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.

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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) but summit 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.

Talking about the weather …

September is here.  When I visited this site two months ago we were in the midst of the heatwave and the samples I collected from the Wear at Wolsingham were different to any that I have seen at this location before, dominated by small green algae (see “Summertime blues …”).   As I drove to Wolsingham this time, I could see the first signs of autumn in the trees and the temperatures are more typical of this time of year.   We have had rain, but there has not been a significant spate since April and this means that there has been nothing to scour away these unusual growths and return the river to its more typical state.

That does not mean, however, that there have been no changes in the algae on the submerged stones.  Some of these differences are apparent as soon as I pick up a stone.  Last month, there was a thin crust on the surface of the stones; that is still here but now there are short algal filaments pushing through, and the whole crust seems to be, if anything, more consolidated than in July, and I can see sand grains amidst the filaments.   Biofilms in healthy rivers at this time of year are usually thin, due to intense grazing by invertebrates, so I’m curious to know what is going on here this year.

A cobble from the River Wear at Wolsingham, showing the thick biofilm interspersed with short green filaments.   Note, too, the many sand grains embedded in the biofilm.  The bare patch at the centre was created when I pulled my finger through it to show how consolidated it had become.  The cobble is about 20 centimetres across.

Many of the organisms that I can see when I peer at a drop of my sample through my microscope are the same as those I saw back in July but there are some conspicuous differences too.   There are, for example, more desmids, some of which are, by the standards of the other algae in the sample, enormous.   We normally associate desmids with soft water, acid habitats but there are enough in this sample to suggest they are more than ephemeral visitors.   And, once I had named them, I saw that the scant ecological notes that accompanied the descriptions referred to preferences for neutral and alkaline, as well as nutrient-rich conditions.  Even if I have not seen these species here before, others have seen them in similar habitats, and that offers me some reassurance.    In addition to the desmids, there were also more coenobia of Pediastrum boryanum and Coelastrum microporum compared to the July sample.

A view of the biofilm from the River Wear at Wolsingham on 1 September 2019. 

There were also more diatoms present than in my samples from July – up from about 13 percent of the total in July to just over 40 per cent in September.   The most abundant species was Achnanthidium minutissimum, but the zig-zag chains of Diatoma vulgare were conspicuous too.  The green filaments turned out to be a species of Oedogonium, not only a different species to the one I described in my previous post but also with a different epiphyte: Cocconeis pediculus this time, rather than Achnanthidium minutissimum.   I explained the problems associated with identifying Oedogonium in the previous post but, even though I cannot name the species, I have seen this form before (robust filaments, cells 1.5 to 2 times as long as broad) and associate it with relatively nutrient-rich conditions.  That would not normally be my interpretation of the Wear at Wolsingham but this year, as I have already said, confounds our expectations.   I did not record any Cladophora in this sample but am sure that, had I mooched around for longer in the pools at the side of the main channel, I would have found some filaments of this species too.

Desmids and other green algae from the River Wear at Wolsingham, 1 September 2019.  a. Closterium cf. acerosum; b. Closteriumcf. moniliferum; c. Cosmarium cf. botrysis; d. Closterium cf. ehrenbergii; e. Coelastrum microporum; f. Pediastrum boryanum.   Scale bar: 50 micrometres (= 1/20th of a millimetre).  

It is not just the differences between months this year that I’m curious about.  I did a similar survey back in 2009 and, looking back at those data, I see that my samples from August and September in that year had a very different composition.   There was, I remember, a large spate in late July or early August, and my August sample, collected a couple of weeks later had surprised me by having a thick biofilm dominated by the small motile diatom Nitzschia archibaldii.   My hypothesis then was that the spate had washed away many of the small invertebrates that grazed on the algae, meaning that there were few left to feed on those algae that survived the storm (or which had recolonised in the aftermath)..   As the algae divided and re-divided, so they started to compete for light, handing an advantage to those that could adjust their position within the biofilm.   This dominance by motile diatoms was, in my experience of the upper Wear, as uncommon as the assemblages I’m encountering this summer, though probably for different reasons.

Other algae from the River Wear at Wolsingham, September 2018.    The upper image shows Diatoma vulgare and the lower image is Oedogonium with epiphytic Cocconeis pediculus.   Scale bar: 20 micrometres (= 1/50th of a millimetre).

I suspect that it is the combination of high temperatures and low flows (more specifically, the absence of spates that might scour away the attached algae) that is responsible for the present state of the river.  This, along with my theory behind the explosion of Nitzschia archibaldii in August 2009, both highlight the importance of weather and climate in generating some of the variability that we see in algal communities in rivers (see “How green is my river?”).   The British have a reputation for talking about the weather.   I always scan the weather forecasts in the days leading up to a field trip, mostly to plan my attire and make sure that I will, actually, be able to wade into the river.  Perhaps I also need to spend more time thinking about what this weather will be doing to the algae I’m about to sample.

A hitchhiker’s guide to algae …

One of the recurring themes of this blog is the hidden delights of natural history for anyone prepared to take a closer look at unprepossessing locations, so it is appropriate that we have found some quite rich habitats within walking distance of our home in County Durham.   I’ve written before about visits to Crowtrees, a local nature reserve (see “More pleasures in my own backyard” and “Natural lenses”) and Heather is also writing a series of posts about the ever-changing flora of this small vale at the foot of the Permian limestone escarpment (see “Crowtrees LNR July 2018 part 2: gentians to grasses” for the most recent and links back to previous ones).   I visited again last week, taking Brian Whitton along for company.

His interest was the red alga Chroothece ricteriana, which I described in one of my earlier posts about Crowtrees but we did not find it on this particular visit.   Instead, my eye was drawn to soft clouds of green filaments that floated just above the bed of the pond.   When I looked closely under my microscope, I saw that these were thin filaments of Oedogonium.  Typically, these had no reproductive organs, so cannot be named (see “Love and sex in a tufa-forming stream” for a rare exception), but all showed characteristic “cap cells” (see lower illustration).

Growths of Oedogonium in Crowtrees pond, August 2018.   The frame width is about 30 centimetres.   The photograph at the top of the post shows Brian Whitton searching for algae during our visit.

The diatom Achnanthidium minutissimum was growing on small stalks attached to the Oedogonium filaments, often alone but also in pairs and stacks of four, as the diatom cells divided and re-divided.  Oedogonium is a rougher alga to the touch than filamentous genera such as Draparnaldia, Stigeoclonium and Spirogyra, and often carries epiphytes, and I presume the lack of mucilage is a factor in this.   Achnanthidium minutissimum is a diatom that is very common on the upper surface of submerged stones in both lakes and rivers, but it is not fussy and I often see it as an epiphyte if conditions are right.  In this case, I suspect that the very hard water of Crowtrees Pond is a factor: calcium carbonate is constantly being precipitated from the water to create a thin layer of “marl” (see photo in “Pleasures in my own backyard”).   This makes life difficult for a tiny diatom that cannot move, so hitch-hiking a ride on the back of a filamentous alga that floats about the lake bottom makes a lot more sense.

Oedogonium filaments with epiphytic Achnanthidium minutissimum, from Crowtrees pond, August 2018.  Scale bar: 20 micrometres (= 1/50th of a millimetre).  

Oedogonium is an adaptable genus.  It is also common in the River Ehen (soft water, low nutrients) and I also find it in lowland polluted rivers too.  Being able to name the species would, I am sure, help us to better understand the ecology but this is, as I have already mentioned, problematic (see “The perplexing case of the celibate alga”).   However, in each of the cases I’ve mentioned, the epiphytes are different (Achnanthidium minutissimum here, Tabellaria flocculosa and Fragilaria species in the Ehen, Rhoicosphenia and Cocconeis placentula in enriched lowland rivers) and I suspect that these might offer an easier way to interpret the habitat than the filaments themselves, at least until someone finds a stress-free way of naming them.

Comparing algae on a summer’s day …

I wrote about the effect of the long period of low flow in the River Wear a few weeks ago (see “Summertime Blues …”) and have, now, completed two dioramas depicting the state of the river in the main channel and in a filamentous algae-dominated backwater.  The first of these is dominated by free-living green algae, either single cells or coenobia (see note at end), which is a big contrast to the situation I recorded two months earlier when the assemblage was dominated by diatoms, with patches of filamentous green algae (see “Spring comes slowly up this way” and “A question of scale”).

I sent a small sample of the Wolsingham biofilm to Dave John for his opinion on the green algae, and he sent back a list with twenty one different green algae that he had found.  Fortunately, this confirmed my own original list, with Keratococcus bicaudatus, Scenedesmus, Desmodesmus and Monoraphidium all featuring.   He also commented that Keratococcus is hard to differentiate from Chlorolobium (which is also in his list) and that most of the green alga on his list are usually considered to be planktonic (Keratococcus and Chlorolobium are exceptions) although, as my earlier post suggested, these definitely formed a distinct biofilm on the surface of stones this year in the River Wear.

A diorama showing the biofilm in the River Wear at Woslingham, July 2018.   You can see coenobia of Demodesmuss communis (centre), Scenedesmus sp. (left) and Coelastrum microporum (right – half tucked behind a mineral particle, along with single cells of Keratococcus bicaudatus (upright cells) and Monoraphidium.  There are also some cells of Achnanthidium minutissimum on short stalks in the foreground and a cluster of Fragilaria gracilis cells in the background.

There seems to be little hard evidence on the habit of Keratococcus and Chlorobium apart from references to a preference for benthic habitats.   I have drawn them as upright cells, drawing on their similarity in form to Characium, for which there is better evidence of an upright habit (although Characium tends to grow on other algae, rather than on hard surfaces).  Whereas I often have a strong sense of the three dimensional arrangement of organisms within benthic biofilms, so little has been written about the preferences of these green algae that, apart from the Keratococcus, I have had to show them as a jumble of cells and coenobia across the picture frame.

The second diorama depicts the tangle of filamentous green algae that I found in the pools beside the main channel.  As I mentioned in my earlier post, these are species that I do not normally find at this site and are here, I presume, due to the long period of unusually warm weather and low flows.   One difference between these communities and that captured in my first diorama is that there is a more obvious organisation of the constituents here: the Cladophora filaments, though appearing as a tangle to us, form the foundation upon which epiphytes grow directly, but also around which Melosira filaments are entangled, rather like the lianas in a tropical rain forest.   The quantity of diatoms around the Cladophora is so great that their brown pigments completely mask the Cladophora’s green cells but note how the density of Cocconeis cells reduces towards the tips – the youngest parts of the filaments.

Depiction of filamentous algae growing in the margins of the River Wear at Wolsingham in July 2018, showing epiphytic Cocconeis pediculus and entangled Melosira varians.

There have been some recurring themes in my posts this summer: one is that UK rivers have been behaving quite differently to previous years, due to a combination of low flows (more accurately, a lack of the scour associated with high flows) and warm, well-lit conditions.   The low flows have also resulted, to some extent, in rivers becoming more physically heterogeneous, with side-pools and silty areas developing distinct assemblages of algae quite different to those encountered in the main channel.   Sometimes, the sum of these effects is for rivers to look less healthy than is usually the case.

The Wear at Wolsingham is one of those sites that I like to think I know well, having visited the location so many times over the past 30 years.  It is reassuring, in a rather humbling way, to know that it still has the capacity to surprise me.

Dave’s list of green algae from the Wolsingham biofilm, July 2018

Desmids
Closterium moniliferum
Closterium acerosum
Cosmarium botrytis
Cosmarium venustum
Staurastrum striatum

‘Chlorococcalean’ algae
Acutodesmus dimorphus
Coelastrum astroideum
(very small and atypical)
Coelastrum microporum (very small and atypical)
Chlorolobion braunii
Desmococcus olivaceum (subaerial species)
Desmodesmus communis
Desmodesmus subspicatus
Keratococcus bicaudatus

Monoraphidium arcuatum
Monoraphidium contortum
Monoraphidium griffithsia
Monoraphidium irregulare
Scenedesmus arcuatus
Pseudopediastrum boryanum
Tetradesmus obliquus
Tetraedron minimum

Note

A coenobium is a colony in which the cell number is fixed at the time of formation and not augmented subsequently.   Coenobia are particularly common in the Chlorococcalees.

Two-faced diatoms …

Back in March I reflected on the challenges involved in discriminating species of Gomphonema (see “Baffling biodiversity …”).   That there were several species in the sample which prompted the article was indisputable; that some of those species were, individually, quite variable was also clear.  The former issue I resolved, to some extent, by reference back to Hutchinson’s “Paradox of the Plankton” but the latter was harder to explain.

Part of the problem stems, I suspect, from the reliance on morphology to characterise species.  We assume that, because a group of organisms share a set of visible characteristics, then they must also share genes which determine those characteristics and that, in turn, implies a common ancestry.   Turning that assumption on its head, we assume that groups of microscopic algae that appear different to each other belong to different species.   However, a dog lover might point out that Chihuahuas and Great Danes look very different but are, in fact, the same species.   One of the challenges of those of us who study algae is deciding just how much variation in form is typical within a species, and at what point differences are such that they represent more than one species.

Gomphonema sarcophagus from Pitsford Water, Northamptonshire, showing Janus cells.  Photographs by Ingrid Jüttner.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

So what should we make of the diatom valves in the image above?   The valve outlines and breadths are similar but the striae densities are so different that we might think that they belong to two separate species.   However, I recently stumbled, by chance, on a 1998 paper by Stacy McBride and Robert Edgar which discussed the topic of “Janus cells”.  Janus, you may remember, is the Roman god of time and is depicted with two faces, one looking back to the past and the looking to the future. His name has been appropriated, in this context, to describe diatoms that have frustules comprising two valves with different characteristics.   A few genera show consistent differences between the two valves – in Cocconeis and Planothidium, for example, one valve has a raphe whilst the other does not – and there are also differences in striae densities between the raphe and rapheless valves.   The term “Janus cell” is applied to diatoms where there are marked differences between the two valves but this is not a fundamental characteristic of the species or genus.   So, in the example above, we see some forms with much denser striae (11-13 in 10 mm) than others (7-8 in 10 mm).

We don’t know, from just looking at variability in populations, that this is not polymorphism within the species, in much the same way that some humans have attached ear lobes and others do not.   But, as diatom populations grow in number by repeated divisions of single cells, we can assume that most are clones of a small number of genotypes and, therefore, that the differences are due to ontogenetic variation.   What is interesting here is that this variation seems to create two distinct outcomes – coarsely or finely striated valves.  Some have suggested that such variation may be determined by differences in environmental conditions; however, the co-existence in a single population argues against this.

Gomphonema, as I have mentioned in earlier posts, is a genus that challenges taxonomists.  And, because ecologists depend upon taxonomists to give them a means of sorting diatom valves and frustules into meaningful categories, the environmental signals we get from Gomphonema species are often quite confused too.   The possibility of encountering Janus cells just throws one more curve ball into the mix.

Reference

McBride, S.A. & Edgar, B.K. (1998).   Janus cells unveiled: frustular morphometric variability in Gomphonema angustatum.   Diatom Research 13:293-310.

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

Summertime blues …

My reflections on the effects of the heatwave on freshwater algae continued with the latest of my regular visits to the River Wear at Wolsingham.  A comparison of the picture above with that at the head of “Spring comes slowly up this way …” says it all: the sun was shining and the gravel berms that I usually use to enter the river were occupied by families with barbeques whilst their children splashed around in the water.   At times such as this, a grown man picking up stones and then vigorously brushing their tops with a toothbrush would have invited too many questions, so I slunk off 100 metres or so downstream and found a quieter spot to explore.

The biofilm in the main channel of the River Wear at Wolsingham, July 2018. 

The first thing I noticed was that the biofilm coating the submerged stones at the bottom of the river had a greenish tinge, rather than its usual chocolate brown appearance.  It also was more crusty and less slimy to the touch than I usually see in this river.  When I got a specimen under the microscope, I could see that the composition was completely different to that which I had observed in previous months.   Most samples from this location that I’ve looked at in the past have been dominated by diatoms, with occasional spring flourishes of filamentous green algae.  Today, however, the sample was dominated by small green algae – a group that I am not very confident at identifying.   My rough estimate is that these formed about three quarters of all the algae that I could see, with diatoms and cyanobacteria each accounting for about half of the remainder.   The most abundant greens were a tiny single-celled alga that I tentatively identified as Keratococcus bicaudatus, along with a species of Scenedesmus and Desmodesmus communis.   There were also a number of cells of Monoraphidium arcuatum and some of Ankistrodesmus sp.

Two views of biofilms from the River Wear, Wolsingham in January 2018.   Left: from the main channel; right: from pools at the edge of the channel.

Green algae from the River Wear at Wolsingham, July 2018: a. Desmodesmus communis; b. Monoraphidium arcuatum; c. Scenedesmus sp.; d. unidentified, possibly Keratococcus bicaudatus.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

However, there were also pools at the side of the channel, away from the main current but not so cut off that they were isolated from the river itself.   These were dominated by dense, brown filamentous growths, very similar in appearance to the Melosira varians flocs I described in “Some like it hot …”.  The filaments, however, felt coarser to the touch and, in close-up, could be seen to be branched, even without recourse to a microscope.   Once I got these under the microscope, I could see that they were filaments of Cladophora glomerata, another green alga, but so smothered with epiphytic diatoms (mostly Cocconeis pediculus) that they appeared brown in colour.

This combination of Cladophora glomerata and Cocconeis pediculus in the backwaters were as much of a surprise as the green-algae-dominated biofilms in the main channel.   These are species usually associated with enriched rivers (see “Cladophora and friends”) and, whilst I have seen Cladophora in the upper Wear before, it is an unusual occurrence.   Just as for the prolific growths of Melosira varians described in “Some like it hot …” it is tempting to leap to the conclusion that this must be a sign that the river is nutrient-rich.  However, the same conditions will apply here as there: “nutrients” are not the only resource that can limit plant growth and a steady trickle of phosphorus combined with warm, sunny conditions is just as likely to lead to prolific growths as a more conventionally “polluted” river.

Cladophora filaments smothered by the diatom Cocconeis pediculus in a pool beside the River Wear at Wolsingham, July 2017.   The frame width of the upper image is about 1 cm; the scale bar on the lower images is 20 micrometres (= 1/50th of a millimetre).

Another way to think of these situations is that, just as even healthy people are occasionally ill, so healthy streams can go through short periods when, based on a quick examination of plants and animals present, they exhibit symptoms associated with polluted conditions or simply (as for the first sample I described) different to what we usually expect to find.   A pulse of pollution might have passed downstream or, as seems to be happening at the moment, an unusual set of conditions lad to different organisms thriving.   Just as the ability to fight off infection forms part of a doctor’s understanding of “health”, so I expect that the River Wear will, in a few weeks time, be back to its usual state.   Healthy ecosystems, just like healthy humans, show “resilience”.   The irony is that, in this case, the “symptoms” are most obvious at a time when we are enjoying a summer better than any we’ve had in recent years.