It is commonly believed that E. coli, which has evolved as a symbiont of warm-blooded animals, should die-off very quickly once released from the animal hosts to the natural environment. However, recent studies have reported E. coli strains that persisted in the natural environment as genetically distinct, self-sustaining populations. Not only does this phenomenon challenge the use of E. coli as an indicator of fecal pollution in the aquatic environments, it also poses an important question about the adaptation and evolution of E. coli in the natural environment. Many studies have shown that prophages (i.e. DNA of phages residing in the genome of bacterial cells) are responsible for genome diversification and subsequent niche expansion of pathogenic E. coli from one host species to anot...[ Read more ]

It is commonly believed that E. coli, which has evolved as a symbiont of warm-blooded animals, should die-off very quickly once released from the animal hosts to the natural environment. However, recent studies have reported E. coli strains that persisted in the natural environment as genetically distinct, self-sustaining populations. Not only does this phenomenon challenge the use of E. coli as an indicator of fecal pollution in the aquatic environments, it also poses an important question about the adaptation and evolution of E. coli in the natural environment. Many studies have shown that prophages (i.e. DNA of phages residing in the genome of bacterial cells) are responsible for genome diversification and subsequent niche expansion of pathogenic E. coli from one host species to another. However, there has been no investigation on the diversities and functions of prophages in environmental E. coli. Therefore, it is not known whether prophages are involved in niche expansion of E. coli from the animal hosts to the natural environment. Using two E. coli strains (E1140 and E1728) isolated from marine sediment, we investigated for the first time the diversity of prophages carried by E. coli that extant in a natural environment. The results showed that the two strains belonged to the same ancestral lineage; however, they had different genome arrangement and carried different diversities of prophages. Sequence analysis on these prophages has found several fitness factors that are related to the survival in nutrient poor environments. Prophage sequences that were previously known for bacteria indigenous to the marine environment were also found in E1140, suggesting the possibility of horizontal gene transfer. By injecting the prophage of E1140 into a third E. coli strain (isolated from pig feces), an increase in survival time of the third strain in seawater microcosm was observed. These findings altogether suggested prophage-mediated genetic events as a possible pathway for E. coli to evolve and survive in the natural environment.