Towards a water-wise world Annual report 2014

Small changes in bacterial population effectively registered 

Next Generation Sequencing to monitor drinking water quality

27 December 2014BTO


Next Generation DNA sequencing makes it possible to make a “finger print” of the microbial composition of (drinking) water. If the bacterial composition of the water changes slightly, for example because a small quantity of contaminated water mixes in with the drinking water, this can be read in the microbial finger print. Within the water sector’s joint research programme (BTO), KWR and Vitens are together developing a very sensitive method to use Next Generation Sequencing to monitor drinking water quality at critical moments in water treatment processes and in the distribution system.

Bacterial populations are frequently made up of a whole “haystack” of different types of bacteria. You can identify these bacteria on the basis of their DNA. And, what is more, you can look for the specific DNA fragment of a single type of bacterium, that is, for “the needle in the haystack”. Thanks to new microbiological techniques you can take an even smarter approach. “With Next Generation DNA sequencing,” says Leo Heijnen, “you immediately look at the whole haystack, on the basis of a fragment that is present in the vast majority of bacteria, but which has a slightly different base pair composition in each species.” Next Generation Sequencing uses a DNA fragment of 500 base pairs, which can be found in 90-95 percent of all bacteria. By isolating the DNA from a water sample, then amplifying it with PCR, and subsequently having it analysed by a specialist laboratory using Next Generation Sequencing, you receive a huge amount of data in return. By processing these data with the proper software, you can discover which bacterial species are present in the water sample, and also get an indication of their numbers.

Finger print

KWR works with and for Vitens on the application of this new molecular/biological technique, so that Vitens can make a “finger print” of water samples. The company mainly wants to know whether small changes in the composition of the water are perceptible in changes in the finger print. “Imagine, for example, that you have drinking water which, as a result of a leakage, contains a small amount of surface water,” explains Bendert de Graaf of Vitens. “Would this be reflected in a small change in the bacterial finger print? And could you, on the basis of such a finger print, quickly designate the water as being good or bad?”

Sensitive measurement method

To answer these questions, within the water sector’s joint research programme (BTO), the method developed is first tested on artificial water samples, consisting of mixtures of drinking water and surface water in various proportions. The method proves to be so sensitive that it registers the presence of 0.1 ml of surface water in a litre of drinking water. The method is then tested in practice. After having replaced a pipe, Vitens measures the quantities of E. coli and enterococci in the water, following the method prescribed by regulations. As a result, in one of the samples only one colony formation unit per 100 ml was detected; this is this method’s detection limit. The same sample is then pre-treated and sent to be analysed with Next Generation Sequencing. The results show that the sample contains various bacteria of faecal origin. This method also registers changes in the bacterial population that occur when water treatment filters are cleaned. Next Generation Sequencing is thus a very sensitive and promising measurement method, with a number of application possibilities. “To enable the routine use of this technique in the future, however, the analysis itself would have to become a little faster and cheaper,” says De Graaf. “More development is also needed with regard to the processing of the large amounts of data involved. The software now being used is fine for scientific research, but it’s too complex for daily use in the lab.”

Monitoring the microbial composition of drinking water

In the coming period, Vitens, together with Wetsus, will be working on monitoring possible changes in the microbial composition of drinking water at critical moments in its treatment – for example, when the filter medium is cleaned or replaced – and in the distribution system – for example, in the case of repairs, mixing or leakages. KWR will be using the method in a variety of research projects, including research aimed at identifying the factors and bacteria present in biofilm that influence the regrowth of Aeromonas bacteria in water pipes.

© 2017 KWR Watercycle Research Institute

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