Phylogeny of Photorhabdus and Xenorhabdus based on universally conserved protein-coding sequences and implications for the taxonomy of these two genera. Proposal of new taxa: X. vietnamensis sp. nov., P. luminescens subsp. caribbeanensis subsp. nov., P. luminescens subsp. hainanensis subsp. nov., P. temperata subsp. khanii subsp. nov., P. temperata subsp. tasmaniensis subsp. nov., and the reclassification of P. luminescens subsp. thracensis as P. temperata subsp. thracensis comb. nov

Systematics, diversity and biogeography of entomopathogenic nematodes and their bacterial symbionts

Since the discovery of the first entomopathogenic nematode in 1923, our understanding of their systematics and biogeography has advanced significantly. This review outlines the historical development of research on systematics of entomopathogenic nematodes and their bacterial symbionts, while presenting the current state of knowledge in these fields. Additionally, we evaluate the status of several recently described but dubious EPN species and provide an updated list of valid Heterorhabditis and Steinernema species. Finally, we summarize existing data on the geographical distribution of entomopathogenic nematode species and draw general conclusions about their biogeography.

The first 100 years in the history of entomopathogenic nematodes

The field of entomopathogenic nematology has grown exponentially since the discovery of the first species, Steinernema kraussei (=Aplecatna kraussei), in 1923. Initially, entomopathogenic nematodes (EPN) were solely viewed as a curiosity. The discovery of the nematode-bacteria association in 1965 and the incipient research for mass production motivated their recognition as biological control agents for agricultural pests. Subsequent studies were focused on the discovery of new species and/or populations, the early studies to understand the biotic and abiotic factors that contribute to their performance in the field and success in insect pest management. However, as we entered the 21st century, and with the advent of molecular biology, research on these organisms took a fascinating turn, unraveling a deeper understanding of the complex symbiotic relationship EPN has with their bacterial symbionts and the insect host. Furthermore, because of their experimental tractability, EPNs have proven to be model organisms that are used among various biological sciences to gain further insights into host-symbiont, host-pathogen interactions, population dynamics, and as resources for pharmaceutical bioprospecting. This special issue commemorates the first 100 years of research in entomopathogenic nematology and summarizes the contributions of ten symposia and presentations at the 100th Anniversary of the First EPN Discovery Congress in Logroño, Spain (https://www.icvv.es/english/epn). This specific article focuses on the historical review of EPN, their bacterial partners and the numerous and diverse applications in disciplines in basic such as phylogeny, biogeography, symbiosis, and soil biology and ecology, or more applied venues such as formulation and mass production, application technology, commercialization and regulation, from 1923 to the present time.

Steinernema keralense n. sp., a new entomopathogenic nematode (Nematoda: Steinernematidae) from India

In this study, morphological and molecular features were used to identify a new Steinernema sp. from Kerala, India. Morphological and molecular features provide evidence for placing the new species into the longicaudum clade. The new species is characterized by the following morphological features: infective juveniles with a body length of 1067 μm (914-1268 μm); a distance from the anterior end to excretory pore of 82 μm (73-92 μm); a distance from anterior end to nerve ring of 105 μm (91-118 μm). The distinguishing feature of the infective juveniles of S. keralense n. sp. is the presence of seven ridges in the mid-body region, while all other species classified within the logicaudum clade to date are characterized by eight ridges. The first-generation males are characterised by 25 genital papillae, very short spicules, with a length of 68 μm (60-72 μm), and the SW% ratio is 136 (114-169). The new species is further characterized by sequences of the internal transcribed spacer and partial 28S regions of the ribosomal DNA. Phylogenetic analyses show that S. keralense n. sp. is closely related to species within the longicaudum clade.

Comparative pathogenicity of entomopathogenic nematodes symbiotic bacteria- distinct intra- and inter-species variation

This study aimed to achieve two main objectives: first, to determine whether the virulence factors of symbiotic bacteria of entomopathogenic nematodes (EPNs) against insect hosts are cell-associated or secreted, and to shed light on the underlying mechanisms of pathogenicity; and second, to identify and evaluate the standalone pathogenicity of symbiotic bacteria associated with entomopathogenic nematodes against Tenebrio molitor. Three bacterial species, Xenorhabdus nematophila (A41, SC, A18 and SF), Photorhabdus kayaii, and P. thracensis, were isolated and characterized via phylogenetic analysis of 16S-rRNA and gyrB genes. Bioassays involved injecting T. molitor larvae with bacterial suspensions, cell-free supernatants, immersing them in bacterial suspensions, and incorporating various bacterial treatments into their diet. Lethal concentrations (LC50) and lethal times (LT50) were determined based on observed mortality trends within specified periods. No mortality was recorded in T. molitor larvae when they were immersed in bacterial suspensions or fed diets incorporating various bacterial treatments. Among injection-based trials, X. nematophila strains A41, SC, and SF demonstrated remarkable virulence through low LC50 values in bacterial suspension tests, whereas X. nematophila A18 stood out in intracellular suspension trials. Interestingly, P. thracensis triggered mortality exclusively during extracellular suspension testing. However, no discernible effects emerged when employing non-invasive techniques such as soaking or spiking the insect's diet. Overall, our investigation highlights significant intra-species/inter-species variation in the pathogenicity profiles of nematode-associated bacteria towards T. molitor across diverse application modes, emphasizing the importance of tailored implementation approaches in utilizing microbials as effective biocontrol agents. The variation in susceptibility of host to cell suspension, cellular extract, and cell-free suspension of the studied bacteria indicates that the existence of living bacteria or intercellular secretions may be essential for certain isolates to establish a successful infection. In order to optimize the use of symbiotic bacteria as a biocontrol agent, it is important for future research to focus on identifying genes that encode for intercellularly secreted proteins and exploring alternate delivery methods. This will help in realizing the full potential of these beneficial bacteria in IPM programs.

Symbiotic bacteria associated with entomopathogenic nematodes showed molluscicidal activity against Biomphalaria glabrata, an intermediate host of Schistosoma mansoni

BACKGROUND

Biomphalaria glabrata acts as the intermediate host of schistosomes that causes human schistosomiasis. Symbiotic bacteria, Xenorhabdus and Photorhabdus associated with Steinernema and Heterorhabditis, produce secondary metabolites with several biological activities. Controlling B. glabrata is a potential strategy to limit the transmission of schistosomiasis. The aims of this study were to identify Xenorhabdus and Photorhabdus bacteria based on recA sequencing and evaluate their molluscicidal activity against B. glabrata snail.

RESULTS

A total of 31 bacterial isolates belonging to Xenorhabdus (n = 19) and Photorhabdus (n = 12) (X. ehlersii, X. stockiae, X. indica, X. griffinae, P. luminescens, P. akhurstii, and P. laumondii subsp. laumondii were molecularly identified based on recA sequencing. Five isolates of bacterial extracts showed potential molluscicide, with 100% snail mortality. P. laumondii subsp. laumondii (bALN19.5_TH) showed the highest effectiveness with lethal concentration (LC) values of 54.52 µg/mL and 89.58 µg/mL for LC50 and LC90, respectively. Histopathological changes of the snail were observed in the head-foot region, which showed ruptures of the epithelium covering the foot and deformation of the muscle fiber. A hemocyte of the treated snails was observed in the digestive tubules of the digestive glands. The hermaphrodite glands of treated snails showed a reduction in the number of spermatozoa, degeneration of oocytes, and deformation and destruction in the hermaphrodite gland. In addition, liquid chromatography-tandem mass spectrometry (LC-MS/MS) of three symbiotic bacteria contained compounds such as GameXPeptide, Xenofuranone, and Rhabdopeptide.

CONCLUSIONS

Five bacterial extracts showed good activity against B. glabrata, especially P. laumondii subsp. laumondii and X. stockiae, which produced virulent secondary metabolites resulting in the death of the snails. They also caused histopathological alterations in the foot, digestive glands, and hermaphrodite glands of the snails. This study suggests that extracts from these bacteria show promise as molluscicides for the control of B. glabrata.

Xenorhabdus bharatensis sp. nov., Xenorhabdus entomophaga sp. nov., Xenorhabdus siamensis sp. nov., and Xenorhabdus thailandensis sp. nov. Isolated from Steinernema Entomopathogenic Nematodes

Four Gram-stain-negative bacterial strains, CS20T, AUT15.5T, XENO-11T, and CCN3.3T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel species within the genus Xenorhabdus (Gammaproteobacteria, Morganellaceae). In this study, we described these new species using whole-genome phylogenomic reconstructions, sequence identity values from core genome sequences, and phenotypic characterization. Phylogenetic reconstructions based on 16S rRNA gene sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T, (ii) strain AUT15.5T is closely related to X. budapestensis DSM 16342T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The 16S rRNA gene sequence similarity value between strain CS20T and X. stockiae DSM 17904T is 97.8%, between strain AUT15.5T and X. budapestensis DSM 16342T is 98.1%, between strain XENO-11T and X. khoisanae DSM 25463T is 97.8%, and between strain CCN3.3T and X. griffiniae DSM 17911T is 98.6%. Phylogenomic reconstructions using whole-genome sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T and X. innexi DSM 16336T, (ii) strain AUT15.5T is closely related to X. indica DSM 17382T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains CS20T, AUT15.5T, XENO-11T, and CCN3.3T and the type strains of their more closely related species are below the 70% and the 95-96% divergence thresholds, respectively, used for prokaryotic species delineation. Hence, we propose the following four new species: Xenorhabdus bharatensis sp. nov. (the type strain is CS20T=CCM 9320T=CCOS 2070T), X. entomophaga sp. nov. (the type strain is XENO-11T=CCM 9389T=CCOS 2111T), X. siamensis sp. nov. (the type strain is AUT15.5T=CCM 9405T=CCOS 2116T), and X. thailandensis sp. nov. (the type strain is CCN3.3T=CCM 9406T=CCOS 2115T). The following biochemical tests may be useful for differentiating the novel species from their more closely related taxa: acetoin production, arginine dihydrolase, citrate utilization, gelatinase, glucose oxidation, indole production, and tryptophan deaminase. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.

A temperature-induced metabolic shift in the emerging human pathogen Photorhabdus asymbiotica

Photorhabdus is a bacterial genus containing both insect and emerging human pathogens. Most insect-restricted species display temperature restriction, unable to grow above 34°C, while Photorhabdus asymbiotica can grow at 37°C to infect mammalian hosts and cause Photorhabdosis. Metabolic adaptations have been proposed to facilitate the survival of this pathogen at higher temperatures, yet the biological mechanisms underlying these are poorly understood. We have reconstructed an extensively manually curated genome-scale metabolic model of P. asymbiotica (iEC1073, BioModels ID MODEL2309110001), validated through in silico gene knockout and nutrient utilization experiments with an excellent agreement between experimental data and model predictions. Integration of iEC1073 with transcriptomics data obtained for P. asymbiotica at temperatures of 28°C and 37°C allowed the development of temperature-specific reconstructions representing metabolic adaptations the pathogen undergoes when shifting to a higher temperature in a mammalian compared to insect host. Analysis of these temperature-specific reconstructions reveals that nucleotide metabolism is enriched with predicted upregulated and downregulated reactions. iEC1073 could be used as a powerful tool to study the metabolism of P. asymbiotica, in different genetic or environmental conditions.

IMPORTANCE

Photorhabdus bacterial species contain both human and insect pathogens, and most of these species cannot grow in higher temperatures. However, Photorhabdus asymbiotica, which infects both humans and insects, can grow in higher temperatures and undergoes metabolic adaptations at a temperature of 37°C compared to that of insect body temperature. Therefore, it is important to examine how this bacterial species can metabolically adapt to survive in higher temperatures. In this work, using a mathematical model, we have examined the metabolic shift that takes place when the bacteria switch from growth conditions in 28°C to 37°C. We show that P. asymbiotica potentially experiences predicted temperature-induced metabolic adaptations at 37°C predominantly clustered within the nucleotide metabolism pathway.

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.

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

Entomopathogenic nematodes of the genera Steinernema and Heterorhabditis, along with their bacterial symbionts from the genera Xenorhabdus and Photorhabdus, respectively, are important biological control agents against agricultural pests. Rapid progress in the development of genomic tools has catalyzed a transformation of the systematics of these organisms, reshaping our understanding of their phylogenetic and cophlylogenetic relationships. In this review, we discuss the major historical events in the taxonomy and systematics of this group of organisms, highlighting the latest advancements in these fields. Additionally, we synthesize information on nematode-bacteria associations and assess the existing evidence regarding their cophylogenetic relationships.

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.

Biocontrol potential of six Heterorhabditis bacteriophora strains isolated in the Azores Archipelago

Entomopathogenic nematodes (EPNs) are closely associated with Popillia japonica and potentially used as their biological control agents, although field results proved inconsistent and evoked a continual pursuit of native EPNs more adapted to the environment. Therefore, we surveyed the Azorean Archipelago to isolate new strains of Heterorhabditis bacteriophora and to evaluate their virulence against the model organism Galleria mellonella under laboratory conditions. Six strains were obtained from pasture and coastal environments and both nematode and symbiont bacteria were molecularly identified. The bioassays revealed that Az172, Az186, and Az171 presented high virulence across the determination of a lethal dose (LD50) and short exposure time experiments with a comparable performance to Az29. After 72 hours, these virulent strains presented a mean determination of a lethal dose of 11 infective juveniles cm-2, a lethal time (LT50) of 34 hours, and achieved 40% mortality after an initial exposure time of only 60 minutes. Az170 exhibited an intermediate performance, whereas Az179 and Az180 were classified as low virulent strains. However, both strains presented the highest reproductive potential with means of 1700 infective juveniles/mg of larvae. The bioassays of the native EPNs obtained revealed that these strains hold the potential to be used in biological control initiatives targeting P. japonica because of their high virulence and locally adapted to environmental conditions.

Enhancing mass production of Heterorhabditis bacteriophora: influence of different bacterial symbionts (Photorhabdus spp.) and inoculum age on dauer juvenile recovery

The entomopathogenic nematode Heterorhabditis bacteriophora (Nematoda: Rhabditidae) is used in biological insect control. Their dauer juveniles (DJs) are free-living and developmentally arrested, invading host insects. They carry cells of their bacterial symbiont Photorhabdus spp. in the intestine. Once inside the insect´s hemolymph the DJs perceive a food signal, triggering them to exit the DJ stage and regurgitate the Photorhabdus cells into the insect's haemocoel, which kill the host and later provide essential nutrients for nematode reproduction. The exit from the DJ stage is called "recovery". For commercial pest control, nematodes are industrially produced in monoxenic liquid cultures. Artificial media are incubated with Photorhabdus before DJs are added. In absence of the insect's food signal, DJs depend on unknown bacterial food signals to trigger exit of the DJ stage. A synchronized and high DJ recovery determines the success of the industrial in vitro production and can significantly vary between nematode strains, inbred lines and mutants. In this study, fourteen bacterial strains from H. bacteriophora were isolated and identified as P. laumondii, P. kayaii and P. thracensis. Although the influence of bacterial supernatants on the DJ recovery of three inbred lines and two mutants differed significantly, the bacterial impact on recovery has a subordinate role whereas nematode factors have a superior influence. Recovery of inbred lines decreased with age of the DJs. One mutant (M31) had very high recovery in bacterial supernatant and spontaneous recovery in Ringer solution. Another mutant (M88) was recovery defective.

Steinernema shori n. sp., a new entomopathogenic nematode (Nematoda: Steinernematidae) from India

In this study, morphological and molecular features were used to identify a new Steinernema sp. from Chhattisgarh, India. Morphological and molecular features provide evidence for placing the new species into the "bicornutum" clade. The new species is characterized by the following morphological features: infective juveniles with a body length of 587 (494-671) μm; a distance from the anterior end to excretory pore of 46 (43-50) μm; a distance from anterior end to nerve ring of 72 μm (61-85 μm); and E% of 88 (77-97). The first-generation males are characterised by 27 genital papillae and very short spicules, with a length of 61 μm (53-67) μm. The SW% and GS% ratio of S. shori n. sp. are 139 (107-190) and 75 (62-90), respectively. The new species is further characterized by sequences of the internal transcribed spacer and partial 28S regions of the ribosomal DNA. Phylogenetic analyses show that S. shori n. sp. is most closely related to S. abbasi, S. kandii, and S. yirgalemense.

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.

Association of Rahnella victoriana, Enterobacter hormaechei subsp. hoffmannii and Citrobacter braakii with walnut decline

Persian walnut (Juglans regia) has a considerable economic importance worldwide. However, the vigor and vitality of walnut trees were heavily affected by bark canker during the last few years. Irregular longitudinal cankers in the outer bark, stem tissue necrosis, and bleeding with black-colored exudates walnut trees were observed in Kermanshah, Hamedan, Markazi, Alborz, Isfahan, Qom, Semnan, and Razavi Khorasan provinces in western, central and eastern Iran during 2018 and 2019. A total of 150 symptomatic samples were collected from affected walnut trees in order to identify bacteria associated with walnut decline. Two-hundred sixty strains with a metallic green sheen were isolated on EMB-agar medium. The pathogenicity of all strains was proved by inoculating a suspension of the bacterial strains under the bark of immature walnut fruits cv. 'Hartley'. Ninety-five strains caused necrosis and a dark-colored region in the mesocarp around the inoculation site 14 days post-inoculation. Moreover, 12 representative strains induced necrotic and black-colored tissues in the bark of young green twigs of two-year old walnut seedling cv. 'Chandler'. The strains were classified into four categories based on conventional phenotypic characters confirmed with the 16S rRNA gene sequences. A phylogenetic tree based on the concatenated sequences of two housekeeping gene fragments, gyrB and infB, indicated that strains including I1, Q6, and S6 were grouped in a cluster with Gibbsiella quercinecans FBR97^T as well as strains I2, I5, and KE6 were clustered with Rahnella victoriana FRB 225^T. Moreover, strains MR1, MR3, and MR5 were grouped with the Enterobacter hormaechei subsp. hoffmannii DSM 14563^T. The phylogenetic analyses based on the partial sequencing of housekeeping genes including fusA, pyrG, and leuS revealed that strains KH1, KH3, and KH7 belong to Citrobacter braakii species. To the best of our knowledge, this is the first report of C. braakii and E. hormaechei as plant pathogens and R. victoriana associated with walnut decline.

Draft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya

As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only 27 species have been described to date. In this study, a novel Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 - this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils - were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70 % of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1 and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70 % of species-specific genes encoded unknown functions. Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae . The functions encoded by most species-specific genes in the X. griffiniae clade remain unknown.

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.

The endosymbiont and the second bacterial circle of entomopathogenic nematodes

Single host-symbiont interactions should be reconsidered from the perspective of the pathobiome. We revisit here the interactions between entomopathogenic nematodes (EPNs) and their microbiota. We first describe the discovery of these EPNs and their bacterial endosymbionts. We also consider EPN-like nematodes and their putative symbionts. Recent high-throughput sequencing studies have shown that EPNs and EPN-like nematodes are also associated with other bacterial communities, referred to here as the second bacterial circle of EPNs. Current findings suggest that some members of this second bacterial circle contribute to the pathogenic success of nematodes. We suggest that the endosymbiont and the second bacterial circle delimit an EPN pathobiome.

Comparative genomics and informational content analysis uncovered internal regions of the core genes rpoD, pepN and gltX for an MLSA with genome-level resolving power within the genus Pseudomonas

In the field of prokaryotic taxonomy, there has been a recent transition towards phylogenomics as the gold standard approach. However, genome-based phylogenetics is still restrictive for its cost when managing large amounts of isolates. Fast, cheap, and taxonomically competent alternatives, like multilocus sequence analysis (MLSA) are thus recommendable. Nevertheless, the criteria for selecting the conserved genes for MLSA have not been explicit for different bacterial taxa, including the broadly diverse Pseudomonas genus. Here, we have carried out an unbiased and rational workflow to select internal sequence regions of Pseudomonas core genes (CG) for a MLSA with the best phylogenetic power, and with a resolution comparable to the genome-based ANI approach. A computational workflow was established to inspect 126 complete genomes of representatives from over 60 Pseudomonas species and subspecies, in order to identify the most informative CG internal regions and determine which combinations in sets of three partial CG sequences have comparable phylogenetic resolution to that of the current ANI standard. We found that the rpoD^346-1196-pepN^1711-2571-gltX^86-909 concatenated sequences were the best performing in terms of phylogenetic robustness and resulted highly sensitive and specific when contrasted with ANI. The rpoD-pepN-gltX MLSA was validated in silico and in vitro. Altogether, the results presented here supports the proposal of the rpoD-pepN-gltX MLSA as a fast, affordable, and robust phylogenetic tool for members of the Pseudomonas genus.

Entomopathogenic Nematodes and Their Symbiotic Bacteria from the National Parks of Thailand and Larvicidal Property of Symbiotic Bacteria against Aedes aegypti and Culex quinquefasciatus

Simple Summary

Entomopathogenic nematodes (EPNs) are insect-parasitizing nematodes of the genera Heterorhabditis and Steinernema that are symbiotically associated with the symbiotic bacteria Photorhabdus and Xenorhabdus, respectively. Heterorhabditis indica, H. baujardi, Heterorhabditis SGmg3, Steinernema guangdongense, S. surkhetense, S. minutum, and S. longicaudum were isolated from soil samples in the national parks of Thailand. For symbiotic bacterial isolates, P. luminescens subsp. akhurstii, P. luminescens subsp. hainanensis, P. luminescens subsp. australis, Xenorhabdus stockiae, X. indica, X. griffiniae, X. japonica, and X. hominickii were isolated from those EPNs. In mosquito larvicidal bioassays, Photorhabdus isolates were effective against both Aedes aegypti and Culex quinquefasciatus. In conclusion, a wide diversity of entomopathogenic nematodes and symbiotic bacteria was found in the national parks of Thailand. Moreover, isolated Photorhabdus bacteria were shown to have potential as biocontrol agents to control culicine mosquitoes.

Abstract

Entomopathogenic nematodes (EPNs) are insect parasitic nematodes of the genera Het-erorhabditis and Steinernema. These nematodes are symbiotically associated with the bacteria, Photorhabdus and Xenorhabdus, respectively. National parks in Thailand are a potentially rich resource for recovering native EPNs and their symbiotic bacteria. The objectives of this study are to isolate and identify EPNs and their bacterial flora from soil samples in four national parks in Thailand and to evaluate their efficacy for controlling mosquito larvae. Using a baiting method with a Galleria mellonella moth larvae and a White trap technique, 80 out of 840 soil samples (9.5%) from 168 field sites were positive for EPNs. Sequencing of an internal transcribed spacer resulted in the molecular identification of Heterorhabditis nematode isolates as H. indica, H. baujardi and Heterorhabditis SGmg3, while using 28S rDNA sequencing, Steinernema nematode species were identified as S. guang-dongense, S. surkhetense, S. minutum, S. longicaudum and one closely related to S. yirgalemense. For the symbiotic bacterial isolates, based on recA sequencing, the Photorhabdus spp. were identified as P. luminescens subsp. akhurstii, P. luminescens subsp. hainanensis and P. luminescens subsp. australis. Xenorhabdus isolates were identified as X. stockiae, X. indica, X. griffiniae, X. japonica and X. hominickii. Results of bioassays demonstrate that Photorhabdus isolates were effective on both Aedes aegypti and Culex quinquefasciatus. Therefore, we conclude that soil from Thailand’s national parks contain a high diversity of entomopathogenic nematodes and their symbiotic bacteria. Photorhabdus bacteria are larvicidal against culicine mosquitoes and may serve as effective biocontrol agents.

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).

Description of Oscheius cyrus n. sp. (Nematoda: Rhabditidae) as new entomopathogenic nematode from Iran

A new species of the genus Oscheius, Oscheius cyrus n. sp., collected in the moist soils taken from forest heights in the north of Iran, is recorded. A comprehensive description, comprising molecular (internal transcribed spacer (ITS), 18S, and 28S rDNA genes) information, morphometrics data, light microscope and scanning electron microscope images, is supplied. The species resembles Oscheius myriophilus. However, the highest ranges for female body length, female tail, infective juvenile tail length, median bulb, absence of epiptygma and lateral field incisures number vary. The new species was distinguished from Oscheius insectivorus by the general lip region. The male was not found. Molecular analysis showed that the new species has the most similarity to O. myriophilus both in the ITS and 18S regions. Morphological and molecular data confirmed its belonging to the Insectivora-group. Furthermore, the species of Ochrobactrum pseudogrignonense was reported as a dominant associated bacterium of the new Oscheius species. Finally, the mortality of the host after seven days varied from 20% to 82.5%, depending on nematodes' concentration.

Nematophilic bacteria associated with entomopathogenic nematodes and drug development of their biomolecules

The importance of Xenorhabdus and Photorhabdus symbionts to their respective Steinernema and Heterorhabditis nematode hosts is that they not only contribute to their entomopathogenicity but also to their fecundity through the production of small molecules. Thus, this mini-review gives a brief introductory overview of these nematophilic bacteria. Specifically, their type species, nematode hosts, and geographic region of isolations are tabulated. The use of nucleotide sequence-based techniques for their species delineation and how pangenomes can improve this are highlighted. Using the Steinernema–Xenorhabdus association as an example, the bacterium-nematode lifecycle is visualized with an emphasis on the role of bacterial biomolecules. Those currently in drug development are discussed, and two potential antimalarial lead compounds are highlighted. Thus, this mini-review tabulates forty-eight significant nematophilic bacteria and visualizes the ecological importance of their biomolecules. It further discusses three of these biomolecules that are currently in drug development. Through it, one is introduced to Xenorhabdus and Photorhabdus bacteria, their natural production of biomolecules in the nematode-bacterium lifecycle, and how these molecules are useful in developing novel therapies.

Insecticidal activities of the local entomopathogenic nematodes and cell-free supernatants from their symbiotic bacteria against the larvae of fall webworm, Hyphantriacunea

The fall webworm (FWW), Hyphantria cunea Drury (Lepidoptera: Erebidae), is an invasive and polyphagous insect pest of many economically important crops such as hazelnuts, apple, and mulberry. Recently, there have been an increasing number of reports about the damaging activities of FWW from hazelnut growing areas of Turkey indicating that currently existing control methods fail to satisfy the expectations of growers. Entomopathogenic nematodes (EPNs) in the Steinernematidae and Heterorhabditidae (Nematoda: Rhabditida) families and the symbiotic bacteria they carry in their intestine have a great potential for the management of many agriculturally important pests. In this study, the symbiotic bacteria of local EPN species (Heterorhabditis bacteriophora AVB-15, Steinernema feltiae KCS-4S, and Steinernema bicornotum MGZ-4S) recovered from the central Anatolia region was characterized using recA gene region as Photorhabdus luminescens, Xenorhabdus bovienii and Xenorhabdus budapestensis. The contact (25, 50, 100, 200 IJs/Petri) and oral efficacies of the infective juveniles (IJs) (25, 50, 100, 200 IJs/leaf) of these EPN isolates determined on 3rd/4th instar larvae, and cell-free supernatants from the identified symbiotic bacteria were evaluated separately on the 3rd and 4th larval instars of FWW in Petri dish environment under laboratory conditions (25 ± 1 °C, 60% of RH). In the Petri dish bioassays of EPN species, the most pathogenic isolate at the 1st DAT and 4th DAT was S. feltiae which caused 50% mortality at the highest concentration (200 IJs/Petri) and the highest mortality rate (97.5%) were achieved at 4th DAT by H. bacteriophora AVB-15 isolate. Surprisingly, the mortality rates were generally higher at the lowest concentrations and 82.5% mortality were reached 4th DAT by S. bicornotum at the lowest concentration (25 IJs/leaf) in the leaf bioassays. Mortality rates were higher in both Petri dish and filter paper efficacies of cell-free supernatants at the 2nd DAT and the highest mortality (87.5%) was reached in the contact efficacy studies when applied X. bovienii KCS-4S strain. The results suggest that the tested EPN species and CFSs have good potential for biological control of the larvae of FWW and can contribute to the IPM programs of FWW. However, the efficacy of both IJs of EPNs and CFSs of their symbiotic bacteria on larvae of FWW requires further studies to verify their efficiency in the field.

Xenorhabdus spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes

Mounting concern over the misuse of chemical pesticides has sparked broad interest for safe and effective alternatives to control plant pests and pathogens. Xenorhabdus bacteria, as pesticidal symbionts of the entomopathogenic nematodes Steinernema species, can contribute to this solution with a treasure trove of insecticidal compounds and an ability to suppress a variety of plant pathogens. As many challenges face sound exploitation of plant-phytonematode interactions, a full useful spectrum of such interactions should address nematicidal activity of Xenorhabdus. Steinernema-Xenorhabdus complex or Xenorhabdus individually should be involved in mechanisms underlying the favorable side of plant-nematode interactions in emerging cropping systems. Using Xenorhabdus bacteria should earnestly be harnessed to control not only phytonematodes, but also other plant pests and pathogens within integrated pest management plans. This review highlights the significance of fitting Xenorhabdus-obtained insecticidal, nematicidal, fungicidal, acaricidal, pharmaceutical, antimicrobial, and toxic compounds into existing, or arising, holistic strategies, for controlling many pests/pathogens. The widespread utilization of Xenorhabdus bacteria, however, has been slow-going, due to costs and some issues with their commercial processing. Yet, advances have been ongoing via further mastering of genome sequencing, discovering more of the beneficial Xenorhabdus species/strains, and their successful experimentations for pest control. Their documented pathogenicity to a broad range of arthropods and pathogens and versatility bode well for useful industrial products. The numerous beneficial traits of Xenorhabdus bacteria can facilitate their integration with other tactics for better pest/disease management programs.

Larvicidal activity of Photorhabdus and Xenorhabdus bacteria isolated from insect parasitic nematodes against Aedes aegypti and Aedes albopictus

Aedes aegypti and Aedes albopictus are important vectors for several arboviruses such as the dengue virus. The chemical control of Aedes spp., which is usually implemented, affects both humans and the environment. The biological control of Aedes spp. with entomopathogenic bacteria such as Photorhabdus and Xenorhabdus may be an alternative method that can overcome such issues. This study aimed to isolate and identify Photorhabdus and Xenorhabdus bacteria from entomopathogenic nematodes (EPNs) collected in Thailand and evaluate their larvicidal properties in controlling A. aegypti and A. albopictus. Colony morphology and recA sequencing of the 118 symbiotic isolated bacteria indicated that most were P. luminescens subsp. akhurstii and X. stockiae with minor prevalence of P. luminescens subsp. hainanensis, P. asymbiotica subsp. australis, X. indica, X. griffiniae, X. japonica, X. thuongxuanensis, and X. eapokensis . The larvicidal bioassay with the third- and fourth-instar mosquito larvae suggested that a whole-cell suspension of X. griffiniae (bMSN3.3_TH) had the highest efficiency in eradicating A. aegypti and A. albopictus, with 90 ± 3.71% and 81 ± 2.13% mortality, respectively, after 96 h exposure. In contrast, 1% of ethyl acetate extracted from X. indica (bSNK8.5_TH) showed reduced mortality for A. aegypti of only 50 ± 3.66% after 96 h exposure. The results indicate that both X. griffiniae (bMSN3.3_TH) and X. indica (bSNK8.5_TH) could be used as biocontrol agents against Aedes larvae.

Pre- and post-association barriers to host switching in sympatric mutualists

Coevolution between mutualists can lead to reciprocal specialization, potentially causing barriers to host switching. Here, we conducted assays to identify pre- and post-association barriers to host switching by endosymbiotic bacteria, both within and between two sympatric nematode clades. In nature, Steinernema nematodes and Xenorhabdus bacteria form an obligate mutualism. Free-living juvenile nematodes carry Xenorhabdus in a specialized intestinal receptacle. When nematodes enter an insect, they release the bacteria into the insect hemocoel. The bacteria aid in killing the insect and facilitate nematode reproduction. Prior to dispersing from the insect, juvenile nematodes must form an association with their symbionts; the bacteria must adhere to the intestinal receptacle. We tested for pre-association barriers by comparing the effects of bacterial strains on native verses non-native nematodes via their virulence towards, nutritional support of, and ability to associate with different nematode species. We then assessed post-association barriers by measuring the relative fitness of nematodes carrying each strain of bacteria. We found evidence for both pre- and post-association barriers between nematode clades. Specifically, some bacteria were highly virulent to non-native hosts, and some nematode hosts carried fewer cells of non-native bacteria, creating pre-association barriers. In addition, reduced infection success and lower nematode reproduction were identified as post-association barriers. No barriers to symbiont switching were detected between nematode species within the same clade. Overall, our study suggests a framework that could be used to generate predictions for the evolution of barriers to host switching in this and other systems.

The relevance of studying insect-nematode interactions for human disease

Vertebrate-parasitic nematodes cause debilitating, chronic infections in millions of people worldwide. The burden of these so-called 'neglected tropical diseases' is often carried by poorer socioeconomic communities in part because research on parasitic nematodes and their vertebrate hosts is challenging and costly. However, complex biological and pathological processes can be modeled in simpler organisms. Here, we consider how insight into the interactions between entomopathogenic nematodes (EPN), their insect hosts and bacterial symbionts may reveal novel treatment targets for parasitic nematode infections. We argue that a combination of approaches that target nematodes, as well as the interaction of pathogens with insect vectors and bacterial symbionts, offer potentially effective, but underexplored opportunities.

Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC)

Antimicrobial multidrug resistance (MDR) is a global challenge, not only for public health, but also for sustainable agriculture. Antibiotics used in humans should be ruled out for use in veterinary or agricultural settings. Applying antimicrobial peptide (AMP) molecules, produced by soil-born organisms for protecting (soil-born) plants, seems a preferable alternative. The natural role of peptide-antimicrobials, produced by the prokaryotic partner of entomopathogenic-nematode/bacterium (EPN/EPB) symbiotic associations, is to sustain monoxenic conditions for the EPB in the gut of the semi-anabiotic infective dauer juvenile (IJ) EPN. They keep pathobiome conditions balanced for the EPN/EPB complex in polyxenic (soil, vanquished insect cadaver) niches. Xenorhabdus szentirmaii DSM16338(T) (EMC), and X. budapestensis DSM16342(T) (EMA), are the respective natural symbionts of EPN species Steinernema rarum and S. bicornutum. We identified and characterized both of these 15 years ago. The functional annotation of the draft genome of EMC revealed 71 genes encoding non-ribosomal peptide synthases, and polyketide synthases. The large spatial Xenorhabdus AMP (fabclavine), was discovered in EMA, and its biosynthetic pathway in EMC. The AMPs produced by EMA and EMC are promising candidates for controlling MDR prokaryotic and eukaryotic pathogens (bacteria, oomycetes, fungi, protozoa). EMC releases large quantity of iodinin (1,6-dihydroxyphenazine 5,10-dioxide) in a water-soluble form into the media, where it condenses to form spectacular water-insoluble, macroscopic crystals. This review evaluates the scientific impact of international research on EMA and EMC.

A Review of Entomopathogenic Nematodes as a Biological Control Agent for Red Palm Weevil, Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae) is a severe pest of palm trees worldwide. The development and feeding activities of R. ferrugineus larvae inside the trunk damage palm trees. However, the absence of noticeable infestation signs at an early stage contributes to the spread of the attack. Integrated pest management (IPM) has been introduced to control R. ferrugineus infestation by implementing various approaches and techniques. The application of chemical pesticides has shown impressive results. However, biological control should be applied as an alternative solution due to adverse environmental impacts and pest resistance issues. One example is the use of entomopathogenic nematodes (EPNs) as biological control agents, which can forage and attack targeted pests without compromising the environment and other nontarget organisms. EPNs and their symbiotic bacteria have a mutualistic interaction that can kill the host within a short period of time. Therefore, this review emphasizes the effectiveness of entomopathogenic nematodes and their symbiotic bacteria against R. ferrugineus.

Xenorhabdus lircayensis sp. nov., the symbiotic bacterium associated with the entomopathogenic nematode Steinernema unicornum

Xenorhabdus is a symbiotic group of bacteria associated with entomopathogenic nematodes of the family Steinernematidae. Although the described Steirnernema species list is extensive, not all their symbiotic bacteria have been identified. One single motile, Gram-negative and non-spore-forming rod-shaped symbiotic bacterium, strain VLS^T, was isolated from the entomopathogenic nematode Steinernema unicornum. Analyses of the 16S rRNA gene determined that the VLS^T isolate belongs to the genus Xenorhabdus, and its closest related species is Xenorhabdus szentirmaii DSM 16338^T (98.2 %). Deeper analyses using the whole genome for phylogenetic reconstruction indicate that VLS^T exhibits a unique clade in the genus. Genomic comparisons considering digital DNA-DNA hybridization (dDDH) values confirms this result, showing that the VLS^T values are distant enough from the 70 % threshold suggested for new species, sharing 30.7, 30.5 and 30.3 % dDDH with Xenorhabdus khoisanae MCB, Xenorhabdus koppenhoeferi DSM 18168^T and Xenorhabdus miraniensis DSM 18168^T, respectively, as the closest species. Detailed physiological, biochemical and chemotaxonomic tests of the VLS^T isolate reveal consistent differences from previously described Xenorhabdus species. Phylogenetic, physiological, biochemical and chemotaxonomic approaches show that VLS^T represents a new species of the genus Xenorhabdus, for which the name Xenorhabdus lircayensis sp. nov. (type strain VLS^T=CCCT 20.04^T=DSM 111583^T) is proposed.

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).

A study on Xenorhabdus and Photorhabdus isolates from Northeastern Thailand: Identification, antibacterial activity, and association with entomopathogenic nematode hosts

Xenorhabdus and Photorhabdus are gram negative bacteria that can produce several secondary metabolites, including antimicrobial compounds. They have a symbiotic association with entomopathogenic nematodes (EPNs). The aim of this study was to isolate and identify Xenorhabdus and Photorhabdus species and their associated nematode symbionts from Northeastern region of Thailand. We also evaluated the antibacterial activity of these symbiotic bacteria. The recovery rate of EPNs was 7.82% (113/1445). A total of 62 Xenorhabdus and 51 Photorhabdus strains were isolated from the EPNs. Based on recA sequencing and phylogeny, Xenorhabdus isolates were identified as X. stockiae (n = 60), X. indica (n = 1) and X. eapokensis (n = 1). Photorhabdus isolates were identified as P. luminescens subsp. akhurstii (n = 29), P. luminescens subsp. hainanensis (n = 18), P. luminescens subsp. laumondii (n = 2), and P. asymbiotica subsp. australis (n = 2). The EPNs based on 28S rDNA and internal transcribed spacer (ITS) analysis were identified as Steinernema surkhetense (n = 35), S. sangi (n = 1), unidentified Steinernema (n = 1), Heterorhabditis indica (n = 39), H. baujardi (n = 1), and Heterorhabditis sp. SGmg3 (n = 3). Antibacterial activity showed that X. stockiae (bMSK7.5_TH) extract inhibited several antibiotic-resistant bacterial strains. To the best of our knowledge, this is the first report on mutualistic association between P. luminescens subsp. laumondii and Heterorhabditis sp. SGmg3. This study could act as a platform for future studies focusing on the discovery of novel antimicrobial compounds from these bacterial isolates.

Photorhabdus spp.: An Overview of the Beneficial Aspects of Mutualistic Bacteria of Insecticidal Nematodes

The current approaches to sustainable agricultural development aspire to use safer means to control pests and pathogens. Photorhabdus bacteria that are insecticidal symbionts of entomopathogenic nematodes in the genus Heterorhabditis can provide such a service with a treasure trove of insecticidal compounds and an ability to cope with the insect immune system. This review highlights the need of Photorhabdus-derived insecticidal, fungicidal, pharmaceutical, parasiticidal, antimicrobial, and toxic materials to fit into current, or emerging, holistic strategies, mainly for managing plant pests and pathogens. The widespread use of these bacteria, however, has been slow, due to cost, natural presence within the uneven distribution of their nematode partners, and problems with trait stability during in vitro culture. Yet, progress has been made, showing an ability to overcome these obstacles via offering affordable mass production and mastered genome sequencing, while detecting more of their beneficial bacterial species/strains. Their high pathogenicity to a wide range of arthropods, efficiency against diseases, and versatility, suggest future promising industrial products. The many useful properties of these bacteria can facilitate their integration with other pest/disease management tactics for crop protection.

Identification of Photorhabdus symbionts by MALDI-TOF MS

Species of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies. High-level discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results therefore suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.

Genome announcement of Steinernema khuongi and its associated symbiont from Florida

Citrus root weevil (Diaprepes abbreviates) causes significant yield loss in citrus, especially in Florida. A promising source of control for this pest is biological control agents, namely, native entomopathogenic nematodes (EPNs) within the genus Steinernema. Two species of endemic EPN in Florida are S. diaparepesi, abundant within the central ridge, and S. khuongi, dominating the flatwood regions of the state. These citrus-growing regions differ significantly in their soil habitats, which impacts the potential success of biological control measures. Although the genome sequence of S. diaprepesi is currently available, the genome sequence of S. khuongi and identity of the symbiotic bacteria is still unknown. Understanding the genomic differences between these two nematodes and their favored habitats can inform successful biological control practices. Here, MiSeq libraries were used to simultaneously sequence and assemble the draft genome of S. khuongi and its associated symbionts. The final draft genome for S. khuongi has 8,794 contigs with a total length of ∼82 Mb, a largest contig of 428,226 bp, and N50 of 46 kb; its BUSCO scores indicate that it is > 86% complete. An associated bacterial genome was assembled with a total length of ∼3.5 Mb, a largest contig at 116,532 bp, and N50 of 17,487 bp. The bacterial genome encoded 3,721 genes, similar to other Xenorhabdus genomes. Comparative genomics identified the symbiotic bacteria of S. khuongi as Xenorhabdus poinarii. These new draft genomes of a host and symbiont can be used as a valuable tool for comparative genomics with other EPNs and its symbionts to understand host range and habitat suitability.

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).

Competition and Co-existence of Two Photorhabdus Symbionts with a Nematode Host

Photorhabdus spp. (Enterobacteriales: Morganellaceae) occur exclusively as symbionts of Heterorhabditis nematodes for which they provide numerous services, including killing insects and providing nutrition and defence within the cadavers. Unusually, two species (Photorhabdus cinerea and Photorhabdus temperata) associate with a single population of Heterorhabditis downesi at a dune grassland site. Building on previous work, we investigated competition between these two Photorhabdus species both at the regional (between insects) and local (within insect) level by trait comparison and co-culture experiments. There was no difference between the species with respect to supporting nematode reproduction and protection of cadavers against invertebrate scavengers, but P. cinerea was superior to P. temperata in several traits: faster growth rate, greater antibacterial and antifungal activity and colonisation of a higher proportion of nematodes in co-culture. Moreover, where both bacterial symbionts colonised single nematode infective juveniles, P. cinerea tended to dominate in numbers. Differences between Photorhabdus species were detected in the suite of secondary metabolites produced: P. temperata produced several compounds not produced by P. cinerea including anthraquinone pigments. Bioluminescence emitted by P. temperata also tended to be brighter than that from P. cinerea. Bioluminescence and pigmentation may protect cadavers against scavengers that rely on sight. We conclude that while P. cinerea may show greater local level (within-cadaver) competitive success, co-existence of the two Photorhabdus species in the spatially heterogeneous environment of the dunes is favoured by differing specialisations in defence of the cadaver against differing locally important threats.

Temperature Restriction in Entomopathogenic Bacteria

Temperature plays an important role in bacteria-host interactions and can be a determining factor for host switching. In this study we sought to investigate the reasons behind growth temperature restriction in the entomopathogenic enterobacterium Photorhabdus. Photorhabdus has a complex dual symbiotic and pathogenic life cycle. The genus consists of 19 species but only one subgroup, previously all classed together as Photorhabdus asymbiotica, have been shown to cause human disease. These clinical isolates necessarily need to be able to grow at 37°C, whilst the remaining species are largely restricted to growth temperatures below 34°C and are therefore unable to infect mammalian hosts. Here, we have isolated spontaneous mutant lines of Photorhabdus laumondii DJC that were able to grow up to 36-37°C. Following whole genome sequencing of 29 of these mutants we identified a single gene, encoding a protein with a RecG-like helicase domain that for the majority of isolates contained single nucleotide polymorphisms. Importantly, provision of the wild-type allele of this gene in trans restored the temperature restriction, confirming the mutations are recessive, and the dominant effect of the protein product of this gene. The gene appears to be part of a short three cistron operon, which we have termed the Temperature Restricting Locus (TRL). Transcription reporter strains revealed that this operon is induced upon the switch from 30 to 36°C, leading to replication arrest of the bacteria. TRL is absent from all of the human pathogenic species so far examined, although its presence is not uniform in different strains of the Photorhabdus luminescens subgroup. In a wider context, the presence of this gene is not limited to Photorhabdus, being found in phylogenetically diverse proteobacteria. We therefore suggest that this system may play a more fundamental role in temperature restriction in diverse species, relating to as yet cryptic aspects of their ecological niches and life cycle requirements.

A survey of entomopathogenic nematodes and their symbiotic bacteria in agricultural areas of northern Thailand

Entomopathogenic nematodes (EPNs) Steinernema and Heterorhabditis and their symbiotic bacteria, Xenorhabdus and Photorhabdus, have been successfully used for the control of insect pests. The objectives of this study were to survey the EPNs and symbiotic bacteria in the agricultural areas of the Phitsanulok province, Thailand, and to study the association between the soil parameters and presence of EPNs. We collected 200 soil samples from 40 soil sites in agricultural areas (field crops, horticulture crops and forest). The prevalence of EPNs was 8.0% (16/200). Fifteen of the EPN isolates were molecularly identified (based on 28S ribosomal DNA and internal transcribed spacer regions) as Steinernema siamkayai. Seven isolates of Xenorhabdus stockiae were identified using recombinase A sequencing. Phylogenetic analysis revealed that all the Steinernema and Xenorhabdus isolates were closely related to S. siamkayai (Indian strain) and X. stockiae (Thai strain), respectively. Significantly more EPNs were recovered from loam than from clay. Although the association between soil parameters (pH, temperature and moisture) and the presence of EPNs was not statistically significant, the elevation levels of the soil sites with and without EPNs were found to be different. Moreover, statistical comparisons between the agricultural areas revealed no significant differences. Therefore, we concluded that S. siamkayai is associated with X. stockiae in agricultural areas and that there is no association between the soil parameters of agricultural areas and presence of EPNs, except for soil texture and the elevation. Steinernema siamkayai may be applied as a biocontrol agent in agricultural areas.

Antibacterial activity of Xenorhabdus and Photorhabdus isolated from entomopathogenic nematodes against antibiotic-resistant bacteria

Xenorhabdus and Photorhabdus, symbiotically associated with entomopathogenic nematodes (EPNs), produce a range of antimicrobial compounds. The objective of this study is to identify Xenorhabdus and Photorhabdus and their EPNs hosts, which were isolated from soil samples from Saraburi province, and study their antibacterial activity against 15 strains of drug-resistant bacteria. Fourteen isolates (6.1%), consisting of six Xenorhabdus isolates and eight Photorhabdus isolates, were obtained from 230 soil samples. Based on the BLASTN search incorporating the phylogenetic analysis of a partial recA gene, all six isolates of Xenorhabdus were found to be identical and closely related to X. stockiae. Five isolates of Photorhabdus were found to be identical and closely related to P. luminescens subsp. akhurstii. Two isolates of Photorhabdus were found to be identical and closely related to P. luminescens subsp. hainanensis. The remaining isolate of Photorhabdus was found to be identical to P. asymbiotica subsp. australis. The bacterial extracts from P. luminescens subsp. akhurstii showed strong inhibition the growth of S. aureus strain PB36 (MSRA) by disk diffusion, minimal inhibitory concentration, and minimal bactericidal concentration assay. The combination between each extract from Xenorhabdus/Photorhabdus and oxacillin or vancomycin against S. aureus strain PB36 (MRSA) exhibited no interaction on checkerboard assay. Moreover, killing curve assay of P. luminescens subsp. akhurstii extracts against S. aureus strain PB36 exhibited a steady reduction of 10⁵ CFU/ml to 10³ CFU/ml within 30 min. This study demonstrates that Xenorhabdus and Photorhabdus, showed antibacterial activity. This finding may be useful for further research on antibiotic production.

Bradyrhizobia associated with Laburnum anagyroides, an exotic legume grown in Poland

We isolated 18 rhizobial strains from root nodules of a leguminous shrub Laburnum anagyroides (common laburnum) grown in Southeast Poland as an exotic plant. With the use of BOX-PCR fingerprinting, the isolates were clustered into 2 main groups and one separate lineage, which was congruent with the ITS-RFLP results. The phylogenetic trees constructed based on 16S rRNA and combined atpD, dnaK, glnA, and recA gene sequence data separated the representative strains into three evolutionary lineages within the Bradyrhizobium jicamae supergroup, with Bradyrhizobium algeriense and Bradyrhizobium valentinum as the closest relatives. The nodA and nifH gene phylogenies proved that the L. anagyroides symbionts carry a symbiotic gene variant known as Clade IV, representing the symbiovar retamae. Phenotypic characteristics of the isolates and reference strains are also reported. Our study of the rhizobia nodulating L. anagyroides growing in Poland complements earlier few findings on the symbiotic associations of this Genisteae species.

First Record of the Entomopathogenic Nematode Steinernema litorale (Filipjev) (Rhabditida: Steinernematidae) and Its Symbiotic Bacterium from Turkey, and Its Efficacy Capability

The entomopathogenic nematode Steinernema litorale was isolated from Çamkoru Nature Park located in Ankara, Turkey, in September 2018. Steinernema litorale was recovered in 1 of 67 soil samples from a natural forest area; the soil was characterised as sandy loam. The isolated nematode S. litorale was identified based on morphological and molecular parameters. The symbiotic bacterium of S. litorale was determined as Xenorhabdus bovienii. Steinernema litorale was found for the first time in Turkey and the Middle East. The virulence of the isolate was tested on Galleria mellonella larvae. Different concentrations of the nematode (10, 25, 50, 75, and 100 infective juveniles (IJs/larvae) were used. While the LC₅₀ values at 48 h, 72 h, and 96 h were 153.419, 51.005, and 15.439 IJs, respectively, and the LT₅₀ values at 75 IJs and 100 IJs showed that this isolate is capable to control insect larvae within 50.083 and 36.266 h, respectively.

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome

BACKGROUND

The holistic view of bacterial symbiosis, incorporating both host and microbial environment, constitutes a major conceptual shift in studies deciphering host-microbe interactions. Interactions between Steinernema entomopathogenic nematodes and their bacterial symbionts, Xenorhabdus, have long been considered monoxenic two partner associations responsible for the killing of the insects and therefore widely used in insect pest biocontrol. We investigated this "monoxenic paradigm" by profiling the microbiota of infective juveniles (IJs), the soil-dwelling form responsible for transmitting Steinernema-Xenorhabdus between insect hosts in the parasitic lifecycle.

RESULTS

Multigenic metabarcoding (16S and rpoB markers) showed that the bacterial community associated with laboratory-reared IJs from Steinernema carpocapsae, S. feltiae, S. glaseri and S. weiseri species consisted of several Proteobacteria. The association with Xenorhabdus was never monoxenic. We showed that the laboratory-reared IJs of S. carpocapsae bore a bacterial community composed of the core symbiont (Xenorhabdus nematophila) together with a frequently associated microbiota (FAM) consisting of about a dozen of Proteobacteria (Pseudomonas, Stenotrophomonas, Alcaligenes, Achromobacter, Pseudochrobactrum, Ochrobactrum, Brevundimonas, Deftia, etc.). We validated this set of bacteria by metabarcoding analysis on freshly sampled IJs from natural conditions. We isolated diverse bacterial taxa, validating the profile of the Steinernema FAM. We explored the functions of the FAM members potentially involved in the parasitic lifecycle of Steinernema. Two species, Pseudomonas protegens and P. chlororaphis, displayed entomopathogenic properties suggestive of a role in Steinernema virulence and membership of the Steinernema pathobiome.

CONCLUSIONS

Our study validates a shift from monoxenic paradigm to pathobiome view in the case of the Steinernema ecology. The microbial communities of low complexity associated with EPNs will permit future microbiota manipulation experiments to decipher overall microbiota functioning in the infectious process triggered by EPN in insects and, more generally, in EPN ecology.

Evolution and taxonomy of nematode-associated entomopathogenic bacteria of the genera Xenorhabdus and Photorhabdus: an overview

Entomopathogenic bacteria from the genera Photorhabdus and Xenorhabdus are closely related Gram-negative bacilli from the family Enterobacteriaceae (γ-Proteobacteria). They establish obligate mutualistic associations with soil nematodes from the genera Steinernema and Heterorhabditis to facilitate insect pathogenesis. The research of these two bacterial genera is focused mainly on their unique interactions with two different animal hosts, i.e. nematodes and insects. So far, studies of the mutualistic bacteria of nematodes collected from around the world have contributed to an increase in the number of the described Xenorhabdus and Photorhabdus species. Recently, the classification system of entomopatogenic nematode microsymbionts has undergone profound revision and now 26 species of the genus Xenorhabdus and 19 species of the genus Photorhabdus have been identified. Despite their similar life style and close phylogenetic origin, Photorhabdus and Xenorhabdus bacterial species differ significantly in e.g. the nematode host range, symbiotic strategies for parasite success, and arrays of released antibiotics and insecticidal toxins. As the knowledge of the diversity of entomopathogenic nematode microsymbionts helps to enable the use thereof, assessment of the phylogenetic relationships of these astounding bacterial genera is now a major challenge for researchers. The present article summarizes the main information on the taxonomy and evolutionary history of Xenorhabdus and Photorhabdus, entomopathogenic nematode symbionts.

Isolation, identification, and pathogenicity of Steinernema carpocapsae and its bacterial symbiont in Cauca-Colombia

In Colombia, identification of entomopathogenic nematodes (EPN’s) native species is of great importance for pest management programs. The aim of this study was to isolate and identify EPNs and their bacterial symbiont in the department of Cauca-Colombia and then evaluate the susceptibility of two Hass avocado (Persea americana) pests to the EPNs isolated. EPNs were isolated from soil samples by the insect baiting technique. Their bacterial symbiont was isolated from hemolymph of infected Galleria mellonella larvae. Both organisms were molecularly identified. Morphological, and biochemical characterization was done for the bacteria. Susceptibility of Epitrix cucumeris and Pandeleteius cinereus adults was evaluated by individually exposing adults to 50 infective juveniles. EPNs were allegedly detected at two sampled sites (natural forest and coffee cultivation) in 5.8% of the samples analyzed. However, only natural forest EPN’s could be isolated and multiplied. The isolate was identified as Steinernema carpocapsae BPS and its bacterial symbiont as Xenorhabus nematophila BPS. Adults of both pests were susceptible to S. carpocapsae indicating this EPN potential for its management. The results of this study constitute the first record of S. carpocapsae in Colombia and the susceptibility of P. cinereus to this EPN.

Cyclo(tetrahydroxybutyrate) production is sufficient to distinguish between Xenorhabdus and Photorhabdus isolates in Thailand

Bacteria of the genera Photorhabdus and Xenorhabdus produce a plethora of natural products to support their similar symbiotic life cycles. For many of these compounds, the specific bioactivities are unknown. One common challenge in natural product research when trying to prioritize research efforts is the rediscovery of identical (or highly similar) compounds from different strains. Linking genome sequence to metabolite production can help in overcoming this problem. However, sequences are typically not available for entire collections of organisms. Here, we perform a comprehensive metabolic screening using HPLC-MS data associated with a 114-strain collection (58 Photorhabdus and 56 Xenorhabdus) across Thailand and explore the metabolic variation among the strains, matched with several abiotic factors. We utilize machine learning in order to rank the importance of individual metabolites in determining all given metadata. With this approach, we were able to prioritize metabolites in the context of natural product investigations, leading to the identification of previously unknown compounds. The top three highest ranking features were associated with Xenorhabdus and attributed to the same chemical entity, cyclo(tetrahydroxybutyrate). This work also addresses the need for prioritization in high-throughput metabolomic studies and demonstrates the viability of such an approach in future research.

Photorhabdus khanii subsp. guanajuatensis subsp. nov., isolated from Heterorhabditis atacamensis, and Photorhabdus luminescens subsp. mexicana subsp. nov., isolated from Heterorhabditis mexicana entomopathogenic nematodes

Two Gram-negative, rod-shaped, non-spore-forming bacteria, MEX20-17^T and MEX47-22^T, were isolated from the digestive system of Heterorhabditis atacamensis and Heterorhabditis mexicana entomopathogenic nematodes, respectively. Their 16S rRNA gene sequences suggest that strains MEX20-17^T and MEX47-22^T belong to the γ-Proteobacteria and to the genus Photorhabdus. Deeper analyses using housekeeping-gene-based and whole-genome-based phylogenetic reconstruction suggest that MEX20-17^T is closely related to Photorhabdus khanii and that MEX47-22^T is closely related to Photorhabdus luminescens. Sequence similarity scores confirm these observations: MEX20-17^T and P. khanii DSM 3369^T share 98.9 % nucleotide sequence identity (NSI) of concatenated housekeeping genes, 70.4 % in silico DNA-DNA hybridization (isDDH) and 97 % orthologous average nucleotide identity (orthoANI); and MEX47-22^T and P. luminescens ATCC 29999^T share 98.9 % NSI, 70.6 % isDDH and 97 % orthoANI. Physiological characterization indicates that both strains differ from all validly described Photorhabdus species and from their more closely related taxa. We therefore propose to classify MEX20-17^T and MEXT47-22^T as new subspecies within P. khanii and P. luminescens, respectively. Hence, the following names are proposed for these strains: Photorhabdus khanii subsp. guanajuatensis subsp. nov. with the type strain MEX20-17^T (=LMG 30372^T=CCOS 1191^T) and Photorhabdus luminescenssubsp. mexicana subsp. nov. with the type strain MEX47-22^T (=LMG 30528^T=CCOS 1199^T). These propositions automatically create Photorhabdus khanii subsp. khanii subsp. nov. with DSM 3369^T as the type strain (currently classified as P. khanii), and Photorhabdus luminescenssubsp. luminescenssubsp. nov. with ATCC 29999^T as the type strain (currently classified as P. luminescens).

Evolutionary dynamics of origin and loss in the deep history of phospholipase D toxin genes

Background

Venom-expressed sphingomyelinase D/phospholipase D (SMase D/PLD) enzymes evolved from the ubiquitous glycerophosphoryl diester phosphodiesterases (GDPD). Expression of GDPD-like SMaseD/PLD toxins in both arachnids and bacteria has inspired consideration of the relative contributions of lateral gene transfer and convergent recruitment in the evolutionary history of this lineage. Previous work recognized two distinct lineages, a SicTox-like (ST-like) clade including the arachnid toxins, and an Actinobacterial-toxin like (AT-like) clade including the bacterial toxins and numerous fungal homologs.

Results

Here we expand taxon sampling by homology detection to discover new GDPD-like SMase D/PLD homologs. The ST-like clade now includes homologs in a wider variety of arthropods along with a sister group in Cnidaria; the AT-like clade now includes additional fungal phyla and proteobacterial homologs; and we report a third clade expressed in diverse aquatic metazoan taxa, a few single-celled eukaryotes, and a few aquatic proteobacteria. GDPD-like SMaseD/PLDs have an ancient presence in chelicerates within the ST-like family and ctenophores within the Aquatic family. A rooted phylogenetic tree shows that the three clades derived from a basal paraphyletic group of proteobacterial GDPD-like SMase D/PLDs, some of which are on mobile genetic elements. GDPD-like SMase D/PLDs share a signature C-terminal motif and a shortened βα1 loop, features that distinguish them from GDPDs. The three major clades also have active site loop signatures that distinguish them from GDPDs and from each other. Analysis of molecular phylogenies with respect to organismal relationships reveals a dynamic evolutionary history including both lateral gene transfer and gene duplication/loss.

Conclusions

The GDPD-like SMaseD/PLD enzymes derive from a single ancient ancestor, likely proteobacterial, and radiated into diverse organismal lineages at least in part through lateral gene transfer.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1302-2) contains supplementary material, which is available to authorized users.