The natural history of numbers

I have made a few facetious comments in this blog about the tendency for ecologists to spend more time staring at spreadsheets than engaging directly with the organisms and habitats they are trying to understand.   There is, of course, a balance that needs to be struck.   We can learn a lot from analysing big datasets that would not have occurred to a biologist who spent all his or her time in the field.  And, I have to admit, somewhat grudgingly, there is a beauty to the numerical landscapes that becomes apparent when a trained eye is brought to bear on data.

I’ve been involved in a project for the European Commission which has been trying to find good ways of converting the ecological objectives that we’ve established for the Water Framework Directive into targets for the pressures that lead to ecosystem degradation.   The key principle behind this work is summarised in the graph below: if the relationship between the biology (expressed as an Ecological Quality Ratio, EQR) and a pressure (in this case, the phosphorus concentration in a river or lake) can be expressed as a regression line then we can read off the phosphorus concentration that relates to any point on the biological scale.   (Note that there are many other ways of deriving a threshold phosphorus concentration, but this simple approach will suffice for now.)

PvEQR_1pressure

Relationship between biology (expressed as an Ecological Quality Ratio, EQR) and phosphorus concentration for a hypothetical dataset.  The blue line indicates the least squares regression line, the horizontal green line is the position of the putative good/moderate status boundary and the vertical green line is the phosphorus concentration at this boundary position.  Coefficient of determination, r2= 0.89 (rarely achieved in real datasets!)

This is fine if you have a strong relationship between your explanatory and response variables and you are confident that there is a causal relationship between them.  Unfortunately, neither of these criteria are fulfilled in most of the datasets we’ve looked at; in particular, it is rare for the biota in rivers to be so strongly controlled by a single pressure.  This means that, when trying to establish thresholds, we also need to think about how a second pressure might interact with the factor we’re trying to control.   If this second pressure has an independent effect on the biota then we might expect some sites that would have had high EQRs if we just considered phosphorus might now be influenced by this second pressure, so the EQR at these sites will fall below the regression line we’ve just established.   When we plot the relationship between EQR and phosphorus taking this second pressure into account, our data no longer fits a neat straight line, but now has a “wedge” shape, due to the many sites where the second pressure overrules the effect of phosphorus.   If you were tempted to put a simple regression line through this new cloud of data, you would see the coefficient of determination, r2, drop from 0.89 to 0.35.  Note, too, how the change in slope means that the position of the phosphorus boundary also falls.   More worryingly, we know that, for this hypothetical dataset, the new line does not represent a causal relationship between biology and phosphorus.  That’s no good if you want to use the relationship to set phosphorus targets and, indeed, you now also need to think about how to manage this second pressure.

PvEQR_2pressures

The same relationship as that shown in the previous graph, but this time with an interaction from a second pressure.  The blue line is the regression line established when phosphorus alone was considered, and the red line is the regression between EQR and phosphorus in the presence of this second pressure.

My purpose in this post is not to talk about the dark arts of setting targets for nutrient concentrations that will support healthy ecosystems but, rather, to talk about data landscapes.  Once we saw and started to understand the meaning of “wedge”-shaped data, we started to see similar patterns occurring in all sorts of other situations.   The previous paragraph and graph, for example, assumed that the factor that confounded the biology-phosphorus relationship was detrimental to the biology, but some factors can mitigate the effect of phosphorus, giving an inverted wedge, as in the next diagram.  Once again, the blue line shows the regression line that would have been fitted if this was a pure biology versus phosphorus relationship.

PvEQR_2pressures_#2

The same relationship, but this time with a second factor that mitigates against the effect of phosphorus.  Note how the original relationship now defines the lower, rather than the upper, edge of the wedge. 

Wedge-shaped data crop up in other situations as well.  The next graph shows the number of diatoms I recorded in a study of Irish streams and there is a distinct “edge” to the cloud of data points.   At low pH (acid conditions), I rarely found more than 10-15 species of diatom whereas, at circumneutral conditions, I sometimes found 10-15 species but I could find 30 or more.   Once again, we are probably looking at a situation where, although pH does exert a pressure on the diatom assemblage, lots of other factors do too, so we only see the effect of pH when its influence is strong (< pH 5) when its influence is very strong.

Ntaxa_v_pH_FORWATER

The number of diatom species recorded across a pH gradient in Irish streams.  Unpublished data.

In this case, the practical problem is that the link between species number and pH is weak so it is hard to derive useful information from the number of species alone.   It would be dangerous to conclude, for example, that the ecology at a site was impacted by acidification on the strength of a single sample.  On the other hand, if you visited the site several times and always recorded low species numbers, then you have a pretty good indication that there was a problem (not necessarily low pH; toxic metals would have a similar effect).   Whether such a pattern would be spotted will depend on how often a site is visited and the sad reality is that sampling frequencies in the UK are now much lower than in the past.

However, this post is not supposed to be about the politics of monitoring (evidence-based policy is so much easier when you don’t collect enough uncomfortable evidence) but about the landscapes that we see in our data, and what these can tell us about the processes at work.   Just as a field biologist can look up from the stream they are sampling and gain a sense of perspective by contemplating the topography of the surrounding land, so we should also be aware of the topography of our data before blithely ploughing ahead with statistical analyses.

with_Geoff_&amp;_Heliana

With Geoff Phillips and Heliana Teixaira – fellow-explorers of data landscapes in our project to encourage consistent nutrient boundaries across the European Union.

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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.

Casting the net wide …

A  month or so ago I wrote a couple of posts about the green algae that were thriving in the River Wear this summer (see “Keeping the cogs turning …” and “More green algae from the River Wear”).  In one of those, I promised to write a post about a related genus, Hydrodictyon.   I did try to find some recent populations but ran out of time so have fallen back on some old pictures along with more of Chris Carter’s spectacular photography.

Hydrodictyon reticulatum is commonly called the “water net” and can form extensive, and sometimes nuisance, growths, either floating in a lake or a slow-flowing river, or as a mat at the edge (see photos below).   The cylindrical cells are arranged in pentagons or hexagons which can be visible with the naked eye (hence the net-like appearance).   These have a mode of asexual reproduction that results in tiny zoospores being formed inside each cell.  Each of these develops into a small daughter cell whilst still inside the mother cell, and the ends of these daughters then join together to form mini-nets.  You can see this happening in Chris’ image at the top of the post: there are some young cells in the foreground with a mature “mother” cell full of “daughter” cells forming their own nets inside.  Eventually, the wall of the mother-cell disintegrates and the daughter net is released.

A mat of Hydrodictyon reticulatum from the lower River Tweed; b. macro, and, c. microscopic views of coenobia of H. reticulatum from Thrapston Lake, Northampton (b. and c. by Chris Carter).

This is an extremely effective way of enabling Hydrodictyon reticulatum to spread quickly when conditions favour its growth and the image below shows just how extensive these mats can be.   It is a species that is more common in the warmer parts of the world but it does occur in the UK as far north as Scotland and Brian Whitton has predicted that it is a species that is likely to be favoured in some climate warning scenarios.   Some authors have suggested that Hydrodictyon favours nutrient-rich water, but some of the locations where I have found it (the River Tweed in Scotland, Sunbiggin Tarn in Cumbria) do not meet this criterion.  Rather, I suggest that well-lit, relatively undisturbed summer conditions are the key factor and that this is more likely to be the case in lowland areas that are, in many cases, also rich in nutrients.  It is more likely to be a correlation than a cause, in other words.   Whatever the cause, there is a huge dichotomy between the beauty of the organism under the microscope and the nuisance that it can cause.

A huge growth of Hydrodictyon reticulatum at Manor Farm Weir on the Jubilee River (a flood alleviation channel of the River Thames near Maidenhead).  Photo: Environment Agency.

This mode of asexual reproduction – in which the zoospores aggregate inside the parent – is also a feature of Pediastrum.  Even though the shapes and dimensions of the organisms are very different, they share some fundamental properties.   Molecular phylogenetic studies have also shown that there is a close affinity between Hydrodictyon, Pediastrum and the other genera I mentioned in “Keeping the cogs turning …”.   However, their habits and ecology are very different and that raises some interesting questions about a different matter entirely … the subject of my next post.

Reference

John, D.M., Pentecost, A. & Whitton B.A. (2001).  Terrestrial and freshwater eukaryotic algae.   pp. 148-149.  In: The Changing Wildlife of Great Britain and Ireland (edited by D.L. Hawksworth).   Taylor & Francis, London.

Krienitz, L. & Bock, C. (2012).  Present state of the systematics of planktonic coccoid green algae of inland waters.   Hydrobiologia 698: 295-326.

 

Algae from the Alto Duoro …

From the highlands of Serra da Estrela w headed north-west towards the vineyards of the Duoro Valley from which the grapes that make port are picked.  I’m supposed to be on holiday but, as the narrow road twists and turns down a steep hillside, with vineyards on both sides, I see a case study in how humans alter rivers and their catchments to suit their needs.  I wonder if the passengers on the cruise ships that move sedately through this beautiful landscape have any idea of just how difficult this same journey would have been just fifty years ago.   Now there are 51 large dams within the watershed, regulating the flow and, at the same time, generating much-needed hydroelectricity.   Before these were in place, the only way to get the port from the quintas in the Alto Duoro to Porto was to load the barrels onto a “barco rabelo”, and then to plot a perilous path through the rapids before using a combination of sail, oars and oxen to make the slow journey back upstream (you can see videos of these journeys on YouTube).

A replica of a barco rabelo moored in the Rio Duoro at Porto, September 2018.

The Rio Douro is a type of river that is rare in the UK but very common throughout the rest of Europe in that it crosses (and, for part of its course, forms) national boundaries.  There are a few rivers in Ireland which straddle borders (the Foyle is one, and some of the headwaters of the Shannon can be found in County Fermanagh) but, mostly, this is a complication that our river managers do not have to face.  By contrast, eighty per cent of the Rio Douro’s catchment lies in Spain (where it is called the Duero) and it is actually the largest watershed on the Iberian Peninsula.   The whole European project, and its environmental policy in particular, makes so much more sense when you are looking at a well-travelled river.

Our immediate objective was the Quinta do Bomfin at Pinhão, which produces grapes for Cockburns’, Dow’s and Taylor’s ports.  However, after a morning walking through the vineyards and following a tour of the winery (the robot that has replaced human grape treaders has, we learned, been carefully calibrated to match the pressure that a human foot exerts, lest the grape seeds are crushed, imparting bitterness to the resulting wine) plus some port tasting, the lure of the river was too strong.

A view across the Douro Valley from Quinta do Bomfin at Pinhão.   This, and the previous two photographs, were taken by Heather Kelly.

The river bank at Pinhão is lined with rip rap (loose stones) enclosed in mesh cages to protect it from erosion from the waves created by the many cruise ships that make their way up the river with tourists.   This, along with the floating jetties at which they embark and disembark, meant that it was not easy to get access to the river; however, I eventually found a small slipway close to the point where a small tributary joins.  There were a few loose stones with a green film in shallow water that I could just reach, plus some algal mats coating the concrete of the slipway at water level.   I managed to get small samples of each to bring back for closer examination, attracting the usual curious stares from passers-by in the process.

The mats on the slipway were composed of an alga (technically, a cyanobacterium) that has featured in this blog on several occasions in the past: Phormidium autumnale (see “In which the spirit of Jeremy Clarkson is evoked”).   This is the time of year when the Douro is at its lowest so living at this point on the slipway means that it spends a small part of the year exposed to the air, but most of it submerged.

Phormidium cf autumnale on a slipway beside the Rio Douro at Pinhão, September 2018.  The left hand image shows the mats on the lower part of the slipway; the right hand image shows individual filaments.  Scale bar: 20 micrometres (= 1/50th of a millimetre).

The stones beside the slipway had a thick greenish film which, when I looked at it under a microscope, turned out to consist largely of bundles of thin cyanobacterial filaments belonging to a relative of Phormidium: Homoeothrix janthina (kindly identified for me by Brian Whitton).   Homoeothrix differs from Phormidium in that the filament are often slightly tapered, rather than straight-sided and usually aggregated into colonies, often growing vertically towards the light rather than intertwined to form mats.   It is a genus that I see in the UK (including, sometimes, in the River Wear) but which I have not previously written about on this blog.   The photos below show tufts of filaments but it would be quite easy to imagine several of these clumps joined together to form a hemispherical colony, before I disrupted them with my vigorous sampling technique.

Left: the rip rap at the edge of the Douro at Pinhão from which I sampled algae in September 2018; right: the stone after vigorous brushing with a toothbrush.

Bundles of filaments of Homoethrix janthina from the River Douro at Pinhão. Scale bar: 20 micrometres (= 1/50th of a millimetre).

Many of my posts try to make the link between the algae that I find in lakes and rivers and physical and human factors in those water bodies and their surroundings.  That is not an easy task in a large river basin such as that of the Douro as there is so much more of a hinterland including large towns in Spain such as Valladolid.   The river, to some extent, integrates all of these influences and, whereas the vines around Pinhão have their roots in nutrient-poor granite and schist soils, the river’s journey to this point has covered a range of different rock types, including chalky clay soils in the Spanish part of the catchment and the water reflect this.   This cocktail of physical alteration and pollution, shaken up with a dash of international relations, recurs in the largest rivers throughout Europe and is either a fascinating challenge for an ecologist or a complete pain in the backside, depending on your point of view.

I’ll come back to the Douro in a few weeks, once I’ve had a chance to have a closer look at the diatoms.  Meanwhile, I have one more stop on my travels along the Rio Douro, at the port lodges of Vila Nova de Gaia to try some vintage port …

Reference

Bordalo, A.A., Teixeira, R. & Wiebe, W.J. (2006).  A water quality index applied to an international shared river basin: the case of the Douro River.  Environmental Management 38: 910-920.

The end of the journey: port maturing in barrels at Cockburn’s lodge in Vila Nova de Gaia.

 

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.

More green algae from the River Wear

Having discussed some of the recent name changes in green algae in the previous post, I thought that I would continue this theme using some of the other taxa that I found in the samples I collected from the River Wear a couple of weeks ago.   The plate below shows some specimens that, 20 years ago, I would not have hesitated to call Scenedesmus, characterised by coenobia of either four cells or a multiple of four cells arranged in a row.   Over 200 species, and 1200 varieties and forms have been recognised although there were also concerns that many of these so-called “species” were, in fact, variants induced by environmental conditions.  A further problem is that Scenedesmus and relatives do not have any means of sexual reproduction.  This means that any mutation that occurs and which does not have strong negative effects on the organism will be propagated rather than lost through genetic processes.  Working out what differences are really meaningful is always a challenge, especially when dealing with such tiny organisms.

Scenedesmus and Desmodemus species from the River Wear, Wolsingham, September 2018.  a. and b. Scenedesmus cf ellipticus; c. Desmodesmus communis.   Scale bar: 20 micrometres (= 1/50th of a millimetre).

The onset of the molecular era shed some new light onto these problems but, in the process, recognised differences within the genus itself that necessitated it being split into three, two of which are on the plate below.  Scenedesmus, in this modern sense, has cells with obtuse (rounded) apices and mucilage surrounding the cells whilst Desmodesmus has distinct spines at the apices of marginal cells and, sometimes, shorter ones elsewhere too.   In addition to these there is Acutodesmus, which is similar to Scenedesmus (i.e. without spines) but whose cells have more pointed (“acute”) ends and which does not have any surrounding mucilage.   A further genus, Pectinodesmus, has been split away from Acutodesmus on the basis of molecular studies, although there do not seem to be any features obvious under the light microscope which can differentiate these.

The genera Ankistrodesmus and Monoraphidium present a similar situation.  In the past, these long needle- or spindle-shaped cells would all have been considered to be Ankistrodesmus.   Some formed small bundles whilst others grew singly and this, along with a difference in their reproductive behaviour, was regarded as reason enough for splitting them into two separate genera.   Both were present in the Wear this summer, but only Monoraphidium presented itself to me in a manner that could be photographed.  Two species are shown in the plate below.   Recent molecular studies seem to not just support this division but also suggest that each of these could, potentially, be divided into two new genera, so we’ll have to watch out for yet more changes to come.

Monoraphidium species from the River Wear, Wolsingham, September 2018.  a. and b.: M. griffthii; c. M. arcuatum.  Scale bar: 20 micrometres (= 1/50th of a millimetre).

The final illustration that I managed to obtain is of another common coenobium-forming alga, Coelastrum microporum.   Though the three-dimensional form makes it a little harder to see, cell numbers, as for Pediastrum, Scenedesmus and Desmodesmus, are multiples of four.  I apologise if the picture is slightly out of focus, but it is a struggle to use high magnification optics on samples such as these.  The oil that sits between the lens and the coverslip conveys the slight pressure from fine focus adjustments directly to the sample, meaning that the cells move every time I try to get a crisper view.  That means it is impossible to use my usual “stacking” software.   The answer is to use an inverted microscope so that the lens was beneath the sample.  However, I do this type of work so rarely that the investment would not be worthwhile.

That’s enough for now.   I’m off on holiday for a couple of weeks, so the next post may be from Portugal and perhaps I will also find time to sample the River Duoro as well as the products of the vineyards in it’s catchment…

Coelastrum microporum from the River Wear,Wolsingam, Septmber 2018.  Scale bar: 20 micrometres (= 1/50th of a millimetre).

References

An, S.S., Friedl, T. & Hegewald, E. (2008).  Phylogenetic relationships of Scenedesmus and Scenedesmus-like coccoid green algae as inferred from ITS-2 rDNA sequence comparisons.   Plant Biology 1: 418-428.

Hegewald, E., Wolf, M., Keller, A., Friedl, T. & Krienitz, T. (2010).  ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus.   Phycologia 49: 325-355.

Krienitz, L. & Bock, C. (2012).  Present state of the systematics of planktonic coccoid green algae of inland waters.   Hydrobiologia 698: 295-326.

Krienitz, L., Bock, C., Nozaki, H. & Wolf, M. (2011).   SSU rRNA gene phylogeny of morphospecies affiliated to the bioassay alga “Selanastrum capricornutum” recovered the polyphyletic origin of crescent-shaped Chlorophyta.  Journal of Phycology 47: 880-893.

Trainor, F.R. & Egan, P.F. (1991).  Discovering the various ecomorphs of Scenedesmus: the end of a taxonomic era.   Archiv für Protistenkunde 139: 125-132.

Keeping the cogs turning …

A few algae lift my soul when I see them under the microscope through their beauty.   To see such intricate yet symmetrical organisation in something too small to be visible with the naked eye never ceases to amaze and delight me.   One of the genera that has that effect is the green alga Pediastrum, which forms cog-like colonies: flat plates of cells whose outer members bear horn-like projections.   One of its representatives, Pediastrum boryanum, was common in the River Wear when I visited recently (see previous post).   You can see, from the illustration above (the scale bar is 20 micrometres – 1/50th of a millimetre – long), the characteristic disc-like arrangement of cells, always in multiples of four (there are 16 in the colony above).   There are many species of Pediastrum, differing in the shape of both the inner and marginal cells, and the number and length of the horns.

I have found Pediastrum on many occasions in the Wear in the past, but never quite as abundant as it was in my most recent samples.  Pediastrum boryanum is the species I find most often, here and elsewhere, but other species occur too.  I have also found Pediastrum in some unusual places, including deep in lake sediments when I was searching for fossil pollen grains and there is evidence that the cell walls of Pediastrum contain both silica and a sporopollenin-like material (sporopollenin is the extremely tough material found in the outer walls of pollen grains (which probably explains why it had survived the fierce mix of chemicals that we used to prepare the lake sediments for pollen analysis).   I am guessing that the sporopollenin and silica both add some structural integrity to the cells.   There are references in the literature to Pediastrum being planktonic but I often find it in samples from submerged surfaces and associated with submerged macrophytes, so I suspect that it is one of those species that moves between different types of habitat.  It should not really be a surprise that a relatively large colonial alga with a payload of silica and sporopollenin in addition to the usual cellulose cell wall, is going to be common in benthic films in a river towards the end of a long, dry summer.

Pediastrum is another genus that has been shaken up in recent years as a result of molecular studies.  According to these, Pediastrum boryanum should now be called Pseudopediastrum boryanum although the Freshwater Algal Flora of the British Isles continues to use the old name.   Not everyone agrees with this split (see McManus and Lewis’ paper in the list below) but the divisions suggested by molecular data do also seem to match differences in morphological characteristics of the group (see Table below).

Pediastrum is part of the family Hydrodictyaceae and, as I was writing this, it occurred to me that I have never written about another interesting member of this family, Hydrodictyon reticulatum.  As I like to accompany my posts with my own photographs, I spent part of yesterday afternoon tramping around a location where I have found Hydrodictyon in the past.   All I got for my troubles, however, was two damp feet, so that post will have to wait for another day.

 

Differentiating characteristics of Pediastrum and similar genera (after Krienitz & Bock, 2011).

Genus Features
Pediastrum Flat coenobia with intercellular spaces, marginal cells with two lobes
Lacunastrum Flat coenobia with large intercellular spaces, marginal cells with two lobes
Monactinus Flat coenobia with large intercellular spaces, marginal cells with one lobes
Parapediastrum Flat coenobia with intercellular spaces, marginal cells with two lobes, each divided into two projections
Pseudopediastrum Flat coenobia without intercellular spaces, marginal cells with two lobes, each with a single projection
Sorastrum Three-dimensional coenobia, each cell with two or four projections.
Stauridium Flat coenobia without intercellular spaces, marginal cells “trapezoid”* with deep incision to create two lobes, each with a concave surface, though the lobes are not really extended into “projections”

* not all of the illustrations show marginal cells that are strictly “trapezoid” (e.g. with at least one pair of parallel sides).

References

Buchheim, M., Buchheim, J., Carlson, T., Braband, A., Hepperle, D., Krienitz, L., Wolf, M. & Hegewald, E. (2005).  Phylogeny of the Hydrodictyaceae (Chlorophyceae): inferences from rDNA data.  Journal of Phycology 41: 1039-104.

Good, B.H. & Chapman, R.L. (1978).  The ultrastructure of Phycopeltis (Chroolepidaceae: Chlorophyta). I. Sporopollenin in the cell walls.  American Journal of Botany 65: 27-33.

Jena, M., Bock, C., Behera, C., Adhikary, S.P. & Krienitz, L. (2014).  Strain survey on three continents confirms the polyphyly of the genus Pediastrum (Hydrodictyaceae, Chlorophyceae).  Fottea, Olomouc 14: 63-76.

Krienitz, L. & Bock, C. (2012).  Present state of the systematics of planktonic coccoid green algae of inland waters.   Hydrobiologia 698: 295-326.

McManus, H.A. & Lewis, L.A. (2011).  Molecular phylogenetic relationships in the freshwater family Hydrodictyaceae (Sphaaeropleales, Chlorophyceae), with an emphasis on Pediastrum duplex.   Journal of Phycology 47: 152-163.

Millington, W.F. & Gawlik, S.R. (1967).  Silica in the wall of PediastrumNature (London) 216: 68.