Escherichia coli isolated from surface soil in an agricultural landscape

E. coli are deposited into soil with feces and undergo subsequent population decline with concomitant environmental selection. Environmentally persistent strains exhibit longer survival times during this selection process and some environmentally adapted strains from soil and sediments have been reported. A georeferenced collection of E. coli isolates was developed comprising 3,329 isolates from 1,428 soil samples that were collected from a landscape spanning the transition from the grasslands to the eastern deciduous forest biomes. Genomes of 944 isolates were sequenced for the purposes of determining how deposition in soil might affect selection for persistence or virulence traits, given that E. coli are rapidly dispersed to soil as a non-host environment. Libraries for sequencing were generated using Illumina Nextera XTTM kits, sequenced using paired 100 bp reads on an Illumina HiSeq 4000 at Macrogen Clinical Laboratories.