A very dilute compost heap …

It is hard to believe that this idyllic view is within a kilometre of the centre of Newcastle.   We are standing in Jesmond Dene, a steep-sided valley that is now, thanks to the largesse of Lord Armstrong in the 19th century, now a public park.  From the point of view of someone teaching freshwater ecology to undergraduates it is a godsend, as it means that we have a fine location for fieldwork within walking distance of the university.  And, because I teach Geography undergraduates, all I need to do is tell them the location and assume that their spatial awareness will lead them to the right place at roughly the right time.  It usually works.

Don’t be misled by the Arcadian scene in this photograph: for most of its length the Ouseburn is an unprepossessing stream with a multitude of problems, which is one of the reasons why I bring the students here in the first place.  We get them to sample the water, which they analyse in the laboratory over the next couple of weeks, and also collect a sample of invertebrates from the stream bed.  But, most importantly, I just want to get them to start thinking about the factors that driver a river ecosystem.

In the lectures beforehand, I make the point that we need to think beyond the stream channel itself if we are to understand its ecology and the visit to the Ouseburn helps to reinforce this.   That sun-dappled scene above is conveying an important truth: that a lot of the sunlight is intercepted by the leaves of the surrounding trees before it can reach the stream itself.   If we thought about ecology solely in terms of the stream channel we might conclude that this means less energy to fuel the stream ecosystem.  However, look at the photograph below of some of my students peering into the tray containing the invertebrates they have just collected.  Around them in the stream are leaves shed by the surrounding trees.   And, in that tray, we find a range of invertebrates but, most commonly, freshwater shrimp (Gammarus pulex), freshwater hoglouse (Asellus aquaticus) both of which are as happy feeding on the rotting remains of leaves from the surrounding trees as they are on food produced within the stream.

Left: Invertebrate sampling at Jesmond Dene, October 2017. Note the dead leaves in the stream, creating a natural food supply for the bugs.  Right: a Petri dish containing the contents from one pond net.  Note the large numbers of freshwater shrimp, Gammarus pulex (see inset).  

This is the time of year when gardeners are raking up piles of leaves and dumping them on their compost heaps.   When I peer into our compost heap I see a writhing mass of invertebrate animals also feeding on dead and decaying vegetation.  There are many segmented worms in both our compost heap and the samples we get from the Ouseburn, although most of the other animals are quite different (slugs, mostly, in our compost heap).   They may not be as exciting as the hyenas and vultures that perform similar functions on African savannahs but they play an essential role in driving nature’s cycles, turning death back into life (or, at least, into the raw materials on which new life will grow).  All flesh is grass…

Two compost bins: useful metaphors for how energy flows through stream ecosystems.

That’s the first lesson that I want to get across to the students: a river, in its natural state, is really a very, very dilute compost heap, full of organisms custom-built to recycle dead and decaying organic matter.   What I don’t tell them is that bringing them to the Ouseburn is a cop-out for me, as a lecturer whose real skills lay with algae rather than invertebrates.  If I took them to a stream further up the Tyne Valley where the hand of man was less obvious, we would have found many more types of invertebrates, and would have been able to demonstrate a much wider range of ways of feeding than we saw in the Ouseburn.  In particular, I would have expected to see stonefly nymphs and caddisfly larvae, some of which have tough jaws capable of ripping apart leaves, as well as mayfly nymphs, some of which will graze directly on algae.

The idea of a “grazer”, however, needs a little qualification.   Freshwater ecologists like to classify bugs into neat categories based on their food preferences as this helps them understand how energy flows through ecosystems.  The bugs-eye view of algae, however is that they are just one of many types of digestible energy found on and around the stream beds they inhabit.  Some ecologists prefer to lump “grazers” into a larger category of “collector-gatherers” that are relatively unfussy about what type of organic matter they eat and will cheerfully hoover up detritus that other organisms have left behind.

That “detritus” is, by the way, a euphemism for, amongst other things, the downloaded remains of the stonefly nymph’s vegetarian dinner.  Freshwater ecologists refer to this as “fine particulate organic matter” but the rest of us have a wealth of scatological language on which to draw.   That’s another lesson that I want to convey to my students: streams contain a lot of small organisms investing a lot of their valuable time searching for and eating other animal’s poo.   And that means that trout and other predators in these aquatic food-webs are eating a mixture of herbivores (the “shredders” plus the bugs that feed directly on algae) plus a lot of invertebrates that are a lot less fussy about food hygiene.   Next time you sit down to eat grilled trout, remember that you are basically eating reprocessed poo.


Bloor, M.C., (2011).  Dietary Preference of Gammarus pulex and Asellus aquaticus during a laboratory breeding programme for ecotoxicological studies. International Journal of Zoology 2011: article ID 294394, http://dx.doi.org/10.1155/2011/294394.

Cummins, K.W. (1983).  Trophic relations of aquatic insects.  Annual Review of Entomology 18: 183-206.

Kelly, D.W., Dick, J.T.A. & Montgomery, W.I.  (2002). The functional role of Gammarus (Crustacea, Amphipoda): shredders, predators, or both?   Hydrobiologia 485: 199-203.

Macus, J.H., Sutcliffe, D.W. & Willoughby, L.G. (1978).  Feeding and growth of Asellus aquaticus (Isopoda) on food items from the littoral of Windermere, including green leaves of Elodea Canadensis.  Freshwater Biology 8: 505-519.

Willoughby, L.G. (1983).  Feeding behaviour of Gammarus pulex (L.) (Amphipoda) on Nitella.  Crustaceana 44: 245-250.


What a difference a storm makes …

I was back at Croasdale Beck last week and noticed a rather dramatic change to the meander just upstream from our regular sampling spot.   If you look at the photograph that heads the post “A tale of two diatoms …”, you’ll see the stream flowing around this meander.  Now, however, it has cut a new, shorter channel that bypasses the meander altogether.   We visited the stream just a few days after Storm Ophelia had passed through although, judging by the grass growing on the gravel of the abandoned meander, it was not necessarily this particular event that reshaped the stream.

Croasdale Beck is an unruly tributary of the River Ehen, rising on the fells above Ennerdale Water and tumbling down across rough grazing land and some semi-improved pasture (as in the picture above) before joining the Ehen in Ennerdale Bridge.   This is not the first time that we have seen conspicuous changes in the channel after a storm.  The magnitude of the flood is illustrated by the hydrograph below, which went off-scale for a period, as the discharge exceeded 3000 mega litres per day (300 MLD is the approximate limit for safe wading, in my experience).   I noticed that there was much less green algae present than we usually record at this time of year, although the diatom film was still quite thick.   Some of the stones that I picked up to sample had the slimy biofilm on the underside, suggesting that they had been recently rolled by the flooded river.   Croasdale Beck has no lake to buffer the rise and fall of the floodwaters and a huge amount of energy is carried down in a short period of time as the water surges downstream.

By the time we had arrived, the floodwaters had subsided and the sheep were contentedly grazing the surrounding land.  The stream itself was almost back to base flow (in contrast to the River Ehen which was still only just wadable).  Only the meander looked different …

The hydrograph for the River Ehen, as the aftereffects of Storm Ophelia make their way downstream.

Winning hearts and minds …

I write several of my posts whilst travelling, though am always conscious of the hypocrisy of writing an environmentally-themed blog whilst, at the same time, chalking up an embarrassing carbon footprint.  Last month, however, I participated in my first “eConference”, in which the participants were linked by the internet.  With over 200 people from all over Europe, and beyond, attending for all or part of the three days, there was a substantial environmental benefit and whilst there was little potential for the often-useful “off-piste” conversations that are often as useful as the formal programme of a conference, there were some unexpected benefits.  I, for example, managed to get the ironing done whilst listening to Daniel Hering and Annette Battrup-Pedersen’s talks.

You can find the presentations by following this link: https://www.ceh.ac.uk/get-involved/events/future-water-management-europe-econference.   My talk is the first and, in it, I tried to lay out some of the strengths and weaknesses of the ways that we collect and use ecological data for managing lakes and rivers.  I was aiming to give a high level overview of the situation and, as I prepared, I found myself drawing, as I often seem to do, on medical and health-related metaphors.

At its simplest, ecological assessment involves looking at a habitat, collecting information about the types of communities that are present and match the information we collect to knowledge that we have obtained from outside sources (such as books and teachers) and from prior experience in order to guide decisions about future management of that habitat. At its simplest, this may involve categoric distinctions (“this section of a river is okay, but that one is not”) but we often find that finer distinctions are necessary, much as when a doctor asks a patient to articulate pain on a scale of one to ten.  The doctor-patient analogy is important, because the outcomes from ecological assessment almost always need to be communicated to people with far less technical understanding than the person who collected the information in the first place.

I’ve had more opportunity than I would have liked to ruminate on these analogies in recent years as my youngest son was diagnosed with Type I diabetes in 2014 (see “Why are ecologists so obsessed with monitoring?”).   One of the most impressive lessons for me was how the medical team at our local hospital managed to both stabilise his condition and teach him the rudiments of managing his blood sugar levels in less than a week.   He was a teenager with limited interest in science so the complexities of measuring and interpreting blood sugar levels had to be communicated in a very practical manner.  That he now lives a pretty normal life stands testament to their communication, as much to their medical, skills.

The situation with diabetes offers a useful parallel to environmental assessment: blood sugar concentrations are monitored and evaluated against thresholds.  If the concentration crosses these thresholds (too high or too low), then action is taken to either reduce or increase blood sugar (inject insulin or eat some sugar or carbohydrates, respectively).   Blood sugar concentrations change gradually over time and are measured on a continuous scale.  However, for practical purposes they can be reduced to a simple “Goldilocks” formula (“too much”, “just right”, “not enough”).  Behind each category lie, for a diabetic, powerful associations that reinforce the consequences of not taking action (if you have even seen a diabetic suffering a “hypo”, you’ll know what I mean).

Categorical distinctions versus continuous scales embody the tensions at the heart of contemporary ecological assessment: a decision to act or not act is categorical yet change in nature tends to be more gradual.   The science behind ecological assessment tends to favour continuous scales, whilst regulation needs thresholds.  This is, indeed, captured in the Water Framework Directive (WFD): there are 38 references to “ecological status”, eight in the main text and the remainder in the annexes.  By contrast, there are just two references to “ecological quality ratios” – the continuous scale on which ecological assessment is based – both of which are in an annex.   Yet, somehow, these EQRs dominate conversation at most scientific meetings where the WFD is on the agenda.

You might think that this is an issue of semantics.  For both diabetes and ecological assessment, we can simply divide a continuous measurement scale into categories so what is the problem?   For diabetes, I think that the associations between low blood sugar and unpleasant, even dangerous consequences are such that it is not a problem.  For ecological assessment, I’m not so sure.  Like diabetes, our methods are able to convey the message that changes are taking place.  Unlike diabetes, they are often failing to finish the sentence with “… and bad things will happen unless you do something”.   EQRs can facilitate geek-to-geek interactions but often fail to transmit the associations to non-technical audiences – managers and stakeholders – that make them sit up and take notice.

I’d like to think that we can build categorical “triggers” into methods that make more direct links with these “bad things”.  In part, this would address the intrinsic uncertainty in our continuous scales (see “Certainly uncertain …”) but it would also greatly increase the ability of these methods to communicate risks and consequences to non-technical audiences (“look – this river is full of sewage fungus / filamentous algae – we must do something!”).   That’s important because, whilst I think that the WFD is successful at setting out principles for sustainable management of water, it fails if considered only as a means for top-down regulation.   In fact, I suspect that Article 14, which deals with public participation, is partly responsible for regulators not taking action (because “costs” are perceived as disproportionate to “benefits”) than for driving through improvements.   We need to start thinking more about ensuring that ecologists are given the tools to communicate their concerns beyond a narrow circle of fellow specialists (see also “The democratisation of stream ecology?”).   Despite all the research that the WFD has spawned, there has been a conspicuous failure to change “hearts and minds”.  In the final analysis, that is going to trump ecological nuance in determining the scale of environmental improvement we should expect.

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.

It’s all about the algae

Just a short post to point you all towards an article I wrote for Royal Society of Biology’s magazine The Biologist.  It is a broad overview of the reasons why we use algae to assess the condition of our lakes and rivers in Europe and is illustrated with three of Chris Carter’s beautiful images, and the print edition will have even more of these.  Take the figure legends with a pinch of salt (we didn’t write these!): neither Tolypella nor Chaetophora are particularly common in the UK.   Navicula, on the other hand, is common but the legend makes no mention of this.

Whilst I have your attention, I will also point you towards a short article that I wrote for the most recent Phycological Bulletin, the newsletter of the Phycological Society of America.  This offers a few more hints to anyone thinking about entering the Hilda Canter-Lund competition next year.

Certainly uncertain …

Back in May I set out some thoughts on what the diatom-based metrics that we use for ecological assessment are actually telling us (see “What does it all mean?”).  I suggested that diatoms (and, for that matter, other freshwater benthic algae) showed four basic responses to nutrients and that the apparent continua of optima obtained from statistical models was the result of interactions with other variables such as alkalinity.   However, this is still only a partial explanation for what we see in samples, which often contain species with a range of different responses to the nutrient gradient.  At a purely computational level, this is not a major problem, as assessments are based on the average response of the assemblage. This assumes that the variation is stochastic, with no biological significance.  In practice, standard methods for sampling phytobenthos destroy the structure and patchiness of the community at the location, and our understanding is further confounded by the microscopic scale of the habitats we are trying to interpret (see “Baffled by the benthos (1)”).  But what if the variability that we observe in our samples is actually telling us something about the structure and function of the ecosystem?

One limitation of the transfer functions that I talked about in that earlier post is that they amalgamate information about individual species but do not use any higher level information about community structure.  Understanding more about community structure may help us to understand some of the variation that we see.   In the graph below I have tried to visualise the response of the four categories of response along the nutrient/organic gradient in a way that tries to explain the overlap in occurrence of different types of response.   I have put a vertical line on this graph in order that we can focus on the community at one point along the pollution gradient, noting, in particular, that three different strategies can co-exist at the same level of pollution.  Received wisdom amongst the diatom faithful is that the apparent variation we see in ecological preferences amongst the species in a single sample reflects inadequacies in our taxonomic understanding.  My suggestion is that this is partly because we have not appreciated how species are arranged within a biofilm.  I’ve tried to illustrate this with a diagram of a biofilm that might lead to this type of assemblage.

Schematic diagram showing the response of benthic algae along a nutrient/organic gradient.  a.: taxa thriving in low nutrient / high oxygen habitats; b.: taxa thriving in high nutrient / high oxygen habitats; c.: taxa thriving in high nutrient / low oxygen habitats; d.: taxa thriving in high nutrients / very low oxygen habitats.   H, G., M, P and B refer to high, good, moderate, poor and bad ecological status.

The dominant alga in many of the enriched rivers in my part of the world is the tough, branched filamentous green alga Cladophora glomerata.   This, in turn, creates micro-habitats for a range of algae.  Some algae, such as Rhoicosphenia abbreviata, Cocconeis pediculus and Chamaesiphon incrustans, thrive as epiphytes on Cladophora whilst others, such as C. euglypta are often, but not exclusively, found in this microhabitat.  Living on Cladophora filaments gives them better access to light but also means that their supply of oxygen is constantly replenished by the water (few rivers in the UK are, these days, so bereft of oxygen to make this an issue).   All of these species fit neatly into category b. in my earlier post.

Underneath the Cladophora filaments, however, there is a very different environment.  The filaments trap organic and inorganic particulate matter which are energy sources for a variety of protozoans, bacteria and fungi.   These use up the limited oxygen in the water, possibly faster than it can be replenished, so any algae that live in this part of the biofilm need to be able to cope with the shading from the Cladophora plus the low levels of oxygen.   Many of the species that we find in highly polluted conditions are motile (e.g. Nitzschia palea), and so are able to constantly adjust their positions, in order to access more light and other resources.   They will also need to be able to cope with lower oxygen concentrations and, possibly, with consequences such as highly reducing conditions.  These species will fit into categories c. and d. in the first diagram.

A stylised (and simplified) cross-section through a biofilm in a polluted river, showing how different algae may co-exist.   The biofilm is dominated by Cladophora glomerata (i.) with epiphytic Rhoicosphenia abbreviata (ii.), Cocconeis euglypta (iii.) and Chamaesiphon incrustans (iv.) whilst, lower down in the biofilm, we see motile Nitzschia palea (v.) and Fistulifera and Mayamaea species (vi.) growing in mucilaginous masses.

However, as the cross-section above represents substantially less than a millimetre of a real biofilm, it is almost impossible to keep apart when sampling, and we end up trying to make sense of a mess of different species.   The ecologists default position is, inevitably, name and count, then feed the outputs into a statistical program and hope for the best.

A final complication is that river beds are rarely uniform.  The stones that make up the substrate vary in size and stability, so some are rolled by the current more frequently than others.  There may be patches of faster and slower flow associated with the inside and outsides of meanders, plus areas with more or less shade.   As a result, the patches of Cladophora will vary in thickness (some less stable stones will lack them altogether) and, along with this, the proportions of species exhibiting each of the strategies.  The final twist, therefore, is that the vertical line that I drew on the first illustration to illustrate a point on a gradient is, itself, simplistic.  As the proportions vary, so the position of that line will also shift.  Any one sample (itself the amalgamation of at least five microhabitats) could appear at a number of different points on the gradient.  Broadly speaking, uncertainty is embedded into the assessment of ecological status using phytobenthos as deeply as it is in quantum mechanics.  We can manage uncertainty to some extent by taking care with those aspects that are within our control.   However, in the final analysis, a sampling procedure that involves an organism 25,000 times larger than most diatoms blundering around a stream wielding a toothbrush is invariably going to have limitations.

The same schematic diagram as that at the start of this article, but with the vertical line indicating the position of a hypothetical sample replaced by a rectangle representing the range of possibilities for samples at any one site.