Molecular methods to monitor water quality can address current and historical pollution. Molecular measurements of enteric markers from sediments can aid in the evaluation of historical water quality using a singular index and be used to analyze correlations to climate and human impact. However, the stability of the markers in defined storage conditions and durations is uncertain. The goals of this dissertation were to: 1) investigate how storage conditions and duration affected concentrations of enteric molecular markers in water samples; and 2) evaluate the correlations of historical anthropogenic and climate variables with the deposition of persistent enteric markers in sediment cores from the Lake St. Clair watershed. Autoclaved water from the Red Cedar River was seeded with 10% (vol/vol) raw sewage and stored in liquid suspension (LS) or attached to a solid matrix (SM). Enterococci (ENT) 23S rDNA, Escherichia coli (EC) uidA, and Bacteroides thetataiotaomicon (BT) 1,6 alpha-mannanase were measured with quantitative polymerase chain reaction (qPCR) in order to evaluate their persistence for up to 28 and 366 days at 4o (long term and short term studies), and 27o and 37oC (short term study only). Five linear and non-linear best-fit models were fit to the indicator concentrations. Persistence of the indicators was enhanced on SM (p < 0.001), and decreased with time (p < 0.001). Persistence was also dependent on indicator species in the short term and long term studies (p < 0.001, and p = 0.001, respectively). The least to most persistent indicators were: BT < EC < ENT. The time needed for 90% decay of the indicators, T90, calculated with the best-fit models in the short term study (and long term study) ranged from 1 day for BT in LS at 37 ̊C to > 28 days for ENT and EC on SM at all temperatures (and 35.8 days for EC in LS to 164 days for ENT on SM at 4°C). At 4°C, the T90 values were greater in the long term study compared to the short term study. This study suggests that storage of water samples at 4°C attached to a solid matrix can increase the persistence of markers from fecal indicators.Surface sediments from Anchor Bay, northwestern Lake St. Clair (AB), and the mouth of the Clinton River (CR) were spiked with EC and Enterococcus faecium. qPCR measurements of ENT 23S rDNA and EC uidA extracted from 17 DNA extraction methods were compared. Within each location, Kruskal-Willis tests confirmed few significant differences between the concentrations of the indicators. The optimal method included a bead beating step with a DNA sorption blocker followed by centrifugation. This method evaluated the concentrations of ENT 23S rDNA and EC uidA in sediment cores from AB and CR, representing the years c.1757 - 2012, and c.1895 - 2012, respectively. EC concentrations in the AB and CR cores increased with year, and ranged from 1.42 x 106 to 16.9 x 106 cell equivalents (CE) per g-dry wt, and 1.81 x 106 to 8.46 x 106 CE per g-dry wt, respectively. ENT concentrations in the CR core increased with year, and ranged from 3 x 103 to 990 x 103 CE per g-dry wt. The ENT concentrations in the AB core experienced two steady states: ~1 x 104, and ~2 x 105 CE per g-dry wt during c.1757 – c.1878, and c.1902 – c.2010, respectively. ENT concentrations in both cores were correlated to river discharge (p = 0.046), while EC concentrations were correlated to air temperature (p = 0.018), and total nitrogen and total carbon concentrations (p = 0.038, and 0.029, respectively). Also, ENT and EC concentrations were significantly correlated to population in watershed (p = 0.003 and 0.023, respectively). This study offers a novel analysis of ≥ 100 years of the management of the Clinton River watershed.
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