Waterbodies throughout Northwest Indiana, specifically tributaries to Lake Michigan and its coastal waters, have long suffered from bacterial pollution. While many potential fecal inputs to these waterbodies exist, effluent or leakage from the 30,000 domestic septic tanks within the region presents a particular health hazard. This project surveyed 15 distinct aquatic resources, with multiple samples collected within most, under both wet and dry conditions throughout 2019 to determine the extent of E. coli pollution, the potential for human fecal inputs as the cause, and specific identification of septic systems as a pollution source. Over the course of the project, my lab collected over 170 water samples and 39 fecal samples. Our data showed that 60% of samples exceeded the Indiana state ambient/recreational water quality criterion of 235 MPN E. coli per 100 mL, with ~18% of samples exceeding 1000 MPN E. coli per 100 mL. We analyzed samples exceeding the water quality criterion for human-specific bacterial markers using the EPA’s Human Bacteroides quantitative PCR (qPCR) assay to determine if human fecal inputs were a source of the pollution. Of the 96 samples analyzed by qPCR, ~40% had probable human contamination, and 17% had a high probability of human fecal inputs. DNA amplicon sequencing of the microbial community was performed for water and fecal samples to determine if key fecal microbes could be detected in water samples to provide a better resolution of various fecal inputs that might contribute E. coli to each waterbody. The results of random forest model built with key sequences from fecal taxa showed that nearly all samples contained a complex mixture of fecal sources. This study confirms that, while human fecal inputs are not the sole source of E. coli to local waterways, they are a significant and widespread problem throughout Northwest Indiana, particularly in areas that receive runoff and/or near surface groundwater flows from residential areas with a high density of septic systems. Download the Final Report for more details.

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Communities along the Lake Michigan shoreline throughout Northwest Indiana have a high prevalence of septic tank use due to the topography of the dune landscape. Homes with septic systems older than their intended life are common and can be a source of bacterial pathogens to surface water and groundwater, making coastal beaches particularly vulnerable to septic pollution. While water quality is the typical metric for human health, recent studies suggest that pathogens in beach sand may pose a greater risk to human health due to more extensive contact. This project addressed an emerging issue along the coast of Lake Michigan in Northwest Indiana: microbiological pollution of beach sands due to failing septic systems. We sampled the beaches in the Long Beach community along a ~1.5 km stretch spanning areas with known septic system failures. We analyzed beach sand and lake water for E. coli by culture-based methods, human fecal bacterial DNA markers through qPCR, and the presence of potential bacterial pathogens through community 16S rRNA amplicon sequencing. Data from this study showed variable concentrations of these indicators in sand and that higher densities of E. coli and human markers correlated with recent rainfall. Lake water samples showed much lower E. coli concentrations, suggesting that the sand may retain any septic-derived inputs or that significant dilution and circulation of water occurs. Sequencing results indicate that both commensal human gut bacteria and potential human pathogens were present in multiple samples. Download the Final Report for more details.

Water samples were collected during the summer of 2021 from waterbodies predetermined by map analysis to be upstream of, downstream of, or within neighborhoods using septic systems rather than municipal sewer lines. Most sites were sampled at least twice, under wet and dry conditions, depending on the presence of water and accessibility of the site. Samples were analyzed for E. coli concentrations using the IDEXX Colilert™ system. Samples were filtered to retain bacterial cells for DNA extraction and subsequent molecular analysis for human fecal markers. The USEPA Human Bacteroides quantitative PCR assay was used to detect the presence of Bacteroides dorei 16S rRNA, which is an indicator that human fecal pollution is present. The project met or exceeded completion goals for sample collection and laboratory analysis. Of the >70 samples collected, 86% exceeded state water quality criteria for E. coli (>235 MPN/100 mL); and 75% of samples had at least detectable human fecal markers. Regionally, E. coli and human fecal markers did not strongly correlate, suggesting that sources are inconsistent or that other fecal sources also contribute to the bacterial pollution problem. Download the Final Report for more details.