Photorhabdus antumapuensis sp. nov., a novel symbiotic bacterial species associated with Heterorhabditis atacamensis entomopathogenic nematodes

Abstract

One motile, Gram-negative, non-spore-forming and rod-shaped symbiotic bacterium, strain UCH-936T, was isolated from Heterorhabditis atacamensis nematodes. Results of biochemical, physiological, molecular and genomic analyses suggest that it represents a new species, which we propose to name Photorhabdus antumapuensis sp. nov. Digital DNA–DNA hybridization shows that strain UCH-936T is more closely related to Photorhabdus kleinii DSM 23513T, but shares solely 50.5 % similarity, which is below the 70% cut-off value that delimits species boundaries in bacteria. Phylogenetic reconstructions using whole-genome sequences show that strain UCH-936T forms a unique clade, suggesting its novel and distinct taxonomic status again. Similarly, comparative genomic analyses shows that the virulence factor flagella-related gene fleR, the type IV pili-related gene pilL and the vibriobactin-related gene vibE are present in the genome of strain UCH-936T but absent in the genomes of its closest relatives. Biochemically and physiologically, UCH-936T differs also from all closely related Photorhabdus species. Therefore, Photorhabdus antumapuensis sp. nov. is proposed as a new species with the type strain UCH-936T (CCCT 21.06T=CCM 9188T=CCOS 1991T).

Systematics and phylogeny of the entomopathogenic nematobacterial complexes Steinernema–Xenorhabdus and Heterorhabditis–Photorhabdus

“…2 ). In 2018 and 2021, the use of whole-genome sequences for taxonomic purposes was introduced for the genera Photorhabdus and Xenorhabdus , respectively, to align with the gold standards for bacterial taxonomy at that time [ 117 , 126 ]. Now, novel bacterial species are described based on a well-supported phylogenomic separation as phylogenomic trees often capture intra- and interspecific variability, and based on overall genomic relatedness indices (OGRIs) such as average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH).…”

“…sonorensis"* [ 167 ] H. atacamensis P. antumapuensis, P. khanii subsp. guanajuatensis [ 124 , 126 ] H. downesi megidis P. cinerea, P. temperata [ 117 ] H. marelatus P. tasmanensis [ 117 ] H. megidis P. cinerea, P. temperata [ 117 ] H. safricana P. laumondii subsp. laumondii [ 168 ] H. zealandica P. tasmaniensis, P. heterorhabditis subsp.…”

Photorhabdus aballayi sp. nov. and Photorhabdus luminescens subsp. venezuelensis subsp. nov., isolated from Heterorhabditis amazonensis entomopathogenic nematodes

“…The genus Photorhabdus was proposed by Boemare et al in 1993 to describe symbiotic bacteria of Heterorhabditis entomopathogenic nematodes [17]. Since then, several species and subspecies have been described [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. Currently, the genus Photorhabdus contains 28 valid taxa: 22 species, six of which are divided into different subspecies.…”