20:20 hindsight …

Last week saw the publication of a paper that has undergone a slow gestation through the year.   It’s an opinion piece published in the new open access journal Metabarcoding and Metagenomics and describes some of the lessons I learned during the development of a new diatom metric based on metabarcoding data.   The science behind these projects is written up in reports and papers, but that only tells part of the story.  Applied science needs a context, and my paper is more about how the new science fits into a wider process of managing change in large and ponderous government agencies.

That’s where my title comes from: “Adapting the (fast-moving) world of molecular ecology to the (slow-moving) world of environmental regulation”.   The new science of metabarcoding is developing fast and some of the assumptions that we made at the start of the project have now been overtaken by developments in methods.  Yet the regulatory systems into which these methods will be integrated need to be stable and continual “tweaks” to optimise the system would not be welcome.   “Ponderous”, in this context, is not necessarily a bad thing.  Imagine driving in your local area and finding all the speed limits had changed at the whim of an official and without any consultation or advance warning.  Finding a balance between these two needs: for the best possible methods and a stable basis for regulation seems to be one of the biggest challenges those of us with an interest in molecular ecology face over the next few years.

My own view, reflecting back over the discussions I’ve had over the past few years, is that this is possible, but that the UK’s environment agencies will need some major structural changes for this to come about.   As I was reviewing the proofs of the paper, I came across Tim Harford’s fascinating podcast Cautionary Tales and, in particular, an episode called “How Britain Invented, then Ignored, Blitzkrieg”.  The point he made in this episode was that improvements to individual components of a system (tanks, in his example) have little value if the overall architecture within which those components operate are not also regularly updated.   He cited a paper by Rebecca Henderson and Kim Clark which, had I seen it sooner, would have strengthened the principal argument in my paper.

Henderson and Clark’s examples were drawn from manufacturing industry, but we can use the same kind of language to make their framework relevant to ecological assessment.   Broadly speaking, an ecological assessment method (using diatoms, in this case, but it could also be invertebrates, macrophytes or fish) is one component in a larger decision-making “machine”.  Replacing the existing methods, based on specialist biologists painstakingly analysing samples to identify and enumerate the taxa present by one based on metabarcoding technology constitutes a “modular innovation”, using the terminology in the table below.   That might well work in some cases (replacing an analogue by a digital telephone, for example, doesn’t fundamentally affect the way we communicate with one another).  However, the question that Henderson and Clark were asking was what happens when an innovation interacts differently with other components, in which case a shift in the entire product design might be necessary.

A framework for defining innovation (after Henderson and Clark, 1990)

  Core concepts
Reinforced Overturned
Linkages between core concepts and components

Unchanged

 

Incremental innovation

 

Modular innovation

Changed

 

Architectural innovation

Radical innovation

Harford used the comparative fortunes of IBM and Apple in his podcast (Henderson and Clark’s paper was written before the tech revolutions, otherwise I’m sure they would have done so too).  Apple did not invent the mouse or the graphical user interface, but they were able to fit these into a radical new architecture of components, opening up an enormous market for consumer-friendly gadgets.  IBM, by contrast, was the market leader for mainframe computers, but its thinking and organisational structures were so focussed on these that they were not nimble enough to adapt to this new world.

The question that arises when using metabarcoding in a regulatory capacity is whether this technology just constitutes a “modular innovation” or whether a broader refit of the organisations that use the technology is necessary in order to maximise their benefits. My argument is that metabarcoding constitutes a “radical innovation” partly because the way that individuals interpret  metabarcoding data is different to the way that they would traditional data, which means that the value that a biologist can add to evidence for a regulatory decision on his/her locale will change, and because the gathering of evidence by traditional means constituted an “unstructured training program” for freshwater biologists that gave them a broad awareness of freshwater ecology in their region.

Furthermore, the rate of development of these new technologies is such that a better way needs to be find of balancing innovation and regulatory stability beyond the very ponderous approach in force in the UK at the moment.  There are ways of doing this, but the mindset in the administrations needs to change before these can be implemented and there would also need to be more administrators to oversee this process, a big ask in a public sector still limping along on much reduced budgets.

One of the biggest lessons we learned was, in fact, that if you want to learn lessons you need to get stuck in and have a go.  There are plenty of review papers in the academic literature now saying how metabarcoding might be used for ecological assessment, and plenty of discussion about these new technologies within the hierarchies of the government agencies. But you can only go so far with theory: not all of the challenges we encountered were anticipated and, certainly, not all the assumptions that drove the original commissioning of the project turned out to be correct.   The only way of testing these was to take a step into the unknown.  We learned the hard way, but maybe future projects will benefit.

Reference

Henderson, R.M. & Clark, K.B. (1990).  Architectural innovation: the reconfiguration of existing product technologies and the failure of existing firms.  Administrative Science Quarterly 35: 9-30.

 

The devil lies in the detail …

Our latest ring test* slide took us on a vicarious journey to the beautiful River Don in Aberdeenshire.  Maybe because I have been doing this job for so long, but the quality of the landscape was clear to me as I peered through my microscope 500 kilometres away: the range of diatoms that I could see would not have thrived anywhere with more than the lightest touch from humankind.

One of the clues for me lay in some of the smallest diatoms on the slide.   It took some discussion amongst my fellow experts, but we eventually came up with a list of five different species of Achnanthidium (all illustrated below) which, together, constituted about a third of all the diatoms on the slide (admittedly, because they are small, they constitute rather less than a third of the total volume of diatoms, but that is another story ….).   The mere presence of several Achnanthidium species is, in my experience, usually a sign of high habitat quality (see “Baffled by the benthos (2)”) but unravelling the identities of the different species with a light microscope is challenging.

Achnanthidium-minutissimum-Medwin_WaterAchnanthidium minutissimum from Medwin Water, Scotland. Photographs from the Diatom Flora of Britain and Ireland by Ingrid Jüttner.  Scale bar: 10 micrometres (= 1/100thof a millimetre). 

Achnanthidium_pyrenaicum_Towie

Achnanthidium pyrenaicum from the River Don, Towie, Aberdeenshire.  Photographs by Lydia King.  Scale bar: 10 micrometres (= 1/100thof a millimetre). 

The genus Achnanthidium is a good example of the delicate co-existence between “identification” and “taxonomy” in the world of diatoms.   Individuals from this genus are usually small so anyone using a light microscope for routine analyses will be working right at the optical limits of their equipment whilst anyone with a serious interest in taxonomy will depend upon a scanning electron microscope for the insights needed for critical differentiation between species.

This divergence between the working methods of “identifiers” and “taxonomists” means that it is rarely possible to name every individual of Achnanthidium with complete confidence.  The ones that present clearly in valve view (i.e. face-up) can mostly be assigned to a species based on features we can see with a light microscope, but it is not always straightforward for those seen in girdle view (i.e. on their side) or which are partly obscured by other diatoms or extraneous matter on the slide.   In this example from the River Don, we also noticed that smaller individuals of A. gracillimum lost their characteristic rostrate/sub-capitate ends and were, as a result, not easy to differentiate from A. pyrenaicum.

Achnanthidium_gracillium_Towie_Water

Achnanthidium gracillimum from the River Don, Towie, Aberdeenshire.  Photographs by Lydia King.   Scale bar: 10 micrometres (= 1/100thof a millimetre). 

What continues to mystify me is why so many closely-related species can live in such close proximity. It is Achnanthidium that prompt this question here, but other genera display similar tendencies (see “When is a diatom like a London bus?”).  And this immediately generates another question: why are more people not asking this question of diatoms and, indeed, microscopic algae in general?

The answer to that question falls into two parts. The first is that understanding the precise ecological requirements of microscopic algae is not a trivial task, and assumes that you are able to get several closely-related species to live in culture (which, itself, assumes you know the precise ecological requirements of each … you see the problem?).   There is, as a result, a tendency to avoid experimental approaches and, instead, look for how species associate with likely environmental variables in datasets collected from sites exhibiting strong gradients of conditions.   However, this assumes that the forces that drive the differentiation between species work at the same scale at which we sample (see “Our patchwork heritage …” for more on this).

Underlying this, however, is a deeply-held belief, dating back at least forty years, that the niches of freshwater diatoms are determined primarily by the chemistry of the overlying water.   This is a dogma that has served us well when using diatoms for understanding the effects of environmental pollution but which is, ultimately, a limitation when trying to explain why we found five separate Achnanthidium species in a single sample, all exposed to the same stream water.

Achnanthidium_lineare_&_affine_Towie

Achnanthidium lineare (first three images from the left) and A. affine (two images on the right) from River Don, Towie, Aberdeenshire.  Photographs by Lydia King.  Scale bar: 10 micrometres (= 1/100thof a millimetre). 

I will go one step further: this dogma is so deeply held that referees rarely challenge the weak evidence that is produced to demonstrate different responses to environmental conditions between closely-related species.  There are certainly variations in environmental preferences between Achnanthidium species, but these are best expressed as trends rather than unambiguous differences and I have never seen such trends subject to rigorous statistical testing.

I blame better microscopes: greater magnification and resolution has revealed such a baffling amount of diversity that all the energy of bright diatomists is absorbed unravelling this rather than trying to explain what it all means (see “The meaning of … nothing”).  If we were bumbling along with the quality of equipment that Hustedt depended upon, then maybe we would be cheerfully lumping all these forms together and focussing on functional ecology instead.   Maybe.

* see “Reaching a half century” for more about the ring test scheme

Follow the data, stupid …

A perennial problem with ecology is that it is a discipline that is far better at describing problems than it is at solving them. The Water Framework Directive (WFD) encapsulates this: after nineteen years, we have a pretty good idea of the condition of Europe’s waters but have made very little progress in restoring the half that do not yet achieve good ecological status.

The reason for this is, I suspect, because describing the problem is a task that lies squarely within the remit of a scientist whilst finding solutions requires interactions that go beyond the boundaries of science, encountering vested interests along the way.   The agricultural sector’s enthusiasm for the environment is tempered by their desire to maximise yield and earn a living from the land, politicians are wary of regulations that may deter business or raise prices for the consumer and all of us are too wedded to the luxuries that the modern world offers.

The WFD can be seen as an embodiment of the social contract, articulated by philosophers such as Thomas Hobbes whereby individuals forego some rights in order to transcend the state of nature (“… nasty, brutish and short.”) and give us access to the benefits of an ordered society.  In this case, we all consent to forego some freedoms in return for a share in the benefits that a healthy aquatic environment will bring to all of us.   “Freedom” might seem like a weighty word in this context but anyone who has watched their sewerage charges creep steadily upwards over the past twenty years should recognise this as the price we pay for the freedom to flush away life’s less desirable by-products.

The problem is defining the point at which we hand over our natural rights to a higher authority.   We understand this when driving: an urban speed limit of 30 miles per hour reflects the point at which the risk we pose to other road users are deemed societally unacceptable and our right to drive as fast as we wish has to be curtailed.  If we can translate that principle into environmental governance then we can set “speed limits” for the major pressures that impact on the aquatic environment.   How do we get from an ecologist’s understanding of a “healthy” river (“good ecological status”, in WFD parlance) to the “speed limit” for nutrients, widely recognised as one of the major pressures affecting both freshwater and marine systems?

That’s been the focus of some work I’ve been doing under the auspices of the European Commission’s Joint Research Centre, one strand of which has just been published in Science of the Total Environment.  This paper looked at the threshold concentrations for nutrients (phosphorus and nitrogen) used by EU countries, noting the very wide range of values chosen as the national “speed limit”.   The situation is complicated because, just as is the case for roads, different types of rivers require different limits and we had to look for variation between countries amidst an array of variation within countries.   What emerged, however, was a clear relationship between the threshold values and the method used to set the standard.  Those that had applied statistical or modelling techniques to national data generally had tighter thresholds than those that relied upon “expert judgement”.  I’ve included the two figures from this paper that make this point.

Poikane_et_al_2019_Fig7

Range of good/moderate lake phosphorus (a) and nitrogen (b) threshold values grouped by method used to determine the value. Different letters indicate groups that are statistically different (p ≤ 0.05).   Fig. 7 from Poikane et al. (2019).

“Expert judgement” is one of those slippery terms that often creeps into official reports.   There needs to be space within a decision-making process for an experienced professional to see through the limitations of available evidence and present a reasoned alternative.  However, “expert judgement” too often becomes a shorthand for cutting corners and, in this case, grabbing numbers from the published literature that seem vaguely plausible.  There is also a darker side because, having unhitched decision-making from the evidence, “expert judgement” can become a euphemism for the “art of the possible”.  I have seen this occur during discussions around setting and revising river phosphorus standards in the UK: the regulators themselves are under pressure to balance environmental protection with economic development and tight standards can potentially limit what can be done in a catchment.

Another of our recent papers (this one’s not open-access, I’m afraid) shows that setting standards using empirical models is far from straightforward and we also recognise that standard setting is just one part of a longer process of nutrient management.   However, setting inappropriate standards simply as an expedience seems completely barmy, as you are never going to attain your desired ecological benefits.   The cynical view might be that, as the process of environmental change is invariably greater than the electoral cycle, there is limited accountability associated with such decisions, compared with more immediate political capital kudos from bringing investment and jobs to a region.

Poikane_et_al_2019_Fig8

Range of good/moderate river phosphorus (a) and nitrogen (b) threshold values grouped method used to determine the value. Different letters indicate groups that are statistically different (p ≤ 0.05).   Fig. 8 from Poikane et al. (2019).

All of our work has shown that, in most cases, the relationship between biology and nutrients is weak and, for this reason, large datasets are needed if robust inferences are to be drawn.  This leads to one further consequence of our work: setting environmental standards may only be possible if countries pool their data in order to produce big enough datasets with which to work.  This is particularly the case for smaller countries within the EU, but also applies to water body types that may be relatively infrequent in one country but are more widespread elsewhere.   I had recent experience of this when working on the Romanian stretches of the Danube: they simply did not have a wide enough gradient of conditions in their own territory, and we had to incorporate their data into a larger dataset in order to see the big picture (see “Beyond the Tower of Babel …”).    Writing about the benefits of international collaboration as the Brexit deadline looms obviously has a certain irony, but it needs to be said.  Far from being the distant and unaccountable law maker of Brexiteer mythology, in this field the European Commission has been quietly encouraging Member States to share experience and promote best practice.  One can only speculate about the future of the UK environment once free of Brussels oversight.

References

Philips, G., Teixeira, H., Poikane, S., Salas, F. & Kelly, M.G. (2019).   Establishing nutrient thresholds in the face of uncertainty and multiple stressors: a comparison of approaches using simulated data sets.   Science of the Total Environment684: 425-433.

Poikane, S., Kelly, M.G., Salas Herrero, F., Pitt, J.-A., Jarvie, H.P., Claussen, U., Leujak, W., Solheim, A.L., Teixera, H. & Phillips, G. (2019).  Nutrient criteria for surface waters under the European Water Framework Directive: Current state-of-the-art, challenges and future outlook.  Science of the Total Environment 695.  

Note on figures:

The methods used by Member States to derive nutrient thresholds are described in more detail in Poikane et al. (2019).   In brief, the approaches are:

1 – regression between nutrient and biological response;

2 – modelling;

3 – distribution of nutrient concentrations in water bodies classified (using ecological criteria) as high, good or moderate status;

4 – distribution of nutrient concentrations in all water bodies using an arbitrary percentile;

5 – expert judgement.  This includes values taken from the literature or from older European Directives. For example, for nitrate, the common use of the value 5.65 mg-N L−1 in freshwaters is likely to be derived from the guideline value of 25 mg L−1 of nitrate in the Nitrates Directive (91/676/EEC) or now repealed Drinking Water Directive (80/778/EC).

6 – The so-called OSPAR Comprehensive Procedure is used widely in coastal and transitional waters. In this, a water body is considered to be an ‘Eutrophication Problem Area’ if actual status deviates 50% or more from reference conditions.

7 – insufficient information.

The only way is up …

Ehen_Mill_Feb19

How does an alga move upstream?   I’m curious because, I am now seeing populations of Lemanea fluviatilisabout four kilometres further upstream in the River Ehen than when I first started my regular visits in 2013.   I can explain the presence of the organism partly through changes in the hydrology of the river: a small tributary, Ben Gill, that had been diverted into the lake in Victorian times was reconnected to the river in 2014 and this introduced periodic pulses of intense energy to the river that had immediate effects on the substrate composition.  Lemanea fluviatilisis a species that thrives in the fastest-flowing sections of streams so I am quite prepared to believe that even a small shift in the hydrology of this very regulated river might make the habitat more conducive.

But that does not explain how it got there in the first place.   If the alga was occurring a few kilometres further downstream we would not have any such problems: the upstream populations would provide innocula and, if the habitat conditions changed at the downstream location, then some of those propagules might be able to establish at the downstream locations.   But what about movement in the other direction?

There has been relatively little published on this topic in recent years.  I have a review by Jørgen Kristiansen from 1996 that considers the dispersal of algae but most of the references that he cites are quite a lot older than this and I have not seen much published subsequently.   He lists our options: dispersal by water, by organisms, by air currents and by human activity.   Let’s consider each in the context of Lemaneain the River Ehen.   Lemanea, like most red algae, has a complicated life cycle with the potential for dispersal in both the haploid and diploid phases, but that is probably more detail than we need right now.  We’ll just outline the options in broad terms:

Water:the linear flow of the river means that it is almost impossible for the downstream population to provide inocula for the new upstream locations.  It may be possible for populations from further upstream in the catchment to seed the new locations.  I have not seen Lemaneain any of the streams that flow into Ennerdale Water (from which the Ehen emerges) but my knowledge of the catchment is not exhaustive.   Likelihood: very low to low.

Lemanea_at_Mill_Feb19

Young shoots of Lemanea fluviatillis(bottom right) growing on a submerged boulder in the River Ehen at a location where I have not previously seen it.   These are growing alongside thick growths of diatoms (yellow-brown in colour) and patches of green filamentous algae.

Organisms:much of the older literature is concerned with the possibility of living algae or their propagules being transported in mud attached to bird’s feet or feathers and this cannot be ruled out.   There is also a recent study showing how mink may act as a vector for Didymosphenia geminata in Chile.  The Ehen also has aquatic mammals (such as otters) that could be acting as vectors for Lemanea, as well as migratory fish such as salmon and trout that could move propagules upstream.   There is also some evidence that some algae can survive passage through mammalian and invertebrate guts, and this, too, may provide a means for Lemaneato spread upstream.    Likelihood: low to medium.

Air currents / wind:quite a lot has been written about airborne dispersal of algae, with even Darwin making a contribution (see reference in Kristiansen).  The key hazard in airborne dispersal is desiccation so, in the case of Lemanea, the most likely lifecycle stages that could be dispersed in this way would be the diploid carpospores or haploid monospores. This, however, would assume that there were times during the year when the relevant life-cycle stages were exposed and, as Lemaneais a species that I usually find in the Ehen only fully-submerged, this is not very feasible.  Likelihood: low.

Human activity:there is evidence that Didymosphenia geminatacan be transported between sites attached to waders and new records often correspond with patterns of recreational use (references in Bergey & Spaulding – see below).   When we work in the Ehen we prefer to move downstream in order to minimise the risk of moving organisms on our kit, and we also clean our kit before we start.   However, a lot of people work in this part of the Ehen and it only takes one dirty wader to introduce a propagule.   Likelihood: low to medium.

We’ll almost certainly never know for sure why Lemanea fluviatilisis now thriving four kilometres further upstream than it was five years ago.  It is, however, worth bearing in mind that, given enough time, even a low probability may yield a positive result.   So none of the four hypotheses can be ruled out for sure.   Three of the possibilities are entirely natural, with one – movement by the stream itself – being constrained by the direction of flow.  Biological vectors look like a very plausible means of moving algal propagules around catchments but, for this to work, we need wildlife-friendly corridors around the river to support the animals and birds.  The upper Ehen has these, but many other rivers do not.

Actually, having a number of options all with a relatively low likelihood adds to the sense of mystery that every ecologist should have when they approach the natural world.  When cause and effect are too predictable, we tend to focus on engineering the right “solution”.  The truth, in our muddled and unpredictable world, is often that nudging several factors in the right direction will give us a more resilient outcome, even though we may have to wait longer for it to happen.

Reference

Bergey, E.A. & Spaulding, S.A. (2015). Didymosphenia: it’s more complicated.  BioScience65: 225.

Kristiansen, J. (1996).  Dispersal of freshwater algae – a review.  Hydrobiologia336: 151-157.

Leone, P.B., Cerda, J., Sala, S. & Reid, B. (2014).  Mink (Neovision vision) as a natural vector in the dispersal of the diatom Didymosphenia geminataDiatom Research29: 259-266.

Raven, J.A. (2009).  The roles of the Chantransia phase of Lemanea (Lemaneaceae, Batrachospermales, Rhodophyta) and of the ‘Mushroom’ phase of Himanthalia (Himanthaliaceae, Fucales, Phaeophyta).  Botanical Journal of Scotland46: 477-485.

Life out of water …

Last time I wrote, I mentioned that those diatom genera that did not have to be permanently submerged in order to thrive (so-called “aerophilous diatoms”) often appeared together in samples.   Having seen some Luticola muticaearly in my analysis of the sample from Castle Eden Burn, it was no surprise to find Diadesmisand Simonsenialater in the same analysis.   If anything, the biggest surprise was that I did not also find Hantzschia amphioxys, another habitué of the damp fringes of diatom society.

A quick analysis of my database puts these thoughts into context.   There are 6500 samples in my database, so we can see, from the total number of records of each of the aerophilous genera that these are relatively scarce in the samples I encounter.  That is largely because my sampling approaches are biased against the habitats where these thrive (more about this below).   Aerophilous diatoms are more common than you might think; it is scientists with a yearning to learn more about them that is in short supply.

Hantzschiaand Simonseniaare both less frequent and less abundant than the other two genera, never occurring in numbers exceeding ten per cent of the total but, when they form more than one per cent of the total, there is a very high chance that you will also find other aerophilous taxa in the sample.   Humidophilaand Luticolaare sometimes found in higher numbers, and when this is the case, then the proportion of other aerophilous taxa is also often high: 75 per cent of samples where Humidophilais abundant, for example, have at least one other aerophilous taxon present at one per cent or more.

Frequency of other aerophilous genera in samples with Hantzschia, Humidophila, Luticolaand Simonsenia.    Each genus is represented by two rows: records where it formed 10 per cent or more of the total number of valves and records where it formed more than one per cent.   Similarly, records for other aerophilous genera are also stratified into those where they comprise more than 10 per cent of the total and those where they comprise more than one per cent.  

Genus number of records   other aerophilous genera
>10% >1%
Hantzschia 147 >10% n/a n/a
>1% 0.50 0.70
Humidophila 248 >10% 0.25 0.75
>1% 0.09 0.29
Luticola 630 >10% 0.09 0.35
>1% 0.05 0.16
Simonsenia 61 >10% n/a n/a
>1% 0.50 1.00

Over the years, I have come to use this information informally as a way of knowing whether the results of an analysis are likely to be giving me useful insights into ecological condition.   Many of the samples I analyse are collected by other people and sent to me.   These samplers should have been working to protocols that ensure that they check that the stones they choose were fully submerged for some time prior to their visit.  However, the person collecting the sample may have to make a judgement about river and lake level fluctuations in the period before their visit.  Finding lots of cells of aerophilous taxa in a sample is a good hint that something is awry.

The German method for ecological status assessment actually uses the proportion of aerophilous taxa as a check on the reliability of an assessment.    I suspect that they are not the only ones, but They have a list of 46 species that they regard as aerophilous taxa, and use a threshold of five per cent in a sample as a threshold.   The genera I’ve discussed all feature prominently, along with representatives of 19 other genera. Most of these are represented by only one or two species, although there are seven species of Nitzschia, five of Pinnulariaand six of Stauroneis.   I suspect that some species on this list are more tolerant of desiccation than others. We do not know enough of the physiological mechanisms behind this tolerance but it would seem that a few genera (Hantzschia, Humidophila, Luticiola) have definitely got this hard-wired into their genotypes, whilst other genera have members which are mostly aquatic in their habit but with a few exceptions able to survive out of water for some time.   I, personally, would trust the five per cent threshold if it was restricted to the hardcore aerophilous genera, with other taxa on the list providing supporting evidence. I would also add the proviso that there should be more than one aerophilous taxon contributing to that five per cent.  I would be happier, too, if there were a few experimental studies behind these lists and thresholds but, as ever with the world of diatoms, taxonomists are several steps ahead of the physiologists and so we are heavily dependent on anecdotal information when interpreting results.

List of taxa regarded as aerophilous in the German system for assessing ecological status in rivers. 

Name Authority
Achnanthes coarctata (Brébisson) Grunow in Cleve & Grunow 1880
Chamaepinnularia parsura (Hustedt) C.E.Wetzel & Ector in Wetzel et al. 2013
Cosmioneis incognita (Krasske) Lange-Bertalot in Werum & Lange-Bertalot 2004
Denticula creticola (Østrup) Lange-Bertalot & Krammer 1993
Diploneis minuta Petersen 1928
Eolimna subadnata  (Hustedt) G. Moser, Lange-Bertalot & Metzeltin 1998
Fallacia egregia (Hustedt) D.G. Mann 1990
Fallacia insociabilis (Krasske) D.G. Mann 1990
Fistulifera pelliculosa (Brébisson ex Kützing) Lange-Bertalot 1997
Halamphora montana (Krasske) Levkov 2009
Halamphora normanii (Rabenhorst) Levkov 2009
Hantzschia abundans Lange-Bertalot 1993
Hantzschia amphioxys (Ehrenberg) Grunow 1880
Hantzschia elongata (Hantzsch) Grunow 1877
Hantzschia graciosa Lange-Bertalot 1993
Hantzschia subrupestris Lange-Bertalot 1993
Hantzschia vivacior Lange-Bertalot 1993
Humidophila aerophila (Krasske) Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Humidophila brekkaensis (J.B.Petersen) D. Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Humidophila contenta (Grunow) Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Humidophila perpusilla (Grunow) Lowe, Kociolek, Johansen, Van de Vijver, Lange-Bertalot & Kopalová, 2014
Luticola cohnii (Hilse) D.G. Mann 1990
Luticola dismutica (Hustedt) D.G.Mann1990
Luticola mutica (Kützing) D.G. Mann 1990
Luticola nivalis (Ehrenberg) D.G. Mann 1990
Luticola nivaloides (W.Bock) J.Y.Li & Y.Z.Qi 2018
Luticola paramutica (W. Bock) D.G. Mann 1990
Luticola pseudonivalis (W.Bock) Levkov, Metzeltin & A.Pavlov 2013
Luticola saxophila (W.Bock ex Hustedt) D.G.Mann 1990
Mayamaea nolensoides (W. Bock) Lange-Bertalot 2001
Melosira dickiei (Thwaites) Kützing 1849
Muelleria gibbula (Cleve) Spaulding & Stoermer 1997
Neidium minutissimum Krasske 1932
Nitzschia aerophila Hustedt 1942
Nitzschia bacillarieformis Hustedt 1922
Nitzschia disputata J.R. Carater 1971
Nitzschia harderi Husedt 1949
Nitzschia modesta Hustedt 1950
Nitzschia terrestris (J.B. Petersen) Hustedt 1934
Nitzschia valdestriata Aleem & Hustedt 1951
Orthoseira dendroteres (Ehrenberg) Genkal & Kulikovskiy in Kulikovskiy et al. 2010
Orthoseira roseana (Rabenhorst) Pfitzer 1871
Pinnularia borealis Ehrenberg 1843
Pinnularia frauenbergiana E. Reichardt 1985
Pinnularia krookii (Grunow) Hustedt 1942
Pinnularia largerstedtii (Cleve) Cleve-Euler 1934
Pinnularia obscura Krasske 1932
Simonsenia delognei (Grunow) Lange-Bertalot 1979
Stauroneis agrestis J.B. Petersen 1915
Stauroneis borrichii (J.B.Petersen) J.W.G.Lund 1946
Stauroneis gracillima Hustedt 1943
Stauroneis lundii Hustedt 1959
Stauroneis muriella J.W.G. Lund 1946
Stauroneis obtusa Lagerstedt 1873
Surrirella terricola Lange-Bertalot & Alles 1996
Tryblionella debilis Arnott ex O’Meara 1873

Reference

Schaumburg, J., Schranz, C., Steizer, D., Hofmann, G., Gutowski, A. & Forester, J. (2006).  Instruction protocol for the ecological assessment of running waters for implementation of the EC Water Framework Directive: macrophytes and phytobenthos.  Bavarian Environment Agency

Return to the Serra da Estrela

towards_manteigas

Back in October I wrote about the algae and other plants that I had found in a small stream draining the Serra da Estrela mountains in Portugal (see “Notes from the Serra da Estrela”).  I’ve now had a chance to look more closely at the diatoms that I found there, and can offer a few thoughts on the ecology of the stream.

I collected two samples from the stream: one by brushing the top surface of the granite stones with a toothbrush and the other from the darker patches that I described in the earlier post.   These were a mix of algae and mosses, with the former dominated by cyanobacterial filaments and diatoms.   I merged the two samples prior to digesting them, but the biofilm on the submerged rocks was very thin so it is the diatoms from the dark patches that dominate the slide that I prepared from this stream.   As my preliminary observations suggested, motile diatoms were very abundant in this sample, with Surirella roba, Navicula angustaand N. exilis all common, along with some Pinnularia and Nitzschia.   I do not often find motile diatoms to be quite so abundant in fast-flowing upland streams, but I suspect that this is because I look in the wrong places.   Our standard sampling method involves scrubbing the tops of submerged stones which, in this type of stream at least, are not situations where motile diatoms thrive.  By contrast, the tangle of cyanobacterial filaments and dead organic matter creates a very different environment, where an ability to adjust position in order to move away from densely-shaded areas and, perhaps, from situations where bacteria and fungi had used up all the available oxygen, was an advantage.

surirella_roba_unhais_sep18

Surirella robafrom the stream at Unhais de Serra, September 2018; a. – f.: valve views; g. – i.: girdle views. Scale bar: 10 micrometres (= 1/100thof a millimetre). The photo at the top of the post shows the view along the valley of the Rio Zêzere towards Mantiegas in the Serra da Estrela.

misc_diatoms_unhais_sep18

Miscellaneous diatoms from the stream at Unhais de Serra, September 2018: a. – d.: Cocconeis placentula, complete frustule, rapheless valve and two raphe valves; e. – g.: Navicula exilis; h. N. angusta; i. – k.: Pinnularia subcapitata, two valve views and a girdle view.  Scale bar: 10 micrometres (= 1/100thof a millimetre). 

A chain-forming species of Fragilariawas abundant in the original sample although, by the time I had prepared a slide, the chain had disintegrated into individuals or pairs of cells.  These all belonged to a member of the Fragilaria capucinacomplex, though I am not sure which one. There were also a few cells of the free-living (i.e. non-chain-forming) Fragilaria gracilis.    Eunotia minoror a close relative was also present, sometimes also forming short chains and, finally, I found a number of cells of Cocconeis placentula(possibly var. klinoraphis).

These are all diatoms that I would expect to find in a stream draining a hard rock such as granite in an area that is remote from any industrial or mining influences that might lead to artificial acidification.   There are mines in the area, but these are further south.  These do have a measurable effect on the biology of local streams, as the references at the end of this post attest.   However, this particular stream appears to be in rude health.

A curious side-effect of the years that I have spent looking at diatoms is that a sample such as this can evoke the environments from which it came: an assemblage of soft-water circumneutral diatoms conjures, in my mind, a particular landscape.   The label on the slide, of course, takes me straight back to our time in the Serra da Estrela but, in a more general sense, the diatoms capture an essence that transcends any one particular time or place.   Analysing diatom slides can become an escape from the humdrum and a chance to remember warmer days …

fragilaria_unhais_sep18

Fragilaria species from the stream at Unhais de Serra, September 2018: a. – g.: chain-forming member of Fragilaria capucina complex (a.-c.: valve views; d.-g.: girdle views); h.-j.Fragilaria gracilis.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

eunotia_cf_minor_unhais_sep18

Eunotiacf. minorfrom the stream at Unhais de Serra, September 2018: j. – n.: valve views; o. valve view of a related species; p. girdle views. Scale bar: 10 micrometres (= 1/100thof a millimetre). 

References

Luis, A.T., Teixeira, P., Almeida, S.F.P., Matos, J.X. & Silva, E.F. (2004).  Environmental impact of mining activities in the Lousal area (Portugal): Chemical and diatom characterization of metal-contaminated stream sediments and surface water of Corona stream.  Science of the Total Environment409: 4312-4325.

Silva E.F., Almeida, S.F.P., Nunes, M.L. & Fredrik, A.T.L. (2009). Heavy metal pollution downstream the abandoned Coval da Mó mine (Portugal) and associated effects on epilithic diatom communities.  Science of the Total Environment407: 5620-5636.

A day out in Wasdale

Irt_LundBridge_Nov18

A few days after my trip to Weardale I found myself beside the River Irt, a few hundred metres below the point where it flows out of Wastwater, in the western part of the Lake District.   Whereas the River Wear drains a catchment underlain by Carboniferous rocks, including a high proportion of limestone (see “Co. Durham’s secret Karst landscape”), the Irt’s catchment is largely underlain by ancient volcanic rocks, resulting in much softer water.   I was curious to see how different the algae were here compared to those in the Wear.

The river bed at this point is dominated by boulders of granite, which host a patchwork of mosses, filamentous algae and discrete growths of diatoms (visible on the right-hand side of the figure below).  Between these there were areas of pebbles and gravels, suggesting good habitat for freshwater mussels.   The patches of filamentous algae (mostly no more than a couple of centimetres in length) were a mixture of Mougeotiaand Zygnema, similar to the forms that I find in the River Ehen, a 30 minute drive to the north.   These two species differ in the form of their chloroplasts (Mougeotiahas a flat plate whilst Zygnemahas two star-shaped chloroplasts, attached by thin cytoplasmic strands to resemble an animal skin stretched on a frame) but are closely-related, both belonging to the family Zygnemtaceae.

Irt_substratum_Nov18

An underwater photograph of the substratum of the River Irt in November 2018 showing patches of filamentous green algae, mosses and (on the right-hand side) diatoms growing on granite boulders.

Irt_greens_Nov18

Filamentous green algae from the River Irt, November 2018.   The upper photograph shows cells from a filament of Mougeotiawhilst the lower image shows two filaments of Zygnema. Scale bar: 20 micrometres (= 1/50thof a millimetre).

In between the tufts of filamentous algae were apparently bare patches of rock (they almost certainly had a very thin biofilm that would be hard to sample in isolation from the lusher algal growths that shared their habitat) and some conspicuous orange-brown growths of colonial diatoms.  These turned out to be almost pure growths ofGomphonema hebridense, or a close relative (I can’t give a definitive answer until I have examined cleaned material), growing on long mucilaginous, sometimes branched, stalks to create a veritable “bush” of diatoms.  There were a few other species of diatom growing within this bush, most notably some cells of Achnanthidium (cf.) caledonicumthat seemed to be growing on short stalks attached to the Gomphonemastalks, but also a few cells of Gomphonema capitatum(which also grows on long stalks) and some chains of Tabellaria flocculosa.

Gomphonema hebridenseis a diatom that I have written about several times before, as it is also common in the River Ehen, and also presents a number of interesting challenges to taxonomists (see “Diatoms and dinosaurs”). Whatever future studies reveal, however, the presence of colonies of this (or these) species that are visible with the naked eye is something I associate with only the cleanest rivers in the country during the cooler times of year.  It should not have been a great surprise to me to find it flowing out of one of the most pristine lakes in England (see “The Power of Rock …”).

Gomphonema_Irt_x1000_Nov18

A close up of cells within a colony of Gomphonemacf hebridense.  Several mucilaginous stalks are also visible as well as (top left) a cell of Achnanthidiumcf caledonicum.   Scale bar: 10 micrometres (= 100th of a millimetre).

The predominance of boulders over smaller, more easily moved stones, suggests a river that has more energy than the River Ehen, one of my regular Lake District haunts.   Both flow out of lakes whose catchments include some of the wildest and most mountainous terrain in the country.   Lakes tend to act as shock absorbers in catchments, slowing down the water that pours off the fells after heavy rain.   Streams in this part of the world that have no such impediments to flow tend to have rocky, mobile beds and relatively sparse algal communities.   By contrast, the Irt and Ehen just below their respective lakes have relatively lush growths of algae.   The substrates of the two rivers, however, are very different: the Ehen having very few boulders in comparison to the Irt, due to the presence of a weir at the outfall. This allows Ennerdale Water to be used as a water supply for the towns of north west Cumbria but, at the same time, turns the lake into an even more effective hydrological shock absorber.  Yet more of the energy that should be washing smaller stones down the river is no longer available except after the most exceptional storms.

That’s my working hypothesis, then: the Irt is a river that is subject to just enough high energy events to move the rocky substrates around yet no so many that rich algal communities cannot develop between these.  The Ehen, by contrast, has fewer events, leading to fewer opportunities for the algae to be scoured away, whilst unregulated streams such as Croasdale Beck (see “What a difference a storm makes …”) have such regular scouring spates that the algal communities are usually sparse.   I might be wrong, of course and I might be back in a years time with a better hypothesis.  Until then …