What is microbial source tracking?

Microbial source tracking is a suite of DNA-based techniques used to determine the sources of fecal bacteria in an aquatic environment, such as a lake, river or stream.

Knowing the source of fecal contamination — livestock, domestic animals, wildlife or humans — allows resource managers to make more informed water quality management decisions.

Why is fecal contamination dangerous?

Fecal contamination in water puts people and animals at immediate risk of illness from disease-causing organisms. There are also economic impacts: beach closures; damage to shellfish harvesting and aquaculture; and the contamination of crops and other agricultural products.

Traditional techniques for examining contaminated water measure the amount of fecal indicator bacteria (FIB) in a sample. This can tell us whether there’s fecal matter in a watershed, but doesn’t identify the source.

Microbial source tracking (MST) gives water resource managers a powerful tool to understand the source of contamination and mitigate its effects — or stop it all together.

Why do we need to identify the source of bacteria?

Suppose a popular swimming beach is found to be contaminated with fecal bacteria. The beach is near a river that drains into the ocean, and this river is fed by multiple streams.

We know there’s fecal contamination in the water, but from where?

An off-leash dog park that’s up the river? Migratory flocks of Canada geese resting on the beach? A leaky sewer that’s leaching into a brook? Or is it a combination of all three?

With microbial source tracking and quantitative real-time PCR (qPCR) technology, we can pinpoint the bacteria’s source.

MST analyzes the genetic material present in fecal bacteria to determine the specific microorganisms present, and then compares that to a database of known microorganisms from a wide range of sources.

How can MST distinguish fecal contamination between animal species?

Animals’ unique diets and behaviors create different microbial communities in their digestive tracts. These microorganisms can be used as indicators of the source of the contamination. For example, certain bacteria or viruses that are found in the feces of cows may not be found in the feces of pigs, and vice versa.

DNA extracted from a single water sample can be used to identify the presence of multiple MST markers, giving an exact proportion of bacteria from each potential contaminant.