Using Phylogenetics for Fecal Source
Tracking in the SNEP Region

SNEP

The Palmer River begins in Rehoboth, Massachusetts in a mainly forested area before flowing
alongside agricultural operations as it meanders its way south to the Rhode Island state border and
eventually into the Barrington-Warren River and Narragansett Bay. While the Palmer River Watershed
is fairly bucolic and agrarian, it, like many other watersheds in our region, is facing the ever-increasing
pressure of suburbanization. But with agriculture and suburbanization comes pollution. In 1992 the
Rhode Island Department of Environmental Management (RIDEM) listed portions of the river as
impaired for recreation and shellfish consumption due to high levels of fecal coliform; the
Massachusetts Department of Environmental Protection (MassDEP) followed suit in 2002. Shellfish
beds were closed, and recreational activities were restricted for safety. The source of the fecal
contamination was thought to be from crops, cattle and dairy farms, failing or illicitly connected septic
systems, and waterfowl.

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To begin lessening the fecal contamination coming from
farms, the Palmer River watershed was included in the
National Water Quality initiative (NWQI) in 2012. Being an
NWQi watershed makes Natural Resources Conservation
Service (NRCS) project funding and expertise available and
can often lead to opportunities for other sources of
funding such as Clean Water Act (CWA) section 319
nonpoint source management funds. The funding typically
goes to on-the-farm agricultural conservation practices, or
best management practices (BMPs) as they are
sometimes referred, that decrease the amount of
pollution entering our waters while often increasing
agricultural efficiency. In the Palmer River watershed,
practices included creating grass buffers along waterways,
improved litter and manure storage, livestock exclusion
fences, and protecting heavy use areas from erosion, to
name a few.

Water quality sampling in the Palmer River Watershed

To understand how these practices were improving the water quality of the Palmer River, MassDEP,
RIDEM, and the U.S Environmental Protection Agency (EPA) New England Regional Lab collaborated to
collect traditional water samples between 2012 and 2019. As part of this monitoring effort, samples
were collected from 2017-2019 for a novel analysis to determine specific sources of fecal
contamination using the "PhyloChip" (Developed by Lawrence Berkley National Labs).

Southeast New England Program
www.epa.gov/snecwrp


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Using Phylogenetics for Fecal Source SNEP

Tracking in the SNEP Region

Applying this technique to ambient water samples tells you about its bacterial community composition
which can then be compared to those normally found in the gut of various animals and humans. This
comparison, in turn, gives us an idea of who or what has been contaminating the water with their feces.
Traditional water quality sampling for e. coli, fecal coliform bacteria, and Enterococci, while extremely
useful, can only indicate the potential that harmful fecal bacteria are present; whereas the PhyloChip can
not only determine likely fecal contamination, but its mammalian source as well. It can also be used to
determine if specific known, harmful species of bacteria are present.

The Southeast New England Program (SNEP) used 50 of the samples collected in 2018 in the Palmer
River to conduct a pilot study using the PhyloChip. Samples were selected based on spatial and temporal
representativeness, and their likelihood of fecal contamination. These results can be used to tell us
which fecal source(s) is polluting the water segment. We learned that while cow, pig, pet, and horse
contamination was present, human and waterfowl contamination occurred more often in more
locations. The results indicate that farm-based contamination may not contribute as heavily to water
quality impairment and shellfish bed closure as failing septic systems and Canadian geese (read the full
report here). SNEP in conjunction with EPA's New England Regional Lab is currently working to analyze
another set of Palmer River samples from 2019 to get an idea of contamination source changes over a
longer time scale.

The results from this pilot, as well as others being conducted by EPA Region 1, are beginning to show the
utility of this advanced, innovative, technique for tracking the sources, as well as spatial and temporal
distribution, of fecal contamination in watersheds. Future studies may also include evaluation of the
"sinks" of fecal contamination such aquaculture operations and shellfish beds.

For more information please contact: Dombroski.ian@epa.gov

SNEP

Southeast New England Program
www.epa.gov/snecwrp


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