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.

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A year in the life of the River Wear …

After six bimonthly visits to the River Wear at Wolsingham during 2018, I can now step back and have a look at the complete dataset to see what patterns emerge.   Over the course of the year, I have visited the site six times and recorded a total of 107 species: 5 Cyanobacteria, 32 green algae, 69 diatoms and one red alga.  The true figure is probably higher than this, as the green algae include a number of “LRGT” (see “Little round green things …”) and certainly did not receive the same level of attention as the diatoms.

This crude enumeration of species, however, disguises some interesting seasonal patterns with, as I described in “Summertime Blues” and “Talking about the weather …”, abundant growths of green algae during the heatwave and associated low flow periods.  This can be seen clearly in the bar chart showing the seasonal changes in the river: diatoms predominate in the early part of the year whilst green algae are very scarce.  The bloom of the green filamentous alga Ulothrix zonata that I expected to see in March was missing due, I suspected, to the hard weather we experienced in late Feburary (see “The mystery of the alga that wasn’t there …”) but, by the summer, the river had taken on a very different complexion and was dominated by small green algae.   The last sample of the year, collected in November, showed a return to diatom dominance with a late autumn showing of Ulothrix zonata(see “The River Wear in November …”).

wear_summary_2018

Relative proportions (by approximate biovolume) of the main groups of algae found in the River Wear at Wolsingham during 2018.  

Looking back at records of a similar exercise in 2009, I see that the beginning and end of the year were quite similar, with thick biofilms dominated by diatoms; however, the algae in the summer of 2009 were very different to those I found in 2018.  My 2009 exercise involved monthly rather than bimonthly visits and I see that I recorded more Cyanobacteria in June and July than I found in Summer 2018.  These were mostly filaments of Phormidium retziiand tufts of Homoeothrix varians, which I assumed to be a consequence of intense grazing (there is evidence that invertebrates find Cyanobacteria to be less palatable than other algae).  By July, Cyanobacteria comprised over half the total biovolume of algae; however, there was a major spate soon after my visit.  I was surprised to find, when I visited in August, a noticeably thicker biofilm smothering the rocks and, when I looked closely, this was dominated by the small motile diatom Nitzschia archibaldii.   The Cyanobacteria had disappeared almost completely.   I attributed this change to the invertebrate grazers being washed away by the spate, allowing the algae to grow unhindered.  As the biofilm grew in thickness, so the algal cells start to shade each other, and a diatom that can glide through the biofilm has an advantage over any that are stuck to one place.  Diatoms remained dominant for the remainder of the year, although my November sample came just after another storm and the stones I sampled were completely bare.

wear_summary_2009

Relative proportions (by approximate biovolume) of the main groups of algae found in the River Wear at Wolsingham during 2009.   A sample was collected in November but no living algae were recorded from it.

Overall, however, the similarities between the years outweighed the differences in the summer assemblages, whilst the composition of communities between late autumn and late spring was remarkably similar across the two years.   The changes in summer 2018 extended beyond just a shift in the balance of algae in favour of greens: there were also changes in the composition of diatoms too.  In fact, the changes in diatoms proved to be quite powerful mirrors of the changes in the community as a whole.  I have demonstrated this in datasets spanning a number of sites in the past but it is reassuring to see that they are also reflecting patterns within one site.   On the other hand, if I only had examined the diatoms, I would have missed some of the most interesting changes in the river over the course of the year.

Another observation is that no single sample from 2018 contained more than a quarter of the total algal diversity that I recorded over the course of the year.  Every month saw some new arrivals and some departures (or, more likely in some cases, a few taxa that were present had dropped below my analytical detection limit).  Some of these were expected (the seasonal dynamics of Ulothirx zonata, for example); others not (e.g. dominance by Keratococcus bicaudatusin the summer).  I discussed this in “A brief history of time-wasting …” and, in honour of that post, am not going to repeat myself here. In an age when our environmental regulators are cutting back on the amount of data that they gather, I shall go into 2019 reflecting on Yuval Noah Harari’s comment that “the greatest scientific discovery was the discovery of ignorance”.

Mystery, wonder and joy

My Advent reading this year was Michael McCarthy’s The Moth Snowstorm: Nature and Joy (John Murray, 2015), a meditation on the reasons why humans love the natural world, and how engagement with nature can, in turn, be beneficial for our wellbeing.   His personal fascinations with butterflies, moths and birds provide most of the examples but, as I was reading this book at the same time as I was writing the previous post on “little round green things”.  As a result, I found myself reflecting on my own fascinations with the microscopic world.

A characteristic of ecologists, I have realised, is that there is almost always a tension between their scientific training and a primeval emotional response to nature.   This is not unique to ecology: geologists and astronomers certainly share it, but it is not a universal trait of scientists.  In those disciplines where it occurs, however, interactions with the natural world occasionally transcend strictly dispassionate objective observation and spill over into the language of joy and wonder.   “Joy” being, in McCarthy’s words, “concentrated happiness” whilst “wonder” is “a sort of astonished cherishing or veneration … often involving an element of mystery”.   We are straying away from the language of science and towards a religious and spiritual dimension that many ecologists would, I suspect, be reluctant to acknowledge.

“Mystery” is the word that ties together the disparate worlds of science and religion.   It implies “missing knowledge”, but much more than just an absence of necessary facts.   Every time I peer at samples from the River Ehen through my microscope I get the full gamut of joy-wonder-mystery-related emotions even though I have seen similar views many times before.   Part of this can be attributed to “missing knowledge” but not all.  I am acutely aware of my own shortcomings as I struggle to identify the organisms that I see, as well as the limitations of the taxonomic literature on which I depend.  I am, in addition, perpetually astonished that so much diversity can live on such a small scale and, even when I have done my best to name the algae present, I still struggle to explain why the communities differ over the space of a few metres and between our monthly visits.

Ehen_Mill_181212

Regular visits for five years have not diminished my wonder at the microscopic world of the River Ehen: this submerged boulder has obvious patches of brown diatoms and green algae, but also gaps where the algae are much less abundant. We can make coarse predictions about which species are likely to be found in particular locations, but the factors that determine their distribution on much finer scales are still shrouded in mystery.

The word “mystery” in short, carries an emotional heft that simply “not knowing” does not.  It rises above ignorance, partly because mystery, by definition, implies an awareness of this lack of knowledge.   The word “mystery”, in a modern, scientific context, also links to the concept of complexity, recognising that interactions between variables is often such that it is very difficult to predict outcomes.   That “astonished cherishing” that forms part of McCarthy’s definition of wonder needs to include an element of wariness.  We approach – or, at least, we should approach – ecosystems in the same cautious manner that Moses approached the burning bush.   Whether or not you believe in a higher power, recognition of both the complexity of nature and our limited understanding of this is humbling.   Humility, in turn, generates reverence, and we have completed the journey from the hard, dispassionate language of science to the fringes of spirituality and religion.

None of this precludes trying to improve our understanding of the natural world, nor of using this knowledge to inform decision-making.   What I have written above is no more than the Precautionary Principle, albeit expressed in quasi-mystical language.   Whilst the Precautionary Principle is an instrument of policy, my interpretation is more personal.   Each of us, individually, should be finding time to revel in the wonder of nature which, in turn, will fuel the sense of mystery and, in turn, temper any inclination to rush to intemperate conclusions.

Ehen_181212_diatoms

Some of the diatoms that are abundant in the River Ehen.  Top left: colonies of Gomphonema(see “Diatoms and dinosaurs” for more about this species); top right: colonies of Fragilaria tenera, which shares the habitat with at least two other similar representatives of the same genus; bottom left: Tabellaria flocculosa.  Genetic studies suggest that this, too, is probably a complex of morphologically-similar species.   Scale bar: 20 micrometres (= 1/50thof a millimetre).

We should, however, never assume that joy, wonder and a sense of mystery are ever-presents in the make-up of ecologists.   McCarthy makes the point that a love of nature is not a universal human attribute, although a propensity to love nature may be.   Just as that propensity can be nurtured through adolescence into an adult appreciation of the natural world, so a failure to exercise that appreciation as an adult can lead to it withering again.   I am acutely conscious that ecologists of middling seniority and above often spend more time staring at spreadsheets and in teleconferences than they do engaging directly with nature.  Within government agencies the reduction of time available for field ecology since the onset of austerity in the UK means that I often now deal with people who are unable to conjure visual images from the words and numbers that populate their datasets.  And, in my own work, I have to consciously make time to observe the natural world beyond the tight constraints of my professional life.

Above all, never forget that this love of nature exists in the first person, present tense or not at all. Natural history documentaries on the television and (dare I say) blogs such as mine are the herbs and spices that enliven your diet, but the naturalist’s basic sustenance needs a commitment that goes beyond staring at a spreadsheet or sitting on a couch.

 

The River Wear in November

Wear_Wolsingham_181119

I was back at the River Wear last week for my final visit of the year.   The heatwave that dominated the summer seems like an aeon ago as I plunged my arm into the cold water to find some stones and take some photographs.  I’m curious to see what is here, though.   The river has surprised me several times already this year.  Has it reverted to type as the British climate has regained a semblance of normality, or will the changes that we saw in the summer (see “Summertime blues …” and “Talking about the weather …”) still have consequences for the algae growing on the river bed?

The river bed itself had many patches of green filamentous algae which, on closer examination, turned out to be my old friend Ulothrix zonata, an alga that is common in these parts and which has a distinct preference for early spring conditions (see “Bollihope Bavakakra” and references therein).   A closer look showed two types of filament present: the normal vegetative ones with a single chloroplast encircling the cell but also some where the cell contents have divided to produce zoospores which are released and which, if they land on a suitable surface, will produce new vegetative filaments.   The “parent” filaments, themselves, are produced as zygotes, produced back in the spring, germinate.  The zygotes are the product of sexual reproduction, triggered by lengthening days (see reference in earlier post) and are dormant through the summer, only germinating once day length shortens and temperatures start falling.

Wear_Wolsingham_bed_Nov18

The river bed of the River Wear at Wolsingham, November 2018, showing conspicuous growths of Ulothrix zonata.

Ulothrix_zonata_Nov18

Magnified views of Ulothrix zonatafilaments from the River Wear at Wolsingham.  The upper image shows a vegetative filament and the lower image shows filaments where the cell contents have divided up prior to the release of zoospores.  Scale bar: 20 micrometres (= 1/50thof a millimetre).

The areas between the patches of Ulothrix zonatawere covered with a thick film, composed primarily of diatoms, in contrast to the situation on my last two visits when non-filamentous green algae predominated.  This time, it was Achnanthidium minutissimumdominated my count (about 70% of cells) although, because they are relatively small, they comprised just under half of the total volume of algae present.   Other diatoms bumped this up to about 70 per cent of the total volume, with motile cells of Navicula and Nitzschia, which were so abundant at the start of the year, beginning to appear in numbers again.   The green cells that dominated my counts in July and September now only constitute about five per cent of the total.   The River Wear, in other words, has shaken off the effects of the summer, just as a healthy human gets over a winter cold, and is now back to its old self.

Wolsingham_181119_#1

A view down my microscope whilst examining samples from the River Wear at Wolsingham showing the predominance of Achnanthidium minutissimum with (on the right-hand side) a filament of a narrow Ulothrix (not U. zonata).  

Entomoneis in three dimensions

I’ve written about the genus Entomoneison a few occasions in the past (see “A typical Geordie alga …”).   It is a challenging species to understand partly because the cells often do not survive digestion in the strong oxidizing agents that we routinely use to understand the structure of diatom cell walls, and partly because of its unusual three-dimensional architecture.   I’ve commented on this before, using some of Chris Carter’s photos to illustrate this (see “The really rare diatom show”).  Now, thanks to yet more careful work from Chris, we have a new set of photos with which to understand this species.

The underlying problem of a complicated geometry (the frustule [cell wall] is actually twisted in two planes) is compounded by the shallow depth of field that is available when viewing organisms at high magnifications. The first of Chris’ images shows how most diatomists will encounter Entomoneis: as a cleaned cell mounted on a slide and shows how the girdle bands bands (the silica “spacers” between the two valves) seem to present a particular problem.  Look, in particular, at the arrangement of these in the left-hand image, focused on the top of the cell, and note how they appear to cross over one another.  Compare this to image that is focused on the bottom of the cell.  By contrast, a cell that has not been subjected to the strong oxidising agents that we use to “clean” diatoms prior to observation presents quite a different view, as seen in the second set of three photographs.   The contrast is poorer here, as the cell is not mounted in a high-resolution mountant (the reason diatomists “clean” their samples in the first place) but we can, nonetheless, see the girdle bands.   When Chris focuses on the top of the cell. the girdle bands are clearly visible, not criss-crossed, and diagonal across the cell. At the other extreme (focus on bottom of cell) the bands are still just visible, sloped the other way somewhat obscured by the cell contents but, most importantly, not presenting a gaping hole.

B Entomoneis naphrax mount.jpg

A cell of Entomoneisthat has been cleaned and mounted in Naphrax before being photographed at three focus levels using simple brightfield microscopy.  The left-hand image is focussed on the top of the cell and shows how the girdle bands appear to cross one another whilst the right hand image is focussed on the bottom of the cell and shows a chasm in the centre of the cell where the girdle bands have collapsed. The middle image shows an intermediate focal plane where the apices are in focus: this is where the girdle bands are attached.

C Entomoneis alcohol mount.jpg

A cell of Entomoneisthat has been mounted in alcohol before being photographed at three focus levels. The contrast is much poorer here but at one extreme (focus on top of cell ie towards observer) the bands are clearly visible, not criss-crossed, and diagonal across the cell. At the other extreme (focus on bottom of cell) the bands are still just visible, sloped the other way but somewhat obscured by the cell contents.

What we think is happening is that the girdle bands are so weak that they collapse as soon as the frustule is dried or hits hot Naphrax; this collapse can be either towards the observer or away from the observer, creating a slightly different optical effect in each case.   Most of the time, however, the bands detach completely leaving isolated valves – sometimes with some straggly bits attached.  Chris thinks that almost all the published images of this taxon are misleading: usually flattened either optically or by software in order to give a sharp image for presentation and, in the process, disguising this detail.

These images all show us what Entomoneis looks like in girdle-view, the way we are most likely to encounter an intact cell when looking down a light microscope.  The next two plates show it from above (“valve view”) and in apical view (i.e. looking at the cell from one end), both of which are not often seen during routine observation.    The pair of valve views show the outline at different focal levels, and we can see how the thin wing (keel) is twisted towards the viewer; this twist is also present in the main (cylindrical) part of the cell but is not visible in these photographs.   The series of photographs in the next plate takes this further: the sequence along the top shows an apical view at several points of focus.  Some particulate matter is caught within the open structure of the frustule and acts as a reference point when comparing the two views. The thin keel with its thickened edge (containing the raphe) shows clearly. The body of the cell is not symmetrical because of the twist; the girdle band section is at the bottom of the inverted U section and is demarcated by ridges associated with each band: the number of bands can be estimated as shown on the enlarged fourth section. The other valve must have detached without holding onto any girdle bands.

A Entomoneis valve view in alcohol.jpg

Valve view of an alcohol mounted celul of Entomoneisat two focus levels.

D Entomoneis semicell in apical view in alcohol.jpg

An alcohol mounted semicell of Entomoneis caught in both apical (top row, showing several points of focus) and girdle views (bottom right).  The image at the bottom left shows a slightly magnified version of the fourth apical view indicating the location of the girdle bands on the opposite sides of the valve (indicated by the vertical red lines).

Entomoneis highlights the limitations of using two-dimensions to portray algae.  The answer, Chris and I agree, would be a three-dimensional model (see “Taking desmids to the next dimension …”) that we could pick up and view from all angles.  Another option is to use a scanning electron micrograph (SEM), and the two references at the end of this article contain several useful images.   However, most of us are still going to encounter Entomoneisprimarily via the light microscope.  Having a sense of the three-dimensional form of an alga lodged in your mind makes it much easier to interpret the flattened two-dimensional images that we routinely encounter.  Prior to the era of SEMs, the three-dimensional form of Entomoneis, and, indeed, its true taxonomic position, was very difficult to appreciate.   Both the 1930 and 1990s editions of the Süsswassflora von Mitteleuropaplaced it with Naviculawhereas we now understand enough about the form of the raphe to know that Entomoneis is more closely related to Surirella(see Round et al.,referenced below).  It is a good reminder that the study of diatoms has always been limited by the technology available.   Our toys may have changed enormously over the past hundred years but the gaps in our understanding remain …

References

Round, F.E., Crawford, R.M. & Mann, D.G. (1990).  The Diatoms: Biology and Morphology of the Genera.  Cambridge University Press, Cambridge.

Dalu, T., Taylor, J.C., Richoux, N.B. & Froneman, P.W. (2015).  A re–examination of the type material of Entomoneis paludosa(W Smith) Reimer and its morphology and distribution in African waters.  Fottea15: 11-25.

The Imitation Game

About a year ago, I made a dire prediction about the future of diatom taxonomy in the new molecular age (see “Murder on the barcode express …“).   A year on, I thought I would return to this topic from a different angle, using the “Turing Test” in Artificial Intelligence as a metaphor.   The Turing Test (or “Imitation Game”) was derived by Alan Turing in 1950 as a test of a machine’s ability to exhibit intelligent behaviour, indistinguishable from that of a human (encapsulated as “can machines do what we [as thinking entities] can do?”).

My primary focus over the past few years has not been the role of molecular biology in taxonomy, but rather the application of taxonomic information to decision-making by catchment managers.   So my own Imitation Game is not going to ask whether computers will ever identify microscopic algae as well as humans, but rather can they give the catchment manager the information they need to make a rational judgement about the condition of a river and the steps needed to improve or maintain that condition as well as a human biologist?

One of the points that I made in the earlier post is that current approaches based on light microscopy are already highly reductionist: a human analyst makes a list of species and their relative abundances which are processed using standardised metrics to assign a site to a status class. In theory, there is the potential for the human analysts to then add value to that assignment through their interpretations.  The extent to which that happens will vary from country to country but there two big limitations: first, our knowledge of the ecology of diatoms is meagre (see earlier post) and, in any case, diatoms represent only a small part of the total diversity of microscopic algae and protists present in any river.   That latter point, in particular, is spurring some of us to start exploring the potential of molecular methods to capture this lost information but, at the same time, we expect to encounter even larger gaps in existing taxonomic knowledge than is the case for diatoms.

One very relevant question is whether this will even be perceived as a problem by the high-ups.  There is a very steep fall-off in technical understanding as one moves up through the management tiers of environmental regulators.   That’s inevitable (see “The human ecosystem of environmental management…“) but a consequence is that their version of the Imitation Game will be played to different rules to that of the Environment Agency’s Poor Bloody Infantry whose game, in turn, will not be the same as that of academic taxonomists and ecologists.  So we’ll have to consider each of these versions separately.

Let’s start with the two extreme positions: the traditional biologist’s desire to retain a firm grip on Linnaean taxonomy versus the regulator’s desire for molecular methods to imitate (if not better) the condensed nuggets of information that are the stock-in-trade of ecological assessment.   If the former’s Imitation Game consists of using molecular methods to capture the diversity of microalgae at least as well as human specialists, then we run immediately into a new conundrum: humans are, actually, not very good at doing this, and molecular taxonomy is one of the reasons we know this to be true.  Paper after paper has shown us the limitations of taxonomic concepts developed during the era of morphology-based taxonomy.  In the case of diatoms we are now in the relatively healthy position of a synergy between molecular and morphological taxonomy but the outcomes usually indicate far more diversity than we are likely to be able to catalogue using formal Linnaean taxonomy to make this a plausible option in the short to medium-term.

If we play to a set of views that is interested primarily in the end-product, and is less interested in how this is achieved, then it is possible that taxonomy-free approaches such as those advocated by Jan Pawlowski and colleagues, would be as effective as methods that use traditional taxonomy.   As no particular expertise is required to collect a phytobenthos sample, and the molecular and computing skills required are generic rather than specific to microalgae, the entire process could by-pass anyone with specialist understanding altogether.  The big advantages are that it overcomes the limitations of a dependence on libraries of barcodes of known species and, as a result, that it does not need to be limited to particular algal groups.  It also has the greatest potential to be streamlined and, so, is likely to be the cheapest way to generate usable information.   However, two big assumptions are built into this version of the Imitation Game: first, there is absolutely no added value from knowing what species are present in a sample and, second, that it is, actually, legal. The second point relates to the requirement in the Water Framework Directive to assess “taxonomic composition” so we also need to ask whether a list of “operational taxonomic units” (OTUs) meets this requirement.

In between these two extremes, we have a range of options whereby there is some attempt to align molecular barcode data with taxonomy, but stopping short of trying to catalogue every species present.  Maybe the OTUs are aggregated to division, class, order or family rather than to genus or species?   That should be enough to give some insights into the structure of the microbial world (and be enough to stay legal!) and would also bring some advantages. Several of my posts from this summer have been about the strange behavior of rivers during a heatwave and, having commented on the prominence and diversity of green algae during this period, it would be foolish to ignore a method that would pick up fluctuations between algal groups better than our present methods.   On the other hand, I’m concerned that an approach that only requires a match to a high-level taxonomic group will enable bioinformaticians and statisticians to go fishing for correlations with environmental variables without needing a strong conceptual behind their explorations.

My final version of the Imitation Game is the one played by the biologists in the laboratories around the country who are simultaneously generating the data used for national assessments and providing guidance on specific problems in their own local areas.   Molecular techniques may be able to generate the data but can it explain the consequences?  Let’s assume that method in the near future aggregates algal barcodes into broad groups – greens, blue-greens, diatoms and so on, and that some metrics derived from these offer correlations with environmental pressures as strong or stronger than those that are currently obtained.   The green algae are instructive in this regard: they encompass an enormous range of diversity from microscopic single cells such as Chlamydomonas and Ankistrodesmus through colonial forms (Pediastrum) and filaments, up to large thalli such as Ulva.   Even amongst the filamentous forms, some are signs of a healthy river whilst others can be a nuisance, smothering the stream bed with knock-on consequences for other organisms.   A biologist, surely, wants to know whether the OTUs represent single cells or filaments, and that will require discrimination of orders at least but in some cases this level of taxonomic detail will not be enough.   The net alga, Hydrodictyon(discussed in my previous post) is in the same family as Pediastrumso we will need to be able to discriminate separate genera in this case to offer the same level of insight as a traditional biologist can provide.   We’ll also need to discriminate blue-green algae (Cyanobacteria) at least to order if we want to know whether we are dealing with forms that are capable of nitrogen fixation – a key attribute for anyone offering guidance on their management.

The primary practical role of Linnaean taxonomy, for an ecologist, is to organize data about the organisms present at a site and to create links to accumulated knowledge about the taxa present.    For many species of microscopic algae, as I stressed in “Murder on the barcode express …”, that accumulated knowledge does not amount to very much; but there are exceptions.  There are 8790 records on Google Scholar for Cladophora glomerata, for example, and 2160 for Hydrodictyon reticulatum.  That’s a lot of wisdom to ignore, especially for someone who has to answer the “so what” questions that follow any preliminary assessment of the taxa present at a site.  But, equally, there is a lot that we don’t know and molecular methods might well help us to understand this.   There will be both gains and losses as we move into this new era but, somehow, blithely casting aside hard-won knowledge seems to be a retrograde step.

Let’s end on a subversive note: I started out by asking whether “machines” (as a shorthand for molecular technology) can do the same as humans but the drive for efficiency over the last decade has seen a “production line” ethos creeping into ecological assessment.   In the UK this has been particularly noticeable since about 2010, when public sector finances were squeezed.   From that point on, the “value added” elements of informed biologists interpreting data from catchments they knew intimately started to be eroded away.   I’ve described three versions of the Imitation Game and suggested three different outcomes.  The reality is that the winners and losers will depend upon who makes the rules.  It brings me back to another point that I have made before (see “Ecology’s Brave New World …”): that problems will arise not because molecular technologies are being used in ecology, but due to how they are used.   It is, in the final analysis, a question about the structure and values of the organisations involved.

References

Apothéloz-Perret-Gentil, L., Cordonier, A., Straub, F., Iseili, J., Esling, P. & Pawlowksi, J. (2017).  Taxonomy-free molecular diatom index for high-throughput eDNA monitoring.   Molecular Ecology Resources17: 1231-1242.

Turing, A. (1950).  Computing machinery and intelligence.  Mind59: 433-460.

Notes from the Serra de Estrela

At the end of my last post I suggested that the next time I wrote it may be from Portugal.   In reality, tiredness and, to be frank, a steady consumption of Vino Verde intervened and this post may be about Portugal but is not, alas, written from that country.   Our travels took us from Lisbon northwards to Covilhã, a town on the edge of the Serra da Estrela mountain range, then onwards to the Duoro valley and Porto, and finally back to Lisbon.   The lower part of the Duoro is the home to many of the Vino Verde vineyards, although our focus was mostly on the vineyards further upstream from which the grapes for port are grown.  I’ll write more about the Duoro in a later post but, first, I want to take you on a journey to the Serra da Estrela.

These are the highest mountains in mainland Portugal (there is a higher point in the Azores) with a summit at 1993 metres at Torre.  Unusually, for the highest peak in a mountain range, there is a road all the way to the top, along with a couple of shops and a small bar/restaurant.   On the day we visited, a couple of hardy cyclists had toiled their way up from the plains but most of the visitors had driven up.   We had stopped on our route up from Covilhã to explore the granite landscape and botanise so felt that we had earned our bica and Pastéis de Nata by the time we got to the very top.

Much as I appreciate a summit that satisfies a caffeine addiction, the real interest lies elsewhere, with the road up from Covilhã passing through some dramatically-eroded granite outcrops, composed of huge boulders apparently perched precariously on top of each other.  These resemble the granite “tors” we find in Dartmoor in south-west England, and have a similar origin.   The area around the tors had distinctive vegetation that will, no doubt, be described in greater length in a post on Heather’s blog before too long.   The free-draining sandy soils that the granite landscape creates mean that there was not a lot of surface water for me to indulge my own passions, so I will have to take you to another part of the Serra da Estrela for the remainder of this post.

Granite landscapes near Torre in the Serra da Estrela Natural Park in northern Portugal, September 2018.  

We found an inviting stream as we were walking near Unhais de Serra, at the southern end of the Natural Park.  The first plants to catch our eye were a submerged Ranunculus species with finely-divided leaves and five-petelled white flowers sitting at the water surface.   As well as these, we could see shoots of patches of water dropwort (Oenanthe sp.) and, looking more closely, several of these appeared to be growing out of dark coloured patches which turned out to be a submerged moss overgrown with algae (more about which a little later).   I am guessing that, once the rains come, much of these mini-ecosystems will be washed downstream leaving just a few moss stems to be colonised again next year.

Submerged vegetation in the stream at Unhais de Serra in September 2018 (40°15’44” N 7°37’21” W).  The top photograph shows a Ranunculus species and the lower photograph shows mosses overgrown with algae (a mixture of Cyanobacterial filaments, diatoms and coccoid green algae), within which young plants of Oenanthe sp. have taken root (top photograph: Heather Kelly).

Somewhat to my surprise there were also some patches of Lemanea.   This is a red algal genus that I usually associate with late winter and spring in my own part of the world, so I had not expected to find such prolific growths at this time of year at lower latitudes.   Maybe Iberian species of Lemanea behave differently to those with which I am familiar?

The Lemanea species found in the stream at Unhais de Serra in September 2018.  The top photograph shows it growing in situ and the lower photograph is a close-up.  The filaments are about a millimetre wide.

The dark film itself contained a variety of algae, some of which I have put in a plate below.   There were some cyanobacterial filaments which looked like Oscillatoria to me but which were not moving (their life between collection and examination was less than ideal).  There were also a large number of diatoms, mostly Navicula and Surirella.  Again, both would have been moving around in a healthy sample but were static when I got around to examining them; the chloroplasts in the Surirella, in particular, were not in very good condition).  I also saw some chains of Fragilaria species and several small green algae (especially Monoraphidium, discussed in the previous post).  I’ll return to the diatoms in a future post, once I have been able to get permanent slides prepared and examined but first impression is that I am looking at a community from a low nutrient, circumneutral environment.

Some of the algae living in the dark films overgrowing mosses in the stream at Unhais de Serra in September 2018.   a. – c.: Navicula angusta; d. –g. Surirella cf. roba; h. – i. two different chain-forming Fragilaria sp.; j. – k.: Navicula cf cryptocephala; l. – m.: Oscillatoria sp.    Scale bar: 20 micrometres (= 1/50th of a millimetre). 

The diatoms, in particular, reiterate the important point that notwithstanding the huge number of new species that have been described in recent years, it is possible to peer through a microscope at a sample from anywhere in Europe and see a familiar set of outlines that, for the most part, give a consistent interpretation of environmental conditions wherever you are (see, for example, “Lago di Maggiore under the microscope”).   That same rationale applies, to some extent to other organism groups too: we have recently shown this for macrophytes in shallow lakes for example.   Likewise, the geology here was shaped by the same broad forces that created the landscape of south-west England even if local climate means that the flora surrounding the tors in the Serra da Estrela is adapted to more arid conditions than that on Dartmoor.    It is important that, when we travel, we see the differences but, perhaps even more important in this fractured age, that we see the similarities too.

References

Chapuis, I.S., Sánchez-Castillo, P.M. & Aboal Sanchero, M. (2014).  Checklist of freshwater red algae in the Iberian Penisula and the Balearic Islands.   Nova Hedwigia 98: 213-232.

Poikane, S., Portielje, R., Deny, L., Elferts, D., Kelly, M., Kolada, A., Mäemets, H., Phillips, G., Søndergaard, M., Willby, N. & van den Berg, M. (2018).   Macrophyte assessment in European lakes: Diverse approaches but convergent views of ‘good’ ecological status.  Ecological Indicators 94: 185-197.