Genomic characteristics and phenotype of a new species Bdellovibrio bacteriopascens sp. nov., isolated from soil of Mexico

Abstract

A predatory, motile, Gram-negative bacterium, 22V T , was isolated from a soil sample collected from Tamaulipas, Mexico, which forms plaques on Vibrio parahaemolyticus prey. It was identified as a member of the genus Bdellovibrio based on its 16S rRNA gene sequence. It has a circular genome of 3,601,631 bp with 3,437 protein-coding genes, one rRNA gene cluster and a G+C (mol%) content of 46.7 mol%. Phylogenetic analysis based on the 16S rRNA gene, concatenated housekeeping genes and core genes placed 22V T as a member of a new species. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values of <21%, <80% and <78%, respectively, between 22V T and other known species in the genus Bdellovibrio are below the threshold for species delineation. 22V T can prey on Gram-negative bacteria, including nine strains from seven genera ( Escherichia, Klebsiella , Proteus , Pseudomonas, Salmonella , Shigella and Vibrio ). By fluorescence and cryo-electron microscopy, 22V T was observed as a tiny, motile bacterium that invaded the periplasmic space of host cells to form bdelloplasts, supporting a periplasmic predatory lifestyle. The unique rRNA gene cluster was located on a genomic island near an incomplete prophage. The rRNA gene yielded a phylogeny that conflicts with the phylogeny based on the core genes or housekeeping genes, suggesting that this rRNA gene cluster was obtained by horizontal transfer. Based on the phenotypic and phylogenomic results, 22V T represents a novel species in the genus Bdellovibrio , for which Bdellovibrio bacteriopascens sp. nov. is proposed. The type strain is 22V T (=ATCC TSD- 365 T =CM-CNRG 933 T ).