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

Four Gram-negative bacterial strains isolated from Steinernema africanum entomopathogenic nematodes were biochemically and molecularly characterized to determine their taxonomic position. Results of 16S rRNA gene sequencing indicated that they belong to the class Gammaproteobacteria, family Morganellaceae, genus Xenorhabdus, 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 bovienii T228(T), is 99.4%. We therefore selected only one of them, XENO-1(T), for further molecular characterization using whole genome-based phylogenetic reconstructions and sequence comparisons. Phylogenetic reconstructions show that XENO-1(T) is closely related to the type strain of X. bovienii, T228(T), 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-1(T) and X. bovienii T228(T) are 96.3 and 71.2%, respectively, suggesting that XENO-1(T) represents a novel subspecies within the X. bovienii species. Noteworthy, the dDDH values between XENO-1(T) and several other X. bovienii strains 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-1(T) represents 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-1(T) to a new subspecies within X. bovienii. ANI and dDDH values between XENO-1(T) and 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 and in silico genomic comparisons show that XENO-1(T) exhibit a unique physiological profile that differs from all the Xenorhabdus species with validly published names and from their more closely related taxa. Based on this, we propose that strain XENO-1(T) represents a new subspecies within the X. bovienii species, for which we propose the name X. bovienii subsp. africana subsp. nov, with XENO-1(T) (=CCM 9244(T)=CCOS 2015(T)) as the type strain.

Automated summary

Four Gram-negative bacterial strains isolated from Steinernema africanum entomopathogenic nematodes were identified as a novel subspecies within the genus Xenorhabdus, named X. bovienii subsp. africana subsp. nov, with the type strain XENO-1(T). The strains exhibited a high similarity to X. bovienii T228(T) but showed distinct physiological profiles. The taxonomic position was determined by 16S rRNA gene sequencing, whole genome-based phylogenetic reconstructions, and ANI and dDDH values calculation.