Role of Low-Affinity Calcium System Member Fig1 Homologous Proteins in Conidiation and Trap-Formation of Nematode-trapping Fungus Arthrobotrys oligospora

A palisade-shaped membrane reservoir is required for rapid ring cell inflation in Drechslerella dactyloides

Fusion of individual vesicles carrying membrane-building materials with the plasma membrane (PM) enables gradual cell expansion and shape change. Constricting ring (CR) cells of carnivorous fungi triple in size within 0.1-1 s to capture passing nematodes. Here, we investigated how a carnivorous fungus, Drechslerella dactyloides, executes rapid and irreversible PM expansion during CR inflation. During CR maturation, vesicles carrying membrane-building materials accumulate and fuse, forming a structure named the Palisade-shaped Membrane-building Structure (PMS) around the rumen side of ring cells. After CR inflation, the PMS disappears, with partially inflated cells displaying wavy PM and fully inflated cells exhibiting smooth PM, suggesting that the PMS serves as the reservoir for membrane-building materials to enable rapid and extensive PM expansion. The DdSnc1, a v-SNARE protein, accumulates at the inner side of ring cells and is necessary for PMS formation and CR inflation. This study elucidates the unique cellular mechanisms underpinning rapid CR inflation.

Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus

Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-dwelling nematode-trapping fungi (NTF). In particular, the NTF Arthrobotrys oligospora secretes food and sex cues to lure nematodes to its mycelium and is triggered to develop specialized trapping devices. Captured nematodes are then invaded and digested by the fungus, thus serving as a food source. In this study, we examined the transcriptomic response of A. oligospora across the stages of sensing, trap development, and digestion upon exposure to the model nematode Caenorhabditis elegans. A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. Two-thirds of the predicted secretome of A. oligospora was up-regulated in the presence of C. elegans at all time points examined, and among these secreted proteins, 38.5% are predicted to be effector proteins. Furthermore, functional studies disrupting the t-SNARE protein Sso2 resulted in impaired ability to capture nematodes. Additionally, genes of the DUF3129 family, which are expanded in the genomes of several NTF, were highly up-regulated upon nematode exposure. We observed the accumulation of highly expressed DUF3129 proteins in trap cells, leading us to name members of this gene family as Trap Enriched Proteins (TEPs). Gene deletion of the most highly expressed TEP gene, TEP1, impairs the function of traps and prevents the fungus from capturing prey efficiently. In late stages of predation, we observed up-regulation of a variety of proteases, including metalloproteases. Following penetration of nematodes, these metalloproteases facilitate hyphal growth required for colonization of prey. These findings provide insights into the biology of the predatory lifestyle switch in a carnivorous fungus and provide frameworks for other fungal-nematode predator-prey systems.

Multiple Roles of the Low-Affinity Calcium Uptake System in Drechslerella dactyloides, a Nematode-Trapping Fungus That Forms Constricting Rings

(1) Background: the low-affinity calcium uptake system (LACS) has been shown to play a crucial role in the conidiation and formation of adhesive nets and knobs by nematode-trapping fungi (NTF), but its involvement in the formation of constricting rings (CRs), mechanical traps to capture free-living nematodes, remains unexplored. (2) Methods: we investigated the function of two LACS genes (DdaFIG_1 and DdaFIG_2) in Drechslerella dactyloides, an NTF that forms CRs. We generated single (DdaFIG_1Ri and DdaFIG_2Ri) and double (DdaFIG_1,2Ri) knockdown mutants via the use of RNA interference (RNAi). (3) Results: suppression of these genes significantly affected conidiation, trap formation, vegetative growth, and response to diverse abiotic stresses. The number of CRs formed by DdaFIG_1Ri, DdaFIG_2Ri, and DdaFIG_1,2Ri decreased to 58.5%, 59.1%, and 38.9% of the wild-type (WT) level, respectively. The ring cell inflation rate also decreased to 73.6%, 60.6%, and 48.8% of the WT level, respectively. (4) Conclusions: the LACS plays multiple critical roles in diverse NTF.

Integrating nanotechnology with plant microbiome for next-generation crop health

Nanotechnology has enormous potential for sustainable agriculture, such as improving nutrient use efficiency, plant health, and food production. Nanoscale modulation of the plant-associated microbiota offers an additional valuable opportunity to increase global crop production and ensure future food and nutrient security. Nanomaterials (NMs) applied to agricultural crops can impact plant and soil microbiota, which offers valuable services to host plants, including the acquisition of nutrients, abiotic stress tolerance, and disease suppression. Dissecting the complex interactions between NMs and plants by integrating multi-omic approaches is providing new insights into how NMs can activate host responses and functionality as well as influence native microbial communities. Such nexus and moving beyond descriptive microbiome studies to hypothesis-driven research will foster microbiome engineering and open up opportunities for the development of synthetic microbial communities to provide agronomic solutions. Herein, we first summarize the significant role of NMs and the plant microbiome in crop productivity and then focus on NMs effects on plant-associated microbiota. We outline three urgent priority research areas and call for a transdisciplinary collaborative approach, involving plant scientists, soil scientists, environmental scientists, ecologists, microbiologists, taxonomists, chemists, physicists, and stakeholders, to advance nano-microbiome research. Detailed understanding of the nanomaterial-plant-microbiome interactions and the mechanisms underlying NMs-mediated shifts in the microbiome assembly and functions may help to exploit the services of both nano-objects and microbiota for next-generation crop health.

DhFIG_2, a gene of nematode-trapping fungus Dactylellina haptotyla that encodes a component of the low-affinity calcium uptake system, is required for conidiation and knob-trap formation

Calcium ion (Ca²⁺) is a universal second messenger involved in regulating diverse processes in animals, plants, and fungi. The low-affinity calcium uptake system (LACS) participates in acquiring Ca²⁺ from extracellular environments under high extracellular Ca²⁺ concentration. Unlike most fungi, which encode only one protein (FIG1) for LACS, nematode-trapping fungi (NTF) encode two related proteins. AoFIG_2, the NTF-specific LACS component encoded by adhesive network-trap forming Arthrobotrys oligospora, was shown to be required for conidiation and trap formation. We characterized the role of DhFIG_2, an AoFIG_2 ortholog encoded by knob-trap forming Dactylellina haptotyla, in growth and development to expand our understanding of the role of LACS in NTF. Because repeated attempts to disrupt DhFIG_2 failed, knocking down the expression of DhFIG_2 via RNA interference (RNAi) was used to study its function. RNAi of DhFIG_2 significantly decreased its expression, severely reduced conidiation and trap formation, and affected vegetative growth and stress responses, suggesting that this component of LACS is crucial for trap formation and conidiation in NTF. Our study demonstrated the utility of RNAi assisted by ATMT for studying gene function in D. haptotyla.

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

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

Tools and basic procedures of gene manipulation in nematode-trapping fungi

Nematode-trapping fungi (NTF) are the majority of carnivorous microbes to capture nematodes through diverse and sophisticated trapping organs derived from hyphae. They can adopt carnivorous lifestyles in addition to saprophytism to obtain extra-nutrition from nematodes. As a special group of fungi, the NTF are not only excellent model organism for studying lifestyle transition of fungi but also natural resources of exploring biological control of nematodes. However, the carnivorous mechanism of NTF remains poorly understood. Nowadays, the omics studies of NTF have provided numerous genes and pathways that are associated with the phenotypes of carnivorous traits, which need molecular tools to verify. Here, we review the development and progress of gene manipulation tools in NTF, including methodology and strategy of transformation, random gene mutagenesis methods and target gene mutagenesis methods. The principle and practical approach for each method was summarized and discussed, and the basic operational flow for each tool was described. This paper offers a clear reference and instruction for researchers who work on NTF as well as other group of fungi.

SNARE Protein DdVam7 of the Nematode-Trapping Fungus Drechslerella dactyloides Regulates Vegetative Growth, Conidiation, and the Predatory Process via Vacuole Assembly

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins play conserved roles in membrane fusion events in eukaryotes and have been documented to be involved in fungal growth and pathogenesis. However, little is known about the roles of SNAREs in trap morphogenesis in nematode-trapping fungi (NTF). Drechslerella dactyloides, one of the constricting ring-forming NTF, captures free-living nematodes via rapid ring cell inflation. Here, we characterized DdVam7 of D. dactyloides, a homolog of the yeast SNARE protein Vam7p. Deletion of DdVam7 significantly suppressed vegetative growth and conidiation. The mutation significantly impaired trap formation and ring cell inflation, resulting in a markedly decreased nematode-trapping ability. A large vacuole could develop in ring cells within ~2.5 s after instant inflation in D. dactyloides. In the ΔDdVam7 mutant, the vacuoles were small and fragmented in hyphae and uninflated ring cells, and the large vacuole failed to form in inflated ring cells. The localization of DdVam7 in vacuoles suggests its involvement in vacuole fusion. In summary, our results suggest that DdVam7 regulates vegetative growth, conidiation, and the predatory process by mediating vacuole assembly in D. dactyloides, and this provides a basis for studying mechanisms of SNAREs in NTF and ring cell rapid inflation. IMPORTANCE D. dactyloides is a nematode-trapping fungus that can capture nematodes through a constricting ring, the most sophisticated trapping device. It is amazing that constricting ring cells can inflate to triple their size within seconds to capture a nematode. A large centrally located vacuole is a unique signature associated with inflated ring cells. However, the mechanism underpinning trap morphogenesis, especially vacuole dynamics during ring cell inflation, remains unclear. Here, we documented the dynamics of vacuole assembly during ring cell inflation via time-lapse imaging for the first time. We characterized a SNARE protein in D. dactyloides (DdVam7) that was involved in vacuole assembly in hyphae and ring cells and played important roles in vegetative growth, conidiation, trap morphogenesis, and ring cell inflation. Overall, this study expands our understanding of biological functions of the SNARE proteins and vacuole assembly in NTF trap morphogenesis and provides a foundation for further study of ring cell rapid inflation mechanisms.

DdaCrz1, a C2H2-Type Transcription Factor, Regulates Growth, Conidiation, and Stress Resistance in the Nematode-Trapping Fungus Drechslerella dactyloides

The Ca²⁺/calmodulin-dependent signaling pathway regulates diverse cellular processes. Calcineurin is a calcium-dependent phosphatase acting in fungi mainly through Crz1, a zinc finger transcription factor. Although the likely involvement of Ca²⁺ in fungal carnivorism has been documented, how Crz1 functions in nematode-trapping fungi remains unknown. Here, we identified the Crz1 gene (named as DdaCrz1) in Drechslerella dactyloides, a species that forms constricting rings to trap nematodes. The deletion of DdaCrz1 significantly reduced hyphal growth and conidiation, trap formation, and ring cell inflation. Moreover, the mutation increased sensitivity to Mn²⁺ but decreased sensitivity to Ca²⁺, Mg²⁺, Zn²⁺, and Li⁺. Similarly, the mutant showed increased tolerance to osmotic stress but was more sensitive to Congo red, a cell wall-damaging agent. Our results confirmed the critical roles of the Ca²⁺/calmodulin-dependent signaling pathway in regulating growth, conidiation, and the stress response, and suggested its involvement in trapping nematodes.

Regulatory Mechanism of Trap Formation in the Nematode-Trapping Fungi

Nematode-trapping (NT) fungi play a significant role in the biological control of plant- parasitic nematodes. NT fungi, as a predator, can differentiate into specialized structures called “traps” to capture, kill, and consume nematodes at a nutrient-deprived condition. Therefore, trap formation is also an important indicator that NT fungi transition from a saprophytic to a predacious lifestyle. With the development of gene knockout and multiple omics such as genomics, transcriptomics, and metabolomics, increasing studies have tried to investigate the regulation mechanism of trap formation in NT fungi. This review summarizes the potential regulatory mechanism of trap formation in NT fungi based on the latest findings in this field. Signaling pathways have been confirmed to play an especially vital role in trap formation based on phenotypes of various mutants and multi-omics analysis, and the involvement of small molecule compounds, woronin body, peroxisome, autophagy, and pH-sensing receptors in the formation of traps are also discussed. In addition, we also highlight the research focus for elucidating the mechanism underlying trap formation of NT fungi in the future.

Intercropping Walnut and Tea: Effects on Soil Nutrients, Enzyme Activity, and Microbial Communities

The practice of intercropping, which involves growing more than one crop simultaneously during the same growing season, is becoming more important for increasing soil quality, land-use efficiency, and subsequently crop productivity. The present study examined changes in soil physicochemical properties, enzymatic activity, and microbial community composition when walnut (Juglans spp.) was intercropped with tea (Camellia sinensis L.) plants in a forest and compared with a walnut and tea monocropping system. The results showed that walnut–tea intercropping improved the soil nutrient profile and enzymatic activity. The soil available nitrogen (AN), available phosphorus (AP), available potassium (AK), organic matter (OM) content, and sucrase activity were significantly boosted in intercropped walnut and tea than in monocropping forests. The interaction between crops further increased bacterial and fungal diversity when compared to monoculture tea forests. Proteobacteria, Bacteroidetes, Firmicutes, Chlamydiae, Rozellomycota, and Zoopagomycota were found in greater abundance in an intercropping pattern than in monoculture walnut and tea forest plantations. The walnut–tea intercropping system also markedly impacted the abundance of several bacterial and fungal operational taxonomic units (OTUs), which were previously shown to support nutrient cycling, prevent diseases, and ameliorate abiotic stress. The results of this study suggest that intercropping walnut with tea increased host fitness and growth by positively influencing soil microbial populations.

The fucose-specific lectin gene AOL_s00054g276 affects trap formation and nematocidal activity of the nematophagous fungus Arthrobotrys oligospora

Nematode-trapping fungi are natural enemies of nematodes in nature. Arthrobotrys oligospora, a typical nematode-trapping fungus with a clear genetic background, can capture and infect nematodes by forming adhesive three-dimensional networks. Lectins, a class of glycoproteins containing glycosyl-specific recognition domains, play an important role in biological recognition. However, the fucose-specific lectins have rarely been studied regarding the process of preying on nematodes. In this study, we characterized the biological role of the fucose-specific lectin encoding gene AOL_s00054g276 (g276) in A. oligospora. The gene g276 was first deleted based on homologous recombination, then the phenotype and nematocidal activity of the Δg276 mutant was evaluated. The results showed that the deletion of gene g276 delayed trap formation and weakened its nematocidal activity; however, mycelial growth, conidia production, conidial germination rates, and adaption to environmental stresses were not affected. Our results suggest that the fucose-specific lectin encoding gene g276 might be associated with the morphogenesis of this fungus, and its deletion resulted in a significantly low density of three-dimensional traps (P < 0.05) and a significantly low nematode-tapping efficiency (P < 0.001). These findings provide a basis for further elucidating the mechanism of A. oligospora preying on nematodes and lay a foundation for the development and utilization of fungal-derived lectins for nematode control in future.

DdaSTE12 is involved in trap formation, ring inflation, conidiation, and vegetative growth in the nematode-trapping fungus Drechslerella dactyloides

Ste12 transcription factors, downstream of mitogen-activated protein kinase (MAPK) signalling pathways, are exclusively found in the fungal kingdom and regulate fungal mating, development, and pathogenicity. The nematode-trapping fungus Drechslerella dactyloides can capture free-living nematodes using constricting rings by cell inflation within 1 s when stimulated by nematodes entering the rings. The MAPK signalling pathways are involved in the trap formation of nematode-trapping fungi, but their downstream regulation is not clearly understood. In this study, disruption of the DdaSTE12 gene in D. dactyloides disabled cell inflation of constricting rings and led to an inability to capture nematodes. The number of septa of constricting rings and the ring cell vacuoles were changed in ΔDdaSTE12. Compared with the wild type, ΔDdaSTE12 reduced trap formation, conidiation, and vegetative growth by 79.3%, 80.3%, and 21.5%, respectively. The transcriptomes of ΔDdaSTE12-3, compared with those of the wild type, indicated that the expression of genes participating in trap formation processes, including signal transduction (Gpa2 and a 7-transmembrane receptor), vesicular transport and cell fusion (MARVEL domain-containing proteins), and nematode infection (PEX11 and CFEM domain-containing proteins), is regulated by DdaSTE12. The results suggest that DdaSTE12 is involved in trap formation and ring cell inflation, as well as conidiation and vegetative growth, by regulating a wide range of downstream functions. Our findings expanded the roles of Ste12 homologous transcription factors in the development of constricting rings and provided new insights into the downstream regulation of the MAPK signalling pathway involved in nematode predation. KEY POINTS: • DdaSTE12 was the first gene disrupted in D. dactyloides. • DdaSTE12 is related to ring cell inflation, vegetative growth, and conidiation. • DdaSTE12 deletion resulted in defects in trap formation and ring development.

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.

Plants and Associated Soil Microbiota Cooperatively Suppress Plant-Parasitic Nematodes

Disease suppressive soils with specific suppression of soil-borne pathogens and parasites have been long studied and are most often of microbiological origin. As for the plant-parasitic nematodes (PPN), which represent a huge threat to agricultural crops and which successfully defy many conventional control methods, soil progression from conducive to suppressive state is accompanied by the enrichment of specific antagonistic microbial consortia. However, a few microbial groups have come to the fore in diminishing PPN in disease suppressive soils using culture-dependent methods. Studies with cultured strains resulted in understanding the mechanisms by which nematodes are antagonized by microorganisms. Recent culture-independent studies on the microbiome associated with soil, plant roots, and PPN contributed to a better understanding of the functional potential of disease suppressive microbial cohort. Plant root exudation is an important pathway determining host-microbe communication and plays a key role in selection and enrichment of a specific set of microbial antagonists in the rhizosphere as first line of defense against crop pathogens or parasites. Root exudates comprising primary metabolites such as amino acids, sugars, organic acids, and secondary metabolites can also cause modifications in the nematode surface and subsequently affect microbial attachment. A positive interaction between hosts and their beneficial root microbiota is correlated with a low nematode performance on the host. In this review, we first summarized the historical records of nematode-suppressive soils and then focused on more recent studies in this aspect, emphasizing the advances in studying nematode-microbe interactions over time. We highlighted nematode biocontrol mechanisms, especially parasitism, induced systemic resistance, and volatile organic compounds using microbial consortia, or bacterial strains of the genera Pasteuria, Bacillus, Pseudomonas, Rhizobium, Streptomyces, Arthrobacter, and Variovorax, or fungal isolates of Pochonia, Dactylella, Nematophthora, Purpureocillium, Trichoderma, Hirsutella, Arthrobotrys, and Mortierella. We discussed the importance of root exudates in plant communication with PPN and soil microorganisms, emphasizing their role in microbial attachment to the nematode surface and subsequent events of nematode parasitism. Comprehensive understanding of the plant-beneficial microbial consortia and the mechanisms underlying disease suppression may help to develop synthetic microbial communities for biocontrol of PPN, thereby reducing nematicides and fertilizers inputs.

Calcium Transport Proteins in Fungi: The Phylogenetic Diversity of Their Relevance for Growth, Virulence, and Stress Resistance

The key players of calcium (Ca²⁺) homeostasis and Ca²⁺ signal generation, which are Ca²⁺ channels, Ca²⁺/H⁺ antiporters, and Ca²⁺-ATPases, are present in all fungi. Their coordinated action maintains a low Ca²⁺ baseline, allows a fast increase in free Ca²⁺ concentration upon a stimulus, and terminates this Ca²⁺ elevation by an exponential decrease – hence forming a Ca²⁺ signal. In this respect, the Ca²⁺ signaling machinery is conserved in different fungi. However, does the similarity of the genetic inventory that shapes the Ca²⁺ peak imply that if “you’ve seen one, you’ve seen them all” in terms of physiological relevance? Individual studies have focused mostly on a single species, and mechanisms elucidated in few model organisms are usually extrapolated to other species. This mini-review focuses on the physiological relevance of the machinery that maintains Ca²⁺ homeostasis for growth, virulence, and stress responses. It reveals common and divergent functions of homologous proteins in different fungal species. In conclusion, for the physiological role of these Ca²⁺ transport proteins, “seen one,” in many cases, does not mean: “seen them all.”