16S rDNA-based phylogeny of non-symbiotic bacteria of Entorno-pathogenic nematodes from infected insect cadavers

Harnessing nature's arsenal: Ochrobactrum bacteria metabolites in the battle against root- knot nematode - Insights from in vitro and molecular docking studies

Agricultural Productivity and plant health are threatened by the root-knot nematode. The use of biocontrol agents reduces the need for chemical nematicides and improves the general health of agricultural ecosystems by offering a more environmentally friendly and sustainable method of managing nematode infestations. Plant-parasitic nematodes can be efficiently managed with the use of entomopathogenic nematodes (EPNs), which are widely used biocontrol agents. This study focused on the nematicidal activity of the secondary metabolites present in the bacteria Ochrobactrum sp. identified in the EPN, Heterorhabditisindica against Root-Knot Nematode (Meloidogyne incognita). Its effect on egg hatching and survival of juveniles of root- knot nematode (RKN) was examined. The ethyl acetate component of the cell-free culture (CFC) filtrate of the Ochrobactrum sp. bacteria was tested at four different concentrations (25 %, 50 %, 75 % and 100 %) along with broth and distilled water as control. The bioactive compounds of Ochrobactrum sp. bacteria showed the highest suppression of M. incognita egg hatching (100 %) and juvenile mortality (100 %) at 100 % concentration within 24 h of incubation. In this study, unique metabolite compounds were identified through the Gas Chromatography- Mass Spectrometry (GC-MS) analysis, which were found to have anti- nematicidal activity. In light of this, molecular docking studies were conducted to determine the impact of biomolecules from Ochrobactrum sp. using significant proteins of M. incognita, such as calreticulin, sterol carrier protein 2, flavin-containing monooxygenase, pectate lyase, candidate secreted effector, oesophageal gland cell secretory protein and venom allergen-like protein. The results also showed that the biomolecules from Ochrobactrum sp. had a significant inhibitory effect on the different protein targets of M. incognita. 3-Epimacronine and Heraclenin were found to inhibit most of the chosen target protein. Among the targets, the docking analysis revealed that Heraclenin exhibited the highest binding affinity of -8.6 Kcal/mol with the target flavin- containing monooxygenase. Further, the in vitro evaluation of 3- Epimacronine confirmed their nematicidal activity against M. incognita at different concentrations. In light of this, the present study has raised awareness of the unique biomolecules of the bacterial symbiont Ochrobactrum sp. isolated from H. indica that have nematicidal properties.

The genome of a steinernematid-associated Pseudomonas piscis bacterium encodes the biosynthesis of insect toxins

Several species of soil-dwelling Steinernema nematodes are used in the biocontrol of crop pests, due to their natural capacity to kill diverse lepidopteran species. Although this insect-killing trait is known to be augmented by the nematodes' Xenorhabdus endosymbionts, the role of other steinernematid-associated bacterial genera in the nematode lifecycle remains unclear. This genomic study aimed to determine the potential of Pseudomonas piscis to contribute to the entomopathogenicity of its Steinernema host. Insect larvae were infected with three separate Steinernema cultures. From each of the three treatments, the prevalent bacteria in the haemocoel of cadavers, four days post-infection, were isolated. These three bacterial isolates were morphologically characterised. DNA was extracted from each of the three bacterial isolates and used for long-read genome sequencing and assembly. Assemblies were used to delineate species and identify genes that encode insect toxins, antimicrobials, and confer antibiotic resistance. We assembled three complete genomes. Through digital DNA-DNA hybridisation analyses, we ascertained that the haemocoels of insect cadavers previously infected with Steinernema sp. Kalro, Steinernema sp. 75, and Steinernema sp. 97 were dominated by Xenorhabdus griffiniae Kalro, Pseudomonas piscis 75, and X. griffiniae 97, respectively. X. griffiniae Kalro and X. griffiniae 97 formed a subspecies with other X. griffiniae symbionts of steinernematids from Kenya. P. piscis 75 phylogenetically clustered with pseudomonads that are characterised by high insecticidal activity. The P. piscis 75 genome encoded the production pathway of insect toxins such as orfamides and rhizoxins, antifungals such as pyrrolnitrin and pyoluteorin, and the broad-spectrum antimicrobial 2,4-diacetylphloroglucinol. The P. piscis 75 genome encoded resistance to over ten classes of antibiotics, including cationic lipopeptides. Steinernematid-associated P. piscis bacteria hence have the biosynthetic potential to contribute to nematode entomopathogenicity.

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.

Draft Genome Sequence of a Noncognate Bacterium, Achromobacter sp. Strain Bel, Associated with a Rhabditid Entomopathogenic Nematode

Achromobacter sp. strain Bel is a noncognate bacterium associated with a rhabditid entomopathogenic nematode of the Oscheius genus. Its draft genome sequence is 6.62 Mb with a G+C content of 65.4%. The genome highlights important genes which could play a role in entomopathogenicity.

The population structure of Ochrobactrum isolated from entomopathogenic nematodes indicates interactions with the symbiotic system

Entomopathogenic nematodes (EPNs) form specific mutualistic associations with bioluminescent enterobacteria. In Heterorhabditidis indica, Ochrobactrum spp. was identified beside the symbiont Photorhabdus luminescens but its involvement in the symbiotic association in the EPNs remains unclear. This study describe the population structure and the diversity in Ochrobactrum natural populations isolated from EPNs in the Caribbean basin in order to question the existence of EPN-specialized clones and to gain a better insight into Ochrobactrum-EPNs relationships. EPN-associated Ochrobactrum and Photorhabdus strains were characterized by multi-locus sequence typing, Pulsed-Field Gel Electrophoresis fingerprinting and phenotypic traits. Population study showed the absence of EPN-specialized clones in O. intermedium and O. anthropi but suggested the success of some particular lineages. A low level of genetic and genomic diversification of Ochrobactrum isolated from the natural population of Caribbean nematodes was observed comparatively to the diversity of human-associated Ochrobactrum strains. Correspondences between Ochrobactrum and P. luminescens PFGE clusters have been observed, particularly in the case of nematodes from Dominican Republic and Puerto Rico. O. intermedium and O. anthropi associated to EPNs formed less biofilm than human-associated strains. These results evoke interactions between Ochrobactrum and the EPN symbiotic system rather than transient contamination. The main hypothesis to investigate is a toxic/antitoxic relationship because of the ability of Ochrobactrum to resist to antimicrobial and toxic compounds produced by Photorhabdus.

Analysis of microbial diversity in apple vinegar fermentation process through 16s rDNA sequencing

Based on SPME-GC-MS analysis, it could be found that the production of acetic acid, phenethyl acetate, and isoamyl acetate gradually increased in the apple vinegar fermentation broth with the fermentation time. Consequently, in order to systematically explore the dynamic changes of microbial diversity and metabolites in the process of apple vinegar fermentation, 16S rDNA were sequenced and analyzed in this work. The present results showed that bacterial diversity was rich and exhibited a certain variation during the dynamic fermentation process of apple vinegar. Furthermore, Lactococcus and Oenococcus were the predominant bacteria in the pre-fermentation (alcoholic fermentation) of apple vinegar, while the dominant bacteria in the middle and late fermentation stages (acetic acid fermentation) were Lactococcus and Acetobacter. In addition, during the whole fermentation process of apple vinegar, Lactococcus was the most dominant bacteria, Oenococcus was the unique species in the stage of alcohol fermentation, and Acetobacter increased rapidly in the stage of acetic acid fermentation. In conclusion, our finding provided a theoretical basis for the processing technology of apple vinegar fermentation, and a theory evidence for the safety and health assessment of apple vinegar.

A human-food web-animal interface on the prevalence of food-borne pathogens (Clostridia and Enterococcus) in mixed veterinary farms

In the present work, we addressed the impact of a human-food web-animal interface on the prevalence of food-borne pathogens in mixed farms of Tamil Nadu, India. We have isolated and identified six strains of Clostridium sp. and five strains of Enterococcus sp. from food and animal sources disposed near to the veterinary and poultry farms. Phylogenetic relationships of these strains were inferred from their homologies in 16S rDNA sequences and rRNA secondary structures. The strain PCP07 was taxonomically equivalent to C. botulinum confirmed by neurotoxin-specific PCR primers, followed by mouse bioassay. Other Clostridial and Enterococcal isolates have shown a phylogenetic similarity to the C. bifermentans and E. durans isolated from veterinary farms, respectively. Results of our study revealed that a human-food web-animal interface has influenced the disease incidence and prevalence of these isolates in the poultry to veterinary farms, where human food acted as a likely transmittance vehicle for their infections.

Identification of an entomopathogenic bacterium, Xenorhabdus ehlersii KSY, from Steinernema longicaudum GNUS101 and its immunosuppressive activity against insect host by inhibiting eicosanoid biosynthesis

Steinernema longicaudum GNUS101, an entomopathogenic nematode, was isolated from soils in Korea. Its internal transcribed space sequence was highly similar to the known S. longicaudum species. Infective juveniles (IJs) of S. longicaudum were highly virulent to lepidopteran and coleopteran insects. Two different bacteria were isolated from the hemolymph of lepidopteran larvae infected with S. longicaudum. They exhibited blue and red colonies on nutrient bromothymol blue agar. The red-colored bacterium was identified as Enterococcus mundtii KHY while the blue-colored bacterium was identified as Xenorhabdus ehlersii KSY based on 16S rRNA sequencing and biochemical characters. The bacterial species showed different growth rates, with X. ehlersii KSY growing more slowly than E. mundtii KHY. Both bacteria were entomopathogenic, but showed differences in suppressing host immune responses. X. ehlersii KSY, but not E. mundtii KHY, showed inhibitory activity against cellular immune responses of Spodoptera exigua larvae including hemocyte-spreading behavior and nodule formation in bacteria-cultured broth. Its immunosuppressive activity was reversed by adding arachidonic acid, an eicosanoid biosynthesis precursor. Furthermore, organic extracts of X. ehlersii KSY using hexane or ethyl acetate showed inhibitory activity against cellular immune responses of S. exigua larvae. Arachidonic acid addition to S. exigua larvae infected with X. ehlersii significantly rescued the survival rate of target insect. Of the two bacteria isolated from S. longicaudum GNUS101, only X. ehlersii induced immunosuppression of target insect by inhibiting eicosanoid biosynthesis.

Ignatzschineria cameli sp. nov., isolated from necrotic foot tissue of dromedaries (Camelus dromedarius) and associated maggots (Wohlfahrtia species) in Dubai

Five bacterial strains, UAE-HKU57^T, UAE-HKU58, UAE-HKU59, UAE-HKU60 and UAE-HKU61, were isolated in Dubai, UAE, from necrotic foot tissue samples of four dromedaries (Camelus dromedarius) and associated maggots (Wohrlfartia species). They were non-sporulating, Gram-negative, non-motile bacilli. They grew well under aerobic conditions at 37 °C, but not anaerobically. The pH range for growth was pH 7.0-9.0 (optimum, pH 7.5-8.0) and the strains could tolerate NaCl concentrations (w/v) up to 2 % (optimum, 0.5 %). They were catalase- and cytochrome oxidase-positive, but caseinase-, gelatinase- and urease-negative. Their phenotypic characters were distinguishable from other closely related species. Phylogenetic analyses of the almost-complete 16S rRNA gene and partial 23S rRNA gene, gyrB, groEL and recA sequences revealed that the five isolates were most closely related to undescribed Ignatzschineria strain F8392 and Ignatzschineria indica, but in most phylogenies clustered separately from these close relatives. Average nucleotide identity analysis showed that genomes of the five isolates (2.47-2.52 Mb, G+C content 41.71-41.86 mol%) were 98.00-99.97% similar to each other, but ≤87.18 % similar to other Ignatzschineriaspecies/strains. Low DNA relatedness between the five isolates to other Ignatzschineriaspecies/strains was also supported by Genome-to-Genome Distance Calculator analysis. The chemotaxonomic traits of the five strains were highly similar. They were non-susceptible (intermediate or resistant) to tetracycline and resistant to trimethoprim/sulphamethoxazole. The name Ignatzschineria cameli sp. nov. is proposed to accommodate these five strains, with strain UAE-HKU57^T (=CCOS1165^T=NBRC 113042^T) as the type strain.