What does it all mean?

Just over a quarter of a century ago, my friend and colleague Steve Juggins and a group of other palaeoecologists came up with a clever way to relate the composition of diatom samples taken from different levels of a sediment core to the environmental conditions of the lake at the time that these diatoms were alive.   At the heart of this was a set of statistical tools called “transfer functions” and the use of these has proliferated over subsequent years, spilling from diatoms to many other groups of organisms and from palaeoecological studies to contemporary investigations of man’s impact on the environment.   So pervasive have these methods become that Steve returned to the subject a few years ago and critiqued the many misuses of the method that he was seeing in the literature.

The principle behind the use of transfer functions is that each species has a characteristic response to an environmental pressure gradient (in early studies this was pH) which could be portrayed as a unimodal (approximately bell-shaped curve).   The point along the gradient where a species is most abundant represents the “optimum” condition, the level of the pressure where the species thrives best.  The average of the optima of all organisms in a sample, Steve and colleagues showed, could be then used to estimate the value of the pressure.   This unlocked the door to quantitative reconstructions of changes in acidification of lakes in the UK and Scandinavia that, in turn, ultimately shaped environmental policy. It was one of the most impressive achievements of applied ecologists in the 20th century.

A diagrammatic representation of the principle behind transfer functions: each organism has a characteristic response to the predominant pressure (nutrient/organic pollution in this case).

Part of the reason for their success in building strong predictive models was, I suspect, that the pollutant that they were focussed upon had a direct effect on the physiology of the cells which, in turn, created strong selective pressures on the community.   Another reason was that palaeoecological samples condense all the habitat variation within a lake (plankton v benthic, seasonal differences etc) into a single assemblage.   This, then, begs the question of how well we should expect transfer functions to perform when applied to assemblages which represent much narrower windows of space and time, and when the pollutants of interest exert indirect rather than direct effects on the organisms.   Or, to recast that question another way, are some of the problems we encounter interpreting diatom indices from rivers another form of the misuse of transfer functions that Steve dissects in his review?

It is easy to believe that transfer functions do work when applied to contemporary diatom assemblages from rivers.   If you evaluate datasets you will almost certainly find that the “optima” for all the species do appear to be arranged along a continuum along the pressure gradient.  The question that we need to ask is whether this represents a causal relationship or is just a statistical artefact?  I touched on this issue in “What we expect is often what we get …” but, in that post, I was mostly interested in how samples react along a gradient, not the response of individual species.  I suspect that, given the importance of alkalinity in freshwater algal ecology (see “Ecology in the Hard Rock Café”), this must influence the distribution of optima along a nutrient gradient.   This will be compounded when sample sizes are small, as the likelihood is that the sample optimum will not correspond exactly to the “true” optimum for the species in question (a question Steve has also addressed in a more recent paper – see reference list below).  Finally, this is all embedded within a larger problem: that most of the work I have discussed here involves statistical inference from datasets compiled from samples collected from a range of sites in a region, but is intended to address changes in time rather than space (so-called “space-for-time substitution – see reference by Pickett below).   There has been relatively little testing of species preferences under controlled experimental conditions.

In practice, I suspect, the physiological response of benthic algae to nutrients is less complicated than our noisy graphs suggest.   I set out a version of this in “What we expect is often what we get …”.   That post dealt primarily with communities of microalgae; this is the same basic scheme (with some slight revisions) but posed in terms of the physiological response of the organisms.  It borrows from the habitat matrix conceptual model of Barry Biggs, Jan Stevenson and Rex Lowe (which, itself, builds on earlier work on terrestrial plants by Phil Grime and colleagues).

An alternative explanation for the response of benthic algae to nutrients and organic pollution.  a., b., c. and d. are explained in the text.

  1. Low nutrients / high oxygen concentrations – the “natural state” in most cases. Biggs et al. referred to species adapted to such conditions “stress-adapted” as they can cope in situations where nutrients are scarce. Associated with TDI scores 1 and 2.  Examples: Hannaea arcus, Achnanthidium minutissimum, Tabellaria flocculosa.
  2. high nutrients / no “secondary effects” of eutrophication – these are “competitive” species in Biggs et al.’s template and can thrive when there is anthropogenic enrichment of nutrients. Ideally, this group would consist of species that have a physiological adaptation that allows them to thrive when nutrients are plentiful though, in practice, our understanding is based mostly on inference from spatial patterns. The “window” where such species can thrive is wide, and will overlap with the two states described below, in many cases.  Associated with TDI scores 3 and 4.  Examples: Amphora pediculus, Rhoicosphenia abbreviata, Cocconeis pediculus.  Cladophora glomerata would be a good example of a non-diatom that belongs to this group.
  3. high nutrients plus “secondary effects” of eutrophication – this category extends the habitat template of Biggs et al. to include organisms whose are reacting to secondary effects  of nutrient enrichment (e.g. shade and low oxygen) rather than to the elevated nutrients per se and is, consequently, difficult to differentiate from a direct response to organic pollution. Associated with TDI scores 4 and 5. Examples include several species of Nitzschia as well as Mayamaea and Fistulifera, amongst others.   Importantly, this group may co-exist with representatives from group b. – perhaps inhabiting different zones of the biofilm that typically blend together when a sample is taken.
  4. high nutrients / very low oxygen – a final category that represents extreme situations when an ability to cope with reducing conditions is beneficial, and where diatoms that are facultative heterotrophs may thrive. Associated with TDI score 5. Heterotrophic fungal and bacterial growths (“sewage fungus”) may also be abundant.  Once again, there is likely to be some overlap between this and other groups.   Technically, this group is more likely to be associated with serious organic pollution than with nutrients; however, it will be found at sites where nutrient concentrations are high and it is possible that an association with nutrients may be inferred from spatial patterns.

We are left, in other words, with a choice between deriving optima along a continuous scale based on inferences from spatial patterns within which we know that there are significant confounding variables or dividing species into a few physiologically-defined categories for which there is not very much experimental underpinning.   Neither is ideal, and some of our recent analyses suggest that, in terms of model strength, there is little to choose between them.   The former, in my view, suggests an artificially high level of precision that is unrealistic, given the current state of knowledge.   The latter, on the other hand, links the data to a conceptual model rather than simply relying upon the numbers that squirt out at the far end of a statistical process.

That does not mean that such an approach might not be appropriate for some other groups of organisms.  The reason why I urge simplicity for diatoms is largely because of the scale of the habitats that we are sampling, in relation to the wider patterns of variability.  A continuous series of optima may be appropriate in some cases too.   Macrophytes surveys, for example, encompass all visible organisms found along a 100 m stretch.   These will have a range of life history and nutrient acquisition strategies: some of these will take up nutrients from the water, some from the sediments.  Different types of sediment will vary in the supply of phosphorus and nitrogen, and so on.   There will still be issues of confounding variables and risks of inferring from correlative rather than causal relationships, but perhaps the overall patchiness experienced over the survey length will create a more complex web of interactions between nutrients and community that justifies a continuous scale.

For diatoms, however, simplicity is probably the best choice.   In the absence of definitive evidence one way or the other we apply Occam’s Razor (“entities should not be multiplied unnecessarily”) and opt for the simpler of the two hypotheses pending evidence to the contrary.   This, in turn, may address a deeper issue: that of finding robust answers to complex problems (see “Unravelling causal thickets …”).   Inference from statistical models is only as good as the conceptual models that underpin those models and, I fear, we too often are so lost in the detail of the many confounding variables that we lose sight of our goals.  Being able to understand our observations in terms of ecological process is the first step to finding robust solutions to our problems.

References

Bennion, H., Juggins, S. & Anderson, N.J. (1996).  Predicting epilimnetic phosphorus concentrations using an improved diatom-based transfer function and its application to lake eutrophication management. Environmental Science & Technology 30: 2004-2007.

Biggs, B.J.F., Stevenson, R.J. & Lowe, R.L. (1991). A habitat matrix conceptual model for stream periphyton. Archiv für Hydrobiologie 143: 21-56.

Birks, H.J.B.,  Line, J.M., Juggins, S., Stevenson, A.C. & ter Braak, C.J.F.  (1990). Lake surface-water chemistry reconstructions from palaeolimnological data. Diatoms and pH reconstruction. Philosophical Transactions of the Royal Society of London Series B 327: 263-278.

Juggins, S. (2013).  Quantitative reconstructions in palaeolimnology: new paradigm or sick science?  Quaternary Science Reviews 64: 20-32.

Kelly, M.G., King, L. & Ní Chatháin, B. (2009).  The conceptual basis of ecological status assessments using diatoms.  Biology and Environment: Proceedings of the Royal Irish Academy 109B: 175-189.

Pickett, S.T.A. (1988).  Space-for-time substitution as an alternative to long-term studies.  Pp. 110-135.   In: Long-term Studies in Ecology: Approaches and Alternatives (edited by G.E.. Likens).  Springer-Verlag, New York.

Reavie, E.D. & Juggins, S. (2011).  Exploration of sample size and diatom-based indicator performance in three North American phosphorus training sets.  Aquatic Ecology 45: 529-538.

Back to the Himalayas …

It is always nice to tie up loose ends left in earlier posts, so I was pleased to find a recent paper that put a name on a diatom that I had illustrated, but not been able to name, during my examination of material from a high altitude lake in Ladakh (see “Diatoms from Pangong Tso”).   I had assumed that this was a species of Gomphonema; however, Pat Kociolek and colleagues have placed it in a completely new genus, Gomphosinica.

Following their paper, the diatom that was abundant in the littoral of Pangong Tso is most likely Gomphosinica lacustris and this would be the first record of the genus in India.  The type location for this species is Kalakule Lake in the Kunlum Mountains of Xianjiang Province, northwest China, some 800 km north of Ladakh, and on the other side of the Tibetan Plateau.   They describe their sample as “planktonic in the lake”, whereas the populations I described formed distinct growths in the littoral zone (see “Return to Pangong Tso”).  They also have recorded it from Sichuan province, in southwest China.   Pangong Tso actually marks the Indian-Chinese border, so it should not be a great surprise to have found it here.

Altogether, Pat Kociolek and colleagues found three new species of Gomphosinica in China, and transferred a previously-described species of Gomphonema found in Nepal to the genus.  However, they also found four species in Montana, in the USA, and made one further transfer of a Gomphoneis first described from the Great Lakes.  Bear in mind, too, that Gomphosinica species are distinctive, so it is unlikely that the absence of Gomphosinica in regions other than China and the USA is an oversight on the part of diatomists.  There is clearly more to learn about the biogeography of this genus.

Having said that Gomphosinica is distinctive, it is hard to say exactly how it differs from Gomphonema based on what we can see with the light microscope alone.  The distinctive features can only be seen with scanning electron microscope, and it would be interesting to get some molecular barcodes from members of this genus to see how these compare with those from Gomphonema and relatives.  This might also shed some light on the differences between the North American and Asian species.

The same journal part also contained a paper on diatoms from the Doon Valley, near Dehra Dun in Uttarakhand, which may shed some light on the diatoms that I found nearby in the Ganges at Rishikesh (see “Diatoms from a holy river”).   I named these using the identification literature that I had to hand (mostly from Europe) and included “Gomphonema pumilum” in my list.  This new paper suggests that there may be local species which look very similar, including G. juettnerii and G. doonensis.   My population does not fit the dimensions of either of these exactly, and my inclination would still be that at least the larger of the two specimens I illustrated is G. pumilum, but there is enough in this paper to remind me that trusting a European flora when studying the diatoms of Asia is dangerous.   Whether these diatoms actually fill different niches in their respective ecosystems, or whether they are just genetically-distinct forms of what is, basically, food for relatively unfussy invertebrate larvae on both continents is a question for another day.

Note: the photograph at the top of the post is an early-evening view of a river in the Outer Himalaya Zone in the vicinity of Dehra Dun.

Reference

Karthick, B., Nautiyal, R., Kociolek, J.P. & Ramachandra, T.V. (2015).  Two new species of Gomphonema (Bacillariophyceae) from Doon Valley, Uttarakhand, India.  Nova Hedwigia, Beiheft 144: 166-174.

Kociolek, J.P., You, Q-M., Wang, Q-X. and Liu, Q. (2015).  A consideration of some interesting freshwater gomphonemoid diatoms from North America and China, and the description of Gomphosinica gen. nov..  Nova Hedwigia, Beiheft 144: 175-198.

Lost in detail?

In my first post of 2017, I wrote “I fear, microscopic benthic algae may be ecology’s Sirens, sitting on submerged rocks and luring the unsuspecting into a world of taxonomic detail that is too rarely accompanied by profound ecological insight” (see “Not so bleak midwinter?”).   That was a post about Ennerdale Water and the River Ehen and I return to that same remote and beautiful part of north-west England to put some flesh onto the bones of that statement.

I chose a slide Ennerdale Water for the latest “ring test” which tests the competence of the analysts involved in routine ecological assessments using diatoms.   Everyone analyses the same slide and sends their results to me and I sort through and note areas of disagreement.   In this case, there was quite a lot of disagreement even amongst the experienced analysts but, as if to prove the point in my opening paragraph, this did had only a small effect on the conclusions that people reached on the quality of the ecosystem that the sample represented.

One of the areas of disagreement was a population of Brachysira that some described as Brachysira brebissonii whilst others suggested it was B. intermedia.   My inclination, following the illustrations in Hofmann et al’s Diatomeen im Süsswassser-Benthos von Mitteleuropa, was to call it B. intermedia as the illustrations of B. brebissonii show more broadly-rounded ends than were apparent in the Ennerdale population.  However, Bryan Kennedy, a member of our scheme, has been looking into the taxonomy of this genus as part of his PhD and directed me towards a paper by Bart van der Vijver, in which he had examined the type material for B. brebissonii (as “Navicula brebissonii Brébisson).  His illustrations show a population with more acute ends than Hofmann et al.’s illustrations.  Its shape is, in fact, much closer to that of the examples of B. intermedia that they illustrate.  Yet, we were all agreed, this taxonomic ambiguity had little effect on the interpretation that an ecologist would reach.  Most Brachysira species (with the curious exception of the type species, B. aponina) are associated with circumneutral to slightly acid water and low nutrients.   The species of the genus vary in their preference for alkalinity and hardness but, generally, indicate high quality conditions.

Another of the species present in the same sample was Frustulia crassinervia, which presents an interesting counterpoint to the situation I described for Brachysira brebissonii.   In this case, there was another possible candidate, Frustulia saxonica and, in fact, the rhombic-lanceolate outline of the Ennerdale Water population did suggest this species.  However, the clearly protracted ends and the size are more characteristic of F. crassinervia which was the name that the majority of experienced analysts opted for.   Once again, however, both species have similar ecological requirements: soft, often peaty water with low levels of enrichment.

Frustulia crassinervia from the south-east end of Ennerdale Water (circa NY 127 140), July 2016, scale bar: 10 micrometres (= 1/100th of a millimetre).  The top illustration shows Brachysira brebissonii from the same location.   Photographs by Lydia King.

The difference between the situation for Brachysira and Frustulia is that, in the case of Frustulia, the traditional morphological taxonomy is underpinned by molecular studies whereas, in the case of Brachysira, we only have morphological evidence on which to base names.   The interesting point is that the molecular studies of Frustulia suggest that there is no genetic difference between F. crassinervia and F. saxonica.   This alone does not mean that they are not separate species (they did not look at the whole genome), but it does suggest that more work is needed before we have a full understanding of the limits of the species in this genus.   A similar study on Brachysira (and, indeed, on any genus with a surfeit of recently described species separated purely on morphological criteria) might emphasise that differences in shape to which traditional taxonomists assign so much importance are real or it might not.   That would, at least, give people such as myself who use diatoms to gain a wider perspective of ecological health a better insight into where we really need to put in time and effort to discriminate between species.   In the post I mentioned at the start of this article I referred to the nineteenth century scientist Alexander von Humbolt and his concern that scientists got so bogged down in detail that they missed the big picture (“naturgemälde”). Some things never change …

Reference

Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011).  Diatomeen im Süßwasser-Benthos von Mitteleuropa.  A.R.G. Gantner Verlag K.G., Rugell.

Lange-Bertalot, H. & Moser, G. (1994).  Brachysira.  Monographie der Gattung.  Bibliotheca Diatomologica 29: 1-212.

Urbánková, P., Scharfen, V. & Kulichová, J. (2016).  Molecular and automated identification of the diatom genus Frustulia in northern Europe.  Diatom Research 31: 217-229.

Van der Vijver, B. (2014).  Analysis of the type material of Navicula brachysira Brébisson with the description of Brachysira sandrae, a new raphid diatom (Bacillariophyceae) from Iles Kerguelen (TAAF, sub-Antarctica, southern Indian Ocean).  Phytotaxa 184: 139-147.

Veselá, Urbánková, P.,Černá, K. & Neustupa, J. (2012). Ecological variation within traditional diatom morphospecies: diversity of Frustulia rhomboides sensu lato (Bacillariophyceae) in European freshwater habitats.  Phycologia 51: 552-561.

Note:

In an earlier post about diatoms from this location (see “Reflections from Ennerdale’s far side …”) I showed some images of live cells of Stenopterobia sigmatella but added a comment to say that there was a very similar species, S. densestriata, that I could not rule out on the basis of observations of live cells alone.   I now have had the opportunity to have a looked at cleaned material as well and can confirm that the population in Ennerdale Water is, indeed, S. sigmatella.  S. sigmatella has less than 24 striae in 10 micrometres whilst S. densestriata, as the name suggests, has more (> 26 / 10 micrometres).   S. densestriata is also shorter (< 110 micrometres) and narrows to more acutely-rounded ends.

We also found a few valve of S. delicatissima, the other member of the genus that has been recorded from the UK.

Stenopterobia spp. from Ennerdale Water, July 2016.  i.: part of a cleaned valve of S. sigmatella; j. S. delicatissima.   Scale bar: 10 micrometres (= 100th of a millimetre).  Photographs by Lydia King.

Ecology in the Hard Rock Café …

Before I was diverted by the delights of Bukhara and Samarkand, I was writing about the struggles that aquatic plants have to undergo in order to obtain the carbon that they need for photosynthesis (see “Concentrating on carbon …”).   In this post, I want to show the scale of the effect of inorganic carbon supply on the diatoms that we find in freshwaters.

My earlier post pointed out that aquatic plants have two possible sources of carbon to use for photosynthesis: dissolved carbon dioxide or bicarbonate.   The latter is derived, ultimately, from the rocks through which the water seeps before ending up in a stream or river.   Calcium carbonate, in turn, reacts with hydrogen ions in the water to form the bicarbonate that plants can use for photosynthesis.   A rock such as limestone, which is made of calcium carbonate, for example, provides a better supply than a hard siliceous rock such as granite.

Aquatic biologists use the term “alkalinity” to refer to the relative amounts of carbon dioxide, bicarbonate and carbonate in water.   This can confuse people as, in this context, “alkalinity” has little to do with the pH of the water itself and, indeed, water that is alkaline (i.e. has pH > 7) does not have to have a high alkalinity.   For now, just accept that low alkalinity water has little bicarbonate relative to dissolved carbon dioxide, whilst high alkalinity water has mostly bicarbonate and relatively little dissolved carbon dioxide.   In practice, alkalinity is a good indicator of the geology underlying the catchment from which a sample was collected, with low values associated regions of hard rocks (such as the Ordovician granites in Ennerdale’s catchment) and high values particularly associated with limestone and chalk.

I’ve spent a quarter of a century trying to understand how diatoms react to pollution and one of the surprising by-products of those studies is the realisation that alkalinity is just as important as pollution in determining the diatoms that are found at a site.   This is the case for most groups of freshwater organisms, but the scale of the effect on diatoms is particularly strong, as the graph below indicates.

Relationship between alkalinity and the average TDI at 430 UK river sites (r2 = 0.52).   The blue line shows a regression line fitted to the 10th percentile using the “quantreg” package in R. 

This graph shows a data from 430 UK sites where at least one TDI (Trophic Diatom Index) measurement was available, with alkalinity plotted on a logarithmic scale on the x axis and the TDI on the y axis.   There is a clear relationship between the two variables with about half of all the variation in the TDI accounted for by alkalinity (i.e. geology) alone, and this is manifest, in particular, by alkalinity setting a “floor” below which the TDI is unlikely to fall at any given alkalinity value (indicated by the blue line).  The red line, then, indicates the variation in TDI due to other factors, mostly human pressures such as eutrophication.

The blue line, in other words, indicates the best that the TDI is likely to be at any given alkalinity and if we were to look at samples which plot close to this line we will see quite marked differences in the diatoms as we moved from the low end towards the high.   When alkalinity is low, we will find Tabellaria flocculosa, some Brachysira species (e.g. B. neoexilis) and maybe a few Eunotia species too.  As alkalinity increases, so the diatom assemblage will be dominated by Achnanthidium minutissimum and relatives, but we will also see Hannaea arcus and Fragilaria gracilis, amongst other species.   We will see some Achnanthidium and Fragilaria species at low alkalinity, too, but either different to those at moderate to high alkalinity or in lower numbers.

There are several possible explanations for this but Brian Moss, in a classic paper from 1972, suggested that the availability of dissolved carbon dioxide was a major factor.  The “soft water” species, in other words, were better adapted to life without bicarbonate but were out-competed in moderate and hard water where the supply of bicarbonate was greater.   Very roughly, this switch from domination by free carbon dioxide users to bicarbonate users occurs at no more than 20 mg L-1 CaCO3.   There is more going on than just the supply of inorganic carbon: low alkalinity water is more likely to have low pH, which brings a separate set of challenges to aquatic organisms, and very high alkalinity water is often associated with productive agricultural areas.  This means that effects at both ends of the scale may be hard to separate completely from human pressures.  However, the broad story that emerges is that hard rock, in ecology as in music, is not to everyone’s taste.

Reference

Moss B. (1973).  The influence of environmental factors on the distribution of freshwater algae: an experimental study. II. The role of pH and the carbon-dioxide-bicarbonate system.  Journal of Ecology 61: 157-177.

Daniel and his den of diatoms …

After contemplating astronomy-without-optics at Ulug Beg’s observatory (see previous post) we walked ten minutes down the road to another of Samarkand’s sights, the mausoleum of Daniyar (the Old Testament prophet Daniel, also venerated by Muslims).  This was a much plainer structure than the polychromatic wonders we had seen elsewhere in the city and, no doubt as a result, fewer visitors.  Daniel’s sarcophagus runs the entire length of the building: the legend is that his severed leg has continued to grow, necessitating an eighteen metre tomb.  The presence of a group of pilgrims, praying with an Iman, reminded me that our word “holiday” is a concatenation of “holy day”, and that pilgrims were the original tourists, both in this part of the world and in Europe.

Our guidebook mentioned an ancient spring on the site, offering me my first opportunity to mix business and pleasure. Unfortunately, the spring was dry but, following the valley up a steep hillside, we reached a graveyard, beside which there was a water trough whose bottom, when I peered inside, was covered with dark brown circular patches, up to about half a centimetre across.  I had not really come prepared for diatom sampling but managed to commandeer an empty water bottle into which I scraped some of these colonies using a piece of plastic that I found lying on the ground nearby.   The water bottle was then stuffed into my rucksack as we continued our explorations, cutting across country towards another set of monuments that we could see on the horizon (Colin Thurbron describes the same journey in reverse in his excellent book The Lost Heart of Central Asia).   Once we were back at our hotel, I let the sample settle overnight, poured off the supernatant and then added an equal volume of local vodka to the remaining suspension.  As in India last year, this is the quickest and least hazardous way of keeping diatoms in reasonable condition when on the road (see “Diatoms from the Valley of Flowers”).

Left: the water trough near Daniyar’s mausoleum, Samerkand from which my diatom sample was collected and, right, the circular colonies of diatoms on the bottom of the water trough.  The largest of these colonies is about half a centimetre across.

Several freshwater diatoms form conspicuous colonies but what intrigued me about these particular growths was that the colonies were disc-shaped, reflecting horizontal growth with little vertical development.  Once back from my travels, I had a look under the microscope and was surprised to see that they were composed of almost-pure growths of either Achnanthidium minutissimum or a very close relative (my observations were on the vodka-preserved specimens and I have not yet had a chance to look at cleaned valves).   This is an extremely common constituent of biofilms all over the world but I have never seen it forming discrete colonies in this way.  I suspect that, given time, all of these colonies would merge to form a continuous biofilm and that, in a natural ecosystem (rather than a water trough), grazing by invertebrates would then control the biomass so that they formed a subaquatic and microscopic “turf”.   Maybe what I am seeing is the early stage of colonisation in a situation where there are, as yet, no grazers?   It is very hard to tell an ecological story from a single, brief visit to any habitat but that would be my opening gambit.

Microscopic views of Achnanthidium minutissimum colonies from the water trough near Daniyar’s mausoleum, Samarkand, April 2017.  The left hand image was taken at x100 magnification and shows a colony (or fragment) that is about 650 micrometres across.  The right hand image was taken at x1000 magnification.   Scale bar: 10 micrometres (= 1/100th of a millimetre).

Achnanthidium minutissimum was not the only familiar plant (in the broadest sense) that we saw on our travels.   The grazed grassland between Daniyar’s mausoleum and Bibi Khanym mosque, our next objective, contained several flowers familiar from home (see Heather’s blog) and our trip to the Tien’shan mountains a few days later revealed many more, including a steep-sided valley full of hawthorn bushes.   It is a good reminder that, however far from home we are, and however exotic our surroundings, we are still in the broad temperate belt around the Eurasian continent that allows a measure of biogeographical continuity across this area.  Some of the plants we saw in the wild in Uzbekistan are garden plants in north-west Europe (the tulip is a good example) but several others thrive in the wild in both places.

Botanising in the grassland between Daniyar’s mausoleum and Bibi Khanym mosque, Samerkand, April 2017.

Decoration on mausoleums at the Shar-i-Zinda complex in Samerkand, near the Bibi Khanym mosque and Daniyar’s mausoleum.  The photograph at the top of this post shows the exterior of Daniyar’s mausoleum.

Ecology’s Brave New World …

My travels have brought me to the kick-off conference of DNAqua-net at the University of Duisburg-Essen in Germany, to give a plenary talk on our progress towards using high throughput next generation sequencing (NGS) for ecological assessment.   I went into the meeting feeling rather nervous as I have never given a full length talk to an audience of molecular ecologists before but it was clear, even before I stood up, that we were in the almost unique position of having a working prototype that was under active consideration by our regulatory bodies.   Lots of the earlier speakers showed promising methods but few had reached the stage where adoption for nationwide implementation was a possibility.   There was, as a result, audible intake of breath as I mentioned, during my talk, that, from 2017, samples would no longer be analysed by light microscopy but only by NGS.

That, in turn, brought some earlier comments by Florian Leese, DNAqua-net chair, into sharp focus.  He had talked about managing the transition from “traditional” ecology to the Brave New World of molecular techniques; something that weighs heavily on my mind at the moment.   In fact, I said, in my own talk, that the structures and the values of the organisations that were implementing NGS were as important as the quality of the underlying science.   And this, in turn, raised another question: what is an ecologist?

If that sounds too easy, try this: is an ecologist more than just someone who collects ecological data?   I have put the question like this because one likely scenario for routine use of environmental DNA, once in routine use, is that sampling will be delegated to lowly technicians who will dispatch batches to large laboratories equipped with the latest technology for DNA extraction, amplification and sequencing on an enormous scale (see “Replaced by a robot?”) and the results will be fed into computer programs that generate the answer to the question that is being posed.

The irony, for me, is that the leitmotif of my consultancy since I started has been helping organisations apply ecological methods consistently across the whole country so that the results generate represent real differences in the state of the environment and not variations in the practice or competence of the ecologists who collected the data.  Over the past decade, I helped co-ordinate the European Commission’s intercalibration exercise, which extended the horizons of this endeavour to the extremities of the European Union.   The whole process of generating ecological information had to be broken down into steps, each has been taken apart and examined and put back together to, we hoped, produce a more effective outcome.  There was, nonetheless, ample opportunity for the ecologist to bring higher cognitive skills to the process, in sampling and surveying, species identification and, ultimately, in interpreting the data.

I often use the example of McDonalds as a model for what we are trying to achieve, simply because it is a brand with which everyone is familiar and we all know that their products will taste the same wherever we go (see “Simplicity is the ultimate sophistication …“).   I admire them for that because they have achieved what ecologists involved in applying EU legislation should desire most: a completely consistent approach to a task across a territory.   But that same consistency means that one is never tempted to pop into a McDonalds on the off chance that the chef has popped down to the market to buy some seasonal vegetables with which to whip up a particularly appetising relish.   If you want the cook to have used his or her higher cognitive abilities to enhance your dining experience you do not go to a McDonalds.

But that is where we could end up as we go down the road of NGS.  A reader of my post “A new diatom record from West Sussex” commented tartly that there would be no chance of that diatom being spotted once the Environment Agency replaced their observant band of diatom analysts by NGS and he was right.   Another mentioned that he had recently passed on a suspicion of a toxic pollution event to the local staff based on observations on the sample that were not captured by the metrics that are used to classify ecological status.  Again, those insights will not be possible in our Brave New World.

Suppose we were somehow able to run a Monte-Carlo permutation test on all the possible scenarios of where we might be in twenty years, in terms of the application of NGS to ecological assessment.  Some of those outcomes will correspond to Donald Baird’s vision of “Biomonitoring 2.0” but some will not and here, for the sake of playing Devil’s Advocate, is a worst-case scenario:

In an effort to reduce costs, a hypothetical environmental regulator outsources eDNA sampling to a business service company such as Group 4 or Capita.   They batch the samples up and dispatch them to the high throughput laboratory that provides the lowest quote.   The sequencing results are uploaded straight to the Cloud and processed according to an automated “weight of evidence” template by data analysts working out of Shanghai, Beijing or Hyderabad before being passed back to staff in the UK.   At no point is a trained ecologist ever required to actually look at the river or stream.  I should stress that this “year zero” scenario will not come about because NGS is being used but because of how it is used (and a post in the near future will show how it is possible to use NGS to enhance our understanding of the UK’s biodiversity).   It brings us back to the question of the structure and values of the organisation.

What I would like to see is a system of ecological assessment that makes full use of the higher cognitive abilities of the biologists responsible for ecological assessment.  Until now a lot of a biologist’s skill goes into identifying organisms in order to make the list of species upon which assessments are based.  It should be possible to use the new genetic technologies to free ecologists to play a greater role in interpretation and decision-making.  However, that will not come about when they are being used in situations where there is an overwhelming desire to reduce costs.  One of the lessons that we need to learn, in other words, is that there is more to applying molecular ecology than simply developing the method itself.

Reference

Baird, D.J. & Hajibabaei, M. (2012). Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology 21: 2039-2044.Date

 

Reflections from Ennerdale’s Far Side …

ennerdale_far_end_170105

Ennerdale Water is, as I have described in earlier posts, is a lake of two halves, with a south eastern end influenced by granite and the north western end by softer mudstones and sandstones.  That has a big effect on the algae that we find in the littoral zone, with Cyanobacteria (blue-green algae) abundant in the south-east end and Chlorophyta (green algae) more conspicuous at the other end.   Diatoms are conspicuous in the littoral zone all around the lake, although there are some differences in the types of species encountered.  That is a story for another day, but I did find one species in some of the samples I collected from the south-eastern end that point to one other influence on the ecology of Ennerdale’s littoral zone.

Look at the photograph at the start of this post.  It was taken as I walked up to the south-eastern end (circa NY 127 140) and shows the view up the lake, with Angler’s Crag visible on the left hand shore in the distance.   The River Liza enters the lake on the right hand side (just out of the frame) and the low lying area between the River Liza and the raised ground where I was standing is an area of wet heath with a range of Sphagnum species and several boggy pools.   The shoreline of the lake itself is formed by a shingle spit which acts as a barrier between the wet heath and the lake itself.

ennerdale_gravel_bar_170105

The shingle spit separating the wet heath at the south-east end of Ennerdale from the lake itself.   Photographed in January 2017.

Several of the diatoms that I found at this end of the lake were species that I associate with acid conditions although, curiously, the limited chemical data that we have does not show a lower pH here than elsewhere in the lake.   I suspect that the proximity to the acid Sphagnum heath may lead to occasional pulses of acid water entering this area and exerting a subtle effect on the attached algae before being diluted by the water of the lake as a whole.   Of the species that I found, the most intriguing was Stenopterobia sigmatella, a long, sigmoid diatom with a single plate-like chloroplast.

The genus Stenopterobia fulfils most of my criteria for a genuinely rare diatom (see “A “red list” of endangered British diatoms”).   I only have 11 records in my dataset of 6500 samples, and in only one case did Stenopterobia constitute more than one percent of the diatoms in the sample.   These samples are all from acid habitats (mean pH: 6.1), with low nutrient concentrations (never more than 2 mg L-1 reactive phosphorus).  Those for which we have location information are plotted below.   The record in East Anglia needs further investigation (meaning: “I don’t believe it … but I haven’t had a chance to track down the slide for a closer look”). If we ignore this, the distribution is confined to mountainous regions of western Britain, and these Ennerdale samples also fit this trend, although the lake has soft water and is circumneutral rather than acid.

Stenopterobia sigmatella is another diatom with a sigmoid outline, and this brings me back to a question that I have posed before (see “Nitzschia and a friend …”): what advantages does a sigmoid outline confer on a diatom?  I cannot think of any other genera of algae that has species with a sigmoid outline, which only adds to the mystery. All of the diatoms that are sigmoid are motile, so I guess that the explanation may be linked to movement, but I don’t know for sure what the reason may be.   For all of the rich diversity that we see in diatoms, there is still, to pick up on a phrase from my biography of Humboldt, a “poverty of meaning” …

stenopterobia_sigmatella_en

Stenopterobia cf sigmatella from Ennerdale Water, October 2016 and January 2017.  Scale bar: 10 micrometres (= 1/100th of a millimetre).

stenopterobia_distribution_

A distribution map of records of Stenopterobia in Great Britain.   S. curvula is a synonym for S. sigmatella (see taxonomic note below).  Map prepared by Susannah Collings (see “Why do you look for the living among the dead?” for more details of how this was done)

stenopterobia_densestriata_

A valve of Stenopterobia densestriata.  Photograph from the ADIAC database (photographer: Micha Bayer).  Scale bar: 10 micrometres (= 1/100th of a millimetre).

Taxonomic note

I have used the name “Stenopterobia sigmatella” in this post, but this still needs confirmation as there is a closely-related species, S. densestriata (Hustedt) Krammer 1987 (see image above).  S. sigmatella has < 24 striae in 10 micrometres whilst S. densestriata has > 26 striae in 10 micrometres.  S. densestriata also has slightly smaller overall dimensions.

David Mann made the following comment about Stenopterobia sigmatella on the website Common Freshwater Diatoms of Britain and Ireland (predecessor to the new Diatom Flora of Britain and Ireland: “A nomenclatural mess. For most of the 20th century, this species was referred to (wrongly) as S. intermedia. Ross (in Hartley, 1986) stated that there is an earlier name, sigmatella, that could be applied to this species and made a new combination S. sigmatella. Unfortunately, this was wholly ignored by Krammer (in Lange-Bertalot & Krammer, 1987; and see Krammer & Lange-Bertalot, 1988) who made the new combination S. curvula. However, Nitzschia curvula of W. Smith is preceded by N. sigmatella of Gregory (1856, 1854, respectively).”   The references can all be found on the Common Freshwater Diatoms website.