Selective Survival of Escherichia coli Phylotypes in Freshwater Beach Sand

Fecal pollution monitoring still relies on E. coli enumeration, despite the fact that this organism can survive for prolonged periods and has been shown to be easily transported from sand into surrounding waters through waves and runoff, thus no longer representing recent fecal pollution events. Here, we demonstrate experimentally that regardless of the host source, certain genetically distinct subgroups, or phylotypes, survive longer than others under conditions typical of Great Lakes beach sites. ABSTRACT Escherichia coli is used as an indicator of fecal pollution at beaches despite evidence of long-term survival in sand. This work investigated the basis for the survival of E. coli through field microcosm experiments and phylotypic characterization of >1,400 E. coli isolates recovered from sand, sewage, and gulls, enabling the identification of long-surviving populations and environmental drivers of their persistence. Microcosms containing populations of E. coli from each source (n = 176) were buried in the backshore of Lake Michigan for 45 and 96 days under several different nutrient treatments, including unaltered native sand, sterile autoclaved sand, and baked nutrient-depleted sand. The availabilities of carbon and nitrogen, as well as competition with the indigenous community, were major factors that influenced E. coli survival. E. coli Clermont phylotypes B1 and A were the dominant phylotypes surviving seasonally (>6 weeks), regardless of source and nutrient treatment, whereas cryptic clade and D/E phylotypes survived over the winter (>300 days). Autoclaved sand, presumably supplying nutrients through increased availability, promoted growth, and the presence of the indigenous microbial community reduced this effect. Screening of 849 sand E. coli isolates from four freshwater beaches demonstrated that B1 and D/E were the most common phylotypes recovered. Analysis by quantitative PCR (qPCR) for the Gull2, Lachno3, and HB human markers demonstrated that only 25% of the samples had evidence of gull waste and none of the samples had evidence of human waste. These findings suggest that the prevalence of E. coli in sand could be attributed more to long-term-surviving populations than to new fecal pollution. IMPORTANCE Fecal pollution monitoring still relies on E. coli enumeration, despite the fact that this organism can survive for prolonged periods and has been shown to be easily transported from sand into surrounding waters through waves and runoff, thus no longer representing recent fecal pollution events. Here, we demonstrate experimentally that regardless of the host source, certain genetically distinct subgroups, or phylotypes, survive longer than others under conditions typical of Great Lakes beach sites. We found that nutrients were a major driver of survival and could actually promote growth and that the presence of native microorganisms modulated these effects. These insights into the dynamics and drivers of survival will improve the interpretation of E. coli measurements at beaches and inform strategies that could focus on reducing nutrient inputs to beaches or maintaining a robust natural microbiome in beach sand.