Molecular biology to track water quality
The power of molecular biology means that techniques like PCR coupled with sequence analysis can be used to monitor the environment and audit the presence, and even abundance, of different organisms. This is particularly helpful when it comes to the aquatic realm. And Cambridge University’s Max Stammnitz has been showing quite how useful along the River Cam, the training ground for a certain famous rowing team, as he told Chris Smith...
Max - Many of our friends in Cambridge who regularly row and swim have reported to us that there are infections, severe infections, occasionally occurring involving people's eyes and open wounds, leading to hospitalisations in certain cases. So that is one aspect of the biological problem that we were facing. And then on the other hand, our team of students that then later formed, it was all composed by geneticists interested in applying DNA analysis methods to problems all around us outside the lab. And then these two things basically came together in the so-called PuntSeq project
Chris - And you thought, right, hey presto, we can put together the challenge of trying to find out why there are infections in waterways in our rowing friends, and apply some new technology and genetics knowledge to try and solve it?
Max - Exactly. You basically track biological activity or microbial life in the water sources through their DNA footprints, as we like to say. So you can essentially take a sample, in our case fresh water from the river Cam, extract the bacterial DNA from that and then analyse it with a very modern DNA sequencing platform that gives us a lot of data on bacterial species and abundancies.
Chris - So you can actually get some idea as to the burden of a particular bacteria type in the water? Because that's one criticism of doing this sort of thing. It's so sensitive that you end up with a signal for a particular bacteria, but it's so rare in real terms that it's not going to pose any kind of threat, really, so you've got around that?
Max - Yes and no. To a certain extent you can say, across the range of samples that you take along the waterway, is a bacterial species increasing or decreasing in numbers. Do we have a suspect sewage pipe that might lead into the water source? Then we might suspect that certain bacteria that might cause infections through wastewater sources, that they are likely to be found downstream of that. But it's true that, without additional laboratory work, you cannot necessarily say whether a bacterium that you spot with this DNA platform, whether it is actually harmful. So we see this method more as an early stage typification of your local water source rather than find an answer to 'hey, this is making people sick or not'.
Chris - Indeed, because what you can't say is that, from that DNA signal, this came from a viable organism.
Max - That's true. Yeah. We might in fact have looked at lots of dead bacteria. But there's a reason why these dead bacteria are floating in the water, right? They must come from somewhere. So we think that even if, you know, we trace mostly dead organisms, it is interesting to see where these might've come from and what their roles might be, even if it's further upstream of the source where you're sampling.
Chris - Did you get an answer for your rower friends?
Max - Yes, we think so. Downstream of the city of Cambridge, there is a large waste water treatment plant. So the waste waters, after treatment, are basically fed back into the river. And we do see certain spikes of bacteria after that that we can associate with pathogenic bacteria. We didn't follow up on it through much lab work, to be very honest, we entered a little collaboration with Public Health England and sent some of our suspect candidates' DNA to them to verify whether these could actually be pathogens or not. And most of their results were similar along our lines that you cannot, a hundred percent, be sure that there's enough infectious material. But you can definitely say that in certain spots we find bacteria such as pseudomonas aeruginosa. So we can say these bacteria are present, be they alive or dead. We cannot necessarily say, okay, on this particular day, if you were to fall in and your immune system might've not been the strongest, you would have been a likely candidate to fall ill from that. But you can certainly see that, from this point onwards, it's much easier to reduce the candidate list of pathogens in a given water source. I mean, overall, we were able to measure more than 600 different bacterial genres. So you reduce it down from a huge list of potential candidates. And besides the whole biomedical question, you also get an insight into, you know, just the biodiversity, just through DNA analysis.
Chris - The mere fact that you've proved that this can work though, presumably what you could do is to choose some very reliable indicator species that have a good specificity for contamination of the water with other threats, and then use those almost like a bacterial canary down the coal mine, where if you detect those, which are rare under normal circumstances, but a strong predictor of contamination of the water with, for instance, sewage, you could then use this very successful and sensitive technique to say, well, look, this water looks contaminated, it would be a bad time to go rowing today.
Max - That's correct. Yes. To be very honest, there are ways to do that still that are much cheaper and that really just pinpoint the indicator species for other purposes. We could actually already see it working, for example, since we took samples both in the earlier spring months and later in summer, we could see that throughout this time, the number of cyanobacteria increased in certain spots. And we think maybe these could be used as indicators towards, you know, algae, flowering periods. So not necessarily just about pathogens, but also about other biological processes that happen in these sources.