Rapid microbial surveillance using Nanopore DNA sequencing

Wastewater treatment plants depend heavily on microbial communities to clean sewage water, which has to pass strict nutrient requirements before the effluent goes into waterways. The biological processes are generally stable. However, problems do occur occasionally, can arise quickly and lead to process breakdown. To mitigate this, operators have to act fast to control problematic microbes. With current methods, it is often impossible to predict a system crash before it is too late. Monitoring the microbial community for critical changes is tedious, as the process from sample to results take several days and requires expert knowledge as well as expensive lab facilities.
With the development of cheap, portable real-time sequencing (Oxford Nanopore MinION) it is now possible to detect problematic microorganisms, such as pathogens or process critical bacteria from wastewater treatment plants, onsite in a matter of hours. Rapid and effective protocols for DNA extraction need to be developed to use with Oxford Nanopore kits, along with bioinformatic tools to obtain results fast and without user intervention. This will provide actionable information to plant operators in time to mitigate a process breakdown. The developed protocols and tools will ultimately allow plant operators to monitor and report the microbial status as a routine measurement alongside simple process characteristics such as pH and temperature.