Tracing bacteria with DNA techniques
With the help of DNA analysis, one can today quickly and reliably show what organisms are present in water, the extent of their presence and their possible sources.
The quality of surface water in the Netherlands is carefully protected. KWR, in a commission from the Dutch Directorate for Public Works and Water Management, is conducting research into methods to quickly and effectively determine the presence of pathogenic bacteria in outdoor bathing water. “For reasons of public health,” says Edwin Kardinaal, “it is important to know whether particular indicator bacteria, originating in human and animal faeces, are present in bathing water. If they are present, this can be an indication of the presence of pathogens as well. Cyanobacteria, also known as blue-green algae, also require our close attention, since they are capable of producing toxic substances that can be harmful to humans and animals.”
Before, one had to grow cultures or carry out microscopic counts to determine the concentration of certain bacteria. But research conducted by molecular mocrobiologists
Leo Heijnen and Bart Wullings has led to various new detection and characterisation methods, which draw on the opportunities offered by DNA techniques. “With DNA techniques you can essentially take a sample in the morning and have a result in the afternoon,” says Edwin Kardinaal. “Therefore you can tell much faster whether the water standards have been exceeded.”
Brieftly, DNA research involves isolating DNA and artificially reproducing pieces of DNA (PCR) that are characteristic of a particular species or group. One can determine the concentration of an organism through quantitative DNA techniques (qPCR). “This technique also offers the possibility of showing – for the Water Framework Directive, for instance – ‘DNA traces’ of higher organisms, such as fish and reptiles, and to discover more about their distribution patterns. Every living animal spreads environmental DNA (eDNA) into the water environment, through the loss of skin cells and excretion of faeces, for instance.”
Apart from its research into pathogens, blue-green algae and eDNA, KWR also applies DNA methods to trace the sources of faecal pollution: What are the origins of this pollution in (bathing) water, and how much of a risk does it represent? DNA studies of the bacteria found in samples taken at various locations in 2012 show that birds are major contributors to the contamination of bathing locations. Other risk factors are the limited hygiene of the swimmers themselves and the runoff from fields where cows graze. “In 2013, we will focus on the development of methods to determine the specific contribution of dogs to faecal pollution,” says Kardinaal. Looking to the future, he expects that our approach in five years’ time will be quite different. “We won’t any longer be growing cultures on a mass scale and will be making more use of DNA techniques. The new knowledge we acquire should lead to adjustments in the regulatory framework. But this is a slow process, which could stand in the way of the development of new techniques.”
© 2018 KWR Watercycle Research Institute