Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov

Abstract

Bacterial symbionts are crucial for the infectivity and success of entomopathogenic nematodes as biological control agents. The current understanding of the symbiotic relationships is limited by taxonomic uncertainties. Here, we used whole-genome sequencing and traditional techniques to reconstruct the phylogenetic relationships between all described Photorhabdus species and subspecies as well as 11 newly isolated symbiotic bacteria of Heterorhabditis nematodes, including the unreported bacterial partner of H. beicherriana. In silico DNA-DNA hybridization, orthologous average nucleotide identity and nucleotide sequence identity of concatenated housekeeping genes scores were calculated and set into relation with current cut-off values for species delimitation in bacteria. Sequence data were complemented with biochemical and chemotaxonomic markers, and ribosomal protein fingerprinting profiles. This polyphasic approach resolves the ambiguous taxonomy of Photorhabdusand lead to the proposal for the elevation of most of them into a higher taxon and the creation of several new taxa: 15 new species, one of which is newly described: Photorhabdus bodei sp. nov. (type strain LJ24-63^T=DSM 105690^T=CCOS 1159^T) and the other 14 arise through the proposal of elevating already described subspecies to species, and are proposed to be renamed as follows: Photorhabdus asymbioticasubsp. australis as Photorhabdus australis sp. nov., Photorhabdus luminescenssubsp. akhurstii as Photorhabdus akhurstii sp. nov., Photorhabdus luminescenssubsp. caribbeanensis as Photorhabdus caribbeanensis sp. nov., Photorhabdus luminescenssubsp. hainanensis as Photorhabdus hainanensis sp. nov., Photorhabdus luminescenssubsp. kayaii as Photorhabdus kayaii sp. nov., Photorhabdus luminescenssubsp. kleinii as Photorhabdus kleinii sp. nov., Photorhabdus luminescenssubsp. namnaonensis as Photorhabdus namnaonensis sp. nov., Photorhabdus luminescenssubsp. noenieputensis as Photorhabdus noenieputensis sp. nov., Photorhabdus luminescenssubsp.laumondii as Photorhabdus laumondii sp. nov., Photorhabdus temperatasubsp. cinerea as Photorhabdus cinerea sp. nov., Photorhabdus temperatasubsp. khanii as Photorhabdus khanii sp. nov., Photorhabdus temperatasubsp. stackebrandtii as Photorhabdus stackebrandtii sp. nov., Photorhabdus temperatasubsp. tasmaniensis as Photorhabdus tasmaniensis sp. nov., and Photorhabdus temperatasubsp. thracensis as Photorhabdus thracensis sp. nov. In addition, we propose the creation of two new subspecies, one of which arises through the reduction of rank: Photorhabdus laumondii subsp. laumondii comb. nov. (basonym: P. luminescenssubsp. laumondii) and the second one is newly described: Photorhabdus laumondii subsp. clarkei subsp. nov. (type strain BOJ-47^T=DSM 105531^T=CCOS 1160^T). Finally, we propose to emend the description of three species, which results from the proposal of elevating three subspecies to the species status: Photorhabdus asymbiotica, Photorhabdus temperata and Photorhabdus luminescens, formerly classified as Photorhabdus asymbioticasubsp. asymbiotica, Photorhabdus temperatasubsp.temperata and Photorhabdus luminescenssubsp. luminescens, respectively.

Keywords: Heterorhabditis; OrthoANI; Photorhabdus; isDDH; phylogenomics; polyphasic classification; reclassification; whole-genome sequencing.