Molecular Biology

The Biology Program's Molecular Section uses microbial source tracking (MST) analyses to identify sources of fecal contamination in Florida’s waterbodies. Fecal indicator bacteria (FIB), like Escherichia coli (E. coli) and Enterococci, are commonly found in human and animal waste but can also live naturally in soil, sediment, water, periphyton and biofilms.

Standard methods used for detecting FIB are culture based and cannot discriminate between enteric (living in the gut of a host animal) and environmental bacteria not associated with fecal waste or elevated health risks. MST analyses help distinguish between potential contamination sources using genetic markers, as the genetic composition of bacteria differs between human and non-human sources.

DEP’s molecular laboratory uses quantitative polymerase chain reaction (qPCR) assays to investigate fecal contamination in surface waters. This involves collection and filtration of water samples to capture bacteria, extraction of the bacterial DNA, and amplification of target DNA by qPCR, which quantifies the amount of specific DNA present in the sample. This amount indicates how much fecal bacteria from a specific animal species is present in the sample, which provides information about whether that animal is contributing to the elevated bacteria levels in the waterbody.

Results from qPCR analyses are used in combination with microbiological and chemical analyses to determine sources of fecal bacteria. Molecular lab offers host-associated qPCR assays that can detect fecal waste from humans (HF183), seabirds (Gull2), all birds (GFD), all ruminants (BacR).The molecular toolbox also includes EPA patented qPCR markers for human (HumM2), cattle (CowM2) and canine (DG3).

Identifying the source of fecal bacteria is an essential step in prioritizing restoration activities. Levels of bacteria above surface water quality thresholds may lead to a waterbody being classified as impaired.

Staff at DEP aim to restore all impaired water bodies but must prioritize those that pose the greatest threat to public health. Waters impacted by human waste are more likely to cause adverse health effects than those impacted by animal waste and are given the highest restoration priority. Microbial source tracking studies help the department rapidly identify the dominant sources of fecal contamination and communicate any risks associated with human exposure.

By targeting anthropogenically enriched water bodies for restoration, DEP staff can best protect public health and the environment in Florida.