Identification of Photorhabdus symbionts by MALDI-TOF MS

Description of Heterorhabditis americana n. sp. (Rhabditida, Heterorhabditidae), a new entomopathogenic nematode species isolated in North America

BACKGROUND

Heterorhabditis are important biological control agents in agriculture. Two Heterorhabditis populations, S8 and S10, were isolated from agricultural soils in the United States of America. Molecular analyses, based on mitochondrial and nuclear genes, showed that these populations are conspecific and represent a novel species of the "Bacteriophora" clade. This species was named Heterorhabditis americana n. sp. and is described in this study.

METHODS

To describe H. americana n. sp., we carried out phylogenetic reconstructions using multiple genes, characterized their morphology, conducted self-crossing and cross-hybridization experiments, and isolated and identified their symbiotic bacteria.

RESULTS

Heterorhabditis americana n. sp. is molecularly and morphologically similar to H. georgiana. Morphological differences between the males of H. americana n. sp. and H. georgiana include variations in the excretory pore position, the gubernaculum size, the gubernaculum-to-spicule length ratio, the tail length, and the body diameter. Infective juveniles (IJs) of H. americana n. sp. differ from H. georgiana IJs because H. americana n. sp. IJs have an invisible bacterial cell pouch posterior to the cardia and a small posterior phasmid, whereas H. georgiana IJs have a visible bacterial cell pouch and an inconspicuous phasmid. Hermaphrodites of H. americana n. sp. and H. georgiana are differentiated by the body length, the nerve ring distance from the anterior end, the excretory pore distance from the anterior end, the anal body diameter, and the c' ratio. Females of H. americana n. sp. can be differentiated from H. georgiana females by the anal body diameter and the c' ratio. Reproductive isolation was confirmed, as H. americana n. sp. does not produce viable offspring with any of the species of the "Bacteriophora" clade. Heterorhabditis americana n. sp. is associated with the symbiotic bacterium Photorhabdus kleinii.

CONCLUSIONS

Based on the observed morphological and morphometric differences, the distinct phylogenetic placement, and the reproductive isolation, the nematode isolates S8 and S10 represent a novel species, which we named Heterorhabditis americana n. sp. This study provides a detailed characterization of this novel species, contributing to enhancing our knowledge of species diversity and evolutionary relationships of the Heterorhabditis genus.

Direct analysis and identification of the intestinal microflora of shrimps for their geographical traceability via mass spectrometry and bacterial library searching

The expansion of the seafood market has led to an increased probability of food fraud. The development of rapid and reliable traceability methods for aquatic food products is of utmost importance. In this study, direct analysis and identification of the intestinal microbiota of aquatic foods were conducted. The validity of using BacteriaMS database searching for the identification of bacteria was assessed and demonstrated through analyzing prepared bacterial mixtures. We focused on shrimp as a model for aquatic food products and utilized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the intestinal microflora of Chinese shrimp (Fenneropenaeus chinensis) collected from three different aquaculture farms in China. It was found that the most dominant bacteria found in shrimps' intestines could serve as a basis for distinguishing shrimps' geographical origin. The most dominant bacteria in the intestines varied among shrimps from different origins but remained identical for shrimps from the same origin. The reliability of the method in tracing the geographic origin of aquatic products was further validated by analysis of black tiger shrimp (Penaeus monodon) from different origins. The findings show that the utilization of MALDI-TOF MS for the analysis of the microbial community in the intestines of shrimp samples combined with bacterial library searching can offer a rapid, accurate, and feasible method that can be employed for determining shrimps' geographical origin. The present protocol was successfully utilized for the traceability of origins of Chinese shrimp (Fenneropenaeus chinensis) and black tiger shrimp (Penaeus monodon). It is promising to extend the present protocol to other aquatic products with regional characteristics to help combat food fraud in the aquatic product market.

Photorhabdus viridis sp. nov. Isolated from Heterorhabditis zealandica Entomopathogenic Nematodes

A novel bacterial species, Photorhabdus viridis sp. nov., represented by strain GreenT, isolated from Heterorhabditis zealandica MJ2C entomopathogenic nematodes, is described. Phylogenetic reconstructions using 16S rRNA gene sequences show that strain GreenT is closely related to P. thracensis DSM 15199 T. The 16rRNA gene sequences of these two strains are 98.8% identical. Phylogenetic reconstructions using whole-genome sequences show that strain GreenT is closely related to P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T. Digital DNA-DNA hybridization (dDDH) values between strain GreenT and its three more close relative species, P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T, are 49%, 59%, and 59%, respectively. In addition, average nucleotide identity (ANI) values between GreenT and P. tasmaniensis DSM 22387 T, P. thracensis DSM 15199 T, and P. temperata DSM 14550 T are 92.4%, 94.4%, and 94.6%, respectively. The novel species also differs in their biochemical capacities from the biochemical capacities of their more closely related taxa. The following biochemical tests may be particularly useful in this context: Arginine dihydrolase, gelatinase, and glucose and mannitol oxidation. Given the clear phylogenetic separation, the sequence divergence values, and the phenotypic differences, we conclude that strain GreenT represents a novel bacterial species, for which we propose the name Photorhabdus viridis sp. nov. with GreenT (= CCM 9407 T = CCOS 2117 T = MJ2CT) as the type strain. Our study contributes to a better understanding of the taxonomy and biodiversity of an important bacterial group with great biotechnological and agricultural potential.

Unearthing the power of microbes as plant microbiome for sustainable agriculture

In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.

Photorhabdus africana sp. nov. isolated from Heterorhabditis entomopathogenic nematodes

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-LCT, was therefore molecularly, biochemically, and morphologically characterized to describe the novel bacterial species. Phylogenetic reconstructions using 16S rRNA gene sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. The 16rRNA gene sequences between CRI-LCT and P. laumondii subsp. laumondii TT01T are 99.1% identical, and between CRI-LCT and P. laumondii subsp. clarkei BOJ-47T are 99.2% identical. Phylogenetic reconstructions using whole genome sequences show that CRI-LCT is closely related to P. laumondii subsp. laumondii TT01T and to P. laumondii subsp. clarkei BOJ-47T. Moreover, digital DNA-DNA hybridization (dDDH) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T are 65% and 63%, respectively. In addition, we observed that average nucleotide identity (ANI) values between CRI-LCT and its two relative species P. laumondii subsp. laumondii TT01T and P. laumondii subsp. clarkei BOJ-47T 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-LCT represents a novel bacterial species, for which we propose the name Photorhabdus africana sp. nov. with CRI-LCT (= CCM 9390T = CCOS 2112T) as the type strain. The following biochemical tests allow to differentiate P. africana sp. nov. CRI-LCT 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.

Xenorhabdus aichiensis sp. nov., Xenorhabdus anantnagensis sp. nov., and Xenorhabdus yunnanensis sp. nov., Isolated from Steinernema Entomopathogenic Nematodes

Three bacterial strains, XENO-2T, XENO-7T, and XENO-10T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel Xenorhabdus species. In this study, we describe these new species by whole-genome and whole-proteome phylogenomic reconstructions, by calculating sequence identity scores using core genome sequences, and by phenotypic characterization. Phylogenomic reconstructions using ribosomal and house-keeping genes, and whole-genome and whole-proteome sequences show that XENO-2T and XENO-10T are closely related to Xenorhabdus japonica DSM 16522T and that XENO-7T is closely related to Xenorhabdus bovienii subsp. africana XENO-1T and to X. bovienii subsp. bovienii T228T. The dDDH values between XENO-2T and XENO-10T and between XENO-2T and X. japonica DSM 16522T are 56.4 and 51.8%, respectively. The dDDH value between XENO-10T and X. japonica DSM 16522T is 53.4%. The dDDH values between XENO-7T and X. bovienii subsp. africana XENO-1T and between XENO-7T and X. bovienii subsp. bovienii T228T are 63.6 and 69.4%, respectively. These dDDH values are below the 70% divergence threshold for prokaryotic species delineation. The newly described species are highly pathogenic to G. mellonella larvae, grow at pH between 5 and 9 (optimum 5-7), at salt concentrations of 1-3% (optimum 1-2%), and temperatures between 20 and 37 °C (optimum 28-30 °C). Biochemical tests such as lysine decarboxylase, ornithine decarboxylase, urease, gelatinase, citrate utilization, indole and acetoin production, and cytochrome oxidase tests allow to differentiate the novel species from their more closely related species. Considering these genetic and phenotypic divergencies, we propose the following new species: Xenorhabdus aichiensis sp. nov. with XENO-7T (= CCM 9233T = CCOS 2024T) as the type strain, Xenorhabdus anantnagensis sp. nov., with XENO-2T (= CCM 9237T = CCOS 2023T) as the type strain, and Xenorhabdus yunnanensis sp. nov., with XENO-10T (= CCM 9322T = CCOS 2071T) as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.

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

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, APURE^T and JAR^T, 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 APURE^T and JAR^T are closely related to Photorhabdus luminescens subsp. luminescens ATCC 29999^T and to P. luminescens subsp. mexicana MEX47-22^T. Moreover, digital DNA-DNA hybridization (dDDH) values between APURE^T and P. luminescens subsp. luminescens ATCC 29999^T, APURE^T and P. luminescens subsp. mexicana MEX47-22^T, and APURE^T and JAR^T are 61.6, 61.2 and 64.1 %, respectively. These values are below the 70 % divergence threshold that delimits prokaryotic species. dDDH scores between JAR^T and P. luminescens subsp. luminescens ATCC 29999^T and between JAR^T and P. luminescens subsp. mexicana MEX47-22^T 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, APURE^T and JAR^T represent two different taxa, for which we propose the names: Photorhabdus aballayi sp. nov. with APURE^T (=CCM 9236^T =CCOS 2019^T) as type strain and Photorhabdus luminescens subsp. venezuelensis subsp. nov. with JAR^T (=CCM 9235^T =CCOS 2021^T) as type strain. Our study contributes to a better understanding of the biodiversity of an important bacterial group with enormous biotechnological and agricultural potential.

Acinetobacter nematophilus sp. nov., Alcaligenes nematophilus sp. nov., Enterobacter nematophilus sp. nov., and Kaistia nematophila sp. nov., Isolated from Soil-Borne Nematodes and Proposal for the Elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the Species Level

Four bacterial strains, A-IN1T, A-TC2T, E-TC7T, and K-TC2T, isolated from soil-borne nematodes of the species Oscheius tipulae and Acrobeloides bodenheimeri, were found to represent new species of the genera Acinetobacter, Alcaligenes, Enterobacter, and Kaistia, respectively. In this study, we described these new species using a polyphasic taxonomic approach that included whole-genome and whole-proteome phylogenomic reconstructions, core genome sequence comparisons, and phenotypic characterization. Phylogenomic reconstructions using whole-genome and whole-proteome sequences show that A-IN1T is closely related to Acinetobacter guillouiae DSM 590T and to Acinetobacter bereziniae LMG 1003T. The dDDH values between A-IN1T and these latest strains are 25.1 and 39.6%, respectively, which are below the 70% divergence threshold for prokaryotic species delineation. A-TC2T is closely related to Alcaligenes faecalis subsp. faecalis DSM 30030T and to Alcaligenes faecalis subsp. phenolicus DSM 16503T. The dDDH values between A-TC2T and these latest strains are 47.0 and 66.3%, respectively. In addition, the dDDH values between Alcaligenes faecalis subsp. faecalis DSM 30030T, Alcaligenes faecalis subsp. phenolicus DSM 16503T, and Alcaligenes faecalis subsp. parafaecalis are always lower than 70%, demonstrating that the three strains represent species within the genus Alcaligenes rather than subspecies within Alcaligenes faecalis. E-TC7T is closely related to Enterobacter kobei DSM 13645T, Enterobacter chuandaensis 090028T, and to Enterobacter bugandensis STN0717-56T. The dDDH values between E-TC7T and these strains are 43.5, 42.9, and 63.7%, respectively. K-TC2T is closely related to Kaistia terrae DSM 21341T and to Kaistia defluvii JCM 18034T. The dDDH values between these strains are 29.2 and 30.7%, respectively. Several biochemical tests allow to differentiate the type strains of the newly described species from the type strains of their more closely related species. Based on the results of this polyphasic taxonomic approach, the following new species are proposed: Acinetobacter nematophilus sp. nov. with A-IN1T (=CCM 9231T =CCOS 2018T) as the type strain, Alcaligenes nematophilus sp. nov. with A-TC2T (=CCM 9230T =CCOS 2017T) as the type strain, Enterobacter nematophilus sp. nov. with E-TC7T (=CCM 9232T =CCOS 2020T) as the type strain, and Kaistia nematophila sp. nov. with K-TC2T (=CCM 9239T =CCOS 2022T) as the type strain. In addition, we propose the elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the species level. Therefore, we propose the creation of Alcaligenes parafaecalis sp. nov. with DSM 13975T as the type strain, and Alcaligenes phenolicus sp. nov. with DSM 16503T as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of bacteria associated with soil-borne nematodes.

Entomopathogenic potential of bacteria associated with soil-borne nematodes and insect immune responses to their infection

Soil-borne nematodes establish close associations with several bacterial species. Whether they confer benefits to their hosts has been investigated in only a few nematode-bacteria systems. Their ecological function, therefore, remains poorly understood. In this study, we isolated several bacterial species from rhabditid nematodes, molecularly identified them, evaluated their entomopathogenic potential on Galleria mellonella larvae, and measured immune responses of G. mellonella larvae to their infection. Bacteria were isolated from Acrobeloides sp., A. bodenheimeri, Heterorhabditis bacteriophora, Oscheius tipulae, and Pristionchus maupasi nematodes. They were identified as Acinetobacter sp., Alcaligenes sp., Bacillus cereus, Enterobacter sp., Kaistia sp., Lysinibacillus fusiformis, Morganella morganii subsp. morganii, Klebsiella quasipneumoniae subsp. quasipneumoniae, and Pseudomonas aeruginosa. All bacterial strains were found to be highly entomopathogenic as they killed at least 53.33% G. mellonella larvae within 72h post-infection, at a dose of 106 CFU/larvae. Among them, Lysinibacillus fusiformis, Enterobacter sp., Acinetobacter sp., and K. quasipneumoniae subsp. quasipneumoniae were the most entomopathogenic bacteria. Insects strongly responded to bacterial infection. However, their responses were apparently little effective to counteract bacterial infection. Our study, therefore, shows that bacteria associated with soil-borne nematodes have entomopathogenic capacities. From an applied perspective, our study motivates more research to determine the potential of these bacterial strains as biocontrol agents in environmentally friendly and sustainable agriculture.

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

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).

Potential of Oscheius tipulae nematodes as biological control agents against Ceratitis capitata

A survey to collect soil nematodes with potential to control Ceratitis capitata flies was carried out in different locations in Tunisia. Several nematode isolates were recovered, laboratory colonies were established, and their taxonomic identities were determined based on molecular methods. Among all the recovered nematode isolates, two of them, Oscheius tipulae TC2 and OC2, were evaluated for their capacity to control C. capitata flies and for their ability to kill and reproduce on Galleria mellonella larvae. Our results show a great potential of these two isolates as biocontrol agents as they kill C. capitata eggs and pupae and interfere with the metamorphosis of C. capitata larvae. More specifically, TC2 and OC2 nematodes killed 39 and 31% of C. capitata eggs, respectively, impaired the metamorphosis of up to 77% and up to 67% of C. capitata larvae, respectively, and killed up to 66% and up to 58% of C. capitata pupae, respectively. The efficacy of TC2 and OC2 nematodes was particularly high on C. capitata pupae, and significant insect mortalities were observed even at concentrations of 1 and 5 nematodes/pupae, respectively. We also found that TC2 and OC2 nematodes efficiently kill and reproduce in G. mellonella larvae, suggesting that these insects could be used for mass-multiplication of these nematodes. These results reveal the potential of O. tipulae to complement integrated pest management programs against C. capitata flies.

Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product

Two lactic acid bacterial strains (IMAU80584T and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to Lentilactobacillus rapi . However, phylogenetic tree analyses of two housekeeping genes, rpoA (encoding RNA polymerase alpha subunit) and pheS (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from L. rapi DSM 19907T, forming an infra-specific subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between IMAU80584T and L. rapi DSM 19907T were 93.1 and 52.8 %, respectively. Strains IMAU80584T and IMAU92037 are distinguished from L. rapi DSM 19907T because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584T was 42.3 mol%. The major cellular fatty acids were C16 : 0, C18 : 1  ω9t and summed feature 5 (C18 : 0 ante and/or C18 : 2  ω6c and/or C18 : 2  ω9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584T and IMAU92037 could be considered as a novel subspecies in the species L. rapi with the proposed name Lentilactobacillus rapi subsp. dabitei subsp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).

Multi-locus phylogenetic analyses uncover species boundaries and reveal the occurrence of two new entomopathogenic nematode species, Heterorhabditis ruandica n. sp. and Heterorhabditis zacatecana n. sp

Species of the nematode genus Heterorhabditis are important biological control agents against agricultural pests. The taxonomy of this group is still unclear as it currently relies on phylogenetic reconstructions based on a few genetic markers with little resolutive power, specially of closely related species. To fill this knowledge gap, we sequenced several phylogenetically relevant genetic loci and used them to reconstruct phylogenetic trees, to calculate sequence similarity scores, and to determine signatures of species- and population-specific genetic polymorphism. In addition, we revisited the current literature related to the description, synonymisation, and declaration as species inquirendae of Heterorhabditis species to compile taxonomically relevant morphological and morphometric characters, characterized new nematode isolates at the morphological and morphometrical level, and conducted self-crossing and cross-hybridization experiments. The results of this study show that the sequences of the mitochondrial cytochrome C oxidase subunit I (COI) gene provide better phylogenetic resolutive power than the sequences of nuclear rRNA genes and that this gene marker can phylogenetically resolve closely related species and even populations of the same species with high precision. Using this gene marker, we found two new species, Heterorhabditis ruandica n. sp. and Heterorhabditis zacatecana n. sp. A detailed characterization of these species at the morphological and morphometric levels and nematode reproduction assays revealed that the threshold for species delimitation in this genus, using COI sequences, is 97% to 98%. Our study illustrates the importance of rigorous morphological and morphometric characterization and multi-locus sequencing for the description of new species within the genus Heterorhabditis, serves to clarify the phylogenetic relationships of this important group of biological control agents, and can inform future species descriptions to advance our efforts towards developing more tools for sustainable and environmentally friendly agriculture.

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

Two Gram-negative, rod-shaped bacteria, H1^T and H3^T, isolated from the digestive tract of Heterorhabditis 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 Morganellaceae, and to the Photorhabdus genus. Deeper analyses using whole genome-based phylogenetic reconstructions show that strains H1^T and H3^T are closely related to P. akhurstii DSM 15138^T, to P. hainanensis DSM 22397^T, and to P. namnaonensis PB45.5^T. In silico 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 P. akhurstii DSM 15138^T, P. hainanensis DSM 22397^T, and P. namnaonensis PB45.5^T, respectively, and that strain H3^T shares 76.6, 69.4, and 59.2 % dDDH with P. akhurstii DSM 15138^T, P. hainanensis DSM 22397^T, and P. namnaonensis PB45.5^T, respectively. Physiological and biochemical characterization reveals that these two strains differ from most of the validly described Photorhabdus 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 P. akhurstii, and H1^T as a new species within the Photorhabdus genus, in spite that H1^T shares 70.6 % dDDH with P. akhurstii 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 P. akhurstii DSM 15138^T cluster apart in the phylogenetic trees and that dDDH scores between strain H1^T and other P. akhurstii strains are lower than 70 %. Hence, the following names are proposed: Photorhabdus hindustanensis sp. nov. with the type strain H1^T (=IARI-SGMG3^T,=KCTC 82683^T=CCM 9150^T=CCOS 1975^T) and P. akhurstii subsp. bharatensis subsp. nov. with the type strain H3^T (=IARI-SGHR2^T=KCTC 82684^T=CCM 9149^T=CCOS 1976^T). These propositions automatically create P. akhurstii subsp. akhurstii subsp. nov. with DSM 15138^T as the type strain (currently classified as P. akhurstii).

Photorhabdus heterorhabditis subsp. aluminescens subsp. nov., Photorhabdus heterorhabditis subsp. heterorhabditis subsp. nov., Photorhabdus australis subsp. thailandensis subsp. nov., Photorhabdus australis subsp. australis subsp. nov., and Photorhabdus aegyptia sp. nov. isolated from Heterorhabditis entomopathogenic nematodes

Three Gram-stain-negative, rod-shaped, non-spore-forming bacteria, BA1^T, Q614^T and PB68.1^T, isolated from the digestive system of Heterorhabditis entomopathogenic nematodes, were biochemically and molecularly characterized to clarify their taxonomic affiliations. The 16S rRNA gene sequences of these strains suggest that they belong to the Gammaproteobacteria, to the family Morganellacea, and to the genus Photorhabdus. Deeper analyses using whole genome-based phylogenetic reconstructions suggest that BA1^T is closely related to Photorhabdus akhursti, that Q614^T is closely related to Photorhabdus heterorhabditis, and that PB68.1^T is closely related to Photorhabdus australis. In silico genomic comparisons confirm these observations: BA1^T and P. akhursti 15138^T share 68.8 % digital DNA-DNA hybridization (dDDH), Q614^T and P. heterorhabditis SF41^T share 75.4 % dDDH, and PB68.1^T and P. australis DSM 17609^T share 76.6  % dDDH. Physiological and biochemical characterizations reveal that these three strains also differ from all validly described Photorhabdus species and from their more closely related taxa, contrary to what was previously suggested. We therefore propose to classify BA1^T as a new species within the genus Photorhabdus, Q614^T as a new subspecies within P. heterorhabditis, and PB68.1^T as a new subspecies within P. australis. Hence, the following names are proposed for these strains: Photorhabdus aegyptia sp. nov. with the type strain BA1^T(=DSM 111180^T=CCOS 1943^T=LMG 31957^T), Photorhabdus heterorhabditis subsp. aluminescens subsp. nov. with the type strain Q614^T (=DSM 111144^T=CCOS 1944^T=LMG 31959^T) and Photorhabdus australis subsp. thailandensis subsp. nov. with the type strain PB68.1^T (=DSM 111145^T=CCOS 1942^T). These propositions automatically create Photorhabdus heterorhabditis subsp. heterorhabditis subsp. nov. with SF41^T as the type strain (currently classified as P. heterorhabditis) and Photorhabdus australis subsp. australis subsp. nov. with DSM17609^T as the type strain (currently classified as P. australis).