The way things were …

Writing the previous post led me to contemplate how much things had changed over the time that I have been working in this field.  Back in the early 1990s when I first set out to look at the response of diatoms to nutrients in streams, few in the National Rivers Authority (NRA, predecessor to the Environment Agency) regarded phosphorus as a serious pollutant in rivers, and most biologists thought about ecological quality solely in terms of organic pollution and invertebrates.   In order to investigate the effect of nutrients, I wanted to visit sites where organic pollution was not a problem.

I was helped in this task by the work done by biologists at the then Institute for Freshwater Ecology (now Centre for Ecology and Hydrology) who had just developed the early versions of RIVPACS (“River Invertebrate Prediction and Classification System”) which established the principle of expressing ecological quality as the observed quality / expected quality.  This, in turn, required an ability to predict the “expected” condition for any stream.   The work that had developed these equations started from a dataset of invertebrate and environmental data collected from a wide range of “unpolluted” running water sites which, in those far off days, was compiled by asking biologists working for the Regional Water Authorities (predecessors to the NRA) for their recommendations of sites that were of “good” or “fairly good” quality.  Nowadays, screening sites to be used for calibrating ecological methods is a much more rigorous procedure but this was the first tentative step on a long journey and “expert judgement” was as good a place to start as any.

The paper that emerged from this exercise (see reference below) analysed data from these “unpolluted” sites and classified them into eight groups.  Each of these groups consisted of sites that shared similar invertebrate assemblages which reflected similarities in the habitat, from upland, fast flowing becks to deep, wide slow-flowing rivers in the lowlands.  The authors included a useful table that listed the physical and chemical characteristics of each of these groups and I noticed that the phosphorus concentrations reported for these spanned a very wide range.   This meant that I could use these as the basis for putting together a sampling program that spanned a long gradient of nutrient pressure without the complications of organic pollution.   The outcome of that work was the first of the two papers referenced in my previous post.

Time has moved on and I thought it would be interesting to revisit these “unpolluted” sites to see how they would be classified using the UK’s current standards for phosphorus.  This highlights a striking difference between the prevailing idea of “unpolluted” in the early 1980s and the present day, as all of these groups had average concentrations that equate to substantial enrichment by modern standards; in half the groups this average concentration would be classified as “poor status” whilst the maximum concentrations in three groups equates to “bad status”.   Whatever way you look at it now, these sites were far from “unpolluted”.

Classification of TWINSPAN end-groups of unpolluted river sites in Great Britain based on Armitage et al. (1984) along with average and maximum phosphorus concentrations recorded in each group and the phosphorus status based on current environmental standards.  M = moderate status; P = poor status; B = bad status.

I am not being critical of the approach taken by Patrick Armitage and colleagues.  In many ways, I regard the work of this group as one of the most significant contributions to the science of ecological assessment in my lifetime.   I am just intrigued to see how the thinking of ecologists and regulators has moved on in the thirty years or so since this paper was published.  I know from my own early conversations with NRA biologists that inorganic nutrients were not perceived as a problem in rivers until the early 1990s.   It was probably the European Community’s Urban Wastewater Treatment Directive (UWWTD) that started to draw the attention of biologists in the UK to these problems, and which led to the development of stricter environmental standards for nutrients, though not without opposition from several quarters.

This, then is a situation where good legislation provided the impetus needed to start the process.  There were places in the UK – rivers in the Norfolk Broads, for example – where nutrients were already being regulated, but these were special circumstances and nutrient problems in most rivers were largely ignored. Indeed, as I said in my previous post, phosphorus was not even measured routinely in many rivers.   I heard via my professional grapevine that it was the Netherlands who had made the case for the clauses in the UWWTD concerning regulating nutrients, as their stretches of the lower Rhine were subject to numerous problems caused by unregulated inputs of nutrients from countries upstream.   I do not know if this is true, but it is certainly plausible.   However, once the need to control eutrophication in rivers was codified in UK law, then the debate about how to evaluate it started, one of the outcomes of which was more funding for me to develop the Trophic Diatom Index (referenced in the previous post).  And, gradually, over time, concentrations in rivers really did start to fall (see “The state of things, part 2”).   I’d like to think the TDI played a small part in this; though this might also mean that I am partially responsible for the steep increase in water charges that everyone endured in order to pay for better water quality …


Armitage, P.D., Moss, D., Wright, J.F. & Furse, M.T. (1984).  The performance of a new biological water quality score system based on macroinvertebrates over a wide range of unpolluted running-water sites.  Water Research 17: 333-347.

The challenging ecology of a freshwater diatom?


Amphora pediculus from Polly Brook, Devon, December 2016. Scale bar: 10 micrometres (= 1/100th of a millimetre).

The images above show one of the commonest diatoms that I find in UK waters.  It is a tiny organism, often less than 1/100th of a millimetre long, which means that it tests the limits of the camera on my microscope.  In recent months, however, it is not just the details on Amphora pediculus’ cell wall that I am struggling to resolve: I also find myself wondering how well we really understand its ecology.

The received wisdom is that Amphora pediculus favours hard water, does not like organic pollution and is relatively tolerant of elevated concentrations of inorganic nutrients.  This made it a very useful indicator species in a period of my career when we were using diatoms to identify sewage work s where investment in nutrient-removal technology might yield ecological benefits.  There were many nutrient-rich rivers, particularly in the lowlands, where any sample scraped from the upper surface of a stone was dominated by these tiny orange-segment-shaped diatom valves.   Unfortunately, twenty years on, many of those same rivers have much lower concentrations of nutrients (see “The state of things, part 2”) but still have plenty of Amphora pediculus.   Did I get the ecology of this species wrong?

The graph below shows some data from the early- and mid- 1990s showing how the abundance of Amphora pediculus was related to phosphorus.   The vertical lines on this graph show the average position of the boundaries between phosphorus classes based on current UK standards.   Records for A. pediculus are clustered in the “moderate” and “poor” classes, supporting my initial assertion that this species is a good indicator of nutrient-enriched conditions, but there are also samples outside this range where it is also abundant, so A. pediculus is only really useful when it is one of a number of strands of evidence.


The relationship between Amphora pediculus and reactive phosphorus in UK rivers, based on data collected in the early-mid 1990s.  Vertical lines show the average boundaries between high and good (blue), good and moderate (green), moderate and poor (orange) and poor and bad (red) status classes based on current UK standards and the two arrows show the optima based on this dataset (right) and data collected in the mid-2000s (left).

If we weight each phosphorus measurement in the dataset by the proportion of Amphora pediculus at the same site (i.e. so that sites where A. pediculus is abundant are given greater weight), we get an idea of the point on the phosphorus gradient where A. pediculus is most abundant.   We can then infer that this is the point at which conditions are most suitable for the species to thrive.  In ecologist’s shorthand, this is called the “optimum” and, based on these data, we can conclude that the optimum for A. pediculus is 154 ug L-1 phosphorus.  The right hand arrow indicates this point on the graph below. However, I then repeated this exercise using another, larger, dataset, collected in the mid-2000s.   This yielded an optimum of 57 ug L-1 phosphorus (the left hand arrow on the graph), less than half of that suggested by the 1990s dataset.   There are, I think, two possible explanations:

First, the 1990s phosphorus gradient was based on single phosphorus samples collected at the same time that the diatom sample was collected (mostly spring, summer and autumn) whilst the mid-2000s phosphorus gradient was based (mostly) on the average of 12 monthly samples.  As phosphorus concentrations, particularly in lowland rivers, tend to be higher in summer than at other times of the year, it is possible that part of the difference between the two arrows is a result of different approaches.  (For context, in the 1990s, when I first started looking at the effect of nutrients in rivers, phosphorus was not routinely measured in many rivers, so we had no option but to do the analyses ourselves, and certainly did not have the budget or time to collect monthly samples).

However, another possibility is that the widespread introduction of phosphorus stripping in lowland rivers in the period between the mid-1990s and mid-2000s means that the average concentration of phosphorus in the rivers where conditions favour Amphora pediculus have fallen.   In other words, A. pediculus is tolerant of high nutrient conditions but is not that bothered about the actual concentration.   My guess is that it thrives under nutrient-rich conditions so long as the water is well-oxygenated and, as biochemical oxygen demand is generally falling, and dissolved oxygen concentrations rising (see “The state of things, part 1”), this criterion, too is widely fulfilled.   I suspect that both factors probably contribute to the change in optima.

But the second point in particular raises a different challenge:  We often slip into casual use of language that implies a causal relationship between a pressure such as phosphorus and biological variables whereas, in truth, we are looking at correlations between two variables.   Causal relationships are, in any case, quite hard to establish and the effect that we call “eutrophication” is really the result of interactions between a number of factors acting on the biology.   All of these simplifications mean that it is useful, from time to time, to look back to see if assumptions made in the past still hold.   In this case, I suspect that some of our indices might need a little fine-tuning.  There is no disgrace in this: the evidence we had in the 1990s led us to both to a conclusion about the relative sensitivity of Amphora pediculus to nutrients but also fed into a large-scale “natural experiment” in which nutrient levels in UK rivers were steadily reduced.   When we evaluate the results of that natural experiment we see we need to adjust our hypotheses.  That’s the nature of science.  As the sign on the door of a friend who is a parasitologist reads: “if we knew what we were doing, it wouldn’t be research”.


The 1990s dataset (89 records) is mostly based on data used in:

Kelly M.G. & Whitton B.A. (1995).   A new diatom index for monitoring eutrophication in rivers.   Journal of Applied Phycology 7: 433-444.

The mid-2000s dataset (1145 records) comes from:

Kelly, M.G., Juggins, S., Guthrie, R., Pritchard, S., Jamieson, B.J., Rippey, B, Hirst, H & Yallop, M.L. (2008).   Assessment of ecological status in UK rivers using diatoms.   Freshwater Biology 53: 403-422.

This is not a nitrate standard …

Much of my professional life takes place in the collision zone between ecology and bureaucracy.   These make uneasy partners: ecologists like to think of themselves as Lone Rangers riding out to put the world to rights rather than as small cogs in big administrative machines, but the reality is that environmental regulators need both “carrots” and “sticks”, and wielding the latter makes them part of the criminal justice system, with all the responsibilities – and paperwork – that that implies.

I’ve spent quite a lot of time over the past few years working on developing standards for nutrients in freshwaters.   Roughly speaking, I have been helping to define the freshwater equivalent of the 30 miles per hour speed limit.   Speed limits work partly because everyone understands the dangers of driving too fast in urban areas, and partly because we know that there is a good chance of being caught by a speed camera if we drive too fast.   And so it is (or should be) for pollutants: the lower dashed line on the graph of phosphorus in the Ouseburn in the previous post is the “30 mph” limit based on an understanding of how phosphorus interacts with freshwater ecology.   There is a lot I could write about how these values are derived (a subject for another day) but that, in a nutshell, is what we are trying to achieve.

When my students are analysing the data from the Ouseburn, they find standards for ammonia, BOD and phosphorus relatively easily via the UK TAG website but they come to me each year wondering why they cannot find equivalent values for nitrate.  The UK TAG document says “we consider the general understanding of this [nitrogen] to be insufficient at present for it to be used as a basis for setting standards or conditions.”  This was disingenuous in the extreme because I know that DEFRA has been extremely reluctant to set standards for nitrogen as this would focus attention on agricultural pollution which is both much harder to manage and would incur the ire of the farming lobby.   A few years ago, Nigel Willby and I calculated the nitrogen concentrations that would support good status in UK rivers as a by-product of a project to revise phosphorus standards.  We had the data we needed and it struck us that no-one would turn down our “buy one, get one free” initiative.   Not so.  Our figures for nitrogen were quietly excised from our report using the very good argument that it was going to be a hard enough job to argue the case for tighter phosphorus standards without confusing the issue with nitrogen too.  Since then, little has happened, as far as I know, to push nitrogen up the regulatory agenda.

The table below shows these values simply to indicate the values of oxidised nitrogen (which is mostly as nitrate rather than nitrite) that are associated with different levels of ecological status in UK rivers.  They have no regulatory significance, but should give us a rough idea of how much nitrogen is “too much” when we are trying to understand the ecology of a river.

Predicted Total Oxidised Nitrogen (nitrate-N + nitrite-N)  concentrations associated with EQR values modelled for two altitudes (20 and 200 m asl) and four alkalinities (10, 50, 100 and 200 mg L-1 CaCO3).   Boundaries are normalised at 0.8 (high/good), 0.6 (good/moderate), 0.4 (moderate/poor) and 0.2 (poor/bad)); 0.7 and 0.9, therefore, represent conditions at the middle of their respective status classes.


Applying these values to the Ouseburn, a lowland, hard water river, we see that most of the values lie below this threshold except for those from Woolsington, the headwater stretches which are surrounded by agricultural land where there is likely to be extensive use of artificial fertilisers.   The open circles on the right of the graph are values collected by my students each autumn, which may explain why they are lower than the annual mean values that the closed circles to the left represent.  But note, too, the high values in the Airport tributary in the early 1990s.   These occur at about the same time as the high ammonium concentrations that I discussed in “Part of the problem?”.   The ammonium that the airport released into the stream has a nitrogen atom bound to four hydrogen atoms using strong bonds.   Some microorganisms are able to break these bonds and use the energy that is released to drive their own cells.   This is what we see in Airport tributary where the high nitrate is the result of a two-step process that breaks down the ammonium first to nitrite and then to nitrate.


Trends in concentrations of nitrogen as nitrate in the Ouseburn over time.  Woolsington is upstream of the airport, Airport tributary (Abbotswood Burn) receives runoff from Newcastle Airport and Jesmond Dene is about 10 km downstream from the airport.  Closed symbols are annual means of data collected by the National Rivers Authority and Environment Agency; open symbols are means of data collected and analysed by Newcastle University Geography students in October (once also in February) of each yearThe dashed line is the UK environmental standard for reactive phosphorus to support “good ecological status.

The final graph shows concentrations of nitrogen as ammonium and nitrate at the three sites we’ve been examining, along with the (official) standard for nitrogen as ammonium plus my unofficial guide value for healthy nitrate-nitrogen concentrations.  This gives us four quadrants, with bottom left representing situations where both forms of nitrogen are at concentrations that should not significantly impair ecology.   This is the case at the two sites downstream from the airport from the mid-1990s onwards, once ammonia concentrations were under control.

The top right quadrant, by contrast, has just a small number of values from Airport tributary from the early 1990s, when high ammonia was rapidly oxidised to yield high nitrate-nitrogen concentrations too.   A further cluster of sites, mostly from Airport Tributary and Jesmond Dene, also have high ammonium concentrations, although nitrate-nitrogen concentrations are below the threshold.  Finally, at the top left, we have values from Woolsington where concentrations of nitrogen as ammonium are low but nitrate-nitrogen concentrations may be a problem, due to agriculture.

For a river that is less than 20 kilometres from source to mouth, there is a lot happening in the Ouseburn, which makes it ideal for students to become acquainted with the complexities of environmental regulation.   You can read the history of pollution control in the graphs of data too: from intercepting toxic point sources in the 1980s to more general concerns about overflowing storm sewers in the 2000s and, now, more interest in diffuse nutrient pollution from farmland in the headwaters.   That, too, is a good lesson for undergraduates: pollution, itself, is not an unambiguous concept and its definition has evolved as our understanding increases.  One lesson that we can draw from this episode about nitrate standards is that the scientific argument about sensible levels of any pollutant can quickly become obscured by politics and vested interests.  That can never be a good thing.


Relationship between nitrogen as ammonium and as nitrate in the Ouseburn between 1989 and 2016.  The diagonal line has slope = 1 and the horizontal and vertical dashed lines indicate the position of the maximum concentrations that are likely to support good ecological status.   There is no differentiation between Environment Agency data and data collected by Newcastle University students on this graph.

Diatoms from a holy river …


Having written about the diatoms I found in the Ganges headwaters a week or so ago (see “Diatoms from the Valley of Flowers”) I now travel about 250 kilometres downstream, descending 3000 metres in the process, to the holy city of Rishikesh on the Ganges itself.   As in the Valley of Flowers, I had time and space for a single sample, and scrambled down to one of the many ghats, toothbrush in hand, to get a sample (and amuse the locals).  You can see a photograph of me collecting the sample at the end of “A cautionary tale”.  The ghat I chose was just under water at the time of collection, but the water level was fluctuating throughout our visit, so it might have been deeper at times, and probably fully exposed for periods too.  As we were in Rishikesh towards the end of the monsoon period, the chances are that it spent more time submerged than exposed in the weeks before our arrival, but I cannot be sure.

My sample comes from the flat surface of a concrete ghat, roughly at water level at the time I visited (the river was running across my feet as I sampled) but the biofilm on the surface of the ghat was so thin that I wondered if I had any algae at all in my bottle at the end of some ferocious brushing with my toothbrush.   The plate below gives an indication of the diversity of diatoms that, despite my forebodings, I found on the slide that I prepared.  Of these, Adlafia minuscula var. muralis was the most abundant organism and this, along with Nitzschia palea, which was also frequent, suggested that the water at Rishikesh was quite enriched.   Halamphora montana, which was also frequent, is a species that can thrive in intermittently wet conditions, consistent with its presence on a ghat that was not fully submerged.  In contrast to these, Gomphonema pumilum (which was also frequent) and Achnanthidium minutissimum (rare) are more often associated with cleaner water.


Diatoms from the River Ganges at Rishikesh, September 2016.  a.  c.: Gomphonema pumilum; d.: Navicula sp.; e. Adlafia minuscula var. muralis; f. Achnanthidium minutissimum; g. Cymbella sp.; h., i.: Halamphora montana; j. Cocconeis euglypta; k. Nitzschia cf inconspicua; l. Nitzschia palea.  Scale bar: 10 micrometres (= 100th of a millimetre).

As you can see from the photograph at the top of the post, and from images in earlier posts, Rishikesh sits just at the foot of the Himalayas, just at the point where the Ganges enters the Deccan Plateau.  Were I to turn around and photograph the view in the opposite direction, the landscape would be flat for as far as the eye can see.   There is, nonetheless, a substantial population in the Ganges valley upstream of Rishikesh, with several substantial towns, the largest being Srinagar, a city of 150,000 on the Alaknanda tributary.   Sewage treatment in these areas is rudimentary so a high organic loading would not be surprising.

The low numbers of algae is no great surprise.  I recall sampling streams in Nigeria during the wet season and finding very little: the high, scouring flows and turbid water both make conditions difficult for algae at times such as these.   The predominance of indicators of poor water quality may also be a consequence of the monsoon, as the heavy rains not just overload the limited sewerage systems, but also wash organic matter into the rivers from terrestrial sources.   There is some evidence that water quality is worse during this period than it is during either the pre- or post-monsoon period.

There is, however, a belief that the Ganges has peculiar powers of self-purification. I recall Eric Newby writing about this in his classic book Slowly Down The Ganges, and there does seem to be limited evidence that Ganges water has some novel anti-microbial capabilities.   I do, nonetheless, wonder at the health consequences of performing an immersive “puja” in such a polluted river.   The irony is that the term “pollution” actually has its origins in religion, relating the defilement of holy places by man, so the state of the holy Ganges may have the dubious honour of being truly polluted in both the original and modern senses of the word.


Nautiyal, C.S. (2009). Self-Purificatory Ganga Water Facilitates Death of Pathogenic Escherichia coli O157:H7.  Current Microbiology 58: 25-29.

Tareq, S.M., Rahamen, S.M., Rikta, S.Y., Nazrul Islam, S.M. & Sultana, M.S. (2013).  Seasonal variation in water quality in the Ganges and Brahmaputra River, Bangladesh.  Jahangirnagar University Environmental Bulletin 2: 71-82.

Primed for the unexpected?

I was in Nottingham last week for a CIEEM conference entitled “Skills for the future” where I led a discussion on the potential and pitfalls of DNA barcoding for the applied ecologist.  It is a topic that I have visited in this blog several times (see, for example, “Glass half full or glass half empty?”).  My original title was to have been “Integrating metabarcoding and “streamcraft” for improved ecological assessment in freshwaters”; however, this was deemed by the CIEEM’s marketing staff to be insufficiently exciting so I was asked to come up with a better one.  I was mildly piqued by the implication that my intended analysis of how to blend the old with the new was not regarded as sufficiently interesting so sent back “Metabarcoding: will it cost me my job?” as a facetious alternative.  They loved it.

So all I had to do was find something to say that would justify the title.   Driving towards Nottingham it occurred to me that the last time I should have made this trip was to Phil Harding’s retirement party.  I was invited, but had a prior engagement.  I would have loved to have been there as I have known Phil for a long time.  And, as I drew close to my destination, it occurred to me that Phil’s career neatly encapsulated the development of freshwater ecological assessment in the UK over the past 40 years.  He finished his PhD with Brian Whitton (who was also my supervisor) in the late 1970s and went off to work for first North West Water Authority and then Severn Trent Water Authority.   When the water industry was privatised in 1989, he moved to the National Rivers Authority until that was absorbed into the Environment Agency in 1995.   Were he more ambitious he could have moved further into management, I am sure, but Phil was able to keep himself in a jobs that got him out into the field at least occasionally throughout his career.   That means he has experienced the many changes that have occurred the past few decades first hand.


Phil Harding: early days as a biologist with North West Water Authority in the late 70s

Phil had a fund of anecdotes about life as a freshwater biologist.  I remember one, in particular, about sampling invertebrates in a small stream in the Midlands as part of the regular surveys that biologists performed around their areas.   On this particular occasion he noticed that some of the invertebrate nymphs and larvae that he usually saw at this site were absent when he emptied out his pond net into a tray.   Curious to find out why, he waded upstream, kicking up samples periodically to locate the point at which these bugs reappeared in his net.   Once this had happened, he knew that he was upstream of the source of the problem and could focus on searching the surrounding land to find the cause.   On this occasion, he found a farmyard beside a tributary where there was a container full of pesticides that had leaked, poisoning the river downstream.

I recount this anecdote at intervals because it sums up the benefits of including biology within environmental monitoring programmes.   Chemistry is very useful, but samples are collected, typically, no more than once a month and, once in the laboratory, you find a chemical only if you set out to look for it and only if it was present in the river at the time that the sample was collected.  Chemical analysis of pesticides is expensive and the concentrations in rivers are notoriously variable, so the absence of a pesticide in a monthly water sample is no guarantee that it was never there.  The invertebrates live in the river all the time, and the aftershocks of an unexpected dose of pesticide are still reverberating a few weeks later when Phil rolls up with his pond net.   But the success of this particular incident depends on a) Phil being alert enough to notice the change and b) having time for some ad hoc detective work.

This encapsulates the “streamcraft” which formed part of my original title.   This is the ability to “read” the messages in the stream that enable us to understand the processes that are taking place and, in turn, the extent to which man’s activities have altered these (see “Slow science and streamcraft”).  It is something you cannot be taught; you have to learn it out in the field, and the Environment Agency and predecessors was, for a long while, well set up to allow this process of personal development.    Changes over the past few years, in the name of greater efficiency (and, to be fair, in the face of enormous budget cuts) have, I fear, seriously eroded this capability, not least because biologists spend far less time in the field, and are no longer responsible for collecting their own invertebrate or diatom samples.


Phil Harding: forty years on, sampling algae in the River Ashop in Derbyshire.

In my talk, I was thinking aloud about the interactions between metabarcoding and the higher level cognitive skills that a good biologist needs.   I feared that, in the wrong hands, it could be yet another means by which the role of the biologist was eroded to that of a technician feeding samples into one end of a series of swish machines, before staring at spreadsheets of data that emerged from the other end.   All the stages where the old school biologist might parse the habitat or sample s/he was investigating and collect signs and indications of its condition over and above the bare minimum set in the protocol were stripped away.

A further reason why this might be a problem is that molecular ecology takes a step backwards from the ideal of biological assessment.  Much as the chemist only sees what his chosen analyses allow him to see, so the molecular biologist will only “see” what his particular set of primers reveal.   Moreover, their interpretation of the spreadsheets of data that emerge is less likely to be qualified by their direct experience of the site because their time is now too precious, apparently, to allow them to collect samples for routine assessments.

A few points emerged out of the discussion that followed (the audience included representatives of both Environment Agency and Natural England).    First, we agreed that metabarcoding is not, itself, the problem; however, applying metabarcoding within an already-dysfunctional organisation might accentuate existing problems.  Second, budgets are under attack anyway and metabarcoding may well allow monitoring networks to be maintained at something approaching their present scale.  Third, the issue of “primers” was real but, as we move forward, it is likely that the primer sets will be expanded and a single analysis might pick up a huge range of information.  And, finally, the advent of new technologies such as the MinION might put the power of molecular biology directly into the hands of field biologists (rather than needing high throughput laboratories to harness economies of scale).

That last point is an important one: molecular ecology is a fast moving field with huge potential for better understanding of the environment.    However, we need to be absolutely clear that an ability to generate huge amounts of data does will not translate automatically into that better understanding.   We will still need biologists with an ability to exercise higher cognitive skills and, therefore, organisations will need to provide biologists with opportunities to develop those skills. Metabarcoding, in other words, could be a good friend to the ecologist but will make a poor master.  In the short term , the rush to embrace metabarcoding because it is a) fashionable and b) cheap may erode capabilities that have taken years to develop  and which will be needed it we are to get the full potential out of these methods.   What could possibly go wrong?

Who will watch the watchmen now?


There can only be one topic to write about today.   On Thursday, the UK voted, by a narrow margin, to leave the European Union and entered a period of uncertainty and instability as the nature of the “divorce” is agreed between London and Brussels.   I know that most of my UK readers were in favour of staying in the EU but at least one was in favour of exit.  And, as I know from personal experience that the EU is a far-from-perfect organisation, I am happy to accept that there is scope for intelligent people to hold different opinions on the benefits of membership.   I also accept that being anti-EU does not necessarily equate with being anti-Europe, or a “Little Englander”.  I do believe, however, that the “out” campaigns presented a distorted view of EU policy particularly on immigration, in order to play on the fears of sections of the populace.

However, what is done is done and now attention must focus on the nature of the future agreement between the UK and the EU.   As the dust settles and the bluster dies down, we awoke to a horrible truth: the “out” campaign actually have no more idea of what the future will look like than anyone else.   We now enter a period of negotiation with 27 countries, several of whom are both annoyed and worried by the UK decision, and they are not going to roll over quietly and let UK politicians dictate terms.

I have grave concerns for the UK environment after an EU exit.   The campaigns from both sides involved stripping down highly complicated arguments to a few key points that would have traction with the electorate, and then rebutting the other side’s efforts at the same. It was, in short, a campaign decided more by political process than by principle.   Unfortunately, this is exactly how environmental policy is decided at the highest level.   The sad truth is that most people’s awareness of environmental problems comes from the media, not direct experience.   Press stories can synergise with a general sense that summers are different now to when we were young to reinforce fears of global warming.  At the same time, the patterns are not so robust that naysayers cannot spin their own interpretations.   The same applies to the aquatic environment: we have (thankfully) passed the stage when many rivers looked (and smelt) appalling.  The reason we know that our rivers are polluted now is more due to media accounts, and the reason we know that they are improving is due to the Environment Agency’s press releases.  Beyond a dedicated band of anglers, few of us have enough direct experience to challenge either set of statements.

That’s where the EU played a role.   They provided a level of scrutiny above that provided by domestic politics.   I spent much of the past 15 years working towards definitions of the health of the aquatic environment that were applicable throughout Europe.   That provides a benchmark against which claims of rivers improving or declining in quality can be judged.   Bearing in mind that Europe extends from the Arctic Circle to the Mediterranean and from the Alps to areas that are below sea level, this was not an easy task, and what we have is a “work in progress” rather than a definitive product.  But it is a positive step that, to push a metaphor, “detoxifies” debates about the state of the environment.

Unfortunately, interventions such as this represent exactly the sort of loss of “sovereignty” that Ian Duncan-Smith, Nigel Farage, Boris Johnson and others decry.   So let’s unpick just what “sovereignty” might mean in this instance: it would mean DEFRA deciding on criteria to define the health of the aquatic environment, irrespective of the views of experts elsewhere in Europe.   Bear in mind that DEFRA also has responsibility for agriculture (high political sensitivities), my comments above about the susceptibility of environmental policy to “spin” and the general advocacy for “small government” from the right, and this cannot be good news for the environment.  I predict that the clause in the Water Framework Directive that allows “less stringent objectives” under certain circumstances (article 4, paragraph 5) will be applied very broadly in the UK, once scrutiny from Brussels is loosened.

What to do?   We may have to wait and see how the “Brexit” negotiations unfold.  My hope is that free access to European markets will require the UK to stay signed-up to legislation that ensures a “level playing field” for business, and that the environment will be part of this package.  This would be similar to the deal that Norway has at present, and Norwegian colleagues continue to make substantial and valuable contributions to debates on how EU environment policy is implemented.  That would mean “business as usual” for the UK environment.

However, changes in the Tory party may bring a more obstreperous breed of politician to the negotiating table and we cannot rule out the possibility that rattles will be thrown out of the pram.   Plan B, therefore, may be for independent, non-Governmental bodies such as the river trusts to steps in to scrutinise UK environment policy and measure claims against evidence.   As the Environment Agency will be even more liable to funding cuts once obligations to the EU no longer exist, such bodies will also need to watch that sufficient evidence is being collected, and maybe to collect some evidence themselves.  All that will take money, and I don’t know where that will come from.   But we need to start preparing for a world in which the “watchmen” return to being political pawns answerable only to Westminster and Whitehall.

Cadaques_2012Memories of happier times in Europe: Cadaqués in north-eastern Spain, June 2012.  The top picture shows vineyards near Bäd Dürkheim, Rhineland-Pfalz, Germany (circa. 2000), the area where my love affair with continental Europe started in 1972.  

Bollihope Burn in close-up

Bollihope Burn does not disappear dramatically down a single swallow hole in the way that Gaping Gill swallows up Fell Beck on the slopes of Ingleborough.  Rather, there is a gradual diminishment of flow, as the river percolates through the joints in the limestone, before the remnants of the stream swirl down a final sinkhole (see “Co. Durham’s secret Karst landscape”).   I was intrigued to see how the organisms that inhabited Bollihope Burn reacted to these stresses so got down on my knees close to this final sinkhole to get a closer look.

My waterproof Olympus TG2 (see “Getting close to pearl mussels with my underwater camera”) set to super-macro mode is equivalent to putting my head under the surface of the water and then peering at the rock through a magnifying glass … but gets fewer odd looks from passers-by.   Fortunately, this is an isolated corner of Weardale and passers-by were limited to a few rabbits, because sticking a camera into a stream to take a photograph of a stone is, itself, odd enough to attract stares from most people.

These close-up views of freshwater algae in their natural habitat continue to surprise me.  It is only in the last few years that waterproof digital cameras with macro facilities have fallen to an affordable price.  Before this, underwater photography required special kit that few freshwater biologists could afford.  Yet, removing a stone to photograph the algal growths meant that the algae were never photographed in their natural habitat, and were deprived of the buoyancy that the water afforded them.   I have plenty of photographs of green or brown gunk composed of different algae but, with the algae removed from their context, these photographs offer few insights into the biology of the stream bed.  The photograph below, however, shows a community with a distinct structure – a “turf” of near-vertical filaments waving in the gentle eddies of the stream as it swirls around before disappearing down the swallow hole.


A cobble in Bollihope Burn, close to the swallow hole, covered by a short “turf” of algae, April 2016.   Scale bar: approximately two centimetres.

Under the microscope, the structure of this “turf” starts to reveal itself.   The filaments appear to be aggregations of diatoms around dying filaments of the green alga Ulothrix zonata.   This is an alga that is common in Pennine streams in the winter and early Spring but which disappears as the weather starts to warm up. It often forms very conspicuous green patches on the river bed for a short period of time, as in the following picture, which I took a few kilometres away from my current location, in the River Wear at Wolsingham.   The difference in appearance between the alga in the two photographs is mostly due to the Bollihope population being smothered with diatoms whilst the Wolsingham population was virtually a pure growth of Ulothrix.   This may be partly due to the Bollihope picture being taken taken two months later than the Wolsingham image.   Ulothrix zonata produces copious quantities of mucilage and the Wolsingham population was slimy to the touch.  I rarely see epiphytes on this or any other slime-producing algae in their healthy state.   However, Ulothrix is a species that thrives in cold water.   Indeed, a study has shown that when the water starts to warm up and the day length increases, the Ulothrix filaments switch into their dispersal and reproductive modes and that is what may be happening here.   As the rate of photosynthesis declines, so there is less carbohydrate from which the slime molecules can be made and, as a result, less of a deterrence to any diatom looking for a perch.   From now until next winter, Ulothrix zonata will not be very obvious in the streams that I visit.  This is because the zygotes which are produced by sexual reproduction lie dormant until day length decreases and temperature drops.   At this point, they germinate and divide to produce zoospores which, in turn, grow into new Ulothrix zonata filaments.


Growths of Ulothrix zonata on cobbles in the River Wear at Wolsingham, February 2009. 

The photographs taken under the microscope illustrate this well.  On the left hand side there is one of the few healthy looking Ulothrix filaments that I found, with a chloroplast wrapped around the inside of the cell wall   On the right hand side you can see that the chloroplasts have gone, replaced by dark green blobs which are (I think) bundles of gametes awaiting release.   More significantly, you can also see several diatoms around the Ulothrix filament, taking advantage of it to lift themselves up above the rock surface.

The paradox is that these algae are entering their senescent phase just as most of the plant life in Weardale is flourishing.   This is probably not a coincidence: life in cold water means fewer grazing invertebrates and less shade to intercept the precious winter sunlight.   I suspect that algae, once masters of the planet, have gradually adapted and evolved to live a subordinate life, flourishing in those periods of the year when most of us are content to stay indoors.


Ulothrix zonata from Bollihope Burn, April 2016.  The left hand image shows a healthy vegetative filament; the right hand image shows zoospore production and colonisation by diatom epiphytes. 


Graham, J.M., Graham, L.E. & Kranzfelder, J.A. (1985).  Light, temperature and photoperiod as factors controlling reproduction in Ulothrix zonata (Ulvophyceae).  Journal of Phycology 21: 235-239.

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