Population structure and persistence of Escherichia coli in ditch sediments and water in the Seven Mile Creek Watershed

Escherichia coli is currently used as an indicator of fecal contamination in freshwater systems based on the assumption that it does not grow or survive outside of the host. However, recent studies have reported the growth and persistence of E. coli in various habitats such as soil, sands and sediments. While the majority of studies examining the growth and survival of E. coli in sediments have been performed primarily under laboratory conditions, there is, however, only limited field investigations concerning the growth and survival of this bacterium in sediments and its partitioning to overlaying water. Furthermore, the contributions of sediment adapted E. coli to water quality impairment in ditches or tile lines have not yet been assessed. Therefore, in this study, we examined the population structure of E. coli and determined whether ditch sediments can serve as reservoirs of environmental E. coli in the Seven Mile Creek (SMC) watershed, a minor watershed located in south central Minnesota. We also examined the potential factors that might influence the spatial and temporal distribution of E. coli populations present in the SMC watershed. Horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique (HFERP) was used to examine the population structure of E. coli in the SMC watershed, and host source-specific PCR assays targeting Bacteroidetes were used to identify potential host sources of fecal bacteria in the SMC watershed. Results of these studies indicated that seasonal variation in the population density of E. coli is likely influenced by parameters such as temperature and flow events (rainfall and runoff events). Furthermore, we report that despite an annual shift in population structure, viable E. coli strains were isolated repeatedly from temperate ditch sediments and water across all three years. Therefore, sites likely contain a mixture of newly acquired and resident E. coli strains. HFERP fingerprint analyses indicated that the resident strains were likely growing in sediments and surviving through the winter freeze-thaw cycles. Sediment-borne E. coli strains had HFERP DNA fingerprints that were unique to this location and distinct from known sources of E. coli (from fecal origin), suggesting that these E. coli strains became naturalized to the SMC sediments. Furthermore, multivariate analysis of variance (MANOVA) indicated that there was mixing of bacteria between sites during flow conditions, which likely influenced the distribution and mobility of naturalized E. coli within the watershed. Additionally, mixing occurred between the sediment and water column, and this may have resulted in the re-suspension of sediment-borne naturalized E. coli into the overlaying water, leading to an apparent increase in the observed levels of E. coli. These results suggest that ditch sediments are temporal sinks of E. coli and that these indigenous populations might contribute significantly to population levels of E. coli measured in water quality studies. This confounds the use of E. coli as an indicator of fecal contamination of waterways, and has implications for future water quality monitoring and TMDL determinations.