Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Biology and Microbiology

First Advisor

Volker S. Brozel


Escherichia coli, multi-niche, pasture, phylogroup, SESOM, survival


Escherichia coli strains are naturally present as either commensals or pathogens in the gastrointestinal tract of mammals and some other vertebrates. Until recently, it was assumed that E. coli are solely associated with the gut and are unable to survive outside of a host for a long period of time, the basis of its use as an indicator organism. Recent reports suggest that E. coli can become naturalized to several tropical, subtropical or temperate soils and aquatic environments, where they have been isolated repeatedly. Several studies have shown that these strains are capable of surviving and proliferating in the environment under suitable conditions. Not only have these strains adapted to the environment but also, several studies have revealed that they are genetically distinct from their gut-associated counterparts. In this dissertation, I focused to understand the genomic versatility and adaptation strategies of E. coli in pasture and pond ecosystems. The objectives of my research were (I) to determine the E. coli diversity and niche partitioning in pasture and pond ecosystems, (II) to compare the growth and extended survival of environmental E. coli isolates and E. coli O157:H7 in soil organic matter, (III) to determine E. coli fitness in soil by determining the antibiotic resistance, presence of virulence genes and susceptibility to grazing by Dictyostelium discoideum, and (IV) to compare the genotypic and phenotypic diversity of 20 representative isolates. These objectives were achieved as follows. Sampling of the pasture and pond environments in this study involved various representative sample types of two ecosystems. Phylogrouping and phylogenetic analysis of mutS and uidA genes were used to determine the diversity within the E. coli populations obtained, and to find out if any possible unique environmental strains exist or any of these isolates belongs to one of the previously described Escherichia clades. Furthermore, to determine the survival ability of isolates in soil a long-term survival study was conducted in liquid soil organic matter (SESOM) at 25 °C as well as in sterile soil outside over winter. The ability of E. coli to survive in various environments depends on several factors. The fitness of these isolates to survive in soil and aquatic environments was determined by biofilm and RDAR (red, dry and rough) formation, antibiotic resistance, presence of virulence genes and protozoan grazing susceptibility. Comparative analyses of the whole genome sequences of 20 isolates were conducted using EDGAR computational platform and R programming. A Phenotypic microarray assay was used to obtain the nutrient utilization profile of 20 isolates. The results of pasture isolate studies indicated the existence of environmental E. coli that are phylogenetically distinct from bovine fecal isolates, and which are able to better maintain populations in the soil environment. The pond isolates showed a distribution pattern of genotypic and phenotypic traits among isolates of various sample sources based on their niche preferences. Population genetic analysis of both the uidA and mutS genes supported the existence of three separate populations in the pond ecosystem. The bovine feces isolates belonged to one population and the snail isolates were of two, whereas the sediment, plant, and water isolates were an admixture of three different populations. The antibiotic resistance pattern of snail and bovine feces isolates were very different from sediment, plant and water isolates. The environmental strains were found to be more resistant to protozoan grazing, suggesting these strains may have developed some mechanism to avoid grazing, thereby displaying enhanced survival in soil. E. coli isolates from pasture soil and bovine feces displayed a high genotypic and phenotypic diversity within phylogroups. However the genotype diversity did not mirror the phenotypic distribution. Further implementation of transcriptome, proteome and metabolomics data is necessary to understand the genotype and phenotypic relatedness of organisms. These results suggest that E. coli strains with the potential to be pathogenic are able to maintain populations in the environment more broadly than previously thought. The presence of naturalized or environmental populations of E. coli in soil and aquatic environments renders the use of this bacterium as an indicator organism ambiguous at best. The ability to distinguish between environmental and host associated strains could allow for more accurate use of E. coli as an indicator for recent fecal contamination.

Library of Congress Subject Headings

Escherichia coli -- Genetics.
Evolutionary genetics.
Niche (Ecology)
Virulence (Microbiology) -- Genetic aspects.


Includes bibliographical references



Number of Pages



South Dakota State University



Rights Statement

In Copyright