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

Abstract

Six Gram-negative, rod-shaped bacterial strains isolated from Heterorhabditis amazonensis entomopathogenic nematodes were characterized to determine their taxonomic position. 16S rRNA and gyrB gene sequences indicate that they belong to the class Gammaproteobacteria , family Morganellaceae and genus Photorhabdus , and that some of them are conspecifics. Two of them, APURET and JART, were selected for further molecular characterization using whole genome- and whole-proteome-based phylogenetic reconstructions and sequence comparisons. Phylogenetic reconstructions using whole genome and whole proteome sequences show that strains APURET and JART are closely related to Photorhabdus luminescens subsp. luminescens ATCC 29999T and to P. luminescens subsp. mexicana MEX47-22T. Moreover, digital DNA–DNA hybridization (dDDH) values between APURET and P. luminescens subsp. luminescens ATCC 29999T, APURET and P. luminescens subsp. mexicana MEX47-22T, and APURET and JART are 61.6, 61.2 and 64.1 %, respectively. These values are below the 70 % divergence threshold that delimits prokaryotic species. dDDH scores between JART and P. luminescens subsp. luminescens ATCC 29999T and between JART and P. luminescens subsp. mexicana MEX47-22T are 71.9 and 74.8 %, respectively. These values are within the 70 and 79 % divergence thresholds that delimit prokaryotic subspecies. Based on these genomic divergence values, APURET and JART represent two different taxa, for which we propose the names: Photorhabdus aballayi sp. nov. with APURET (=CCM 9236T =CCOS 2019T) as type strain and Photorhabdus luminescens subsp. venezuelensis subsp. nov. with JART (=CCM 9235T =CCOS 2021T) as type strain. Our study contributes to a better understanding of the biodiversity of an important bacterial group with enormous biotechnological and agricultural potential.

Taxonomic and molecular characterization of a new entomopathogenic nematode species, Heterorhabditis casmirica n. sp., and whole genome sequencing of its associated bacterial symbiont

“…The strains were further subcultured and maintained on LB agar plates at 28 °C. An initial molecular characterization, using 16S rRNA gene sequences, was carried out to determine the taxonomic affiliation of the obtained bacterial cultures as described previously [ 3 , 4 , 17 , 56 ]. Phylogenetic reconstruction and sequence comparisons based on whole genome sequences were carried out to confirm the taxonomic affiliation of the obtained bacterial cultures as described previously [ 3 , 55 , 56 ].…”

“…An initial molecular characterization, using 16S rRNA gene sequences, was carried out to determine the taxonomic affiliation of the obtained bacterial cultures as described previously [ 3 , 4 , 17 , 56 ]. Phylogenetic reconstruction and sequence comparisons based on whole genome sequences were carried out to confirm the taxonomic affiliation of the obtained bacterial cultures as described previously [ 3 , 55 , 56 ]. Briefly, genomic DNA was extracted and purified using the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich, Switzerland) following the manufacturer’s instructions.…”

“…The final assemblies were polished using Pilon 1.22 [ 59 ]. Phylogenetic relationships were reconstructed based on the assembled genomes and the genome sequences of all valid published species of the genus [ 3 , 55 , 56 ]. For this, core genome alignments were created using Roary 3.6.2 [ 60 ].…”

Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes

“…One of the nematode strains isolated was designated here as CRI-LC. It was identified as previously described [ 36 ]. Briefly, genomic DNA from about 20 females was extracted using the genomic DNA isolation kit from QIAamp DNA Mini Kit (Qiagen, Valencia, CA) following the manufacturer’s instructions.…”

“…To harmonize the taxonomy of the bacteria symbiotically associated with both genera of entomopathogenic nematodes, Boemare et al (1993) proposed to create the genus Photorhabdus to accommodate the bacterial species associated with Heterorhabditis nematodes, and to maintain the genus Xenorhabdus for the bacterial species associated with Steinernema nematodes [ 19 ]. Since its creation, several Photorhabdus species and subspecies have been described [ 18 – 36 ] . Currently, the Photorhabdus genus contains 30 valid taxa: 23 species, 6 of which are divided into different subspecies.…”