Extracellular enzymes and the pathogenesis of nematophagous fungi

Proteomic insights into nematode-trapping fungi Arthrobotrys oligospora after their response to chitin

Introduction

Nematode-trapping fungi (NTFs) can produce various chitinases to degrade nematode body wall and eggshell chitin during predation. However, the regulatory mechanisms of their expression of chitinases still remain unclear. The primary objective of this study was to elucidate the differential protein profile of A. oligospora, an NTF, in response to chitin.

Material and Methods

Colloidal chitin was added to induce the culture of A. oligospora, and the phenotypic differences before and after induction were observed under inverted microscope. The differential proteins before and after mycelium induction were screened by liquid chromatography-tandem mass spectrometry. The differentially expressed chitinase was expressed in Pichia yeast, and the recombinant enzyme was incubated with Caenorhabditis elegans and its egg suspension to explore its biological activity.

Results

It was found that there was a significant acceleration in the mycelial growth post chitin interaction in A. oligospora. A total of 1,124 differentially expressed proteins (DEPs) were identified between the control group (AO-c) and the experimental group (AO-e), with 183 upregulated and 941 downregulated. Gene Ontology analysis revealed that the DEPs acted in various metabolic processes with catalysis and binding functions. Kyoto Encyclopedia of Genes and Genomes analysis associated these proteins primarily with signalling pathways related to glucose metabolism. Three chitinases were significantly modulated among DEPs. Moreover, enzymatic activity assays demonstrated that one of them effectively degraded C. elegans and its eggs.

Conclusion

These findings suggest that A. oligospora can significantly alter its protein expression profile in response to chitin, thereby facilitating its sugar metabolism and mycelial development. Our study provided new insights into the regulatory mechanisms of nematode predation in A. oligospora.

Antagonistic activity of Pochonia chlamydosporia against three helminth eggs and characterization of its serine protease

To address the economic burden caused by livestock parasitic diseases, particularly gastrointestinal nematodes (GIN) and liver flukes, which are exacerbated by growing anthelmintic resistance, researchers are increasingly focusing on biological control strategies as a promising solution. Among these, the fungus Pochonia chlamydosporia has demonstrated promising helminth control properties. This study explored the potential of P. chlamydosporia in controlling helminth infections by examining its effects on helminth eggs. P. chlamydosporia was cultured on 2 % water agar (WA) plates, and the eggs of three parasite species (Fasciola hepatica, Parascaris spp., and Nematodirus oiratianus) were placed on these plates. The impact of the fungus on the eggs was assessed using light microscopy and scanning electron microscopy (SEM). Eggs were introduced into a liquid medium to stimulate P. chlamydosporia' s predatory activity. The culture filtrate was tested for protease activity and its efficacy against nematode eggs was evaluated. The extracellular alkaline serine protease was purified and characterized through ammonium sulfate precipitation and Sephadex G - 100 chromatography. P. chlamydosporia showed type 1, type 2, and type 3 effects on eggs. (Type 1 effect: physiological and biochemical impact without morphological damage to the eggshell, with visible hyphae adhering to the eggshell; Type 2 effect: lytic effect causing morphological changes in both the embryo and eggshell, without hyphal penetration; Type 3 effect: lytic effect with morphological changes in the embryo and eggshell, along with hyphal penetration and internal egg colonization). Light microscope and SEM observations revealed that P. chlamydosporia destroyed the eggs through mycelial growth, appressoria formation, penetration, and degradation stages. Moreover, the addition of nematode eggs stimulated the secretion of extracellular proteins, including proteases, with induction filtrate showing high ovicidal activity. The molecular mass of the protease was approximately 40 kDa estimated by SDS-PAGE. The optimum activity of the protease was at pH 10 and 60 ℃. The purified protease was highly sensitive to phenylmethyl sulfonyl fluoride (PMSF), indicating it belonged to the serine protease family. The findings suggest that P. chlamydosporia could be an effective biological control agent for helminth diseases in livestock.

In vitro ovicidal studies on egg-parasitic fungus Pochonia chlamydosporia and safety tests on mice

Introduction

The control of parasites infections in livestock is an ongoing concern, with parasites developing resistance to commonly used antiparasitic drugs. The current study investigated in vitro the destructive effect of the fungus Pochonia chlamydosporia on the eggs and oocysts of several equine parasites, as well as assessing the safety of the fungus in mice.

Methods

S. equinus, P. equorum, Anoplocephala spp eggs and Eimeria spp. oocysts were treated with P. chlamydosporia. The prepared preparation was also administered to mice, and the physiological indexes and lesions of major tissues and organs, as well as pathological sections of tissue, were then observed.

Results

P. chlamydosporia exhibited varying degrees of efficacy in the control of S. equinus, P. equorum, Anoplocephala spp eggs and Eimeria spp. oocysts. The acute toxicity test demonstrated that there was no death or toxicity symptom observed in the mice, with no significant difference in clinical observations, such as respiration, mental state, appetite, or feces, between the control and treated mice after the feeding of the biological preparation of P. chlamydosporia.

Discussion

These findings suggested that administration of P. chlamydosporia would be safe to use in livestock and provided a rationale for its potential clinical application, pending further analyses.

Biocontrol agents and their potential use as nano biopesticides to control the tea red spider mite (Oligonychus coffeae): A comprehensive review

Tea red spider mite (TRSM), Oligonychus coffeae Nietner, is one of the major pests that cause considerable crop losses in all tea-growing countries. TRSM management often involves the use of multiple chemical pesticides that are linked to human health risks and environmental pollution. Considering these critical issues, employing biocontrol agents is a potential green approach that may replace synthetic pesticides. This review study aims to discuss the efficacy of plant extracts, entomopathogenic microorganisms, and predators in controlling TRSM. This study includes 44 botanical extracts, 14 microbial species, and 8 potential predators used to control TRSM, along with their respective modes of action. Most of the botanical extracts have ovicidal, adulticidal, and larvicidal activity, ranging from 80 to 100 %, attributed to bioactive compounds such as phenols, alcohols, alkaloids, tannins, and other secondary metabolites. Among microbial pesticides, Purpureocillium lilacinum, Metarhizium robertsii, Aspergillus niger, Pseudomonas fluorescens, and Pseudomonas putida are highly effective against TRSM without causing any harm to the nontarget beneficial insects. Besides, some predators, including green lacewings, ladybirds, and phytoseiid mites have the potential to control TRSM. Employing these biocontrol agents simultaneously in tea plantations could be more effective in preventing TRSM. Nevertheless, their high biodegradability rate, uneven distribution, and uncontrolled release pose challenges for large-scale field applications. This study also explores how nanotechnology can enhance sustainability by addressing the limitations of biopesticides in field conditions. This review study could contribute to the search for potential biocontrol agents and the development of commercial nano biopesticides to control TRSM.

Insights into the efficient degradation mechanism of extracellular proteases mediated by Purpureocillium lilacinum

Protease secretion is crucial for degrading nematode cuticles using nematophagous fungus Purpureocillium lilacinum, but the secretion pattern of protease remains poorly understood. This study aimed to explore the degradation mechanism of proteases by investigating the characteristics of protease secretion under various carbon and nitrogen sources, and different carbon to nitrogen (C:N) ratios in P. lilacinum. The results showed that corn flour as a carbon source and yeast extract as a nitrogen source specifically induced protease secretion in P. lilacinum. P. lilacinum produced significant amounts of gelatinase and casein enzyme at C:N ratios of 10:1, 20:1, and 40:1, indicating that higher C:N ratios were more beneficial for secreting extracellular proteases. Proteomic analysis revealed 14 proteases, including 4 S8 serine endopeptidases and one M28 aminopeptidase. Among four S8 serine peptidases, Alp1 exhibited a high secretion level at C:N ratio less than 5:1, whereas PR1C, PR1D, and P32 displayed higher secretion levels at higher C:N ratios. In addition, the transcription levels of GATA transcription factors were investigated, revealing that Asd-4, A0A179G170, and A0A179HGL4 were more prevalent at a C:N ratio of 40:1. In contrast, the transcription levels of SREP, AreA, and NsdD were higher at lower C:N ratios. The putative regulatory profile of extracellular protease production in P. lilacinum, induced by different C:N ratios, was analyzed. The findings offered insights into the complexity of protease production and aided in the hydrolytic degradation of nematode cuticles.

A systematic review on products derived from nematophagous fungi in the biological control of parasitic helminths of animals

Nematophagous fungi have been widely evaluated in the biological control of parasitic helminths in animals, both through their direct use and the use of their derived products. Fungal bioproducts can include extracellular enzymes, silver nanoparticles (AgNPs), as well as secondary metabolites. The aim of this study was to conduct a systematic review covering the evaluation of products derived from nematophagous fungi in the biological control of parasitic helminths in animals. In total, 33 studies met the inclusion criteria and were included in this review. The majority of the studies were conducted in Brazil (72.7%, 24/33), and bioproducts derived from the fungus Duddingtonia flagrans were the most commonly evaluated (36.3%, 12/33). The studies involved the production of extracellular enzymes (48.4%, 16/33), followed by crude enzymatic extract (27.2%, 9/33), secondary metabolites (15.1%, 5/33) and biosynthesis of AgNPs (9.1%, 3/33). The most researched extracellular enzymes were serine proteases (37.5%, 6/16), with efficacies ranging from 23.9 to 85%; proteases (31.2%, 5/16), with efficacies from 41.4 to 95.4%; proteases + chitinases (18.7%, 3/16), with efficacies from 20.5 to 43.4%; and chitinases (12.5%, 2/16), with efficacies ranging from 12 to 100%. In conclusion, extracellular enzymes are the most investigated derivatives of nematophagous fungi, with proteases being promising strategies in the biological control of animal helminths. Further studies under in vivo and field conditions are needed to explore the applicability of these bioproducts as tools for biological control.

Endoglucanase H from Aspergillus westerdijkiae Plays an Important Role in the Virulence on Pear Fruits

Aspergillus westerdijkiae can infect many agricultural products including cereals, grapes, and pear. Pathogenic fungi secrete diverse effectors as invasive weapons for successful invasion the host plant. During the pathogen-host interaction, 4486 differentially expressed genes were observed in A. westerdijkiae with 2773 up-regulated and 1713 down-regulated, whereas 8456 differentially expressed genes were detected in pear fruits with 4777 up-regulated and 3679 down-regulated. A total of 309 effector candidate genes were identified from the up-regulated genes in A. westerdijkiae. Endoglucanase H (AwEGH) was significantly induced during the pathogen-host interaction. Deletion of AwEGH resulted in altered fungal growth and morphology and reduced conidia production and germination compared to the wild-type. Further experiments demonstrated that AwEGH plays a role in cell wall integrity. Importantly, disruption of AwEGH significantly reduced the fungal virulence on pear fruits, and this defect can be partly explained by the impaired ability of A. westerdijkiae to penetrate host plants.

Linking the protease activity to the nematicidal action of edible mushroom

Biological control using edible mushrooms as natural enemies is a sustainable alternative for pest management. Despite the well-established literature on toxins and secondary metabolites produced by these fungi in the biochemical control of nematodes, the nematicidal activity of proteases from different Pleurotus species is yet to be investigated. Therefore, this study aimed to correlate protease to the nematicidal activity of different mushrooms, Pleurotus sp., P. ostreatus (SB), P. ostreatus (Pearl), and P. djamor. For such a purpose, we performed motility assays of Panagrellus sp. at different time intervals, 6, 12, and 24 h for each of the mushrooms. In addition, the protease activity was measured using different pH (5, 7, and 9) and fermentation time intervals (45 and 75 days). Furthermore, we also evaluated the effect of this cell-free extract on Panagrellus sp. In response to these experiments, all edible mushrooms showed a reduction over 82% for the nematode-feeding activity (p < 0.01). The cell-free crude extract of each of the fungi studied showed nematocidal activity (p < 0.01). For the 45-day fermentation, P. djamor exhibited statistical significance (p < 0.01) compared with the others, reaching a reduction percentage of 73%. For the 75-day fermentation, Pleurotus sp. and P. ostreatus (Pearl) showed significant differences compared with the other fungi (p < 0.01), with reduction percentages of 64 and 62%, respectively. Herein, protease activity was associated with the nematicidal action of different Pleurotus species in controlling Panagrellus sp.

Biodegradation and valorization of feather waste using the keratinase-producing bacteria and their application in environmentally hazardous industrial processes

Poultry feathers are widely discarded as waste worldwide and are considered an environmental pollutant and a reservoir of pathogenic bacteria. Therefore, developing sustainable and environmentally friendly methods for managing feather waste is one of the important environmental protection requirements. In this study, we investigated a rapid and eco-friendly method for the degradation and valorization of feather waste using keratinase-producing Pseudomonas geniculata H10, and evaluated the applicability of keratinase in environmentally hazardous chemical processes. Strain H10 completely degraded chicken feathers within 48 h by producing keratinase using them as sources of carbon, nitrogen, and sulfur. The culture contained a total of 402.8 μM amino acids, including 8 essential amino acids, which was higher than the chemical treatment. Keratinase was a serine-type metalloprotease with optimal temperature and pH of 30 °C and 9, respectively, and showed relatively high stability at 10-40 °C and pH 3-10. Keratinase was also able to degrade various insoluble keratins such as duck feathers, wool, human hair, and nails. Furthermore, keratinase exhibited more efficient depilation and wool modification than chemical treatment, as well as novel functionalities such as nematicidal and exfoliating activities. This suggests that strain H10 is a promising candidate for the efficient degradation and valorization of feather waste, as well as the improvement of current industrial processes that use hazardous chemicals.

Antimicrobial Traits of Beauveria bassiana Against Rhizoctonia solani, the Causal Agent of Sheath Blight of Rice Under Field Conditions

Beauveria bassiana, an entomopathogenic fungus, has recently drawn attention worldwide not only as a potential biocontrol agent against insect pests but also for its other beneficial roles as plant disease antagonist, endophyte, plant growth promoter, and beneficial rhizosphere colonizer. In the present study, 53 native isolates of B. bassiana were screened for antifungal ability against Rhizoctonia solani, the causal agent of sheath blight of rice. Also, the mechanisms underlying such interaction and the responsible antimicrobial traits involved were studied. Following this, potential B. bassiana isolates were assayed against the reduction of sheath blight of rice under field conditions. The results showed that B. bassiana exhibited antagonistic behavior against R. solani with a percent mycelial inhibition recorded maximum of up to 71.15%. Mechanisms behind antagonism were the production of cell-wall-degrading enzymes, mycoparasitism, and the release of secondary metabolites. The study also deciphered several antimicrobial traits and the presence of virulent genes in B. bassiana as a determinant of potential plant disease antagonists. Under field conditions, combined application of the B. bassiana microbial consortium as a seed treatment, seedling root dip, and foliar sprays showed reduced sheath blight disease incidence and severity up to 69.26 and 60.50%, respectively, along with enhanced plant-growth-promoting attributes. This is one of the few studies investigating the antagonistic abilities of the entomopathogenic fungus B. bassiana against phytopathogen R. solani and the underlying mechanisms involved.

Ada2 and Ada3 Regulate Hyphal Growth, Asexual Development, and Pathogenicity in Beauveria bassiana by Maintaining Gcn5 Acetyltransferase Activity

The histone acetyltransferase (HAT) Gcn5 ortholog is essential for a variety of fungi. Here, we characterize the roles of Ada2 and Ada3, which are functionally linked to Gcn5, in the insect-pathogenic fungus Beauveria bassiana. Loss of Ada2 and Ada3 led to severe hyphal growth defects on rich and minimal media and drastic decreases in blastospore yield and conidiation capacity, with abnormal conidia-producing structures. ΔAda2 and ΔAda3 exhibited a delay in conidial germination and increased sensitivity to multiple chemical stresses and heat shock. Nearly all their pathogenicity was lost, and their ability to secrete extracellular enzymes, Pr1 proteases and chitinases for cuticle degradation was reduced. A yeast two-hybrid assay demonstrated that Ada2 binds to Ada3 and directly interacts with Gcn5, confirming the existence of a yeast-like Ada3-Ada2-Gcn5 HAT complex in this fungus. Additionally, deletion of the Ada genes reduced the activity of Gcn5, especially in the ΔAda2 strain, which was consistent with the acetylation level of histone H3 determined by Western blotting. These results illustrate the dependence of Gcn5 enzyme activity on Ada2 and Ada3 in fungal hyphal growth, asexual development, multiple stress responses, and pathogenicity in B. bassiana. IMPORTANCE The histone acetyltransferase Gcn5 ortholog contributes significantly to the growth and development of various fungi. In this study, we found that Ada2 and Ada3 have critical regulatory effects on Gcn5 enzyme activity and influence the acetylation of histone H3. Deletion of Ada2 or Ada3 decreased the fungal growth rate and asexual conidial yield and increased susceptibility to multiple stresses in Beauveria bassiana. Importantly, Ada genes are vital virulence factors, and their deletion caused the most virulence loss, mainly by inhibiting the activity of a series of hydrolytic enzymes and the dimorphic transition ability. These findings provide a new perspective on the function of the Gcn5 acetyltransferase complex in pathogens.

Recent Advances in Life History Transition with Nematode-Trapping Fungus Arthrobotrys oligospora and Its Application in Sustainable Agriculture

Parasitic nematodes cause great annual loss in the agricultural industry globally. Arthrobotrys oligospora is the most prevalent and common nematode-trapping fungus (NTF) in the environment and the candidate for the control of plant- and animal-parasitic nematodes. A. oligospora is also the first recognized and intensively studied NTF species. This review highlights the recent research advances of A. oligospora as a model to study the biological signals of the switch from saprophytism to predation and their sophisticated mechanisms for interacting with their invertebrate hosts, which is of vital importance for improving the engineering of this species as an effective biocontrol fungus. The application of A. oligospora in industry and agriculture, especially as biological control agents for sustainable purposes, was summarized, and we discussed the increasing role of A. oligospora in studying its sexual morph and genetic transformation in complementing biological control research.

Identification, Pathogenicity, and Culture Conditions of a New Isolate of Cordyceps javanica (Hypocreales: Cordycipitaceae) From Soil

This study decribes a highly effective insecticidal isolate of Cordyceps javanica (Frieder. & Bally) (Hypocreales: Cordycipitaceae) named IJ-tg19, which was isolated from soil. Spray bioassays were performed with IJ-tg19 on Myzus persicae (Sulzer) (Hemiptera: Aphididae) adults, third-instar nymphs of Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae), and third-instar larvae of Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae) to determine the pathogenicity of the isolate. The corrected mortality rates for all three pests were 100% when the conidia concentration was 1 × 106 conidia/ml, the lowest concentration in this study, and the median survival times (MST) were 4, 4, and 3 d. The MST shortens with increasing conidia concentration. The effects of laboratory culture conditions on the sporulation and growth of the isolate were also studied. This isolate had the greatest conidia production and fastest growth rate on malt extract agar medium at 25°C. The amount of conidia produced had positive correlation to light duration, with the highest production at 24 hr light. The growth of mycelium can adapt to a moderately alkaline environment, but the optimum conidial production occurred at the pH of 7. Our finding and research will be useful in biocontrol programs that are considering using the new isolate of C. javanica against greenhouse pests.

Trichoderma longibrachiatum T6: A nematocidal activity of endochitinase gene exploration and its function identification

Endochitinase is a natural extracellular protein in Trichoderma longibrachiatum T6, which can degrade the eggshell of Heterodera avenae significantly, however the related genes that coding this protein was rarely characterized. In the present study, the endochitinase 18-5 gene (T6-Echi18-5) of T. longibrachiatum T6 was cloned and sequenced. The expression level of T6-Echi18-5 gene in T. longibrachiatum T6 was induced and increased after the H. avenae cysts inoculation. The full-length cDNA sequence of T6-Echi18-5 was 1671 bp that contained an ORF of 1275 bp, corresponding to 424 amino acids with a 45.9 kDa molecular weight. A single band of 60.04 kDa was detected and identified using SDS-PAGE and Western blot analysis after transferring the T6-Echi18-5 gene to Escherichia coli BL21 Rosetta (DE3). The concentration of purified recombinant T6-Echi18-5 protein was 1.53 mg·ml^-1, and the optimal temperature and pH were 50 °C and 5.0, respectively. The eggshell and content were dissolved and exuded from 4 to10 days after treatment with the purified recombinant T6-Echi18-5 protein. The relative inhibition rate of eggs hatching was 86.79 % at 12 days after treatment. Our study demonstrated the key role of T6-Echi18-5 gene in degrading the H. avenae eggshell and inhibiting the eggs hatching.

Making "Sense" of Ecology from a Genetic Perspective: Caenorhabditis elegans, Microbes and Behavior

Our knowledge of animal and behavior in the natural ecology is based on over a century's worth of valuable field studies. In this post-genome era, however, we recognize that genes are the underpinning of ecological interactions between two organisms. Understanding how genes contribute to animal ecology, which is essentially the intersection of two genomes, is a tremendous challenge. The bacterivorous nematode Caenorhabditis elegans, one of the most well-known genetic animal model experimental systems, experiences a complex microbial world in its natural habitat, providing us with a window into the interplay of genes and molecules that result in an animal-microbial ecology. In this review, we will discuss C. elegans natural ecology, how the worm uses its sensory system to detect the microbes and metabolites that it encounters, and then discuss some of the fascinating ecological dances, including behaviors, that have evolved between the nematode and the microbes in its environment.

Strategy of Nematophagous Fungi in Determining the Activity of Plant Parasitic Nematodes and Their Prospective Role in Sustainable Agriculture

In this review, we supply a framework for the importance of nematophagous fungi (nematophagous fungi [NF]) and their role in agricultural ecosystems. We characterize the taxonomy, diversity, ecology, and type of NF, depending on their interaction with plant-parasitic nematodes (PPNs). We described potential mechanisms of NF in the control of PPNs, the efficiency and methods of utilization, and the use of nematicides in sustainable agriculture. We explain the utilization of NF in nanotechnology as a new approach. NF are significant in the soil for having the effective potential for use in sustainable agriculture. These types of fungi belong to wide taxa groups, such as Ascomycota, Basidiomycota, and other groups. Diverse NF are available in different kinds of soil, especially in soils that contain high densities of nematodes. There is a relationship between the environment of nematodes and NF. NF can be divided into two types according to the mechanisms that affect nematodes. These types are divided into direct or indirect effects. The direct effects include the following: ectoparasites, endoparasites, cyst, or egg parasites producing toxins, and attack tools as special devices. However, the indirect effect comprises two groups: paralyzing toxins and the effect on the life cycle of nematodes. We explained the molecular mechanisms for determining the suitable conditions in brief and clarified the potential for increasing the efficacy of NF to highly impact sustainable agriculture in two ways: directly and indirectly.

Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus

Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.

Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics

Soft rot pectobacteria are devastating plant pathogens with a global distribution and a broad host range. Pectobacterium aroidearum L6, previously isolated from leaves of Syngonium podophyllum, is a pectolytic bacterial pathogen that causes typical soft rot on S. podophyllum. There is a shortage for genome data of P. aroidearum, which seriously hinders research on classification and pathogenesis of Pectobacterium. We present here the complete genome sequence of P. aroidearum L6. The L6 strain carries a single 4,995,896-bp chromosome with 53.10% G + C content and harbors 4,306 predicted protein-coding genes. We estimated in silico DNA-DNA hybridization and average nucleotide identity values in combination with the whole-genome-based phylogeny from 19 Pectobacterium strains including P. aroidearum L6. The results showed that L6 and PC1 formed a population distinct from other populations of the Pectobacterium genus. Phylogenetic analysis based on 16S rRNA and genome sequences showed a close evolutionary relationship among Pectobacterium species. Overall, evolutionary analysis showed that L6 was in the same branch with PC1. In comparison with 18 Pectobacterium spp. reference pathogens, strain L6 had 2,712 gene families, among which 1,632 gene families were identified as orthologous to those strains, as well as 1 putative unique gene family. We discovered 478 genes, 10.4% of the total of predicted genes, that were potentially related to pathogenesis using the Virulence Factors of Pathogenic Bacteria database. A total of 25 genes were related to toxins, 35 encoded plant cell-wall degrading enzymes, and 122 were involved in secretion systems. This study provides a foundation for a better understanding of the genomic structure of P. aroidearum and particularly offers information for the discovery of potential pathogenic factors and the development of more effective strategies against this pathogen.

Understanding the Transcriptional Changes During Infection of Meloidogyne incognita Eggs by the Egg-Parasitic Fungus Purpureocillium lilacinum

The egg-pathogenic fungus Purpureocillium lilacinum parasitizes on nematode eggs, and thus, it is used as a good biocontrol agent against plant root-knot nematodes. However, little is known about the transcriptional response of P. lilacinum while infecting nematode eggs. This study presents the whole transcriptome sequencing of P. lilacinum and transcriptome-wide gene expression analysis of P. lilacinum upon infecting the eggs of Meloidogyne incognita compared to non-infecting controls. A transcriptomic library of P. lilacinum was used as reference gene set and six transcriptomic libraries of the non-infecting control and P. lilacinum infecting M. incognita eggs were constructed, respectively, comprising three biological replicates of each. A total of 1,011 differently expressed genes (DEGs) were identified in the infecting samples, including 553 up-regulated and 458 down-regulated genes compared to the non-infecting control samples. Furthermore, functional enrichment analysis exhibited that these DEGs were primarily involved in oxidative phosphorylation, oxidoreductase activity, and metabolic processes. Fifteen DEGs were randomly selected to verify the RNA sequencing results through quantitative real-time polymerase chain reaction (qPCR). The study focused on P. lilacinum genes that were strongly expressed upon infecting M. incognita eggs. These DEGs were primarily involved in detoxification, parasitic behavior, and nutritional utilization. This study contributes significantly to the understanding of the molecular mechanisms underlying the parasitic action of P. lilacinum on nematode eggs and provides a valuable genetic resource for further research on parasitic behavior of P. lilacinum. Notably, this study examined the transcriptomics of P. lilacinum infecting M. incognita eggs at only one time point. Since there were fungi at different stages of the infection process at that time point, the transcriptional profiles are not precisely examining one specific stage in this process.

Suppression of root-knot nematode Meloidogyne incognita on tomato plants using the nematode trapping fungus Arthrobotrys oligospora Fresenius

AIM

The aims of the study were to isolate and characterize the nematode trapping fungus, Arthrobotrys oligospora, to investigate the suppressive and predacious activities of the fungus against Meloidogyne incognita and to study the potentiality of A. oligospora in controlling root-knot caused by M. incognita on tomato plants.

METHODS AND RESULTS

Arthrobotrys oligospora (MRDS 300) was isolated from sandy soil samples collected from Al-Beheira, Egypt. In vitro experiments revealed a high efficiency of the fungus in capturing and suppressing M. incognita second juveniles (J₂ ). Microscopic observations showed that the fungus develops adhesive traps consisting of loops of hyphae. Moreover, an in vitro experiment showed that the culture filtrate of A. oligospora had a high toxic effect on the nematode. Pot experiments carried out in two seasons (2018-2019) showed that A. oligospora significantly suppressed root knot on tomato plants caused by M. incognita. The number of females, galls and nematodes in different developing stages were reduced significantly. The treatment with A. oligospora had a prominent effect on enhancing plant growth.

CONCLUSION

Arthrobotrys oligospora had significant suppressive and predacious effects against root-knot nematode, M. incognita. The fungus developed different forms of trapping devices in addition to secreting toxic metabolites to M. incognita. The fungus had a plant-growth promoting effect.

SIGNIFICANCE AND IMPACT OF THE STUDY

Arthrobotrys oligospora (MRDS 300) is a potential biological control agent that can be utilized in controlling the root-knot diseases caused by M. incognita.

Biocontrol of Melolontha spp. Grubs in Organic Strawberry Plantations by Entomopathogenic Fungi as Affected by Environmental and Metabolic Factors and the Interaction with Soil Microbial Biodiversity

The efficacy of two strains of two Beauveria species (B. bassiana and B. brongniartii), individually or as co-inoculants, to control Melolontha sp. grubs was assessed in two organic strawberry plantations in relation to the environmental conditions, their abundance after soil inoculation, and their in vitro chitinolytic activity, thereby also verifying their impact on soil microbial communities. A reduction of the grubs' damage to strawberry plants was observed when compared to the untreated control in one plantation, irrespective of the strain used and whether they were applied as single or as co-inoculum. The metabolic pattern expressed by the two fungi in vitro was different: B. bassiana showed a higher metabolic versatility in the use of different carbon sources than B. brongniartii, whose profile was partly overlapped in the co-inoculum. Similar differences in the chitinolytic activity of each of the fungi and the co-inoculum were also pointed out. A higher abundance of B. bassiana in the soils receiving this species in comparison to those receiving B. brongniartii, together with its in vitro metabolic activity, could account for the observed diverse efficacy of pest damage control of the two species. However, environmental and climatic factors also affected the overall efficacy of the two bioinocula. According to the monitoring of the two species in soil, B. bassiana could be considered as a common native species in the studied locations in contrast to B. brongniartii, which seemed to be a non-endemic species. Nevertheless, the inoculation with both species or the co-inoculum did not consistently affect the soil microbial (fungi and bacteria) biodiversity, as expressed by the operational taxonomic unit (OTU) number and Shannon-Wiener diversity index based on terminal restriction fragment length polymorphism (TRFLP) data. A small transient increase of the share of the inoculated species to the total fungal community was noted by the analysis of genes copy numbers only for B. brongniartii at the end of the third growing season.

Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome

Rhizosphere microbes influence one another, forming extremely complex webs of interactions that may determine plant success. Identifying the key factors that structure the fungal microbiome of the plant rhizosphere is a necessary step in optimizing plant production. In a long-term field experiment conducted at three locations in the Canadian prairies, we tested the following hypotheses: (1) diversification of cropping systems influences the fungal microbiome of the canola (Brassica napus) rhizosphere; (2) the canola rhizosphere has a core fungal microbiome, i.e., a set of fungi always associated with canola; and (3) some taxa within the rhizosphere microbiome of canola are highly interrelated and fit the description of hub taxa. Our results show that crop diversification has a significant effect on the structure of the rhizosphere fungal community but not on fungal diversity. We also discovered and described a canola core microbiome made up of one zero-radius operational taxonomic unit (ZOTU), cf. Olpidium brassicae, and an eco-microbiome found only in 2013 consisting of 47 ZOTUs. Using network analysis, we identified four hub taxa in 2013: ZOTU14 (Acremonium sp.), ZOTU28 (Sordariomycetes sp.), ZOTU45 (Mortierella sp.) and ZOTU179 (cf. Ganoderma applanatum), and one hub taxon, ZOTU17 (cf. Mortierella gamsii) in 2016. None of these most interacting taxa belonged to the core microbiome or eco-microbiome for each year of sampling. This temporal variability puts into question the idea of a plant core fungal microbiome and its stability. Our results provide a basis for the development of ecological engineering strategies for the improvement of canola production systems in Canada.

Purpureocillium lilacinum and Trichoderma virens for biological control of trichostrongylid parasites of sheep: an in vitro evaluation

The study evaluated the ovicidal activity of enzymatic extracts of Purpureocillium lilacinum and Trichoderma virens against trichostrongylid eggs from sheep. Filtered extract (FE) and macerated crude extract (MCE) were prepared from fungal cultures in minimal broth. In the experiment, 100 trichostrongylid eggs, obtained from the feces of naturally infected sheep, were exposed to fungal extracts for 24 and 48 hours/25°C. In the control group, eggs were incubated in minimal broth. The number of L1 larvae was ascertained. Each treatment consisted of four repetitions and the experiment was repeated five times. It was observed that the effect of FE and MCE of P. lilacinum and T. virens on egg hatchability differed from that of the control group. MCE of T. virens and P. lilacinum showed higher ovicidal activity than FE over both periods and at 48 hours of exposure, respectively. From the percentage reductions in hatchability of the eggs, MCE was shown to be superior to FE for both fungi. This study demonstrated the ovicidal potential of these fungi against trichostrongylid eggs. However, further studies are needed in order to identify the molecules responsible for the ovicidal effects, and to evaluate the behavior of fungal extracts in biotic and abiotic interactions.

Fungi-Nematode Interactions: Diversity, Ecology, and Biocontrol Prospects in Agriculture

Fungi and nematodes are among the most abundant organisms in soil habitats. They provide essential ecosystem services and play crucial roles for maintaining the stability of food-webs and for facilitating nutrient cycling. As two of the very abundant groups of organisms, fungi and nematodes interact with each other in multiple ways. Here in this review, we provide a broad framework of interactions between fungi and nematodes with an emphasis on those that impact crops and agriculture ecosystems. We describe the diversity and evolution of fungi that closely interact with nematodes, including food fungi for nematodes as well as fungi that feed on nematodes. Among the nematophagous fungi, those that produce specialized nematode-trapping devices are especially interesting, and a great deal is known about their diversity, evolution, and molecular mechanisms of interactions with nematodes. Some of the fungi and nematodes are significant pathogens and pests to crops. We summarize the ecological and molecular mechanisms identified so far that impact, either directly or indirectly, the interactions among phytopathogenic fungi, phytopathogenic nematodes, and crop plants. The potential applications of our understanding to controlling phytophagous nematodes and soilborne fungal pathogens in agricultural fields are discussed.

Optimization of the Fermentation Media and Parameters for the Bio-control Potential of Trichoderma longibrachiatum T6 Against Nematodes

The cereal cyst nematode Heterodera avenae is one of the important soil-borne pathogens of cereal crops and causes high yield losses worldwide. Trichoderma spp. formulations are applied as commercial bio-control agents against soil-borne plant pathogens such as H. avenae. However, the relationship between Trichoderma longibrachiatum fermentation parameters and its bio-control potential against H. avenae has not been exclusively established. In the present study, the effect of 10 different fermentation media and conditions on the nematicidal activity of T. longibrachiatum T6 (T6) was evaluated with a single-factor method and a Plackett-Burman design, and the interaction between different fermentation parameters was investigated by a Box-Behnken design. The variables for enhancing the nematicidal activity of T6 culture filtrates were explored and optimized using response surface methodology (RSM). The Minor Medium (MM) plus wheat bran-2 medium was found to be the most effective fermentation medium for T6 culture filtrates against the second stage juveniles (J2s) of H. avenae. The maximum mortality of the J2s was obtained using the T6 culture filtrates under the following fermentation conditions: initial pH 6, 28°C culture temperature, 180 rpm rotating speed, 60 ml of fermentation media, 7 days of incubation time, and 1 ml of inoculation volumes. Among these parameters, the initial pH, inoculation volume, and incubation day were identified as the most significant parameters and critical independent variables for enhancing the nematicidal activity of the T6 culture filtrates. After further optimizations based on statistical predictions, the highest nematicidal activity (92.42%) was obtained with the T6 culture filtrates fermented under an initial pH of 6.06, an inoculation volume of 1.62 ml, and an incubation time of 7.15 days. The nematicidal activity was increased approximately by as high as 1.07% compared with that before optimization. Bio-control efficacy of T6 culture filtrates was 83.88% at the 70th day after wheat seeds sowing in greenhouse experiments. The results from the validation experiments agreed with the model predictions. Our study has improved the bio-control potential of Trichoderma spp. against the plant-parasitic nematodes H. avenae and provided a cost-efficient bio-resource in the future development of novel bio-control agents.

Effect of Heterodera schachtii female age on susceptibility to three fungal hyperparasites in the genus Hyalorbilia

Three closely related nematophagous fungi in the genus Hyalorbilia were compared for their ability to parasitize females and eggs of Heterodera schachtii at different developmental stages. DoUCR50, StM, and ARF were originally isolated from Heterodera schachtii, Meloidogyne incognita, and Heterodera glycines, respectively. Phylogenetic analysis and pairwise sequence analysis showed that DoUCR50 and StM are more closely related to each other than they are to ARF. DoUCR50 parasitism suppressed 100% of the J2 hatch from 3-week-old H. schachtii females and 75% of the hatch from 4-week-old females. Eggs within 5-week-old females were resistant to parasitism, and hatch of J2 was unaffected by exposure to DoUCR50. StM and ARF did not reduce the hatch of J2 from H. schachtii females of any age. Eggs removed from females and spread onto water agar cultures of the fungi were mostly resistant to parasitism. DoUCR50 parasitized only 16% of such eggs from 3-week-old females. Extracellular hydrolytic enzyme production by the three fungal strains grown on PDA or parasitized H. schachtii females was evaluated using API ZYM (bioMérieux) test strips. All three fungi produced extracellular hydrolytic enzymes when grown on PDA or H. schachtii females. Trypsin-like protease activity was uniquely detected in DoUCR50 grown on PDA and H. schachtii females, with the highest activity associated with the fungus grown on parasitized females.

Identification and Nematicidal Characterization of Proteases Secreted by Endophytic Bacteria Bacillus cereus BCM2

The endophytic bacterium Bacillus cereus BCM2 has shown great potential as a biocontrol organism against Meloidogyne incognita, which causes severe root-knot diseases in crops. In our previous study, the metabolite of BCM2 showed high nematicidal activity against the M. incognita second-stage juveniles. However, the mechanism employed by endophytic bacteria to infect and kill nematodes is still unclear. Here, we investigate both the endophytic bacterial extracellular proteins with nematicidal activity and their mechanism of killing nematodes. The first step was detecting the nematicidal activities of crude proteins. The results show that the nematode mortality rate reached 100% within 72 h, and the crude proteins damaged both the cuticle and eggshell, before finally destroying the targets. This suggests possible proteinaceous pathogeny in BCM2. Throughout the process, the fine-detail changes in the nematode cuticle and the intestinal structure were observed using scanning electron microscopy and transmission electron microscopy. These images show that BCM2 extracellular proteins did not damage the internal organization of the nematode but did severely damage its cuticle, which led to content leakage. From the crude proteins, chitosanase, alkaline serine protease, and neutral protease were purified and identified. The M. incognita-B. cereus BCM2 microenvironment simulation demonstrates that BCM2 adheres to the surface of nematodes and helps the metabolites that were produced by BCM2 to rapidly recognize and kill M. incognita. This relationship between plants, endophytic bacteria, and nematodes offers insight into the biological mechanisms that can be utilized for of nematode management.

The pH sensing receptor AopalH plays important roles in the nematophagous fungus Arthrobotrys oligospora

There is well-conserved PacC/Rim101 signaling among ascomycete fungi to mediate environmental pH sensing. For pathogenic fungi, this pathway not only enables fungi to grow over a wide pH range, but it also determines whether these fungi can successfully colonize and invade the targeted host. Within the pal/PacC pathway, palH is a putative ambient pH sensor with a seven-transmembrane domain. To characterize the function of a palH homolog, AopalH, in the nematophagous fungus Arthrobotrys oligospora, we knocked out the encoding gene of AopalH through homologous recombination, and the transformants exhibited slower growth rates, greater sensitivities to cationic and hyperoxidation stresses, as well as reduced conidiation and reduced trap formation, suggesting that the pH regulatory system has critical functions in nematophagous fungi. Our results provide novel insights into the mechanisms of pH response and regulation in fungi.

Signal pathways involved in microbe-nematode interactions provide new insights into the biocontrol of plant-parasitic nematodes

Plant-parasitic nematodes (PPNs) cause severe damage to agricultural crops worldwide. As most chemical nematicides have negative environmental side effects, there is a pressing need for developing efficient biocontrol methods. Nematophagous microbes, the natural enemies of nematodes, are potential biocontrol agents against PPNs. These natural enemies include both bacteria and fungi and they use diverse methods to infect and kill nematodes. For instance, nematode-trapping fungi can sense host signals and produce special trapping devices to capture nematodes, whereas endo-parasitic fungi can kill nematodes by spore adhesion and invasive growth to break the nematode cuticle. By contrast, nematophagous bacteria can secrete virulence factors to kill nematodes. In addition, some bacteria can mobilize nematode-trapping fungi to kill nematodes. In response, nematodes can also sense and defend against the microbial pathogens using strategies such as producing anti-microbial peptides regulated by the innate immunity system. Recent progresses in our understanding of the signal pathways involved in microbe-nematode interactions are providing new insights in developing efficient biological control strategies against PPNs. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.

Exposure of Toxocara canis eggs to Purpureocillium lilacinum as a biocontrol strategy: an experimental model evaluation

Abstract Purpureocillium lilacinum is a nematophagous fungus used in biological control against some parasites, including Toxocara canis. This study researched the infectivity of embryonated T. canis eggs after exposure to the fungus P. lilacinum. T. canis eggs were exposed to P. lilacinum for 15 or 30 days and subsequently administered to Swiss mice (n=20). Control group consisted of mice who received T. canis embryonated eggs without fungal exposure. Forty-eight hours after infection, heart, lung, and liver from animals of each group were collected to assess larval recovery. The organs of mice that received embryonated eggs exposed to the fungus showed a lower average larval recovery (P<0.05) suggesting that exposure of T. canis eggs to P. lilacinum was able to reduce experimental infection. Under the evaluated conditions, the interaction time between the fungus and the parasite eggs was not a significant factor in larvae recovery. P. lilacinum may be considered a promising T. canis biological control agent. However, further studies are needed to determine a protocol for the use of this fungus as a biological control agent.

Suppression of Meloidogyne incognita by the Entomopathogenic Fungus Lecanicillium muscarium

The entomopathogenic fungus Lecanicillium muscarium (Petch) Zare and Gams is currently being developed as a biocontrol agent against insect pests, as well as some plant-pathogenic fungi and bacteria. Data about its activity against plant-parasitic nematodes exist, but are relatively limited. To expand this understanding, we investigated the biocontrol efficiency of three isolates of L. muscarium (Lm) against the root knot nematode, Meloidogyne incognita, in both in vitro and in vivo conditions. In our experiments, the maximum number of nematode eggs, juveniles (J2s), females, and egg masses that were parasitized were quantified after a 72-h exposure to the fungus. The isolate Lm1 was designated as the best biocontrol agent against nematode eggs as well as J2s. It showed the highest colonization of eggs and significantly decreased egg hatching events. The results from two additional isolates, Lm2 and Lm3, were also significant (P = 0.05) but less pronounced than those observed with Lm1. L. muscarium treatments had significant (P = 0.05) positive effects on plant shoot and root growth compared with the growth of control plants. These results suggest the effectiveness of the fungus may be due to either the infection of eggs and J2s, or the production of secondary metabolites that induced plant defense mechanisms and lead to systemic resistance. Our study demonstrates that L. muscarium could be used as a potential biocontrol agent against root knot nematodes.

Predator-prey interactions of nematode-trapping fungi and nematodes: both sides of the coin

Nematode-trapping fungi develop complex trapping devices to capture and consume nematodes. The dynamics of these organisms is especially important given the pathogenicity of nematodes and, consequently, the potential application of nematode-trapping fungi as biocontrol agents. Furthermore, both the nematodes and nematode-trapping fungi can be easily grown in laboratories, making them a unique manipulatable predator-prey system to study their coevolution. Several different aspects of these fungi have been studied, such as their genetics and the different factors triggering trap formation. In this review, we use the nematode-trapping fungus Arthrobotrys oligospora (which forms adhesive nets) as a model to describe the trapping process. We divide this process into several stages; namely attraction, recognition, trap formation, adhesion, penetration, and digestion. We summarize the latest findings in the field and current knowledge on the interactions between nematodes and nematode-trapping fungi, representing both sides of the predator-prey interaction.

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.

Taxonomic Resolution of the Nematophagous Fungal Isolate ARF18 via Genome Sequencing

The taxonomically uncharacterized nematophagous fungus ARF18, which parasitizes cysts, juveniles, and adults of the soybean cyst nematode (Heterodera glycines), was proposed as a nematode biological control agent in 1991. A 46.3-Mb draft genome sequence of this fungus is presented, and a tentative taxonomic identification as a novel species of Brachyphoris is proposed.

Random mutagenesis analysis and identification of a novel C2H2-type transcription factor from the nematode-trapping fungus Arthrobotrys oligospora

Arthrobotrys oligospora is a typical nematode-trapping fungus. In this study, 37 transformants of A. oligospora were obtained by REMI (restriction enzyme mediated integration) method and phenotypic properties of nine transformants were analyzed. The nine transformants showed differences in growth, conidiation, trap formation, stress tolerance, and/or pathogenicity among each other and with those of the parental wild-type strain (WT). The insertional sites of the hph cassette were identified in transformants X5 and X13. In X5, the cassette was inserted in the non-coding region between AOL_s00076g273 (76g273) and AOL_s00076g274 (76g274) and the transcription of 76g274, but not 76g273, was enhanced in X5. 76g274p had two conserved domains and was predicted as a nucleoprotein, which we confirmed by its nuclear localization in Saccharomyces cerevisiae using the green fluorescent protein-fused 76g274p. The transcription of 76g274 was stimulated or inhibited by several environmental factors. The sporulation yields of 76g274-deficient mutants were decreased by 70%, and transcription of several sporulation-related genes was severely diminished compared to the WT during the conidiation. In summary, a method for screening mutants was established in A. oligospora and using the method, we identified a novel C₂H₂-type transcription factor that positively regulates the conidiation of A. oligospora.

Nematode-Trapping Fungi

Nematode-trapping fungi are a unique and intriguing group of carnivorous microorganisms that can trap and digest nematodes by means of specialized trapping structures. They can develop diverse trapping devices, such as adhesive hyphae, adhesive knobs, adhesive networks, constricting rings, and nonconstricting rings. Nematode-trapping fungi have been found in all regions of the world, from the tropics to Antarctica, from terrestrial to aquatic ecosystems. They play an important ecological role in regulating nematode dynamics in soil. Molecular phylogenetic studies have shown that the majority of nematode-trapping fungi belong to a monophyletic group in the order Orbiliales (Ascomycota). Nematode-trapping fungi serve as an excellent model system for understanding fungal evolution and interaction between fungi and nematodes. With the development of molecular techniques and genome sequencing, their evolutionary origins and divergence, and the mechanisms underlying fungus-nematode interactions have been well studied. In recent decades, an increasing concern about the environmental hazards of using chemical nematicides has led to the application of these biological control agents as a rapidly developing component of crop protection.

Substrate-induced changes in dynamics and molecular motions of cuticle-degrading serine protease PL646: a molecular dynamics study

Cuticle-degrading serine proteases secreted by nematophagous fungi can degrade the nematode cuticle during the infection processes.

Improvement of chitinase Pachi with nematicidal activities by random mutagenesis

Chitinase, an enzyme that can degrade the main compositions of insect intestine and cuticle, has been used in the bio-control field. Our previous work has reported the chitinase Pachi with nematicidal activity (Caenorhabditis elegans). In the present study, to improve the chitinolytic and nematicidal activities of Pachi, a random mutant library was constructed by error-prone PCR and screened by bacteriophage T7-based high-throughput screening system. One mutant, Pachi_N35D was obtained from about 10, 000 clones. The kinetics analysis revealed that Pachi_N35D exhibited a 63% decrease in K_m value against chitosan, a 2.1-fold enhancement in k_cat/K_m value and a 1.2-fold increase in specific activity over the wild-type Pachi. Moreover, the mortality analysis against Caenorhabditis elegans showed that the 50% lethal concentration (LC₅₀) of Pachi_N35D is 309.6±1.1μg/ml and a 20% increase in nematicidal activity over the wild-type Pachi (with a LC₅₀ value of 387.3±31.7μg/ml). The structure modeling and superimposition indicated that the substitution N35D reduced the distance between substrate and substrate-binding site Asp141, finally resulting in an increase in substrate affinity, catalytic efficiency and specific activity. These results provide useful information for the study of structure-function relationship of Pachi and lay a foundation for its potential applications in agro-biotechnology.

Effect of Paecilomyces lilacinus, Trichoderma harzianum and Trichoderma virens fungal extracts on the hatchability of Ancylostoma eggs

BACKGROUND

Ancylostoma species have demanded attention due to their zoonotic potential. The use of anthelmintics is the usual method to prevent environmental contamination by Ancylostoma eggs and larvae. Nematophagous fungi have been widely used in their biological control due to the fungus ability to capture and digest free nematode forms.

AIMS

The aim of this study was to evaluate the effect of four different fungal extracts of Paecilomyces lilacinus (n=2), Trichoderma harzianum (n=1) and Trichoderma virens (n=1) isolates on the hatchability of Ancylostoma eggs.

METHODS

Fungal extracts consisted of fungal broth culture supernatant without filtration (crude extract) and filtered broth (filtered extract), macerated mycelium (crude macerate), and macerated mycelium submitted to filtration (filtered macerate). The Ancylostoma eggs were obtained from the feces of naturally infected dogs. In vitro assays were performed in five replicates and consisted of four treatments and one control group.

RESULTS

The activity of the fungal extracts of each evaluated fungus differed (p<0.05) from those of the control group, showing significant ovicidal activity. The hatching of the eggs suffered reduction percentages of 68.43% and 47.05% with P. lilacinus, and 56.43% with T. harzianum, when crude macerate extract was used. The reduction with the macerate extract of T. virens was slightly lower (52.25%) than that for the filtered macerate (53.64%).

CONCLUSIONS

The results showed that all extracts were effective in reducing the hatchability of Ancylostoma eggs. The ovicidal effect observed is likely to have been caused by the action of hydrolytic enzymes secreted by the fungi.

Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

Background

Subtilisin-like serine proteases or Subtilases in fungi are important for penetration and colonization of host. In Hypocreales, these proteins share several properties with other fungal, bacterial, plant and mammalian homologs. However, adoption of specific roles in entomopathogenesis may be governed by attainment of unique biochemical and structural features during the evolutionary course. Due to such functional shifts Subtilases coded by different family members of Hypocreales acquire distinct features according to respective hosts and lifestyle. We conducted phylogenetic and DIVERGE analyses and identified important protein residues that putatively assign functional specificity to Subtilases in fungal families/species under the order Hypocreales.

Results

A total of 161 Subtilases coded by 10 species from five different families under the fungal order Hypocreales was included in the analysis. Based on the presence of conserved domains, the Subtilase genes were divided into three subfamilies, Subtilisin (S08.005), Proteinase K (S08.054) and Serine-carboxyl peptidases (S53.001). These subfamilies were investigated for phylogenetic associations, protein residues under positive selection and functional divergence among paralogous clades. The observations were co-related with the life-styles of the fungal families/species. Phylogenetic and Divergence analyses of Subtilisin (S08.005) and Proteinase K (S08.054) families of proteins revealed that the paralogous clades were clear-cut representation of familial origin of the protein sequences. We observed divergence between the paralogous clades of plant-pathogenic fungi (Nectriaceae), insect-pathogenic fungi (Cordycipitaceae/Clavicipitaceae) and nematophagous fungi (Ophiocordycipitaceae). In addition, Subtilase genes from the nematode-parasitic fungus Purpureocillium lilacinum made a unique cluster which putatively indicated that the fungus might have developed distinctive mechanisms for nematode-pathogenesis. Our evolutionary genetics analysis revealed evidence of positive selection on the Subtilisin (S08.005) and Proteinase K (S08.054) protein sequences of the entomopathogenic and nematophagous species belonging to Cordycipitaceae, Clavicipitaceae and Ophiocordycipitaceae families of Hypocreales.

Conclusions

Our study provided new insights into the evolution of Subtilisin like serine proteases in Hypocreales, a fungal order largely consisting of biological control species. Subtilisin (S08.005) and Proteinase K (S08.054) proteins seemed to play important roles during life style modifications among different families and species of Hypocreales. Protein residues found significant in functional divergence analysis in the present study may provide support for protein engineering in future.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0793-y) contains supplementary material, which is available to authorized users.

CAZyme content of Pochonia chlamydosporia reflects that chitin and chitosan modification are involved in nematode parasitism

Pochonia chlamydosporia is a soil fungus with a multitrophic lifestyle combining endophytic and saprophytic behaviors, in addition to a nematophagous activity directed against eggs of root-knot and other plant parasitic nematodes. The carbohydrate-active enzymes encoded by the genome of P. chlamydosporia suggest that the endophytic and saprophytic lifestyles make use of a plant cell wall polysaccharide degradation machinery that can target cellulose, xylan and, to a lesser extent, pectin. This enzymatic machinery is completed by a chitin breakdown system that involves not only chitinases, but also chitin deacetylases and a large number of chitosanases. P. chlamydosporia can degrade and grow on chitin and is particularly efficient on chitosan. The relevance of chitosan breakdown during nematode egg infection is supported by the immunolocalization of chitosan in Meloidogyne javanica eggs infected by P. chlamydosporia and by the fact that the fungus expresses chitosanase and chitin deacetylase genes during egg infection. This suggests that these enzymes are important for the nematophagous activity of the fungus and they are targets for improving the capabilities of P. chlamydosporia as a biocontrol agent in agriculture.

Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1

Purpureocillium lilacinum is a promising nematophagous ascomycete able to adapt diverse environments and it is also an opportunistic fungus that infects humans. A microbial inoculant of P. lilacinum has been registered to control plant parasitic nematodes. However, the molecular mechanism of the toxicological processes is still unclear because of the relatively few reports on the subject. In this study, using Illumina paired-end sequencing, the draft genome sequence and the transcriptome of P. lilacinum strain 36-1 infecting nematode-eggs were determined. Whole genome alignment indicated that P. lilacinum 36-1 possessed a more dynamic genome in comparison with P. lilacinum India strain. Moreover, a phylogenetic analysis showed that the P. lilacinum 36-1 had a closer relation to entomophagous fungi. The protein-coding genes in P. lilacinum 36-1 occurred much more frequently than they did in other fungi, which was a result of the depletion of repeat-induced point mutations (RIP). Comparative genome and transcriptome analyses revealed the genes that were involved in pathogenicity, particularly in the recognition, adhesion of nematode-eggs, downstream signal transduction pathways and hydrolase genes. By contrast, certain numbers of cellulose and xylan degradation genes and a lack of polysaccharide lyase genes showed the potential of P. lilacinum 36-1 as an endophyte. Notably, the expression of appressorium-formation and antioxidants-related genes exhibited similar infection patterns in P. lilacinum strain 36-1 to those of the model entomophagous fungi Metarhizium spp. These results uncovered the specific parasitism of P. lilacinum and presented the genes responsible for the infection of nematode-eggs.

Genetic improvement of the nematicidal fungus Lecanicillium attenuatum against Heterodera glycines by expression of the Beauveria bassiana Cdep1 protease gene

Lecanicillium attenuatum is an important nematophagous fungus with potential as a biopesticide against plant-parasitic nematodes. The Pr1A-like cuticle-degrading protease (Cdep1) gene originating from the entomopathogenic fungus Beauveria bassiana was transformed into the nematophagous fungus L. attenuatum using a polyethylene-glycol mediated protoplast-based transformation system. Protease activity was increased 0.64- to 1.63-fold 2-10d after growth in the transformed L. attenuatum. Inhibition of egg-hatching and J2 motility of soybean cyst nematodes (Heterodera glycines) by cell-free fungal culture filtrates were enhanced by 17-76% 2-14d and 43-152% 1-13d after incubation, respectively.