Bacteria can mobilize nematode-trapping fungi to kill nematodes

Electron-Transferring Flavoprotein and Its Dehydrogenase Required for Fungal Pathogenicity in Arthrobotrys oligospora

Electron transfer flavoprotein (ETF) plays an important function in fatty acid beta oxidation and the amino acid metabolic pathway. It can provide pathogenicity to some opportunistic fungi via modulating cellular metabolite composition. Arthrobotrys oligospora is a typical invasion fungus to nematodes. Its ETF characterization is still unknown. Here, we showed that the mutations of A. oligospora ETF (Aoetfα and Aoetfβ) and its dehydrogenase (Aoetfdh) led to severe defects in mitochondrial integrity and blocked fatty acid metabolism. The pathogenicity-associated trap structures were completely suppressed when exposed to nematode-derived ascarosides and nutrition signals, including ammonia and urea. Compared to the wild-type strain, the nematode predatory activity was significantly reduced and delayed. But surprisingly, the rich nutrition could restore the massive trap and robust predatory activity in the mutant Aoetfβ beyond all induction cues. Moreover, the deletion of Aoetfβ has led to the accumulation of butyrate-like smell, which has a strong attraction to Caenorhabditis elegans nematodes. Ultimately, ETF and its dehydrogenase play a crucial role in nematode-trapping fungi, highlighting mitochondrial metabolite fluctuations that are connected to pathogenesis and further regulating the interactions between fungi and nematodes.

Nematode-trapping fungus Arthrobotrys oligospora recruited rhizosphere microorganisms to cooperate in controlling root-knot nematodes in tomato

AIMS

The objective of this study was to elucidate the role and mechanism of changes in the rhizosphere microbiome following Arthrobotrys oligospora treatment in the biological control of root-knot nematodes and identify the key fungal and bacterial species that collaborate with A. oligospora to biocontrol root-knot nematodes.

METHODS AND RESULTS

We conducted a pot experiment to investigate the impact of A. oligospora treatment on the biocontrol efficiency of A. oligospora against Meloidogyne incognita infecting tomatoes. We analyzed the rhizosphere bacteria and fungi communities of tomato by high-throughput sequencing of the 16S rRNA gene fragment and the internal transcribed spacer (ITS). The results indicated that the application of A. oligospora resulted in a 53.6% reduction in the disease index of M. incognita infecting tomato plants. The bacterial diversity of rhizosphere soil declined in the A. oligospora-treated group, while fungal diversity increased. The A. oligospora treatment enriched the tomato rhizosphere with Acidobacteriota, Firmicutes, Bradyrhizobium, Sphingomonadales, Glomeromycota, and Purpureocillium. These organisms are involved in the utilization of rhizosphere organic matter, nitrogen, and glycerolipids, or play the role of ectomycorrhiza or directly kill nematodes. The networks of bacterial and fungal co-occurrence exhibited a greater degree of stability and complexity in the A. oligospora treatment group.

CONCLUSIONS

This study demonstrated the key fungal and bacterial species that collaborate with the A. oligospora in controlling the root-knot nematode and elaborated the potential mechanisms involved. The findings offer valuable insights and inspiration for the advancement of bionematicide based on nematode-trapping fungi.

Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity

Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.

Urea regulates soil nematode population by enhancing the nematode-trapping ability of nematode-trapping fungi

As the most abundant animal in the soil, nematodes are directly or indirectly involved in almost all soil ecological processes. Studying soil nematode population regulation is essential to understanding soil ecological processes. This study found urea combines nematode-trapping fungi to regulate the population of soil nematodes. In soil, compared with no urea, adding 0.2 mg/mL urea after applying Arthrobotrys oligospora and Dactylellina ellipsospora reduced the number of nematodes by 34.7% and 31.7%. Further, the mechanism of urea couple nematode-trapping fungi to regulate the nematode population was explored in the medium environment. The results showed that the addition of 0.2 mg/ml urea accelerated the trap formation of A. oligospora and D. ellipsosporas by 50% and 46.5%, and increased the yield of traps of A. oligospora and D. ellipsosporas by 39.5% and 40.6%, thus, the predatory efficiency of A. oligospora and D. ellipsospora on nematodes was increased by 34.2% and 32.7%. In conclusion, urea regulates the predation ability of A. oligospora and D. ellipsosporas to regulate the soil nematode population. This study deepens the understanding of the regulatory pathways of the soil nematodes but also provides a potential new strategy for harmful nematode bio-control.

DNA methylation plays important roles in lifestyle transition of Arthrobotrys oligospora

Trap formation is the key indicator of carnivorous lifestyle transition of nematode-trapping fungi (NTF). Here, the DNA methylation profile was explored during trap induction of Arthrobotrys oligospora, a typical NTF that captures nematodes by developing adhesive networks. Whole-genome bisulfite sequencing identified 871 methylation sites and 1979 differentially methylated regions (DMRs). This first-of-its-kind investigation unveiled the widespread presence of methylation systems in NTF, and suggested potential regulation of ribosomal RNAs through DNA methylation. Functional analysis indicated DNA methylation's involvement in complex gene regulations during trap induction, impacting multiple biological processes like response to stimulus, transporter activity, cell reproduction and molecular function regulator. These findings provide a glimpse into the important roles of DNA methylation in trap induction and offer new insights for understanding the molecular mechanisms driving carnivorous lifestyle transition of NTF.

Biotic interactions in soil and dung shape parasite transmission in temperate ruminant systems: An integrative framework

Gastrointestinal helminth parasites undergo part of their life cycle outside their host, such that developmental stages interact with the soil and dung fauna. These interactions are capable of affecting parasite transmission on pastures yet are generally ignored in current models, empirical studies and practical management. Dominant methods of parasite control, which rely on anthelmintic medications for livestock, are becoming increasingly ineffective due to the emergence of drug-resistant parasite populations. Furthermore, consumer and regulatory pressure on decreased chemical use in agriculture and the consequential disruption of biological processes in the dung through nontarget effects exacerbates issues with anthelmintic reliance. This presents a need for the application and enhancement of nature-based solutions and biocontrol methods. However, successfully harnessing these options relies on advanced understanding of the ecological system and interacting effects among biotic factors and with immature parasite stages. Here, we develop a framework linking three key groups of dung and soil fauna-fungi, earthworms, and dung beetles-with each other and developmental stages of helminths parasitic in farmed cattle, sheep, and goats in temperate grazing systems. We populate this framework from existing published studies and highlight the interplay between faunal groups and documented ecological outcomes. Of 1756 papers addressing abiotic drivers of populations of these organisms and helminth parasites, only 112 considered interactions between taxa and 36 presented data on interactions between more than two taxonomic groups. Results suggest that fungi reduce parasite abundance and earthworms may enhance fungal communities, while competition between dung taxa may reduce their individual effect on parasite transmission. Dung beetles were found to impact fungal populations and parasite transmission variably, possibly tied to the prevailing climate within a specific ecological context. By exploring combinations of biotic factors, we consider how interactions between species may be fundamental to the ecological consequences of biocontrol strategies and nontarget impacts of anthelmintics on dung and soil fauna and how pasture management alterations to promote invertebrates might help limit parasite transmission. With further development and parameterization the framework could be applied quantitatively to guide, prioritize, and interpret hypothesis-driven experiments and integrate biotic factors into established models of parasite transmission dynamics.

Fungi beyond limits: The agricultural promise of extremophiles

Global climate changes threaten food security, necessitating urgent measures to enhance agricultural productivity and expand it into areas less for agronomy. This challenge is crucial in achieving Sustainable Development Goal 2 (Zero Hunger). Plant growth-promoting microorganisms (PGPM), bacteria and fungi, emerge as a promising solution to mitigate the impact of climate extremes on agriculture. The concept of the plant holobiont, encompassing the plant host and its symbiotic microbiota, underscores the intricate relationships with a diverse microbial community. PGPM, residing in the rhizosphere, phyllosphere, and endosphere, play vital roles in nutrient solubilization, nitrogen fixation, and biocontrol of pathogens. Novel ecological functions, including epigenetic modifications and suppression of virulence genes, extend our understanding of PGPM strategies. The diverse roles of PGPM as biofertilizers, biocontrollers, biomodulators, and more contribute to sustainable agriculture and environmental resilience. Despite fungi's remarkable plant growth-promoting functions, their potential is often overshadowed compared to bacteria. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with many terrestrial plants, enhancing plant nutrition, growth, and stress resistance. Other fungi, including filamentous, yeasts, and polymorphic, from endophytic, to saprophytic, offer unique attributes such as ubiquity, morphology, and endurance in harsh environments, positioning them as exceptional plant growth-promoting fungi (PGPF). Crops frequently face abiotic stresses like salinity, drought, high UV doses and extreme temperatures. Some extremotolerant fungi, including strains from genera like Trichoderma, Penicillium, Fusarium, and others, have been studied for their beneficial interactions with plants. Presented examples of their capabilities in alleviating salinity, drought, and other stresses underscore their potential applications in agriculture. In this context, extremotolerant and extremophilic fungi populating extreme natural environments are muchless investigated. They represent both new challenges and opportunities. As the global climate evolves, understanding and harnessing the intricate mechanisms of fungal-plant interactions, especially in extreme environments, is paramount for developing effective and safe plant probiotics and using fungi as biocontrollers against phytopathogens. Thorough assessments, comprehensive methodologies, and a cautious approach are crucial for leveraging the benefits of extremophilic fungi in the changing landscape of global agriculture, ensuring food security in the face of climate challenges.

Rare NRPS Gene Cluster for Desferriferrichrome Biosynthesis Controls the Conflict between Trap Formation and Nematicidal Activity in Arthrobotrys oligospora

The formation of the trapping device induced by nematodes has been assumed as an indicator for a switch from saprophytic to predacious lifestyles for nematode-trapping fungi. However, fungal nematocidal activity is not completely synonymous with fungal trap formation. We found that the predominant nematode-trapping fungus Arthrobotrys oligospora harbored a rare NRPS (Ao415) gene cluster that was mainly distributed in nematode-trapping fungi. The gene Ao415 putatively encodes a protein with a unique domain organization, distinct from other NRPSs in other fungi. Mutation of the two key biosynthetic genes Ao415 and Ao414 combined with nontarget metabolic analysis revealed that the Ao415 gene cluster was responsible for the biosynthesis of a hydroxamate siderophore, desferriferrichrome (1). Lack of desferriferrichrome (1) and its hydroxamate precursor (3) could lead to significantly increased Fe3+ content, which induced fungal trap formation without a nematode inducer. Furthermore, the addition of Fe3+ strongly improved fungal trap formation but deleteriously caused broken traps. The addition of 1 significantly attenuated trap formation but enhanced fungal nematicidal activity. Our findings indicate that iron is a key factor for trap formation and provide a new insight into the underlying mechanism of siderophores in nematode-trapping fungi.

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.

Analysis of Nuclear Dynamics in Nematode-Trapping Fungi Based on Fluorescent Protein Labeling

Nematophagous fungi constitute a category of fungi that exhibit parasitic behavior by capturing, colonizing, and poisoning nematodes, which are critical factors in controlling nematode populations in nature, and provide important research materials for biological control. Arthrobotrys oligospora serves as a model strain among nematophagous fungi, which begins its life as conidia, and then its hyphae produce traps to capture nematodes, completing its lifestyle switch from saprophytic to parasitic. There have been many descriptions of the morphological characteristics of A. oligospora lifestyle changes, but there have been no reports on the nuclear dynamics in this species. In this work, we constructed A. oligospora strains labeled with histone H2B-EGFP and observed the nuclear dynamics from conidia germination and hyphal extension to trap formation. We conducted real-time imaging observations on live cells of germinating and extending hyphae and found that the nucleus was located near the tip. It is interesting that the migration rate of this type of cell nucleus is very fast, and we speculate that this may be related to the morphological changes involved in the transformation to a predatory lifestyle. We suggest that alterations in nuclear shape and fixation imply the immediate disruption of the interaction with cytoskeletal mechanisms during nuclear migration. In conclusion, these findings suggest that the signal initiating nuclear migration into fungal traps is generated at the onset of nucleus entry into a trap cell. Our work provides a reference for analysis of the dynamics of nucleus distribution and a means to visualize protein localization and interactions in A. oligospora.

Ammonia and Nematode Ascaroside Are Synergistic in Trap Formation in Arthrobotrys oligospora

Nematode-trapping (NT) fungi are natural predators of the soil living nematodes. Diverse external signals mediate the generation of predatory devices of NT fungi. Among these, broad ascarosides and nitrogenous ammonia are highly efficient inducers for trap structure initiation. However, the overlay effect of ammonia and ascaroside on the trap morphogenesis remains unclear. This study demonstrated that the combination of nitrogenous substances with nematode-derived ascarosides led to higher trap production compared to the single inducing cues; notably, ammonia and Ascr#18 had the most synergistic effect on the trap in A. oligospora. Further, the deletion of ammonia transceptor Amt43 blocked trap formation against ammonia addition in A. oligospora but not for the ascaroside Ascr#18 induction. Moreover, ammonia addition could promote plasma endocytosis in the process of trap formation. In contrast, ascaroside addition would facilitate the stability of intracellular organization away from endocytosis. Therefore, there is a synergistic effect on trap induction from different nitrogenous and ascaroside signals.

Morphological and Phylogenetic Characterization of Five Novel Nematode-Trapping Fungi (Orbiliomycetes) from Yunnan, China

Nematode-trapping fungi are widely studied due to their unique morphological structure, survival strategy, and potential value in the biological control of harmful nematodes. During the identification of carnivorous fungi preserved in our laboratory, five novel nematode-trapping fungi were established and placed in the genera Arthrobotrys and Drehslerella based on morphological and multigene (ITS, TEF, and RPB2) phylogenetic analyses. A. hengjiangensis sp. nov. and A. weixiensis sp. nov. are characterized by producing adhesive networks to catch nematodes. Dr. pengdangensis sp. nov., Dr. tianchiensis sp. nov., and Dr. yunlongensis sp. nov. are characterized by producing constricting rings. Morphological descriptions, illustrations, taxonomic notes, and phylogenetic analysis are provided for all new taxa; a key for Drechslerella species is listed; and some deficiencies in the taxonomy and evolution study of nematode-trapping fungi are also discussed herein.

Involvement of AoMdr1 in the Regulation of the Fluconazole Resistance, Mycelial Fusion, Conidiation, and Trap Formation of Arthrobotrys oligospora

Multidrug resistance (Mdr) proteins are critical proteins for maintenance of drug resistance in fungi. Mdr1 has been extensively studied in Candida albicans; its role in other fungi is largely unknown. In this study, we identified a homologous protein of Mdr (AoMdr1) in the nematode-trapping (NT) fungus Arthrobotrys oligospora. It was found that the deletion of Aomdr1 resulted in a significant reduction in the number of hyphal septa and nuclei as well as increased sensitivity to fluconazole and resistance to hyperosmotic stress and SDS. The deletion of Aomdr1 also led to a remarkable increase in the numbers of traps and mycelial loops in the traps. Notably, AoMdr1 was able to regulate mycelial fusion under low-nutrient conditions, but not under nutrient-rich conditions. AoMdr1 was also involved in secondary metabolism, and its deletion caused an increase in arthrobotrisins (specific compounds produced by NT fungi). These results suggest that AoMdr1 plays a crucial role in the fluconazole resistance, mycelial fusion, conidiation, trap formation, and secondary metabolism of A. oligospora. Our study contributes to the understanding of the critical role of Mdr proteins in mycelial growth and the development of NT fungi.

Nematodes as suppressors and facilitators of plant performance

Plant-nematode interactions are mainly considered from the negative aspect with a focus on plant-parasitic nematodes (PPNs), which is justified considering the agronomic losses caused by PPNs. Despite the fact that PPNs are outnumbered by nonparasitic free-living nematodes (FLNs), the functional importance of FLNs, especially with regard to plant performance, remains largely unknown. Here, we provide a comprehensive overview and most recent insights into soil nematodes by showing direct and indirect links of both PPNs and FLNs with plant performance. We especially emphasize the knowledge gaps and potential of FLNs as important indirect players in driving plant performance such as stimulating the resistance to pests via improving the disease suppressive activity of the rhizobiome. Together, we present a holistic view of soil nematodes as positive and negative contributors to plant performance, accentuating the positive but underexplored role of FLNs.

Activity of chitin/chitosan/chitosan oligosaccharide against plant pathogenic nematodes and potential modes of application in agriculture: A review

Chemical nematicide is the most common method of controlling plant-parasitic nematodes (PPN). Given the negative impact of chemical nematicides on the environment and ecosystem, it is necessary to seek their alternatives and novel modes of application. Chitin oligo/polysaccharide (COPS), including chitosan and chitosan oligosaccharide, has unique biological properties. By producing ammonia, encouraging the growth of antagonistic bacteria, and enhancing crop tolerance, COPSs help suppress PPN growth during soil remediation. COPS is also an effective sustained-release carrier that can be used to overcome the shortcomings of nematicidal substances. This review summarizes the advancements of COPS research in nematode control from three perspectives of action mechanism as well as in slow-release carrier-loaded nematicides. Further, it discusses potential agricultural applications for nematode disease management.

Natural nematicidal metabolites and advances in their biocontrol capacity on plant parasitic nematodes

Covering: 2010 to 2021Natural nematicidal metabolites are important sources of nematode control. This review covers the isolation and structural determination of nematicidal metabolites from 2010 to 2021. We summarise chemical structures, bioactivity, metabolic regulation and biosynthesis of potential nematocides, and structure-activity relationship and application potentiality of natural metabolites in plant parasitic nematodes' biocontrol. In doing so, we aim to provide a comprehensive overview of the potential roles that natural metabolites can play in anti-nematode strategies.

Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants

BACKGROUND

Root-knot nematodes (RKN) are among the most important root-damaging plant-parasitic nematodes, causing severe crop losses worldwide. The plant rhizosphere and root endosphere contain rich and diverse bacterial communities. However, little is known about how RKN and root bacteria interact to impact parasitism and plant health. Determining the keystone microbial taxa and their functional contributions to plant health and RKN development is important for understanding RKN parasitism and developing efficient biological control strategies in agriculture.

RESULTS

The analyses of rhizosphere and root endosphere microbiota of plants with and without RKN showed that host species, developmental stage, ecological niche, and nematode parasitism, as well as most of their interactions, contributed significantly to variations in root-associated microbiota. Compared with healthy tomato plants at different developmental stages, significant enrichments of bacteria belonging to Rhizobiales, Betaproteobacteriales, and Rhodobacterales were observed in the endophytic microbiota of nematode-parasitized root samples. Functional pathways related to bacterial pathogenesis and biological nitrogen fixation were significantly enriched in nematode-parasitized plants. In addition, we observed significant enrichments of the nifH gene and NifH protein, the key gene/enzyme involved in biological nitrogen fixation, within nematode-parasitized roots, consistent with a potential functional contribution of nitrogen-fixing bacteria to nematode parasitism. Data from a further assay showed that soil nitrogen amendment could reduce both endophytic nitrogen-fixing bacteria and RKN prevalence and galling in tomato plants.

CONCLUSIONS

Results demonstrated that (1) community variation and assembly of root endophytic microbiota were significantly affected by RKN parasitism; (2) a taxonomic and functional association was found for endophytic nitrogen-fixing bacteria and nematode parasitism; and (3) the change of nitrogen-fixing bacterial communities through the addition of nitrogen fertilizers could affect the occurrence of RKN. Our results provide new insights into interactions among endophytic microbiota, RKN, and plants, contributing to the potential development of novel management strategies against RKN. Video Abstract.

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.

Establishment of Arthrobotrys flagrans as biocontrol agent against the root pathogenic nematode Xiphinema index

Plant-parasitic nematodes cause devastating agricultural damage worldwide. Only a few synthetic nematicides can be used and their application is limited in fields. Therefore, there is a need for sustainable and environment-friendly alternatives. Nematode-trapping fungi (NTF) are natural predators of nematodes. They capture and digest them with their hyphae and are starting to being used as bio-control agents. In this study, we applied the NTF Arthrobotrys flagrans (Duddingtonia flagrans) against the wine pathogenic nematode Xiphinema index. A. flagrans reduced the number of X. index juveniles in pot cultures of Ficus carica, an alternative host plant for X. index, significantly. Sodium-alginate pellets with A. flagrans spores were produced for vineyard soil inoculation under laboratory conditions. The NTF A. conoides, A. musiformis and A. superba were enriched from several soil samples, showing their natural presence. Trap formation is an energy-consuming process and depends upon various biotic and abiotic stimuli. Here, we show that bacteria of the genus Delftia, Bacillus, Pseudomonas, Enterobacter and Serratia induced trap formation in NTF like A. conoides and A. oligospora but not in A. flagrans in the absence of nematodes. The application of NTF along with such bacteria could be a combinatorial way of efficient biocontrol in nematode-infested soil.

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.

The Multifaceted Gene 275 Embedded in the PKS-PTS Gene Cluster Was Involved in the Regulation of Arthrobotrisin Biosynthesis, TCA Cycle, and Septa Formation in Nematode-Trapping Fungus Arthrobotrys oligospora

The predominant nematode-trapping fungus Arthrobotrys oligospora harbors a unique polyketide synthase-prenyltransferase (PKS-PTS) gene cluster AOL_s00215g responsible for the biosynthesis of sesquiterpenyl epoxy-cyclohexenoids (SECs) that are involved in the regulation of fungal growth, adhesive trap formation, antibacterial activity, and soil colonization. However, the function of one rare gene (AOL_s00215g275 (275)) embedded in the cluster has remained cryptic. Here, we constructed two mutants with the disruption of 275 and the overexpression of 275, respectively, and compared their fungal growth, morphology, resistance to chemical stress, nematicidal activity, transcriptomic and metabolic profiles, and infrastructures, together with binding affinity analysis. Both mutants displayed distinct differences in their TCA cycles, SEC biosynthesis, and endocytosis, combined with abnormal mitochondria, vacuoles, septa formation, and decreased nematicidal activity. Our results suggest that gene 275 might function as a separator and as an integrated gene with multiple potential functions related to three distinct genes encoding the retinoic acid induced-1, cortactin, and vacuolar iron transporter 1 proteins in this nematode-trapping fungus. Our unexpected findings provide insight into the intriguing organization and functions of a rare non-biosynthetic gene in a biosynthetic gene cluster.

Repulsive response of Meloidogyne incognita induced by biocontrol bacteria and its effect on interspecific interactions

The aversive behavior of Caenorhabditis elegans is an important strategy that increases their survival under pathogen infection, and the molecular mechanisms underlying this behavior have been described. However, whether this defensive response occurs in plant-parasitic nematodes (PPNs), which have quite different life cycles and genomic sequences from the model nematode, against biocontrol microbes and affects interspecific interactions in ecological environments remains unclear. Here, we showed that Meloidogyne incognita, one of the most common PPNs, engaged in lawn-leaving behavior in response to biocontrol bacteria such as Bacillus nematocida B16 and B. thuringiensis Bt79. Genomic analysis revealed that the key genes responsible for the aversive behavior of C. elegans, such as serotonin-and TGF-β-related genes in canonical signaling pathways, were homologous to those of M. incognita, and the similarity between these sequences ranged from 30% to 67%. Knockdown of the homologous genes impaired avoidance of M. incognita to varying degrees. Calcium ion imaging showed that the repulsive response requires the involvement of the multiple amphid neurons of M. incognita. In situ hybridization specifically localized Mi-tph-1 of the serotonin pathway to ADF/NSM neurons and Mi-dbl-1 of the TGF-β pathway to AVA neurons. Our data suggested that the repulsive response induced by different biocontrol bacteria strongly suppresses the invasion of tomato host plants by M. incognita. Overall, our study is the first to clarify the pathogen-induced repulsive response of M. incognita and elucidate its underlying molecular mechanisms. Our findings provide new insights into interspecific interactions among biocontrol bacteria, PPNs, and host plants.

Amphiphysin AoRvs167-Mediated Membrane Curvature Facilitates Trap Formation, Endocytosis, and Stress Resistance in Arthrobotrysoligospora

Bin1/Amphiphysin/Rvs (BAR) domain-containing proteins mediate fundamental cellular processes, including membrane remodeling and endocytosis. Nematode-trapping (NT) fungi can differentiate to form trapping structures through highly reorganized cell membranes and walls. In this study, we identified the NT fungus Arthrobotrys oligospora ortholog of yeast Rvs167 and documented its involvement in membrane bending and endocytosis. We further confirmed that the deletion of AoRvs167 makes the fungus more hypersensitive to osmotic salt (Nacl), higher temperatures (28 to 30 °C), and the cell wall perturbation agent Congo red. In addition, the disruption of AoRvs167 reduced the trap formation capacity. Hence, AoRvs167 may regulate fungal pathogenicity through the integrity of plasma membranes and cell walls.

Tubular Sediment-Water Electrolytic Fuel Cell for Dual-Phase Hexavalent Chromium Reduction

A novel tubular sediment-water electrolytic fuel cell (SWEFC) was fabricated for the reduction of Cr(VI) in a dual-phase system. The approach simulates a standing water body with Cr(VI)-contaminated overlying water (electrolyte) and bottom sediment phase with electrodes placed in both the phases, supplemented with urea as a potential electron donor. Cr(VI) reduction efficiency of 93.2 ± 1.3% from electrolyte (in 1.5 h) and 81.2 ± 1.3% from the sediment phase (in 8 h) with an initial Cr(VI) concentration of 1,000 mg/L was observed in a single-cell configuration. The effect of initial Cr(VI) concentration, variation in sediment salinity and pH, and different electron donors on the SWEFC performance were systematically investigated. SWEFC showed enhanced performance with 2.4-fold higher current (193.9 mA) at 400 mg/L Cr(VI) concentration when cow dung was used as a low-cost alternative to urea as an electron donor. Furthermore, reactor scalability studies were carried out with nine-anode and nine-cathode configuration (3 L electrolyte and 2 kg sediment), and reduction efficiencies of 98.9 ± 0.9% (in 1 h) and 97.6 ± 2.2% (in 8 h) were observed from the electrolyte and sediment phases, respectively. The proposed sediment-water electrolytic fuel cell can be an advanced and environmentally benign strategy for Cr(VI) remediation from contaminated sediment-water interfaces along with electricity generation.

Acetylation of Sesquiterpenyl Epoxy-Cyclohexenoids Regulates Fungal Growth, Stress Resistance, Endocytosis, and Pathogenicity of Nematode-Trapping Fungus Arthrobotrys oligospora via Metabolism and Transcription

Sesquiterpenyl epoxy-cyclohexenoids (SECs) that depend on a polyketide synthase-terpenoid synthase (PKS-TPS) pathway are widely distributed in plant pathogenic fungi. However, the biosynthesis and function of the acetylated SECs still remained cryptic. Here, we identified that AOL_s00215g 273 (273) was responsible for the acetylation of SECs in Arthrobotrys oligospora via the construction of Δ273, in which the acetylated SECs were absent and major antibacterial nonacetylated SECs accumulated. Mutant Δ273 displayed increased trap formation, and nematicidal and antibacterial activities but decreased fungal growth and soil colonization. Glutamine, a key precursor for NH₃ as a trap inducer, was highly accumulated, and biologically active phenylpropanoids and antibiotics were highly enriched in Δ273. The decreased endocytosis and increased autophagosomes, with the most upregulated genes involved in maintaining DNA and transcriptional stability and pathways related to coronavirus disease and exosome, suggested that lack of 273 might result in increased virus infection and the acetylation of SECs played a key role in fungal diverse antagonistic ability.

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

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

Precision Probiotics in Agroecosystems: Multiple Strategies of Native Soil Microbiotas for Conquering the Competitor Ralstonia solanacearum

Ralstonia solanacearum (Rs), a soilborne phytopathogen, causes bacterial wilt disease in a broad range of hosts. Common approaches, for example, the direct reduction of the pathogen using classic single broad-spectrum probiotics, suffer from poor colonization efficiency, interference by resident microbiota, and nonnative-microorganism invasion. The soil microbiota plays an important role in plant health. Revealing the intrinsic linkage between the microbiome and the occurrence of disease and then applying it to agroecosystems for the precise control of soilborne diseases should be an effective strategy. Here, we surveyed the differences in the microbiome between healthy and diseased soils used for tomato planting across six climatic regions in China by using 16S rRNA amplicon and metagenomic sequencing. The roles of species associated with disease symptoms were further validated. Healthy soil possessed more diverse bacterial communities and more potential plant probiotics than diseased soil. Healthy soil simultaneously presented multiple strategies, including specifically antagonizing Rs, decreasing the gene expression of the type III secretion system of Rs, and competing for nutrition with Rs. Bacteria enriched in diseased samples promoted the progression of tomato bacterial wilt by strengthening the chemotaxis of pathogens. Therefore, Rs and its collaborators should be jointly combatted for disease suppression. Our research provides integrated insights into a multifaceted strategy for the biocontrol of tomato bacterial wilt based on the individual network of local microbiota.

IMPORTANCE In the current work, the relationship between the soil microbiota and tomato bacterial wilt on a large scale offered us a comprehensive understanding of the disease. The delicate strategy of the microbiota in soil used for growing tomatoes to conquer the strong competitor, Rs, was revealed by microbiome research. The collaborators of Rs that coexist in a common niche with Rs strengthened our understanding of the pathogenesis of bacterial wilt. Bacteria enriched in healthy soil that antagonized pathogens with high specificity provide a novel view for ecofriendly probiotics mining. Our study offers new perspectives on soilborne-pathogen biocontrol in agroecosystems by decoding the rule of the natural ecosystem.

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.

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.

Dietary S. maltophilia induces supersized lipid droplets by enhancing lipogenesis and ER-LD contacts in C. elegans

Dietary and symbiotic bacteria can exert powerful influence on metazoan lipid metabolism. Recent studies have emerged that microbiota have a role in animal obesity and related health disorders, but the mechanisms by which bacteria influence lipid storage in their host are unknown. To reduce the complexity of the relationship between gut microbiota and the host, Caenorhabditis elegans (C. elegans) has been chosen as a model organism to study interspecies interaction. Here, we demonstrate that feeding C. elegans with an opportunistic pathogenic bacterium Stenotrophomonas maltophilia (S. maltophilia) retards growth and promotes excessive neutral lipid storage. Gene expression analysis reveals that dietary S. maltophilia induces a lipogenic transcriptional response that includes the SREBP ortholog SBP-1, and fatty acid desaturases FAT-6 and FAT-7. Live imaging and ultrastructural analysis suggest that excess neutral lipid is stored in greatly expanded lipid droplets (LDs), as a result of enhanced endoplasmic reticulum (ER)-LD interaction. We also report that loss of function mutations in dpy-9 in C. elegans confers resistance to S. maltophilia. Dietary S. maltophilia induces supersized LDs by enhancing lipogenesis and ER-LD contacts in C. elegans. This work delineates a new model for understanding microbial regulation of metazoan physiology.

Arrestin-Coding Genes Regulate Endocytosis, Sporulation, Pathogenicity, and Stress Resistance in Arthrobotrys oligospora

Arrestins are a family of scaffold proteins that play a crucial role in regulating numerous cellular processes, such as GPCR signaling. The Arthrobotrys oligospora arrestin family contains 12 members, which have highly conserved N-terminal and C-terminal domains. In the presence of ammonia, A. oligospora can change its lifestyle from saprotrophic to carnivorous. During this transition, the expression pattern of arrestin-coding (AoArc) genes was markedly upregulated. Therefore, we disrupted seven AoArc genes from A. oligospora to identify their functions. Although individual arrestin mutant strains display similar pathogenesis, phenotypes, and stress resistance, the fundamental data on the roles of AoArc genes in A. oligospora are obtained in this study. Membrane endocytosis in AoArc mutants was significantly reduced. Meanwhile, the capacity of trap device formation against nematodes and ammonia was impaired due to AoArc deletions. We also found that AoArc genes could regulate conidial phenotypes, cell nuclear distribution, pH response, and stress resistance. Results of qRT-PCR assays revealed that sporulation-regulated genes were affected after the deletion of AoArc genes. In particular, among the 12 arrestins, AoArc2 mediates pH signaling in the fungus A. oligospora. Notably, combined with the classical paradigm of arrestin–GPCR signal transduction, we suggest that arrestin-regulated trap formation in A. oligospora may be directly linked to the receptor endocytosis pathway.

Natural Recovery from Fire Disturbance is More Favorable than Assisted Recovery for the Restoration of Soil Nematode-trapping Fungi

Fire is usually considered a severe disturbance factor in environment. Globally, rising temperatures and increasing human activities have intensified the severity and frequency of fire incidents; research on postfire recovery has inevitably become an important focus for ecologists. In terms of the restoration of burned areas, there are usually two primary approaches: natural recovery and assisted recovery. However, there are very few relevant studies that systematically compared these recovery alternatives suggesting which one is more favorable to the overall restoration of an ecosystem, especially to the soil microbes that function as indispensable components of ecosystems. In this study, the restoration of soil nematode-trapping fungi (NTF) was compared between natural and assisted recovery environments. Results showed that although the NTF community structures differed among the sample sites, the counts and diversity of the NTF communities in the upper and lower soil layers in the natural recovery area were higher than those in the assisted recovery and the unburned control areas. These findings suggests that artificial efforts to help ecosystem recovery after fire produce negative effects on the speed and quality of soil NTF community recovery. Instead, natural recovery appears to be the more suitable land management choice after fire disturbance.

Composted Municipal Green Waste Infused with Biocontrol Agents to Control Plant Parasitic Nematodes-A Review

The last few years have witnessed the emergence of alternative measures to control plant parasitic nematodes (PPNs). We briefly reviewed the potential of compost and the direct or indirect roles of soil-dwelling organisms against PPNs. We compiled and assessed the most intensively researched factors of suppressivity. Municipal green waste (MGW) was identified and profiled. We found that compost, with or without beneficial microorganisms as biocontrol agents (BCAs) against PPNs, were shown to have mechanisms for the control of plant parasitic nematodes. Compost supports a diverse microbiome, introduces and enhances populations of antagonistic microorganisms, releases nematicidal compounds, increases the tolerance and resistance of plants, and encourages the establishment of a "soil environment" that is unsuitable for PPNs. Our compilation of recent papers reveals that while the scope of research on compost and BCAs is extensive, the role of MGW-based compost (MGWC) in the control of PPNs has been given less attention. We conclude that the most environmentally friendly and long-term, sustainable form of PPN control is to encourage and enhance the soil microbiome. MGW is a valuable resource material produced in significant amounts worldwide. More studies are suggested on the use of MGWC, because it has a considerable potential to create and maintain soil suppressivity against PPNs. To expand knowledge, future research directions shall include trials investigating MGWC, inoculated with BCAs.

Fatal attraction of Caenorhabditis elegans to predatory fungi through 6-methyl-salicylic acid

Salicylic acid is a phenolic phytohormone which controls plant growth and development. A methyl ester (MSA) derivative thereof is volatile and involved in plant-insect or plant-plant communication. Here we show that the nematode-trapping fungus Duddingtonia flagrans uses a methyl-salicylic acid isomer, 6-MSA as morphogen for spatiotemporal control of trap formation and as chemoattractant to lure Caenorhabditis elegans into fungal colonies. 6-MSA is the product of a polyketide synthase and an intermediate in the biosynthesis of arthrosporols. The polyketide synthase (ArtA), produces 6-MSA in hyphal tips, and is uncoupled from other enzymes required for the conversion of 6-MSA to arthrosporols, which are produced in older hyphae. 6-MSA and arthrosporols both block trap formation. The presence of nematodes inhibits 6-MSA and arthrosporol biosyntheses and thereby enables trap formation. 6-MSA and arthrosporols are thus morphogens with some functions similar to quorum-sensing molecules. We show that 6-MSA is important in interkingdom communication between fungi and nematodes.

Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus Arthrobotrys oligospora in China

Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol agent NTF are geographically and ecologically structured. A previous study reported evidence for ecological adaptation in the model NTF species Arthrobotrys oligospora. However, their large-scale geographic structure, patterns of gene flow, their potential phenotypic diversification, and host specialization remain largely unknown. In this study, we developed a new panel of 20 polymorphic short tandem repeat (STR) markers and analyzed 239 isolates of A. oligospora from 19 geographic populations in China. In addition, DNA sequences at six nuclear gene loci and strain mating types (MAT) were obtained for these strains. Our analyses suggest historical divergence within the A. oligospora population in China. The genetically differentiated populations also showed phenotypic differences that may be related to their ecological adaptations. Interestingly, our analyses identified evidence for recent dispersion and hybridization among the historically subdivided geographic populations in nature. Together, our results indicate a changing population structure of A. oligospora in China and that care must be taken in selecting the appropriate strains as biocontrol agents that can effectively reproduce in agriculture soil while maintaining their nematode-trapping ability.

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.

Extraordinary Multi-Organismal Interactions Involving Bacteriophages, Bacteria, Fungi, and Rotifers: Quadruple Microbial Trophic Network in Water Droplets

Our observations of predatory fungi trapping rotifers in activated sludge and laboratory culture allowed us to discover a complicated trophic network that includes predatory fungi armed with bacteria and bacteriophages and the rotifers they prey on. Such a network seems to be common in various habitats, although it remains mostly unknown due to its microscopic size. In this study, we isolated and identified fungi and bacteria from activated sludge. We also noticed abundant, virus-like particles in the environment. The fungus developed absorptive hyphae within the prey. The bacteria showed the ability to enter and exit from the hyphae (e.g., from the traps into the caught prey). Our observations indicate that the bacteria and the fungus share nutrients obtained from the rotifer. To narrow the range of bacterial strains isolated from the mycelium, the effects of bacteria supernatants and lysed bacteria were studied. Bacteria isolated from the fungus were capable of immobilizing the rotifer. The strongest negative effect on rotifer mobility was shown by a mixture of Bacillus sp. and Stenotrophomonas maltophilia. The involvement of bacteriophages in rotifer hunting was demonstrated based on molecular analyses and was discussed. The described case seems to be an extraordinary quadruple microbiological puzzle that has not been described and is still far from being understood.

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.

Feeding Fungal-Pretreated Corn Straw Improves Health and Meat Quality of Lambs Infected with Gastrointestinal Nematodes

Simple Summary

Non-chemical strategies to control gastrointestinal nematode (GINs) infections are urgently needed to support the sustainable development of the livestock industry. The potential anti-parasitic properties in fungal-pretreated corn straw on health and meat quality of lambs infected with GINs were investigated in this study. In summary, feeding fungal-pretreated corn straw improved health and meat quality, including meat color and tenderness. Improved meat traits were attributed to fungal-pretreated corn straw providing additional dietary protein for lambs and secreting some nematicidal metabolites to repel GINs, which increased PCV and plasma iron content of lambs and reversed negative effects of GINs on meat quality.

Abstract

Infections with gastrointestinal nematodes (GIN) adversely affect meat color in lambs. Although white-rot fungi (WRF) pretreatment increases nutritional value and fiber digestion of corn straw for lambs, whether it can improve meat quality of lambs infected with GINs is unknown. The objective of this experiment was to study effects of feeding WRF-pretreated corn straw on the health and meat quality of lambs infected with GINs. Sixteen healthy Ujumqin lambs were orally drenched with 3rd-stage GINs larvae and randomly divided into two dietary treatments of control (CON) and WRF diets for 70 days of feeding. Results showed that feeding WRF-pretreated corn straw decreased L* and b* values (p < 0.05) and increased a* value (p < 0.01) of both longissimus thoracis et lumborum (LTL) and semimembranosus (SM) muscles of lambs infected with GINs. Feeding WRF-pretreatment corn straw decreased fecal egg count (p = 0.014) and increased packed cell volume (p = 0.013) of lambs from 28 d of feeding and increased plasma iron content (p = 0.008) of lambs from 56 d of the feeding. Feeding WRF-pretreatment corn straw decreased myosin heavy-chain (MyHC)-I (p = 0.032) and MyHC-IIα (p = 0.025) content in LTL muscle and MyHC-I (p = 0.022) and MyHC-IIβ (p = 0.048) in SM muscle of lambs. In conclusion, although there were no significant changes in the content of most amino acids or increased intensity of better flavor compounds, meat quality and health of lambs infected with GINs was significantly improved by feeding WRF-pretreated corn straw due to increased PCV and meat color and tenderness.

Recent Advances in the Development of Environmentally Benign Treatments to Control Root-Knot Nematodes

Root-knot nematodes (RKNs), Meloidogyne spp., are sedentary endoparasites that negatively affect almost every crop in the world. Current management practices are not enough to completely control RKN. Application of certain chemicals is also being further limited in recent years. It is therefore crucial to develop additional control strategies through the application of environmentally benign methods. There has been much research performed around the world on the topic, leading to useful outcomes and interesting findings capable of improving farmers' income. It is important to have dependable resources gathering the data produced to facilitate future research. This review discusses recent findings on the application of environmentally benign treatments to control RKN between 2015 and April 2020. A variety of biological control strategies, natural compounds, soil amendments and other emerging strategies have been included, among which, many showed promising results in RKN control in vitro and/or in vivo. Development of these methods continues to be an area of active research, and new information on their efficacy will continuously become available. We have discussed some of the control mechanisms involved and suggestions were given on maximizing the outcome of the future efforts.

AoStuA, an APSES transcription factor, regulates the conidiation, trap formation, stress resistance and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora

The APSES protein family comprises a conserved class of fungus-specific transcriptional regulators. Some members have been identified in partial ascomycetes. In this study, the APSES protein StuA (AoStuA) of the nematode-trapping fungus Arthrobotrys oligospora was characterized. Compared with the wild-type (WT) strain, three ΔAoStuA mutants grew relatively slowly, displayed a 96% reduction in sporulation capacity and a delay in conidial germination. The reduced sporulation capacity correlated with transcriptional repression of several sporulation-related genes. The mutants were also more sensitive to chemical stressors than the WT strain. Importantly, the mutants were unable to produce mycelial traps for nematode predation. Moreover, peroxisomes and Woronin bodies were abundant in the WT cells but hardly found in the cells of those mutants. The lack of such organelles correlated with transcriptional repression of some genes involved in the biogenesis of peroxisomes and Woronin bodies. The transcript levels of several genes involved in the cAMP/PKA signalling pathway were also significantly reduced in the mutants versus the WT strain, implicating a regulatory role of AoStuA in the transcription of genes involved in the cAMP/PKA signalling pathway that regulates an array of cellular processes and events. In particular, AoStuA is indispensable for A. oligospora trap formation and virulence.

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.

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

Constructed wetlands are ecofriendly, cost effective technology involved in treatment of wastewaters. The goal of this study is focused on characterization of microbial community existing in constructed wetland system planted with Cyperusalternifolius treating sewage contaminated with heavy metals. The characteristics of effluent met the standards of discharge for inland use and irrigation. Microbes in constructed wetland apparently play a pivotal role in the efficiency of system for removal of organics, nutrients, suspended solids and heavy metal. To expose the active players in the lime light, a representative soil sample from the reed bed was collected and characterized for microbial community analysis. Metagenomic studies of the bacterial and fungal flora were identified. Results revealed that the phylum Proteobacteria (38.27%) and Ascomycota (77.47%) dominated in the bacterial and fungal kingdom respectively. However, in the bacterial kingdom at species level major portion remain unclassified except Pseudomonasalcaligenes but in the fungal kingdom at species level only 3.1% remain unclassified. The role of bacteria in wastewater treatment is exemplified in previous reports but the role of fungi in wastewater system needs exploration. However, the findings reveal that the identified microbes might have definitely played a vital role in wastewater treatment. The database available for the identification of bacterial species remain undiscovered for a major portion and requires up gradation. Next generation sequence being a high end technology in microbial ecology decodes the entire community in environmental samples but lack of database limits the identification. Implementation of improvements in the paucity of data bases is essential.

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

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

Metagenomics Study of the Microbes in Constructed Wetland System Treating Sewage

Constructed wetlands are ecofriendly, cost effective technology involved in treatment of wastewaters. The goal of this study is focused on characterization of microbial community existing in constructed wetland system planted withCyperusalternifoliustreating sewage contaminated with heavy metals. The characteristics of effluent met the standards of discharge for inland use and irrigation. Microbes in constructed wetland apparently play a pivotal role in the efficiency of system for removal of organics, nutrients, suspended solids and heavy metal. To expose the active players in the lime light, a representative soil sample from the reed bed was collected and characterized for microbial community analysis. Metagenomic studies of the bacterial and fungal flora were identified. Results revealed that the phylum Proteobacteria (38.27%) and Ascomycota (77.47%) dominated in the bacterial and fungal kingdom respectively. However, in the bacterial kingdom at species level major portion remain unclassified exceptPseudomonasalcaligenesbut in the fungal kingdom at species level only 3.1% remain unclassified. The role of bacteria in wastewater treatment is exemplified in previous reports but the role of fungi in wastewater system needs exploration. However, the findings reveal that the identified microbes might have definitely played a vital role in wastewater treatment. The database available for the identification of bacterial species remain undiscovered for a major portion and requires up gradation. Next generation sequence being a high end technology in microbial ecology decodes the entire community in environmental samples but lack of database limits the identification. Implementation of improvements in the paucity of data bases is essential.

Bacterial-fungal interactions: ecology, mechanisms and challenges

Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.

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.

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

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