Applied Science Associates, Inc.

New Bedford Harbor water quality study uses DNA fingerprinting analysis and shows animal sources of fecal coliform many times that of humans

Contact: Nicole Whittier
Phone: 401-789-6224
June, 2004

For years, people have been concerned about pollution in New Bedford (MA) Harbor, with a "red flag" raised over what human beings and water treatment plants might be dumping into the bay. A recently completed study of water quality in New Bedford Harbor, commissioned by the New Bedford Harbor Trustee Council and conducted by Applied Science Associates (ASA), took a new approach to evaluate sources contributing pollution to the harbor. The study combined a field sampling program and computer modeling with DNA fingerprinting analysis to identify and quantify sources contributing fecal coliform (FC) to the waters of Outer New Bedford Harbor.

The results of the computer modeling, combined with the DNA analysis, indicate that humans are not the most significant source of FC in the study area. The study concluded that humans accounted for only a small fraction (~7-15%) of the analyzed samples of FC entering the harbor. DNA analysis reveals birds to be the dominant source of FC in the harbor, with rodents and raccoons also significant contributors.

Background

Potential for FC contamination is the primary concern affecting the decision of the Massachusetts Division of Marine Fisheries to restrict harvesting of shellfish in Outer New Bedford Harbor. This study was conducted to characterize the sources and distribution of FC in the harbor.

Pollution from sewage has long been thought to be a serious water quality problem in New Bedford Harbor, with a number of man-made sources potentially contributing FC to the harbor. Because no one knew how much fecal material came from each of these potential sources, the primary source of the FC in the harbor was uncertain. Candidates included failing septic systems along Boys and Girls Creeks and the west shore of Sconticut Neck and local sewage treatment facilities such as the Fairhaven Water Pollution Control Facility (FWPCF), which was not required to chlorinate its effluent between November and March of each year. Additionally, a number of combined sewer outflows (CSOs) that discharged raw sewage during significant storm events had once been located along the harbor shoreline, although the City of New Bedford has recently eliminated most of the outer harbor CSOs. Natural sources were also thought to contribute to the high fecal counts found in the bay, though the magnitude of their contribution was uncertain.

Details of the Study

A multi-phase approach, incorporating both fieldwork and modeling, was taken in this study. First, a field survey was conducted by EA Engineering, Science and Technology, Inc., under the direction of ASA, to characterize the FC sources contributing to and resulting FC levels found in the harbor. Water samples from the field program were then subjected to DNA fingerprinting analysis to determine the origin of the FC at each of the identified sources. Finally, a modeling study was undertaken to evaluate the effect of each of the identified sources on the distribution of FC in the outer harbor.

Water samples were collected at 21 stations in and around New Bedford Harbor. These stations were carefully selected so as to adequately characterize the origins and magnitudes of the FC sources and the resulting FC levels. Sampling began in April 2002 and continued until July 2003. The field program also included intensive sampling of two storm events. Historical data indicated that there were many instances of FC concentrations exceeding the 14 MPN/100 ml regulatory threshold for shellfishing prior to 2000. There has been dramatic improvement since 2000, but the field survey still found numerous occasions on which FC concentrations exceeded the regulatory threshold, with FC concentrations as high as 920,000 MPN/100 ml reported.

Samples from two dry periods and one of the intensively sampled storm events were subjected to a bacterial source tracking analysis to determine the biological origin of the fecal coliform. Two different bacterial fingerprinting techniques were used in this analysis: DNA Ribotyping and the F-Specific (F+ or FRNA) coliphage method. DNA Ribotyping analysis, which can distinguish human and non-human (e.g., horse, cow, deer, chicken, bird, etc.) sources, was performed by Dr. Hemant Chikarmane's laboratory located at Cape Cod Community College in Barnstable, MA. The F-Specific coliphage analysis was conducted at Dr. David Smith's laboratory at the University of Rhode Island's Graduate School of Oceanography in Narragansett, RI. This method uses the differences between human and animal RNA to determine the organisms associated with the fecal pollution in the water.

Hydrodynamic modeling of Outer New Bedford Harbor was performed to obtain detailed currents in the harbor using ASA's Boundary Fitted Hydrodynamic (BFHYDRO) model calibrated with historical data of winds, tides and currents in the harbor. Results from the hydrodynamic model were then used in conjunction with data on FC source concentrations from the field survey to conduct a series of pollutant fate and transport simulations using ASA's Boundary Fitted Mass Transport (BFMASS) model. Model simulations were conducted for three key scenarios: 1) typical dry conditions (excluding November-December period); 2) typical storm conditions; and 3) dry conditions during the November-December period.

Conclusions

The conclusions from the computer modeling combined with the DNA fingerprint analysis indicate that humans are a minor source of FC relative to other animals for New Bedford Harbor. DNA fingerprinting techniques indicate that birds are the dominant source of FC in the harbor, with rodents and raccoons also significant contributors. Humans were found to account for only a small fraction (~7-15%) of the total FC entering the outer harbor. The study was able to distinguish fecal coliform from humans, goose, rats, deer, seagulls, raccoons, horses and cows in the New Bedford area.

FC concentrations were found to be relatively low throughout most of the harbor, with higher concentrations limited to near-shore areas. ASA's computer modeling indicates that sources within Inner New Bedford Harbor contributed significant amounts of FC to the outer harbor during November and December. This period coincides with a period during which the FWPCF was not required to chlorinate its effluent, but it is uncertain whether this was the source of the observed FC. FWPCF has subsequently begun treating its effluent with UV radiation as a requirement for ongoing permitting, eliminating any FC contributions from this source as a future concern. FC counts during the storm events were significantly higher than those observed during dry periods.