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 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  (= 1/100th 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.

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


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