide, a broad, shallow, riffled stretch, skirting the small town of Wolsingham roughly at the point where Weardale broadens out from a narrow Pennine valley to the gentler landscape of the Durham coalfield.  There are a couple of small towns upstream but the ecological condition of the river is still good.  Although there are still concerns about concentrations of heavy metals arising from the mines that are scattered around the upper parts of the valleys, I can see no serious effects of toxic pollution when I look at the plants and animals that live at Wolsingham.

If you follow this blog you will not be surprised to hear that, even in the depths of winter, algal communities in the River Wear are thriving Most of the larger stone surfaces are covered with a discernible brown film, up to a couple of millimetres thick.   The very top layer is dark brown in colour, with a lighter brown layer beneath this.   When I put a sample of this under my microscope, I saw that it was dominated by gliding cells of Navicula lanceolata, though other diatoms were also present (described in more detail in “The ecology of cold days”) and there were also a few thin filaments of a blue-green alga.

A submerged cobble photographed in situ in the River Wear at Wolsingham, January 2018, covered with a thick diatom-dominated biofilm.

I’ve included a picture of the view down my microscope because one of the questions that I’ve been trying to answer over the past few years is how we construct an understanding of the microscopic world using microscopy (see “The central dilemma of microscopy” and “Do we see through a microscope?”).   Of course, a single view field of view does not convey all the information I require, so my understanding is actually built up from observations of a large number of separate fields.  The boat-shaped cells of Navicula lanceolata were almost ubiquitous in these, as were patches of amorphous organic matter (“fine particulate organic matter” – see “A very dilute compost heap …”).  In total, I found 15 different species of algae in my preliminary analysis, of which Navicula lanceolata comprised about half of the total, with thin filaments of the cyanobacterium Phormidium and the diatom Achnanthidium minutissimum each constituting about 15 per cent.

A view of the biofilm from the River Wear, Wolsingham in January 2018.

However, my earlier comment about the biofilms having distinct layers means that simply observing what organisms are present will not tell us the whole story about how those organisms are organised within the biofilm (see “The multiple dimensions of submerged biofilms …”) so the next step is to hypothesise how these organisms might be arranged in the biofilm before I disrupted their microhabitat with my sampling.   The schematic diagram below attempts to capture this, but with a few provisos.  First, I said that the biofilm was a couple of millimetres thick but my portrayal only shows about a tenth of a millimetre; second, there is considerable spatial and temporal variation in biofilms and my depiction amalgamates my direct observations in January 2018 with information gleaned from a number of other visits.   Gomphonema olivaceum (probably a complex of two or three species in this particular case), for example, is often more prominent than it was last week, and I have also omitted Achnanthidium minutissimum altogether.   I suspect that this is less abundant in the mature biofilms but that the cobble surface is a patchwork of different thicknesses, reflecting different types of disturbance.   That raises another issue: the scale at which we generally collect samples is greater than the scales at which the forces which shape biofilms operate.   The whole image below, for context, occupies about the same width as a single bristle on the toothbrush that I used to collect the sample.

It is difficult to convert what we “see” back to the original condition when working under such constraints and, inevitably, decisions are guided by what others before us have written.  That brings a different set of problems: Isaac Newton may have seen further by “standing on the shoulders of giants” but Leonardo da Vinci’s usually rigorous objectivity lapsed on at least one occasion when his eye was led by assumptions he had inherited from earlier generations (see “I am only trying to teach you to see …”).   What my picture is actually showing, in other words, is a mixture of what I saw and what I think I should have seen.   This two-way process in art extends from the very earliest drawings we make through to the most sophisticated Old Masters so I am in good company.  In truth, I am not trying to depict a particular point in space or time so much as to encapsulate the idea of a biofilm from that river that is more than a random aggregation of cells.

A schematic view of the vertical structure of a submerged biofilm from the River Wear, Wolsingham, January 2018.   a., Navicula lanceolata (valve view); b., N. lanceolata (girdle view); c. Navicula gregaria (valve view); d. N. gregaria (girdle view); e. Gomphonema olivaceum (valve view); f. G. olivaceum (girdle view); g. Phormidium; h. inorganic particles; i. fine particulate organic matter.  Scale bar: 20 micrometres (= 1/40th of a millimetre).

References

You can find out more about the condition of the River Wear (or any other river or lake) using the Environment Agency’s excellent Catchment Planning webpages

Three good books that discuss the relationship between pictorial representation and the mind are:

Cox, Maureen (1992).  Children’s Drawings.   Penguin, Harmondsworth.

Gombrich, E.H. (1977) Art and Illusion: a study in the psychology of pictorial representation.   5th Edition.  Phaidon, London.

Hamilton, James (2017).  Gainsborough: a Portrait.   Weidenfield & Nicholson, London.

 

 

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Algae behaving selfishly …

My most recent trip to Ennerdale Water was on a wonderful windless winter day, offering perfect reflections of the snow-dusted peaks beyond the lake. It was a cold day but I was well wrapped-up and could enjoy both the long-distance views and the close-ups of nature around the lake’s margins.   One of the small streams that I crossed as I skirted the perimeter of the lake had patches of green algae growing on its submerged stones and even a quick examination showed it to be coarser than the green algae that covered most of the larger stones on the lake bed itself, as well on those in the River Ehen, just below the outfall.   When I managed to get specimens under my microscope I saw that the algae on the lake bed was Spirogyra (which I have seen here before; see “A lake of two halves”) whilst that in the inflow stream was Oedogonium.

I’ve written about Oedogonium before, and lamented the problems we face when we try to identify the species within this large genus (see “The perplexing case of the celibate alga”).   Ironically, a couple of weeks after I wrote this, I encountered a population of Oedogonium in another Cumbrian stream that did have sexual organs (see “Love and sex in a tufa-forming stream”).  However, this was the exception that proves the rule, as I have not seen a sexually-mature population of Oedogonium since.  The population I found beside Ennerdale was not sexually mature either but it did show a different, but equally effective, means of going forth and multiplying.

In the left hand diagram below we see a vegetative cell from an Oedogonium filament that has split open, allowing a vesicle to be extruded within which a single zoospore has formed.   This has a ring of flagella at one end, resembling a monk’s tonsure (you can just see these flagella in the photograph).   The other two photographs show the monk’s bald pate, though the fringe of flagella is not very clear.    The transparent vesicle swells and eventually ruptures, releasing the zoospore, which swim around for an hour or so, before settling on a new substratum and growing into new filaments.

Zoospores of Oedogonium from a stream flowing into Ennerdale Water, January 2018.   Scale bar: 25 micrometres (= 1/40th of a millimetre). 

In my material, the new filaments were mostly attached to mature Oedogonium filaments; however, this is probably partly an artefact and, in the field, they would almost certainly also settle on rocks and other surfaces too.   You can see, in the diagram below, how the “bald” end of the zoospore has started to differentiate into a holdfast that will secure the cell to the substrate whilst, over time, the other end will start to divide to produce the first cells of the new filament.  The whole process is described in a series of papers by Jeremy Pickett-Heaps (see reference list below).

Why did I see zoospore formation in this particular sample?   I don’t know for sure but it may be because I let a longer than usual time elapse between collecting and examining the sample.   This one had sat around in a cool box and fridge for four days, whereas I usually manage to check them within 24 hours.   Neglect can be a useful tool in the phycologist’s arsenal, as many freshwater algae see no need to indulge in anything more taxing than routine cell division for as long as the habitat keeps them replenished with whatever light, nutrients and other resources that they need.   Only when this is no longer the case do the algae start to channel resources into survival strategies.

Oedogonium zoospores germinating into new filaments, both epiphytic on mature filaments.   From a stream flowing into Ennerdale Water, January 2018. .   Scale bar: 25 micrometres (= 1/40th of a millimetre). 

Although I used the phrase “go forth and multiply” in an earlier paragraph, these Oedogonium cells are actually “going forth” rather than “multiplying” as the process we are watching only produces a single new cell.  However, were this zoospore to be released in a stream rather than a sample bottle, then there is a good chance that it would have been washed downstream and that a few of the many zoospores might have settled on a suitable habitat away from the constraints of their former home.   Asexual reproduction is a dispersal mechanism that results in the spread of genetically-identical copies of the parent cell.  For a sessile organism, this strategy allows a single genotype to move on from less-favourable locations and to exploit the potential of nearby locations.

The word “reproduction” is misleading as the mixing of genetic material that we associate with sex doesn’t take place.  The end product is a clone of a successful Oedogonium filament growing somewhere else.   However, taking the “sex” out of “asexual” removes a huge potential for innuendo, and readers who have battled this far through a post on nondescript green filaments deserve a reward.  So let’s finish with Woody Allen’s definition of masturbation as “sex with someone you love” and suggesting that the cytological huffing and puffing involved in zoospore production may not have the romance of sex but nor does it lead to any of the complications which result from sex either.   The alga gets offspring that are 100% identical to itself, just slightly further downstream and there is no risk of mixing with inferior genotypes.   That’s about as “selfish” as the “selfish gene” can get.

References

Pickett-Heaps, J. (1971).   Reproduction by zoospores in Oedogonium. I. Zoosporogenesis.   Protoplasma 72: 275-314.

Pickett-Heaps, J. (1971).   Reproduction by zoospores in Oedogonium. II. Emergence of the zoospore and the motile phase. Protoplasma 74: 149-167.

Pickett-Heaps, J. (1972).   Reproduction by zoospores in Oedogonium. III. Differentiation of the germling.  Protoplasma 74: 169-173.

Pickett-Heaps, J. (1972).   Reproduction by zoospores in Oedogonium. IV. Cell division in the germling and the possible evolution of the wall rings.   Protoplasma 74: 195-212.

See also “The River Ehen in March” for some further perspectives on asexual reproduction in algae.

View from near our sampling site on Croasdale Beck, looking towards Ennerdale Bridge, January 2018.

 

Change is the only constant …

The diatoms I saw in my sample from the littoral of Lake Popovo (described in the previous post) reminded me of an assemblage that I had seen in another lake which, apart from its location, has much in common with Popovo. This lake is Wastwater, in the western part of the English Lake District (see “The Power of Rock …”).  Like Popovo, it is situated in a remote a region of hard volcanic rocks and, as such, has very soft water and is subject to few of the pressures to which most of our freshwaters are subject.  The photograph above shows me sampling Wastwater in about 2006 (more about this photograph, by the way, in “A cautionary tale …”).

I wrote about Wastwater when I was writing my book Of Microscopes and Monsters, the precursor of this blog.   I focussed, in particular, on an experiment that my friend Lydia King had performed as part of the research towards her PhD.  Her previous work had established that there were relationships between the types of algae that she found in lakes in the Lake District and the amount of nutrients that they contained.  She also saw that the types of algae she found depended upon how acid or alkaline the water was.  But the water chemistry only explained a part of the variation in the algae and now she wanted to find out about the variation that was not explained by this.   In particular, she wanted to know how much of the variation was due to the way that the algae interacted with each other.

Lydia’s experiment involved putting clay pots into the shallows at the edge of Wastwater and then watched how the algal communities changed over the course of six weeks.  She also examined small parts of the pots at extremely high magnifications using a scanning electron microscope.   These micrographs, and subsequent conversations with her, had inspired some of my early paintings and I returned to this subject several times, finally producing a series of three pictures that showed changes in the algae over time.

The microbial world of the littoral zone of Wastwater after two weeks of colonisation showing unidentified small unicellular blue-green alga,  unidentified small unicellular green alga; thin filaments of Phormidium,  Achnanthidium minutissimum and Gomphonema parvulum.

The first of these shows the surface of the plant pot after being submerged in Wastwater for two weeks.   You could think of this as a patch of waste ground that was, at the start of the experiment, bare of vegetation.   If we watched this patch over a number of weeks, we would notice some plants appearing: scattered stalks of grass, perhaps some rosebay willow herb, dock or plantains. A gardener might dismiss these as “weeds”, although this term has no ecological meaning but ecologists prefer to think of these as “pioneers”: plants adapted to colonising new habitats, growing quickly (which might mean producing lots of seeds in a short space of time or producing rhizomes or runners) and covering the ground.  This same process has taken place on Lydia’s plant pot in Wastwater: the “weeds” in this case are scattered thin filaments of the blue-green alga Phormidium, the diatoms Achnanthidium minutissimum and Gomphonema parvulum plus a number of spherical green and blue-green cells that she couldn’t identify.   Such is the scale that we are working at that this open landscape still contains about 92000 cells per square centimetre.

The microbial world of the littoral zone of Wastwater after three weeks of colonisation.   The composition is similar to that in the previous figure but the density of cells is greater.

When she came back a week later, much of the empty space had been infilled; there were now about 300,000 cells per square centimetre.  These mostly belonged to the same species that she had found the week before.  The difference is that they are now rubbing up against each other and this has some important consequences.  All plants need light and nutrients to grow and algae are no exceptions.   Sunlight provides the energy for photosynthesis but now, at week three, the density of algae is such that there is a chance that some of the light will be intercepted by a neighbouring cell.   The total amount of sunlight that filters through the water to the pot surface is already much lower than that available at the lake surface; now it has to be shared out between many more cells.   At this point, properties such as fast growth rates that helped our pioneers to colonise the plant pot become less relevant, and it is algae that are better adapted to capturing the limited light that will survive.

So when Lydia came back to Wastwater after six weeks, she saw a very different community of algae on her pots.   There was still a lot of Achnanthidium minutissimum, but rising above these was the elegant art deco shape of Gomphonema acuminatum (also found in Lake Popovo) which, importantly for our story, grows on a long stalk.  There are also cells of “Cymbella affinis” (the correct name at the time that Lydia was working but see comments in the previous post about the nomenclatural history of this species).   This, too, grows on a long-stalk, the better to grow above the Achnanthidium and other pioneers.   If we continue to use the analogy of a patch of wasteland, then it has now reached the point where it has been invaded by shrubs such as hawthorn and blackthorn.   However, in a terrestrial habitat this would happen two or three years after the first pioneers had arrived, not six weeks as Lydia had observed for the algae.   She also found the diatom called Tabellaria flocculosa which forms filaments.  These often start out loosely-attached to the substratum but more often break free and become entangled around the other algae.   In our “wasteland” analogy, these would be the brambles.

The microbial world of the littoral zone of Wastwater after five weeks of colonisation.  Gomphonema acuminatum, “Cymbella affinis” and Tabellaria flocculosa have now joined the assemblage seen in the two earlier dioramas.

The experiment finished shortly after this, terminated when the apparatus was overturned.  Whether by a wave or by vandalism, Lydia will never know but this event is, itself, a metaphor for the harsh world in which benthic algae have to survive.  In real life, the many cobbles in the littoral zone will be rolled by wave action or, as we have seen in other posts, invertebrate grazers could have removed much of the “shrubbery”, leaving a “pasture” composed of the tough, fast-growing species such as Achnanthidium minutissimum to dominate samples.   The “successions” we see in the microscopic world not only take place much more quickly than those in the macro world, but they also rarely have a stable “climax”: just a brief pause before the next onslaught from the physical, chemical and biological processes that shape their existence.

References

King, L., Barker, P. & Jones, R.I. (2000). Epilithic algal communities and their relationship to environmental variables in lakes of the English Lake District. Freshwater Biology 45: 425-442.

King, L., Jones, R.I. & Barker, P. (2002). Seasonal variation in the epilithic algal communities from four lakes of different trophic state. Archiv für Hydrobiologie 154: 177-198.

Diatom hunting in the Pirin mountains

I started 2018 peering down my microscope at a sample that I collected whilst in Bulgaria back in the summer.   I have written about my trip to the Pirin mountains before (see “Desmids from the Pirin mountains”) but the diatom sample that I collected from Lake Popovo had remained unexamined since I got back.

I had waded into the littoral zone of this steep-sided corrie lake and picked up a few of the smaller stones, which I had then scrubbed with the toothbrush stowed in my rucksack to remove the thin film of diatoms.  These, like most of the algae that I collect on my travels, get treated to a bath in local spirits to ease the journey back to the UK.  This is not an ideal preservative for soft-bodied algae but is not a problem when your primary interest is diatoms with their tough silica cell walls.  Once I got back, I had them prepared and mounted ready for inspection, but then got distracted by other things and have only just got around to having a proper look.

The two most abundant taxa were the Achnanthidium minutissimum complex (probably at least three species) and Cymbella excisiformis.  Together, these constituted over eighty per cent of all the diatoms in the sample.  Ten years ago, I would have called the organism I was calling Cymbella excisiformis by a different name, Cymbella affinis, but opinions have shifted more than once.  The original Diatomeen im Süsswasser-Benthos von Mitteleuropa has images of C. affinis that are actually C. tumidula, and also describes C. excisa as a separate species.   However, the most recent view is that C. affinis and C. excisa are two names for the same species, with C. affinis taking precedence.   To confuse matters yet further, the population illustrated below shows a gradation of features from “C. affinis” to “C. excisiformis”, suggesting that the use of length:width as a discriminating factor is over simplistic.  Krammer tried to explain his rationale for distinguishing between these species in his 2002 monograph but he uses the name “C. excisa” for the organism called “C. affinis” in our 2017 English edition.  Confused?  You will be ….

Cymbella excisiformis” from Lake Popovo, Pirin Mountains, Bulgaria, August 2017.   Based on Lange-Bertalot et al. (2017)’s criteria of length:breadth 4.2-5.3 in C. excisiformis compared to 3.1 – 3.8 in C. affinis, images a., b. and c. are C. excisiformis whilst d., e., f. and g. are C. affinis.   Scale bar: 10 micrometres (= 1/100th of a millimetre).

This is another good example of points that I have made several times before: that we should always try to identify populations rather than single cells, and that we should treat dimensions stated in the literature as indicative rather than definitive (see “More about Gomphonema vibrio”).    Length:width, in particular, can change a lot during the life-cycle of the diatom.

Species of Gomphonema were also present in the sample.  Though not numerically abundant (none constituted more than one per cent of the total count), they included some large cells which, in addition, have extensive mucilaginous stalks, so their contribution to total biomass is greater than their low abundance suggests.   I’ll write more about the ecology of these species in the next post.   Finally, I also found other Cymbella species, as well as some Encyonema and Encyonopsis, and a few valves of Eucocconeis flexella, a relative of Achnanthidium and Cocconeis which has a distinctive diagonal raphe.

Gomphonema spp. from Lake Popovo, Pirin mountains, Bulgaria, August 2017.   h., i.: G. acuminatum; j.: G. truncatum; k.: unidentified girdle view; l.: G. pumilum.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

There is, at this point in time, no official Bulgarian method for assessing the ecological status of lakes using diatoms so I have evaluated Lake Popovo as if it were a low alkalinity lake in the UK instead.  Using the method we developed, this one sample has an Ecological Quality Ratio of 0.92, which puts it on the border between high and good status.   Looking around the lake, I see no reason why it should not be firmly in high status but, at the same time, I am using an evaluation method that was designed for lakes 2000 kilometres away, so maybe we should not expect perfect results.    However, I have performed similar exercises at other lakes far from the UK and also got similar results (see “Lago di Maggiore under the microscope”) which points to a basic robustness in this approach.

The outflow of Lake Popovo leads into a cascade that ends in the first of a series of lakes, the “Fish Popovski” lakes.   I wrote about the desmids in this lake back in September (see “”Desmids from the Pirin mountains”) and will return to this sample in order to describe the diatoms in another post.   But, meanwhile, the assemblage at Popovo reminded me of the littoral algae in another lake that I really should tell you about …

Miscellaneous diatoms from Lake Popovo, Pirin mountains, Bulgaria, August 2017.   m.: Cymbella sp.; n.: Encyonema neogracile; o. and p.: Eucocconeis flexella (raphe valve and girdle view respectively).  Scale bar: 10 micrometres (= 1/100th of a millimetre).

Lake Popovo, photographed from close to the location from which my sample was collected.  The brass plate on the rock at the right hand side gives the altitude as 2234 metres above sea level.  The photograph at the top of the post shows Lake Popovo against a backdrop of the Pirin mountains.

References

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

Krammer, K. (2002).  Diatoms of Europe volume 3: Cymbella.   A.R.G. Gantner Verlag K.G., Ruggell, Germany.

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.

The UK lake diatom assessment method is described in:

Bennion, H., Kelly, M.G., Juggins, S., Yallop, M.L., Burgess, A., Jamieson, J. & Krokowski, J. (2014).  Assessment of ecological status in UK lakes using benthic diatoms.  Freshwater Science 33: 639-654.

Details of the calculation can be found in the UK TAG method statement.

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”

Reference

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. www.theLancet.com/plantary-health 1: e48-e49.

Note

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.