Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Fcu in a soil microenvironment at low temperature

In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11fcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11fcu in soils is associated with a complex interplay of metabolic networks.

Automated summary

In this study, the metabolic genes and networks that affect the persistence of pathogenic Escherichia coli O104:H4 strain C227/11fcu in agricultural soil microenvironments at low temperature were explored. RNA sequencing analysis revealed differential expression of over 1500 genes at 1 and 4 weeks compared to the initial time point, including stress response genes and genes involved in primary metabolism. Genes and gene sets related to the uptake of carbohydrates and amino acids were significantly upregulated in low nutrient environments. These transcriptome analysis results suggest a complex interplay of metabolic networks in the persistence of C227/11fcu in soils.