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.

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Rolling stones gather no moss …

Back in early July I mused on how rivers changed over time (see “Where’s the Wear’s weir?”) and reflected on how this shapes our expectations about the plants and animals that we find.  In that post, I compared a view of the River Tees today with the same view as captured by J.R.W Turner at the end of the 18th century.   The photograph above is taken about 40 kilometres further upstream from Egglestone Abbey and shows the River Tees as it tumbles along in a narrow valley between Falcon Clints and Cronkley Scar.   I’ve written about this stretch of river before (see “The intricate ecology of green slime” and “More from Upper Teesdale”) and it is an idyllic stretch.   It all looks, to the uninitiated, very natural, almost untouched by the hand of man.

However, a couple of kilometres beyond this point we turn a corner and are confronted by a high waterfall, Cauldron Snout, formed where the river cascades over the hard Whin Sill.   Scrambling up the blocky dolerite is not difficult so long as you have a head for heights but, on reaching the top, a wall of concrete comes into view.  This is the dam of Cow Green Reservoir, constructed between 1967 and 1971 and highly controversial at the time.  The purpose of the reservoir was to regulate the flow in the River Tees, in particular ensuring that there was sufficient flow in the summer to ensure a steady supply for the industries of Teeside (most of which have, subsequently, closed).  My first visit to Cauldron Snout was in the early 1980s on a Northern Naturalist Union field excursion led by David Bellamy.  As we scrambled down Cauldron Snout, Tom Dunn, an elderly stalwart of the NNU, told me how much more impressive Cauldron Snout had been before the dam was closed.

Now look back at the picture at the top of this post.   The dark patches on the tops of the boulders emerging from the water are growths of the moss Schistidium rivulare, which thrives on the tops of stable boulders that are occasionally submerged.    The old adage “a rolling stone gathers no moss” is, actually, true, leaving me wondering how much less of this moss an walker beside this river in the mid-1960s might have seen.   How many more powerful surges of storm-fuelled water would have there been to overturn the larger boulders on which Schistidium rivulare depends?   Bear in mind, too, that two major tributaries, the Rivers Balder and Lune, also have flow regimes modified by reservoirs and the potential for subtle alteration of the view that Turner saw at Egglestone increases.   I wrote recently about how differences in hydrological regime can affect the types and quantities of algae that are found (see “A tale of two diatoms …”).   I may have stood at exactly the same place where Turner had sat when he drew the scene at Egglestone, but I was looking at a very different river.

The dam of Cow Green Reservoir looming above the top of Cauldron Snout in Upper Teesdale National Nature Reserve, Co. Durham, July 2017.  The picture at the top of this post shows the Tees a couple of kilometres downstream from Cauldron Snout.

Trevor Crisp from the Freshwater Biological Association showed that the consequences of Cow Green Reservoir on the River Tees extend beyond alterations to the flow.  Impounding a huge quantity of water in one of the coolest parts of the country also affects the temperature of the river, due to water’s high specific heat capacity.  This means that there is not just a narrower range of flows, but also a narrower range of temperature recorded.   The difference between coolest and warmest temperatures in the Tees below Cow Green dropped by 1 – 2 °C, which may not seem a lot, but one consequence is to delay the warming of the river water in Spring by about a month, which delays the development of young trout.  However, Crisp and colleagues went on to show that any reduction in growth rate due to lower temperatures was actually offset by other side-effects of the dam (such as a less harsh flow regime) to result in an increase in the total density of fish downstream.   Others have shown significant shifts in the types of invertebrate that he found in the Tees below Cow Green, with a decrease in taxa that are adapted to a harsh hydrological regime, as might be expected.   Maize Beck, a tributary which joins just below Cauldron Snout, and which has a natural flow regime, shows many fewer changes.

One conclusion that we can draw from all this is that healthy ecosystems such as the upper Tees are fairly resilient and can generally adapt to a certain amount of change, as Trevor Crisp’s work on the fish shows us. The big caveat on this is that the upper Tees is relatively unusual in having no natural salmon populations, as the waterfall at High Force presents a natural obstacle to migration.  Had this not been present, then all potential spawning grounds upstream of the reservoir would have been lost.   A second caveat is that there is still a lot that we do not know.   The studies of the river that followed the closure of the dam focussed on lists of the animal and plant species found; a modern ecologist might have put more effort into understanding the consequences for ecological processes, the “verbs” in ecosystems, rather than in the “nouns”.  Who knows how different energy pathways are now, compared to the days before regulation, and what the long-term consequences of such changes might be?  Schistidium rivulare is a good example of the limitations of our knowledge: its presence offers insights into the hydrology of the river, but we know relatively little about the roles that these semi-aquatic mosses play in the river ecosystem.   Knowing that there is much that we do not know should, at least, keep us humble as we struggle to find the balance between preserving natural landscapes and their sustainable use in the future.

Note

Twenty years ago, I would have recognised Schistidium rivulare, if not in the field, then at least after a quick check under the microscope.  Now, however, my moss identification skills are rusty and I had to turn to Pauline Lang to get this moss named.   I mentioned in “The Stresses of Summertime …” how the ecologist’s niche becomes the office not the field.  One danger is that we remain familiar with names (as I am with S. rivulare and other aquatic mosses) but, through lack of practice, lose the craft that connects those names to the living organisms.

References

Armitage, P.D. (2006).   Long-term faunal changes in a regulated and an unregulated stream – Cow Green thirty years on.  River Research and Applications 22: 957-966.

Crisp, D.T. (1973).  Some physical and chemical effects of the Cow Green (upper Teesdale) impoundment.  Freshwater Biology 7: 109-120.

Crisp, D.T., Mann, R.H.K. & Cubby, P.R. (1983).  Effects of regulation on the River Tees upon fish populations below Cow Green Reservoir.  Journal of Applied Ecology 20: 371-386.

Lang, P.D. & Murphy, K.J. (2012).  Environmental drivers, life strategies and bioindicator capacity of bryophyte communities in high-latitude headwater streams.  Hydrobiologia 612: 1-17.

The stresses of summertime …

One reaches a stage in an ecological career when your “niche” becomes the office not the field and you are expected to focus your hard-earned experience on data that others have collected.  That means that I spend more time than I wish – even in the summer – staring at computer screens and writing reports – and far too little time engaging directly with nature.   Today’s post is the result of a Saturday’s excursion around some of the more enigmatic parts of the Yorkshire Dales National Park (the enigma being, basically, that we spent most of our time in Cumbria, not Yorkshire).

The photograph above shows a steam locomotive hauling a train along the Settle to Carlisle railway as it makes its way through Mallerstang, the upper part of the Eden Valley.   It is a beautiful little valley, hidden away from the main tourist drags and the sight of a steam train imparted a sense that we were somehow detached, albeit briefly, from the modern world.   The river channel itself lies amidst the ribbon of woodland in the valley bottom.

The River Eden in Mallerstang (SD 778 985) with (right) a large pebble with a Cyanobacterial film.

Curious to see what kind of life thrives in such a heavily shaded stream, I hopped over a fence, pushed through some bankside vegetation, crouched down and lent out as far as possible to grab a few of the stones from the streambed.   As I would have expected in a stream in such a location, the slippery film on the stone surface was thin (this is the time of year when the algae and other microbes can barely grow fast enough to keep up with the voracious appetites of the invertebrates that inhabit the crevices among the rocks) but, when I held it up to the light, there was a distinct greenish tinge that piqued my curiosity.

Under the microscope, this green tinge revealed itself to be due to numerous filaments of a thin, non-heterocystous cyanobacterium (blue-green alga), similar to that which I see in the River Ehen (see “’Signal’ or ‘noise’?”).  There, Phormidium autumnale forms tough leathery mats whereas here there was no obvious arrangement of the filaments.   In fact, the filaments seemed to be randomly organised within a mass of organic matter that made photography difficult and the photograph below is of one that had glided into a clear space on the coverslip.   I was surprised that there were relatively few diatoms present but, amidst the clumps of cyanobacteria and organic matter, I could see cells of Gomphonema pumilum, though it was very definitely sub-dominant to the Phormidium.  That was not very easy to photograph either, and my images have been built-up using Helicon Focus stacking software.

Some of the algae living on stones in the upper River Eden, August 2017: a. Phormidium cf autumnale; b. and c.: Gomphonema cf pumilum.  Scale bar: 10 micrometres (= 100th of a centimetre). 

I have seen other streams where non-heterocystous cyanobacteria thrive during the summer months and suspect that their unpalatability relative to other algae may play a part in this.  This is partially induced by the proximity of grazers – a recent study suggested that filaments of Phormidium did not need to come into contact with the grazer itself, only to detect chemicals associated with the grazer in the ambient water.  This, in turn, can promote production of a tougher sheath, making the filaments less palatable.   I’m always a little surprised that aquatic invertebrates find diatoms, with their silica cell walls, palatable, but I see enough midge larvae greedily hoovering-up diatoms to recognise that they know something that I do not.

My brief visit to the upper River Eden reminds me that summer can be a tough time for stream algae.   Not only is this the time that the invertebrate larvae are scouring rock surfaces for algae to serve as the fuel that will catapult them into their brief adult phases, but also the trees are in full leaf, limiting the amount of energy that the algae can capture in order to power their own growth.   Not surprising, then, that so many algae – diatoms and other groups alike – are more prolific in the winter, when the invertebrates are not so active and there is less shade from marginal trees (see “Not so bleak midwinter?” and “A winter wonderland in the River Ehen”).   I’ll probably be sitting indoors staring at spreadsheets and writing reports this winter too, but I’ll still be looking for excuses to get out and explore nature’s hidden diversity.

Pendragon Castle, guarding the entrance to Mallerstang in the upper Eden Valley. 

Reference

Fiałkowska, E.  & Pajdak-Stós, A. (2014).  Chemical and mechanical signals inducing Phormidium (Cyanobacteria) defence against their grazers.   FEMS Microbiology Ecology 89: 659-669.

As if through a glass darkly …

Life used to be so easy: I stared down my microscope, named the diatoms I could see, counted them and, from these data, made an evaluation of the quality of the ecosystem that I was studying.   Along with the majority of my fellow diatomists, I conveniently ignored the fact that I was looking at dead cell walls rather than living organisms.   My work on molecular barcodes as an alternative to traditional microscopy has been revelatory as I try to reconcile these two types of data.   At one level, what I see down the microscope is a benchmark for what I should expect to see in my barcode output.  Yet, at the same time, the differences between the two types of data show up the limitations of traditional data – and the assumptions that underpin the ways that we work.

Take a look at the plate below which shows two of the most common diatoms in UK rivers: Ulnaria ulna is one of the largest that I encounter regularly whilst Achnanthidium minutissimum is often one of the most abundant in my samples, particularly when the level of human pressure is relatively low.  When we analyse samples with the light microscope, we record individuals, so both of these score “1” in my data book despite the fact that U. ulna is about 100x larger (by volume) than A. minutissimum.

Specimens of Ulnaria ulna (top) and Achnanthidium minutissimum (bottom).  Both are from cultures used for obtaining sequences for the reference library for our molecular barcoding project.   Scale bar: 10 µm.   Photographs: Shinya Sato, Royal Botanic Gardens, Edinburgh.

When we analyse a sample using Next Generation Sequencing (NGS), we count not cell walls but copies of the rbcL gene, which provides the blueprint for Rubisco, a key photosynthetic enzyme.   As I write, there is no clear understanding of how the number of rbcL copies relates to the number of individuals.  We know that each chloroplast within a cell will have at least one copy of this gene, and usually several. There is also some evidence that larger chloroplasts have more copies of the gene than smaller ones and there is also likely to be a measure of environmental control.  The key message that I try to get across in my talks is that NGS data are different to the data we are used to gathering using microscopy.  These differences do not mean that it is wrong, just that we need to leave some of our preconceptions before starting to interpret this new type of data.

However, we could also argue that counting the number of copies of the gene for an important photosynthesis enzyme should be giving us a better insight into the contribution of a species to primary productivity than counting the number of cell walls.  In other words (whisper this …), rbcL might not just be different, it might be better, especially if our purpose is to understand the contribution the various species in the biofilm make to primary productivity in stream ecosystem.  At the moment there are plenty of problems with the NGS-based method, not least the fact that we often cannot assign half the copies of the rbcL gene in a sample to a species, but the situation is improving all the time …

Some recent work pushes this a little further.   Jodi Young and colleagues at Princeton University have demonstrated large variation in the kinetics of Rubisco in diatoms, and in their carbon-concentrating mechanisms (see “Concentrating on carbon …” for more about these).  Although their work is focussed on marine phytoplankton, the variation within Rubisco and carbonic anhydrases could go some way to explaining the sensitivity of diatoms to inorganic carbon (see “Ecology in the Hard Rock Café …”).   In other words, rbcL is not an irrelevant DNA sequence, as the term “barcode” may imply (in contrast to barcodes based on the ITS region, for example), it is deeply implicated in the reasons why a species lives in particular place.

And yet, and yet, and yet …  The same could be argued for morphology, up to a point at least.   The shape of a Gomphonema or a Navicula also helps us to understand the organism’s relationship with its environment.   The problem is that modern taxonomists tend to focus on a much finer level of detail – on the arrangement and structure of the various pores on the silica frustule, for example – and offer few insights into what these minute differences mean in terms of the ecophysiology of the organisms.  Even at the whole-cell scale, information on habit, which is linked to form (Gomphonema tending to live on stalks or short mucilage pads secreted from their foot poles for at least part of their life-cycle, for example) is rarely incorporated into assessment systems.   The move from using light microscopy to using NGS, in other words, means replacing an imperfect system with which we are familiar with one that we are still learning to understand.  Both offer unique information and the gains from using one approach rather than the other, will be offset by losses of insight.

That leaves us with two big challenges over the couple of years, as UK diatom-based assessments move from light microscopy to NGS.  The first is to work harder to understand what NGS outputs are actually telling us about the environment over and above the minimalist ecological status indices that spew out of our “black box” computer programs.   The second is to maintain an understanding of the properties of whole organisms and how these interact with one another and with their environments.   I guess I should add a third challenge to this pair: persuading middle managers who have at best a sketchy understanding of diatoms and phytobenthos and already-stretched budgets that any of this matters …

References

Badger, M.R. & Price, G.D. (2003).  The role of carbonic anhydrase in photosynthesis.  Annual Review of Plant Biology 45: 369-392.

Young, J.N. & Hopkinson, B.M.M. (2017).  The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms.  Journal of Experimental Botany doi: 10.1093/jxb/erx130.

Young, J.N., Heureux, A.M.C., Sharwood, R.E., Rickaby, R.E.M., Morel, F.M.M. & Whitney, S.M. (2016).  Large variations in the Rubisco kinetics of diatoms reveals diversity among their carbon-concentrating mechanisms.  Journal of Experimental Botany 67: 3445-3456.

Unlikely neighbours …

One of the lessons I learned from writing “A tale of two diatoms …” is that we can often learn more about the ecology of a species by contrasting its behaviour with that of another species rather than by just relating the distribution of that species to features of its environment.  I came across another example of this when I was writing up the results of the latest “ring-test” that UK diatom analysts undertake to maintain their competence.

The sample came from a stream in east Devon (the one that had a walk-on part in “The challenging ecology of a freshwater diatom”).  This stream receives effluent from a small sewage works but our sample comes from just upstream of this works.   We know that the stream downstream of the sewage works is quite polluted but were also interested in the condition of the stream above the works.   This has proved to be challenging and, it seems, there are some pollution sources, including septic tanks and runoff from fields, that mean that the stream already shows signs of impact before it reaches the sewage works.   There are, however, mixed messages when we look at the aquatic flora, and some of the diatoms that are abundant are characteristic of low or only slight enrichment.

One feature of the stream that was quite unusual was a relatively large number of cells of Reimeria uniseriata, a relative of Reimeria sinuata which is quite common.  Both of these are illustrated below: note that R. uniseriata tends to be slightly larger and has distinctly punctate striae.  However, when I looked at the distribution of these species in response to water chemistry, I could see few differences, with most of the records suggesting a preference for water with low or slightly elevated phosphorus concentrations.   Reimeria sinuata is more common than R. uniseriata and when the latter is found, the former is usually present too.  They seem to be able to share their habitat quite comfortably.

Reimeria sinuata from Polly Brook, Devon, December 2016.   a. – f.: valve views; g.: girdle view focussed on ventral side.  Scale bar: 10 micrometres (= 1/100th of millimetre).  Photos: Lydia King.

Reimeria uniseriata from Polly Brook, December 2016.  h., i.: valve views; j.: girdle view focussed on dorsal side; k., l.: girdle views focussed on ventral side.   Scale bar: 10 µm (= 1/100th of millimetre).  Photos: Lydia King.

In other words, we cannot learn very much from looking at differences in the distribution of these two species of Reimeria, given our current state of knowledge.  There is, however, one other “compare and contrast” within the data that I collected from Polly Brook that is more intriguing.   If Reimeria sinuata, in particular, usually indicates a healthy stream, possibly with a little nutrient enrichment, Rhoicosphenia abbreviata is more often associated with enriched conditions.   We have met this diatom before (see “Cladophora and friends” amongst other posts) and I have explained that it is often found growing as an epiphyte on other algae.  We rarely see situations where both species are abundant at the same time, as the graph below shows.

The relative distribution of Reimeria sinuata and Rhoicosphenia abbreviata in the 6500 UK stream and river samples in the DARES dataset.   The horizontal and vertical lines indicate 10% relative abundance of each species.

When I started looking at stream algae there was a prevailing assumption that there were strong causal relationships between the species of diatom that were found at a site and the level of chemical pressures.  In the case of phosphorus, in particular, I am now not convinced that the evidence supports this whilst, at the same time, am more convinced that we should be able to, at the very least, describe what a healthy stream algal community looks like and give reasons.  I use the word “describe” because I think that many of us have been preoccupied with counting and measuring, often at the expense of a qualitative understanding.  These two species illustrate my point as when I look down a microscope and see Reimeria sinuata, I can usually assume that the stream where it was growing was reasonably healthy, even if the nutrients are a little higher than would be ideal.  On the other hand, seeing lots of cells of Rhoicosphenia makes me suspect that there has been a breakdown in the functioning of the healthy community.  These conclusions would be irrespective of what the chemistry or the values that biological indices told me.

Two species is barely enough to base a credible assessment upon but we could stir more into the mix: I often find Reimeria sinuata with Achnanthidium minutissimum, and that, in in summer especially, suggests strong top-down control by grazers, which means that pathways of energy flow have not been disrupted.   And Rhoicosphenia, as I have already mentioned, is associated with Cladophora which, in abundance, suggests a breakdown in these pathways, as shown by Michael Sturt and colleagues from University College, Cork, a few years ago.   That Polly Brook has both Reimeria and Rhoicosphenia in abundance suggests that it might just be at the tipping point between these two states.

The naïve answer to making sure that the upper stretches of Polly Brook do not cross this threshold would be to manage the nutrients.  However that is not quite as easy as it sounds in an agricultural catchment.   It could be that managing other aspects of the riparian environment are equally effective at keeping the stream in a healthy condition but that takes us into areas where the evidence is still accumulating.  It could be that the simplistic determinism that drove much of the development of biological assessment methods actually held back the gathering of that evidence for a long time.  Reimeria sinuata – and it’s cousin, R. uniseriata – stand as two reminders that there is more to the management of aquatic ecosystems than strong correlations.

Reference

Sturt, M.M., Jansen, M.A.K. & Harrison, S.A.C. (2011).  Invertebrate grazing and riparian shade as controllers of nuisance algae in a eutrophic river.  Freshwater Biology 56: 2580-2593.

A tale of two diatoms …

I’ve been writing about the River Ehen in Cumbria since I started this blog, sharing my delight in the diversity of the microscopic world in this small river along with my frustrations in trying to understand what it is that gives this river its character.   We know that the presence of a weir at the outfall of Ennerdale Water has a big influence so, in 2015, we started to look at a nearby stream, Croasdale Beck (photographed above), which is similar in many respects but lacks the regulating influence of a lake and weir.  Maybe, we reasoned, the differences we observed would give us a better understanding of how the regulation of flow in the River Ehen influenced the ecology.

Broadly speaking, any kind of impoundment – whether a natural lake or an artificial reservoir – removes a lot of the energy from a stream that might otherwise roll stones, move sediment downstream and, in the process, dislodge the organisms that live there.   We noticed quite early in our studies, for example, that Croasdale Beck generally had less algae growing on the stones than in the nearby River Ehen, and also that the algal flora here was less diverse.

There were also some quite big differences in the algae between the two streams.  I wrote about one of the Cyanobacteria that are found in Croasdale Beck in “A bigger splash …” but there are also differences in the types of diatoms found in the two streams.  Most diatomists think about ecology primarily in terms of the chemical environment within which the diatoms live but I think that some of the differences that I see between the diatoms in the River Ehen and Croasdale Beck are a result of the different hydrological regimes in the two streams.

Several diatom species are common to both streams but two, in particular, stand out as being common in Croasdale Beck but rare in the River Ehen.  These are Achnanthes oblongella (illustrated in “Why do you look for the living amongst the dead?”) and Odontidium mesodon.  However, a closer look at the data showed that, whilst both were common in Croasdale Beck, they were rarely both common in the same sample.   If Achnanthes oblongella was abundant, then Odontidium mesodon was rare and vice versa, as the left hand graph below shows.   There were also a few situations when neither was abundant.

Odontidium mesodon from Croasdale Beck, Cumbria, July 2015.  Photographs by Lydia King.

The story got more interesting when I plotted the relative proportions of these two taxa against the amount of chlorophyll that we measured on the stones at the time of sample collection (see right hand graph below).   This gives us an idea of the total biomass of algae present at the site (which, in this particular case, are dominated by diatoms).   Achnanthes oblongella was most abundant when the biomass was very low, whilst Odontidium mesodon peaked at a slightly higher biomass, but proportions of both dropped off when the biomass was high.   I should point out that “high” in the context of Croasdale Beck is relatively low by the standards of other streams that we have examined and this adds another layer of complexity to the story.

When the biomass exceeds two micrograms per square centimetre, both Odontidium mesodon and Achnanthes oblongella are uncommon in the biomass, and the most abundant diatoms are Achnanthidum minutissimum, Fragilaria gracilis or, on one occasion, Cocconeis placentula.   A. minutissimum and F. gracilis are both common in the nearby River Ehen but C. placentula is very rarely found there.

The difference between River Ehen and Croasdale Beck is probably largely a result of the very difernt hydrological regimes, though this is an aspect of the ecology of diatoms that has been studied relatively rarely.   The differences within my Croasdale Beck samples is probably also a result of the hydrology, but reflects changes over time.   I suspect that Achnanthes oblongella is the natural “pioneer” species of soft-water, hydrologically-dynamic streams, and that Diatoma mesodon is able to over-grow A. oblongella when the biomass on stones increases due to prolonged periods of relative stability in the stream bed.  That still does not explain what happens when biomass is high and neither are abundant: the dataset is still small and we need to collect some more data to try to understand this. But the point of the post is mostly to remind everyone of the dangers of trying to interpret the ecology of attached stream algae solely in terms of their chemical environment.   And to make the point that a little more understanding of a natural system often fuels, rather than removes, the sense of mystery that is always present in nature.

a. The relationship between representation of Achnanthes oblongella and Odontidium mesodon in samples from Croasdale Beck between May 2015 and January 2017. Both axes are presented on square-root-transformed scales; b. relationship between representation of Achnanthes oblongella and Odontium mesodon and total epilithic biomass (as chlorophyll a). Lines show a locally-weighted polynomial (LOESS) regression fitted to the data.

Taxonomic note

Odontidium mesodon is the correct name for Diatoma mesodon (see “Diatoms from the Valley of Flowers”).   The name Odontidium had fallen out of popular usage, but Ingrid Jüttner and colleagues made the case to resurrect this genus for a few species that would hitherto have been classified in Diatoma.

Achnanthes oblongella, by contrast, is definitely not the correct name for this organism.  Three other names have been proposed: Karayevia oblongella, Psammothidium oblongella and Platessa oblongella.  The first two are not convincing and I have not yet been able to see the paper describing the third.  It will be interesting to see what a combined morphological and genetic study of this species (or, more likely, complex) reveals.

Reference

Jüttner, I., Williams, D.M., Levkov, Z., Falasco, E., Battegazzore, M., Cantonati, M., Van de Vijver, B., Angele, C. & Ector, L. (2015).  Reinvestigation of the type material for Odontidium hyemale (Roth) Kützing and related species, with description of four new species in the genus Odontidium (Fragilariaceae, Bacillariophyta).  Phytotaxa 234: 1-36.

Wetzel, C.E., Lange-Bertalot, H. & Ector, L. (2017): Type analysis of Achnanthes oblongella Østrup and resurrection of Achnanthes saxonica Krasske (Bacillariophyta). Nova Hedwigia Beiheft (in press).

 

Finding the balance …

Gammarus fossarum (Scale bar: 1 millimetre).  Photograph: Drew Constable.

Back in March I wrote about the challenges facing those who planned to implement Next Generation Sequencing (NGS) methods for ecological assessment (see “Ecology’s Brave New World”).  In that post I argued that the success (or otherwise) of using DNA for ecological assessment was as much down to the structure and values of the organisation implementing the method as to the method itself.   More particularly, there were likely to be problems if the process was viewed primarily as a means of gathering ecological data rather than for enhancing the capabilities of ecologists.

This is an important distinction.  Much of an ecologist’s time is spent collecting the basic data, whether in the field or laboratory, from which the condition of a particular habitat can be inferred.   But, with traditional methods, there was always a possibility that this basic data collection could be supplemented by observations and insights made by the ecologist that would inform their judgements.  These people have also added to our knowledge of the UK’s biodiversity over the years (see “A new diatom record from Sussex” for an example).   My fear is that adoption of NGS approaches in order to reduce costs will limit the potential for ecologists to make these serendipitous additions to our understanding of a habitat.

A recent paper by Rosie Blackman and colleagues from the University of Hull and Environment Agency offers a good example of how traditional and DNA-based methods can be complementary.  Rosie had looked at invertebrate assemblages in rivers in England using both approaches and discovered that some of the DNA in her samples came from a species, Gammarus fossarum, not previously recorded in the UK.  Other representatives of this genus of small crustaceans, including the extremely common G. pulex, had been abundant in her samples.  Now, however, going back to her sites with the knowledge that G. fossarum might also be present, she was on the lookout for the subtle differences in morphology that separated G. fossarum from other Gammarus species.  She found it in large numbers at 23 out of 28 sites, spread around the country, and in historical material stored at the Natural History Museum dating back to 1964, suggesting that it has been overlooked by those identifying it by traditional means.

This is a great example of biologists working in the sweet zone where traditional and molecular methods combine to give us new insights that are greater than the sum of their parts.   The shortcomings of traditional morphology-based taxonomy in the past are clear but, at the same time, this was essential for verification step once the presence of Gammarus fossarum had been detected by molecular approaches.   The obvious conclusion is that regulatory organisations should move into the future using both traditional and molecular methods in a complementary manner.   Yet, if you look at that statement from another perspective, I have just advocated increasing the cost of ecological assessment at a time when budgets for such assessments are under extreme pressure.

The likelihood is that, as molecular methods are developed (and if they are shown to be substantially cheaper), traditional approaches to ecological assessment will be dropped.  That would not be a problem were it not that the hours spent in the field and laboratory are an important pathway for graduate ecologists to deepen their understanding of organisms and habitats.   Shifting wholesale to molecular methods without retaining at least some infrastructure for traditional methods will mean first, that future discoveries such as Rosie’s will be harder to validate and, second, that the next generation of ecologists will first encounter these organisms not in a pond net but on a spreadsheet.  That link between a name and an organism with distinctive qualities, and between that organism and particular habitats or conditions, will be lost.

Equally, it is unrealistic to assume that complementary use of both approaches will be the norm.   That will place yet more pressure on already tight budgets and could only happen if everyone was happy to accept that monitoring networks could be much smaller (see “Primed for the unexpected?”).  So how do we retain this “sweet zone” between old and new?   I have not yet heard a satisfactory answer to that question so perhaps we should return to the point I made earlier about the structure and values of the organisations that take on these new methods.  Broadly speaking, the adoption of these methods purely to save money is likely to be the road to perdition, because these savings will look most impressive to the senior levels of management (who are probably not biologists) only if there is a wholesale move to the new methods with no retention of traditional infrastructure.

The tragedy is that, within a decade, molecular technology may have moved on to such an extent that it is possible for a biologist to detect invasive species and make other assessments in real time, rather than having to send samples off to remote high-throughput laboratories in order to maximise economies of scale.  Instruments such as Oxford Nanopore’s Minion are still not the finished article from the point of view of ecological end-users, but it is only a matter of time.   Unfortunately, in the here and now, the infrastructure that generates ecological data is already being dismantled in order to squeeze cost-savings from the shift to NGS.   Whether there will be anyone left to inherit this Brave New World is, I am afraid, open to debate.

Two examples of Oxford Nanopore’s Minion portable DNA analysis systems, which can be plugged into the USB port of a laptop.

Reference

Blackman, R.C., Constable, D., Hahn, C., Sheard, A.M., Durkota, J., Hänfling, B. & Lawson Handley, L. (2017).  Detection of a new non-native freshwater species by DNA metabarcoding of environmental samples – first record of Gammarus fossarum in the UK.  Aquatic Invasions 12 (in press)