The diversity and structure of Escherichia coli populations in fresh water environments

Abstract

Escherichia coli is a well known commensal inhabitant of the gastrointestinal tract of both humans and animals and a highly diverse species. The physiology, biochemistry and genetics of E. coli have been studied extensively over many decades. However, these studies have focussed predominately on the pathogenic and commensal isolates. It has been described that E. coli typically exists in two environments, the primary environment being the gastrointestinal tract of the host and the secondary environment being that environment outside of the host (water, soil and sediments). Upon introduction into the environment outside of the host, the numbers of E. coli steadily decline. Generally, where E. coli is present in the external environment and where its numbers are maintained it is due to a constant direct faecal input from the host. This short lifespan in the environment outside of the host forms the basis for the use of E. coli as an indicator organism for faecal contamination in water systems. In contrast, multiple studies have shown that some E. coli strains have the ability to survive and persist in the external environment in the absence of faecal input from the host. With a large pan-genome and the possibility of horizontal gene transfer (HGT) of desirable traits, E. coli have the potential to adapt to a variety of different niches overcoming drastic changes in conditions in its new environment. In addition, adaptation to the secondary environment is facilitated by the presence of soils and sediments, where in an aquatic environment they provide a source of nutrients and protection from the drastic change in conditions. Here, E. coli has the ability to occupy a new niche and become naturalised within an aquatic environment. The aim of this masters project was to examine and characterise the diversity of E. coli isolates collected from two South African freshwater environments namely, the Roodeplaat and Rietvlei Dams, Pretoria. Specific research questions addressed in this study include: (1) are their unique and genetically differentiated sub-populations within the aquatic environments sample? (2) Is there a link between the unique sub-populations and their sample site? (3) Finally, what is the relationship between sub-populations in terms of gene flow and population structure? Understanding E. coli’s population structure and ecology may shed some light on its evolution and potential to adapt to new environments. Following phylogrouping, AFLP and phylogenetic analysis of the rpoS and uidA genes, the results indicated that the population was highly diverse with the majority of strains grouping together with the sewage isolates. Furthermore, population structure analyses concentrating on gene flow and genetic differentiation revealed that possible environmental groups exist within the population. In particular, two groups of E. coli isolates associated with aquatic plants showed restricted gene flow and definite genetic differentiation. These two groups can also be observed in the rpoS and uidA phylogenetic analyses where they consistently group together in the absence of sewage isolates. These findings demonstrate that some E. coli are not only able to survive outside of their host but have undergone some level of niche separation within the secondary environment. These results raise important questions into the accuracy of using E. coli as an indicator organism. In the long term, this study may aid in understanding the population dynamics of E. coli and the implications of environmental strains on using E. coli in assessing water quality.