The two research projects that occupy most of my time at the moment could not be more different except that the motivation in each case is to make applied ecologists more efficient. The first of these, RAPPER (see “Ecological assessment in the fast lane …”) is old-school natural history, which involves ecologists standing in streams and making observations that can give an insight into stream condition almost straight away (especially if you have a field microscope). The second is exploring the prospects for using molecular barcodes (see “When a picture is worth a thousand base pairs …”). Someone still needs to stand in a stream to collect a sample but that is where the similarity ends. I have been collecting samples for molecular barcode analysis for about a year now but I have been sending my samples to the laboratories of the Food and Environment Research Agency at Sand Hutton in York for analysis.
Two pieces of equipment in FERA’s laboratories emphasise the difference between the ecology with which I am familiar and the Brave New World. The first is the BioRobot that is performs the DNA extractions although it is a disappointment to anyone who expects their robots to resemble R2D2. The second is the Illumina MiSeq next generation sequencing machine which is the heart of the operation, producing the sequences from the genes that we use as barcodes. We have been able to deduce the sequence of DNA bases in genes since the 1970s; however, it was a slow and laborious process. When I was doing my PhD, harassed-looking molecular biology students used to stalk the corridors holding the gels that they used to laboriously construct the DNA sequences, base by base. The Illumina MiSeq produces more sequences in an afternoon than they produced for their entire thesis. And, with the automation that the BioRobot brings to the process, the economics shift to such an extent that producing these sequences could well be faster and cheaper than paying myself and others to count diatoms under the microscope.
DNA preparation and sequencing equipment at FERA’s laboratories in York. Left: the BioRobot used for DNA extraction; right: the Illumina MiSeq next generation sequencing machine.
But the day after I visited FERA I was back in the River Ehen (see “A winter wonderland in the River Ehen”). I’ve sent several samples from here off to be sequenced as part of our present project, and am waiting to see what they reveal, particularly as my colleagues and I have struggled to name all of the diatoms using our traditional microscopic approach. This visit to the Ehen, however, threw up a surprise in the shape of an alga that had appeared at a site where we had not previously seen it. And here is the challenge: the nature of molecular biology is that you need very specific “primers” – molecules that can target precisely the gene of interest. It means that molecular biology is very good for finding what you are looking for, but not so good at noticing the unexpected. That, to me, raises the biggest challenge of the work that we are doing at the moment: how can we couple the undoubted potential of next generation sequencing to the observational skills that field biologists hone over the course of their careers (see “Slow science and streamcraft …”)?