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Using Digital PCR to improve our water

Water droplet

A career in water quality can be incredibly varied and diverse, spanning from work with drinking water, to oceans, rivers, estuaries, or even storm water and wastewater. Due to the incredibly varied and unpredictable nature of water, it can be a very difficult substance to work with.

Blood for example, is very consistent – even though people are individually different, their blood is comprised of mostly the same constituent parts, and for example the pH of blood is relatively consistent. With environmental water samples, there can be large variations in salinity, color, and pH levels amongst other things. Just think of the difference between the water that comes from your kitchen sink, and the water at the beach of from a creek or lake.

I started as a biological oceanographer, studying bacteria and viruses in the open ocean. The further along in my research programme I went, the more and more interested I became in the impact that people are having on the ocean and so now, my main research area lies in area where the land meets the ocean. Most people do not realize it, but that more than half of the world’s people live within 100 km of the ocean.

The idea behind our research program is quite a simple one – we are applying new PCR-based molecular methods to quite old problems. It’s been a long understood fact that pathogens in water can make people ill, however it’s only been in the last few decades that we have been able to directly count the dangerous bacteria and viruses in water and identify them quickly in a water sample.

Using molecular diagnostics in this way enables us to improve the lives of the public. If someone ingests even a small amount of dangerous bacteria like Salmonella or a dangerous virus such as norovirus, someone will almost certainly get ill. To get sick, it only requires that you ingest a few to a few hundred of these microorganisms. Using molecular diagnostics, we are able to measure the bacteria and viruses that we care about, at the very low concentrations that we care about. Using ddPCR, we are able to quantify viruses and bacteria at levels that matter to a single person in the ocean who is swimming or surfing and ingesting water.

Before such methods enabled this level of accuracy, the older methods simply could tell you if the microorganisms were present or not. Therefore, it was much more difficult to draw the line between what was safe and what wasn’t. The lack of quantitative information meant that there were times that a beach was open when it should have been closed, or conversely that a beach was unnecessarily closed, affecting not only people’s ability to go in the ocean, but also the subsequent economy of shops and cafes that benefit from swimmers and surfers.

Closing beaches and protecting water quality can be tricky work. I am a researcher, so I do not typically have to make those decisions, but I do assist people at the State level in making them. The decisions can be difficult to make. Finding the balance between protecting people and overprotecting people can be very tricky. If you constantly tell people the water is contaminated, when it is not clearly of risk to swimmers, then they will start to go in anyway. Alternatively, if you set your water quality thresholds too high, and the beach remains open and people get ill, then they don’t want to go in the water at all, and the economy can suffer. My job, as a researcher and collaborator, is to provide the data to assist in the decision making process, and ddPCR and the new molecular tools allow me to be much more accurate in the data that I provide. With developing technologies such as ddPCR, we are able to more confidently protect people from getting ill and with that, we have the ability to have a real impact on people’s lives.

Rachel Noble
is a Professor and Director of Institute for the Environment, University of North Carolina Institute of Marine Sciences. She is speaking at the qPCR and Digital PCR Congress: USA on Quantifying Pathogenic Viruses and Bacteria using ddPCR in Complex Water Samples.

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