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

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

BACKGROUND

Nematodes of the genus Heterorhabditis are important biocontrol agents as they form a lethal combination with their symbiotic Photorhabdus bacteria against agricultural insect pests. This study describes a new species of Heterorhabditis.

METHODS

Six Heterorhabditis nematode populations were recovered from agricultural soils in Jammu and Kashmir, India. An initial examination using mitochondrial and nuclear genes showed that they belong to a new species. To describe this new species, a variety of analyses were conducted, including reconstructing phylogenetic relationships based on multiple genes, characterizing the nematodes at the morphological and morphometric levels, performing self-crossing and cross-hybridization experiments, and isolating and characterizing their symbiotic bacteria.

RESULTS

The newly discovered species, Heterorhabditis casmirica n. sp., shares 94% mitochondrial cytochrome C oxidase subunit I gene (COI) sequence identity with Heterorhabditis bacteriophora and Heterorhabditis ruandica, and 93% with Heterorhabditis zacatecana. Morphologically, it differs from H. bacteriophora in its infective juvenile phasmids (present vs. inconspicuous) and bacterial pouch visibility in the ventricular portion of the intestine (invisible vs. visible); genital papilla 1 (GP1) position (at manubrium level vs. more anterior), and in its b ratio (body length/neck length), c ratio (tail length/bulb width), and D% [(excretory pore/neck length) × 100]. Other morphological differences include anterior end to the nerve ring distance (77-100 vs. 121-130 μm), V% [(anterior end of vulva/body length) × 100] (46-57 vs. 41-47) in hermaphroditic females; rectum size (slightly longer than the anal body diameter vs. about three times longer), phasmids (smaller vs. inconspicuous), body length (0.13-2.0 vs. 0.32-0.39 mm), body diameter (73-150 vs. 160-220 μm), anterior end to the excretory pore distance (135-157 vs. 174-214 μm), and demanian ratios in amphimictic females. Morphological differences with H. ruandica and H. zacatecana were also observed. Furthermore, H. casmirica n. sp. did not mate or produce fertile progeny with other Heterorhabditis nematodes reported from India. It was also discovered that H. casmirica n. sp. is associated with Photorhabdus luminescence subsp. clarkei symbiotic bacteria.

CONCLUSIONS

The discovery of H. casmirica n. sp. provides novel insights into the diversity and evolution of Heterorhabditis nematodes and their symbiotic bacteria. This new species adds to the catalog of entomopathogenic nematodes in India.

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.

Entomopathogenic nematodes isolated from agricultural areas of Thailand and their activity against the larvae of Aedes aegypti, Aedes albopictus and Culex quinquefasciatus (Diptera: Culicidae)

Entomopathogenic nematodes (EPNs) of the genera Steinernema and Heterorhabditis have been considered to be effective biological control agents for several insects. In this study, we isolated and identified EPNs from soil samples in agricultural areas of northern Thailand and evaluated their efficacy for controlling larvae of three mosquito vector species, Aedes aegypti, Ae. albopictus and Culex quinquefasciatus. A total of 51 of 1,000 soil samples were positive (5.1% prevalence) for EPNs, which were identified through sequencing of the rDNA and ITS to 37 Steinernema isolates (3.7%) and 14 Heterorhabditis isolates (1.4%). For the bioassay, the larvae of mosquitoes were exposed to Steinernema surkhetense (eALN6.3_TH), Steinernema lamjungense (eALN11.5_TH), Heterorhabditis indica (eACM14.2_TH) and Heterorhabditis bacteriophora (eALN18.2_TH). Heterorhabditis bacteriophora showed the highest efficacy against Ae. aegypti and Cx. quinquefasciatus. At 96 h after exposure, the mortality rates were 60.0 and 91.7%, respectively. The EPNs were observed in the dead mosquito larvae, which were mostly found in the thorax followed by the head and abdomen. Some EPNs were dead with melanization, and some were able to survive in the cavity of mosquito larvae. Our results show the low prevalence of EPN in agricultural areas of Thailand. Moreover, H. bacteriophora may be considered an alternative biocontrol agent for managing and controlling these vector mosquitoes.

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.

Steinernema africanum n. sp. (Rhabditida, Steinernematidae), a New Entomopathogenic Nematode Species Isolated in the Republic of Rwanda

Alternatives to hazardous insecticides are urgently needed for an environmentally friendly and effective management of insect pests. One such option is the use of entomopathogenic nematodes (EPN). To increase the availability of EPN with potential for biocontrol, we surveyed agricultural soils in the Republic of Rwanda and collected two Steinernema isolates. Initial molecular characterization showed that they represent a new species, for which we propose the name S. africanum n. sp. To describe this new species, we reconstructed phylogenetic relationships, calculated sequence similarity scores, characterized the nematodes at the morphological level, conducted crossing experiments, and isolated and characterized their symbiotic bacteria. At the molecular level, S. africanum n. sp. is closely related to S. litorale and S. weiseri. At the morphological level, S. africanum n. sp. differs from closely related species by the position of the nerve ring and also because the stoma and pharynx region is longer. The first-generation males have ventrally curved spicules with lanceolate manubrium and fusiform gubernaculum and the second-generation males have rounded manubrium and anteriorly hook-like gubernaculum. Steinernema africanum n. sp. does not mate or produce fertile progeny with any of the closely related species.

Sequestration of cucurbitacins from cucumber plants by Diabrotica balteata larvae provides little protection against biological control agents

Cucurbitaceae plants produce cucurbitacins, bitter triterpenoids, to protect themselves against various insects and pathogens. Adult banded cucumber beetles (Diabrotica balteata), a common pest of maize and cucurbits, sequester cucurbitacins, presumably as a defensive mechanism against their natural enemies, which might reduce the efficacy of biological control agents. Whether the larvae also sequester and are protected by cucurbitacins is unclear. We profiled cucurbitacin levels in four varieties of cucumber, Cucumis sativus, and in larvae fed on these varieties. Then, we evaluated larval growth and resistance against common biocontrol organisms including insect predators, entomopathogenic nematodes, fungi and bacteria. We found considerable qualitative and quantitative differences in the cucurbitacin levels of the four cucumber varieties. While two varieties were fully impaired in their production, the other two accumulated high levels of cucurbitacins. We also observed that D. balteata larvae sequester and metabolize cucurbitacins, and although the larvae fed extensively on both belowground and aboveground tissues, the sequestered cucurbitacins were mainly derived from belowground tissues. Cucurbitacins had no detrimental effects on larval performance and, surprisingly, did not provide protection against any of the natural enemies evaluated. Our results show that D. balteata larvae can indeed sequester and transform cucurbitacins, but sequestered cucurbitacins do not impact the biocontrol potential of common natural enemies used in biocontrol. Hence, this plant trait should be conserved in plant breeding programs, as it has been demonstrated in previous studies that it can provide protection against plant pathogens and generalist insects.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10340-022-01568-3.

Comparative Screening of Mexican, Rwandan and Commercial Entomopathogenic Nematodes to Be Used against Invasive Fall Armyworm, Spodoptera frugiperda

Simple Summary

The fall armyworm is a devastating insect pest of maize that has recently spread from the Americas to Africa and Asia. Synthetic insecticides are currently being used excessively to fight this pest. Safe, effective and more sustainable alternatives are urgently needed. We explore the use of beneficial entomopathogenic nematodes to control the fall armyworm. These tiny soil-born roundworms are lethal parasites of insects, including caterpillars such as the fall armyworm. We tested forty nematode strains from either the native range of the fall armyworm (Mexico), or the area of invasion (Rwanda), and commercial strains. We found that certain strains of local nematodes from the area of invasion can be as effective in infecting and killing fall armyworm as commercial strains or those from the armyworm’s native range. These findings will aid the development of locally acceptable and effective biological control products.

Abstract

The fall armyworm (FAW), Spodoptera frugiperda Smith (Lepidoptera: Noctuidae) is an important pest of maize originating from the Americas. It recently invaded Africa and Asia, where it causes severe yield losses to maize. To fight this pest, tremendous quantities of synthetic insecticides are being used. As a safe and sustainable alternative, we explore the possibility to control FAW with entomopathogenic nematodes (EPN). We tested in the laboratory whether local EPNs, isolated in the invasive range of FAW, are as effective as EPNs from FAW native range or as commercially available EPNs. This work compared the virulence, killing speed and propagation capability of low doses of forty EPN strains, representing twelve species, after placing them with second-, third- and sixth-instar caterpillars as well as pupae. EPN isolated in the invasive range of FAW (Rwanda) were found to be as effective as commercial and EPNs from the native range of FAW (Mexico) at killing FAW caterpillars. In particular, the Rwandan Steinernema carpocapsae strain RW14-G-R3a-2 caused rapid 100% mortality of second- and third-instar and close to 75% of sixth-instar FAW caterpillars. EPN strains and concentrations used in this study were not effective in killing FAW pupae. Virulence varied greatly among EPN strains, underlining the importance of thorough EPN screenings. These findings will facilitate the development of local EPN-based biological control products for sustainable and environmentally friendly control of FAW in East Africa and beyond.