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About Microbiology

Microbiological analyses can indicate when a water body is no longer safe for recreational use and can give insight to sources of pollution. Microbiological analyses include tests for:

  • Fecal indicator bacteria – the microorganisms commonly associated with the gut tract of mammals, some of which can make people sick if ingested,
  • Cyanobacteria and cyanotoxin identification – the microorganisms and toxins associated with harmful algal blooms,
  • Microbial source tracking – the identification of different animal sources of fecal pollution based on microbial communities unique to humans and different animals (typically DNA analyses).

Quality Assurance and Quality Control

Generating data that can be relied upon to advise public health entities and inform the public on the safety of water bodies is paramount. To achieve a high standard of data quality, the laboratories that conduct microbiological assays must follow rigorous QA/QC (Quality Assurance/Quality Control) practices. Laboratories that produce low-quality data undermine project goals and can result in lost time, money, and recreation access.

Quality assurance is comprised of an integrated system of management activities that are in place for standard methods or developed during the planning phase of a unique project. These activities are typically detailed in a project specific QA plan that includes QC requirements and corrective actions for field collections and laboratory analyses. Since microbiological assays include a variety of laboratory methods, QA plans are important tools to ensure the appropriate QC protocols are utilized.

Sample Collection
Sample collection for microbiological analyses require the collector to follow matrix dependent best practices. A sample collection targeting fecal indicator bacteria requires sterile bottles and aseptic technique (the practice of not allowing unintended organisms to contaminate the sample, including from the person collecting the sample), whereas samples being collected for DNA analysis require certified DNA-free collection devices or devices that have been treated to remove nucleic acids, using bleach or specialized DNA removing enzymes.

Sample Handling
Strict sample handling is critical for microbiological analyses. Fecal indicator bacteria are required to be analyzed within specific time constraints depending on the type of sample and regulatory purpose. Samples collected for analysis of nucleic acids (DNA or RNA) often require a preservative or flash freezing in liquid nitrogen, and subsequent storage at -20°C or -80°C.

Laboratory QC
Microbiological assays are unique in that they require aseptic technique to be employed throughout sample processing. To maintain confidence that aseptic technique is appropriately applied, and the results are produced with precision, QC protocols include:

  • Sterility Checks - Confirming new batches of growth media, sterile equipment, and processing supplies do not exhibit growth when introduced to sterile nutrient media.
  • Positive controls - a pure culture of the organism of interest. Ensuring that new media or new assay equipment can grow and detect an organism of interest. Target DNA in the case of PCR based methods.
  • Negative Controls - a known organism that does not react with the test kit or will not grow with the culture media used. Non-target DNA in the case of PCR based methods.
  • Laboratory Duplicates and Precision Analyses- The analysis of samples in duplicate to determine the precision of a test batch and continuous monitoring to ensure sample processing has not imparted unreasonable variance.

Contact Information

For questions regarding Microbiology data, please email:

Data Management

Data management includes measures such as uniform business rules for reporting results and data review. These strategies ensure the usability and accessibility of the data generated for a project.

  Learn more on the Data Management webpage.

Measurement Quality Objectives

The SWAMP Measurement Quality Objectives (MQOs) list the required QC samples, acceptance criteria for QC results, and sample handling guidance for the program organized by analyte group.

Fecal Indicator Bacteria

Cyanotoxins by Ligand-Binding Assays

Cyanotoxins by LC/MS