The essential role of arginine biosynthetic genes in lunate conidia formation, conidiation, mycelial growth, and virulence of nematophagous fungus, Esteya vermicola CBS115803

BACKGROUND

The pinewood nematode (Bursaphelenchus xylophilus) causes severe damage to pine trees. The nematophagous fungus, Esteya vermicola, exhibits considerable promise in the biological control of Bursaphelenchus xylophilus due to its infectivity. Notably, the lunate conidia produced by E. vermicola can infect Bursaphelenchus xylophilus. In the study, we aim to investigate the genes involved in the formation of the lunate conidia of E. vermicola CBS115803.

RESULTS

Esteya vermicola CBS115803 yielded 95% lunate conidia on the complete medium (CM) and 86% bacilloid conidia on the minimal medium (MM). Transcriptomic analysis of conidia from both media revealed a significant enrichment of differentially expressed genes in the pathway related to 'cellular amino acid biosynthesis and metabolism'. Functional assessment showed that the knockout of two arginine biosynthesis genes (EV232 and EV289) resulted in defects in conidia germination, mycelial growth, lunate conidia formation, and virulence of E. vermicola CBS115803 in Bursaphelenchus xylophilus. Remarkably, the addition of arginine to the MM improved mycelial growth, conidiation and lunate conidia formation in the mutants and notably increased conidia yield and the lunate conidia ratio in the wild-type E. vermicola CBS115803.

CONCLUSION

This investigation confirms the essential role of two arginine biosynthesis genes in lunate conidia formation in E. vermicola CBS115803. The findings also suggest that the supplementation of arginine to the culture medium can enhance the lunate conidia yield. These insights contribute significantly to the application of E. vermicola CBS115803 in managing Bursaphelenchus xylophilus infections. © 2023 Society of Chemical Industry.

Establishing Gene Expression and Knockout Methods in Esteya vermicola CBS115803

Pine wilt disease, which is caused by the nematode Bursaphelenchus xylophilus, is one of the most destructive forest diseases worldwide. Esteya vermicola, a nematophagous fungus, has emerged as a promising biological control agent. However, the limited availability of gene function analysis techniques hinders further genetic modification of this fungus. In this study, we employed a combination of enzymes (driselase, snailase, and cellulase) to enzymatically degrade the cell wall of the fungus, resulting in a high yield of protoplasts. Furthermore, by utilizing 0.6 M sucrose as an osmotic pressure stabilizer, we achieved a significant protoplast regeneration rate of approximately 31%. Subsequently, we employed the polyethylene glycol-mediated protoplast transformation method to successfully establish a genetic transformation technique for E. vermicola CBS115803. Additionally, through our investigation, we identified the Olic promoter from Aspergillus nidulans, which effectively enhanced the expression of the DsRed gene encoding a red fluorescent protein in E. vermicola CBS115803. Moreover, we successfully implemented a split-marker strategy to delete the EvIPMD gene in E. vermicola CBS115803. In summary, our findings present valuable experimental methodologies for gene function analysis in E. vermicola CBS115803.

Third Generation Genome Sequencing Reveals That Endobacteria in Nematophagous Fungi Esteya vermicola Contain Multiple Genes Encoding for Nematicidal Proteins

Esteya vermicola is the first recorded endoparasitic nematophagous fungus with high infectivity capacity, attacking the pinewood nematode Bursaphelenchus xylophilus which causes pine wilt disease. Endosymbionts are found in the cytoplasm of E. vermicola from various geographical areas. We sequenced the genome of endobacteria residing in E. vermicola to discover possible biological functions of these widespread endobacteria. Multilocus phylogenetic analyses showed that the endobacteria form a previously unidentified lineage sister to Phyllobacterium myrsinacearum species. The number of genes in the endobacterium was 4542, with 87.8% of the proteins having a known function. It contained a high proportion of repetitive sequences, as well as more Acyl-CoA synthetase genes and genes encoding the electron transport chain, compared with compared with plant-associated P. zundukense Tri 48 and P. myrsinacearum DSM 5893. Thus, this symbiotic bacterium is likely to be more efficient in regulating gene expression and energy release. Furthermore, the endobacteria in nematophagous fungi Esteya vermicola contained multiple nematicidal subtilase/subtilisin encoding genes, so it is likely that endobacteria cooperate with the host to kill nematodes.

Effect of culture conditions on conidia production and enhancement of environmental stress resistance of Esteya vermicola in solid-state fermentation

AIMS

Esteya vermicola is an endoparasitic fungus producing lunate conidia, which kill pine wood nematode (PWN), and PWN could cause pine wilt disease (PWD). The aims of this study were to increase production and confirm the resistance (temperature and UV irradiation) of lunate conidia, and further determine the effective concentrations of conidia infecting PWN.

METHODS AND RESULTS

In this study, rice was used as a carrier to absorb conidial suspension to propagate conidia. The optimal conditions for lunate conidia production were 25°C temperature, 9 days of culture time, 2 : 1 rice/distilled water ratio and 10% inoculum size. The germination rate of E. vermicola cultured on potato dextrose agar was influenced by UV irradiation, similar to growth on rice. Esteya vermicola cultured on rice under heat stress might be more suitable for application in the field. The concentration (1 × 10⁸ conidia per ml) to kill PWN had the highest infectivity among the four conidia concentrations tested after 3 days of inoculation.

CONCLUSIONS

This study showed a rice substrate-supported high-quality conidia production and the optimal infectivity concentration of E. vermicola.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results provide the necessary process of an economical and efficient biological control strategy against PWD.

Development of a Real-Time TaqMan PCR Method for Absolute Quantification of the Biocontrol Agent Esteya vermicola

Esteya vermicola has been used as an effective biocontrol agent for the management of the pinewood nematode, Bursaphelenchus xylophilus. Tools for monitoring the colonization and parasitism patterns of E. vermicola are required for the development of highly effective biocontrol strategies. Because the TaqMan PCR technique is effective for quantification of species in environmental samples, a real-time PCR-based methodology was developed for absolute quantification of E. vermicola via internal standard addition and extrapolation of DNA quantity to hyphal length. Primers and a probe for the 28S ribosomal RNA gene of E. vermicola were designed, and nested TaqMan real-time PCR-based quantification was performed. In addition, internal standard-based yield measurement was correlated to the absolute quantity of target genomic DNA. Moreover, an extrapolation curve obtained by optical microscopy and image analysis of the mycelia was constructed for the measurement of fungal hyphal length. The absolute quantification method developed in the present study provides a sensitive and accurate technique to quantify fungal density in either wood or other substrate samples and can be used as an effective tool for future studies of biocontrol agents.

Differential patterns of ophiostomatoid fungal communities associated with three sympatric Tomicus species infesting pines in south-western China, with a description of four new species

Bark beetles and their associated fungi, which cause forest decline and sometimes high mortality in large areas around the world, are of increasing concern in terms of forest health. Three Tomicus spp. (T.brevipilosus, T.minor and T.yunnanensis) infect branches and trunks of Pinusyunnanensis and P.kesiya in Yunnan Province, in south-western China. Tomicus spp. are well known as vectors of ophiostomatoid fungi and their co-occurrence could result in serious ecological and economic impact on local forest ecosystems. Nonetheless, knowledge about their diversity, ecology, including pathogenicity and potential economic importance is still quite rudimentary. Therefore, an extensive survey of ophiostomatoid fungi associated with these Tomicus species infesting P.yunnanensis and P.kesiya was carried out in Yunnan. Seven hundred and seventy-two strains of ophiostomatoid fungi were isolated from the adult beetles and their galleries. The strains were identified based on comparisons of multiple DNA sequences, including the nuclear ribosomal large subunit (LSU) region, the internal transcribed spacer regions 1 and 2, together with the intervening 5.8S gene (ITS) and the partial genes of β-tubulin (TUB2), elongation factor 1α (TEF1-α) and calmodulin (CAL). Phylogenetic analyses were performed using maximum parsimony (MP) as well as maximum likelihood (ML). Combinations of culture features, morphological characters and temperature-dependent growth rates were also employed for species identification. Eleven species belonging to five genera were identified. These included six known species, Esteyavermicola, Leptographiumyunnanense, Ophiostomabrevipilosi, O.canum, O.minus and O.tingens and four novel taxa, described as Graphilbumanningense, O.aggregatum, Sporothrixpseudoabietina and S.macroconidia. A residual strain was left unidentified as Ophiostoma sp. 1. The overall ophiostomatoid community was by far dominated by three species, representing 87.3% of the total isolates; in decreasing order, these were O.canum, O.brevipilosi and O.minus. Furthermore, the ophiostomatoid community of each beetle, although harbouring a diversity of ophiostomatoid species, was differentially dominated by a single fungal species; Ophiostomacanum was preferentially associated with and dominated the ophiostomatoid community of T.minor, whereas O.brevipilosi and O.minus were exclusively associated with and dominated the ophiostomatoid communities of T.brevipilosus and T.yunnanensis, respectively. Eight additional species, representing the remaining 12.7% of the total isolates, were marginal or sporadic. These results suggested that sympatric Tomicus populations are dominated by distinct species showing some level of specificity or even exclusivity.

A pine wood sample preparation method for high target and quality DNA extraction for detection of Esteya vermicola by PCR from living pine

Esteya vermicola is an endophytic fungus of pine wood nematode with demonstrated biocontrol efficacy. At present, the methods for detection of this fungus from pine wood is still inconvenient and inefficient such as thin-section microscopic observations. In the present study, a simple protocol was developed for wood sample preparation for effective extraction of fungal DNA from wood samples for PCR detection. The protocol of preparation of the sample involves washing in sterile water overnight on a shaking table followed by filtration and centrifugation to obtain the extracted DNA. The result indicates that with this sample preparation protocol, any proper DNA extraction method can be effectively used for the rapid and reliable detection of E. vermicola from pine wood. This method can provide valuable support for follow-up studies with practical applications, such as investigation of the growth rate of E. vermicola and how long it remains viable inside a pine tree.

Comparative genomic analyses reveal the features for adaptation to nematodes in fungi

Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application.

Esteya Vermicola, a Nematophagous Fungus Attacking the Pine Wood Nematode, Harbors a Bacterial Endosymbiont Affiliated with Gammaproteobacteria

Symbioses have played pivotal roles in biological, ecological, and evolutionary diversification. Symbiotic bacteria affect the biology of hosts in a number of ways. Esteya vermicola, an endoparasitic nematophagous fungus, has high infectivity in the pine wood nematode (PWN), which causes devastating ecological damage and economic losses in Asia and Europe. An integration of molecular, phylogenetic, and morphological analyses revealed that surface-sterilized E. vermicola with septate hyphae from different geographic locations harbor bacterial endosymbionts. 16S rRNA gene sequences from four fungal strains all clustered in a well-supported monophyletic clade that was the most closely related to Pseudomonas stutzeri and affiliated with Gammaproteobacteria. The existence and intracellular location of endobacteria was revealed by fluorescent in situ hybridization (FISH). Our results showed that endobacteria were coccoid, vertically inherited, as yet uncultured, and essential symbionts. Ultrastructural observations indicated that young and old endobacteria differed in cell size, cell wall thickness, and the degree of reproduction. The results of the present study provide a fundamental understanding of the endobacteria inside E. vermicola and raise questions regarding the impact of endobacteria on the biology, ecology, and evolution of their fungal host.

The complete mitochondrial genome of nematophagous fungus Esteya vermicola

The complete mitochondrial genome of the Nematophagous fungus Esteya vermicola CBS 115803 was determined using the PacBio RS II sequencing technology. The circular molecule is 47,282bp in length with a GC content of 24.85%. Annotated genes including 14 conserved protein-coding genes, the large and the small rRNA subunit (rnl and rns) and 27 tRNAs. The phylogenetic analysis showed that E. vermicola had close genetic relationship with the genus Sporothrix.

Esteya vermicola Controls the Pinewood Nematode, Bursaphelenchus xylophilus, in Pine Seedlings

Esteya vermicola (Ophiostomataceae) is an endoparasitic fungus that has great potential as a biological control agent against the pinewood nematode Bursaphelenchus xylophilus which causes pine wilt disease. We tested E. vermicola for control of pine wilt disease by spraying E. vermicola conidia on artificial wounds on pine seedlings, and the optimum E. vermicola treatment density and application time were also investigated in the greenhouse. The wounds were similar to those made by sawyer beetles (Coleoptera: Cerambycidae). Esteya vermicola treatments significantly increased the survival rate of pine seedlings that were infected by pinewood nematodes. Wounded plants sprayed with 107 CFU/ml E. vermicola had a 73.0% greater survival rate than nonwounded pine seedlings treated similarly. The treatment of pine seedlings with 107 CFU/ml E. vermicola 14 d before nematode infection increased their survival rate by 90.0%. The number of pinewood nematodes isolated from dead pine seedlings sprayed with E. vermicola was 76% less than the number of pinewood nematodes in the controls. Moreover, infected nematodes and the hyphae of E. vermicola were detected in the dead or wilting pine seedlings. Therefore, spraying E. vermicola on the wounds of pine seedlings made by sawyer beetles provides good control of the pine wilt disease that is caused by pinewood nematodes.