Impact of land-use and fecal contamination on Escherichia populations in environmental samples

<p dir="ltr">Understanding the composition of complex <i>Escherichia coli</i> populations from the environment is necessary for identifying strategies to reduce the impacts of fecal contamination and protect public health. Metabarcoding targeting the hypervariable gene <i>gnd</i> was used to reveal the complex population diversity of <i>E. coli</i> and phenotypically indistinct <i>Escherichia</i> species in water, soil, sediment, aquatic biofilm, and fecal samples from native forest and pastoral sites. The resulting amplicons were cross-referenced against a database containing over 700 different partial <i>gnd</i> sequences from <i>E. coli</i>/non-<i>E. coli Escherichia</i> species. Alpha and beta measures of diversity of <i>Escherichia</i> populations were lowest in feces, soil and sediment compared to water and aquatic biofilm samples. <i>Escherichia</i> populations recovered from extensive freshwater catchments dominated by sheep, beef and dairy farming were extremely diverse but well-separated from a wetland dairy site. In contrast, <i>Escherichia</i> populations from the low-impact native forest site with fewer fecal sources were less diverse. Metabarcoding distinguished <i>E. coli</i> populations important to fecal contamination monitoring from non-<i>E. coli Escherichia</i> environmental populations. These data represent in-depth analysis and geographic stability of <i>Escherichia</i> populations from environmental samples with extensive heterogeneity, and reveal links with diverse fecal sources, land-use and the overall burden of fecal contamination at sample sites.</p>