Diatoms from a holy river …


Having written about the diatoms I found in the Ganges headwaters a week or so ago (see “Diatoms from the Valley of Flowers”) I now travel about 250 kilometres downstream, descending 3000 metres in the process, to the holy city of Rishikesh on the Ganges itself.   As in the Valley of Flowers, I had time and space for a single sample, and scrambled down to one of the many ghats, toothbrush in hand, to get a sample (and amuse the locals).  You can see a photograph of me collecting the sample at the end of “A cautionary tale”.  The ghat I chose was just under water at the time of collection, but the water level was fluctuating throughout our visit, so it might have been deeper at times, and probably fully exposed for periods too.  As we were in Rishikesh towards the end of the monsoon period, the chances are that it spent more time submerged than exposed in the weeks before our arrival, but I cannot be sure.

My sample comes from the flat surface of a concrete ghat, roughly at water level at the time I visited (the river was running across my feet as I sampled) but the biofilm on the surface of the ghat was so thin that I wondered if I had any algae at all in my bottle at the end of some ferocious brushing with my toothbrush.   The plate below gives an indication of the diversity of diatoms that, despite my forebodings, I found on the slide that I prepared.  Of these, Adlafia minuscula var. muralis was the most abundant organism and this, along with Nitzschia palea, which was also frequent, suggested that the water at Rishikesh was quite enriched.   Halamphora montana, which was also frequent, is a species that can thrive in intermittently wet conditions, consistent with its presence on a ghat that was not fully submerged.  In contrast to these, Gomphonema pumilum (which was also frequent) and Achnanthidium minutissimum (rare) are more often associated with cleaner water.


Diatoms from the River Ganges at Rishikesh, September 2016.  a.  c.: Gomphonema pumilum; d.: Navicula sp.; e. Adlafia minuscula var. muralis; f. Achnanthidium minutissimum; g. Cymbella sp.; h., i.: Halamphora montana; j. Cocconeis euglypta; k. Nitzschia cf inconspicua; l. Nitzschia palea.  Scale bar: 10 micrometres (= 100th of a millimetre).

As you can see from the photograph at the top of the post, and from images in earlier posts, Rishikesh sits just at the foot of the Himalayas, just at the point where the Ganges enters the Deccan Plateau.  Were I to turn around and photograph the view in the opposite direction, the landscape would be flat for as far as the eye can see.   There is, nonetheless, a substantial population in the Ganges valley upstream of Rishikesh, with several substantial towns, the largest being Srinagar, a city of 150,000 on the Alaknanda tributary.   Sewage treatment in these areas is rudimentary so a high organic loading would not be surprising.

The low numbers of algae is no great surprise.  I recall sampling streams in Nigeria during the wet season and finding very little: the high, scouring flows and turbid water both make conditions difficult for algae at times such as these.   The predominance of indicators of poor water quality may also be a consequence of the monsoon, as the heavy rains not just overload the limited sewerage systems, but also wash organic matter into the rivers from terrestrial sources.   There is some evidence that water quality is worse during this period than it is during either the pre- or post-monsoon period.

There is, however, a belief that the Ganges has peculiar powers of self-purification. I recall Eric Newby writing about this in his classic book Slowly Down The Ganges, and there does seem to be limited evidence that Ganges water has some novel anti-microbial capabilities.   I do, nonetheless, wonder at the health consequences of performing an immersive “puja” in such a polluted river.   The irony is that the term “pollution” actually has its origins in religion, relating the defilement of holy places by man, so the state of the holy Ganges may have the dubious honour of being truly polluted in both the original and modern senses of the word.


Nautiyal, C.S. (2009). Self-Purificatory Ganga Water Facilitates Death of Pathogenic Escherichia coli O157:H7.  Current Microbiology 58: 25-29.

Tareq, S.M., Rahamen, S.M., Rikta, S.Y., Nazrul Islam, S.M. & Sultana, M.S. (2013).  Seasonal variation in water quality in the Ganges and Brahmaputra River, Bangladesh.  Jahangirnagar University Environmental Bulletin 2: 71-82.

Miniature masterpiece …


I had an hour of spare time in Edinburgh last week, and dived into the Scottish National Gallery, conveniently positioned just five minutes from Waverley station.   There is plenty in the permanent collections to make this a worthwhile diversion but, today, and totally unexpectedly, I was in for a particular, treat, as Carel Fabritus’ The Goldfinch was on display, loaned from the Mauritshuis in The Hague.   It is a tiny picture – measuring just 33.5 by 23 cm – but it is a wonderful little canvas, depicting – as the name suggests –a lifesize goldfinch, one of the most regular visitors to our bird table here in Bowburn.

My interest in Dutch painting occasionally spills over into this blog (see “How to paint like Vermeer” and “A wet afternoon in Berlin”) and Fabritus plays a small but important role in the story of the Dutch Golden Age, being a pupil of Rembrandt but also, possibly, a mentor to Vermeer himself.  He provides the elusive link between these two great masters (though the link with Vermeer is only circumstantial).   He was killed at the young age of 32 just after this picture was painted, when a magazine of gunpowder exploded in the city of Delft where he lived.   Looking at the picture – which is, in effect, a trompe d’oeil – the similarities to Vermeer become apparent: the modest subject matter, the attention to detail and, in particular, the realistic treatment of light and shadow.  The tiny picture draws the viewer into its world and, in Edinburgh, it completely overshadows the much larger works that surround it including, ironically, one by Vermeer himself.

My last encounter with The Goldfinch was via the printed word: Donna Tartt uses an encounter with this picture (on loan to the Met in New York in her treatment) as a plot device in her novel The Goldfinch.   It thus joins Tracy Chevalier’s Girl With A Pearl Earring in the exclusive club of novels named after great Dutch paintings.  That has got me thinking … what other novels have Dutch paintings as their titles?  Send me your suggestions  …


A rare excursion behind a telephoto lens: a goldfinch photographed in our garden, May 2016.

Diatoms from the Valley of Flowers


My visit to the Valley of Flowers in India (see “Into the Valley of Flowers …”) is a fast fading memory but I have finally managed to get the diatom samples that I smuggled into my suitcase properly mounted and spent some time last weekend peering down my microscope and trying to match what I could see with the habitat that I remembered.

The sample I collected came from a first order stream which appeared from the mouth of a glacier a couple of hundred metres above us on the [north] side of the valley.  About 500 metres downstream it joined the Pushpanati River, a tributary of the Aleknanda, itself a tributary of the mighty Ganges.   It was just over a metre wide and a few centimetres deep and had a mixture of pebbles and gravel as its substratum.  Some of the larger stones were encrusted with what looked like growths of Chamaesiphon  (see “A bigger splash …“).  There were also a few flocs of green algae which turned out to be Zygnema, a relative of Mougeotia and Spirogyra ( see “Fifty shades of green …”) with two distinctive star-shaped chloroplasts.  They are not at their best in the photograph below because they made the journey from India to the UK soused in local vodka (a cheap and effective preservative for algae: your liver will not begrudge you this particular experience …).


Vinood, our guide, looking at the stream that I sampled in the Valley of Flowers, August 2016.


Vodka-soused Zygnema sp from a glacier-fed tributary stream of the Pushpanati River (Valley of Flowers),  August 2016.  Scale bar: 20 micrometres (= 1/50th of a millimetre).

The diatoms were a surprise as almost all belonged to a single species, Diatoma mesodon, a species familiar to me from very high quality streams in Europe.  Ninety-five percent of all the diatoms I looked at belonged to this species, an unusually high proportion compared with other samples that I have examined, especially as there are no human pressures in the area that might influence diversity.   The Diatoma cells formed zig-zag chains, though these fell apart during the preparation process and the images just show individual valves.   Other diatoms present in small numbers included Meridion circulare var. constrictum (syn: Meridion constrictum) and two species of Eunotia, all of which suggest relatively soft water.

The low diversity intrigued me.   I have seen very low diversity with headwater streams, possibly because there is low potential for organisms from upstream to “seed” the location.   As small tributaries merge, so incocula from the sparse assemblages of these headwater streams will combine to create more diverse communities downstream.  Curiously, a recent paper argues the opposite: that headwaters are, in fact, hotspots of microbial diversity, and that this declines with increasing distance downstream.   However, this study takes a much broader view than just algae.  The authors suggest that it the close connection between headwater streams and the surrounding catchment leads to soil bacteria being washed into the stream.   So this result does not really contradict my observation; rather it highlights the limited insight that one may glean through looking at a single group of organisms.

Had I had more time (and more samples containers), it would have been interesting to follow the valley as far upstream as possible, to see if the other streams flowing down from the hillside had similar assemblages of algae, or if their algae were different.   My guess is that the patchwork of habitats would mean that the total diversity for the valley (“beta diversity”) would be considerably greater than the diversity at any particular site (“alpha diversity”).   If anyone wants to test this hypothesis, then all they need to do is make a three day journey from Delhi, with an extra day set aside for acclimatisation, followed by a two day hike up to a height of 3500 m.  And don’t forget to pack that bottle of vodka …


Diatoma mesodon from a glacier-fed tributary stream of the Pushpanati River (Valley of Flowers), August 2016.   a. – e.: valve views; f. – g.: girdle views.  Scale bar: 10 micrometres (= 1/100th of a millimetre.


Other diatoms from a glacier-fed tributary stream of the Pushpanati River (Valley of Flowers),  August 2016,  a. – b.: valve and girdle views of Meridion circulare var. constrictum; c. Eunotia islandica; d. E. paratridentula; e. Cymbella cf naviculiformis.  Scale bar: 10 micrometres (= 1/100th of a millimetre).


Besemer, K., Singer, G., Quince, C., Bertuzzo, E., Sloan, W. & Battin, T.J. (2016).  Headwaters are critical reservoirs of microbial diversity for fluvial networks.  Proceedings of the Royal Society of London Series B 280: DOI: 10.1098/rspb.2013.1760

Remembrance in Berlin


This week’s trip to Berlin straddled the results of the US election and the anniversaries of Kristallnacht and the end of the Great War.  And my hotel was less than five minutes from Checkpoint Charlie.  The first reaction to news of the victory of a man who wanted to build a wall between the US and Mexico was to walk to a site where a divisive wall had been taken down within my own lifetime.   Were it not for the ghoulish tourist industry that has sprung up around Checkpoint Charlie, cashing-in on the wall’s notoriety, you would never know that Berlin had ever been a divided city.

If there is one grain of comfort to be gleaned from Donald Trump’s victory it was that it pushed Brexit down the agenda in dinner-time discussions with European colleagues, though the consensus was that both were manifestations of similar social phenomena.   And, many told me, nationalist and anti-EU parties are on the rise in other countries too.  Marianne Le Pen is using Brexit as a springboard to make her own overtures in France, and she is not the only one.   It would be highly ironic if one consequence of Brexit was that the ambition of those who have been arguing for “ever closer union” has to be tempered as a result of anti-EU sentiments encouraged by Brexit.   The other side of this argument is that the UK is generally seen as a voice of moderation within the EU and some fear the loss of our voice against the federalists.

A short walk on from Checkpoint Charlie brought me to the Jüdisches Museum, housed in a wonderful building by Daniel Libeskind (who also designed the 9/11 Memorial in New York: see “Reflecting absence”).   I visited this museum on my first visit to Berlin not long after it opened in 2001 and was impressed by the way that the building itself drew you in and subtly adjusted your mood to fit the ambience of the museum and its message.   The only comparable experience is a visit to one of Europe’s great Romanesque or Gothic cathedrals.   The message of the Jüdisches Museum is not pretty in a time when Trump and Farage are stoking up fears of the “other”: Jewish communities have lived their distinctive lives for well over a thousand years in Europe, often in peace alongside their Christian neighbours, but sometimes not.   The coincidence of the rise of nationalist movements with increased suspicion of Jewish communities is stark.   We need “them” in order to define “us” and the Jews have been the convenient foils for nationalists for time immemorial.   Perhaps Islam now takes that role in Europe?


I wonder, too, if the Jüdisches Museum is somehow symbolic of Germany’s determination to make a Europe that transcends old nationalistic prejudices and limits?  The Second World War feeds the UK’s national myth of a small proud independent nation, the “Few” battling against, and ultimately overcoming, forces of Evil.   Germans walking through the Jüdisches Museum and contemplating the history of the 20th century can only leave with the question “what must I do to ensure that this never happens again?”

Libeskind’s building is more than just a container for the museum’s exhibits: it also speaks directly to visitors.   He created “voids” into his design: empty spaces that extend vertically through the whole museum as a counterpoint to the exhibits themselves.    His intention was that these voids illustrated the absence of Jews from modern German society.   One of these contains an installation, Fallen Leaves, by Menashe Kadishman, an Israeli artist, who has filled the floor of the void with 10,000 faces punched out of steel to represent all the innocent victims of war and violence.   The eleventh hour of the eleventh month passed while I was in the museum but the atmosphere inside was such that there seemed no need to mark that moment.  The building, itself, more than compensates for two minutes of silence that, in UK, we mark at this time.


Menashe Kadishman, Fallen Leaves  / Shalekhet, Jüdisches Museum, Berlin.  

Lucky heather …


The interior of Shetland’s Mainland is rugged and remote and almost completely lacking basic tourist infrastructure such as footpaths that most hikers take for granted.  We located the approximate position of our destination on the skyline using our map then set off across heather-covered blanket bog, slithering down peat hags and across small streams until we reached our destination.  This was not a good time to find that I had left an important part of my sampling kit back in the car.

I searched every pocket of my cagoule and rucksack but I could not find my bag of toothbrushes.   These are the basic sampling tool of every diatomist, perfect for removing most algae growing on the surface of submerged stones.   Yet here I was, in one of the most remote corners of the country,  facing a beautiful small loch, but without any means of collecting a sample.   Jon, my co-worker on this trip, looked around us: “can’t you use a piece of heather?”

And so that is what I did: I pulled up a few shoots of heather, gripped them between two fingers and used these, toothbrush style, to clean the brown film off the surface of stones.   I picked out a few leaves and stems out of the final suspension and poured this into my sample bottle.   Problem solved.


Using a piece of heather (Calluna vulgaris) to sample diatoms from a loch in Shetland, October 2016.  The top photograph shows Lamba Water, Mainland (photographed above), during the same sampling trip.

Several of the stones that I picked up from the littoral zone of Lamba Water had slippery, gelatinous tufts which, when examined closely with the naked eye could be seen to be made of bead-like filaments which I recognised to be the red alga Batrachospermum (see “Algae … cunningly disguised as frog spawn”).    Under the microscope, the beaded appearance resolved into tufts of branches arising from a single main axis which, at low magnification, looked like a bottle brush.   Most of my previous encounters with this genus have been in hard water but Lamba Water has relatively soft water (alkalinity: 7 mg L-1 CaCO3; conductivity: 117 mS cm-1) and a slightly acid pH (6.4) due to the surrounding peat which stained the water a dark brown colour.   Browsing through my Flora, I did notice that many of the species listed do appear to have very broad ranges for conductivity that suggest a low sensitivity for rock type compared to other types of algae.   I would not like to make too much of this as the data in the Freshwater Algal Flora of the British Isles are relatively sparse, but it is something that would be interesting to pursue in the future.


A tuft of Batrachospermum on a submerged cobble in the littoral zone of Lamba Water, Shetland Isles, October 2016.  Scale bar: approximately 1 centimetre.


magnification; right hand image at 400x (scale bar: 20 micrometres (= 1/50th of a millimetre).

One of the characteristics of Shetland is a very diverse geology packed into a relatively small area and the following day’s excursions took us to a very different lake on the other side of Mainland.   This was Loch of Girlsta, much deeper than Lamba Water (it is the only loch on Shetland with a population of Arctic Charr, I understand) and influenced by a narrow band of limestone (although most of the catchment seems to be the standard Shetland blanket bog).   By this time, we were having to contend with rain as well as strong winds and our time on site was limited.  I did, however, have a chance to spot some dark brown hemispherical colonies, mostly 3-4 mm in diameter, on some of the submerged stones.  Although the hemispherical colonies first made me think of Rivularia, when I was back in warm and dry conditions and had a chance to look at it under my microscope, it turned out to be Tolypothrix, the cyanobacterium that we last encountered in Ennerdale Water (see “Tales from the splash zone”) which is, chemically, quite similar to Loch of Girlsta, though perhaps with less peat in the catchment.   Both are in catchments with so little human influence that algae need to resort to nitrogen fixation in order to obtain the nutrients that they need to grow.

As an illustration of the extraordinary geological and ecological diversity that we encountered in such a small area, Loch of Benston, the final loch that we visited, was almost entirely underlain by limestone, and had extensive Chara beds.


Colonies of Tolypothrix cf distorta (arrowed)) on rocks in the littoral zone of Loch of Girlsta, Mainland, Shetland Isles, October 2016. 


Microscopic view of a false branch of Tolypothrix cf distorta from Loch of Girlsta.  Scale bar: 10 micrometres (= 100th of a millimetre).

Back on the mainland (the British mainland, that is, rather than Shetland’s Mainland), it was the autumn colours that struck me, after a few days north of the treeline on Shetland.   The drive back south from Edinburgh took me through the wonderful array of brown, red and yellow hues of the Borders and Durham, itself, always looks spectacular at this time of year.   The diatom samples that I collected with those bunches of heather now need to be processed and, I’m sure, there will be more tales from the northern isles to tell once I’ve had a chance to look at these.


Autumn colours on the Durham riverbanks, October 2016.


Primed for the unexpected?

I was in Nottingham last week for a CIEEM conference entitled “Skills for the future” where I led a discussion on the potential and pitfalls of DNA barcoding for the applied ecologist.  It is a topic that I have visited in this blog several times (see, for example, “Glass half full or glass half empty?”).  My original title was to have been “Integrating metabarcoding and “streamcraft” for improved ecological assessment in freshwaters”; however, this was deemed by the CIEEM’s marketing staff to be insufficiently exciting so I was asked to come up with a better one.  I was mildly piqued by the implication that my intended analysis of how to blend the old with the new was not regarded as sufficiently interesting so sent back “Metabarcoding: will it cost me my job?” as a facetious alternative.  They loved it.

So all I had to do was find something to say that would justify the title.   Driving towards Nottingham it occurred to me that the last time I should have made this trip was to Phil Harding’s retirement party.  I was invited, but had a prior engagement.  I would have loved to have been there as I have known Phil for a long time.  And, as I drew close to my destination, it occurred to me that Phil’s career neatly encapsulated the development of freshwater ecological assessment in the UK over the past 40 years.  He finished his PhD with Brian Whitton (who was also my supervisor) in the late 1970s and went off to work for first North West Water Authority and then Severn Trent Water Authority.   When the water industry was privatised in 1989, he moved to the National Rivers Authority until that was absorbed into the Environment Agency in 1995.   Were he more ambitious he could have moved further into management, I am sure, but Phil was able to keep himself in a jobs that got him out into the field at least occasionally throughout his career.   That means he has experienced the many changes that have occurred the past few decades first hand.


Phil Harding: early days as a biologist with North West Water Authority in the late 70s

Phil had a fund of anecdotes about life as a freshwater biologist.  I remember one, in particular, about sampling invertebrates in a small stream in the Midlands as part of the regular surveys that biologists performed around their areas.   On this particular occasion he noticed that some of the invertebrate nymphs and larvae that he usually saw at this site were absent when he emptied out his pond net into a tray.   Curious to find out why, he waded upstream, kicking up samples periodically to locate the point at which these bugs reappeared in his net.   Once this had happened, he knew that he was upstream of the source of the problem and could focus on searching the surrounding land to find the cause.   On this occasion, he found a farmyard beside a tributary where there was a container full of pesticides that had leaked, poisoning the river downstream.

I recount this anecdote at intervals because it sums up the benefits of including biology within environmental monitoring programmes.   Chemistry is very useful, but samples are collected, typically, no more than once a month and, once in the laboratory, you find a chemical only if you set out to look for it and only if it was present in the river at the time that the sample was collected.  Chemical analysis of pesticides is expensive and the concentrations in rivers are notoriously variable, so the absence of a pesticide in a monthly water sample is no guarantee that it was never there.  The invertebrates live in the river all the time, and the aftershocks of an unexpected dose of pesticide are still reverberating a few weeks later when Phil rolls up with his pond net.   But the success of this particular incident depends on a) Phil being alert enough to notice the change and b) having time for some ad hoc detective work.

This encapsulates the “streamcraft” which formed part of my original title.   This is the ability to “read” the messages in the stream that enable us to understand the processes that are taking place and, in turn, the extent to which man’s activities have altered these (see “Slow science and streamcraft”).  It is something you cannot be taught; you have to learn it out in the field, and the Environment Agency and predecessors was, for a long while, well set up to allow this process of personal development.    Changes over the past few years, in the name of greater efficiency (and, to be fair, in the face of enormous budget cuts) have, I fear, seriously eroded this capability, not least because biologists spend far less time in the field, and are no longer responsible for collecting their own invertebrate or diatom samples.


Phil Harding: forty years on, sampling algae in the River Ashop in Derbyshire.

In my talk, I was thinking aloud about the interactions between metabarcoding and the higher level cognitive skills that a good biologist needs.   I feared that, in the wrong hands, it could be yet another means by which the role of the biologist was eroded to that of a technician feeding samples into one end of a series of swish machines, before staring at spreadsheets of data that emerged from the other end.   All the stages where the old school biologist might parse the habitat or sample s/he was investigating and collect signs and indications of its condition over and above the bare minimum set in the protocol were stripped away.

A further reason why this might be a problem is that molecular ecology takes a step backwards from the ideal of biological assessment.  Much as the chemist only sees what his chosen analyses allow him to see, so the molecular biologist will only “see” what his particular set of primers reveal.   Moreover, their interpretation of the spreadsheets of data that emerge is less likely to be qualified by their direct experience of the site because their time is now too precious, apparently, to allow them to collect samples for routine assessments.

A few points emerged out of the discussion that followed (the audience included representatives of both Environment Agency and Natural England).    First, we agreed that metabarcoding is not, itself, the problem; however, applying metabarcoding within an already-dysfunctional organisation might accentuate existing problems.  Second, budgets are under attack anyway and metabarcoding may well allow monitoring networks to be maintained at something approaching their present scale.  Third, the issue of “primers” was real but, as we move forward, it is likely that the primer sets will be expanded and a single analysis might pick up a huge range of information.  And, finally, the advent of new technologies such as the MinION might put the power of molecular biology directly into the hands of field biologists (rather than needing high throughput laboratories to harness economies of scale).

That last point is an important one: molecular ecology is a fast moving field with huge potential for better understanding of the environment.    However, we need to be absolutely clear that an ability to generate huge amounts of data does will not translate automatically into that better understanding.   We will still need biologists with an ability to exercise higher cognitive skills and, therefore, organisations will need to provide biologists with opportunities to develop those skills. Metabarcoding, in other words, could be a good friend to the ecologist but will make a poor master.  In the short term , the rush to embrace metabarcoding because it is a) fashionable and b) cheap may erode capabilities that have taken years to develop  and which will be needed it we are to get the full potential out of these methods.   What could possibly go wrong?