RUI: Dynamics of Genomic Mosaicism in Non-Host Associated Escherichia Populations

Hope College, Holland MI

Investigators

Abstract

This project aims to address whether Escherichia from watersheds can serve as a reservoir for horizontal gene transfer to host-associated strains such as Escherichia coli, which is a known source of human infections. Watersheds can become contaminated with Escherichia via treated sewage, livestock farming, wild animals, fowl, and sediment runoff from urban and agricultural environments. Several studies revealed that Escherichia may adapt and persist in these environments, and eventually may be able to pass the genes for new traits to host-associated strains such as Escherichia coli. In addition to examining this idea, the data from this study will allow the broader scientific community to evaluate existing water quality monitoring methods. The research for this project will be integrated into authentic research experiences for undergraduate students in STEM fields through course-based research experiences (CREs). In particular, undergraduates in first year and upper level laboratories will actively participate in all aspects of the project. This project focuses on two related scientific goals: 1) characterizing genomic diversity of environmentally derived Escherichia isolates to understand variation in naturally occurring populations over time; and 2) linking profiles of 16S community surveys to observed variation in Escherichia isolate genomes and to environmental changes in a watershed. Remarkable genetic diversity has been characterized by global studies of E. coli through analysis of representative fully sequenced genomes, and targeted studies of pathogen sub-types through hundreds of draft genome sequences of clinical isolates. The preponderance of genomic data is from clinical and host-associated environments. This project produces 720 draft genome sequences of environmentally derived Escherichia isolates. The longitudinal data enable testing hypotheses about genome structure and genetic exchange in naturally occurring, non-host-associated populations through comparative genomics of genome content, arrangement and single nucleotide polymorphisms. The data address long term persistence of Escherichia populations in non-host environments, potentially serving as reservoirs for genetic exchange and renewal of fecal indicator bacteria in bodies of water. Oligotyping will estimate diversity in the Escherichia populations; water samples will produce coupled isolate genome sequences and microbial community 16S rRNA sequences. It is asserted that single nucleotide changes in 16S rRNA represent diversity of genome structure; the data will be used to test this assertion. Fine scale sampling produces longitudinal 16S rRNA microbial community profiles used to understand changes in Escherichia and other microbial populations. Work linking 16S rRNA variation to genome variation enables prediction of population changes based on 16S rRNA surveys alone. High quality recreational and drinking water sources are essential for society, and as water quality monitoring shifts to molecular based approaches, the types of datasets produced here become critical to ascertaining effective and broadly applicable monitoring techniques. A third goal fully incorporates undergraduate students in STEM fields through individual and course-based research experiences (CREs). Over 100 students in courses will gain first-hand knowledge of authentic research. The effectiveness of these experiences will be assessed through convergent mixed methods approaches designed to gauge student attitudes toward STEM fields, comparing effects of individual research experiences and CREs on first year and upper level students.