Endosymbiotic bacteria within the nematode-trapping fungus Arthrobotrys musiformis and their potential roles in nitrogen cycling

Endosymbiotic bacteria (ESB) have important effects on their hosts, contributing to its growth, reproduction and biological functions. Although the effects of exogenous bacteria on the trap formation of nematode-trapping fungi (NTF) have been revealed, the effects of ESB on NTF remain unknown. In this study, we investigated the species diversity of ESB in the NTF Arthrobotrys musiformis using high-throughput sequencing and culture-dependent approaches, and compared bacterial profiles to assess the effects of strain source and culture media on A. musiformis. PICRUSt2 and FAPROTAX were used to predict bacterial function. Our study revealed that bacterial communities in A. musiformis displayed high diversity and heterogeneity, with Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the dominant phyla. The ESB between A. musiformis groups isolated from different habitats and cultured in the same medium were more similar to each other than the other groups isolated from the same habitat but cultured in different media. Function analysis predicted a broad and diverse functional repertoire of ESB in A. musiformis, and unveiled that ESB have the potential to function in five modules of the nitrogen metabolism. We isolated nitrogen-fixing and denitrifying bacteria from the ESB and demonstrated their effects on trap formation of A. musiformis. Among seven bacteria that we tested, three bacterial species Bacillus licheniformis, Achromobacter xylosoxidans and Stenotrophomonas maltophilia were found to be efficient in inducing trap formation. In conclusion, this study revealed extensive ESB diversity within NTF and demonstrated that these bacteria likely play important roles in nitrogen cycling, including nematode trap formation.

2-Furoic acid associated with the infection of nematodes by Dactylellina haptotyla and its biocontrol potential on plant root-knot nematodes

Dactylellina haptotyla is a typical nematode-trapping fungus that has garnered the attention of many scholars for its highly effective lethal potential for nematodes. Secondary metabolites play an important role in D. haptotyla-nematode interactions, but which metabolites perform which function remains unclear. We report the metabolic functions based on high-quality, chromosome-level genome assembly of wild D. haptotyla YMF1.03409. The results indicate that a large variety of secondary metabolites and their biosynthetic genes were significantly upregulated during the nematode-trapping stage. In parallel, we identified that 2-furoic acid was specifically produced during nematode trapping by D. haptotyla YMF1.03409 and isolated it from fermentation production. 2-Furoic acid demonstrated strong nematicidal activity with an LD50 value of 55.05 µg/mL against Meloidogyne incognita at 48 h. Furthermore, the pot experiment showed that the number of galls of tomato root was significantly reduced in the experimental group treated with 2-furoic acid. The considerable increase in the 2-furoic acid content during the infection process and its virulent nematicidal activity revealed an essential synergistic effect during the process of nematode-trapping fungal infection. IMPORTANCE Dactylellina haptotyla have significant application potential in nematode biocontrol. In this study, we determined the chromosome-level genome sequence of D. haptotyla YMF1.03409 by long-read sequencing technology. Comparative genomic analysis identified a series of pathogenesis-related genes and revealed significant gene family contraction events during the evolution of D. haptotyla YMF1.03409. Combining transcriptomic and metabolomic data as well as in vitro activity test results, a compound with important application potential in nematode biocontrol, 2-furoic acid, was identified. Our result expanded the genetic resource of D. haptotyla and identified a previously unreported nematicidal small molecule, which provides new options for the development of plant biocontrol agents.

AfLaeA, a Global Regulator of Mycelial Growth, Chlamydospore Production, Pathogenicity, Secondary Metabolism, and Energy Metabolism in the Nematode-Trapping Fungus Arthrobotrys flagrans

Arthrobotrys flagrans (Duddingtonia flagrans) is a typical nematode-trapping fungus which has been used for nematode biocontrol. The global regulator LaeA is widely distributed in filamentous fungi and plays a crucial role in secondary metabolism and development in addition to pathogenicity in fungal pathogens. In this study, the chromosome-level genome of A. flagrans CBS 565.50 was sequenced and homologous sequences of LaeA were identified in A. flagrans. A. flagrans LaeA (AfLaeA) knockout resulted in slower hyphal growth and a smoother hyphal surface. Importantly, deletion of AfLaeA resulted in the absence of chlamydospores and attenuated glycogen and lipid accumulation in hyphae. Similarly, disruption of the AfLaeA gene led to fewer traps and electron-dense bodies, lower protease activity, and a delay in capturing nematodes. The AfLaeA gene had a large effect on the secondary metabolism of A. flagrans, and both the deletion and overexpression of AfLaeA could yield new compounds, whereas some compounds were lost due to the absence of the AfLaeA. Protein-protein interactions between AfLaeA and another eight proteins were detected. Furthermore, transcriptome data analysis showed that 17.77% and 35.51% of the genes were influenced by the AfLaeA gene on days 3 and 7, respectively. AfLaeA gene deletion resulted in the higher expression level of the artA gene cluster, and multiple differentially expressed genes involved in glycogen and lipid synthesis and metabolism showed opposite expression patterns in wild-type and ΔAfLaeA strains. In summary, our results provide novel insights into the functions of AfLaeA in mycelial growth, chlamydospore production, pathogenicity, secondary metabolism, and energy metabolism in A. flagrans. IMPORTANCE The regulation of biological functions, such as the secondary metabolism, development, and pathogenicity of LaeA, has been reported in multiple fungi. But to date, no study on LaeA in nematode-trapping fungi has been reported. Moreover, it has not been investigated whether or not LaeA is involved in energy metabolism and chlamydospore formation has not been investigated. Especially in the formation mechanism of chlamydospores, several transcription factors and signaling pathways are involved in the production of chlamydospores, but the mechanism of chlamydospore formation from an epigenetic perspective has not been revealed. Concurrently, an understanding of protein-protein interactions will provide a broader perspective on the regulatory mechanism of AfLaeA in A. flagrans. This finding is critical for understanding the regulatory role of AfLaeA in the biocontrol fungus A. flagrans and establishes a foundation for developing high-efficiency nematode biocontrol agents.

Conidia Fusion: A Mechanism for Fungal Adaptation to Nutrient-Poor Habitats

Conidia fusion (CF) is a commonly observed structure in fungi. However, it has not been systematically studied. This study examined 2457 strains of nematode-trapping fungi (NTF) to explore the species specificity, physiological period, and physiological significance of CF. The results demonstrated that only six species of Arthrobotrys can form CF among the sixty-five tested NTF species. The studies on the model species Arthrobotrys oligospora (DL228) showed that CF occurred in both shed and unshed plus mature and immature conidia. Additionally, the conidia fusion rate (CFR) increased significantly with the decrease of nutrient concentration in habitats. The studies on the conidia fusion body (CFB) produced by A. oligospora (DL228) revealed that the more conidia contained in the CFB, the faster and denser the mycelia of the CFB germinated in weak nutrient medium and soil plates. On the one hand, rapid mycelial extension is beneficial for the CFB to quickly find new nutrient sources in habitats with uneven nutrient distribution. On the other hand, dense mycelium increases the contact area with the environment, improving the nutrient absorption efficiency, which is conducive to improving the survival rate of conidia in the weak nutrient environment. In addition, all species that form CF produce smaller conidia. Based on this observation, CF may be a strategy to balance the defects (nutrient deficiency) caused by conidia miniaturization.

Function discovery of a non-ribosomal peptide synthetase-like encoding gene in the nematode-trapping fungus Arthrobotrys oligospora

In this study, the function of a non-ribosomal peptide synthetase-like (NRPS-like) encoding gene AOL_s00188g306 (g306) was investigated to reveal the association between NRPS and nematocidal activity in the nematode-trapping fungus Arthrobotrys oligospora. Sequence analysis indicated that the encoded product of g306 is an adenylation domain of non-ribosomal peptide synthetases and extended short-chain dehydrogenase/reductase domain-containing proteins, and displays a wide substrate spectrum. The Δg306 mutants were more sensitive to chemical stressors than the wild type. Disruption of g306 impeded the nematocidal efficiency of A. oligospora. Metabolomics analysis showed that secondary metabolite biosynthesis and lipid metabolism were altered in the mutants. The phenotypic changes in the mutants can be attributed to the down-regulation of various metabolites, including fatty acyls, prenol lipids, steroidsand steroid derivative, and amino acid derivatives, identified in the present study. This study investigated the association between the non-ribosomal polypeptide-encoding gene g306 and nematicidal activity in A. oligospora, providing a reference for resolving the predation mechanism of nematode-trapping fungus.

Arthrobotrys blastospora sp. nov. (Orbiliomycetes): A Living Fossil Displaying Morphological Traits of Mesozoic Carnivorous Fungi

The evolution of carnivorous fungi in deep time is still poorly understood as their fossil record is scarce. The approximately 100-million-year-old Cretaceous Palaeoanellus dimorphus is the earliest fossil of carnivorous fungi ever discovered. However, its accuracy and ancestral position has been widely questioned because no similar species have been found in modern ecosystems. During a survey of carnivorous fungi in Yunnan, China, two fungal isolates strongly morphologically resembling P. dimorphus were discovered and identified as a new species of Arthrobotrys (Orbiliaceae, Orbiliomycetes), a modern genus of carnivorous fungi. Phylogenetically, Arthrobotrys blastospora sp. nov. forms a sister lineage to A. oligospora. A. blastospora catches nematodes with adhesive networks and produces yeast-like blastospores. This character combination is absent in all other previously known modern carnivorous fungi but is strikingly similar to the Cretaceous P. dimorphus. In this paper, we describe A. blastospora in detail and discuss its relationship to P. dimorphus.

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.

Small-secreted proteins as virulence factors in nematode-trapping fungi

Nematode-trapping fungi (NTF), such as Arthrobotrys flagrans (Duddingtonia flagrans), are soil-borne fungi able to form adhesive trapping networks to attract and catch nematodes. In this forum piece we highlight some of their most fascinating features with a special focus on the role of small-secreted proteins in the predatory interaction.

The STRIPAK component SipC is involved in morphology and cell-fate determination in the nematode-trapping fungus Duddingtonia flagrans

The striatin-interacting phosphatase and kinase (STRIPAK) complex is a highly conserved eukaryotic signaling hub involved in the regulation of many cellular processes. In filamentous fungi, STRIPAK controls multicellular development, hyphal fusion, septation, and pathogenicity. In this study, we analyzed the role of the STRIPAK complex in the nematode-trapping fungus Duddingtonia flagrans which forms three-dimensional, adhesive trapping networks to capture Caenorhabditis elegans. Trap networks consist of several hyphal loops which are morphologically and functionally different from vegetative hyphae. We show that lack of the STRIPAK component SipC (STRIP1/2/HAM-2/PRO22) results in incomplete loop formation and column-like trap structures with elongated compartments. The misshapen or incomplete traps lost their trap identity and continued growth as vegetative hyphae. The same effect was observed in the presence of the actin cytoskeleton drug cytochalasin A. These results could suggest a link between actin and STRIPAK complex functions.

Pathogenicity and Volatile Nematicidal Metabolites from Duddingtonia flagrans against Meloidogyne incognita

Plant parasitic nematodes, especially parasitic root-knot nematodes, are one of the most destructive plant pathogens worldwide. The control of plant root-knot nematodes is extremely challenging. Duddingtonia flagrans is a type of nematode-trapping fungi (NTF), which produces three-dimensional adhesive networks to trap nematodes. In this study, the pathogenicity and volatile organic compounds (VOCs) of the NTF D. flagrans against the plant root-knot nematode, Meloidogyne incognita, were investigated. The predatory process of D. flagrans trapping M. incognita was observed using scanning electron microscopy. Gas chromatography-mass spectrometry analysis of the VOCs from D. flagrans led to the identification of 52 metabolites, of which 11 main compounds were tested individually for their activity against M. incognita. Three compounds, cyclohexanamine, cyclohexanone, and cyclohexanol, were toxic to M. incognita. Furthermore, these three VOCs inhibited egg hatching of M. incognita. Cyclohexanamine showed the highest nematicidal activity, which can cause 97.93% mortality of M. incognita at 8.71 µM within 12 h. The number of hatched juveniles per egg mass after 3 days was just 8.44 when treated with 26.14 µM cyclohexanamine. This study is the first to demonstrate the nematicidal activity of VOCs produced by D. flagrans against M. incognita, which indicates that D. flagrans has the potential to biocontrol plant root-knot nematodes.

Prey sensing and response in a nematode-trapping fungus is governed by the MAPK pheromone response pathway

Detection of surrounding organisms in the environment plays a major role in the evolution of interspecies interactions, such as predator-prey relationships. Nematode-trapping fungi (NTF) are predators that develop specialized trap structures to capture, kill, and consume nematodes when food sources are limited. Despite the identification of various factors that induce trap morphogenesis, the mechanisms underlying the differentiation process have remained largely unclear. Here, we demonstrate that the highly conserved pheromone-response MAPK pathway is essential for sensing ascarosides, a conserved molecular signature of nemaotdes, and is required for the predatory lifestyle switch in the NTF Arthrobotrys oligospora. Gene deletion of STE7 (MAPKK) and FUS3 (MAPK) abolished nematode-induced trap morphogenesis and conidiation and impaired the growth of hyphae. The conserved transcription factor Ste12 acting downstream of the pheromone-response pathway also plays a vital role in the predation of A. oligospora. Transcriptional profiling of a ste12 mutant identified a small subset of genes with diverse functions that are Ste12 dependent and could trigger trap differentiation. Our work has revealed that A. oligospora perceives and interprets the ascarosides produced by nematodes via the conserved pheromone signaling pathway in fungi, providing molecular insights into the mechanisms of communication between a fungal predator and its nematode prey.

Forward genetic screens identified mutants with defects in trap morphogenesis in the nematode-trapping fungus Arthrobotrys oligospora

Nematode-trapping fungi (NTF) are carnivorous fungi that prey on nematodes under nutrient-poor conditions via specialized hyphae that function as traps. The molecular mechanisms involved in the interactions between NTF and their nematode prey are largely unknown. In this study, we conducted forward genetic screens to identify potential genes and pathways that are involved in trap morphogenesis and predation in the NTF Arthrobotrys oligospora. Using Ethyl methanesulfonate and UV as the mutagens, we generated 5552 randomly mutagenized A. oligospora strains and identified 15 mutants with strong defects in trap morphogenesis. Whole-genome sequencing and bioinformatic analyses revealed mutations in genes with roles in signaling, transcription or membrane transport that may contribute to the defects of trap morphogenesis in these mutants. We further conducted functional analyses on a candidate gene, YBP-1, and demonstrate that mutation of that gene was causative of the phenotypes observed in one of the mutants. The methods established in this study might provide helpful insights for establishing forward genetic screening methods for other non-model fungal species.

Polyketide Synthase-Terpenoid Synthase Hybrid Pathway Regulation of Trap Formation through Ammonia Metabolism Controls Soil Colonization of Predominant Nematode-Trapping Fungus

Polyketide synthase-terpenoid synthase (PKS-TPS) hybrid pathways for biosynthesis of unique sesquiterpenyl epoxy-cyclohexenoids (SECs) have been found to be widely distributed in plant pathogenic fungi. However, the natural and ecological functions of these pathways and their metabolites still remain cryptic. In this study, the whole PKS-TPS hybrid pathway in the predominant nematode-trapping fungus Arthrobotrys oligospora was first proposed according to all the intermediates and their derivatives from all the A. oligospora mutants with a deficiency in each gene involved in SEC biosynthesis. Most mutants displayed significantly increased trap formation which was correlated with alteration of the ammonia level. Further analysis revealed that the main metabolites involved in ammonia metabolism were largely increased in most mutants. However, significantly retarded colonization in soil were observed in most mutants compared to the wild-type strain due to significantly decreased antibacterial activities. Our results suggested that A. oligospora used the PKS-TPS hybrid pathway for fungal soil colonization via decreasing fungal nematode-capturing ability. This also provided solid evidence that boosting fungal colonization in soil was the secondary metabolite whose biosynthesis depended on a PKS-TPS hybrid pathway.

Laboratory Maintenance and Culturing of the Nematode-Trapping Fungus Arthrobotrys oligospora

Nematode-trapping fungi (NTF) and nematodes are common and sympatric in nature. The molecular basis that underlies this interkingdom predator-prey interaction remains largely uncharacterized. Both NTF and nematodes can be easily isolated from soil samples. NTF do not form traps in nutrient-rich environments, yet trap morphogenesis can be observed under nutrient-poor conditions and upon simultaneous sensing of the nematode cues. Here, we present protocols for laboratory maintenance and culturing of the model NTF Arthrobotrys oligospora. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Growth of nematode-trapping fungi on solid medium Basic Protocol 2: Growth of nematode-trapping fungi in liquid medium Basic Protocol 3: Collection of conidia from solid medium Support Protocol 1: Preparation of Miracloth filter funnel Basic Protocol 4: Induction of trap morphogenesis Alternate Protocol: Quantitative measurement of trap induction Support Protocol 2: Preparation of synchronized C. elegans L4 Basic Protocol 5: Establishing C. elegans survival rate upon exposure to A. oligospora Basic Protocol 6: Storage of nematode-trapping fungi strains.

Morphological and molecular characterization of Orbilia pseudopolybrocha and O. tonghaiensis, two new species of Orbiliaceae from China

This study examined over 20 fungal specimens of the Orbiliaceae (Orbiliomycetes) from different regions in China. Our analyses based on morphological traits and the ITS rDNA sequences revealed two new Orbilia species with drechslerella-like asexual morphs. These new species are able to trap nematodes with constricting rings. In addition, Orbilia cf. orientalis is reported as a new cryptic Chinese variant of European collections of O. orientalis. All three species are described and illustrated in detail in this paper. Their phylogenetic relationships with other orbiliaceous species were identified based on their ITS sequences.

Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi

Nematode-trapping fungi (NTF) are a group of specialized microbial predators that consume nematodes when food sources are limited. Predation is initiated when conserved nematode ascaroside pheromones are sensed, followed by the development of complex trapping devices. To gain insights into the coevolution of this interkingdom predator-prey relationship, we investigated natural populations of nematodes and NTF that we found to be ubiquitous in soils. Arthrobotrys species were sympatric with various nematode species and behaved as generalist predators. The ability to sense prey among wild isolates of Arthrobotrys oligospora varied greatly, as determined by the number of traps after exposure to Caenorhabditis elegans While some strains were highly sensitive to C. elegans and the nematode pheromone ascarosides, others responded only weakly. Furthermore, strains that were highly sensitive to the nematode prey also developed traps faster. The polymorphic nature of trap formation correlated with competency in prey killing, as well as with the phylogeny of A. oligospora natural strains, calculated after assembly and annotation of the genomes of 20 isolates. A chromosome-level genome assembly and annotation were established for one of the most sensitive wild isolates, and deletion of the only G-protein β-subunit-encoding gene of A. oligospora nearly abolished trap formation. In summary, our study establishes a highly responsive A. oligospora wild isolate as a model strain for the study of fungus-nematode interactions and demonstrates that trap formation is a fitness character in generalist predators of the nematode-trapping fungus family.

Nematode-Trapping Fungi Produce Diverse Metabolites during Predator-Prey Interaction

Nematode-trapping fungi are natural antagonists of nematodes. These predatory fungi are capable of switching their lifestyle from a saprophytic to predatory stage in the presence of nematodes by developing specialized trapping devices to capture and consume nematodes. The biochemical mechanisms of such predator–prey interaction have become increasingly studied given the potential application of nematode-trapping fungi as biocontrol agents, but the involved fungal metabolites remain underexplored. Here, we report a comprehensive liquid–chromatography mass spectrometry (LC–MS) metabolomics study on one hundred wild isolates of nematode-trapping fungi in three different species, Arthrobotrysoligospora, Arthrobotrys thaumasia, and Arthrobotrys musiformis. Molecular networking analysis revealed that the fungi were capable of producing thousands of metabolites, and such chemical diversity of metabolites was notably increased as the fungi switched lifestyle to the predatory stage. Structural annotations by tandem mass spectrometry revealed that those fungal metabolites belonged to various structural families, such as peptide, siderophore, fatty alcohol, and fatty acid amide, and their production exhibited species specificity. Several small peptides (<1.5 kDa) produced by A.musiformis in the predatory stage were found, with their partial amino acid sequences resolved by the tandem mass spectra. Four fungal metabolites (desferriferrichrome, linoleyl alcohol, nonadecanamide, and citicoline) that were significantly enriched in the predatory stage were identified and validated by chemical standards, and their bioactivities against nematode prey were assessed. The availability of the metabolomics datasets will facilitate comparative studies on the metabolites of nematode-trapping fungi in the future.

Sesquiterpenyl Epoxy-Cyclohexenoids and their Signaling Functions in Nematode-Trapping Fungus Arthrobotrys oligospora

In this study, we purified three new sesquiterpenyl epoxy-cyclohexenoid (SEC) analogues, arthrobotrisin D (11) and its two derivatives, from nematode-trapping fungus Arthrobotrys oligospora. Our results revealed that arthrobotrisin type SEC metabolites could be detected in all the test fungal strains from geographically distinct regions grown on different nutrient media, indicative of unique diagnostic character as chemical indicators for A. oligospora. The time course designs over short-term intervals of the fungus under direct contact and indirect contact with living or dead nematodes revealed that arthrobotrisin B and D (6 and 11) displayed significant relationships (positive or negative correlation) with fungal saprophytic and pathogenic stages during a nematode predation event. Interestingly, fungus on nutrient-limiting medium conducive to fungal trap formation could rapidly drop the concentration levels of arthrobotrisins B and D within 6 h when dead nematodes were around, in great contrast to that for living nematodes. Moreover, only in the fungal strain under direct contact with living dominant soil bacteria, arthrobotrisins B and D exhibited significant increase in amounts. Among them, the new SEC, arthrobotrisin D (11) was found to be a key unique metabolic signal for fungal colony growth and fungal interaction with prey and bacteria. Our study suggested that chemical analysis of SEC metabolites in A. oligospora provides a window into the fungal growth status and much valuable information about ecological environments associated with the nematode infections.

Synthesis and role of melanin for tolerating in vitro rumen digestion in Duddingtonia flagrans, a nematode-trapping fungus

We describe the synthesis and a function of melanin in Duddingtonia flagrans, a nematode-trapping fungus. We tested various culture media treated with L-DOPA, glucose and tricyclazole on fungal growth and melanin distribution using infrared spectroscopy (IS), electron paramagnetic resonance (EPR) and transmission electron microscopy (TEM). In vitro rumen digestion was used to test the environmental stress and then to evaluate the capacity of this fungus to trap nematode larvae. The growth and melanization of the fungus after 21 days of incubation at 30°C were best in Sabouraud dextrose medium. IS indicated the presence of melanin in D. flagrans, with similar bands for commercial melanin used as a control, and assigned the values obtained by EPR (g of 2.0051 ± 0.0001) to the production of melanin by the fungus. TEM indicated that melanin was produced in melanosomes but was not totally inhibited by tricyclazole. Within the limits of experimental error, the predatory activity of fungus treated with tricyclazole was drastically affected after 27 h of in vitro anaerobic stress with rumen inoculum. The deposition of melanin particles on the fungal cell wall contributed to the maintenance of D. flagrans predatory abilities after in vitro anaerobic ruminal stress.

The lifestyle transition of Arthrobotrys oligospora is mediated by microRNA-like RNAs

The lifestyle transition of fungi, defined as switching from taking organic material as nutrients to pathogens, is a fundamental phenomenon in nature. However, the mechanisms of such transition remain largely unknown. Here we show microRNA-like RNAs (milRNAs) play a key role in fungal lifestyle transition for the first time. We identified milRNAs by small RNA sequencing in Arthrobotrys oligospora, a known nematode-trapping fungus. Among them, 7 highly expressed milRNAs were confirmed by northern-blot analysis. Knocking out two milRNAs significantly decreased A. oligospora's ability to switch lifestyles. We further identified that two of these milRNAs were associated with argonaute protein QDE-2 by RNA-immunoprecipitation (RIP) analysis. Three of the predicted target genes of milRNAs were found in immunoprecipitation (IP) products of QDE-2. Disruption of argonaute gene qde-2 also led to serious defects in lifestyle transition. Interestingly, knocking out individual milRNAs or qde-2 lead to diverse responses under different conditions, and qde-2 itself may be targeted by the milRNAs. Collectively, it indicates the lifestyle transition of fungi is mediated by milRNAs through RNA interference (RNAi) machinery, revealing the wide existence of miRNAs in fungi kingdom and providing new insights into understanding the adaptation of fungi from scavengers to predators and the mechanisms underlying fungal infections.

Integrated Metabolomics and Morphogenesis Reveal Volatile Signaling of the Nematode-Trapping Fungus Arthrobotrys oligospora

The adjustment of metabolic patterns is fundamental to fungal biology and plays vital roles in adaptation to diverse ecological challenges. Nematode-trapping fungi can switch their lifestyle from saprophytic to pathogenic by developing specific trapping devices induced by nematodes to infect their prey as a response to nutrient depletion in nature. However, the chemical identity of the specific fungal metabolites used during the switch remains poorly understood. We hypothesized that these important signal molecules might be volatile in nature. Gas chromatography-mass spectrometry was used to carry out comparative analysis of fungal metabolomics during the saprophytic and pathogenic lifestyles of the model species Arthrobotrys oligospora. Two media commonly used in research on this species, cornmeal agar (CMA) and potato dextrose agar (PDA), were chosen for use in this study. The fungus produced a small group of volatile furanone and pyrone metabolites that were associated with the switch from the saprophytic to the pathogenic stage. A. oligospora fungi grown on CMA tended to produce more traps and employ attractive furanones to improve the utilization of traps, while fungi grown on PDA developed fewer traps and used nematode-toxic furanone metabolites to compensate for insufficient traps. Another volatile pyrone metabolite, maltol, was identified as a morphological regulator for enhancing trap formation. Deletion of the gene AOL_s00079g496 in A. oligospora led to increased amounts of the furanone attractant (2-fold) in mutants and enhanced the attractive activity (1.5-fold) of the fungus, while it resulted in decreased trap formation. This investigation provides new insights regarding the comprehensive tactics of fungal adaptation to environmental stress, integrating both morphological and metabolomic mechanisms.

IMPORTANCE Nematode-trapping fungi are a unique group of soil-living fungi that can switch from the saprophytic to the pathogenic lifestyle once they come into contact with nematodes as a response to nutrient depletion. In this study, we investigated the metabolic response during the switch and the key types of metabolites involved in the interaction between fungi and nematodes. Our findings indicate that A. oligospora develops multiple and flexible metabolic tactics corresponding to different morphological responses to nematodes. A. oligospora can use similar volatile furanone and pyrone metabolites with different ecological functions to help capture nematodes in the fungal switch from the saprophytic to the pathogenic lifestyle. Furthermore, studies with A. oligospora mutants with increased furanone and pyrone metabolites confirmed the results. This investigation reveals the importance of volatile signaling in the comprehensive tactics used by nematode-trapping fungi, integrating both morphological and metabolomic mechanisms.

radiata Scherff Aqueous Extracts (BPE) for Controlling the Southern Root-Knot Nematode

We tested a formulation composed of a mixture of Bidens pilosa var. radiata extract (BPE) and nematode-trapping fungi for its effects on Meloidogyne incognita. In earlier evaluations of the effects of plant extracts on the hyphal growth of 5 species of nematode-trapping fungi with different capture organs (traps), the growth of all species was slightly inhibited. However, an investigation on the number of capture organs and nematode-trapping rates revealed that Arthrobotrys dactyloides formed significantly more rings and nematode traps than those of the control. An evaluation of simple mixed formulations prepared using sodium alginate showed that nematodes were captured with all formulations tested. The simple mixed formulation showed a particularly high capture rate. Furthermore, in a pot test, although the effects of a single formulation made from the fungus or plant extract were acceptable, the efficacy of the simple mixed formulation against M. incognita root-knot formation was particularly high.

The NADPH oxidase AoNoxA in Arthrobotrys oligospora functions as an initial factor in the infection of Caenorhabditis elegans

Reactive oxygen species (ROS) produced by NADPH oxidases can serve as signaling molecules to regulate a variety of physiological processes in multi-cellular organisms. In the nematophagous fungus Arthrobotrys oligospora, we found that ROS were produced during conidial germination, hyphal extension, and trap formation in the presence of nematodes. Generation of an AoNoxA knockout strain demonstrated the crucial role of NADPH oxidase in the production of ROS in A. oligospora, with trap formation impaired in the AoNoxA mutant, even in the presence of the nematode host. In addition, the expression of virulence factor serine protease P186 was up-regulated in the wild-type strain, but not in the mutant strain, in the presence of Caenorhabditis elegans. These results indicate that ROS derived from AoNoxA are essential for full virulence of A. oligospora in nematodes.

GPH1 is involved in glycerol accumulation in the three-dimensional networks of the nematode-trapping fungus Arthrobotrys oligospora

Turgor is very important for the invasive growth of fungal pathogens. Glycerol, a highly osmotic solvent, is considered to play an important role in turgor generation. The nematophagous fungus Arthrobotrys oligospora mainly lives as a saprophyte. In the presence of nematodes, A. oligospora enters the parasitic stage by forming three-dimensional networks (traps) to capture nematodes. In A. oligospora, we found that glycerol accumulated during nematode-induced trap formation. We demonstrated that deleting gph1, which encodes glycogen phosphorylase, decreased the glycerol content, compared with that of a wild-type strain. Although the number of traps induced by nematodes was not affected in the Δgph1 mutant, the capture rate was lower. Meanwhile, deleting gph1 also affected the growth rate and conidiation capacity of the fungus. These results indicate that glycerol derived from GPH1 is essential for the full virulence of A. oligospora against nematodes.

Interspecific and host-related gene expression patterns in nematode-trapping fungi

BACKGROUND

Nematode-trapping fungi are soil-living fungi that capture and kill nematodes using special hyphal structures called traps. They display a large diversity of trapping mechanisms and differ in their host preferences. To provide insights into the genetic basis for this variation, we compared the transcriptome expressed by three species of nematode-trapping fungi (Arthrobotrys oligospora, Monacrosporium cionopagum and Arthrobotrys dactyloides, which use adhesive nets, adhesive branches or constricting rings, respectively, to trap nematodes) during infection of two different plant-pathogenic nematode hosts (the root knot nematode Meloidogyne hapla and the sugar beet cyst nematode Heterodera schachtii).

RESULTS

The divergence in gene expression between the fungi was significantly larger than that related to the nematode species being infected. Transcripts predicted to encode secreted proteins and proteins with unknown function (orphans) were overrepresented among the highly expressed transcripts in all fungi. Genes that were highly expressed in all fungi encoded endopeptidases, such as subtilisins and aspartic proteases; cell-surface proteins containing the carbohydrate-binding domain WSC; stress response proteins; membrane transporters; transcription factors; and transcripts containing the Ricin-B lectin domain. Differentially expressed transcripts among the fungal species encoded various lectins, such as the fungal fruit-body lectin and the D-mannose binding lectin; transcription factors; cell-signaling components; proteins containing a WSC domain; and proteins containing a DUF3129 domain. A small set of transcripts were differentially expressed in infections of different host nematodes, including peptidases, WSC domain proteins, tyrosinases, and small secreted proteins with unknown function.

CONCLUSIONS

This is the first study on the variation of infection-related gene expression patterns in nematode-trapping fungi infecting different host species. A better understanding of these patterns will facilitate the improvements of these fungi in biological control programs, by providing molecular markers for screening programs and candidates for genetic manipulations of virulence and host preferences.

Factors associated with the suppressiveness of sugarcane soils to plant-parasitic nematodes

Observations in three Australian sugarcane fields suggested that the soil just under the trash blanket (the covering of crop residue that remains on the soil surface after crops are harvested) was suppressive to plant-parasitic nematodes. Roots were concentrated in this upper layer of soil but plant-parasitic nematode populations were relatively low and roots showed few signs of nematode damage. Root biomass was much lower 15 cm further down the soil profile, where root health was poor and populations of plant-parasitic nematodes were 3-5 times higher than near the soil surface. A bioassay in which Radopholus similis (a nematode that does not occur in sugarcane soils) was inoculated into heat-sterilized and untreated soils, confirmed that biological factors were limiting nematode populations in some of the soils, with soil from 0-2 cm much more suppressive than soil from 15-17 cm. Surface soil from one site was highly suppressive, as only 16% of R. similis recoverable from heated soil were retrieved from this soil after 8 days. Numerous soil chemical, biochemical, and biological properties were measured, and non-linear regression analysis identified two major groups of factors that were significantly associated with suppressiveness. One group reflected the amount of organic matter in soil (total C, total N, and labile C) and the other was associated with the size of the free-living nematode community (total numbers of free-living nematodes, and numbers of plant associates, bacterial feeders, fungal feeders, and carnivores). These results suggested that suppressiveness was biologically mediated and was sustained by C inputs from crop residues and roots. Since nematode-trapping fungi in the test soils could not be quantified using traditional dilution plating methods, their possible role as suppressive agents was assessed by generating TRFLP profiles with Orbiliales-specific primers, and by sequencing cloned PCR products. Although the molecular data were obtained from a limited number of samples, the level of suppression was significantly correlated to the number of Orbiliales clone groups and was also related to the number of Orbiliales species and TRFs, suggesting that this group of fungi may have been one of the suppressive factors operating in the test soils.

Effect of Crotalaria juncea Amendment on Squash Infected with Meloidogyne incognita

Two greenhouse experiments were conducted to examine the effect of Crotalaria juncea amendment on Meloidogyne incognita population levels and growth of yellow squash (Cucurbita pepo). In the first experiment, four soils with a long history of receiving yard waste compost (YWC+), no-yard-waste compost (YWC-), conventional tillage, or no-tillage treatments were used; in the second experiment, only one recently cultivated soil was used. Half of the amount of each soil received air-dried residues of C. juncea as amendment before planting squash, whereas the other half did not. Crotalaria juncea amendment increased squash shoot and root weights in all soils tested, except in YWC+ soil where the organic matter content was high without the amendment. The amendment suppressed the numbers of M. incognita if the inoculum level was low, and when the soil contained relatively abundant nematode-antagonistic fungi. Microwaved soil resulted in greater numbers of M. incognita and free-living nematodes than frozen or untreated soil, indicating nematode-antagonistic microorganisms played a role in nematode suppression. The effects of C. juncea amendment on nutrient cycling were complex. Amendment with C. juncea increased the abundance of free-living nematodes and Harposporium anguillulae, a fungus antagonistic to them in the second experiment but not in the first experiment. Soil histories, especially long-term yard waste compost treatments that increased soil organic matter, can affect the performance of C. juncea amendment.

Intercropping Cover Crops with Pineapple for the Management of Rotylenchulus reniformis

Effect of cover crops intercropped with pineapple (Ananas comosus) on Rotylenchulus reniformis population densities and activity of nematode-trapping fungi (NTF) were evaluated in two cycles of cover crop and pineapple. Sunn hemp (Crotalaria juncea), rapeseed (Brassica napus), African marigold (Tagetes erecta), or weeds were intercropped with pineapples. Beds planted with sunn hemp or rapeseed had lower population densities of R. reniformis than African marigold, weeds, or pineapple plots during cover crop growth, and the subsequent pineapple-growing periods. Rapeseed was a good host to Meloidogyne javanica and resulted in high population densities of M. javanica in the subsequent pineapple crop. Fireweed (Erigeron canadensis) occurred commonly and was a good host to R. reniformis. Bacterivorous nematode population densities increased (P </= 0.05) most in sunn hemp, especially early after planting. Nematode-trapping fungi required a long period to develop measurable population densities. Population densities of NTF were higher in cover crops than weeds or pineapples during the first crop cycle (P < 0.05). Although pineapple produced heavier fruits following sunn hemp than in the other treatments (P < 0.05), commercial yields were not different among rapeseed, weed, and sunn hemp treatments.