Xenorhabdus bovienii subsp. africana subsp. nov., isolated from Steinernema africanum entomopathogenic nematodes

Abstract

Four Gram-negative bacterial strains isolated fromSteinernema africanumentomopathogenic nematodes were biochemically and molecularly characterized to determine their taxonomic position. Results of 16S rRNA gene sequencing indicated that they belong to the classGammaproteobacteria, familyMorganellaceae, genusXenorhabdus, and that they are conspecific. The average 16S rRNA gene sequence similarity between the newly isolated strains and the type strain of its more closely related species,Xenorhabdus bovieniiT228T, is 99.4 %. We therefore selected only one of them, XENO-1T, for further molecular characterization using whole genome-based phylogenetic reconstructions and sequence comparisons. Phylogenetic reconstructions show that XENO-1Tis closely related to the type strain ofX. bovienii, T228T, and to several other strains that are thought to belong to this species. To clarify their taxonomic identities, we calculated average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values. We observed that the ANI and dDDH values between XENO-1TandX. bovieniiT228Tare 96.3 and 71.2 %, respectively, suggesting that XENO-1Trepresents a novel subspecies within theX. bovieniispecies. Noteworthy, the dDDH values between XENO-1Tand several otherX. bovieniistrains are between 68.7 and 70.9 % and ANI values are between 95.8 and 96.4 %, which could be interpreted, in some instances, as that XENO-1Trepresents a new species. Considering that for taxonomic description the genomic sequences of the type strains are compared, and to avoid future taxonomic conflicts, we therefore propose to assign XENO-1Tto a new subspecies withinX. bovienii. ANI and dDDH values between XENO-1Tand any other of the species with validly published names of the genus are lower than 96 and 70 %, respectively, supporting its novel status. Biochemical tests andin silicogenomic comparisons show that XENO-1Texhibit a unique physiological profile that differs from all theXenorhabdusspecies with validly published names and from their more closely related taxa. Based on this, we propose that strain XENO-1Trepresents a new subspecies within theX. bovieniispecies, for which we propose the nameX. bovieniisubsp.africanasubsp. nov, with XENO-1T(=CCM 9244T=CCOS 2015T) as the type strain.