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.
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