Effects on plant growth and root-knot nematode infection of an endophytic GFP transformant of the nematophagous fungus Pochonia chlamydosporia

Diversity of microbial, biocontrol agents and nematode abundance on a susceptible Prunus rootstock under a Meloidogyne root gradient infection

Root-knot nematodes (RKNs) of the genus Meloidogyne are one of the most damaging genera to cultivated woody plants with a worldwide distribution. The knowledge of the soil and rhizosphere microbiota of almonds infested with Meloidogyne could help to establish new sustainable and efficient management strategies. However, the soil microbiota interaction in deciduous woody plants infected with RKNs is scarcely studied. This research was carried out in six commercial almond groves located in southern Spain and infested with different levels of Meloidogyne spp. within each grove. Several parameters were measured: nematode assemblages, levels and biocontrol agents in Meloidogyne's eggs, levels of specific biocontrol agents in rhizoplane and soil, levels of bacteria and fungi in rhizoplane and soil, fungal and bacterial communities by high-throughput sequencing of internal transcribed spacer (ITS), and 16S rRNA gene in soil and rhizosphere of the susceptible almond hybrid rootstock GF-677 infested with Meloidogyne spp. The studied almond groves showed soil degradation by nematode assemblies and fungi:bacterial ratio. Fungal parasites of Meloidogyne eggs were found in 56.25% of the samples. However, the percentage of parasitized eggs by fungi ranged from 1% to 8%. Three fungal species were isolated from Meloidogyne eggs, specifically Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperellum. The diversity and composition of the microbial communities were more affected by the sample type (soil vs rhizosphere) and by the geographical location of the samples than by the Meloidogyne density, which could be explained by the vigorous hybrid rootstock GF-677 and a possible dilution effect. However, the saprotrophic function in the functional guilds of the fungal ASV was increased in the highly infected roots vs the low infected roots. These results indicate that the presence of biocontrol agents in almond fields and the development of new management strategies could increase their populations to control partially RKN infection levels.

Parasitism of Hirsutella rhossiliensis on Different Nematodes and Its Endophytism Promoting Plant Growth and Resistance against Root-Knot Nematodes

The endoparasitic fungus Hirsutella rhossiliensis is an important biocontrol agent of cyst nematodes in nature. To determine the potential parasitism of the fungus on a non-natural host, the pinewood nematode (Bursaphelenchus xylophilus) living in pine trees and the endophytic ability of the fungus on plants, in this paper, we first constructed and utilized a green fluorescent protein (GFP)-tagged H. rhossiliensis HR02 transformant to observe the fungal infection process on B. xylophilus and its colonization on Arabidopsis roots. Then, we compared the fungal parasitism on three species of nematodes with different lifestyles, and we found that the fungal parasitism is correlated with nematode species and stages. The parasitic effect of H. rhossiliensis on adults of B. xylophilus is similar to that on second-stage juveniles (J2) of the root-knot nematode Meloidogyne incognita after 24 h of inoculation, although the virulence of the fungus to second-stage juveniles of M. incognita is stronger than that to those of B. xylophilus and Caenorhabditis elegans. Moreover, the endophytism of H. rhossiliensis was confirmed. By applying an appropriate concentration of H. rhossiliensis conidial suspension (5 × 106 spores/mL) in rhizosphere soil, it was found that the endophytic fungus can promote A. thaliana growth and reproduction, as well as improve host resistance against M. incognita. Our results provide a deeper understanding of the fungus H. rhossiliensis as a promising biocontrol agent against plant-parasitic nematodes.

Chitosan Modulates Volatile Organic Compound Emission from the Biocontrol Fungus Pochonia chlamydosporia

Fungal volatile organic compounds (VOCs) are responsible for fungal odor and play a key role in biological processes and ecological interactions. VOCs represent a promising area of research to find natural metabolites for human exploitation. Pochonia chlamydosporia is a chitosan-resistant nematophagous fungus used in agriculture to control plant pathogens and widely studied in combination with chitosan. The effect of chitosan on the production of VOCs from P. chlamydosporia was analyzed using gas chromatography-mass spectrometry (GC-MS). Several growth stages in rice culture medium and different times of exposure to chitosan in modified Czapek-Dox broth cultures were analyzed. GC-MS analysis resulted in the tentative identification of 25 VOCs in the rice experiment and 19 VOCs in the Czapek-Dox broth cultures. The presence of chitosan in at least one of the experimental conditions resulted in the de novo production of 3-methylbutanoic acid and methyl 2,4-dimethylhexanoate, and oct-1-en-3-ol and tetradec-1-ene in the rice and Czapek-Dox experiments, respectively. Other VOCs changed their abundance because of the effect of chitosan and fungal age. Our findings suggest that chitosan can be used as a modulator of the production of VOCs in P. chlamydosporia and that there is also an effect of fungal age and exposure time.

Polydomus karssenii gen. nov. sp. nov. is a dark septate endophyte with a bifunctional lifestyle parasitising eggs of plant parasitic cyst nematodes (Heterodera spp.)

In this study fungal strains were investigated, which had been isolated from eggs of the cereal cyst nematode Heterodera filipjevi, and roots of Microthlaspi perfoliatum (Brassicaceae). The morphology, the interaction with nematodes and plants and the phylogenetic relationships of these strains originating from a broad geographic range covering Western Europe to Asia Minor were studied. Phylogenetic analyses using five genomic loci including ITSrDNA, LSUrDNA, SSUrDNA, rpb2 and tef1-α were carried out. The strains were found to represent a distinct phylogenetic lineage most closely related to Equiseticola and Ophiosphaerella, and Polydomus karssenii (Phaeosphaeriaceae, Pleosporales) is introduced here as a new species representing a monotypic genus. The pathogenicity tests against nematode eggs fulfilled Koch's postulates using in vitro nematode bioassays and showed that the fungus could parasitise its original nematode host H. filipjevi as well as the sugar beet cyst nematode H. schachtii, and colonise cysts and eggs of its hosts by forming highly melanised moniliform hyphae. Light microscopic observations on fungus-root interactions in an axenic system revealed the capacity of the same fungal strain to colonise the roots of wheat and produce melanised hyphae and microsclerotia-like structure typical for dark septate endophytes. Confocal laser scanning microscopy further demonstrated that the fungus colonised the root cells by predominant intercellular growth of hyphae, and frequent formation of appressorium-like as well as penetration peg-like structures through internal cell walls surrounded by callosic papilla-like structures. Different strains of the new fungus produced a nearly identical set of secondary metabolites with various biological activities including nematicidal effects irrespective of their origin from plants or nematodes.

Chitosan and nematophagous fungi for sustainable management of nematode pests

Plants are exposed to large number of threats caused by herbivores and pathogens which cause important losses on crops. Plant pathogens such as nematodes can cause severe damage and losses in food security crops worldwide. Chemical pesticides were extendedly used for nematode management. However, due to their adverse effects on human health and the environment, they are now facing strong limitations by regulatory organisations such as EFSA (European Food Safety Authority). Therefore, there is an urgent need for alternative and efficient control measures, such as biological control agents or bio-based plant protection compounds. In this scenario, chitosan, a non-toxic polymer obtained from seafood waste mainly, is becoming increasingly important. Chitosan is the N-deacetylated form of chitin. Chitosan is effective in the control of plant pests and diseases. It also induces plants defence mechanisms. Chitosan is also compatible with some biocontrol microorganisms mainly entomopathogenic and nematophagous fungi. Some of them are antagonists of nematode pests of plants and animals. The nematophagous biocontrol fungus Pochonia chlamydosporia has been widely studied for sustainable management of nematodes affecting economically important crops and for its capability to grow with chitosan as only nutrient source. This fungus infects nematode eggs using hyphal tips and appressoria. Pochonia chlamydosporia also colonizes plant roots endophytically, stimulating plant defences by induction of salicylic and jasmonic acid biosynthesis and favours plant growth and development. Therefore, the combined use of chitosan and nematophagous fungi could be a novel strategy for the biological control of nematodes and other root pathogens of food security crops.

Nematicidal Property of Clindamycin and 5-hydroxy-2-methyl Furfural (HMF) from the Banana Endophyte Bacillus velezensis (YEBBR6) Against Banana Burrowing Nematode Radopholus similis

Radopholus similis is a burrowing nematode which causes banana toppling disease and is of major economic threat for the banana production. Bacterial endophyte Bacillus velezensis (YEBBR6) produce biomolecules like 5-hydroxy-2-methyl furfural (HMF) and clindamycin in during interaction with Fusarium oxysporum f.sp. cubense. Molecular modelling and docking studies were performed on Radopholus similis protein targets such as calreticulin, cathepsin S-like cysteine proteinase, β-1,4 -endoglucanase, reticulocalbin, venom allergen-like protein and serine carboxypeptidase to understand the mode of action of HMF and clindamycin against Radopholus similis. Structurally validated protein targets of R. similis were docked with biomolecules through AutoDock Vina module in PyRx 0.8 software to predict the binding energy of ligand and target protein. Among the chosen six targets, docking analysis revealed that clindamycin had the maximum binding affinity for β-1,4-endoglucanase (- 7.2 kcal/mol), reticulocalbin (- 7.5 kcal/mol) and serine carboxypeptidase (- 6.9 kcal/mol) in comparison with HMF and the nematicide, carbofuran 3G. Besides, clindamycin also had the maximum binding energy for the target sites calreticulin and venom allergen-like protein compared to the small molecule HMF. Novel molecule, clindamycin produced by B. velezensis served as a potential inhibitor of the target sites associated in interrupting the functions of β-1,4-endoglucanase, reticulocalbin, serine carboxypeptidase, calreticulin, cathepsin S-like cysteine proteinase, and venom allergen-like proteins. Besides, increased binding affinity of clindamycin with the protein target sites facilitated to explore it as a novel nematicidal molecule for the management of banana burrowing nematode R. similis. Thus, present investigation confirmed that, the small molecules clindamycin can be explored for nematicidal activity.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-022-01011-2.

Production of Purpureocillium lilacinum and Pochonia chlamydosporia by Submerged Liquid Fermentation and Bioactivity against Tetranychus urticae and Heterodera glycines through Seed Inoculation

Pochoniachlamydosporia and Purpureocilliumlilacinum are fungal bioagents used for the sustainable management of plant parasitic nematodes. However, their production through submerged liquid fermentation and their use in seed treatment have been underexplored. Therefore, our goal was to assess the effect of different liquid media on the growth of 40 isolates of P. lilacinum and two of P. chlamydosporia. The most promising isolates tested were assessed for plant growth promotion and the control of the two-spotted spider mite (Tetranychus urticae) and the soybean cyst nematode (Heterodera glycines). Most isolates produced > 108 blastospores mL−1 and some isolates produced more than 104 microsclerotia mL−1. Microsclerotia of selected isolates were used to inoculate common bean (Phaseolus vulgaris L.) seeds in greenhouse trials. All fungal isolates reduced the T. urticae fecundity in inoculated plants through seed treatment, while P. chlamydosporia ESALQ5406 and P. lilacinum ESALQ2593 decreased cyst nematode population. Purpureocillium lilacinum was more frequently detected in soil, whereas P. chlamydosporia colonized all plant parts. Pochonia chlamydosporia ESALQ5406 improved the root development of bean plants. These findings demonstrate the possibility of producing submerged propagules of P. chlamydosporia and P. lilacinum by liquid culture, and greenhouse trials support the applicability of fungal microsclerotia in seed treatment to control P. vulgaris pests.

Pochonia chlamydosporia Isolate PC-170-Induced Expression of Marker Genes for Defense Pathways in Tomatoes Challenged by Different Pathogens

Pochonia chlamydosporia is a fungal parasite of nematode eggs. Studies have shown that some strains of Pochonia chlamydosporia can promote plant growth and induce plants’ systemic resistance to root-knot nematodes by colonizing in their roots. This study aimed to verify the effect of the PC-170 strain on tomato growth and systemic resistance. Split-root experiments were conducted to observe the systemic resistance induced by PC-170. To explore the defense pathway that was excited due to the colonization by PC-170, we tested the expression of marker genes for defense pathways, and used mutant lines to verify the role of plant defense pathways. Our results showed that PC-170 can colonize roots, and promotes growth. We found a role for jasmonic acid (JA) in modulating tomato colonization by PC-170. PC-170 can activate tomato defense responses to reduce susceptibility to infection by the root-knot nematode Meloidogyne incognita, and induced resistance to some pathogens in tomatoes. The marker genes of the defense pathway were significantly induced after PC-170 colonization. However, salicylic acid (SA)- and jasmonic acid (JA)-dependent defenses in roots were variable with the invasion of different pathogens. Defense pathways play different roles at different points in time. SA- and JA-dependent defense pathways were shown to cross-communicate. Different phytohormones have been involved in tomato plants’ responses against different pathogens. Our study confirmed that adaptive JA signaling is necessary to regulate PC-170 colonization and induce systemic resistance in tomatoes.

Fungal and Bacterial Endophytes as Microbial Control Agents for Plant-Parasitic Nematodes

Endophytes are symbiotic microorganisms that colonize plant tissues and benefit plants in multiple ways including induced systemic resistance to biotic and abiotic stresses. Endophytes can be sustainable alternatives to chemical nematicides and enhance plant health in a variety of cropping and natural environments. Several in vitro and in vivo studies demonstrated the potential of multiple species of Fusarium and Bacillus against plant-parasitic nematodes in horticultural, agricultural, and fodder crops and in forestry. While there were efforts to commercialize some of the endophytes as bionematicides, a lack of good formulations with consistent field efficacy has been a major hurdle in commercializing endophytes for nematode control. Identification of efficacious and environmentally resilient strains, a thorough understanding of their modes of action, interactions with various biotic and abiotic factors, and developing strategies that improve their effectiveness are critical areas to advance the commercialization of bionematicides based on fungal and bacterial endophytes.

Root Endophytism by Pochonia chlamydosporia Affects Defense-Gene Expression in Leaves of Monocot and Dicot Hosts under Multiple Biotic Interactions

A study was carried out on the effect of the root endophytic fungus Pochonia chlamydosporia on plant systemic signal of defense related genes during fungal or nematode parasitism. Different biotic stress factors were examined, inoculating roots of dicot and monocot hosts with the endophyte, and measuring the expression of defense genes in leaves. A first greenhouse assay was carried out on expression of PAL, PIN II, PR1 and LOX D in leaves of tomato cv Tondino inoculated with Phytophthora infestans (CBS 120920), inoculating or not the roots of infected plants with P. chlamydosporia DSM 26985. In a second assay, plants of banana (Musa acuminata cv Grand Naine) were artificially infected with Fusarium oxysporum f. sp. cubense Tropical race 4 (TR4) and inoculated or not with DSM 26985. In a further experiment, banana plants were inoculated or not with P. chlamydosporia plus juveniles of the root knot nematode (RKN) Meloidogyne incognita. A similar assay was also carried out in vitro with adults and juveniles of the lesion nematode Pratylenchus goodeyi. Differential expression of the defense genes examined was observed for all plant-stress associations, indicative of early, upward systemic signals induced by the endophyte. Changes in expression profiles included a 5-fold down-regulation of PIN II at 2 dai in leaves of tomato plants treated with P. infestans and/or P. chlamydosporia, and the up-regulation of PAL by the endophyte alone, at 2 and 7 dai. In the TR4 assay, PR1 was significantly up-regulated at 7 dai in banana leaves, but only in the P. chlamydosporia treated plants. At 10 dai, PIN II expression was significantly higher in leaves of plants inoculated only with TR4. The banana-RKN assay showed a PR1 expression significantly higher than controls at 4 and 7 dai in plants inoculated with P. chlamydosporia alone, and a down-regulation at 4 dai in leaves of plants also inoculated with RKN, with a PR1 differential up-regulation at 10 dai. Pratylenchus goodeyi down-regulated PIN at 21 dai, with or without the endophyte, as well as PAL but only in presence of P. chlamydosporia. When inoculated alone, the endophyte up-regulated PR1 and LOX. The gene expression patterns observed in leaves suggest specific and time-dependent relationships linking host plants and P. chlamydosporia in presence of biotic stress factors, functional to a systemic, although complex, activation of defense genes.

Putative LysM Effectors Contribute to Fungal Lifestyle

Fungal LysM effector proteins can dampen plant host–defence responses, protecting hyphae from plant chitinases, but little is known on these effectors from nonpathogenic fungal endophytes. We found four putative LysM effectors in the genome of the endophytic nematophagous fungus Pochonia chlamydosporia (Pc123). All four genes encoding putative LysM effectors are expressed constitutively by the fungus. Additionally, the gene encoding Lys1—the smallest one—is the most expressed in banana roots colonised by the fungus. Pc123 Lys1, 2 and 4 display high homology with those of other strains of the fungus and phylogenetically close entomopathogenic fungi. However, Pc123 Lys3 displays low homology with other fungi, but some similarities are found in saprophytes. This suggests evolutionary divergence in Pc123 LysM effectors. Additionally, molecular docking shows that the NAcGl binding sites of Pc123 Lys 2, 3 and 4 are adjacent to an alpha helix. Putative LysM effectors from fungal endophytes, such as Pc123, differ from those of plant pathogenic fungi. LysM motifs from endophytic fungi show clear conservation of cysteines in Positions 13, 51 and 63, unlike those of plant pathogens. LysM effectors could therefore be associated with the lifestyle of a fungus and give us a clue of how organisms could behave in different environments.

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.

Isolates of the Nematophagous Fungus Pochonia chlamydosporia Are Endophytic in Banana Roots and Promote Plant Growth

The biocontrol fungus Pochonia chlamydosporia colonizes banana roots endophytically. Root hairs and root surface were colonized by a stable GFP (green fluorescent protein) transformant of the fungus. Hyphal penetration in root cells was also observed. Spores of P. chlamydosporia 123, significantly increase root and leaf length and weight in banana plantlets (Musa acuminata cv. ‘Dwarf Cavendish’) in growth chamber experiments 30 days post-inoculation. In greenhouse 8-L pot experiments, P. chlamydosporia 123 spore inoculation significantly increases root, corm and leaf length, and leaf weight in banana plants (75 days post-inoculation). Spore inoculation of P. chlamydosporia strains from diverse origin (Pc21, Pc123, Pc399, and Pccat), significantly increase root, corm and leaf length and weight in banana plantlets. Pc21 from Italy was the best colonizer of banana roots. Consequently, this strain significantly increases banana root and leaf length most. Root colonization by P. chlamydosporia was also detected using cultural techniques and qPCR.

Volatile Organic Compounds from Entomopathogenic and Nematophagous Fungi, Repel Banana Black Weevil (Cosmopolites sordidus)

Fungal Volatile Organic Compounds (VOCs) repel banana black weevil (BW), Cosmopolites sordidus (Germar, 1824), the key-pest of banana [Musa sp. (Linnaeus, 1753)]. The entomopathogens Beauveria bassiana (Bb1TS11) and Metarhizium robertsii (Mr4TS04) were isolated from banana plantation soils using an insect bait. Bb1TS11 and Mr4TS04 were pathogenic to BW adults. Bb1TS11, Bb203 (from infected palm weevils), Mr4TS04 and the nematophagous fungus Pochonia clamydosporia (Pc123), were tested for VOCs production. VOCs were identified by Gas Chromatography/Mass Spectrometry-Solid-Phase Micro Extraction (GC/MS-SPME). GC/MS-SPME identified a total of 97 VOCs in all strains tested. Seven VOCs (styrene, benzothiazole, camphor, borneol, 1,3-dimethoxy-benzene, 1-octen-3-ol and 3-cyclohepten-1-one) were selected for their abundance or previous record as insect repellents. BW-starved adults in the dark showed the highest mobility to banana corm in olfactometry bioassays. 3-cyclohepten-1-one (C7), produced by all fungal strains, is the best BW repellent (p < 0.05), followed by 1,3-dimethoxy-benzene (C5). The rest of the VOCs have a milder repellency to BW. Styrene (C1) and benzothiazole (C2) (known to repel palm weevil) block the attraction of banana corm and BW pheromone to BW adults in bioassays. Therefore, VOCs from biocontrol fungi can be used in future studies for the biomanagement of BW in the field.

In Vitro Screening of a Culturable Soybean Cyst Nematode Cyst Mycobiome for Potential Biological Control Agents and Biopesticides

Fungal biological control of soybean cyst nematodes (SCN) is an important component of integrated pest management for soybean. However, very few fungal biological control agents are available in the market. In this study, we have screened fungi previously isolated from SCN cysts over 3 years from a long-term crop rotation field experiment for their ability to antagonize SCN using (i) parasitism, (ii) egg hatch inhibition, and (iii) J2 mortality. We evaluated egg parasitism using an in-vitro egg parasitism bioassays and scored parasitism using the egg parasitic index (EPI) and fluorescent microscopy. The ability of these fungi to produce metabolites causing egg hatch inhibition and J2 mortality was assessed in bioassays using filter-sterilized culture filtrates. We identified 10 high-performing isolates each for egg parasitism and toxicity toward SCN eggs and J2s and repeated the tests after storage for 1 year of cryopreservation at -80°C to validate the durability of biocontrol potential of the chosen 20 isolates. Although the parasitic ability changed slightly for the majority of strains after cryopreservation, they still scored 5/10 on EPI scales. There were no differences in the ability of fungi to produce antinemic metabolites after cryopreservation.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

In vivo infection of Bursaphelenchus xylophilus by the fungus Esteya vermicola

BACKGROUND

As the causal agent of pine wilt disease, Bursaphelenchus xylophilus, is a serious pathogen of forest pine trees. Esteya vermicola is a nematophagous fungus of B. xylophilus and exhibits great potential as a biological control agent. However, the in vivo infection mechanism of E. vermicola on B. xylophilus is unclear. Experiments were conducted to study the colonization of host plant and infection of B. xylophilus by E. vermicola inside pine tree xylem.

RESULTS

A green fluorescent protein (GFP)-tagged E. vermicola transformant was constructed as a biomarker to study the in vivo colonization and infection of B. xylophilus in pine trees. The in vitro infection of B. xylophilus by E. vermicola was observed through GFP expression. The bacilloid conidia produced by trophic hyphae in the body of the nematode are described. Additionally, the monitoring of in vivo colonization by GFP-tagged E. vermicola showed the germination and hyphal extension of this fungus after inoculation. Moreover, B. xylophilus infected by this biocontrol agent were extracted from healthy seedlings and observed in the xylem of trees that were wilting due to pine wilt disease.

CONCLUSION

Evidence of fungal colonization and infection of B. xylophilus by E. vermicola is provided to improve our understanding of the in vivo infection mechanisms used by this nematophagous fungus against B. xylophilus. The infection of B. xylophilus by E. vermicola was inferred to begin with the implantation of propagules, and this inference will require future investigation. The colonization of Esteya vermicola in host pine tree xylem and the in vivo infection of pinewood nematode by E. vermicola were investigated using the green fluorescence protein transformant. © 2020 Society of Chemical Industry.

Colonization of Beauveria bassiana 08F04 in root-zone soil and its biocontrol of cereal cyst nematode (Heterodera filipjevi)

Cereal cyst nematodes cause serious yield losses of wheat in Hunaghuai winter wheat growing region in China. Beauveria bassiana 08F04 isolated from the surface of cysts is a promising biological control agent for cereal cyst nematodes. As the colonization capacity is a crucial criteria to assess biocontrol effectiveness for a microbial agent candidate, we aimed to label B. bassiana 08F04 for efficient monitoring of colonization in the soil. The binary pCAM-gfp plasmid containing sgfp and hph was integrated into B. bassiana 08F04 using the Agrobacterium tumefaciens-mediated transformation. The transformation caused a significant change in mycelial and conidial yields, and in extracellular chitinase activity in some transformants. The cultural filtrates of some transformants also decreased acetylcholinesterase activity and the survival of Heterodera filipjevi second-stage juveniles relative to the wild-type strain. One transformant (G10) had a growth rate and biocontrol efficacy similar to the wild-type strain, so it was used for a pilot study of B. bassiana colonization conducted over 13 weeks. Real-time PCR results and CFU counts revealed that the population of G10 increased quickly over the first 3 weeks, then decreased slowly over the following 4 weeks before stabilizing. In addition, the application of wild-type B. bassiana 08F04 and transformant G10 significantly reduced the number of H. filipjevi females in roots by 64.4% and 60.2%, respectively. The results of this study have practical applications for ecological, biological and functional studies of B. bassiana 08F04 and for bionematicide registration.

Bacillus firmus Strain I-1582, a Nematode Antagonist by Itself and Through the Plant

Bacillus firmus I-1582 is approved in Europe for the management of Meloidogyne on vegetable crops. However, little information about its modes of action and temperature requirements is available, despite the effect of these parameters in its efficacy. The cardinal temperatures for bacterial growth and biofilm formation were determined. The bacteria was transformed with GFP to study its effect on nematode eggs and root colonization of tomato (Solanum lycopersicum) and cucumber (Cucumis sativus) by laser-scanning confocal microscopy. Induction of plant resistance was determined in split-root experiments and the dynamic regulation of genes related to jasmonic acid (JA) and salicylic acid (SA) by RT-qPCR at three different times after nematode inoculation. The bacteria was able to grow and form biofilms between 15 and 45°C; it degraded egg-shells and colonized eggs; it colonized tomato roots more extensively than cucumber roots; it induced systemic resistance in tomato, but not in cucumber; SA and JA related genes were primed at different times after nematode inoculation in tomato, but only the SA-related gene was up-regulated at 7 days after nematode inoculation in cucumber. In conclusion, B. firmus I-1582 is active at a wide range of temperatures; its optimal growth temperature is 35°C; it is able to degrade Meloidogyne eggs, and to colonize plant roots, inducing systemic resistance in a plant dependent species manner.

Pochonia chlamydosporia Induces Plant-Dependent Systemic Resistance to Meloidogyne incognita

Meloidogyne spp. are the most damaging plant parasitic nematodes for horticultural crops worldwide. Pochonia chlamydosporia is a fungal egg parasite of root-knot and cyst nematodes able to colonize the roots of several plant species and shown to induce plant defense mechanisms in fungal-plant interaction studies, and local resistance in fungal-nematode-plant interactions. This work demonstrates the differential ability of two out of five P. chlamydosporia isolates, M10.43.21 and M10.55.6, to induce systemic resistance against M. incognita in tomato but not in cucumber in split-root experiments. The M10.43.21 isolate reduced infection (32-43%), reproduction (44-59%), and female fecundity (14.7-27.6%), while the isolate M10.55.6 only reduced consistently nematode reproduction (35-47.5%) in the two experiments carried out. The isolate M10.43.21 induced the expression of the salicylic acid pathway (PR-1 gene) in tomato roots 7 days after being inoculated with the fungal isolate and just after nematode inoculation, and at 7 and 42 days after nematode inoculation too. The jasmonate signaling pathway (Lox D gene) was also upregulated at 7 days after nematode inoculation. Thus, some isolates of P. chlamydosporia can induce systemic resistance against root-knot nematodes but this is plant species dependent.

Time-dependent effects of Pochonia chlamydosporia endophytism on gene expression profiles of colonized tomato roots

A transcriptome analysis was produced from tomato roots inoculated with the hyphomycete Pochonia chlamydosporia at three different times. Gene expression data were also yielded from fungus grown in vitro or endophytic. A next-generation sequencing (NGS) and network analysis approach were applied. We identified 3.676 differentially expressed tomato genes (DEG), highlighting a core of 93 transcripts commonly down- or upregulated at every time point, shedding light on endophytism process. Functional categories related to plant information-processing system, which recognizes, percepts, and transmits signals, were associated with gene upregulated early in time, with higher representations in processes such as plant defense regulation later in time. Network analysis of a DEG subset showed dominance of MAP kinase hubs in the uninoculated control samples, replaced by an increased centrality of WRKY transcription factor and ETR-ethylene response factor genes in the colonized roots. Fungus genes expressed during progression of plant colonization, therefore related to the host colonization process or endophytism persistence, were also identified. Data provided a high-resolution insight on tomato transcriptome changes as induced by endophytism, highlighting a specific modulation of stress-responsive transcripts, related to a selective activation of defense pathways, likely required by the fungus to establish a persistent endophytic lifestyle.

Consortium of five fungal isolates conditioning root growth and arbuscular mycorrhiza in soybean, corn, and sugarcane

Plant growth and arbuscular mycorrhizal colonization were studied in sugarcane, corn and soybean by applying five plant growth promoting fungi: Beauveria bassiana, Metarhizium anisopliae, Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperella. Sugarcane, corn and soybean were grown in pots under two treatments: (1) inoculation with the fungal consortium and (2) control without inoculation. In the inoculated treatment, fungal spore suspension were applied to the seeds and shoots were sprayed every 28 days. Means were analyzed by analysis of variance and Tukey's test at 5% probability level. The experiment was arranged in a completely randomized design, with six replications. Fungi consortium mediate root growth in soybean and corn, and arbuscular mycorrhizal colonization in soybean and sugarcane. These findings are probably caused by the fungi producing phytohormones and inducing the plants to synthesize phytohormones: auxins for root growth; and jasmonic, abscisic, and salicylic acids with a role in the regulation of mycorrhizal colonization. These effects are important when seeking conservation strategies in agriculture and livestock production, since Fungi consortium can better mediate soil resource acquisition, promoting greater absorption of nutrients and water.

Expression and specificity of a chitin deacetylase from the nematophagous fungus Pochonia chlamydosporia potentially involved in pathogenicity

Chitin deacetylases (CDAs) act on chitin polymers and low molecular weight oligomers producing chitosans and chitosan oligosaccharides. Structurally-defined, partially deacetylated chitooligosaccharides produced by enzymatic methods are of current interest as bioactive molecules for a variety of applications. Among Pochonia chlamydosporia (Pc) annotated CDAs, gene pc_2566 was predicted to encode for an extracellular CE4 deacetylase with two CBM18 chitin binding modules. Chitosan formation during nematode egg infection by this nematophagous fungus suggests a role for their CDAs in pathogenicity. The P. chlamydosporia CDA catalytic domain (PcCDA) was expressed in E. coli BL21, recovered from inclusion bodies, and purified by affinity chromatography. It displays deacetylase activity on chitooligosaccharides with a degree of polymerization (DP) larger than 3, generating mono- and di-deacetylated products with a pattern different from those of closely related fungal CDAs. This is the first report of a CDA from a nematophagous fungus. On a DP5 substrate, PcCDA gave a single mono-deacetylated product in the penultimate position from the non-reducing end (ADAAA) which was then transformed into a di-deacetylated product (ADDAA). This novel deacetylation pattern expands our toolbox of specific CDAs for biotechnological applications, and will provide further insights into the determinants of substrate specificity in this family of enzymes.

Induction of auxin biosynthesis and WOX5 repression mediate changes in root development in Arabidopsis exposed to chitosan

Chitosan is a natural polymer with applications in agriculture, which causes plasma membrane permeabilisation and induction of intracellular reactive oxygen species (ROS) in plants. Chitosan has been mostly applied in the phylloplane to control plant diseases and to enhance plant defences, but has also been considered for controlling root pests. However, the effect of chitosan on roots is virtually unknown. In this work, we show that chitosan interfered with auxin homeostasis in Arabidopsis roots, promoting a 2-3 fold accumulation of indole acetic acid (IAA). We observed chitosan dose-dependent alterations of auxin synthesis, transport and signalling in Arabidopsis roots. As a consequence, high doses of chitosan reduce WOX5 expression in the root apical meristem and arrest root growth. Chitosan also propitiates accumulation of salicylic (SA) and jasmonic (JA) acids in Arabidopsis roots by induction of genes involved in their biosynthesis and signalling. In addition, high-dose chitosan irrigation of tomato and barley plants also arrests root development. Tomato root apices treated with chitosan showed isodiametric cells respect to rectangular cells in the controls. We found that chitosan causes strong alterations in root cell morphology. Our results highlight the importance of considering chitosan dose during agronomical applications to the rhizosphere.

Identification of tomato miRNAs responsive to root colonization by endophytic Pochonia chlamydosporia

The molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots. Their predicted target genes are involved in the plant information processing system, which recognizes, percepts, and transmits signals, with higher representations in processes such as apoptosis and plant defense regulation. RNAseq data showed that predicted miRNA target genes were downregulated in tomato roots after 4, 7, 10, and 21 days post P. chlamydosporia inoculation. The differential expression of four miRNAs was further validated using qPCR analysis. The P. chlamydosporia endophytic lifestyle in tomato roots included an intricate network of miRNAs and targets. Data provide a first platform of DE tomato miRNAs after P. chlamydosporia colonization. They indicated that several miRNAs are involved in the host response to the fungus, playing important roles for its recognition as a symbiotic microorganism, allowing endophytism by modulating the host defense reaction. Data also indicated that endophytism affects tRNA fragmentation. This is the first study on miRNAs induced by P. chlamydosporia endophytism and related development regulation effects in Solanum lycopersicum.

Chitosan Increases Tomato Root Colonization by Pochonia chlamydosporia and Their Combination Reduces Root-Knot Nematode Damage

The use of biological control agents could be a non-chemical alternative for management of Meloidogyne spp. [root-knot nematodes (RKN)], the most damaging plant-parasitic nematodes for horticultural crops worldwide. Pochonia chlamydosporia is a fungal parasite of RKN eggs that can colonize endophytically roots of several cultivated plant species, but in field applications the fungus shows a low persistence and efficiency in RKN management. The combined use of P. chlamydosporia with an enhancer could help its ability to develop in soil and colonize roots, thereby increasing its efficiency against nematodes. Previous work has shown that chitosan enhances P. chlamydosporia sporulation and production of extracellular enzymes, as well as nematode egg parasitism in laboratory bioassays. This work shows that chitosan at low concentrations (up to 0.1 mg ml-1) do not affect the viability and germination of P. chlamydosporia chlamydospores and improves mycelial growth respect to treatments without chitosan. Tomato plants irrigated with chitosan (same dose limit) increased root weight and length after 30 days. Chitosan irrigation increased dry shoot and fresh root weight of tomato plants inoculated with Meloidogyne javanica, root length when they were inoculated with P. chlamydosporia, and dry shoot weight of plants inoculated with both P. chlamydosporia and M. javanica. Chitosan irrigation significantly enhanced root colonization by P. chlamydosporia, but neither nematode infection per plant nor fungal egg parasitism was affected. Tomato plants cultivated in a mid-suppressive (29.3 ± 4.7% RKN egg infection) non-sterilized clay loam soil and irrigated with chitosan had enhanced shoot growth, reduced RKN multiplication, and disease severity. Chitosan irrigation in a highly suppressive (73.7 ± 2.6% RKN egg infection) sterilized-sandy loam soil reduced RKN multiplication in tomato. However, chitosan did not affect disease severity or plant growth irrespective of soil sterilization. Chitosan, at an adequate dose, can be a potential tool for sustainable management of RKN.

Arabidopsis thaliana root colonization by the nematophagous fungus Pochonia chlamydosporia is modulated by jasmonate signaling and leads to accelerated flowering and improved yield

Pochonia chlamydosporia has been intensively studied in nematode control of different crops. We have investigated the interaction between P. chlamydosporia and the model system Arabidopsis thaliana under laboratory conditions in the absence of nematodes. This study demonstrates that P. chlamydosporia colonizes A. thaliana. Root colonization monitored with green fluorescent protein-tagged P. chlamydosporia and quantitative PCR (qPCR) quantitation methods revealed root cell invasion. Fungal inoculation reduced flowering time and stimulated plant growth, as determined by total FW increase, faster development of inflorescences and siliques, and a higher yield in terms of seed production per plant. Precocious flowering was associated with significant expression changes in key flowering-time genes. In addition, we also provided molecular and genetic evidence that point towards jasmonate signaling as an important factor to modulate progression of plant colonization by the fungus. Our results indicate that P. chlamydosporia provides benefits to the plant in addition to its nematophagous activity. This report highlights the potential of P. chlamydosporia to improve yield in economically important crops.

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.

Mechanisms Involved in Nematode Control by Endophytic Fungi

Colonization of plants by particular endophytic fungi can provide plants with improved defenses toward nematodes. Evidently, such endophytes can be important in developing more sustainable agricultural practices. The mechanisms playing a role in this quantitative antagonism are poorly understood but most likely multifactorial. This knowledge gap obstructs the progress regarding the development of endophytes or endophyte-derived constituents into biocontrol agents. In part, this may be caused by the fact that endophytic fungi form a rather heterogeneous group. By combining the knowledge of the currently characterized antagonistic endophytic fungi and their effects on nematode behavior and biology with the knowledge of microbial competition and induced plant defenses, the various mechanisms by which this nematode antagonism operates or may operate are discussed. Now that new technologies are becoming available and more accessible, the currently unresolved mechanisms can be studied in greater detail than ever before.

Chitosan enhances parasitism of Meloidogyne javanica eggs by the nematophagous fungus Pochonia chlamydosporia

Pochonia chlamydosporia (Pc), a nematophagous fungus and root endophyte, uses appressoria and extracellular enzymes, principally proteases, to infect the eggs of plant parasitic nematodes (PPN). Unlike other fungi, Pc is resistant to chitosan, a deacetylated form of chitin, used in agriculture as a biopesticide to control plant pathogens. In the present work, we show that chitosan increases Meloidogyne javanica egg parasitism by P. chlamydosporia. Using antibodies specific to the Pc enzymes VCP1 (a subtilisin), and SCP1 (a serine carboxypeptidase), we demonstrate chitosan elicitation of the fungal proteases during the parasitic process. Chitosan increases VCP1 immuno-labelling in the cell wall of Pc conidia, hyphal tips of germinating spores, and in appressoria on infected M. javanica eggs. These results support the role of proteases in egg parasitism by the fungus and their activation by chitosan. Phylogenetic analysis of the Pc genome reveals a large diversity of subtilisins (S8) and serine carboxypeptidases (S10). The VCP1 group in the S8 tree shows evidence of gene duplication indicating recent adaptations to nutrient sources. Our results demonstrate that chitosan enhances Pc infectivity of nematode eggs through increased proteolytic activities and appressoria formation and might be used to improve the efficacy of M. javanica biocontrol.

Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response

Plant crop yields are negatively conditioned by a large set of biotic and abiotic factors. An alternative to mitigate these adverse effects is the use of fungal biological control agents and endophytes. The egg-parasitic fungus Pochonia chlamydosporia has been traditionally studied because of its potential as a biological control agent of plant-parasitic nematodes. This fungus can also act as an endophyte in monocot and dicot plants, and has been shown to promote plant growth in different agronomic crops. An Affymetrix 22K Barley GeneChip was used in this work to analyze the barley root transcriptomic response to P. chlamydosporia root colonization. Functional gene ontology (GO) and gene set enrichment analyses showed that genes involved in stress response were enriched in the barley transcriptome under endophytism. An 87.5% of the probesets identified within the abiotic stress response group encoded heat shock proteins. Additionally, we found in our transcriptomic analysis an up-regulation of genes implicated in the biosynthesis of plant hormones, such as auxin, ethylene and jasmonic acid. Along with these, we detected induction of brassinosteroid insensitive 1-associated receptor kinase 1 (BR1) and other genes related to effector-triggered immunity (ETI) and pattern-triggered immunity (PTI). Our study supports at the molecular level the growth-promoting effect observed in plants endophytically colonized by P. chlamydosporia, which opens the door to further studies addressing the capacity of this fungus to mitigate the negative effects of biotic and abiotic factors on plant crops.

Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales

Background

The fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales.

Results

The complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae.

Conclusions

We present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0341-8) contains supplementary material, which is available to authorized users.

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.