Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes

Abstract

One Gram-negative, rod-shaped bacterial strain, isolated from an undescribed Heterorhabditis entomopathogenic nematode species was characterized to determine its taxonomic position. The 16S rRNA gene sequences indicate that it belongs to the class Gammaproteobacteria, to the family Morganellaceae, to the genus Photorhabdus, and likely represents a novel bacterial species. This strain, designated here as CRI-LC^T, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LC^T is closely related to P. laumondii subsp. laumondii TT01^T and to P. laumondii subsp. clarkei BOJ-47^T. The 16rRNA gene sequences between CRI-LC^T and P. laumondii subsp. laumondii TT01^T are 99.1% identical, and between CRI-LC^T and P. laumondii subsp. clarkei BOJ-47^T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LC^T is closely related to P. laumondii subsp. laumondii TT01^T and to P. laumondii subsp. clarkei BOJ-47^T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LC^T and its two relative species P. laumondii subsp. laumondii TT01^T and P. laumondii subsp. clarkei BOJ-47^T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LC^T and its two relative species P. laumondii subsp. laumondii TT01^T and P. laumondii subsp. clarkei BOJ-47^T are 95.8% and 95.5%, respectively. These values are below the 70% dDDH and the 95-96% ANI divergence thresholds that delimits prokaryotic species. Based on these genomic divergence values, and the phylogenomic separation, we conclude that CRI-LC^T represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LC^T (= CCM 9390^T = CCOS 2112^T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LC^T from other species of the genus, including its more closely related taxa: β-Galactosidase, citrate utilization, urease and tryptophan deaminase activities, indole and acetoin production, and glucose and inositol oxidation. Our study contributes to a better understanding of the taxonomy and biodiversity of this important bacterial group with great biotechnological and agricultural potential.