Buffers for duffers …

In Ecology in the hard rock café I wrote about the challenges of living in an aquatic world where carbon – one of the raw materials for photosynthesis – was in short supply.   What I did not write about in that post is that this carbon also gives freshwater some useful additional properties.   In brief, rainwater is not pure water, but absorbs carbon dioxide from the atmosphere.  This, in turn, makes rainwater slightly acidic and, when it falls onto rocks, this weak acid dissolves the minerals from which the rock is made.  This adds two other forms of carbon to the water – bicarbonate and carbonate (the latter, particularly, from limestone).

Each of these three types of carbon in freshwater can convert to either of the other two types, with the speed of the reaction depending on the balance between the forms (the “law of mass actions”).  In essence, the reactions proceed until equilibrium is obtained, and this equilibrium, in turn, depends upon the pH of the solution.  These processes are summarised in the diagram below.

Relationship between pH and the proportion of inorganic carbon as free carbon dioxide (or carbonic acid, H2CO3 – orange line), bicarbonate (HCO3 – green line) and carbonate (CO32- – blue line).

The chemistry behind this is not easy to explain but a consequence is that any attempt to shift the pH (e.g. by adding acid) causes an automatic adjustment in the balance between the different forms of carbon.  Some of the hydrogen ions that could make the water acid are, instead , bound up as bicarbonate, and the pH, as a result, does not change.  The greater the quantity of inorganic carbon in the sample, in other words, the greater the capacity of the water to resist changes in pH.   The carbonate, bicarbonate and free carbon dioxide together act as a “buffer”, a chemical shock absorber.   Think of it as equivalent to the responsible use of a credit card or savings account to defer the cost of an unexpected bill (a car repair, for example) so that your current account does not go overdrawn.

Because life largely evolved in well-buffered marine systems, the enzymes that run our cells generally work best within a narrow range of pH (approximately 6-9).   Cells – unicellular life forms in particular – get stressed if pH strays outside this range, so the greater the buffering capacity, the easier it is for cells (life at high pH can bring additional complications, but we don’t have time to go into those here).  “Alkalinity”, as I mentioned in the earlier post, is the measure that ecologists use to assess the strength of the buffer system in a lake or river.  The principle of the measurement is straightforward: we add a dilute acid very slowly and watch what happens to the pH.   At first, nothing happens but, as soon as the water’s natural buffering capacity has been exceeded, pH drops rapidly.

I have a small portable alkalinity titration kit which involves adding drops of bromophenol blue indicator to a sample of stream or lake water.  This gives the water a blue colour when the pH is greater than 4.6.  As the pH falls, the solution becomes colourless and, eventually, turns yellow.   If you look at the graph above you will see that, at pH 4.6 most of the bicarbonate (HCO3) has been converted to carbon dioxide so the buffering capacity is pretty much non-existent.  This means that I can use the quantity of acid that is needed to make the bromophenol blue change colour as a measure of the buffering capacity of the water.

Alkalinity titrations beside Ennerdale Water (see top photograph) using a Hanna HI 3811 alkalinity test kit.  The right hand image shows acid being added to the water sample with a 1 ml pipette.  The blue colour shows that pH has not yet dropped below 4.6.

All this talk of chemical equilibria seems to be a long way from the natural history that is the core business of this blog.  Yet, at the same time, these reactions describe natural phenomena every bit as real as the plants and animals that attract the interest of naturalists.   Geology and chemistry ultimately create the context within which biology flourishes, but it is rare to meet a chemist who can talk with a naturalist’s passion.  I think that this is partly because chemistry tends not to describe tangible features of the landscape but, instead, quickly gets lost in abstract equations.  However, it is also a matter of culture: chemists need clinical separation from the mud and filth to maximise precision, whilst ecologists feel the lure of the field.  There is, nonetheless, a very basic and necessary link between the chemistry and ecology of aquatic systems.   Geology may shape a landscape but chemistry is one of the key mediators that determines the types of plants that cloak the hills and vales.  We ignore it at our peril.


Reflections from a Romanian lake


If you have followed my blog for some time you will know that two of my professional interests are ensuring consistency in the implementation of environmental legislation across the European Union and trying to make ecological assessment as straightforward and understandable as possible. These two interests sometimes collide briefly, particularly when I am travelling, as I have an urge to grab a sample from lakes and rivers that I pass and to make a quick judgement on their quality (see “Lago di Maggiore under the microscope” and “Subsidiarity in action”).   This isn’t quite as straightforward as it seems, as my specialism requires use of a microscope, and travelling light precludes carrying my field microscope on my travels.   Instead, I bring small, discrete samples home and have a look at the diatoms in their live state.  Enough are usually recognisable to allow me to make a rough calculation of the indices that we use to evaluate ecological status.

My visit to Romania included a trip to Lacul Cāldāruşani, on the flat lands of the Wallachian Plain about 40 kilometres north of Bucharest. It is a shallow lake, fringed by reeds (Phragmites australis) and it was from these that we collected our sample.  The reed stems were all smothered with the green alga Cladophora glomerata which, in turn, hosted a rich diatom flora.   Many of these could be either identified, or a plausible guess at their identity made, from the live state, so I was able to make a list of diatoms and, from this, to calculate the indices that we use in the UK to assess the quality of lakes.   My conclusion was that that this was definitely an enriched lake, some way below the standards set by the Water Framework Directive, which agreed with the evidence that my Romanian hosts already had.   That I can travel from near the western edge of the European Union to the eastern edge and still make a robust inference of the quality of the lake says much for the robustness of the methods with which we are dealing.

The most abundant diatom in the sample was Cocconeis pediculus, which lives on the surface of the Cladophora filaments.  This means that it is, in this case at least, an epiphyte on an epiphyte, as the Cladophora was, itself, growing on the reed stems.  Rhoicosphenia abbreviata is another diatom that lives epiphytically on Cladophora, and this was also common in the sample.  As well as these, there were at least three species of Encyonema, mostly free-living but a few in tubes, plus Navicula tripunctata and at least one other species and a few cells of Epithemia sorex.   There was also a rich assortment of green algae, but I had only limited time to dedicate to this sample, so these will have to wait for another day.


Cladophora-smothered sections of submerged stems of Phragmites australis collected from Lacul Cāldāruşani, Romania, June 2016; b. and c. Cocconeis pediculus growing on living and dead filaments of Cladophora glomerata from Lac Cāldāruşani. Scale bar: 10 micrometres (= 1/100th of a millimetre).


Diatoms from Lac Cāldāruşani, Romania, June 2016: a. two cells of Rhoicosphenia abbreviata on a stalk; b. Navicula sp.; c. Navicula tripunctata; d. Epithemia sorex; e. Encyonema sp (E. silesiacum?) growing in mucilaginous tubes.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

One difference between this lake and most lakes in the UK is that the Romanians have a taste for a far broader range of freshwater fish than we do.  We enjoy salmon and trout, but there is not much enthusiasm for eating other freshwater fish here, in contrast to many parts of central and eastern Europe where fish such as carp are both farmed and eaten (we, in the UK, seem to have lost that taste, as many ruined monasteries have “carp ponds”).   Lac Cāldāruşani has a commercial fishery, and this probably contributes to the poor quality of the water.   Many shallow lakes and ponds are stocked with carp in the UK too, but for angling, not commercial fisheries.   Many of these are too small to feature on the regular monitoring programs (which only covers water bodies that are at least 50 Ha in size).   Carp, however, are fish that like to root around in the mud for food and, in the process, stir up the sediments releasing nutrients back into the water where they can be used by algae.   The algae, in turn, die and sink to the bottom where they decay and release the nutrients back to the water, only for another carp to stir them up again.  These shallow lakes are, in effect, not just polluted by this year’s inputs of nutrients, but also by pollution from the preceding decade, which is constantly being recycled as the fish search for food.

From here, we climbed back into the car to visit one other lake.  The story of that lake, however, will have to wait for a future post.


More details about the methods for assessing lake ecological status using diatoms in the following two papers:

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

Kelly, M., Urbanic, G., Acs, E. Bennion, H., Bertrin, V., Burgess, A., Denys, L.,  Gottschalk, S., Kahlert, M., Karjalainen, S.-M., Kennedy, B., Kosi, G., Marchetto, A., Morin, S., Picinska-Fałtynowicz, J., Poikane, S., Rosebery, J. Schoenfelder, I., Schoenfelder, J., Varbiro, G.(2014). Comparing aspirations: intercalibration of ecological status concepts across European lakes for littoral diatoms.   Hydrobiologia 734: 125-141.

How to make an ecologist #7


Casting a plankton net to collect algae, somewhere in Scotland (possibly Loch Earn), April 1985.

At some point between leaving Westfield as a rookie ecologist with an enthusiasm for Sphagnum, and finishing a PhD on mosses at Durham I started the slow metamorphosis into a phycologist.   Brian Whitton expected his PhD students to help out in undergraduate practicals and my lack of phycological training up to that point was not regarded as sufficient reason to excuse me from this duty.   It was a steep learning curve but, in turn, it opened windows onto new worlds that have kept me fascinated ever since.

Brian had an old school natural historian’s approach to undergraduate practicals.   Technicians were sent out to local ponds and came back with handfuls of vegetation which were squeezed and scraped to yield rich harvests of algae. At the start of the practical, no-one had any idea which species might be present; three hours later, with the help of a handful of books in a range of languages (we just looked at the pictures) and cajoling from Brian, the demonstrators, at least, emerged older and wiser.

Straight after Easter, the third year botany students were taken on a week-long field trip to Loch Lomond, staying at University of Glasgow’s Rowadennan Field Centre, and learning about algae at a time when most of them would really have preferred to be getting on with revision for their finals.   However, once they arrived at the field centre, set amidst the forests on the east shore of Loch Lomond in the shadow of Ben Lomond, they usually mellowed.   It was a glorious location. We went out to various lochs and streams, sampled different habitats, collected a few environmental measurements, and then spent time in the laboratory trying to name what we had found.   In the evenings most of us made the three kilometre walk to Rowardennan Hotel for a pint of beer.

On one of the days we made a long excursion, down the east shore of Loch Lomond, then up the west shore, making a short diversion at Tarbet to Loch Long, the only sea loch we visited during the week. Then it was back into the vans and up to the north end of Loch Lomond, stopping at a stream in Glen Falloch before sampling Loch Lubhair and Loch Linhe. The final leg swung south past Loch Venachar to Lake of Menteith in the Trossachs (‘the only lake in Scotland’) before returning to Rowardennan in time for dinner. In one long day we had seen marine and freshwater habitats, sampled hard and soft streams and lakes, planktonic and benthic habitats and seen seaweeds as long as our arms and microscopic algae a 100th of a millimetre in diameter.


Durham University botany undergraduatest getting to know freshwater algae at Rowardennan Field Centre, April 1985.

At this time, the Durham botany degree was strong on biochemistry and molecular biology and notoriously light on traditional botanical skills.   There was a running joke during my postgraduate years that some of our molecular biologist colleague’s plant identification skills ran no further than reading the label on a packet of seeds. Reductionism ruled, with teaching on whole plants and their interactions with the environment pushed to the edges of the course.   The honours botany students were taken on a two week field course to Austria at the end of their second year to learn about alpine plants. This week in Rowardennan dealt with the 75 per cent of UK’s plant diversity that has now dropped off most undergraduate curricula over the past couple of generations. And, once again, the demonstrators, acting as intermediaries between Brian’s extensive knowledge and the near complete ignorance of the students, were probably the principal beneficiaries.

There were other beneficial outcomes to the course. I spent long hours walking to and from the pub sharing our experiences of travelling in the Himalayas with one of the students.   This same individual (and her distinctive orange cagoule) cropped up in more of my photographs than a hypothesis concerning the random distribution of students on 35 mm film would predict.

Reader, I married her.


Durham undergraduates sampling a stream in Scotland during the algae field course, April 1985.

Unmasking the faceless Eurocrats …


My own small contribution to the campaign to keep the UK in the European Union takes the form of a scientific paper. This will probably not raise many eyebrows outside the small band of specialists amongst whom I work but it offer it as an antidote to the rhetoric of the anti-EU campaigners and their scaremongering about the Brussels bureaucracy. I have made no secret that I am pro-EU (see “What has the European Union ever done for us?”) and that I think the UK benefits from EU environmental legislation. What one person thinks to be sensible regulation can easily be portrayed by the disingenuous as excessive red tape peddled by faceless, unelected Brussels bureaucrats.

Our paper deals with about half a sentence in an annex of an 80 page Directive that deals with how EU Member States should assess the quality of lakes.   Should the suspended algae, the attached algae and the larger plants be used to assess lake condition, or can you get the same outcome by just using two of these three components? Interpretation of those few words can, however, result in considerable and recurring expense for a large Member State such as the UK.   Opinion on how they should be interpreted differed between the 28 countries of the EU.   How do you find the balance between the environmental risks associated with lax interpretation of EU law and the extra costs that a stringent reading of the Directive would entail?

I was contracted, along with two colleagues, by the European Commission’s Joint Research Centre to look into this issue by examining the datasets of those countries that had analysed all three components to see how much extra information additional types of monitoring added to a manager’s overview of lake condition.   One additional twist to the problem was that my own particular specialism, the attached algae, was the Cinderella at this particular ecological assessment Ball, with about 60% of EU states deciding that these were not necessary.   Ironically, my career as Fairy Godmother to fellow algal specialists was extremely short-lived, as the outcome of our analyses was that, if a lake had a problem, it could usually be detected using the suspended algae and higher plants (the “ugly sisters” … metaphor overload .. no more of this, I promise).   There are situations when all three are needed to understand how to manage a lake but, for strategic overviews of the condition of a country’s lakes, little was gained by including them.

So what has all this got to do with our EU referendum?   In brief, this was a matter of interpretation discussed by representatives of all Member States at meetings mediated by European Commission representatives.   Having identified a difference of opinion, they brought us in to work on an evidence-based solution which was then discussed, in depth, at another meeting of national representatives (mostly ecologists). Many agreed with our conclusion; a few made the case for continuing to use all three components.   Ecological arguments were put forward by both sides but, in essence, we were debating whether this was an issue that should be decided within or between Member States.   Most were happy that this level of detail could be determined within Member States.   Even if the outcome had been in favour of imposing a more rigorous interpretation of the Directive, it would have been the consensus of Member States enacted through the Commission, not a blanket edict from these (hypothetical) faceless bureaucrats that the right wing press constantly demonises.

An interesting coda to this story is that after our report had been circulated and discussed my colleague at JRC was contacted by people from one Member State who were slightly alarmed by the conclusion.  The point that they made was that devolving responsibility to individual countries would lead to many dropping the use of attached algae, simply on the grounds of financial expediency. I had some sympathy (one of the authors was a fellow consultant who, like me, makes part of his living from this type of work) but it also touched on something that has been exercising my mind over recent months.   Do countries use this type of monitoring because they have to (i.e. the Directive tells them to) or because they need to (i.e. it contributes valuable information to lake management)?   It shifts the onus on us, as advocates of a sub-discipline, to make a reasoned case for the continued use of attached algae, rather than simply assume that “Brussels” will guarantee our livelihood.

Note: the photograph shows Derwent Water in the English Lake District, looking south from Friar’s Crag, July 2015.


Kelly, M.G., Birk, S., Willby, N.J., Denys, L., Drakare, S., Kahlert, M., Karjalainen, S.-M., Marchetto, A., Pitt, J.-A., Urbanič, G. & Poikane, S. (2016). Redundancy in the ecological assessment of lakes: Are phytoplankton, macrophytes and phytobenthos all necessary? Science of the Total Environment http://dx.doi.org/10.1016/j.scitotenv.2016.02.024.

Everything is connected …

I’ve written about a curious group of algae called stoneworts (or charophytes) on a couple of occasions (see “The desert shall rejoice and bloom” and “Croft Kettle through the magnifying glass”. The significance of the name “stonewort” becomes obvious when you pick up a Chara plant, expecting it to be soft and pliable, and are struck by the rough texture of the axes, caused by the deposition of lime.


Chara hispida, photographed by Chris Carter.   Note the main axis and branches, from which whorls of branchlets arise at intervals.

The stoneworts are asssociated with hard water, so this deposition should not be a great surprise (the process by which kettles are coated with lime scale in hard water areas is very similar) however, most of the other plants in these habitats don’t share this property, so what is so special about Chara?   The answer is that, in hard waters, the carbon dioxide that plants need for photosynthesis is in short supply, but much more carbon is available as the bicarbonate ion.   Some aquatic plants can absorb the bicarbonate and then use an enzyme, carbonic anhydrase, to convert this bicarbonate to carbon dioxide. Chara, however, has a different strategy, actively pumping out hydrogen from inside the cells which, in turn, react with the bicarbonate and release carbon dioxide, which can then be absorbed by the plant.   However, as the water is also rich in calcium, a further series of reactions produces insoluble calcium carbonate, generating some additional carbon dioxide in the process As this series of reactions occurs very close to the cells from which the hydrogen ions are leaking, the precipitates end up on the plant surface, creating the rough texture.   The chemistry is way beyond this blog (meaning “… this blogger”) but you can follow it up in the references below.


Marcroscopic view of Chara intermedia showing an internode with a whorl of branchlets, along with spine cells and cortex cells (photograph: Chris Carter).

Another ion that is not very soluble is phosphate and this often gets caught up with the precipitating lime to form calcium phosphate.   This can be beneficial, as this phosphorus might otherwise fuel growth of phytoplankton which, in turn, would shade the Chara.   This means that Chara meadows should be resilient to artificial enrichment of nutrients to a limited extent at least.   However, there is some evidence that this capacity might be much less than was previously thought.   Hawes Water, a small tarn in Lancashire (not to be confused with Haweswater in Cumbria), for example, used to have rich and diverse communities of Chara spp, even in the deepest parts, but now the Chara and other submerged aquatic plants are confined to the shallow margins of the lake.   There is also good evidence of artificial enrichment in this catchment. The surprise is that concentrations of phosphorus in the water are still relatively low, yet the Chara meadows are much reduced compared with their condition fifty years ago.   The team that did this work also looked at another small marl lake, Cunswick Tarn, near Kendal in Cumbria, and found very similar changes.

It suggests a sensitivity to eutrophication that, perhaps, has previously been under-estimated, but it also points to the importance of balancing mechanisms in nature. On the one hand, Chara has some inbuilt capacity to counter-act increased nutrient concentrations. But others have shown that the ability of Chara to precipitate calcium carbonate is, itself, based on the photosynthesis rate.   The Chara meadows will reach a point when their natural capacity to absorb this extra phosphorus will be exhausted and then, as the phytoplankton take advantage of this, the water will get more turbid, reducing the amount of light reaching the Chara.   Less light means less photosynthesis and that will reduce the need for bicarbonate and, in turn, mean less carbonate deposition and less phosphorus removed. The evidence from Hawes Water is that this change happens very quickly: an ecological “domino effect”, if you like. As ever, everything is connected; sometimes in surprising ways.


Chara virgata (with oospores) from the Isle of Skye, photographed by Chris Carter.


McConnaughey, T. (1991). Calcification in Chara corallina: CO2 hydroxylation generates protons for bicarbonate assimilation. Limnology and Oceanography 619-628.

Pentecost, A. (1984). The growth of Chara globularis and its relationship to calcium carbonate deposition in Malham Tarn. Field Studies 6: 53-58.

Walker, N.A., Smith, F.A. & Cathers, I.R. (1980). Bicarbonate assimilation by freshwater charophytes and higher plants: I. Membrane transport of bicarbonate ions is not proven. Journal of Membrane Biology 57: 51-58.

Wiik, E., Bennion, H., Sayer, C.D., Davidson, T.A., McGowan, S., Patmore, I.R. & Clarke, S.J. (2015). Ecological sensitivity of marl lakes to nutrient enrichment: Evidence from Hawes Water, UK   Freshwater Biology 60: 2226-2247.

Wiik, E., Bennion, H., Sayer, C.D., Davidson, T.A., Clarke, S.J., McGowen, S., Prentice, S., Simpson, G.L. & Stone, L. (2015). The coming and going of a marl lake: multi-indicator palaeolimnology reveals abrupte cological change and alternative views of reference conditions.  Frontiers in Ecology and Evolution 3:82. doi: 10.3389/fevo.2015.00082.

A genuinely rare diatom genus?

About ten months ago I speculated on the practicalities of producing a “red list” of British diatoms (see “A red list of endangered British diatoms”).   A couple of weeks ago, I reported on progress towards this goal (see “Why do you look for the living amongst the dead?”) and, today, I can show the first evidence for a genuinely rare freshwater diatom in Great Britain.   Great Britain, alas, rather than the United Kingdom, as we struggled to get the Irish grid references to plot on our graphs, but it is a step in the right direction.

In my post last year, I commented that one of the problems we faced was the taxonomic uncertainty, particularly as there have been so many new species described, often as a result of “splitting” taxa that older books regarded as a single entity.   One of the criteria my intern, Susannah, and I used was a stable taxonomic concept, in order to ensure that older records could be merged with our more recent records.   This does not have to be at the level of species and, indeed, the first subject of our scrutiny was a genus, Tetracyclus. It fits our bill perfectly as it is quite recognizable, despite not being very common, so we can be fairly sure that the chance of an identification error is low.


The left hand map shows all hectads (10 km2) squares from which we have at least one freshwater diatom sample in Great Britain; the right hand map shows those hectads with records of Tetracyclus spp.

As you can see from the map, there are a cluster of locations in the Scottish highlands, three in the Cheviots in Northumberland and a few in Snowdonia. Then there is a record in Pembrokeshire and another in Wiltshire.   That is 23 hectads throughout the UK for all three species, none of which, individually, is found in more than 15 hectads, and therefore each qualifies as “nationally rare” according to JNCC guidelines.   There may be a few more records out there but, at the same time, there is also a risk of false negatives – a single valve, remember, does not necessarily mean that a viable population of the organism is present at the site.   The Wiltshire record worries me, and I need to check that there has not been a transcription error as the record was transferred from notebook to database, and to ensure that the grid reference was recorded correctly.

The literature offers little help when it comes to understanding the habitat of Tetracyclus: West and Fritsch tell us that Tetracyclus lacustris “… prefers hilly districts and is often found in the plankton of mountain lakes” whilst T. rupestris “… occurs on dripping rocks in mountain areas.” Other writers also hint that it might be partly sub-aerial in distribution, which may explain why the records in our dataset only ever record it in small quantities.   Is it possible that our samples, which are mostly from submerged rocks in streams and lake littoral zones, are just picking up a few stray cells that have been washed away from their preferred habitat?   We can interpret each dot, perhaps, as indicating that the species was “present in the vicinity”.

We should also point out that one of the Snowdonian locations on the map is Llyn Perfeddau, the lake from which the first Tetracyclus lacustris specimens were described, back in 1843 by John Ralfs.   Allan Pentecost re-visited Llyn Perfeddau in 2014 but was unable to find it in his samples, which adds to the mystique that this genus and species exert.

So are these three Tetracyclus species the first bona fide candidates for a UK (or GB) red list of diatoms?   Each fulfils the criterion of “nationally rare”, being found in less than 15 hectads, albeit with the provisos set out above. However, rarity alone is not sufficient to place a species on a red list; we also need to demonstrate that it is vulnerable or endangered.   This implies knowledge of trends over time, not just patterns in space.   The default under such circumstances is to consider whether the locations where it is found are fragmented and are, themselves, threatened or vulnerable.   The restricted distribution in low nutrient waters in mountainous and northern areas does suggest that changes in land management or climate change could affect the small isolated populations that we do have, so a designation of “vulnerable” is probably appropriate.   Though I doubt that WWF will be replacing their panda logo with a diatom any time soon.


Pentecost A. (2014). In search of the Welsh Tetracyclus. The Phycologist 88: 42-43.


Glass half full or glass half empty?


I’m tapping away at the back of a conference hall during the UK eDNA working group at the University of Bangor, absorbing the latest developments in the use of molecular technologies for applied ecology. Things have moved fast over the last couple of years, with one method, for the detection of Great Crested Newt, having moved out of the research laboratory and into widespread use. Several other methods – including our own method for ecological assessment using diatoms – are drawing close to the stage where their adoption by end-users is a real possibility, and lots more good ideas were bouncing around during the sessions and during the breaks.

The fascination of much of this work lies in the interplay between the new and the old, using the sensitivity of molecular tools to push our understanding of what traditional methods have told us. At the same time, the new methods are largely underpinned by libraries of reference barcode sequences that provide the essential link between the ‘old’ and the ‘new’, and these are wholly dependent upon specialists rooted in old-school taxonomy.

Here’s the rub: if the goal is to produce methods for ecological assessment, then the point will come when the research scientists step back and the end-users start to use it.   At this point, real world exigencies take over and, with the public sector battered by funding cuts, any opportunity to save money will be grasped. What this means is that we cannot assume the same depth of ecological knowledge in the users as in the developers. This was not always the case as the Environment Agency had a cadre of extremely capable ecologists, with a deep knowledge their local rivers and broad understanding of ecology. I don’t believe that this was knowledge that they were taught, rather that they learnt it on the job, seeing streams in all of their moods as they collected samples, poring over identification guides as they named their specimens and sharing knowledge with colleagues.   The result was a depth of understanding which, in turn, they drew upon to advise colleagues involved in regulation and catchment management.

In the last few years this system has come under scrutiny as managers have searched for cost savings. Environment Agency biologists are no longer expected to collect their own samples, which are taken for them by a separate team in the misguided assumption that highly-trained biologist will be more productive if they stay in the laboratory and focus on using their specialist identification skills. Moving to molecular techniques will just continue this process.   Once the excitement of the research is over, the methods will be ripe for economies of scale; sample processing will be a task for molecular biological technicians, and the first time an ecologist encounters the sample it will be as processed output from a Next Generation Sequencing machine.

The function of the laborious process of collecting and analysing ecological samples is not just to produce the data that underpins evidence-driven catchment management. It also allows biologists to acquire the experience that lets them interpret these data sensitively and wisely.   The urge to find short-term savings has focussed on the quantifiable (how many samples can a laboratory process) and ignored the unquantifiable (how good is the advice that they offer their colleagues?).   I don’t think the full calamity of what we are seeing will hit for a few years because most of the ecology staff in the Environment Agency have done their apprenticeships in the field. Over time, however, a new generation will join the organisation for whom computer print-outs may be the closest they get to encountering river and stream life.

I am basically enthusiastic about the potential that molecular technologies can offer to the applied ecologist but we do need to be aware that implications of these approaches extend beyond issues of analytical performance characteristics and cost. This is because ecology is more about making lists of what organisms we find at a particular location (and, judging by the presentations, this seems to be the focus of most current studies) but about what those organisms do, and how they fit together to form ecosystems and food webs. OK, so you can read about Baetis rhodani in a textbook, but that is never going to be the same experience as watching it scuttle across the tray where you’ve dumped the contents of your pond net, or of observing a midge larva graze on algae under a microscope. The problem is that we cannot put a value on those experiences, in the same way that the cost of processing a sample can be calculated.

This is a theme that I’ve explored several times already (see “When a picture is worth a thousand base-pairs …”, “Simplicity is the ultimate sophistication: McEcology and the dangers of call centre ecology” and “Slow science and streamcraft”) but it bears repeating, simply because it is an issue that falls through the cracks of most objective appraisals of ecological assessment.   The research scientists tend to see purely in terms of the objective collection and interpretation of data, whilst managers look at it in terms of the cost to produce an identifiable product.   It is more than both of these: it is a profession.   The challenge now is to integrate molecular methods into the working practices of professional “frontline” ecologists, and how we prevent this professionalism being degraded to a series of technical tasks, simply because the bean counters have worked out that this is the most efficient way to distribute their scarce resources around the organisation.


Biggs, J., Ewald, N., Valentini, A., Gaboriaud, C., Dejean, T., Griffiths, R.A., Fosterd, J., Wilkinson, J.A., Arnell, A., Brothertone, P., Williams, P. & Dunna, F. (2015). Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt (Triturus cristatus). Biological Conservation 183: 19-28.