Rapid Detection and Quantitation of Active Microorganisms

The detection and rapid quantitation of active microorganisms in complex microbial communities are important for informing process monitoring and control and risk assessment in the water sector. However, DNA sequencing, data acquisition, and data interpretation are time-consuming and require advanced expertise, and these methods may not provide insights into the viability or activity of detected microorganisms. Enabling rapid turnaround times on sample-to-data acquisition and analyses, and determining whether detected microorganisms are active would represent a breakthrough for the sector. This project developed an easy-to-use, rapid Nanopore sequencing protocol for microbial species detection, quantitation, and replication rate estimation. The ability to obtain quantitative estimates and replication rates of microbial species within an hour may allow for DNA-sequencing-aided real-time process control. The specific objectives of this project were to (1) develop and optimize the experimental and computational components of the protocol for rapid microbial detection, quantitation, and replication rate estimation, (2) test the protocol in the management of microbial community structure for a biological nutrient removal system, and (3) develop a guidance manual and training workshops to allow for broader application of the protocol. Published in 2026. Research partners: Great Lakes Water Authority and HRSD.