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Water quality testing gets reimagined with new DNA sequencing technology

A more efficient method of DNA sequencing is making it easier for utilities to proactively manage water quality.

Scientists at the Australian Water Quality Centre (AWQC) in Adelaide, a unit within SA Water, are using high-throughput DNA sequencing technology to more comprehensively analyse water samples for common biological contaminants.

The AWQC is the first water laboratory in Australia to apply this technology to water quality analysis. This has significant implications for public health, research, conservation efforts and improving conditions within water treatment plants.

Conventional methods for detecting faecal contamination require days for culturing, and then they only target specific bacteria.

Additionally, if contamination by faecal matter from livestock or agricultural activity is suspected, scientists have to spend hours performing microscopy to search for and count parasites such as Giardia or Cryptosporidium, which can be easily missed.

The benefit of the new technology is that all bacteria can be determined from the one test, and this same analysis also reveals what vertebrates, fish and other organisms have been present in the water. This combined information provides a more comprehensive picture of all possible contamination inputs.

“There are already rigorous treatment processes in place at our plants across the state, but this new technology allows a more targeted approach,” said SA Water's Senior Manager of Laboratory Services Karen Simpson.

The AWQC has acquired two pieces of specialised equipment to perform this DNA analysis.

DNA extraction, purification, fragmentation and amplification are performed using the ION Chef. The amplified fragments tether to a small bead, which sits in one of millions of wells on a semiconducting chip.

The chip is then placed in the ION S5, which reads the DNA using next-gen sequencing (NGS) methods.

The AWQC's Molecular Scientist Lisa Teakle explained that a computer pieces together the fragments to generate complete sequences for each organism. These are then compared against reference sequences available in databases such as Greengenes, allowing organisms – like livestock, native fish, humans and microbes – that have been in contact with the water to be identified.

DNA sequencing reduces the time to perform the water analysis and has far greater accuracy than traditional methods. This allows water treatment plants to implement a rapid, targeted response to contaminants, and notify the public much earlier when applicable, thus significantly reducing the number of potential impacts.

The use of this technology also has major implications for conservation campaigns. Teakle explained that the high degree of accuracy and non-invasive nature means it can be used to monitor the presence of native and invasive species, organisms that are typically elusive (such as platypuses) or ones that were previously unknown within the waterways, thus negating restrictions imposed by conventional catch and release methods.

“It is very useful to know the diversity and abundance of aquatic life in water sources, as they can be indicators of a healthy water system; the ION Chef and ION S5 technology is helping us do just this,” Simpson said.

Finally, the technology can be used to help detect and characterise nitrifying bacteria in wastewater treatment plants, which can be difficult to culture in lab conditions.

Bacteria such as Nitrosomonas sp. lower ammonia levels in wastewater plants by breaking it down into molecules that are useable energy sources for themselves and other bacteria.

This increases the effectiveness of the wastewater treatment process in reducing nutrient levels in discharges, helping to prevent the occurrence of algal blooms, which can potentially suffocate and release toxins into water systems.

Currently the AWQC is using this technology to gain better insight into these ‘good’ bacterial communities in the hopes of being able to grow them on a larger scale and incorporate them into the treatment process as a way to increase their energy and chemical efficiency.

“Nitrifying bacteria are very sensitive to environmental and operational factors,” Simpson said.

“However, there has been no known work undertaken on the connection of the population of nitrifiers using NGS to operational performance and process stability.

“With this in mind, tremendous scope exists for the use of molecular-based monitoring tools to assist with optimising the functional performance of the activated sludge process.”

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