Photorhabdus hindustanensis sp. nov., Photorhabdus akhurstii subsp. akhurstii subsp. nov., and Photorhabdus akhurstii subsp. bharatensis subsp. nov., isolated from Heterorhabditis entomopathogenic nematodes

Abstract

Two Gram-negative, rod-shaped bacteria, H1^T and H3^T, isolated from the digestive tract of <i>Heterorhabditis</i> entomopathogenic nematodes were biochemically and molecularly characterized to determine their taxonomic positions. The 16S rRNA gene sequences of these strains indicate that they belong to the Gammaproteobacteria, to the family <i>Morganellaceae</i>, and to the <i>Photorhabdus</i> genus. Deeper analyses using whole genome-based phylogenetic reconstructions show that strains H1^T and H3^T are closely related to <i>P. akhurstii</i> DSM 15138^T, to <i>P. hainanensis</i> DSM 22397^T, and to <i>P. namnaonensis</i> PB45.5^T. <i>In silico</i> genomic comparisons confirm these observations and show that strain H1^T shares 70.6, 66.8, and 63.5 % digital DNA-DNA hybridization (dDDH) with <i>P. akhurstii</i> DSM 15138^T, <i>P. hainanensis</i> DSM 22397^T, and <i>P. namnaonensis</i> PB45.5^T, respectively, and that strain H3^T shares 76.6, 69.4, and 59.2 % dDDH with <i>P. akhurstii</i> DSM 15138^T, <i>P. hainanensis</i> DSM 22397^T, and <i>P. namnaonensis</i> PB45.5^T, respectively. Physiological and biochemical characterization reveals that these two strains differ from most of the validly described <i>Photorhabdus</i> species and from their more closely related taxa. Given the clear phylogenetic separations, that the threshold to discriminate species and subspecies is 70 and 79% dDDH, respectively, and that strains H1^T and H3^T differ physiologically and biochemically from their more closely related taxa, we propose to classify H1^T and H3^T into new taxa as follows: H3^T as a new subspecies within the species <i>P. akhurstii</i>, and H1^T as a new species within the <i>Photorhabdus</i> genus, in spite that H1^T shares 70.6 % dDDH with <i>P. akhurstii</i> DSM 15138^T, score that is slightly higher than the 70 % threshold that delimits species boundaries. The reason for this is that H1^T and <i>P. akhurstii</i> DSM 15138^T cluster apart in the phylogenetic trees and that dDDH scores between strain H1^T and other <i>P. akhurstii</i> strains are lower than 70 %. Hence, the following names are proposed: <i>Photorhabdus hindustanensis</i> sp. nov. with the type strain H1^T (=IARI-SGMG3^T,=KCTC 82683^T=CCM 9150^T=CCOS 1975^T) and <i>P. akhurstii</i> subsp. <i>bharatensis</i> subsp. nov. with the type strain H3^T (=IARI-SGHR2^T=KCTC 82684^T=CCM 9149^T=CCOS 1976^T). These propositions automatically create <i>P. akhurstii</i> subsp. <i>akhurstii</i> subsp. nov. with DSM 15138^T as the type strain (currently classified as <i>P. akhurstii</i>).