Michael McCarthy: Nature Studies

Here’s a link to an interesting article in today’s Independent about the state of England’s chalk streams.   They are not, says Environment Editor Michael McCarthy, in a very good condition, pointing to the problems of “diffuse pollution” (a catch-all phrase for all the pollutants that find their way into our rivers across the land, rather than via industrial or sewage effluents).   Principal amongst these is the run-off of agricultural chemicals, particularly nutrients.   This leads, says McCarthy, quoting members of the Salmon and Trout Association, to the growth of “blanket weed”, filamentous algae such as Cladophora glomerata.  Blanket weed smothers the gravel on the river bed which, in turn, makes life difficult for the bugs on which the trout and salmon feed.


The River Wylye at Kingston Deverill: a classic example of an English chalk stream. photographed in May 2010.

All this forms a narrative that has been repeated many times by river users and environmental scientists, including many in the Environment Agency.  The condition even has a name: Chalk Stream Malaise.   The problem is that there is no “smoking gun” to link the run-off to the decline of salmon and trout beyond reasonable doubt.   I had to research the literature on this as part of a study a few years back and was surprised about how little hard evidence I could find.  The circumstantial evidence is strong, so long as you cast your net wider than just English chalk streams, but I could not find one paper in a peer-reviewed literature that demonstrated an unambiguous link between nutrients and blanket weed, or between blanket weed and salmon and trout populations, specifically in chalk streams.   The reality is that there is much else happening in the surrounding catchments, including over-abstraction by water companies, which also affects stream ecology.   Nor are nutrients the sole consequence of increased agricultural production: silt and pesticides also enter the rivers and have their own effects, all of which are difficult to disentangle from one another. The result is a plot of interweaving motives and alibis that would make Hercule Poirot blanch.

See also streams of consciousness, my post from 21 August.

‘Speed dating’ with diatoms …

The day after the meeting about RAPPER, I was supposed to lead an informal workshop on rapid ecological assessment using algae.  However, heavy rain earlier in the week and especially on the night before meant that the streams were turbid and swollen, making it impossible to see what was growing on the river bed.  The few stones that we did manage to pull out from the stream margins suggested that most of the algae had been scoured away by the spate.

Instead, we retreated to the classroom after lunch for an alternative exercise that I had thought up.  The idea was this: Maria and I had diatom slides from seven sites which we circulated around the group.   Each person had five minutes to look at a slide, make some notes on its composition and then to guess the quality of the stream that the sample came from.   When I explained this in the pub the night before, a colleague said “ah … .like speed dating, but with diatoms.”


“Speed dating” with diatoms: rapid assessment of ecological status, Penrith, October 2013.

The dozen or so participants varied in experience; some of those with experience came from outside UK or had previously worked on lakes rather than rivers, and I gave them very little background information about the type of streams each sample came from.  Nonetheless, we found 60% of these “speed dating” analyses gave the same result as the detailed analyses that Maria and I had already performed.  People tended to make lists of the most common genera, occasionally picking out the more distinct species, and based their judgements on these.   Even fairly basic knowledge of diatom ecology allowed them to recognise that a sample with lots of Nitzschia was likely to come from a polluted stream whilst one with Tabellaria and Achnanthidium was more likely to come from a clean one.

I told Rick Battarbee about this exercise in the bar later in the evening and he recalled a similar experience in the early days of his research on acidification.  Asked whether a forest in Scotland was responsible for acidifying a water course, he had taken a field microscope and walked up through the catchment, taking samples from the stream at intervals and checking their composition.   He said that it was easy to see to pick out key indicators and whether or not there were marked changes in composition.  In this case, the composition of diatoms from reaches in and below the forest were the same as those in the moorland stretches above the forest, quickly ruling out the original suspicion.

Like RAPPER, which I mentioned in the previous post, approaches such as this have the potential to make biologists much more flexible and reactive.   We need to adjust techniques, for sure, but more important, perhaps, we need to adjust attitudes, both of the biologists themselves and of their managers.   Quick “look-sees” performed in the field with a portable microscope could quickly rule out some hypotheses whilst focus attention on areas within catchments where more detailed investigations are needed.   We are already in a good position to adopt this approach as many biologists already have the basic diatom identification skills plus some ability to differentiate the larger algae.  We just need that attitude shift.  As is so often the case, better science is not always the answer; better use of existing knowledge could yield just as much sooner and at a lower cost.

A RAPPER in da Lake District …



An early morning view across the Lake District fells from Blencathra Field Studies Centre, October 2013.

I am writing this post in my bedroom in Blencathra Field Studies Centre which is, in a strange way, close to where my professional journey started.   I went to Flatford Mill Field Studies Centre for an ecology field course as part of my sixth form studies.   That was over thirty years ago and Flatford Mill is over 300 miles from where I am writing, yet the presence of sixth formers on a similar course here this week takes me on a sentimental journey back through time.

My course took place over a sunny week in June or July, rather than the bleak, wet October day that I have just experienced.   I slept in Willie Lott’s Cottage, familiar as the building on the left-hand side of Constable’s painting The Hay Wain and we spent our days in the fields, streams and saltmarshes around Debden Vale.   I remember one part of the course particularly vividly: we had sampled a small stream and the tutor was picking invertebrates we had found out of a tray and explaining to us how each was adapted to different environmental conditions.  There was a mayfly larva, with feathery gills along its back which meant, we were told, that it needed a constant supply of well-oxygenated water if it was to survive.   And there was a bright red midge larva, which used haemoglobin (the same compound found in human blood) to scavenge oxygen, allowing it to thrive in polluted waters.

Ecological assessment today is still based on relatively simple relationships between the functional ecology of different organisms and water quality.  There is something particularly elegant about a method that has direct practical applications yet could still be explained in terms that made sense to sixth form students.  As I look at the bewildering verbiage that fills academic journals today I wonder whether the gains from new research justify the barriers that complexity can create between specialists and the public.  I worry that the science that is designed to fill journals often forgets the need to communicate our outputs with stakeholders.

My own musings on these issues seemed to chime with thoughts from some colleagues in the Environment Agency and SEPA and we spent part of Thursday brain-storming a new method for rapid assessment.   Our working title for this is RAPPER – Rapid Assessment of PeriPhyton Ecology in Rivers.  The method involves wading through streams recording the different types of algal growth that we could see with the naked eye.   Some of these can be identified in the field; others need to be taken back to the laboratory to be identified with a microscope.   Part of my own motivation is to be able to capture the essence of those sunny days at Flatford Mill, by having a method that was accessible to non-specialists.  But that is not the only possible benefit: RAPPER complements existing approaches to give greater confidence in the decisions that regulators need to make.  It also allows biologists to cover several sites in a day, locating possible hot spots that can then be examined using more detailed methods.

First results are encouraging: we had data from different parts of the country that gave us optimism that the method was working, and that it was worth continuing trials next year, once we had made  a few modifications.  The biologists who had collected the data had generally commented positively on the method.   We agreed some changes, agreed to collate more data and to make more analyses, then to continue the trials next year.  And, maybe, I’ll be looking for some opportunities to try the method out with students and sixth formers, and see if I can enthuse the next generation about the joys of freshwater ecology.

Simplicty is the Ultimate Sophistication: McEcology and the dangers of call centre ecology

I’ve just had a short ‘opinion’ paper published in the journal Ecological Indicators, with the title ‘Simplicity is the ultimate sophistication: building capacity to meet the challenges of the Water Framework Directive’.   One of my big concerns over recent years has been how we translate developments in science into advances in practice particularly when the government agencies that are responsible for our environment are under severe financial constraints.

My big concern is that an effective if rather labour-intensive approach to ecological assessment in the UK is currently being unpicked to accommodate new science (necessary as the Water Framework Directive makes new demands) but, at the same time, more efficient (i.e. ‘cheaper’) business models are also being imposed.  

I use the term ‘McEcology’ to summarise what is going on.     You might have heard the derogatory term ‘McJob’ used to describe a low-paid dead-end job with few career prospects so you might think I’m just riding a popular bandwagon here.   But read on.

Just over ten years ago I was on my way to a meeting to develop some Europe-wide standards for ecological assessment.   At Lille station I passed a McDonalds and remember thinking that it would be nice if we ecologists could get our methods to the point where the end-product was as consistent, across Europe, as a Big Mac.  

I think we have made progress towards this goal over the past decade (see posts on intercalibration) but I’ve also watched some less attractive aspects of the fast food business model being imported.   The essence to producing homogeneous food is often a tightly-controlled ‘production line’ and this approach is increasingly used in ecology, with different individuals responsible for sampling, sample preparation, sample analysis and data interpretation.    In theory, this makes better use of the training of specialist ecologists, allowing them to focus on high-level skills such as data interpretation.   In practice, I suspect that the time ecologists spend travelling around catchments collecting samples and, in the process, observing rivers in all their moods, gives them a level of insight that will soon be lost.   The ‘fast food’ model may be acceptable if the ‘product’ is data but not if it is advice or guidance tailored to a particular water body or an explanation comprehensible to a stakeholder.    

A second concern I addressed was whether advances in science were actually contributing to this slip towards McEcology, as innovations often lead to increased complexity which can push methods out of the capabilities of the “generalist” and limit their use to “specialists”.   We get to the point where knowledge of a particular technique or group of organisms trumps knowledge of a geographic area in determining who is best suited to a task.  

The risk is that the search for short-term economies undermines the professionalism of ecologists.  The old UK model where a team of ecologists acted as a “family doctor” practice for a region, developing extensive local knowledge through close contact over a number of years is at risk of being replaced with a “call centre” model where ecologists become increasingly desk-bound, samples are collected by lower paid staff working to tight schedules and processed by technicians who may not work in the same part of the country, or even in the same country at all.  

The title of my paper “simplicity is the ultimate sophistication” comes from a quotation attributed to Leonardo da Vinci.  Innovation is all very well but if it breaks the links between biologists and the field, we risk losing accumulated wisdom resulting in poorer decision-making.   On the other hand, if we have a good knowledge of the underlying ecological processes, we should be able to develop a set of much simpler methods that allow ‘generalist’ ecologists to collect information on many attributes of ecosystems.  This encourages a more joined-up view of ecosystems and, ultimately, better decision making.

This is not just theory: we’re already making a few tentative steps towards this goal and the next post will talk about one of these in more detail.

At last … a red alga that really is red …

The bed of some parts of the River Ehen on my last visit had a distinctly pinkish-red hue, which is a sure sign that we are moving towards autumn and winter.   This is Audouinella hermanii, which we have already met in earlier posts.   Having written recently about a green alga that is actually red, and also described Lemanea, a red alga that is typically olive-green in colour, it was reassuring to finally encounter a red alga that is unequivocally red in colour.


A rock from the River Ehen, near Ennerdale Bridge, with a thick coating of Audouinella hermanii. Photographed in October 2013.

The red colour in Audouinella and other red algae is due to a pigment called phycoerythrin.  This is a protein-based pigment which is also found in blue-green algae.  By contrast, the carotenoids which gave Haematococcus its bright colour are lipid-based.     The astaxanthin of Haematococcus is, as we saw on 6 October, a natural sunscreen but phycoerythrin and many carotenoids have a different role inside the algae.

Phycoerythrin appears red to us because it is reflecting red light whilst at the same time absorbing other wavelengths.   Beccause blue light penetrates water to a greater depth than light of longer wavelengths, phycoerythrin allows red algae to absorb this and use the energy for photosynthesis.  We can think of the phycoerythrin (and, indeed, many carotenoids) as “turbochargers” for the photosynthetic apparatus, allowing the algae that contain them to live in a wider range of habitats.

This argument works in coastal areas, where red algae can live at great depths where relatively little light penetrates but why should Audouinella be so common in the River Ehen?    The same reasoning applies: the stretch of river where I found Audouinella was heavily shaded and this species is most common in autumn and winter when the sun’s rays are much weaker.  Again, the phycoerythrin gives the normal photosynthetic apparatus a boost to help it make the most of the light that is available.


Cells of Gomphonema truncatum growing within the Audouinella colonies in the River Ehen near Ennerdale Bridge, 9 October 2013.   The two left hand images are in “valve view” whilst those on the right are in “girdle view”.   Scale bar: 10 micrometres (= 100th of a millimetre).

Whilst examining the Audouinella under my microscope, I noticed some clumps of diatom cells that looked like inverted Coke bottles.   These are a species known as Gomphonema truncatum which grows on long mucilaginous stalks which branch to form bush-like colonies.   Unlike Coke bottles, Gomphonema cells are not round, so the characteristic shape is only seen when peering down onto the flat surface of the cell.   When viewed from the side, the cell is wedge-shaped.  Diatomists refer to these two different views as “valve view” and “girdle view” respectively.   Note, too, the characteristic yellow-brown appearance of the chloroplasts.  This is due to the carotenoid fucoxanthin which, like Audouinella’s pigments, gives a boost to the photosynthetic machinery when natural light is in short supply.

Ruth Patrick, 1907-2013

I was pleased to see The Independent running an obituary to Ruth Patrick, who died a couple of weeks ago. She was one of the pioneers behind our current use of algae as indicators of the health of aquatic ecosystems whose work led to the 1972 Clean Water Act in the USA which, in turn, paved the way for the Water Framework Directive in Europe.

About crackers, peanut butter and marmite …

I’m a sucker for good metaphors and analogies when I’m teaching. These are great for linking the ideas that I am trying to communicate with things with which the students are already familiar. One of my favourite analogies for stream ecology comes from a 1974 review paper by the US ecologist Kenneth Cummins. He was describing the process by which leaves which fall into streams at this time of year are broken down by the organisms that live in the stream in order to release their energy. There are a number of aquatic invertebrates, termed “shredders”, whose mouthpieces are specially adapted to tearing apart these leaves. They gain their nutrition from the leaves, so the theory goes, with the partially-digested leaf material emerging from their intestines, in due course, as “fine particulate organic matter”. That itself is a euphemism. Go figure.
But leaves alone do not make a particularly nutritious diet. In fact, the shredders are not living solely on these leaves. As soon as a leaf falls from the tree it is vulnerable to attack from bacteria and fungi. Like the invertebrates (like humans eating spinach, too), they can gain nutrition from this leaf, and the enzymes they produce help to soften up the tissues making it easier for the shredders to tear apart. Once in the water, the dead leaf will also be colonised by algae whose photosynthesis will produce oxygen which will replace that used by the various bugs as they break the leaf down. The combination of fungi, bacteria and algae also add to the nutritional content of the leaf. Cummin’s great analogy was that the leaf was akin to a ‘cracker’ whilst the microbial life was akin to ‘peanut butter’. A single cracker, as you know, is not itself greatly nutritious, but we tend to use crackers as ‘carriers’ for protein- and energy-rich foods such as cheese or, in Cummin’s example, peanut butter. An even better analogy for a UK reader is a cracker spread with Marmite which really is microbial-based nutrition.
Metaphor and analogies have their limitations, of course. But in an age where science is increasingly quantitative, the importance of having strong mental images of systems before you start taking them apart and counting and measuring the various components must be emphasised. It is a tradition that goes back at least as far as Leonardo da Vinci, and possibly further.


Cummins, K.W. (1974). Structure and function of stream ecosystems. Bioscience 24: 631-641.

An encounter with a green alga that is red

One of my favourite walks in the northern Pennines is along the Nent valley from Foreshield to Alston, the highest market town in England, and back. It is just a few miles long and the walk is far from strenuous, but it is a beautiful little valley and to be able to walk in shirtsleeves in late September is an unexpected bonus.

The irony is that the River Nent is one of the most polluted rivers in the region, bearing the drainage from numerous mines and spoil heaps on the surrounding hillsides.  I’ve written about the effect of the toxic mine effluents on the River Nent elsewhere (see ‘East of Eden’ in Of Microscopes and Monsters) but today my attention has been grabbed by an alga that I did not mention in that account.   I am standing at the point where the river flows over a limestone pavement, at Gossipgate, a kilometre or so above Alston itself, and looking down at a rock hollow that has a bright lipstick-red crust.


The River Nent flowing past limestone pavement at Gossipgate, just above Alston, Cumbria and (right) a hollow on the limestone pavement with a crust of Haematococcus pluvialis.

Under the microscope, this crust reveals itself as a series of spherical cells, almost entirely filled with red pigment.  The name of this alga is Haematococcus pluvialis, and it is characteristic of situations which dry out frequently.  It is not just found in rock hollows, such as the ones I saw beside the River Nent; another favourite haunt is in bird baths.  Surprisingly, given its colour, this alga is more closely related to green algae such as Bulbochaete than it is to the group we commonly call “red algae”.   Conversely, if you think back to posts on Audouinella and Lemanea, you will recall that red algae are not necessarily red.   The red colour in Haematococcus is a compound called astaxanthin.    The red cells that I saw at the River Nent are actually cysts which allow the cell to survive periods out of the water.   Because the cells are exposed to the full glare of the sun, they produce astaxanthin as a natural sunscreen.


Left: Resting cells of Haematococcus pluvialis from the River Nent.  Scale bar: 20 micrometres (1/50th of a millimetre); right: Haematococcus in a bird bath in London.

You may be surprised to know that you have probably eaten astaxanthin within the past month, and almost certainly consumed many related compounds.   The intense red colour of astaxanthin means that it is a popular food additive and Haematococcus is grown commercially for this purpose.   Astaxanthin is the reason why the flesh of farmed salmon is often redder in colour than the flesh of wild salmon, but it is added to many other foods as well during the production phase.  If you saw “algae” on a menu, you might well turn up your nose and order something different.  However, algae creep into your diet in all sorts of unexpected ways without you ever knowing.