When is a sample not a sample?


If you have followed this blog over the years, you will probably have worked out that the only inevitable outcome of a close study of diatoms is that you are older at the end than you were at the start. Whether you are also wiser is, alas, not guaranteed.   The older : wiser ratio can vary quite a lot, depending on what, exactly, you are studying and a further factor to stir into the mix is that a freelance ecologist such as myself needs to be prepared to forego the pursuit of wisdom if the price is right.

And so it is that I have spent a fair part of my time since Christmas staring down my microscope at a batch of samples that I have been sent whilst, at the same time, cursing my pecuniary instincts.   These samples are one part of a large survey and, I know, are not collected by people with any experience of freshwater algae.  Judging by the muddy sludge that I get in some of the sample tubes, I am not wholly sure that all can be trusted to distinguish a stream from a field, let alone find stones likely to yield a representative crop of diatoms.   But when, I wondered, after an hour hunting around a slide for fragments of diatoms to identify, do I throw up my hands and say “enough”?

The two photographs in this post are from one of these irksome slides.  In both cases, there is a single diatom but, also, quite a lot of mineral matter.   I would expect maybe five to ten diatoms in a field of view on a well-prepared slide from a good sample,.  In this one, there were more fields of view without diatoms than there were with (typically, I had to scroll past two empty fields between each identifiable diatom, but there could be as many as four or five empty fields between diatoms).   In theory, my first action when confronted with a slide such as this is to make another, more concentrated slide but this will also concentrate all that mineral matter.


A field of view with a single valve of Achnanthidium minutissimum (top right) from a sample from an unnamed stream.   The image at the top of the post shows a different field view, this time with a single valve of Cocconeis euglypta.  Note the large quantity of inorganic matter in the sample.

Here then, are a few questions to ask when you encounter a very sparse slide.

  • Who collected the sample? Do you trust them or not?   A lot of samples these days are collected by people who have little understanding of the ecology of benthic algae and who will not know when a sample is unlikely to yield enough diatoms for analysis;
  • Is there a lot of particulate matter that has resisted oxidation during the preparation stages? These might be telling you something about the habitat itself: mineral particles suggest a depositional, rather than an erosional, habitat.  Some organic materials, particularly from peaty habitats, are also resistant, and can obscure diatoms, unless a dilute preparation is made;
  • What is the state of the diatoms that are present on the slide? If a large proportion are broken, this may suggest that there was not a viable community of algae at the time the sample was collected and you are, in fact, counting diatoms that have been washed in from elsewhere in the catchment;
  • Do the diatoms that you do find in a sample tell a consistent story? Sometimes the diatoms I find in a sparse sample have ecological profiles which, when combined, suggests a particular interpretation but, on other occasions, I see samples that are both very sparse and very diverse, with species representative of several different environments.  When the ecological profiles are not broadly consistent then, again, it is a warning that you may be dealing with washed-in diatoms and fragments, and not an assemblage that is telling you much about the site in question.

I believe that you should be able to count at least 100 valves and have answered the second, third and fourth questions after no more than an hour’s analysis.  This is a good point at which to decide whether it is worth pushing on to complete the analysis or abandon the count.   I try to make this clear in my terms and conditions, emphasising that it takes about as long to decide that a sample cannot be analysed as it does to perform an analysis on a “normal” sample.   I should also emphasise that these suggestions apply to samples from rivers and lake littoral zones and different criteria may need to be applied when dealing with other types of samples (e.g. for palaeoecological or forensic work).

The judgements that you need to make are easier if you have direct knowledge of the site from which the sample was collected; however, this is often not possible.   As “streamcraft” is undervalued by managers (see “Primed for the unexpected” for my most recent moan on this topic), the natural habitat of the diatom analyst is the laboratory not the field and sample collection is often delegated to less-highly trained individuals.   The determination of my fellow analysts to wring every last mote of knowledge from empty silica frustules has also contributed to a greater focus on the laboratory, rather than the field.   Most of the time, to be fair, sample quality is not a factor.  We produced some PowerPoint presentations a few years ago to help people collect diatom samples (see “A cautionary tale…” for the whole story) and, let’s be honest, collecting a decent diatom sample should not be rocket science.   The question underlying all of these is whether or not the diatoms you have on a slide are an accurate representation of the assemblage of living diatoms present at a particular point in space and time.   If you cannot say “yes” with confidence, then you will certainly be older, but no-one will be any wiser.


A cautionary tale …


I was asked for a picture of someone sampling diatoms to include in a presentation this week and dug out the image above, one of my favourites, taken by my son Edward when he joined me on a sampling trip to the Lake District some years ago.   It shows me collecting diatoms from the littoral zone of Wastwater, with the Wastwater Screes in the background.   I like the composition, which captures the grandeur of the location and have used it several times.   Unfortunately, the Environment Agency did not agree with me.   They did not quibble with the aesthetics but refused to use it on a leaflet about diatoms because I was not wearing appropriate health and safety gear.   Seriously.

Let’s put this in context: I work for myself and have no employees.  It is in my own interests to keep myself healthy and safe.   If, when sampling the shallow margins on a warm summer’s day I choose to go barefoot and not wear a lifejacket or gloves, that is a decision that I can take, based on my on site assessment of risks and hazards.   The Environment Agency is a large bureaucracy that has to adhere to health and safety legislation and minimise the risk of being sued for negligence in the event that a member of staff has an accident whilst out sampling.   That creates a very different mindset and, inevitably, a rather top-down and inflexible approach to these matters.

We have had run-ins over the years with the Environment Agency over the years on these issues, usually involving the tier of management just above those who still remember the last time they wore a pair of waders.  One of the most bizarre occurred just after a consortium I was leading had started to develop a Water Framework Directive-compatible method for ecological assessment.   We needed samples from all over the country and these were to be collected by biologists working for the Environment Agency and sister agencies in Scotland and Northern Ireland.  We budgeted for training workshops to make sure that these biologists knew how we wanted the samples to be collected; however, at our first meeting after the budget was confirmed, we were told that the biology teams did not have time to attend these training workshops.

We thought on our feet as the meeting progressed: we could, perhaps, produce a training video that could be distributed to laboratories instead of gathering them in one place.  That sounded like a good idea but we had no idea how to go about this, or what it would cost.   On the way back home I browsed WHSmith’s magazine racks at a train station and bought a copy of “What Video” magazine, which had a 30 day trial copy of Adobe Premiere on the front cover.   I then got together with Marian Yallop, a member of our team from Bristol University, and we spent a day collecting diatom samples in the River Wylye in Wiltshire whilst a colleague from her department videoed us.  I then used Premiere to splice these clips together and put them into PowerPoint presentations that took viewers step-by-step through the principles and practice of sampling diatoms.   You can see those PowerPoints (now somewhat dated) by following this link.   We spent about the same time on these presentations as we would have done organising and delivering workshops, so I thought that this was a good outcome, and that we should have generated some goodwill as a result.  I was, however, in for a bit of a surprise.

Our project manager was pleased with the outputs, as was her counterpart in SEPA.  However, a couple of weeks later, the official response filtered down to us: the presentations could not be used as we had not adhered to all of the Environment Agency’s health and safety procedures whilst collecting the samples.   Our cardinal sin was not to wear gloves, a practice that we (and SEPA) regarded as a decision to be made by the sampler based on their own appraisal of the site but which the Environment Agency regarded as non-negotiable.  Some acrimonious emails and telephone calls followed.   Eventually, just before all of that hard-earned goodwill evaporated completely, a compromise was found, with a confessional slide being introduced at the start of the presentation.  We managed to wave two fingers at the establishment by titling the slide “This slide was inserted by the Environment Agency” lest anyone thought that it was our idea.

Since then, the presentations have sat on the DARES website and people from far-flung parts of the world have come up to me to say that how helpful it was to see diatom sampling being performed, rather than just reading about it, so I think that the overall outcome was positive.   But there is a useful lesson for us all tucked away for those of us who deal with large bureaucracies such as the Environment Agency.  You always have to remember that most of the people who deal with your reports and outputs work at a sufficient distance from the project not to realise how contractors have moulded their work around shifting circumstances.  These people will cheerfully undermine any goodwill that you have built up at the slightest hint that outputs do not fit perfectly into established procedures.  It is probably not a deliberate attempt to sabotage a hard-won outcome on their part, but it happens.  You often need a thick skin in this business.  And gloves.  Even when you don’t think that they are necessary.


Sampling diatoms from the River Ganges at Rishiketh, September 2016.