Little pond of horrors …

One of the highlights of the British Phycological Society’s recent meeting in Plymouth was a talk by Sebastian Hess from the University of Cologne about amoebae which preyed upon microscopic algae.  His presentation included several video clips, one of which featured the aptly-named Vampyrella attaching itself to the outside of an alga cell and slowly sucking out its contents.   The clip drew audible gasps from the audience, none of whom had walked into a dryly-named session on “Algal interactions across the tree of life” expecting the tropes of a horror movie to be displayed before their eyes.

The link to the YouTube video below gives you some idea of the predatory nature of these organisms.   They are not technically parasites but “protoplast feeders”, penetrating the cell wall of the victim and consuming the cell contents by a process known as “phagocytosis”.   Although these organisms have been known for a long time (they were first described in 1865), it is only in recent years that the diversity of these organisms has become apparent.  That’s because, like many unicellular organisms, it is difficult to fully appreciate the differences just by peering at them through a microscope.  It has only with the advent of environmental DNA analyses that this has been understood.   We now know, for example, that the species found in freshwater, soil and marine environments are all different and that each vampyrellid is fairly specific to a particular group of algae (more about Sebastian Hess’ work can be found here.

The vampyrellid amoeba Arachnomyxa cryptophaga feeding on the green alga Eudorina elegans, from the German YouTube channel “Nicht interessant”

Those of us who are interested in algae tend to go on about their importance in trapping the sun’s energy via photosynthesis but rather less time thinking about how that energy then passes from the algae through to higher trophic levels.   I often see chironomid larvae feeding on algae when examining samples (see, for example, “More about very hungry chironomids”) but these tend to use the larger filamentous algae as supports while they graze on the smaller epiphytes (mostly diatoms in the streams I look at) which grow on the surface of the filaments.   The vampyrellids, by contrast, have powerful enzymes that can punch holes in the though cell walls of filamentous algae so that they can suck out the contents.   At the simplest level that creates a tasty meal for the vampyrellid but, from a broader ecological perspective, these amoebae are turning large unpalatable chunks of carbon that an insect larva cannot manipulate into its mouth into smaller nuggets that could, in theory, be consumed by small beasts.  These small beasts, in turn, fuel the slightly larger bugs which may be prey for a fish.   The vampyrellids, in other words, help keep carbon pumping through the aquatic ecosystem.

It is not just predatory amoebae that perform this function.  Another talk at the Plymouth meeting by Davis Laundon of the Marine Biological Association showed that microscopic fungi may play a similar role.   Again, I’ve mentioned these organisms before (see “Little bugs have littler bugs upon their backs to bite ‘em …”) but not really reflected on what role they play in an aquatic ecosystem.  Davis worked in marine rather than freshwater ecosystems but the same principle seems to be at play: large chain-forming diatoms such as Chaetoceros are too big for many zooplankton grazers to feed upon but thraustochytrid fungi inadvertently convert these big indigestible hunks of carbon into bite-sized portions which then fuels the ecosystem in Plymouth Sound.

Coincidentally, my own interest in the microscopic world started when I read about amoebae in school textbooks, and my earliest natural history explorations involved trying to find amoebae in local ponds, usually without success (when I was in Nigeria, protozoans returned the favour … but that’s another story).   Even now, I do not regard amoebae as particularly easy organisms to observe and have not tried to identify them.  However, once your eyes (and mind) are tuned to noticing particular phenomena in nature, there is a positive feedback loop and you start to notice these phenomena more and more.  I suspect I have been suffering from “amoeba blindness” for some time.  Last year I wrote an essay about what we see and don’t see when peering down a microscopeand Marian Yallop, one of my co-authors, included some photographs of amoebae, reminding me of my earlier fascination with these unicellular organisms.  I’ll be watching out for these as I examine samples, and trying to learn a little more about them during 2020.


A plate from showing interactions between algae and other protists from Kelly et al. (2019).  A. A ciliate has consumed a variety of live pennate and centric diatoms and cyanobacterial filaments. B. Algae autofluorescing red and cyanobacterial filaments yellow within the ciliate. C. Other protists e.g. Vorticella select relatively smaller soft-bodied green algae. D. This amoeboid protist had previously consumed two relatively large diatoms E. Some reorganising of the cell contents is required to shuffle these engulfed cells to the periphery. F. Exocytosis takes place to release the partially digested cells, and the amoeba rapidly moves away. This sequence of events lasted a few minutes. Images (A-B, D-F) were taken from biofilm material from Winford Brook, North Somerset, UK by Marian Yallop; Image C was taken from the Danube at Zimmern, Baden-Württemberg, Germany by Lydia King.


Hess, S., Sausen, N. & Melkonian, M. (2012).   Shedding light on vampires: the phylogeny of vampyrellid amoebae revisited.  PLoS One 7: e31165. 

Hess, S.& Melkonian, M. (2013).   The Mystery of Clade X: Orciraptor gen. nov. and Viridiraptor gen. nov. are Highly Specialised, Algivorous Amoeboflagellates (Glissomonadida, Cercozoa).  Protist 164: 706-747.

Kelly, M.G., King, L.. & Yallop, M.L. (2019).  As trees walking: the pros and cons of partial sight in the analysis of stream biofilms.  Plant Ecology and Evolution 152: 120-130.  


This week’s other highlights:

Wrote this whilst listening to: PJ Harvey

Cultural highlight: Tutankhamun: Treasures of the Golden Pharaoh at the Saatchi Gallery in London.   Was looking forward to seeing Girl From The North Country, a musical based around Bob Dylan’s songs, on the same trip to London but it was cancelled 40 minutes before the start due to cast illness.

Currently reading: Nine Lives: In Search of the Sacred in Modern India by William Dalrymple

Culinary highlight: Mildreds, a vegetarian restaurant in London’s Soho.   You can’t book ahead, so we had to wait for a table.   We spent this time at the closest pub, which just happened to be the John Snow, featured in “A drink of water with John Snow”, a post from 2013.  Mildreds was worth the wait, particularly for the desserts.  I was diagnosed as lactose-intolerant last year and normally gaze miserably at dessert menus packed with dairy-rich offerings.  Mildreds, however, is fully vegan throughout January, so the entire dessert menu was there for the choosing.

Quantifying our ignorance …


I am fairly sure that I am not a popular person after my latest choice of slide for the “ring test”, the regular calibration exercise that UK and Irish diatomists perform.   I had noticed a few taxa that we had not seen in previous ring tests in a sample I collected during my visit to the Shetland Islands back in May 2019 (see “Hyperepiphytes in the Shetland Islands”) but, on closer examination, the sample proved to be both highly diverse and very challenging.  The seven experienced analysts who provide the benchmark analyses for the ring test found, between them, over 150 different species: some we could name with confidence, but others we could match to no published description.  Amongst those was the species of Achnanthidium photographed below.   It might be Achnanthidium digitatum or possibly A. ertzii but, then again, it does not quite match the characteristics of either of these so, once again, we have left it unnamed (you can find the original descriptions of both these species in the reference list).

According to Algaebase there are 116 species of Achnanthidium that are currently accepted but descriptions of these are scattered through the literature so it is really hard to be confident that you have found a new species during a routine survey.  This is particularly the case when we only have light microscopical analyses with which to work, as the small size of Achnanthidium species means that you really need a scanning electron microscope to see the fine details clearly.  This, however, assumes that the pool of unnamed Achnanthidium species is finite and that the 116 species on Algaebase is a significant proportion of the total number of Achnanthidium species.  A recent study by Eveline Pinseel and colleagues based on samples from Arctic regions offers hints that there is still plenty of diversity within the genus that cannot be linked to named species

This may, however, be a naïve assumption.   My colleague Maria Kahlert, who works in Sweden, comments that she is quite happy looking at samples that I send her from polluted sites in the UK as she can name most of the species (Achnanthidium and otherwise) from her own experience.   It is the samples from pristine habitats that fox her because so many of the forms are different to anything she has encountered in Sweden.  We have, in other words, a neat reversal of the opening line of Anna Karenina (“All happy families are alike, each unhappy family is unhappy in its own way”), with very high beta and gamma diversity of diatoms (probably other microalgae too) as a characteristic of regions with low population density (see “Baffled by the benthos (2)”).  We often miss this in our enthusiasm to fit all that we see down the microscope to published descriptions, but when we take time to look hard, that diversity – and those differences between sites – start to mount up.


The unknown Achnanthidium species from Petta Water, Mainland, Shetland Islands (pictured at the top of the post).  Scale bar: 10 micrometres (= 1/100th of a millimetre).

Let’s think of this as an ecological experiment to understand the diversity of Achnanthidium, following the capture-mark-capture approach.   Capture-mark-recapture is a technique used by ecologists to assess the size of a population.   As it is rarely possible to count all individuals, a portion of the population is collected, marked (a dab of paint on a snail’s back, for example) and released.   Some time later, the population is sampled again, and the proportion of those that bear the mark in this second sample is used as an indicator of the proportion of the population captured by the original sample.   Though devised for population biology, some have used the same principles to understand diversity in other contexts too so might it work as a means of understanding the yet-to-be discovered diversity of diatoms?

What we have in the scattered taxonomic literature is a record of all the Achnanthidium species that have been “captured” (i.e. observed) and “marked” (i.e. described) by taxonomists.   Suppose we now go some locations not previously visited by taxonomists, take some new samples and see 1) how many different forms of Achanthidium we can see and b) how many of these are “recaptured” (i.e. forms that align with previously described species).   Or, thinking about the problem in a different way, the number of named species could be compared with the number of distinct “operational taxonomic units” (“OTUs”) detected by metabarcoding.   More relevantly, how many extra OTUs are added when more lakes and streams are added to the dataset?   There are well-established methods for deriving “rarefaction curves” that might be useful in understanding regional diversity of diatoms, and modifications of “capture-mark-recapture” have been used to understand taxonomic diversity in palaeobiolgoical contexts, so why not in contemporary ecology too?

The Shetland Islands would make an ideal test ground for such a study as they are geologically-diverse habitats providing the types of conditions where Achnanthidium species thrive (low population density and agricultural intensity.   The diatoms of the region were studied about 40 years ago by my late mentor John Carter and although one of his samples yielded the type material for Achnanthidium caledonicum there have been so many developments in Achnanthidum taxonomy subsequently that this archipelago represents a tabula rasa for a modern taxonomist.   Its many remote lochs and streams offer the setting for a natural experiment which sets out, to put it bluntly, to quantify our ignorance.


Achnanthidium caledonicum from Loch Osgaig, Highland Region, Scotland.   Originally described as Achnanthes microcephala f. scotica Carter & Bailey-Watts 1981 (Scale bar: 10 micrometres (= 100th of a millimetre). 


Carter J. R., Bailey-Watts A. E. (1981). A taxonomic study of diatoms from standing freshwaters in Shetland. Nova Hedwigia. 33: 513-630.

Pinseel, E., Vanormelingen, P., Hamilton, P. B., Vyverman, W., Van de Vijver, B., & Kopalova, K. (2017). Molecular and morphological characterization of the Achnanthidium minutissimum complex (Bacillariophyta) in Petuniabukta (Spitsbergen, High Arctic) including the description of A. digitatum sp. nov. European Journal of Phycology 52: 264-280.

Van der Vijver, B., Jarlman, A., Lange-Bertalot, H., Mertens, A., de Haan, M. & Ector, L. (2011).  Four new European Achnanthidium species (Bacillariophyceae).  Algological Studies 136/137: 193-210.

Liow, L.H. & Nichols, J.D. (2010). Estimating Rates and Probabilities of Origination and Extinction Using Taxonomic Occurrence Data: Capture-Mark-Recapture (CMR) Approaches.  The Paleontological Society Papers 16: 81-94).

This week’s other highlights:

Wrote this whilst listening to: Sheku Kanneh-Mason’s recording of Elgar’s Cello Concerto.   Taking me back to his performance at the proms on a warm evening last summer.

Cultural highlight: Sam Mendes’ film 1917 which, coincidentally, uses the River Tees (as featured sporadically in this blog) as one of its locations

Currently reading: I have just finished Good Economics for Hard Times by Abhijit V. Banerjee and Esther Duflo, which I mentioned a couple of weeks ago.  It left me with the feeling that, had both Boris Johnson and Jerermy Corbyn read it and taken on its messages, the election campaign and the UK political landscape might have been very different.

Culinary highlight: OK Diner on the southbound side of the A1 near Grantham.  Felt like we were walking into the opening scene from Pulp Fiction (the one where Tim Roth jumps up onto a table and attempts to rob all the customers).   Escaped with wallet intact.


Hooray for hippo dung …


I’ve only seen hippopotami in the wild once in my life, and then only at a distance in the Yankari game reserve in northern Nigeria.   I took some photos, but these were taken with only a moderately-powerful telephoto lens and crocodiles basking a few metres from where our Land Rover was parked were a more pressing concern.  In any case, the prints from that holiday (years before digital cameras) are now lost.   The photo at the top of this post is, in fact, a pygmy hippopotamus – a different genus to the common hippopotamus (Hexaprotodon liberiensis rather than Hippopotamous amphibious) – taken at smaller wildlife park (a glorified zoo, really) near Jos but it will do for my purposes. 

A couple of years ago, I wrote about the role that bears may play in the transfer of essential nutrients from the ocean to the forests of north-western North America (see “Ecology’s bear necessities”).  I recently came across a paper that described a situation where hippos were responsible for a significant movement of nutrients in the opposite direction: from land to water.   We think of hippopotami as beasts that wallow in muddy water, but that is because they are filmed and photographed when there is enough light.   Hippos are actually nocturnal animals, coming out of the water to feed on the savannah grasslands when it is dark, and resting in pools during the day.    As they rest in their pools, the grass that they eat during the day is slowly digested (hippos are “pseudoruminants”) and, eventually, passes out of their colons as faeces.   That is an important source of carbon, nitrogen and phosphorus for the river, but also of silicon, an essential nutrient for diatoms.   Diatoms form the base of the food chain in Lake Victoria so, consequently, depend upon a constant supply of silica from the surrounding catchment, and the hippos are inadvertent vectors for this.

There is plenty of silicon in the natural environment (it is the second most abundant element on earth, after oxygen) but most is tightly-bound in particles and so is not in a form that is accessible to other organisms.   Some plants, especially grasses, however, use silicon as a means of strengthening and supporting their cells.  In the process, they also provide a measure of protection (as anyone who has been cut by the sharp edge of a grass leaf will know).  The silicon is taken up by the plant’s roots, but is then laid down in the cells as structures called “phytoliths”.  When these phytoliths are released back into the environment via a tortuous path through the hippo’s digestive system, the silicon they contain is in a much more accessible form than when it was trapped into minerals in the savannah soil.

The phytoliths released by the hippos form about three quarters of all the biologically-available silicon in the hippo pools and, when these have made their way down the stream, may also have an effect on the ecology of Lake Victoria.  At this point, the paper gets rather speculative, but noting that there has already been a significant decline in hippo numbers in recent decades, the authors suggest that this may have had an impact on the ability of diatoms to compete with other algae, contributing to the greater dominance of cyanobacteria that has been observed in recent years.

Even allowing for a little academic hyperbole, this is a useful reminder that trying to keep ecology neatly compartmentalised is never a good idea.  Everything is connected to everything else: lakes, rivers, terrestrial systems.  We sort of know this instinctively but, at the same time, scientists spend so much time absorbed by their specialisms that they often forget this too.   The hippopotamus seems to be an unlikely benefactor of tiny diatoms, but maybe that is the fault of our imagination rather than of nature.


Schoelynck, J., Subalusky, A. L., Struyf, E., Dutton, C. L., Unzué-Belmonte, D., Van De Vijver, B., Post, D.M., Rosi, E.J., Meire, P. & Frings, P. (2019). Hippos (Hippopotamus amphibius): The animal silicon pump. Science Advances 5:


A baboon, photographed at Yankari game reserve in 1990.  The photograph at the end of the post shows a waterbuck, photographed on the same visit.

And, once again, some notes on what else I have been up to this week:

Wrote this whilst listening to: Keith Jarrett’s Köln Concert

Cultural highlight: Keith Jarrett’s Köln Concert is so good that I am prepared to enter it under two headings.  Worth listening to Tim Harford’s Cautionary Tales Podcast (Episode 7: Bowie, jazz and the unplayable piano) to learn more about this remarkable piece of music.

Currently reading: Raynor Winn’s The Salt Path.  I’m in south-west England so a book about walking the South West Coast Path seems appropriate.

Culinary highlight: yet to happen.  I’m at a conference at the University of Plymouth, subsisting on breakfast from a chain hotel and lunch from a university catering service that offers few options for those who are lactose-intolerant.




Fit for purpose?



It is sobering to think that the Water Framework Directive (WFD) will be twenty years old this year (23 October, to be precise).  The 70 pages of legalese that comprise this directive have, to a large extent, determined the course of my career over the past two decades (it is a few sentences in Annex V, to be precise, but unravelling and interpreting these has been enough).  Just before this anniversary arrives, however, the European Commission has published a “fitness check”, giving the Directive a thorough once-over before reaching a mixed verdict on its performance.

The report’s conclusion is that the WFD has provided a governance framework for water management but, overall, the condition of Europe’s water bodies has shown little significant improvement since the WFD passed into law.   The original objective – grossly optimistic in hindsight – was for all Europe’s water bodies to be at least at good status by 2015.  Instead, we are still in the situation where less than half are at good status.  There is no doubt that there have been local improvements, and the rate of deterioration may have decreased but this is not the same as a general trend towards better ecological quality in our water bodies.   I’ll offer three possible reasons for the shortcomings, based on my own experience of WFD implementation, in the hope that lessons learned from turning a well-intentioned policy instrument from theory into practice will have some broader lessons as we tackle the climate emergency.

The first lesson is that complex problems, by necessity, spawn complicated legislation.  The Water Framework Directive arose from an attempt, in the early 1990s, to produce a directive addressing the Ecological Quality of Waters.  As debates about this progressed, people realised that you cannot consider the state of the aquatic environment in isolation, without also considering broader economic issues such as water pricing and, indeed, all aspects of catchment management that respects the rights of other legitimate users.  Each of these issues requires a small army of bureaucrats to unpack and apply within the 28 Member States.   In some countries and for some aspects of the legislation, there were procedures in place that simply needed tweaking to be fit-for-purpose.  Some other aspects were, however, completely new for almost everyone.

The whole idea of using the health of an aquatic ecosystem (“ecological status”) as a measure of the long-term sustainability, for example, was something never attempted on such a scale before.  It had been advocated in the academic literature, and there were a few localised attempts to apply the system (RIVPACS in the UK, for example) but, as the sun rose on 23 October 2000, the task of working out how the fine words of Article 4 had to be translated to a practical reality that was both faithful to the intentions of the WFD and that worked within public sector budgets had to start.


A second big issue that was relatively under-acknowledged in the fitness check is that solving environmental problems cannot be achieved without engaging other sectors as well.   A recent review, to which I contributed, highlighted this, emphasising the need, first, to integrate water policy with other sectors (such as agriculture) whilst, at the same time, emphasising the need to demonstrate tangible benefits that extend beyond the subtleties of shifts in ecological parameters.  Bring agriculture on board to achieve more sympathetic management of catchments, in other words, recognise the contributions that farmers make (“public money for public goods”) but also back this up with substantial demonstrations of reduced flood risk for urban areas downstream.   That calls for a level of joined-up thinking across sectors that has not yet been achieved in Europe and which is, perhaps, an opportunity that the UK, shortly to be freed from the leviathan that is the Common Agricultural Policy, may be in a better position to address.  We live in hope.

The third reason may be that the ambition of the WFD may be higher than many politicians and civil servants are happy with.   Article 1 sets out the objective of promoting “sustainable water use based on a long-term protection of available water resources”.  A phrase such as that could have appeared in any of the party manifestos for our recent election but when the scientists unpack this and explain that this will mean that every river in the country needs to have average phosphorus concentrations of well under 0.1 milligrams per litre, and the water planners put a price on this, alone, that runs into hundreds of millions (if not billions) of euros, then that ambition falters.   More particularly, the noisy nature of much ecological and environmental data gives ample opportunity for bureaucrats to prevaricate rather than take steps that are unlikely to play well with the media (the WFD enshrines the “polluter pays” principle and, as we all contribute to urban wastewater loading, this translates to “voter pays”).

As its 20th anniversary approaches, the WFD will have spanned four electoral cycles (assuming national parliaments have five-year terms), at each of which policy wonks will have been thinking less about long term sustainability of water resources and more about short-term swings in voting preferences.   Moreover, since 2008, much of Europe has felt the consequences of the banking crises, with public sector finances often badly affected.  Again, the scientific challenges that the WFD creates provides easy excuses for cash-strapped regulators to kick the can down the road rather than make potentially unpopular decisions.

Governance may be in place, in other words, but a willingness to push this governance to deliver may be lacking.  That, in turn, reflects a perceived unwillingness on the part of the electorate to accept the costs.  Imperfect democracies will always deliver imperfect solutions, particularly when the underlying problems are complex and the opportunity costs are high.


Pictures in this post are from a New Year’s Day walk around the riverbanks in Durham.  New feature for 2020 is a few notes on what else I’ve been up to during the week in which this post gestated:

Wrote this whilst listening to:  Bob Dylan’s John Wesley Harding; Bruce Springsteen’s Nebraska

Cultural highlight: Greta Gerwig’s Little Women.

Currently reading: Good Economics for Hard Times by Abhijit V. Banerjee and Esther Duflo – two Nobel Prize winners setting global problems into a broader economic framework.  Not an easy read but very stimulating.   A good follow-up to Kate Raworth’s Doughnut Economics, which I mentioned in a couple of posts last year.

Culinary highlight: followed a recipe in The Guardian which involved cramming all the leftovers from our Christmas dinner (turkey, stuffing, roast potatoes, parsnips, brussel sprouts) into a loaf tin along with some breadcrumbs and two eggs to bind.  This created a meatloaf which I froze and then produced on New Year’s Day to provide a final reminder of the festive season before the realities of 2020 intruded.  Doubly enjoyable as West Ham had their first win of the Festive Season as it was being demolished.


Carvalho, L., Mackay, E. B., Cardoso, A. C., Baattrup-Pedersen, A., Birk, S., Blackstock, K. L., Borics, G., Borja, A., Feld, C.K., Ferreira, M.T., Globevnik, L., Grizzetti, B., Hendry, S., Hering, D., Kelly, M., Langaas, S., Meissner, K., Panagopoulos, Y., Penning, E., Rouillard, J., Sabater, S., Schmedtje, U., Spears, B.M., Venohr, M., van de Bund, W. & Solheim, A. L. (2019). Protecting and restoring Europe’s waters: An analysis of the future development needs of the Water Framework Directive. Science of the Total Environment 658 1228-1238.

Looking back on 2019


So at least we now know what will happen next: the UK is set to leave the European Union at the end of January 2020.  Then the hard work of deciding on the shape of a future relationship begins.  The Prime Minister has already announced that the transition period will not be extended beyond the end of 2020 which gives a ridiculously short period in which to reach a trade deal.  Whether he takes up the EU’s offer to extend this remains to be seen.  I suspect that, once the bluster dies down and the magnitude of the task ahead is clear, then common sense may prevail.   If we look for some positives amidst the wreckage of progressive politics after the election, then it is that the Prime Minister can no longer be dictated to by the toxic European Research Group.

What are the prospects for the UK environment in 2020?   I wrote about this in the run-up to the election and there is no need to repeat myself.   The Environment Bill will be re-introduced and, with the Conservative majority, I guess there is little prospect of significant change during the Committee stages, despite the reservations that the environment lobby have about some aspects of this.   The bigger question will be how agricultural support is re-organised once the UK is no longer part of the Common Agricultural Policy.   If there is a greater focus on “public money for public goods”, then this can only be good for the environment.  The question that I still cannot answer, after reading the manifesto before the election, is how a re-organised and more environment-friendly agricultural subsidy scheme can be managed and enforced without more skilled people working on the ground.

I also foresee a weaker focus on the UK’s aquatic resources over the next few years.   First, though the Water Framework Directive has been transposed into UK legislation, few believe that the proposed Office for Environmental Protection will have as many teeth as the European Court of Justice.  Second, the focus on the climate emergency will, without specific funding for a larger workforce in DEFRA and associated agencies, will weaken the capability to respond to the challenges that the aquatic environment still poses.   Third, two of the most obvious consequences of climate change at the moment are flooding and drought, so we can expect more of the Environment Agency’s time and resources to be focussed on these issues.  Finally, the state of the UK’s freshwaters is, to be frank, not that high on anyone’s agenda just at the moment.

There is one other trend, independent from Brexit and populism, that we need to resist.   That is the increasing reliance on the media as an intermediary between us and the environment.   On the one hand, we know about the global climate emergency because of pictures piped onto our homes via television and the internet.  On the other hand, we are not noticing the changes that happen in our own back gardens.   This disconnect makes us, I fear, more susceptible to political hype (left and right) and feeds into the issues I wrote about in the previous paragraph.  I started this blog in 2013 mostly as a way of making me look more closely at my own local environment, and I will continue in 2020, because I regard this self-discipline as a necessary corrective to the modern ecologist who spends more time indoors staring at spreadsheets than outside interacting with nature.  If a few of you want to join me on this journey, then I will be delighted to have some company …

20:20 hindsight …

Last week saw the publication of a paper that has undergone a slow gestation through the year.   It’s an opinion piece published in the new open access journal Metabarcoding and Metagenomics and describes some of the lessons I learned during the development of a new diatom metric based on metabarcoding data.   The science behind these projects is written up in reports and papers, but that only tells part of the story.  Applied science needs a context, and my paper is more about how the new science fits into a wider process of managing change in large and ponderous government agencies.

That’s where my title comes from: “Adapting the (fast-moving) world of molecular ecology to the (slow-moving) world of environmental regulation”.   The new science of metabarcoding is developing fast and some of the assumptions that we made at the start of the project have now been overtaken by developments in methods.  Yet the regulatory systems into which these methods will be integrated need to be stable and continual “tweaks” to optimise the system would not be welcome.   “Ponderous”, in this context, is not necessarily a bad thing.  Imagine driving in your local area and finding all the speed limits had changed at the whim of an official and without any consultation or advance warning.  Finding a balance between these two needs: for the best possible methods and a stable basis for regulation seems to be one of the biggest challenges those of us with an interest in molecular ecology face over the next few years.

My own view, reflecting back over the discussions I’ve had over the past few years, is that this is possible, but that the UK’s environment agencies will need some major structural changes for this to come about.   As I was reviewing the proofs of the paper, I came across Tim Harford’s fascinating podcast Cautionary Tales and, in particular, an episode called “How Britain Invented, then Ignored, Blitzkrieg”.  The point he made in this episode was that improvements to individual components of a system (tanks, in his example) have little value if the overall architecture within which those components operate are not also regularly updated.   He cited a paper by Rebecca Henderson and Kim Clark which, had I seen it sooner, would have strengthened the principal argument in my paper.

Henderson and Clark’s examples were drawn from manufacturing industry, but we can use the same kind of language to make their framework relevant to ecological assessment.   Broadly speaking, an ecological assessment method (using diatoms, in this case, but it could also be invertebrates, macrophytes or fish) is one component in a larger decision-making “machine”.  Replacing the existing methods, based on specialist biologists painstakingly analysing samples to identify and enumerate the taxa present by one based on metabarcoding technology constitutes a “modular innovation”, using the terminology in the table below.   That might well work in some cases (replacing an analogue by a digital telephone, for example, doesn’t fundamentally affect the way we communicate with one another).  However, the question that Henderson and Clark were asking was what happens when an innovation interacts differently with other components, in which case a shift in the entire product design might be necessary.

A framework for defining innovation (after Henderson and Clark, 1990)

  Core concepts
Reinforced Overturned
Linkages between core concepts and components



Incremental innovation


Modular innovation



Architectural innovation

Radical innovation

Harford used the comparative fortunes of IBM and Apple in his podcast (Henderson and Clark’s paper was written before the tech revolutions, otherwise I’m sure they would have done so too).  Apple did not invent the mouse or the graphical user interface, but they were able to fit these into a radical new architecture of components, opening up an enormous market for consumer-friendly gadgets.  IBM, by contrast, was the market leader for mainframe computers, but its thinking and organisational structures were so focussed on these that they were not nimble enough to adapt to this new world.

The question that arises when using metabarcoding in a regulatory capacity is whether this technology just constitutes a “modular innovation” or whether a broader refit of the organisations that use the technology is necessary in order to maximise their benefits. My argument is that metabarcoding constitutes a “radical innovation” partly because the way that individuals interpret  metabarcoding data is different to the way that they would traditional data, which means that the value that a biologist can add to evidence for a regulatory decision on his/her locale will change, and because the gathering of evidence by traditional means constituted an “unstructured training program” for freshwater biologists that gave them a broad awareness of freshwater ecology in their region.

Furthermore, the rate of development of these new technologies is such that a better way needs to be find of balancing innovation and regulatory stability beyond the very ponderous approach in force in the UK at the moment.  There are ways of doing this, but the mindset in the administrations needs to change before these can be implemented and there would also need to be more administrators to oversee this process, a big ask in a public sector still limping along on much reduced budgets.

One of the biggest lessons we learned was, in fact, that if you want to learn lessons you need to get stuck in and have a go.  There are plenty of review papers in the academic literature now saying how metabarcoding might be used for ecological assessment, and plenty of discussion about these new technologies within the hierarchies of the government agencies. But you can only go so far with theory: not all of the challenges we encountered were anticipated and, certainly, not all the assumptions that drove the original commissioning of the project turned out to be correct.   The only way of testing these was to take a step into the unknown.  We learned the hard way, but maybe future projects will benefit.


Henderson, R.M. & Clark, K.B. (1990).  Architectural innovation: the reconfiguration of existing product technologies and the failure of existing firms.  Administrative Science Quarterly 35: 9-30.


Reflections from Castle Eden Burn

As 2019 draws to a close, I have looked back at all the data I have collected from Castle Eden Burn over the past twelve months.   I chose this location precisely because it was different to my usual haunts and, despite having visited this Dene and others along the Durham coast for over thirty years, I realised that I had never had a look at the algae.  Dry river beds are not the most obvious hunting grounds for aquatic biologists, after all.   This year, I put that right over the course of a number of visits between January and November and in this post I am summarising what I found.

I found a total of 77 different diatoms in the six samples that I collected, not to mention green and yellow-green algae (see “When the going gets tough …”) and mosses (see “A thousand little mosses …”).   Of these diatoms, 48 were rare and infrequent, only found in one or two samples, and never forming more than one percent of the total number of diatoms present.   Of the remainder, only two were found in every sample (Humidophila contenta-type and Achnanthidium minutissimum) whilst another eight formed at least ten percent of the total on one occasion.  Numbers of each species waxed and waned over the year: Humidophila contenta-type was abundant in the sample from my first visit in January 2019 but relatively scarce thereafter.  In comparison, Luticola frequentissima was very abundant on two occasions (more than 80% of individuals), quite abundant on three other occasions but absent from the sample from my final visit in November.

Some of these differences are due to the variable flow regime: the stream was dry on three occasions, ponded on one and flowing on just two occasions.  Those occasions when there was no running water were those when the proportions of diatoms that are tolerant to desiccation (see “Life out of water …”) were most abundant, forming from 20 to 97 percent of all individuals.  When there was running water, it was motile Nitzschia  species that dominated.    In fact, there was a strong negative correlation between proportions of desiccation-tolerant and motile taxa in the samples, indicating that the diatoms responded rapidly to the changing pressures experienced in the stream.  There was also a relationship between the proportions of desiccation-tolerant diatoms and the number of taxa recorded – the latter is a good measure of the level of physiological stress experienced in a stream.

What of the diatoms themselves?  Humidophila contenta-type was one of the two ever-presents.  It is, however, very small (few of those in our samples were more than a 100th of a millimetre long), making it difficult to photograph and, indeed, to discern many of the features of the valve.   This species sometimes forms short chains though I did not see any in the Castle Eden Burn samples.  It is strange to think that, when I first started to identify diatoms, this was considered to be part of the genus Navicula.   Since then, it has moved into the genus Diadesmis before finally being transferred to the new genus Humidophila by Rex Lowe and colleagues in 2014.    Some recently-described Humidophila species cannot be differentiated from H. contenta without a scanning electron microscope, so I have referred to this as “Humidophila contenta-type”. Humidophila_contenta

Humidophila contenta ag. from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres.   Photograph: Lydia King. 

The most abundant diatom in samples collected during the dry periods was Luticola frequentissima.  I started the year referring to this as “Luticola mutica” but was gently corrected by colleagues more au fait with recent literature than me.   Luticola mutica is larger (length: 11-28 µm; breadth: 6-9.5 µm) and has more widely-spaced striae (16-18 / 10 µm) than L. frequentissima (length: 7 – 13.8 µm breadth: 4.8 – 6.8 µm; striae: 20 -24 / 10 µm).  The specimens in the plate below all fit the description for L. frequentissima.  Some of the large specimens have size ranges that overlap with L. mutica (though even the largest specimen as a striae density consistent with L. frequentissima).   L. mutica is associated with more brackish habitats whilst L. frequentissima prefers freshwaters.


Luticola frequentissima from Castle Eden Burn, Co. Durham, January 2019. Scale bar: 10 micrometres (= 1/100th of a. millimetre).  Photographs: Lydia King.

Simonsenia delognei is another characteristic species of habitats that dry out periodically.   This species, which is in the same family as Nitzschia, is quite small and only lightly silicified so easily overlooked.  It was common early in the year, but rare thereafter.  Whether this is a real characteristic of the species or an artefact of the conditions in Castle Eden Burn this year is difficult to tell as it is not a particularly common species so there are few other records against which this trend can be compared.


Simonsenia delognei from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres (= 1/100thof a millimetre). Photographs: Lydia King.

Two other species of Nitzschia were common: I illustrated N. clausii in “Out of my depth …” and have included photographs of N. sigma here.   I’m intrigued that two of the most conspicuous Nitzschia in this sample are sigmoid in outline.  I’ve visited the question of sigmoid diatoms before, and still don’t have any good explanation why a few diatoms have this outline (see “Nitzschia and a friend …”).  Note, too, that Nitzschia species can be sigmoid in valve view (i.e. looking down from above) or girdle view (i.e. looking from the side), although the great majority of species are straight in both planes.


Nitzschia sigma from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres (= 1/100th of a millimetre).   Photographs: Lydia King.

Finally, one more relative of Nitzschia that was found in a couple of samples, but never in large numbers, was Tryblionella debilis.  The genus Tryblionella was treated as part of Nitzschia for much of the 20th century.   As it appears to form a natural group with some distinctive characteristics, it is now generally treated as a distinct genus, although the molecular evidence indicates a complicated evolutionary history.   The principle characteristic of the genus is a longitudinal undulation on the valve face that is most clearly manifest on those species in the genus which have visible striae.   T. debilis is a small species with striae that are not resolvable with the light microscope; however, the undulations are just apparent as faint longitudinal lines running along the valve face.


Tryblionella debilis from Castle Eden Burn, Co. Durham, January 2019.  Scale bar: 10 micrometres (= 1/100th of a. millimetre).  Photographs: Lydia King.

That’s a lot of diatoms from a stream that is not always a stream.   I am sure that someone with interests in other groups of algae could probably make similarly long lists for some of those, and a more thorough exploration of habitats within the stream could add to the number of diatoms.  That’s before suggesting a molecular study, which might well reveal cryptic diversity (i.e. significant taxonomic variation that is impossible to discern with a light microscope) within the species I have already described.   The greater our capacity to unravel the mysteries of the microscopic world, the more, it seems, we discover we don’t know.


Lowe, R.L., Kociolek, P., Johansen, J.R., Van de Vijver, B., Lange-Bertalot, H. & Kopalová, K. (2014).  Humidophilagen. nov., a new genus for a group of diatoms (Bacillariophyta) formerly within the genus Diadesmis: species from Hawai’i, including one new species.  Diatom Research 29: 351-360.