Transcriptome changes of Escherichia coli, Enterococcus faecalis and Escherichia coli O157:H7 laboratory strains in response to photo-degraded DOM

Authors: OLADEINDE, ADELUMOLA - Environmental Protection Agency (EPA); LIPP, ERIN - University Of Georgia; CHEN, CHIA-YING - Environmental Protection Agency (EPA); MURIHEAD, RICHARD - Agresearch; GLENN, TRAVIS - University Of Georgia; Cook, Kimberly - Kim; MOLINA, MOLINA - Environmental Protection Agency (EPA)

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/30/2018
Publication Date: 5/8/2018
Citation: Oladeinde, A., Lipp, E., Chen, C., Murihead, R., Glenn, T., Cook, K.L., Molina, M. 2018. Transcriptome changes of Escherichia coli, Enterococcus faecalis and Escherichia coli O157:H7 laboratory strains in response to photo-degraded DOM. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2018.00882.
DOI: https://doi.org/10.3389/fmicb.2018.00882

Interpretive Summary: We investigated the effect of manure-derived dissolved organic matter (DOM) on gene expression in three bacterial strains (Escherichia coli C3000, Escherichia coli O157:H7 B6914 and Enterococcus faecalis ATCC 29212). Advanced molecular microbiological techniques were used to compare differential gene expression between bacteria incubated in microcosms containing sunlight irradiated and non-irradiated DOM, for up to 24 h. Results indicate that E. coli and E. faecalis have different mechanisms for removal of reactive oxygen species (ROS) produced from irradiated DOM. They are also able to produce micromolar concentrations of H2O2 from non-irradiated DOM that should be detrimental to other bacteria present in the environment. Notably, this study provides an assessment of the role of two conjugative plasmids carried by the E. faecalis and highlights the differences in the overall survival dynamics of environmentally-relevant bacteria in the presence of naturally-produced ROS.

Technical Abstract: In this study, we investigated gene expression changes in three bacterial strains (Escherichia coli C3000, Escherichia coli O157:H7 B6914 and Enterococcus faecalis ATCC 29212) commonly,used as indicators of water quality and as control strains in clinical, food, and water microbiology laboratories. Bacterial transcriptome responses from pure cultures were monitored in microcosms containing water amended with manure-derived dissolved organic matter (DOM), previously exposed to simulated sunlight for 12 h. We used RNA sequencing (RNA-seq) and quantitative real-time reverse transcriptase (qRT-PCR) to compare differentially expressed temporal transcripts between bacteria incubated in microcosms containing sunlight irradiated and non-irradiated DOM, for up to 24 h.In addition, we used whole genome sequencing simultaneously with RNA-seq to identify single nucleotide variants (SNV) acquired in bacterial populations during incubation. These results indicate that E. coli and E. faecalis have different mechanisms for removal of reactive oxygen species (ROS) produced from irradiated DOM. They are also able to produce micromolar concentrations of H2O2 from non-irradiated DOM, that should be detrimental to other bacteria present in the environment. Notably, this study provides an assessment of the role of two conjugative plasmids carried by the E. faecalis and highlights the differences in the overall survival dynamics of environmentally-relevant bacteria in the presence of naturally-produced ROS.