Scott J. Kenner, Professor, South Dakota School of Mines and Technology Rapid City, South Dakota

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1 Report on USGS 104b Grant Program for: Investigation of the contribution of coliform contamination in runoff from scoured bed sediments Principal Investigators: Jennifer L. Benning, Assistant Professor, South Dakota School of Mines and Technology, Rapid City, South Dakota (605) Scott J. Kenner, Professor, South Dakota School of Mines and Technology Rapid City, South Dakota (605) Arden D. Davis, Professor, South Dakota School of Mines and Technology Rapid City, South Dakota (605) Project Summary This grant opportunity provided funding for research that has focused on characterizing channel bed sediments as a source of coliform bacteria (fecal and E. Coli) contamination in stormwater runoff. Previous studies involving the Arrowhead drainage basin in Rapid City, South Dakota have indicated that there is an elevated fecal coliform bacterial concentration. Because Rapid Creek is assigned the beneficial use of immersion recreation it is required that no single grab sample exceed 400 colony forming units (CFU) per 100 ml or the geometric mean of 5 samples collected over a 30 day period sampled at least 24 hours apart cannot exceed 200 CFU/100mL. Several watershed studies conducted by the principle investigators, the SD Department of Environment and Natural Resources (SDDENR) and others have shown that concentrations of bacteria in runoff exceed water quality criterion, often by orders of magnitude. The objectives of this research were to collect surface runoff and bed sediment samples, both before and after storm runoff events, and analyze each for its bacterial content, use those

2 samples and previously collected data to evaluate growth/decay models for the representation of fecal bacteria in sediments, determine if the runoff sediment is characteristic of the bed sediment, determine the percent contribution to the bacterial loading in the runoff emanating from the sediment, and recommend cost-effective BMPs that will promote the beneficial uses of the surface waters and enhance the economic opportunities associated with those uses for South Dakota. Further details of this summary are provided in the thesis Sediment as a Source of Fecal Coliform in Stormwater Runoff in the Arrowhead and Meade-Hawthorne Drainage Basins by Keri Schiferl (Schiferl, 2011). The first objective in the thesis was to evaluate the soils in the two drainage basins for the presence and growth of Fecal Coliform and E. Coli bacteria in sediments of the main drainage channels of each watershed. Soil and water (when water was present) samples were taken following three storms in each basin to ascertain if the bacteria loads were growing on location and potentially being resuspended during runoff events. While the water concentrations decreased rapidly after the storm events, the soil concentrations remained high for an extended period which indicates the persistence of bacteria in the soils. The next objective was to determine if there were environments in either watershed that were more conducive to bacteria growth. Previous studies have indicated that with an increase in connected impervious area the concentrations of bacteria in the runoff tend to increase. While the Arrowhead drainage is composed of 91.4% pervious area the Meade-Hawthorne drainage is 61.4% pervious with more curb and gutter draining to storm sewer. When the sediment samples were compared for the two, the 25 th percentile for the Meade-Hawthorne drainage was higher than the median value for the Arrowhead basin. There was one sight in the Arrowhead basin that did have extremely high values of sedimental fecal coliform but it was attributed to a silt fence that caused excess buildup of sediment.

3 The third objective was to ascertain the location in the channel with the largest amount of bacteria. It was found that the center of the channel was the sight of the prevalent concentration. This trend was seen at each of the sights in both drainage basins where a bank and middle sample were taken. However this theory cannot be totally validated because of the existence of the silt fence at the Fairway Hills site in the Arrowhead drainage basin and the possibility of an illicit connection to the storm sewer or a leaking sanitary sewer in the Meade drainage basin. The final and main objective of the study was to establish a connection between sediment resuspension and fecal coliform concentrations during runoff events. The sediment sample concentrations originally in MPN/g-dry were averaged and then converted to CFU/100mL for comparison with the EMC values for aqueous fecal coliform measured during runoff events. The potential contributions of fecal coliform from TSS, based on concentrations measured in the drainage substrate samples, did not exceed 3% of the aqueous sample values and therefore it was determined that the main contributor to the aqueous concentrations was coming from upstream rather than resuspension of bacteria growing in the sediment. In summary, fecal coliform bacteria are present, persisting, and growing in the Arrowhead and Meade- Hawthorne drainage basin sediment but they are only a minor contributor to the overall concentration in runoff. Also, the level of urbanization (percent impervious area) does seem to have an effect on the fecal coliform bacterial concentration in the storm water runoff with Arrowhead being the less developed and thus the lower contributor to the Rapid Creek system. Project Extension: In order to continue the work on the Rapid City Storm Water Management Project, it was decided that in 2012 there would be continued storm event sampling in the Arrowhead and Meade-Hawthorne drainage basins to evaluate the effects of increased urbanization (impervious area) on the runoff

4 quantities and fecal coliform bacterial concentrations entering Rapid Creek and to get a better idea of the source of the bacteria in the runoff. Two models have been built using the Environmental Protection Agency s (EPA) Storm Water Management Model (SWMM), calibrated using the parameter optimization software PEST, and validated to assure a high correlation with the measured observations in the two drainage basins at their current state of development. The model representing the Arrowhead basin was then be modified to equal the level of development in the Meade/Hawthorne basin while maintaining the original conveyance structures. This added the ability to evaluate the effect of those conveyance structures on the runoff quantity and quality. To assess the effect of the increased urbanization from a regulatory standpoint, the results from the three models were also compared to previously developed total maximum daily load (TMDL) values for fecal coliform bacteria (FCB). The SWMM model results will be useful for several purposes, such as providing: 1) current estimates of the annual runoff and pollutant loads for the study watersheds; 2) a comparison of pollutant loads between current and future built-up scenarios; and 3) a demonstration of the ability to accurately calibrate a watershed model using observed data. It is expected that the modeled bacterial load results can be used to assess the current urban runoff loads referenced in a recent TMDL Report (Kenner and Smith 2010). This information will help guide future TMDL calculations by providing actual load estimates for urban areas. The effect of increased impervious area on runoff and bacterial loads will benefit urban planning officials that may consider the addition of best-management-practices for new developments in certain areas. To assess the sources of the bacteria in the drainage basins water quality samples were collected during storm events on both of the basins. The samples were analyzed for Total Suspended Solids, Fecal coliform, E. Coli, Nitrate, and Phosphorus. Pyrosequencing has also been utilized to ascertain the biological species that is contributing the highest level of fecal coliform bacteria (Unno, et al., 2010).

5 Pyrosequencing is a method of DNA sequencing that uses the detection of pyrophosphate release to indicate nucleotide incorporation into a synthesized DNA strand allowing the DNA strand to be synthesized and sequenced simultaneously. The method is explained in further detail in the Genome Research article: Pyrosequencing Sheds Light on DNA Sequencing (Ronaghi, 2001). The analysis of the results from the pyrosequencing process is ongoing.

6 References Kenner, D. S., and Smith, R. L. (2010). "Fecal Coliform, Escherichia Coli Bacteria Total Maximum Daily Loads (TMDLs) for Lower Rapid Creek, Pennington County, South Dakota." South Dakota Department of Environment and Natural Resources/South Dakota School of Mines and Technology. Ronaghi, M. (2001). Pyrosequencing Sheds Light on DNA Sequencing. Genome Research, Schiferl, K. (2011). Sediment as a Source of Fecal Coliform in Stormwater Runoff in the Arrowhead and Meade-Hawthorne Drainage Basins. Unno, T., Jang, J., Han, D., Kim, J. H., Sadowsky, M., Kim, O.-S., et al. (2010). Use of Barcoded Pyrosequencing and Shared OTUs to Determine Sources of Fecal Bacteria in Watersheds. Environmental Science and Technology,