How to make an ecologist #6

My PhD studies were my introduction to the world of environmental monitoring, the shady netherworld of Jeremiahs who diagnose and pronounce upon the sorry state of our planet.   The roots of this activity lie in sound fundamental research; the form it takes, however, is strongly dictated by non-scientific circumstances, including politics and legislation.

In my case, the research group that Brian Whitton led had done some pioneering work on the effect of heavy metals on aquatic ecology from the late 1960s and throughout the 1970s. They had used the abandoned lead mines of the northern Pennines to establish general patterns between the concentration of heavy metal in the water and the number and types of aquatic plants and algae that were found.   The environmental and health consequences of heavy metals was one of the most prominent environmental/health issues of the time. This, however, turned out to be a mixed blessing for me.   On one hand, there was already a huge body of research addressing the basic questions; on the other hand, BP, who at the time had a mining subsidiary exploring the feasibility of zinc mining in the north of England, funded my PhD in order to manage any UK-based activities responsibly.   I was to investigate the use of aquatic mosses to monitor the concentrations of heavy metals, following on from the work of a recently-finished student, John Wehr.

Suffice it to say that I produced enough results over the three years of my studies to satisfy the examiners. It was workmanlike stuff, not terribly exciting and not work that I look back upon with great pride.   I got three papers in respectable journals without shaking the foundations of aquatic ecology and they got my career under way. However, even before I finished, I had the feeling that the rest of the world had moved on.   The issue of toxic pollutants in the environment had been simmering away in the scientific literature and popular press since Rachel Carson published Silent Spring in the 1960s.   In 1976, the European Economic Community had passed the Dangerous Substances Directive which limited the amounts of toxic pollutants (including heavy metals) that were allowed to be released into the environment.   By modern standards, it was not a very subtle piece of legislation, and it certainly did not have any ecological nuances that might have stimulated new directions in my research.   What it did mean, however, was that problems posed by heavy metals were on a wane in western Europe by the time I started. There were rivers that still suffered (see “A return to the River Team”) but more due to weak regulation than to a lack of understanding.   Staff in water authorities (forerunners to the Environment Agency) did use mosses to detect intermittent pulses of heavy metals but, as the legislation was written in terms of concentrations of chemicals, the role of biology was secondary.


Caplecleugh Low Level, an abandoned lead mine at Nenthead in the northern Pennines.   This is one of a very small number of slides from the period of my PhD studies, and their aftermath, that has survived.   You can just see the abundant algal growths (Mougeotia) in the channel in the foreground.

One area where heavy metals were still a problem, however, were the abandoned ore fields of the northern Pennines.   The regulators could only regulate extant businesses, but the mining companies who had exploited the minerals here had long since disappeared.   Polluted mine waters continued to pour from abandoned adits into rivers and these created a huge natural laboratory on which to test ideas. I had spent all my life until this point in London; I associated landscapes as majestic as those of the Pennine dales with holidays, not the everyday. Now, however, I had the excuse to get out and explore the hills, looking for suitable locations for experiments or to collect material to work on in the laboratory. I sometimes scheduled field work for the weekends and walk in the hills after I had finished what I needed to do.  The blurring of the boundaries between work and leisure is another recurring, and mostly positive, theme in my career. I know lots of people who need more rigorous compartmentalisation of professional and home life. I’m lucky, perhaps, in that the curiosity that sustains my work can also spill over into something as mundane as a stroll along a river bank.

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.

Hindsight on the foreshore …


Don’t be fooled by this photograph looking across Lago di Maggiore from the village of Angera, where I was staying during a visit to the European Commission’s Joint Research Centre at Ispra, a few kilometres away.   There had been two days of almost constant rain and temperatures little different to those in the UK and the sun came out just before we were due to head to the airport for the homeward journey.   Before the taxi came, however, I found time for a short walk along the lake front, during which time a silty foreshore littered with empty shells caught my eye.   The shells looked like cockle shells, common around our own coast yet this was a freshwater lake.   I scrambled down for a closer look.

The shells belonged to a bivalve mollusc and were an ochre colour, with darker markings and a series of concentric ridges.   I’m not an expert on molluscs but, after a little searching on the web, I think that they probably belong to the Asian clam (Corbicula fluminea), one of a number of alien mollusc species that has become established in Lago di Maggiore in recent years.   The shape of the cell, and the markings rule out the zebra and quagga mussels (Dreissena polymorpha, D. bugensis) whilst another recent invader, the Chinese pond mussel (Sinanodonta woodiana) is much larger (up to 30 cm).


The foreshore at Angera littered with shells and (right) a close-up of the two halves of an Asian Clam shell.   Each is about 2 centimetres long.   February 2016.

There is an irony here, as I have written several blogs about an endangered freshwater bivalve (the pearl mussel – Margaritifera margaritifera, see “’Signal’ or ‘noise’?”) yet this group also contains some of the most notorious invasive species in the world. All originate from Asia but are now widespread in Europe and North and South America, where they cause a large amount of economic damage.

Like all bivalves, Asian clams are filter-feeders. They open their shells slightly and extend two tubes (“siphons”) from their bodies. Water is drawn in through one of these, across the gills, where particulate material is trapped, and out through the other. Fine cilia waft the particulates towards the clam’s mouth.   In a lake such as Maggiore, much of the particulate matter will be suspended algae (“phytoplankton”) and prolific growths of these invasive bivalves can actually reduce the quantities of phytoplankton to such an extent that they have been proposed as solutions to eutrophication problems under some circumstances. Because the phytoplankton, in turn, contains a lot of the phosphorus in the water, this has been referred to as “biological oligotrophication”. The benefits are partly a matter of perception: the bivalves have not removed the nutrients and algae, they have merely relocated them to another part of the lake.   That might bring short-term benefits, but it is not a solution per se.

Unlike zebra mussels, however, Asian clams have an alternate mode of feeding: they extent a muscly foot to pull themselves into the sediments which, in the process, throws up fine particles that can be sucked through the siphons. This “pedal feeding” could play an important role in the functioning of lakes due to the disturbance it causes, allowing oxygen to penetrate the surface layers of the sediment. As phosphorus compounds are generally less soluble in the presence of oxygen than they are in anaerobic conditions, this can further reduce the effects of eutrophication by “locking” the phosphorus into the sediments. The oxygen also fuels microbial processes, including the breakdown of nitrogen compounds limiting the production of nitrous oxide, a potent greenhouse gas in the process. Yet, ironically, the distribution of Corbicula is strongly influenced by temperature and global warming is likely to increase its range.

Local scientists have concluded that eradication of Corbicula and other alien molluscs from Lago di Maggiore is probably impossible as any attempt to remove them will probably disrupt other littoral organisms too. Yet, at the same time, the role that Corbicula plays in the food chain is not clear and it is possible that the spread of this and other bivalves will have knock-on effects for local fisheries. The first record of C. fluminea in Lago di Maggiore was made in 2010. That means that the lake I looked across this week might look like the lake I looked across on my first visit about 10 years ago, but it is nonetheless a different lake under the surface. It’s not the same lake but, as Heroclitus also reminds us (see “What Constable never saw …”), I’m not the same man either.


Kamburska, L., Lauceri, R. & Riccardi, N. (2013a). Establishment of a new alien species in Lake Maggiore (Northern Italy): Anodonta (Sinanodonta) woodiana (Lea, 1834) (Bivalvia: Unionidae). Aquatic Invasions 8: 111–116.

Kamburska, L., Lauceri, R., Beltrami, M., Boggero, A., Cardeccia, A., Guarneri, I.Manca, M. & Riccardi, N. (2013b). Establishment of Corbicula fluminea (O.F. Müller, 1774) in Lake Maggiore: a spatial approach to trace the invasion dynamics. BioInvasions Records 2: 105–117.

McDowell, W.G., Benson, A.J. & Byers, J.E. (2014). Climate controls the distribution of a widespread invasive species: implications for future range expansion. Freshwater Biology 59: 847-857.

Vaughn, C.C. & Hakenkamp, C.C. (2001). The functional role of burrowing bivalves in freshwater ecosystems. Freshwater Biology 46: 1431-1446.

How to make an ecologist #5

Hindsight, curiously, confuses this exercise of looking back over my career, rather than aiding it. Looking back, I see a linear pathway from Harold Wood through to the present, losing sight of the crossroads where chance could have taken me off in entirely different directions.   Contemplating my visit to the site of the former Westfield College (see “How to make an ecologist #4) jogged my memory and reminded me that the process that brought me to Durham was, actually, far from straightforward.

My undergraduate project had convinced me that I wanted to do a PhD, and my first choice of a supervisor was Professor John Harper, at Bangor in North Wales, whose book Population Biology of Plants had been influential in determining the course of my project.   However, he had recently retired and my letter enquiring about opportunities had bounced around his colleagues.   I did go up to Bangor to meet someone in the Agricultural Science department with a view to doing a taught MSc leading into a PhD on the overlap between population biology and grassland agronomy. There was funding for the MSc but, after that, the situation seemed rather vague.

It was not until after I graduated from Westfield that I saw an advert in New Scientist for an MSc in Durham.   Though not concerned with population biology, it fitted in with my undergraduate studies in two ways: the focus was mosses (picking up on my work on Sphagnum) and heavy metals (a specialism of the department in Westfield).   There was also a strong likelihood of the MSc being converted to a PhD.   I applied.   I had never heard of Brian Whitton (my undergraduate years had involved a single first year lecture on algae) but Connie Allen, a postgraduate student in the lab where I had worked on my project, whooped with delight when I told her that I had an interview. He was, she told me, the leading expert on blue-green algae in the country.   I seem to remember that my application included a hand-written, photocopied CV which included a spelling mistake.   That I got the studentship probably says as much about the other candidates as it does about me.

This was one of those crossroads in my life where chance could have taken me off in several different directions.   It is not a simple process of finding a supervisor whose interests dovetail with your own.   You needed financial support and, in the sciences, that came mostly via a studentship that the supervisor had already been awarded.   It is supply-side economics: there was a pool of studentships, and a larger pool of candidates.   The candidates may have their own ideas on what they want to do, but there was no guarantee that a project on that precise topic would come up at the right time.   At the time of my interview I seem to remember that I was not wholly convinced that this was the right project for me but it seemed like the best opportunity at the time.   I booked a train ticket and headed to Durham for an interview.


Durham: the view from the station.

Durham entrances you before even leaving the station.   The train approaches through a wooded cutting, before the landscape drops away; the final approach to the station is across a viaduct, giving panoramic views of the ancient city, with castle and cathedral perched on an incised meander above the River Wear.   I walked down from the station to the town and through cobbled streets winding up towards the cathedral.   Several years later, when I visited Tuscany for the first time, I was struck by the similarity between this small northern English city and the Tuscan towns clustered on hillsides around a basilica.   I think I knew that I would accept the studentship, if offered, even before I got to the interview.

The science laboratories were a short walk away from the town centre, a zone of prosaic architecture to offset the glories of the peninsula.   The Botany Department was based in the Dawson Building, the oldest building on the site, which had once contained the entire science faculty and which is now home to the departments of Archaeology and Anthropology.   When I arrived, Brian Whitton had a suite of labs on the first floor, plus two satellite laboratories elsewhere on the site, relicts of a period just before I had arrived when the research group was much larger.   Although the work I was doing followed on from topics I had studied as an undergraduate, the Botany Department in Durham was a contrast to Westfield in many ways: an air of frantic industry pervaded the corridors in contrast to Westfield’s general serenity.   Research groups were larger, postdocs were more numerous and I got the sense that Durham academics were researchers who taught, rather than teachers who researched.


The Dawson Building on the University of Durham’s science site.  The phycology labs were at the right hand end on the first floor.  

The interview must have been early July 1983; one condition of the studentship was that I started on 1 August, so that I could get started on fieldwork straight away.   When I watched other postgraduate students turn up in October, and then read and plan experiments through the winter months before starting fieldwork the following Spring, I realised the sense of this step. It did mean, however, that I arrived in Durham at the quietest time of year, was dumped in the unprepossessing Parson’s Field House (now demolished), the postgraduate residence, and had little to do in the evenings. In those days before personal computers, however, Brian Whitton encouraged that all his students learned to type.   I bought a manual typewriter and a book on touch typing and spent the summer evenings banging out exercises to develop strength in my fingers.   The first transferable skill that I learned during my postgraduate days was, therefore, the ability to type without looking at the keyboard; a skill that has proved very useful over subsequent years.

What Constable never saw …


This picture depicts a landscape painted from a position within a few metres of that used by John Constable for his painting Flatford Mill, now in Tate Britain (see “Fieldwork at Flatford”).   It shows part of the same scene almost exactly 200 years after he painted his picture, albeit at a somewhat larger scale (the leaves in the background are only a few millimetres long).   It is based upon the handful of pondweed that I pulled out of the River Stour on 30 December, and the algae that are associated with it.   In the foreground, there is a filament of a green alga that we have not named to our complete satisfaction, but which is either an unbranched Cladophora or Chaetomorpha e linum. Also present in the foreground is a chain of the diatom Ellerbeckia arenaria (see “Ellerbeck and Ellerbeckia”) and, at top left and bottom right there are chains of Melosira varians.   The pondweed leaves are smothered with Cocconeis placentula cells and, at the top right there is a cell of Gyrosigma attenuatum gliding across the pondweed leaf.   Proportions are roughly in line with what I saw down my microscope and the cells of Melosira are approximately 20 micrometres (1/50th of a millimetre) in diameter.

Constable never saw this particular scene on the River Stour partly because he was not (as far as we know) a microscopist, but also because Elodea canadensis, whose leaves that create the backdrop for the image, was not introduced to the UK until after he died. The river would have been different in other ways, too: lower concentrations of nutrients and agrochemicals, in particular. There would have been different submerged plants, but maybe some of the algae growing on their leaves would have been different too?   I was involved in a study a few years ago that looked at this question, using aquatic plant specimens from herbaria. None dated back as far as Constable, but we did see some significant shifts in composition of the attached algae in samples from 100 years ago, compared with now.

The Greek philosopher Heraclitus once said: “no man ever steps in the same river twice, for it’s not the same river and he’s not the same man.”   Perhaps we can also say that no-one looks at the same landscape twice, for it, too, is always changing.   There is a paradox here, because landscape has, at its core, a geological form that change infinitesimally slowly whilst at the same time being cloaked in an ever-changing raiment of vegetation. Rivers are a curious mix of a fixed landscape feature and, as recent floods have reminded us, highly dynamic systems.   And landscape is also a matter of scale: Constable lifted his eyes to the horizon and showed a naturalist’s passion for the clouds that scudded over the Vale of Dedham as he painted.   Sometimes he focussed on more intimate events but not with the level of detail that a botanist craves.   We can look across the River Stour towards Flatford Mill and see the view almost unchanged from when Constable was alive. Yet, at the same time, it is almost wholly different. It is a matter of perspective …


Yallop, M., Hirst, H., Kelly, M., Juggins, S., Jamieson, J. & Guthrie, R. (2009). Validation of ecological status concepts in UK rivers using historic diatom samples. Aquatic Botany 90: 289-295.

A return to the River Team


A microscopic view of the River Team, near Causey Arch, showing Cladophora glomerata filaments with epiphytic Cocconeis spp (mostly C. euglypta), Rhoicosphenia abbreviata and the cyanobacterium Chamaesiphon incrustans. At the bottom right hand corner there is a patch of sediment inhabitated by Nitzschia palea.   This is a composite based on various visits over the past few years.   The Rhoicosphenia abbreviata cells in the foreground are approximately 20 micrometres (=1/50th of a millimetre) long.

My intention with my paintings of the submerged world was partly to convey the wonder of the microscopic world to the wider world, but also to provoke a debate with colleagues about what the data that we spent so many hours collecting, actually means.   One consequence of this is that I have to go back to some of my earliest pictures and change them, in response to the feedback I receive.   This picture is a case in point.   To be frank, my original image of the River Team (see “An Indian summer on our riverbanks …”) was one of the earliest that I had produced (back in 2009) and I have learned quite a lot about the media that I use to produce the images in the interim. I had been hunting through my collection of pictures to find one to illustrate a scientific paper that I am writing with colleagues, and ended up producing a completely new image.

These days, the bed of the River Team is usually smothered with lush growths of the green alga Cladophora glomerata although when I first arrived in the region in 1983, you never saw it in the river, as it could not tolerate the high concentrations of zinc released from a battery factory a few kilometres upstream.   That factory has long since closed, but the river still receives effluent from a sewage works, and is one of the few rivers in the north east where I still see sewage fungus.

A quick look at my records for this one short but rather polluted river puts the diversity of the microscopic world into perspective. I have records for 59 different samples on my database from 13 sites, spanning a distance of about 15 kilometres collected between 2004 and the present and these contain 175 different species of diatom. Many of these are not very common (more than half never form more than one per cent of the total and about a quarter were only ever recorded in a single sample) but it is still an impressive total.   That the average number of species per sample was only 36 further puts this number into perspective, and highlights the amount of variation that can be encountered over short distances and over time.   The three diatom species illustrated in my painting were all amongst the top ten, ranked by both frequency of records and abundance but, at the same time, a quick look in the river (see below) or at my picture (above) put this long list of diatom names into perspective.


The bed of the River Team at Causey Arch, April 2009, smothered with Cladophora glomerata.

First, the passer-by’s immediate perception of the river is of the green algae smothering the bed of the river, rather than the diatoms. It was this that stimulated the development of RAPPER (see “The democratisation of stream ecology?”). But, if we want to understand diatom ecology, we cannot ignore the other algae, which create the habitat upon and around which the diatoms live.   The Cladophora filaments have a big influence on the type of diatoms that we find at a site; even if we are not sampling them directly (and it is hard not to include at least a few filaments in every sample), they are providing inocula of diatoms that can colonise other surfaces.

I should not be too dismissive about diatoms, as they have provided the bulk of my income for over twenty years, but I cannot help but howl with frustration, at times, at the lack of engagement of diatom specialists with functional ecology. Over the last twenty years, we have learnt much more about the taxonomy of diatoms, but this has not really filtered through into better approaches for ecological assessment.    Part of this is, I am sure, that the diatomist looks at samples that are so divorced from their context that a suite of analytical and statistical methods has developed which work around this problem.   That works fine for palaeoecology but is a problem when it comes to relating the lists of diatoms that we collect back to the habitats from which we collected them. I have some theories for how this situation has arisen, but these will have to wait for another day.

My next challenge is to incorporate some of the other microbial life that I see as I peer through my microscope.   As well as other algae, shoots of Cladophora are often smothered with filamentous bacteria, and I really ought to think about how to incorporate these into my illustrations, to make the point that there is a profound shift in the energy sources that underpin organically-polluted rivers.   I have tried to incorporate animals before (see “More about Very Hungry Chironomids”) but it was a struggle to understand the complex structure of their mouthparts, as my notes in that post show.   Bacteria are morphologically simpler but, even so, it would be another step outside my comfort zone.

But isn’t that the point?   In science the emphasis is always on specialisation yet, as we learn more and more about one aspect, we run the risk of losing touch with peripheral areas.   And ecology, more than almost any other discipline, needs that holistic overview.   The specialist is always at a disadvantage … though I would not dare say that in front of some of my diatomist friends …