In pursuit of Bulgarian diatoms …

Our visit to Rila Monastery was one of the cultural highlights of our trip to Bulgaria in the summer (see “The art of icons …”) with the added bonus that it is set amidst some spectacular scenery.   The monastery was founded by St Ivan Rilski (“St John of Rila”) in the 10^th century, though the present structures date from the 19^th century.   St Ivan, I gleaned from my reading, shared a love of nature with St Francis and St Cuthbert and Rila’s remote location reflects his desire to live the life of a hermit.

Beyond the monastery the road twists and turns amidst the forest that lines the valley.   Occasionally, the canopy is broken by meadows and orchards of apricot and plum trees.  The apricots were ripe for harvest and at an easy height for foraging as we passed by.   We were too late in the year to find many wild flowers in these meadows but the absence of any of the paraphernalia associated with intensive agriculture made us suspect that these would have been a riot of colour in the spring.    Eventually, we came to a small hamlet set amidst a wider area of meadows, where we refuelled at a small café serving the delicious local bean soup (“bob chorba”) before making our way across the meadow to the stream.

A haystack in a meadow near Rila Monestery, August 2017.

The Rila stream itself flowed through a densely-wooded channel, with a variety of substrates from coarse sand to moss-covered boulders.   The larger stones were mostly granite, reflecting the underlying geology of the region, which almost certainly means that the water was very soft.  The surrounding vegetation and low population density also mean that the water is probably as pure as we are likely to find anywhere in Europe.   I had a toothbrush and sample bottle in the bottom of my rucksack and scrubbed a few cobble-sized stones to remove the thin surface film and stowed this for the journey back down the valley.

Sampling Rila stream at Kirilova meadows, a few kilometres upstream from Rila Monestery in August 2017.   The photograph at the top of the post shows the scenery around Kirilova meadows.

It has taken until now for me to get around to looking at this sample, which turned out to have a large population of Gomphonema rhombicum, along with quite a lot of Achnanthidium minutissimum and relatives, confirming my suspicion of a circumneutral, low nutrient environment.   G. rhombicium is a relatively uncommon diatom, so I was intrigued to have a closer look.  It has a similar outline to G. pumilum, which is very common, but is larger and has a distinct broad lanceolate axial area and, consequently, relatively short striae.   The axial area broadens out a little further at the central area, where there is also a single stigmoid.  I wish now that I had had a look at the sample before digestion as many of the larger Gomphonema species have long mucilaginous stalks, whereas G. pumilum and relatives tend to be attached to the substrate by short mucilaginous pads.   I can find nothing in the literature that alludes to the habit of the living cell and, on this particular occasion, am in no position to judge the shortcomings of my peers.

By coincidence, the type location for Gomphonema rhombicum is given as “Appleby, Westmoreland”, which is just over an hour’s drive from where I live.   The most obvious place to hunt for G. rhombicum would be the River Eden; however, the scant details on the ecology of G. rhombicum that I can find suggest a preference for softer water than found here.  This is a geologically-complex area so there is a possibility of suitable habitat existing in a stream in the vicinity.  If the Eden was the location from which the original population of G. rhombicum was collected, then I suspect that it may have been a casualty of the agricultural intensification that has taken place in this area since it was first described.

Cleaned valves of Gomphonema rhombicum from Rila stream at Kirilova meadows, August 2017.  a. – g. show valve views; h. shows a girdle view.  The scale bar is 10 micrometres (= 100^th of a millimetre).

That leaves me with just one option: a return to the Rila National Park.  I think I can just about live with that.   We stayed at Hotel Pchelina, a few kilometres down the valley from Rila Monestery and our dinner that evening was the most delicious grilled trout that I have ever tasted.  If a return visit was needed to solve the mystery of Gomphonema rhombicum’s habit then I think that is a hardship with which I can just about cope …

Reference

Iserentant, R. & Ector, L. (1996).  Gomphonema rhombicum M. Schmidt (Bacillariophyta): typification et description en microscopie optique.   Bulletin Français de la Pêche et de la Pisciculture 341/342: 115-124.

Ecology’s bear necessities

I found an old box of slides recently, which took me on a nostalgic journey back to British Columbia in 1980 and, in particular, to a weekend fishing trip with my cousin Steve.  We travelled north from Terrace, where he lived, along a series of unsurfaced roads through dense pine forest, passing the ethereal moonscape of Nisga’a Memorial Lava Bed to the Nass River where we cast lures and caught the salmon which became our dinner a few hours later.   The following morning we followed the road past an impressive Piedmont glacier, through the small town of Stewart and, a couple of miles beyond, passed an unmanned border post and entered Alaska.

The tiny settlement of Hyder sat just beyond the border, beyond which the forests close in again around the gravel track that followed a small stream into the hills.   When we pulled up beside the road and got out, however, the overwhelming sensory experience was not the landscape or even the sound of the stream tumbling out of the hills towards the fjord behind us.  It was the stench of rotting fish.   We were witnessing the spawning and subsequent death throes of the Pacific Salmon.   Unlike the Atlantic Salmon (Salmo salar) which can repeat their migration from the sea to freshwater several times, Pacific Salmon (Onchorhynchus spp.) spawn only once in their lifetime.   Exhausted after the exertions of the migration and what is euphemistically referred to as “big bang reproduction”, the salmon become easy prey for bears, one of whom emerged from the forest a hundred metres or so upstream of where we were standing.

My first encounter with the USA.   The border is at the point where the metalled road ends and the gravel track starts.  The building on the left is the US Customs post.   

You can just make out the bear in the photograph at the top of the post (I’ve also circled in another version at the end).  At the time, my camera was a Kodak Instamatic, which had a semi-wide-angle lens.   We all have two appendages dangling from our hips that make up for many of the deficiencies of a wide-angle lens but, on that stream bank in Alaska, I decided that discretion was the better part of valour.   We watched from afar and the multisensory memory is rather more vivid than the somewhat faded Kodachrome slide that I found in the loft.

That would have been the end of the story except that, in the early years of the new millennium, scientific papers started to appear which turned this spectacle from an item on the wildlife tourist’s bucket list to an integral component of the engine that drives the forest ecosystems of the Pacific Northwest.    These forests, like most natural systems, are hungry for nutrients such as nitrogen and phosphorus and the salmon are, in effect, unwitting suppliers of the fertiliser that the trees need.   The Pacific Salmon spend up to five years in the ocean before moving to their spawning grounds.   Those strong muscles that they need to swim upstream and leap up waterfalls are largely protein which is built from nitrogen-containing molecules.  And nitrogen is, coincidentally, the nutrient that trees need most.

A view across Nisga’a Memorial Lava Bed in the Nass River valley, British Columbia.  The lava was the result of a volcanic eruption in about 1700.  This and other photographs in this post were taken with my Kodak Instamatic, which partially explains their poor quality.

By fishing the dying salmon from streams such as this (and even grabbing the leaping salmon before they get to their spawning grounds – see some spectacular footage from David Attenborugh’s Nature’s Great Events here) the bears become the agents by which the salmon’s nutrients are transferred from the Pacific Ocean to the forests.    It has been estimated that up to a quarter of the nitrogen needs of the forest around these streams is supplied in this way.   Indeed, some have suggested that this transfer of nutrients may be so essential to the functioning of this forest ecosystem that the salmon and bears are, in effect, “keystone species” and that their interaction has an effect that is greater than their contributions individually.

Brian Moss used to use this as a pithy illustration of the need to take a very broad view when managing ecosystems.   We all know that rivers flow into the sea but it is not always so obvious how the oceans can have an effect on terrestrial vegetation far inland.   Similarly, we understand how water flows across land and into stream channels but perhaps we have a hazier awareness of the movements in the opposite direction – from the river channel into the depths of the forest.   Salmon spawning in the Pacific Northwest is one of the world’s great wildlife spectacles, but it should also give us cause to pause and consider the complexities of interactions within natural habitats and, in turn, the dangers of meddling.

One more prosaic lessons that I learned from this short trip: if you are going to the USA, take a passport. Actually, I didn’t need one going into Alaska, but when we returned the Canadian border official had rolled out of bed after his Sunday lie-in  and almost didn’t let me back in!

Another species of hairy wildlife in search of salmon, this time on the Skeena River, British Columbia.   On this particular occasion, the salmon did not oblige and I had my first and only encounter with Kentucky Fried Chicken instead.  

References

Helfield, J.M. & Naiman, R.J. (2006).   Keystone interactions: salmon and bear in riparian forests of Alaska.  Ecosystems 9: 167-180.

Naiman, R.J., Bilby, R.E., Schindler, D.E. & Helfield, J.M.  (2002).  Pacific salmon, nutrients, and the dynamics of freshwater and riparian ecosystems.  Ecosystems 2: 399-417.

Quinn, T.P., Carlson, S.M., Gende, S.M. & Rich, H.B. (2009). Transportation of Pacific salmon carcasses from streams to riparian forests by bears.  Canadian Journal of Zoology 87: 195-203.

The scene near Hyder, Alaska, this time with the bear circled, just in case you didn’t believe me.

Michael Gove has made a sensible suggestion …

I found myself buying the Sunday Telegraph for the first time in my life a few days ago, as Michael Gove chose this newspaper to announce his plans for a new environmental regulator.   His proposal links back to points I have made previously about a need for a new type of regulator to take over the role of the European Commission and European Court of Justice in holding the UK governments to account once we have left the EU (see “(In)competent authority” and “Who will watch the watchmen now?”).

Gove is in a difficult position in his role of Secretary of State for the Environment, Food and Rural Affairs.  His instincts, as a leading architect of the “leave” campaign, are against the European Union yet, for the environment at least, he cannot deny that there are many benefits that the EU has brought.   He acknowledges this: “Some of the mechanisms which have developed during our time in the EU which helpfully scrutinise the achievement of environmental targets and standards by Government will no longer exist in the same way, and principles which guide policy will have less scope and coverage than they do now”.   Too right.

His proposal is for a “world-leading body to give the environment a voice and hold the powerful to account, independent of government and able to speak its mind freely”.  That sounds promising, in the same way that Gordon Brown’s decision to make the Bank of England free of political control back in the late 1990s.   Of course, such bodies are never completely independent (witness the way that John Redwood, Jacob Rees-Mogg and others turn on the Bank of England whenever it dares contradict the most optimistic post-Brexit forecasts) but it is a step in the right direction.

So I will await, with interest, the consultation that Michael Gove promises in his Sunday Telegraph article.  I am hoping that this means that the Environment Agency will still be the tool of official government policy whilst this new body will be independent and able to point out shortfalls in performance.  I’m hoping, too, that this will bring some new thinking into environmental regulation, preserving the best of the EU systems whilst, at the same time, shaking up some of the aspects – such as the integration of environmental and agricultural policy – where the EU was notoriously weak.

The elephant in the corner of the room is finance.  The Environment Agency is currently working on a shoestring and, unless more money from Government is forthcoming, they and this new Agency will simply be unable to afford to be “world-leading”.   Somehow the Environment Agency muddles along, thanks to well-motivated staff, but corners are being cut and monitoring the state of the environment – one of the cornerstones of any effort to giving the environment “a voice” – has been a major casualty.

All this is going on whilst Parliament debates the EU (Withdrawal) Bill and we should, perhaps, see Gove’s announcement as a tactical move to head off rebellion in the Tory ranks.   Issues such as whether existing legislation will be amended by primary or secondary legislation under particular scrutiny.   I and others saw the prospect of the fine print in European environmental legislation being quietly written out of the statute books as a particular risk of Brexit so, even if this is a cynical manoeuvre, I am encouraged by Michael Gove’s words.   If nothing else, it demonstrates that even arch-Brexiteers know that they have to make some concessions.   However, we need to watch this story closely as it unfolds over the next few months …

Murder on the Barcode Express …

A long time ago, Agatha Christie imagined a train coming to a halt in a snowdrift somewhere in Croatia.  By the morning, one of the passengers was dead.   Eighty years later, a group, only slightly larger than Hercule Poirot’s pool of suspects, gathered in a room in modern Zagreb to plot another fiendish murder.   The victim, this time, would be  …. traditional diatom taxonomy.

“Murder” is far too strong a term for this particular whodunit; maybe I should say “aiding and abetting” rather than actually committing the crime, but I think the outcome might be the same.  The conspirators in Zagreb are all involved in developing methods that use molecular barcoding to identify diatoms and have been busily collecting sequences of the many diatom species in order to establish the libraries that we need to link these barcodes to the appropriate Linnaean binomial.   Some years into this, we still have no more than about 15% of freshwater diatom species matched to barcodes.  We are starting to think about ways of filling in the gaps more quickly than is possible using the conventional approach of isolating a diatom, growing it in culture and then sequencing the appropriate marker genes.

The most radical of these alternatives is to by-pass Linnaean binomials altogether and classify diatoms by their barcodes alone – as “operational taxonomic units” or OTUs.   Most of us have spent most of our careers using morphology-based taxonomy and any move away seems like an act of treachery towards a fundamental tenet of our craft.  But the time has come to take a dispassionate view and ask what a species name brings to ecology.   At a very practical level, the use of Linnaean binomials makes it much easier for us to compare data with colleagues and with records in the literature.    Taxonomists would argue that their work helps us to understand the relationships between species but, unfortunately, in this particular branch of science, we make little use of these relationships, and the role of taxonomy is primarily to give us a consistent means of organising the myriad tiny pieces of silica which we find in our samples.

That business of consistent naming could, in theory, be performed for barcodes just as efficiently using digital tags as OTUs and this would also work for the 85% of species where the link between traditional morphology-based taxonomy and marker genes has not yet been established.   So what about the link that Linnaean binomials give us to established knowledge?   Here, again, we need to be brutally frank: ecological information for most freshwater diatoms is limited to information about preferences for hardness/alkalinity, inorganic nutrients, organic pollution, acidity and salinity and that information can be replicated very easily by linking files of metabarcoding and environmental data.  There are very few experimental studies that offer insights into the ecology of freshwater benthic diatoms beyond that gained from looking for associations between diatom distribution and a few common variables.

The plotters plotting …  DNAqua-net workshop in Zagreb, November 2017.  The top photograph shows Zagreb cathedral against the skyline.

The problem is not that we do not see the merits of traditional Linnaean taxonomy, it is that we cannot make a strong case for the funding necessary to collect barcodes for all species.   The final downward thrust of the dagger will, in other words, be inflicted by the bureaucrats whose budgets will not stretch to cataloguing the enormous breadth of algal diversity.   Diatoms sit in the awkward middle ground between larger organisms such as fish where any suggestion of not using traditional taxonomy would be greeted with derision and the microbial world where the idea of applying Linnaean binomials to the enormous diversity uncovered by molecular techniques is equally risible.   Diatom names mean little to the bureaucrats who manage our environmental agencies and, given the choice between a spreadsheet of incomprehensible Latin names or one of equally incomprehensible OTUs, all else being equal, they will choose the cheapest.

“All else being equal” is the key phrase.   I think that there is growing awareness now that one downside of barcoding is that it risks sidestepping the need for trained biologists at all: samples will be collected by technicians, processed in high-throughput laboratories and results churned out through black box computer programs.   The situation for diatoms is worse than for most groups of organisms used for ecological assessment because so much attention is given to the laboratory stages of producing a list of taxa and relative abundances.  We are, however, now approaching the point when DNA sequencers can produce data of equivalent sensitivity to that produced by light microscopy.   The message that barcoding has the potential to be a good friend but a poor master could be lost as our paymasters recognise the potential for reducing costs.   What we need to do now is use those “little grey cells” to ensure that good biological insight is not the victim of a heinous crime.

The underwater world of Ennerdale Water …

I’ve tried to capture the world of microscopic benthic algae many times but never, until now, attempted the same effect with plankton.   The picture below illustrates the problem that I face: whereas the benthic flora are organised with, for the most part, a clear three-dimensional structure and known dependencies amongst organisms (species A, for example, being epiphytic on species B), plankton are randomly distributed in a very dilute solution.

A representation of the phytoplankton of Ennerdale Water with cells of Rhodomonas and Kephyrion depicted at a realistic density (c. 1000 – 2000 cells per millilitre).

I had to address two issues in producing this image, which is based on four phytoplankton samples collected by the Environment Agency in the summers of 2014 and 2016: depicting the phytoplankton cells at approximately the correct density and making sense of the list of names that appeared on the list.  Ennerdale Water is a very nutrient-poor lake and cell concentrations during the summer are in the order of 1000 to 2000 per millilitre.  That sounds a large number until you consider the scale at which we are working.   For simplicity, I assumed spherical cells of about 20 micrometres diameter (= 1/50^th of a millimetre) at a density of 1000 cells/ml.    That equates to one cell per micrometre which is 1 mm x 1 mm x 1 mm.   Using these assumptions, each cell is 50 diameters distant from its nearest neighbour, which means the foreground of a picture should contain only two small cells and a lot of blue paint.

Next, I need to know what algae to paint and the problem here is that 85 per cent of the cells in the Environment Agency phytoplankton analyses were described as “picoplankton < 2 micrometres diameter” or “nanoplankton 2-20 micrometres diameter” (the latter divided into flagellates and non-flagellates).  There are, apparently, big difficulties in naming many of the cells found as preservation with Lugol’s Iodine coupled with the long time in storage before analysis can lead to loss of useful diagnostic features.   Cells in the nanoplankton category can, in theory, belong to any one of a number of groups of algae but If I focussed just on those organisms that could be named, I see that the Cryptophyta Rhodomonas lacustris var nannoplanctica (formerly R. minuta var. nannoplanctica) predominates, followed by Chrysophytes, of which Kephyrion is the most abundant.   So these are the two cells that I have put in the foreground.

I subsequently turned up a paper from 1912 by the father and son team of William and George West who looked at the phytoplankton of Ennerdale Water and a number of other lakes in the Lake District and Scotland.  The range of taxa that they found was quite different to that recorded in these recent surveys with samples dominated by desmids and almost no Chrysophytes or Cryptophytes recorded at all. That may, in part, be due to differences in methods – they collected samples using a “silken tow net”, which would probably have missed the very small Chrysophyta and Cryptophyta (an earlier paper by them tells us of the size of the nets but not the mesh itself) .  Some desmids that they found were found in the recent surveys but in much smaller quantities and it is possible that this was partly an artefact of the differences in sampling technique.  The idea of comparing count data from old papers with modern records is appealing but, in most cases, separating genuine changes in composition from differences introduced by sampling and analytical methods is always difficult.

Excuse these ramblings … there is, as you can see, not a lot of pictorial interest in the underwater world of an oligotrophic lake.   If you want excitement, tune into Blue Planet II, David Attenborough’s latest series for the BBC You will find sex and violence galore there.  The underwater world of Ennerdale Water is a quieter, more serene and certainly less televisual place.  Maybe that’s not such a bad thing …

References

Lund, J.W.G. (1948) A rarely recorded but very common British alga, Rhodomonas minuta Skuja. British Phycological Bulletin, 2:3, 133-139.

West, W. & West, G.S. (1909). The British freshwater phytoplankton, with special reference to the desmid-plankton and the distribution of British desmids.   Proceedings of the Royal Society of London Series B 81: 165-206.

West, W. & West, G.S. (1912).  On the periodicity of the phytoplankton of some British lakes.  Journal of the Linnaean Society, Botany 40: 395-432.

The green mantle of the standing pond* …

One of the highlights of a wet and windy weekend at Malham Tarn Field Centre for the annual British Diatomist Meeting was a talk by Carl Sayer on the ecology of a small pond in Norfolk.  The work was not new to me, as I had been the external examiner for Dave Emson’s PhD thesis on which the work was based.  I remember, at the time, making a mental note to write a post once the work was fully in the public domain, and Carl’s talk has finally jogged me into action.

Carl’s starting point was the observation that small ponds are often covered with dense growths of floating aquatic plants such as duckweed (Lemna minor).  Repeated visits to ponds in north Norfolk, close to where he grew up, had shown that this cover of duckweed often lasted for a few years before disappearing, only to reappear some years later.   As this duckweed blocks out sunlight, periods of dominance are likely to have unfortunate consequences for other aquatic plants in the pond and, as these pump oxygen into the water as a by-product of photosynthesis, life for other pond-dwelling organisms – such as the Crucian carp (Carassius carassius) that Carl likes to catch from the pond – will also get tougher.

There’s a lot of questions that could be asked about what’s going on here, and not all can be answered in a single study, but establishing whether these periodic episodes of duckweed dominance were one-offs or if they were regular events is a good place.  Here Carl and Dave  were able to use a well-known association between a diatom – Lemnicola hungarica – and duckweed to track changes in Lemna over time.   Lemnicola hungarica grows attached to the roots of duckweeds and similar species and seems to be unusually fussy about its habitat compared to many diatoms, which means that when Lemnicola is found in the sediments of a pond, that is a fairly good indication that Lemna was abundant when those sediments were being laid down.   In the process, they also discovered another diatom, Sellaphora saugerresii, also seemed to be strongly associated with Lemna, at least in this habitat (it is also common in many rivers were Lemna is sparse or absent).

The relative abundance of a) Lemnicola hungarica and b) Sellaphora saugerresii in surface sediments of north Norfolk ponds with and without Lemna dominance.   The two species are illustrated on the right hand side (S. saugerresii is typically about 10 micrometres  (= 1/100^th of a millimetre) in length).

Armed with this information, Dave and Carl went back to one of Carl’s local ponds and extracted a core of the sediments from the middle in order to see how numbers of Lemnicola hungarica and Sellaphora saugerresii changed through the length of the core.   Because they were also able to date the core, they were able to show that the period when there are documentary records of duckweed dominance coincides with both of these indicators being abundant in the pond sediments.  Below these levels (i.e. further back in time), the relative abundance of these two species waxes and wanes several times, suggesting that the duckweed cover, too, had come and gone over the years.

Left: Dave Emson and the core from Bodham Rail Pit; right: changes in the relative abundance of Lemnicola hungarica and Sellaphora saugerresii at different levels of the core.    The grey rectangle indicates the period during which Lemna is known to have been dominant in the pond (all photos in this post: Carl Sayer).

Quite why this is so is not clear.   There are several species of floating aquatic plant (water hyacinth and Salvinia, the floating fern are two good examples) that are able to cover large areas of standing water bodies in a short period of time and they often do this by vegetative growth rather than by seed.   This means that the plants are mostly clones of a very small number of plants that first colonised the water body.   And this, in turn, may mean that a virus that infects one frond will be able to infect every other frond as well as there is a very narrow range of genotypes within the population.  That’s one possibility but there may be others.

But back to the story: knowing that Lemna abundance fluctuates is not quite the same as being able to describe the consequences of this for the rest of the organisms that inhabit these ponds.   The Crucian carp was the species that attracted Carl to the pond in the first place so it would be good to know whether this species can survive the dark, oxygen-poor years when the surface is covered with duckweed.   They did find scales of Crucian carp in the cores right through the pond’s dark ages suggesting that this tough little fish had managed to hang on.  In 2008, a few years after the most recent duckweed episode, they found just a single carp when they cast their nets out into the pond but there were three by the following spring and, in 2011 there were over 200 juveniles.  So it looks like the carp populations definitely retrench during the duckweed episodes but that they do, eventually, recover.   And, maybe, another generation of north Norfolk natural historians will become enthralled by the aquatic world as a result?

^* King Lear Act III scene IV

References

Buczkó, K. (2007).  The occurrence of the epiphytic diatom Lemnicola hungarica on different European Lemnaceae species.  Fottea, Olomouc 7: 77-84.

Emson, D., Sayer, C.D., Bennion, H., Patmore, I.R. & Rioual, P. (2017).  Mission possible: diatoms can be used to infer past duckweed (lemnoid Araceae) dominance in ponds.  Journal of Palaeolimnology https://doi.org/10.1007/s10933-017-0008-6.