Naturalization of Escherichia coli in New Zealand freshwater streams

Abstract

Escherichia coli is used internationally as a faecal indicator of water quality based on the assumption that this bacterium is exclusively a commensal of the vertebrate gut. However, recent findings show that E. coli can also grow and multiply in water and soils, either in tropical and temperate climates in different parts of the world. It is becoming clear that some strains of E.coli are able to naturalize in the environment and that these populations persist and expand over weeks or months before resolving and being replaced by new apparently naturalized strains. The process by which this naturalization takes place is as yet undescribed and an approach to discriminating naturalized from contaminating commensal E.coli in an aquatic environment is also not available. This research focuses on defining the specific characteristics of naturalized E. coli strains and determining what makes them different from commensal E. coli strains, by using multi-omic tools. The first step of this project was to select potentially naturalized E. coli isolates characterized by a similar genetic profile and retrieved from freshwater stream biofilms overtime at the same location. Then in the second step, the genetic, transcriptomic, metabolic and phenotypic characteristics of this group of isolates have been extensively studied and compared with the corresponding features of commensal E. coli using Affymetrix microarrays, qPCR, carbon substrate utilization assays, metabolomics analyses and phenotypic assays. Results show similarities and differences with commensal E. coli. While both E. coli categories show similar growth rates, catalase and glycogen production, the naturalized isolates possess enhanced biofilm formation capabilities and a red dry and rough (rdar) morphotype. Transcriptomic analyses demonstrate a lower expression of rpoS, the gene encoding the general stress sigma factor (S), the key component of the general stress response for the naturalized strains compared to the commensal strains. Microarray analyses revealed over-expression of 160 genes mostly involved in motility, chemotaxis, energy production and conversion, amino-acid and inorganic ion metabolisms and reduced expression of 87 genes coding for proteins involved in transcription, translation or in unknown functions. Phenotypic macroarrays show that the naturalized isolates use a broader range of substrates although their nutrient utilization profiles are still very close to some human strain profiles. The metabolomic analyses confirm that the naturalized strains favour different metabolic pathways and metabolites indicating different strategies in relation to the different lifestyles. All together these results suggest that naturalized isolates have better abilities to sense, and to move to, an area with greater nutrient resources (chemotaxis and motility), to remain to these areas by colonizing biofilms (via surface appendages) and to incorporate and use different compounds (carbohydrate and amino acids) in an energy-efficient manner. These capabilities would allow a better survival and growth in a stream environment reflecting a more variable environment with stressors such as variations in nutrient availability, temperature and light. Down regulation of rpoS may facilitate the metabolic flexibility of environmental isolates by reducing the energy and resource requirements devoted to the stress responses, in line whith bacteria favouring the less costly metabolic pathways.