Synchronicity in Samarkand …

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I had intended my next post to continue the story of inorganic carbon in freshwater but a holiday has intervened. However, as is often the way with my travel, I have found some unexpected associations with my professional life.

I had wanted to show, using a graph, how much influence inorganic carbon supply (which freshwater biologists refer to, confusingly, as “alkalinity”) had on the types of diatom that are found in rivers. But the simple act of plotting a graph with Excel had, I realised, some unexpected resonances with my current location in Central Asia. I am in Samarkand, in Uzbekistan, a city with a very long history and which numbers Omar Khayyam (1048 – 1141) amongst its previous inhabitants. Omar Khayyam is best known in the West as a poet but was also a noted mathematician and astronomer. Khiva, another ancient city in Uzbekistan, was the birthplace of Muhammad ibn Musa al-Khwarizmi (c.780 – 850) regarded as one of the founders of algebra. Both, in other words, laid the groundwork for the equation y = mx + c, the equation for a straight line that allows me to express the relationship between the diatom assemblage and alkalinity in quantitative terms.

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The relationship between the Trophic Diatom Index and alkalinity in a dataset drawn from UK rivers. More about this will follow in a future post but, for now, it is presented as an example of how biological data often fit y = mx + c, the equation for a straight line (indicated by the red line on the graph)

The point of algebra is that you can work out general principles that apply to a situation regardless of the quantities involved. An equation is simply a means of replacing these quantities with letters or symbols so that you can work out the value of something that you don’t know in terms of things that you do know. One of these ancient mathematicians – we don’t know who, but I am giving Uzbekistan the benefit of the doubt – decided to use the Arabic word “shay” (which means “thing”) to represent the unknown in his equations. When the early algebraic treatises were translated to Spanish in medieval times, “shay” became “xay”, which eventually was shortened to “x”. That, at least, is the legend, and no-one seems to have a better explanation. Whenever we use “x” in an equation, in other words, we should reflect that we are part of a tradition that extends back over 1000 years to the plains of Central Asia.

The straight line equation, however, bucks this neat theory to some extent as, in this realm of algebra, “x” represents the known rather than the unknown entity. The unknown, by convention, is indicated by “y”. “Why “y”?” you might ask and, I am afraid, I cannot help. It may be that there is no sensible explanation (“quarks” are, after all, named after a nonsense word in Finnigan’s Wake) but the etymology of “x” is, you have to admit, too good to waste. Especially when writing from Samarkand.

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Timurlane’s tomb (Gur-i-Amir) in Samarkand. The photograph at the top of the post shows part of the Registan madrasah complex.

And, finally, I could not resist including this image of decoration on the Sher Dor Madrassa at the Registan: evidence that Medieval Islamic scholars knew about centric diatoms?

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Concentrating on carbon …

On the other side of Ennerdale Water I could see plenty more submerged stones, all covered with green filaments but these belonged to different genera to those that I wrote about in my previous post.   Both are genera that we have met previously – Mougeotia, which has flat, plate-like chloroplasts which rotate around a central axis in order to control its rate of photosynthesis – and Spirogyra.  When light levels are low, Mougeotia’s flat chloroplast is perpendicular to the light in order to capture as much energy as possible, but in bright light it rotates so that the plate is parallel to the direction of the light, in order to slow the photosynthesis mechanism down and prevent internal damage (see “Good vibrations under the Suffolk sun” for another approach to this problem).

However, too much sunlight is the least of an alga’s problems in the Lake District.   This post looks at a different challenge facing freshwater algae and our starting point is the spherical nodules, “pyrenoids”, that you should be able to see on the chloroplasts of both Mougeotia and Spirogyra in the images below.   Photosynthesis involves a reaction between water and carbon dioxide to make simple sugars (turning fizzy mineral water into “pop”, in other words).   A submerged alga does not have a problem obtaining the water it needs, but what about carbon dioxide?   Gases are not very soluble in water, so this presents a much bigger problem to the algae.   Explaining why also presents a big problem to a blogger who conscientiously avoided physics and chemistry from age 16 onwards.  Here goes …

Mougeotia from the littoral zone of Ennerdale Water, April 2017.  Scale bar: 20 micrometres (= 50th of a millimetre).

The concentration of a gas in a liquid depends upon the concentration of that gas in the surrounding atmosphere.   As far as we know (and this is still an area of contention amongst geologists), concentrations of carbon dioxide in the deep past were much higher than they are today, in part because there were no land plants to suck it out of the atmosphere for their own photosynthesis.  So the earliest photosynthetic bacteria and, subsequently, algae, lived in water that also had higher concentrations of carbon dioxide.   As land plants spread, so the carbon dioxide concentration in the atmosphere dropped as they used it to fuel their own growth.  As a result, carbon dioxide concentrations in the water also dropped, thus depriving the algae of an essential raw material for photosynthesis.

However, carbon dioxide is not the only source of carbon available to aquatic organisms.   There is also carbon in many rocks, limestone in particular, and this can mineralise to carbonate and bicarbonate ions dissolved in the water.  Aquatic plants can get hold of this alternative carbon supply via an enzyme called carbonic anhydrase.   By concentrating the carbonic anhydrase activity in a small area of the chloroplast, the algal cell can boost the activity of the Rubisco enzyme (which evolved to function at a higher concentration of carbon dioxide).   This whole process is one of a number of forms of “carbon concentrating mechanism” that plants use to turbocharge their photosynthetic engines (see “CAM, CAM, CAM …” on my wife’s blog for more about a terrestrial version of this).

A two-chloroplast form of Spirogyra from the littoral zone of Ennerdale Water, April 2017.  Scale bar: 20 micrometres (= 50th of a millimetre).

Pyrenoids are widespread amongst algae, though a few groups (notably red algae and most chrysophytes) lack them.   Cyanobacteria (blue-green algae) use an organelle called a “carboxysome” for a similar purpose.   The only group of land plants with pyrenoids are the hornworts, relatives of mosses and liverworts.   About half of all hornworts have pyrenoids and a recent study has suggested that the ability to form pyrenoids has evolved up to five times in this group during their evolution.   The appearance of pyrenoids in distinct evolutionary lineages of algae also suggests that there may have been several evolutionary events that precipitated their formation.  And, it is important to stress, some algae which lack pyrenoids have alternative methods of concentrating carbon to enhance Rubisco activity.

So let us end where we started: in the littoral zone of Ennerdale Water on an April morning, gazing at a fine “fur” of filamentous algae clinging to the submerged rocks.   Back in October last year, I talked about how Ennerdale fitted into a pattern of increasing productivity of Cumbrian lakes first noticed by Pearsall in the early part of the 20th century (see “The power of rock …”).   Now we can start to understand that pattern in terms of basic biochemical processes: getting enough carbon from a combination of atmospheric carbon dioxide and the surrounding rocks for Rubisco and the other photosynthetic enzymes to convert to sugars.   In Ennerdale Water, one of the least productive of the Cumbrian lakes, we can see these algae during the winter and spring because the amount of biomass that those biochemical reactions produces is still just ahead of the amount that grazing invertebrates such as midge larvae can remove.  In a month or so, the grazers will have caught up and the rock surfaces will be, to the naked eye at least, bare.

Rubisco is the enzyme whose gene, rbcL, we use for molecular barcoding, subject of many recent posts (see “When a picture is worth a thousand base pairs …”).  My early desire to avoid physics and chemistry at school translated into as little biochemistry as possible whilst an undergraduate and, over the past few-years, I’ve developed a frantic urge to catch-up on all that I missed.   Just wish that those lectures explaining the Calvin cycle had been a little less … tedious …

References

Giordano, M., Beardall, J. & Raven, J.A. (2005).  CO2 concentrating mechanisms in algae: mechanisms, environmental modulation, and evolution.   Annual Review of Plant Biology 56: 99-131.

Villareal, J.C. & Renner, S.S. (2012).  Hornwort pyrenoids, carbon-concentrating structures, evolved and were lost at least five times during the last 100 million years.  Proceedings of the National Academy  of Science of the USA 109: 18873-18878.

 

Spring in Ennerdale …

My latest trip to Ennerdale Water, in the Lake District, has yielded its usual crop of spectacular views and intriguing questions (see “Reflections from Ennerdale’s far side”).   This time, my curiosity was piqued by lush growths of green algae at several locations around the lake shore.  The knee-jerk reaction to such growths is that they indicate nutrient enrichment but I am always sceptical of this explanation, as lush green growth are a common sight in spring (see “The intricate ecology of green slime …”) and these often disappear within a month or two of appearing.

Two points of interest: first, the lake seems to be lagging behind the River Ehen, which flows out of Ennerdale Water.   We often see these lush growths of algae on the river bed in winter but by this time of year the mass of algae there is lower than we saw in the lake littoral.   Second, the lake bed looks far worse (see photograph below, from the north-west corner of the lake) than the actual biomass suggests.

Filamentous algae (Ulothrix aequalis) smothering cobble-sized stones in the littoral zone of Ennerdale Water, April 2017.

Under the microscope, this revealed itself to be unbranched filaments of a green algae, whose cells each contained a single band-shaped chloroplast lapping around most of the perimeter.   This is Ulothrix aequalis, a relative of Ulothrix zonata, which I wrote about a few times last year (see link above).   Like U. zonata, this species is very slimy to the touch and, I suspect, the payload of mucilage adds to the buoyancy of the organism and means that we look down on a fine mesh of filaments which trap light and add to the unsightly appearance of the lake bed at this point.   That this part of the lake shore is close to a tributary stream draining some improved pasture triggers some suspicions of agricultural run-off fuelling the algal growths but, looking back at my notebook, I see that the lake bed was almost clear of green algae when we visited this location in July last year.  I suspect that a return visit this summer would also show a clean river bed.  Appearances can often be misleading (see “The camera never lies?”).

Ulothrix aequalis from the littoral zone of Ennerdale Water, April 2017.   Scale bar: 10 micrometres (= 1/100th of a millimetre).

This was not the only site that we visited that had conspicuous growths of green algae, though the mass of algae was greatest here.   All of the sites at the western end had these growths (see “A lake of two halves” for an explanation of geological differences within the lake) but, curiously, the genus of alga that we found differed from site to site.   In addition to Ulothrix aequalis in this corner of the lake, we found Mougeotia on the south side and Spirogyra close to the outfall.  This diversity of forms is, itself, intriguing, and I have never read a convincing explanation of what environmental conditions favours each of these genera.   I see both spatial and temporal patterns of green algae in the River Ehen too and, again, there is no satisfactory explanation for why the species I find can differ along short distances of the river and between monthly visits.

The Mougeotia and Spirogyra both have another story to tell, but that will have to wait for the next post …

This other Eden …

As I have written a lot over the past year about the positive effects of the EU on UK’s environment, I cannot let last week’s triggering of Article 50 – the formal start of the “Brexit” process – go without a mention.    This time last year I was on the Great Wall of China, reflecting on borders and migration (see “Reflections from the Great Wall”).   As Theresa May’s letter was delivered to Donald Tusk I was, by coincidence, reading another book about boundaries, Rory Stewart’s The Marches.  In this book he describes his travels around the borderlands between Scotland and England, but which also draws upon his own travels and experiences in Iraq, Afghanistan and other parts of central Asia.

A point that he makes more than once in his book is that borders are, in many cases, artificial boundaries which, over time, create the differences that distinguish two cultures.   Scotland and England are, in his view, good examples: neither Hadrian’s Wall nor the present national border were placed with any regard for the identities of the people on either side.  The only natural cultural boundary, in his view, was that between the highland and lowland Scots, roughly coincident with the Highland Boundary Fault.   In the far past, lowland Scottish culture merged seamlessly into northern English culture as you travelled south until, in Medieval times, a more formal border was established.  From that point on, individuals on either side of the border looked north or south respectively and, gradually, over time, distinct “Scottish” and “English” identities emerged.   Those who inhabit the borderlands become, in turn, pawns that distant political powers used to strengthen their hold on the land and, in turn, destabilise those on the other side.

Being an island, of course, accentuates differences between Britain and the rest of Europe but we only have to look at the differences within this island to recognise the artificiality of this British nationalism.   And those stirring speeches that Shakespeare put into the mouth of Henry V?   The real events behind those plays was part of a military campaign by the English monarchy to assert their rights over French territory.   The Plantagenet kings would have been bemused by the idea of the English Channel representing anything more than a natural obstacle that separated two parts of a single polity.   The national identities to which Farage, Johnson and Nicola Sturgeon all appeal are, in other words, relatively recent inventions.

The point of this little essay is to remind ourselves that national identities are far more fluid than the diatribes of our populist politicians are prepared to admit.   And this national identity will continue to evolve in the future.   Nationalism led Europe to some very dark places in the twentieth century and the impetus for the original European experiment was a desire to learn from lessons of the past in order that they should never be repeated.   I do believe that, whatever we think about the bureaucratic Juggernaut that the European Commission has become, the result is a Europe which is slowly transcending historic boundaries.

So what is this post doing in a blog that is supposed to be about natural history and ecology of freshwaters?   If ecology is all about how organisms interact with their environment then we need to pull back the focus from the stream or lake to encompass the actions of humans under that broad heading of “environment”.  And we cannot consider the direct actions of humans – their immediate impacts on our freshwaters – without also considering the cultural and political spheres which regulate those activities.   The UK’s withdrawal from the EU might not seem to be of great relevance to the world of algae which preoccupies most of my posts.  Yet again, by reshaping the laws and regulations that determine how we interact with our environment, our withdrawal is of enormous relevance to every body of fresh water in the land.

Normal business will be resumed next time.

*This royal throne of kings, this sceptred isle,
This earth of majesty, this seat of Mars,
This other Eden, demi-paradise,
This fortress built by Nature for herself
Against infection and the hand of war,
This happy breed of men, this little world,
This precious stone set in the silver sea,
Which serves it in the office of a wall
Or as a moat defensive to a house,
Against the envy of less happier lands,–
This blessed plot, this earth, this realm, this England.
William Shakespeare, King Richard II, Act 2, Scene 1

The photograph shows Crag Lough from Hadrian’s Wall, near Housesteads, photographed in April 2014.

What’s a pretty diatom like you doing in a place like this?

Whilst looking at some samples from an experiment conducted on mesocosms beside a chalk stream, Candover Brook in Hampshire for Mark Ledger and colleagues, I came across a diatom that I had not seen before and which, at first glance, was out of place.   As the images above show, it is a diatom whose cells join together to form chains which, in turn, means that they typically present their sides to the viewer rather than the valve face, which is the way that the writers of identification guides generally assume that we can see. It took some time to track down a couple of cells that were lying face-upwards so that I could try to name the species and some of the few that were lying this way were damaged (see left hand image), perhaps itself a consequence of the naturally strong links between the cells.

Naming the genus was relatively straightforward: the valve shape, fine striae and very narrow axial area (the gap along the median line of the valve face between the two rows of striae) coupled with the tendency to form chains all pointed to Fragilariforma.   However, most of the Fragilariforma that  I encounter are in soft water, often acid habitats whilst this sample was from a flume beside a chalk stream in southern England.   After scratching my head a little more, and sending images to my friend Lydia in Germany, I eventually decided that Fragilariforma nitzschioides was the most likely name for this diatom.  Searching through my records, I found only one other record for this species: from the River Itchen (into which Candover Brook drains) in the mid-1990s.  That must be more than coincidence.   Interestingly, Hoffman et al. (2011) describe the species as “rare” and say that its ecological preferences are “difficult to define”.

The limited records that we have show that this species does not behave in the same way as most other representatives of the genus.   The weighted average of pH for the genus is 6.6 (see graph below), but there are plenty of records extending into more acid waters.  By contrast, the River Itchen population was recorded at pH 8.1 and the pH in Candover Brook will be very similar.   Most of the records for the genus came from relatively soft water, in contrast to the very hard water found in a chalk stream.  The scarcity of records of a species that is well described in the literature also suggests that this might be a genuinely rare diatom (see “A “red list” of endangered British diatoms”).

One other peculiarity of this species is the name itself.   Fragilariforma was one of a number of genera split away from Fragilaria by Dave Williams and Frank Round in 1986, originally as “Neofragilaria”.  Fragilaria nitzschoides, was not formally transferred at the time, presumably because the authors did not have access to the type material.  They presented good evidence for this new genus but a few people – notably Horst Lange-Bertalot – have continued to group these species under Fragilaria.   This is the situation in Diatomeen im Süsswasser-Benthos von Mitteleuropa but, curiously, for Fragilaria nitzschoides, he created the new combination of “Fragilariforma nitzschoides” purely as a synonym (see p. 268).   The good news is that the next version of this book (see “Tales of Hoffman”) does use these new names.

The relationship between Fragilariforma spp and pH (left) and alkalinity (right) in UK rivers, based on the mid-1990s dataset described in “The challenging ecology of a freshwater diatom”.  Vertical lines show the boundaries for high (blue), good (green), moderate (orange) and poor (red) status classes based on current UK standards and the arrows show the location of the River Itchen population of Fragilariforma nitzschoides along these gradients. 

References

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

Williams, D.M. & Round, F.R. (1987).  Revision of the genus Fragilaria.  Diatom Research 2: 267-288.

Williams, D.M. & Round, F.R. (1988).  Fragilariforma nom nov., a new generic name for Neofragilaria Williams & Round.  Diatom Research 3: 265-267.

Comparing comparisons …

Several of the speakers at the DNAqua-net meeting in Essen described work that, essentially, produced a molecular genetic-based “mirror” of current assessment procedures.  That is what we have done and it is a sensible first step because it helps us to understand how the data produced by Next Generation Sequencing (NGS) relate to our current understanding, based on traditional ecological methods.   The obvious way to make such a comparison is to generate both “old” and “new” indices from samples collected from a range of sites spread out along an environmental gradient, and then to look at the relationship between these.   A scatter plot gives you a good visual indication of the nature of the relationship whilst the correlation coefficient indicates its strength.  All well and good but consider the two plots below.   These are based on artificial data that I generated in such a way that both had a Pearson’s correlation coefficient of about 0.95, indicating a highly significant relationship between the two variables.   However, the two plots differ in one important respect: points on the left hand plot are scattered around the diagonal line (indicating slope = 1, i.e. both indices give the same outcome) whilst those on the right hand plot are mostly below this line.

The work that we have done over the past ten years or so means that we are fairly confident that we understand the performance of our traditional indices and, more importantly, that we can relate these to the concepts of ecological status as set out in the Water Framework Directive.   This means that we need to be able to translate these concepts across to any new indices that might replace our existing approaches and the right hand plot indicates one potential problem: at high values, in particular, the new method consistently under-estimates condition compared with the old method.   Note, however, that this has not been picked up by the correlation coefficient, which is the same for both comparisons and, in this post, I want to suggest a better way of comparing two indices.

I made some comparisons of this nature in a paper that I wrote a few years ago and one of the peer reviewers suggested that, rather than use a correlation coefficient I should, in fact, use Lin’s concordance correlation coefficient, which measures the relationship between two variables in terms of their deviation from a 1:1 ratio.  This is an approach widely used in pharmacology and epidemiology to ensure that drugs give equivalent performance to any that they might replace and there is, as a result, a command for performing this calculation within a library of statistical methods for epidemiologists written for R: epiR.   Having downloaded and installed this library, calculation is straightforward:

The standard Pearson’s correlation coefficient can be computed from a base function in R as:

> cor.test(x,y)

And then we load the epiR library:

> library (epiR)

before calculating Lin’s concordance correlation coefficient as:

> epi.ccc(x,y)

If we calculate this coefficient of concordance on the data used to generate each of the plots above we see that it is 0.95 for the left-hand plot (i.e. very similar to Pearson’s correlation coefficient) but only 0.74 for the right hand plot: quite a different result.

Having identified a deviation from a 1:1 relationship, discussion can spin off in several directions.   For the diatoms, for example, we are recognising that data produced by NGS is fundamentally different to that produced by traditional methods and that the number of “reads” associated with a cell does not necessarily align with our traditional counting unit of the frustule (cell wall) or valve.   It is a product partly of cell size, partly of the number of chloroplasts and partly, I suspect, on a variety of environmental factors that we have not yet started to investigate.   The NGS data are not “wrong”, but they are different and using these data without cognisance of the problem might lead to an erroneous conclusion about the state of a site.   So we then have to think about how to rectify this problem, which might involve applying correction factors so that “traditional” indices can continue to be used or deriving new NGS-specific coefficients, which is the approach we have adopted in the UK.   Both approaches have pros and cons but that is a subject for another day …

References

Kelly, M.G. & Ector, L. (2012) Effect of streamlining taxa lists on diatom-based indices: implications for intercalibrating ecological status.  Hydrobiologia 695: 253-263.

Lin, L. I.-K., 1989. A concordance correlation coefficient to evaluate reproducibility. Biometrics 45: 255–268.

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