The Evolution of Microorganism Health Monitoring in Wastewater Treatment: From MLSS to DNA

September 8, 2025

The evolution of microbial monitoring in wastewater treatment has progressed from physical measurements of the biomass as a system to advanced molecular diagnostics, offering even greater clarity around the microbial community.

First-Generation Monitoring: Physical Parameter Measurements

Monitoring microorganism health in wastewater systems has traditionally relied on evaluating bulk physical characteristics of the mixed liquor. Operators measured parameters such as Mixed Liquor Suspended Solids (MLSS), Mixed Liquor Volatile Suspended Solids (MLVSS), Sludge Volume Index (SVI), Oxygen Uptake Rate (OUR), and Mean Cell Residence Time (MCRT) to assess biomass activity and process efficiency. While these metrics still provide essential insight into overall biomass performance and solids handling characteristics, they offer inference of system health and no specific information about members of the biological community itself.

Second-Generation Monitoring: Microscopic Examination

The next major advancement involved direct microscopic observation of the microbial community. Through wet mount microscopy, operators and microbiologists could examine floc structure, the presence and diversity of filamentous organisms, higher life forms such as protozoa and metazoa, and the clarity and biological activity of the bulk water. This technique enables a more nuanced understanding of system health and allows for early warning signs of issues like filamentous bulking, toxicity, or nutrient imbalances.

Third-Generation Monitoring: Molecular Diagnostics

Today, a new approach to monitoring microbial health is through molecular diagnostics, particularly DNA-based methods. In recent years, the cost and time required for high-throughput sequencing have dropped dramatically. These techniques allow for direct identification and quantification of microorganisms, providing a clear and specific profile of the microbial community. The results not only include a list of microbial genera, which can often number in the hundreds, but also categorize them into functional groups such as nitrifying bacteria, sulfur-reducing bacteria, filamentous bacteria, methanogens, and more.

Spotlight on qPCR: Precision Microbial Analysis

Quantitative PCR (qPCR) has emerged as a powerful tool for differentiating between closely related microbial species, including both bacteria and archaea. Known for its precision and reliability—traits that made it a global cornerstone in COVID-19 diagnostics—qPCR helps track specific organisms in your system.

This comprehensive approach has practical value in multiple ways. It can be used to establish a microbial baseline under optimal operating conditions, diagnose the root causes of biological process upsets, or confirm the presence of problematic organisms such as sulfur-reducing bacteria in odor investigations. Molecular monitoring provides a level of clarity and specificity that empowers wastewater professionals to move from reactive troubleshooting towards proactive system optimization.

Technical Consulting

EnviroZyme’s Technical Consulting service includes microscopic, DNA-based analysis, and physical parameters analysis:

By analyzing a sample under the microscope, our team can provide direct insights that help diagnose and correct issues before they escalate.
DNA-based diagnostics deliver a comprehensive profile of your entire microbial community and evaluate the organisms’ functions.
qPCR testing provides facilities with a reliable way to verify, track, and respond to biological dynamics with confidence.
Operational support translates traditional parameters like MLSS, MLVSS, SVI, OUR, and MCRT into meaningful guidance, helping facilities optimize system performance.