Riding the wave of genomics to investigate aquatic coliphage diversity and activity

Abstract

Summary Bacteriophages infecting Escherichia coli (coliphages) have been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that is present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterized coliphages from three coastal locations in the United Kingdom and Poland. Comparative genomics and phylogenetic analysis of phage isolates facilitated the identification of putative new species within the genera Rb69virus and T5virus and a putative new genus within the subfamily Tunavirinae. Furthermore, genomic and proteomic analysis combined with host range analysis allowed the identification of a putative tail fibre that is likely responsible for the observed differences in host range of phages vB_Eco_mar003J3 and vB_Eco_mar004NP2.

Genome sequence and characterisation of coliphage vB_Eco_SLUR29

“…The burst size of vB_Eco_SLUR29 is 22 , which is smaller than the reported values of 194 115, 78 and 51 for vB_Eco-S59, vB_Eco_swan01 and vB_Eco_mar002J2 respectively 12,21 . There is 195 also considerable variation in the latent period for these phages, with vB_Eco_SLUR29 having a 196 substantially longer latent period (21 min) than the reported 4, 12 and 15 min for vB_Eco-S59, 197 vB_Eco_swan01 and vB_Eco_mar002J2 12,21 . However, the reported 4 min latent period of 198 vB_Eco-S59 seems extraordinarily rapid and maybe an artefact of the method used.…”

“…Mash database was constructed of all complete bacteriophage genomes available at the time of 80 analysis (~ 11,000, April 2019) using the following Mash setting: " -s 10000" using a previously 81 described method 12 . Closely related genomes were identified using this database and the `dist` 82 function.…”

“…Core gene analysis for phages within 88 the putative genus Swanvirus was carried out with ROARY using "--e --mafft -p 32 -i 90" 16 . 89 90 Transmission Electron Microscopy 91 TEM was carried out at the University of Leicester Core Biotechnology Services Electron 92 Microscopy using a previously described method 12 . Digital images were collected with a 93…”

“…Tunavirinae, in a clade that is sister to a clade that contains phages of the genus TLsvirus and 175 contains the phages vB_Eco_mar001J1, vB_Eco_mar002J2, vB_EcoS-95, vB_Eco_swan01 and 176 SECphi27. Previously, we have suggested SECphi27, vB_Eco_mar001J1, vB_Eco_mar002J2, 177 vB_Eco_swan01 and pSf1 are members of the same genus 12 >95 % ANI 23 . Using this criterion, vB_Eco_SLUR29, vB_Eco_mar001J1, vB_Eco_mar002J2, 183 vB_EcoS-95, vB_Eco_swan01, SECphi27 and vB_EcoS-95 would form a single species.…”

“…Wether this is a 167 reflection of their abundance or due to small sample sizes remains to be seen. Comparison of 168 vB_Eco_SLUR29 with its closest relatives, reveals they have all been isolated on E.coli K-12 169 MG1655, although many can infect other bacteria within the Enterobacteriaceae (Fig 3) 12,21 . 170 171 Given the high sequence identity between vB_Eco_SLUR29 and its closest relatives, it was 172 unsurprising that it has similar morphological properties when examined by transmission electron 173 microscopy.…”