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.

 

Tidings of Great Joy …

uk_diatom_flora_homepage

About three years ago I was one of a small group of people who met in the bowels of the National Museum of Wales in Cardiff to discuss the options for producing an online guide to the freshwater diatoms of Britain and Europe.   There were, we reasoned, good guides to most of the rest of the algae found on these islands, and plenty of guides to the diatoms of continental Europe.  There was also an active community of people interested in diatoms for a variety of reasons, both professional and recreational.   There had also been well-intentioned initiatives in the past, the most recent of which was a CD-ROM that I helped to produce for the Environment Agency a few years ago.  I wrote about that sorry saga in “The decline and fall of a CD-ROM”.

There are good reasons why it has not been possible to produce a good guide to diatoms in the past, not least of which has been the shifting sands of diatom taxonomy, which creates instability for anyone who is trying to collate information on the present state of play or, for that matter, to put names on the myriad forms of diatoms that one sees when peering down a microscope.   A more practical reason, over the last few years, has been the absence of anyone with the time and resources to mastermind a project but that situation was about to change, thanks to the National Museum of Wales, who gave their diatom curator Ingrid Jüttner time to work on the project.   They also had experience of developing online taxonomic aids, and a basic “shell” for a website that could be adapted to our needs.   The missing link was funding to allow others with practical or academic interests in diatom taxonomy to travel and meet up to support the project.  That problem was solved thanks to generous support from the British Phycological Society.

uk_diatom_flora_nitzschia

The homepage for the genus Nitzschia in the Diatom Flora of Britain and Ireland.

And so, today, the Freshwater Diatom Flora of Britain and Ireland was launched on the National Museum of Wales website and I encourage you all to have a look.   Comparing the swish tablet-friendly website to our CD-ROM is a salutary experience.   That had to be run from a computer with a CD-ROM drive, which meant that either your microscope had to be close to your desktop or you had a laptop or you were constantly dashing across the laboratory to compare the image on the screen with the specimen under your microscope.  There was, at the time, an edict within the Environment Agency that prohibited desktop computers from laboratories, which further complicated the issue.  Now you can check specimens on an iPad as easily as consult a paper flora.  And that is quite important because, in my experience, there are three levels of biological identification.  First, there is a basic pool of species that you can name from memory, then there are rare and difficult specimens that cannot be identified easily and which require you to consult the literature.   Finally, there is a group of species that fall between these two categories that you recognise but for which you may need a “nudge” to match them to the right name.   For these, an aide mémoire that you can consult easily is invaluable.  I always felt that the Lucid software that drove the CD-ROM was a little too clunky to serve this purpose, but a website accessible via a tablet might approach the functionality of my paper-based identification aids.

The diatom flora has images and descriptions of most freshwater genera, and of the most commonly encountered species.  But there is still a long way to go.   The next couple of years will see us start filling in some of the gaps in order to improve coverage, both in the number of species and the amount of information about each.   At the moment, the focus is on valve morphology, but there is more that could be written about live diatoms and about their ecology, for a start.  But we have made the first steps and, importantly for this modern age, we have burst the old paradigm that regards taxonomic literature as stolid inflexible overviews of the state of the art at a point in time, and emerged blinking into a new era where the medium is flexible enough to accommodate change and evolve as our understanding improves.

uk_diatom_flora_ndissipata

The webpage for Nitzschia dissipata in the Diatom Flora of Britain and Ireland, with the description on the left and images on the right.

Diatoms from a holy river …

ganges_at_rishikesh_aug16

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.

rishikesh_diatoms_sep16

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.

Reference

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.

Diatoms from the Valley of Flowers

valley_of_flowers_5_aug16

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 …).

sampling_in_valley_of_flowe

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

zygnema_valley_of_flowers_a

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 …

diat_mesodon_vof_aug16

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_vof_aug16

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).

Reference

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

The power of rock …

In my recent post on Ennerdale Water I referred to the interaction between geology and man in shaping the characteristics of a lake (see “A lake of two halves …”).   As I was writing, I had in mind some famous early work on this topic by Harold (“W.H.”) Pearsall, a botanist who made some of the first tentative steps towards linking patterns and processes in lake ecosystems, whilst working at the universities of Leeds and Sheffield.   He had visited many of the lakes since boyhood and co-opted his father as a field assistant to cycle around the Lake District performing the surveys that formed the basis of this paper.

Pearsall had noted differences in the types of plants growing in the various lakes in the region, and attributed these differences to the geology of the surrounding land.   He took this idea one step further by also suggesting that the lakes became modified as they increased in age, illustrating this by arranging the English Lakes into an “evolutionary sequence”, with Wastwater and Ennerdale Water representing the least evolved, and Windermere and Esthwaite Water representing the most advanced.   His first proposition is now well-established amongst those who study lakes; the second is also generally accepted (I remember writing an essay entitled “Lakes are temporary features of the landscape” as part of my A-level Geography course), although his use of the English Lakes to illustrate this is not.

lake_district_after_pearsal

The lakes of the English Lake District, arranged in the evolutionary sequence proposed by Pearsall: 1: Wastwater; 2: Ennerdale Water; 3: Buttermere; 4: Crummock Water; 5: Hawes Water; 6: Derwent Water; 7: Ullswater; 8: Bassenthwaite Lake; 9: Coniston Water; 10: Windermere; 11: Esthwaite Water.

The graph below makes Pearsall’s case, using his own data (note that his records for Hawes Water refer to the small natural lake that was submerged to form the current Haweswater Reservoir).   The left hand axis shows the proportion of land in the catchment of each lake which was under cultivation (at the time of his study) steadily increasing as we move through his evolutionary sequence.   The right hand axis shows how proportion of the shoreline of each lake that was rocky (down to a depth of 30 feet – 9.2 metres) steadily decreases through the sequence.  He pointed out that both the amount of cultivatable land and the character of the shoreline depended largely on the character of the surrounding country.

pearsall_evolutionary_seque

A graphical representation of Table 1 in Pearsall (1921): “Effects of erosion”.  Lakes are arranged in order of Pearsall’s “evolutionary sequence”.

The next graph shows the same sequence of lakes (excluding Hawes Water) but with the average values of the Lake Trophic Diatom Index (TDI) plotted on the Y axis, and with lakes sub-divided into those with low alkalinity (deriving most of their runoff from the Borrowdale Volcanics and associated hard rocks, including the Ordovician granite discussed in the post about Ennerdale) and those with moderate alkalinity (associated with softer rocks to the north and south of the Borrowdale Volcanics).   This confirms the primary role of geology, with Pearsall’s “primitive” lakes underlain by the Borrowdale Volcanics whilst the more “evolved” are associated with the softer rocks.  Within each category there is an upward trend, rather more pronounced in the moderate alkalinity lakes, as we move through Pearsall’s sequence.  I suspect that this represents the interaction between geology and man, with higher TDI values associated with lakes where there is more agriculture and greater population density.   These factors may, in turn, combine to affect the physical factors within the lake over time, but the implication that a “primitive” lake such as Ennerdale Water might one day “evolve” to have characters similar to those of Windermere is no longer accepted.   On the other hand, he did set up some testable hypotheses that kept freshwater ecologists occupied for a long time subsequently.  As Lao Tzu reminded us: “a journey of a thousand miles begins with a single step”…

pearsall_versus_ltdi

Average lake TDI values (using data from Bennion et al., 2014) for Lake District water bodies, arranged by Pearsall’s evolutionary sequence (no data for Hawes Water).   Open circles are low alkalinity lakes; closed circles are moderate alkalinity lakes.

References

Bennion, H., Kelly, M.G., Juggins, S., Yallop, M.L., Burgess, A., Jamieson, J. & Krokowski, J. (2014).  Assessment of ecological status in UK lakes using benthic diatoms.  Freshwater Science 33: 639-654.

Clapham, A.R. (1971).  William Harold Pearsall.  1891-1964.  Biographical Memoirs of Fellows of the Royal Society 17: 511-540.

Pearsall, W.H. (1921).  The development of vegetation in the English Lakes, considered in relation to the general evolution of glacial lakes and rock basins.  Proceedings of the Royal Society of London Series B 92: 259-285.

Pleasures in my own backyard

Crowtrees_pond_July16

One of the delights of my part of County Durham is the range of natural history that is available without the need to travel great distances.  That, indeed, has been the theme of this blog right from the start (see “Cassop”) and today’s post continues the theme of nature on my doorstep, with a visit to a local nature reserve within walking distance of my house.  Like Cassop Pond, it is at the foot of the Magnesian Limestone escarpment and, at this time of year, the grassland is rich with Northern marsh and Common spotted orchids.   It is, of course, the ponds that draw my attention: they are rich in aquatic plants including, once I start to look closely, beds of the alga Chara, which I’ve written about before (most recently in “Everything is connected …”).  And then, once my eyes are adjusted to looking at natural history at this more intimate scale, I can see that the stones on the bottom of the pond are covered with tiny snails (probably Hydrobiidae) with shells coiled in the shape of an ice-cream cornet.  Freshwater snails crawl across submerged surfaces rasping off attached algae with their tough radula so I started to wonder what snails in this particular pond might be feeding upon.

Crowtrees_stones_July16

Submerged stone from the pond at Crowtrees Nature Reserve, County Durham, covered in Hydrobiidae snails (left: the stone is about 10 cm across) and (right) a stone removed from the bottom of the pond showing the marl-covered part that was exposed and the marl-free part that was buried in the sediment. 

Viewed from just above the water, the surface of the stone looked as if it could be an algal film but, when I picked it up, the stone did not have the yielding texture that I associate with such films, but was a hard, mineral-rich marl.  More intriguingly, it was only present on the exposed surfaces, possibly, I suspect, due to the subtle interactions between chemistry and biology that I wrote about in “Everything is connected …”.

The calcite crystals make it hard to get a good view of the material under the microscope, but I managed to see a number of diatoms, mostly Gomphonema pumilum, or a relative, but also a good number of tiny, slightly asymmetric cells of a species of Encyonopsis, a genus that was, until recently, included in Cymbella, and which is usually a good indication that the water is about as untainted by human influences as it is possible to get.   It is, however, hard to get a really clear view of these under the microscope as they were scooting around.   With valves that are barely more than a hundredth of a millimetre long, I really needed to use an oil immersion objective to see them clearly, but the calcite crystals on the slide made it almost impossible to get a clear view of the live cells.  Not surprisingly, most of what we know comes from studies of carefully-cleaned preparations of the empty frustules.   Encyonopsis shares with Tyrannosaurus Rex the distinction of being an organism better known dead than alive.   It is rather ironic, given that healthy populations are living so close to my house, but that’s very often the case with diatoms.

There was one other abundant alga living amidst the rock (and, indeed, probably the major food source of the snails), but I am having some problems giving it a name, so a full account of that one will have to wait until another day.

Crowtress_diatoms_July16

Diatoms at Crowtrees Nature Reserve, July 2016: a.-d.: Gomphonema (possibly G. pumilum) in girdle and valve views; e.-g.: Encyonopsis sp.   Scale bar: 10 micrometres (= 1/100th of a millimetre).