Plant Science

Origins of E. coli bacteria in soil and crops

Studies of outbreaks affecting humans have led to increased focus on the sources of the E. coli infections. A recent study at JHI has looked at the similarities amongst 29 bacterial isolates sampled from soil and plants at a cereal trial investigating different soil amendments (slurry and compost). The DNA sequences of seven housekeeping genes (the genes involved in maintenance of the bacterial cell) were obtained and this data set was used to estimate the genetic relationships among the isolates. Reference sequences were added to the dataset, including those for E. coli O157. To analyse the data, a phylogenetic network approach was used as there was a possibility that the relationships among the 29 isolates would not be the same across all seven genes due to a process of DNA mixing called horizontal gene transfer (HGT). Due to HGT, a phylogenetic tree may not be the best way of displaying the relationships. Instead, a phylogenetic network was estimated using the NeighborNet split decomposition method. The initial results show that isolates from the same source tend to be more closely related than from other sources and that E. coli appears to be adapting to environmental niches. Future work will aim to understand the basis of this adaptation and the extent to which pathogenic E.coli types survive on crop plants.

phylogenetic network diagram Phylogenetic network showing the relationships among reference E.coli isolates (named) and 29 isolates sampled from different environmental niches ( ).

Further details from: Frank Wright

Article date 2011

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