Rhizosphere Interactions and the Exploitation of Microbial Agents for the Biological Control of Plant-Parasitic Nematodes

AoRan1 Is Involved in Regulating Conidiation, Stress Resistance, Secondary Metabolism, and Pathogenicity in Arthrobotrys oligospora

Arthrobotrys oligospora is a representative nematode-trapping (NT) fungus that is able to capture, kill, and digest nematodes by producing specialized three-dimensional networks (traps) under nutrient-deprived conditions. Ran1 is a serine/threonine protein kinase that can act as a negative regulator of sexual conjugation and meiosis. However, the specific role of Ran1 remains largely unknown in NT fungi. Here, we identified AoRan1 (AOL_s00004g277) via gene disruption, phenotypic analysis, and metabolomic analysis. Our findings reveal that Aoran1 knockout caused a remarkable increase in conidial production, traps, and nematode feeding efficiency. In addition, the absence of Aoran1 resulted in the accumulation of lipid droplets and increased autophagic levels as well as increased tolerance to cell wall synthesis-disturbing reagents and oxidants. Metabolomic analyses also suggested that AoRan1 is involved in multiple metabolic processes, such as fatty acid biosynthesis. In summary, our results suggest that AoRan1 is crucial in conidiation, pathogenicity, and secondary metabolism. This study's results further our understanding of the molecular mechanisms by which AoRan1 regulates conidiation and trap formation in A. oligospora.

How the root bacterial community of Ficus tikoua responds to nematode infection: enrichments of nitrogen-fixing and nematode-antagonistic bacteria in the parasitized organs

Plant-parasitic nematodes (PPNs) are among the most damaging pathogens to host plants. Plants can modulate their associated bacteria to cope with nematode infections. The tritrophic plant-nematode-microbe interactions are highly taxa-dependent, resulting in the effectiveness of nematode agents being variable among different host plants. Ficus tikoua is a versatile plant with high application potential for fruits or medicines. In recent years, a few farmers have attempted to cultivate this species in Sichuan, China, where parasitic nematodes are present. We used 16S rRNA genes to explore the effects of nematode parasitism on root-associated bacteria in this species. Our results revealed that nematode infection had effects on both endophytic bacterial communities and rhizosphere communities in F. tikoua roots, but on different levels. The species richness increased in the rhizosphere bacterial communities of infected individuals, but the community composition remained similar as compared with that of healthy individuals. Nematode infection induces a deterministic assembly process in the endophytic bacterial communities of parasitized organs. Significant taxonomic and functional changes were observed in the endophytic communities of root knots. These changes were characterized by the enrichment of nitrogen-fixing bacteria, including Bradyrhizobium, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and nematode-antagonistic bacteria, such as Pseudonocardia, Pseudomonas, Steroidobacter, Rhizobacter, and Ferrovibrio. Our results would help the understanding of the tritrophic plant-nematode-bacterium interactions in host plants other than dominant crops and vegetables and would provide essential information for successful nematode management when F. tikoua were cultivated on large scales.

A Study of Soil-Borne Fusarium Wilt in Continuous Cropping Chrysanthemum Cultivar 'Guangyu' in Henan, China

Cut chrysanthemum, known as a highly favored floral choice globally, experiences a significant decline in production due to continuous cropping. The adverse physiological effects on cut chrysanthemums result from the degradation of a soil's physical and chemical properties, coupled with the proliferation of pathogens. The "Guangyu" cultivar in Xinxiang, Henan Province, China, has been specifically influenced by these effects. First, the precise pathogen accountable for wilt disease was effectively identified and validated in this study. An analysis was then conducted to examine the invasion pattern of the pathogen and the physiological response of chrysanthemum. Finally, the PacBio platform was employed to investigate the dynamic alterations in the microbial community within the soil rhizosphere by comparing the effects of 7 years of monocropping with the first year. Findings indicated that Fusarium solani was the primary causative agent responsible for wilt disease, because it possesses the ability to invade and establish colonies in plant roots, leading to alterations in various physiological parameters of plants. Continuous cropping significantly disturbed the microbial community composition, potentially acting as an additional influential factor in the advancement of wilt.

Exploring the mechanisms of host-specificity of a hyperparasitic bacterium (Pasteuria spp.) with potential to control tropical root-knot nematodes (Meloidogyne spp.): insights from Caenorhabditis elegans

Plant-parasitic nematodes are important economic pests of a range of tropical crops. Strategies for managing these pests have relied on a range of approaches, including crop rotation, the utilization of genetic resistance, cultural techniques, and since the 1950's the use of nematicides. Although nematicides have been hugely successful in controlling nematodes, their toxicity to humans, domestic animals, beneficial organisms, and the environment has raised concerns regarding their use. Alternatives are therefore being sought. The Pasteuria group of bacteria that form endospores has generated much interest among companies wanting to develop microbial biocontrol products. A major challenge in developing these bacteria as biocontrol agents is their host-specificity; one population of the bacterium can attach to and infect one population of plant-parasitic nematode but not another of the same species. Here we will review the mechanism by which infection is initiated with the adhesion of endospores to the nematode cuticle. To understand the genetics of the molecular processes between Pasteuria endospores and the nematode cuticle, the review focuses on the nature of the bacterial adhesins and how they interact with the nematode cuticle receptors by exploiting new insights gained from studies of bacterial infections of Carnorhabditis elegans. A new Velcro-like multiple adhesin model is proposed in which the cuticle surface coat, which has an important role in endospore adhesion, is a complex extracellular matrix containing glycans originating in seam cells. The genes associated with these seam cells appear to have a dual role by retaining some characteristics of stem cells.

Comparative Transcriptome Analysis Reveals the Molecular Mechanism of Bacillus velezensis GJ-7 Assisting Panax notoginseng against Meloidogyne hapla

The rhizosphere bacteria Bacillus velezensis GJ-7, as a biological control agent (BCA), has significant biological control effects on Meloidogyne hapla, and has strong colonization ability in the root of Panax notoginseng. In this study, we conducted a comparative transcriptome analysis using P. notoginseng plant roots treated with B. velezensis GJ-7 or sterile water alone and in combination with M. hapla inoculation to explore the interactions involving the P. notoginseng plant, B. velezensis GJ-7, and M. hapla. Four treatments from P. notoginseng roots were sequenced, and twelve high-quality total clean bases were obtained, ranging from 3.57 to 4.74 Gb. The Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that numerous DEGs are involved in the phenylpropane biosynthesis pathway and the MAPK signaling pathway in the roots of P. notoginseng with B. velezensis GJ-7 treatments. The analysis results of the two signaling pathways indicated that B. velezensis GJ-7 could enhance the expression of lignin- and camalexin-synthesis-related genes in plant roots to resist M. hapla. In addition, B. velezensis GJ-7 could enhance plant resistance to M. hapla by regulating the expression of resistance-related genes and transcription factors (TFs), including ETR, ERF, ChiB, WRKY22, and PR1. The expression of plant disease resistance genes in the roots of P. notoginseng with different treatments was validated by using real-time quantitative PCR (qRT-PCR), and the results were consistent with transcriptome sequencing. Taken together, this study indicated that B. velezensis GJ-7 can trigger a stronger defense response of P. notoginseng against M. hapla.

Volatile Organic Compounds of Bacillus pumilus Strain S1-10 Exhibit Fumigant Activity Against Meloidogyne incognita

Root-knot nematodes (RKNs) are highly specialized parasites that cause significant yield losses worldwide. In this study, we isolated Bacillus pumilus strain S1-10 from the rhizosphere soil of Zingiber officinale Rosc. plants and evaluated its fumigant activity against Meloidogyne incognita. S1-10 exhibited a strong repellent effect on second-stage juveniles (J2s) of M. incognita, and in vitro assays indicated that S1-10 volatile organic compounds (VOCs) suppressed J2 activity and egg hatching. Under greenhouse conditions, 71 and 79% reductions of nematodes and eggs were detected on plants treated with S-10 VOCs compared with controls. Ten VOCs were identified through gas chromatography and mass spectrometry (GC-MS), of which 2-(methylamino)-ethanol (2-ME) had strong fumigant activity against J2s of M. incognita, with an LC50 value of 1.5 mM at 12 h. These results indicate that S1-10 represents a potential novel biocontrol agent for RKNs.

Antagonistic Bacteria Bacillus velezensis VB7 Possess Nematicidal Action and Induce an Immune Response to Suppress the Infection of Root-Knot Nematode (RKN) in Tomato

Meloidogyne incognita, the root-knot nematode (RKN), a devastating plant parasitic nematode, causes considerable damage to agricultural crops worldwide. As a sedentary root parasite, it alters the root's physiology and influences the host's phytohormonal signaling to evade defense. The sustainable management of RKN remains a challenging task. Hence, we made an attempt to investigate the nematicide activity of Bacillus velezensis VB7 to trigger the innate immune response against the infection of RKN. In vitro assay, B. velezensis VB7 inhibited the hatchability of root-knot nematode eggs and juvenile mortality of M. incognita by 87.95% and 96.66%, respectively at 96 hrs. The application of B. velezensis VB7 challenged against RKN induced MAMP-triggered immunity via the expression of transcription factors/defense genes by several folds pertaining to WRKY, LOX, PAL, MYB, and PR in comparison to those RKN-inoculated and healthy control through RT-PCR. Additionally, Cytoscape analysis of defense genes indicated the coordinated expression of various other genes linked to immune response. Thus, the current study clearly demonstrated the effectiveness of B. velezensis VB7 as a potential nematicide and inducer of immune responses against RKN infestation in tomato.

Evaluation of the mechanism of action of Bacillus spp. to manage Meloidogyne incognita with split root assay, RT-qPCR and qPCR

The goal of this research is to determine the mechanism of action of two Bacillus spp. that can manage Meloidogyne incognita population density in cotton. The overall objectives are 1) determine the efficacy and direct antagonistic capabilities of the Bacillus spp. and 2) determine the systemic capabilities of the Bacillus spp. The greenhouse in planta assay indicated B. amyloliquefaciens QST713 and B. firmus I-1582 could manage M. incognita similarly to the chemical standard fluopyram. An in vitro assay determined that B. firmus I-1582 and its extracted metabolites were able to directly manage M. incognita second stage juveniles by increasing mortality rate above 75%. A split root assay, used to determine systemic capabilities of the bacteria, indicated B. amyloliquefaciens QST713 and B. firmus I-1582 could indirectly decrease the nematode population density. Another species, B. mojavensis strain 2, also demonstrated systemic capabilities but was not a successful biological control agent because it supported a high population density in greenhouse in planta assay and in the split root assay. A RT-qPCR assay was used to confirm any systemic activity observed in the split root assay. At 24 hours both B. amyloliquefaciens QST713 and B. firmus I-1582 upregulated one gene involved in the initial stages of JA synthesis pathway but not another gene involved in the later stages of JA synthesis. These results point to a JA intermediate molecule, most likely OPDA, stimulated by the bacteria rather than JA in a short-term systemic response. After 1 week, the Bacillus spp. stimulated a SA-responsive defense related gene. The long-term systemic response to the Bacillus spp. indicates salicylic acid also plays a role in defense conferred by these bacteria. The final assay was a qPCR to determine the concentration of the bacteria on the cotton roots after 24 days. Bacillus amyloliquefaciens QST713 and B. firmus I-43 1582 were able to colonize the root successfully, with the concentration after 24 days not significantly differing from the concentration at inoculation. This study identifies two bacteria that work via systemic resistance and will help aid in implementing these species in an integrated management system.

Effects of Arugula Vermicompost on the Root-Knot Nematode (Meloidogyne javanica) and the Promotion of Resistance Genes in Tomato Plants

Root-knot nematodes are the most important plantparasitic nematodes worldwide. Many efforts have been made to find non-chemical, risk-free, and environmentally friendly methods for nematode control. In this study, the effects of compost and vermicompost of arugula (Eruca sativa) on Meloidogyne javanica were investigated in three glasshouse experiments. In addition, the expression of the defense-related genes nonexpressor of pathogenesis-related 1 (NPR1) and lipoxygenase 1 (LOX1) was detected in tomato plants treated with vermicompost of arugula at 0, 2, 7, and 14 days after nematode inoculation. The result showed that the vermicompost of arugula significantly reduced the reproduction factor of the nematode by 54.4% to 70.5% in the three experiments and increased the dry weight of shoots of infected tomato plants. Gene expression analysis showed that LOX1 expression increased on the second and seventh day after nematode inoculation, while NPR1 expression decreased. The vermicompost of arugula showed stronger nematode inhibitory potential than the vermicompost of animal manure. The vermicompost of arugula is superior to arugula compost in suppressing the activity of M. javaniva and reducing its impact. It manipulates the expression of resistance genes and could induce systemic resistance against rootknot nematodes.

Antifungal potential of Azotobacter species and its metabolites against Fusarium verticillioides and biodegradation of fumonisin

AIMS

In the study, seven Plant Growth Promoting Rhizobacteria (PGPR) Azotobacter species were screened against three strains of Fusarium verticillioides to test its antifungal activity. Azotobacter strains were tested for the degradation of fumonisin produced by F. verticillioides. Secondary metabolites were isolated and characterized from the Azotobacter strains for the first time.

METHODS AND RESULTS

Potential seven Azotobacter species antifungal activity was tested following the dual culture assay against three starins of Fusarium verticillioides namely FVM-42, FVM-86, MTCC156 estimating the substantial zone of inhibition. Azotobacter species AZT-31 and AZT-50 strains significantly inhibited the growth of F. verticillioides recording drastic growth enhancement of maize under in-vitro conditions by calculating the infection incidence, vigour index and germination percentage. As confirmation, dereplication studies were conducted for the reconfirmation of Azotobacter strains by isolating from rhizoplane. Azotobacter strains played a key role in degradation of fumonisin produced by F. verticillioides reporting 98% degradation at 2hr of incubation with the pathogen. Furthermore, in the study first time we have tried to isolate and characterize the secondary metabolites from the Azotobacter strains exhibiting six compounds from the species AZT-31 (2) and AZT-50 (4). Preliminary in-vitro experiments were carriedout using the compounds extracted to check the reduction of infection incidence (90%) and increase in germination percentage upto 50 to 70% when compared to test pathogen.

CONCLUSION

Azotobacter strains referred as PGPR on influencing the growth of plant by producing certain substances that acts as stimulators on inhibiting the growth of pathogen.

SIGNIFICANCE AND IMPACT OF THE STUDY

Future perspective would be the production of active combination of carboxamide compound and Azotobacter species for preventively controlling the phytopathogenic fungi of plants and crops and also towards the treatment of seeds.

Exploring Anastomosis of Hyphae and Mating-Type Compatibility of Pochonia chlamydosporia Isolates of the Meloidogyne, Heterodera and Globodera Biotypes

The endophytic and nematophagous fungus Pochonia chlamydosporia is an efficient biological control agent of plant-parasitic nematodes. Isolates of the fungus can be allocated to a biotype group according to the nematode host, but it is unknown if genetic interchange can occur between different biotypes, which may affect their parasitic performance. An anastomosis assay was conducted in vitro to assess hyphae vegetative compatibility/incompatibility followed by a PCR-based mating-type assay genotyping of five isolates of P. chlamydosporia var. chlamydoporia of the Meloidogyne sp. (Pc10, Pc190, Pc309), Globodera sp. (Pc280) and Heterodera avenae (Pc60) biotypes, including 16 pairwise isolates combinations in four replicates. Pairwise combinations were tested on glass slides and mycelia were stained to confirm nuclei migration between anastomosing hyphae using fluorescence microscopy. Anastomosis only occurred between mycelium hyphae of the same isolate and biotype. Mating-type PCR-based molecular assays showed that all isolates were heterothallic. The MAT1-1 genotype was found in isolates Pc10, Pc190, Pc280, Pc309, and the MAT1-2 genotype in Pc60. The results showed a vegetative incompatibility among isolates, suggesting the occurrence of such interactions for their respective biotypes. Anastomosis and PCR mating-type results suggest that different fungal biotypes can occur in the same niche but that genetic incompatibility mechanisms, such as mating-type, may limit or impede viable heterokaryosis.

Rhizosphere Bacteria From Panax notoginseng Against Meloidogyne hapla by Rapid Colonization and Mediated Resistance

Root-knot nematodes (RKNs) are soil-borne pathogens that severely affect Panax notoginseng growth and productivity. Thus, there is an urgent need for biological control agents or green nematicides to control root-knot nematodes. Rhizosphere bacteria can effectively control RKNs through different mechanisms. In this study, the three rhizosphere Bacillus strains, isolated from the root of P. notoginseng, were evaluated for the nematicidal activity and biological control efficacy against root-knot nematodes. In addition, we also evaluated the colonization ability of the two bacterial strains with significant biocontrol effect and dynamic regulation of genes related to systemic resistance in P. notoginseng. The rhizosphere Bacillus velezensis GJ-7 and Bacillus cereus NS-2 showed high nematicidal activity against Meloidogyne hapla in vitro and significantly reduced the number of root galls in three different control experiments. The results of colonization experiments showed that the strains GJ-7 and NS-2 colonized P. notoginseng root rapidly and stably. Additionally, the colonization of the strains NS-2 and GJ-7 activated the defense-responsive genes in P. notoginseng. These results indicated that the B. cereus strain NS-2 and B. velezensis strain GJ-7 have the potential for successful ecological niche occupation and enhance plant resistance and therefore could be considered as potential biocontrol agents against root-knot nematodes.

Biological Control of Plant Pathogens: A Global Perspective

The increase in the world population has generated an important need for both quality and quantity agricultural products, which has led to a significant surge in the use of chemical pesticides to fight crop diseases. Consumers, however, have become very concerned in recent years over the side effects of chemical fungicides on human health and the environment. As a result, research into alternative solutions to protect crops has been imposed and attracted wide attention from researchers worldwide. Among these alternatives, biological controls through beneficial microorganisms have gained considerable importance, whilst several biological control agents (BCAs) have been screened, among them Bacillus, Pantoea, Streptomyces, Trichoderma, Clonostachys, Pseudomonas, Burkholderia, and certain yeasts. At present, biopesticide products have been developed and marketed either to fight leaf diseases, root diseases, or fruit storage diseases. However, no positive correlation has been observed between the number of screened BCAs and available marketed products. Therefore, this review emphasizes the development of biofungicides products from screening to marketing and the problems that hinder their development. Finally, particular attention was given to the gaps observed in this sector and factors that hamper its development, particularly in terms of efficacy and legislation procedures.

Soil Microbes Determine Outcomes of Pathogenic Interactions Between Radopholus similis and Fusarium oxysporum V5w2 in Tissue Culture Banana Rhizospheres Starved of Nitrogen, Phosphorus, and Potassium

The contributions of soil biota toward outcomes of pathogenic interactions between Radopholus similis and Fusarium oxysporum V5w2 in tissue culture banana plants starved of nitrogen (N), phosphorus (P), and potassium (K) were investigated. The study was based on three screenhouse factorial experiments (2 × 2 × 2) comprising of potted banana plants with or without R. similis, with or without F. oxysporum V5w2, and either grown in sterile or non-sterile soil. All plants in each of the three experiments received nutrient solutions that were deficient in N, P, or K, respectively. In all the three nutritional regimes, plants inoculated with R. similis were heavily colonized by the nematode with high percentage dead roots and necrosis, while their root biomasses were low. N-starved plants co-inoculated with R. similis and F. oxysporum V5w2 had lower percentage dead roots and tended to have numerically lower nematode density compared to those treated with R. similis only, especially in non-sterile soil. N-starved plants inoculated with R. similis had higher shoot dry weight, were taller with more leaves that were larger, compared to those not inoculated with the nematode. Plants grown in non-sterile soil had lower percentage dead roots, necrosis and R. similis density than those from sterile soil, regardless of the nutrient regime. N-starved plants from non-sterile soil were shorter with smaller leaves having decreased chlorophyll content and lower biomass, compared to those from sterile soil. By contrast, P and K starved plants from non-sterile soil were taller with larger leaves and more biomass, compared to those from sterile soil. Roots inoculated with R. similis had higher endophytic colonization by Fusarium spp., especially when co-inoculated with F. oxysporum V5w2 and grown in sterile soil among the N and K-starved plants. In conclusion, pathogenic interactions between R. similis and F. oxysporum V5w2 are predominantly suppressed by a complex of soil microbes that exert plant growth promoting effects in tissue culture banana plants through N, P, and K dependent processes. Nitrogen is the most important limiting factor in rhizosphere interactions between banana roots, beneficial microbes and the pathogens. Soil sterilization and the stringent aseptic tissue culture techniques still require the development of alternative innovative ways of conserving microbial services for sustainable agriculture.

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.

Fungal communities in bat guano, speleothem surfaces, and cavern water in Madai cave, Northern Borneo (Malaysia)

The island of Borneo is a global biodiversity hotspot. However, its limestone caves are one of its least-studied ecosystems. We report for the first time the fungal species richness, diversity and abundance from Madai cave, situated in north-eastern Borneo. Environmental samples from inside the cave environment were collected (guano, speleothem, and cavern water) via opportunistic sampling. The dilution method was performed for isolation of fungi. Morphological characterisation and molecular analysis of the ITS region were utilised for the identification of isolates. Fifty-five pure cultures of fungi were attained, comprising 32 species from 15 genera, eight orders, and two divisions, Ascomycota and Basidiomycota. Ascomycetes dominated the fungal composition, accounting for 53 (96%) out of 55 total isolates. Penicillium spp. accounted for more than 47.1% of fungal abundance in all sample types. However, Aspergillus spp. had the highest occurrence rate, being isolated from all environmental samples except one. Purpureocillium lilacinum was isolated most frequently, appearing in five separate samples across all three substrates. Annulohypoxylon nitens, Ganoderma australe, Pyrrhoderma noxium, and Xylaria feejeensis were discovered and reported for the first time from the cave environment. This study provides additional data for further research on the mycoflora of Sabah’s various ecosystems, especially limestone caves.

Biocontrol Efficacy of Bacillus cereus Strain Bc-cm103 Against Meloidogyne incognita

Root-knot nematodes (Meloidogyne spp.) are soilborne pathogens that infect vegetable crops and cause major economic losses worldwide annually. Therefore, there is an urgent need for novel nematicides or biological control agents to reduce the damage caused by root-knot nematodes. In this study, we tested efficacy of the Bacillus cereus strain Bc-cm103, isolated from the rhizoplane of Cucumis metuliferus, against Meloidogyne incognita. Strain Bc-cm103 fermentation broth caused 100% mortality of the nematode second-stage juveniles within 12 h and decreased the egg hatching rate by 40.06% within 72 h compared with sterile water. Confocal laser-scanning microscopy revealed that strain Bc-cm103 formed a biofilm on cucumber (C. sativus) roots, which protected the roots from the infection of M. incognita. Additionally, strain Bc-cm103 activated the defense-responsive genes PR1, PR2, LOX1, and CTR1 in cucumber. Furthermore, strain Bc-cm103 significantly reduced the appearance of root galls in pot, split-root, and field tests. These results indicated that B. cereus strain Bc-cm103 had a strong suppressive effect on M. incognita and therefore could be used as a potential biocontrol agent against this pathogen.

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

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

Plants Specifically Modulate the Microbiome of Root-Lesion Nematodes in the Rhizosphere, Affecting Their Fitness

Plant-parasitic nematodes are a major constraint on agricultural production. They significantly impede crop yield. To complete their parasitism, they need to locate, disguise, and interact with plant signals exuded in the rhizosphere of the host plant. A specific subset of the soil microbiome can attach to the surface of nematodes in a specific manner. We hypothesized that host plants recruit species of microbes as helpers against attacking nematode species, and that these helpers differ among plant species. We investigated to what extend the attached microbial species are determined by plant species, their root exudates, and how these microbes affect nematodes. We conditioned the soil microbiome in the rhizosphere of different plant species, then employed culture-independent and culture-dependent methods to study microbial attachment to the cuticle of the phytonematode Pratylenchus penetrans. Community fingerprints of nematode-attached fungi and bacteria showed that the plant species govern the microbiome associated with the nematode cuticle. Bacteria isolated from the cuticle belonged to Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Sphingobacteria, and Firmicutes. The isolates Microbacterium sp. i.14, Lysobacter capsici i.17, and Alcaligenes sp. i.37 showed the highest attachment rates to the cuticle. The isolates Bacillus cereus i.24 and L. capsici i.17 significantly antagonized P. penetrans after attachment. Significantly more bacteria attached to P. penetrans in microbiome suspensions from bulk soil or oat rhizosphere compared to Ethiopian mustard rhizosphere. However, the latter caused a better suppression of the nematode. Conditioning the cuticle of P. penetrans with root exudates significantly decreased the number of Microbacterium sp. i.14 attaching to the cuticle, suggesting induced changes of the cuticle structure. These findings will lead to a more knowledge-driven exploitation of microbial antagonists of plant-parasitic nematodes for plant protection.

Putative LysM Effectors Contribute to Fungal Lifestyle

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

Factors affecting success of biological agents used in controlling the plant-parasitic nematodes

Biological control agents (BCAs) are increasingly used against various plant-parasitic nematode (PPN) pests and offer a favorable alternative to hazardous chemical nematicides. Yet, their lack of efficacy, inconsistent field performance, and/or unfavorable economic factors have generally relegated them to a relatively small sector of pesticide market. Efficacy and biocontrol success can be boosted via holistic grasping of soil biological and ecological factors. Therefore, such factors were highlighted to give better directions for their use. Main points discussed currently are considered to affect the transmission success of these BCAs so that their use must be a way forward in crop protection/pest management. These included improved sampling, grasping BCAs interactions with soil biota and ecology, cost-effective use of BCAs, genetic manipulation for better PPN control, grower acceptance and awareness-raising of BCA techniques, and commercial application.

Bacterial Microbiota Isolated from Cysts of Globodera rostochiensis (Nematoda: Heteroderidae)

The potato cyst nematode (PCN) Globodera rostochiensis is a plant parasite of potato classified into a group of quarantine organisms causing high economic losses worldwide. Due to the long persistence of the parasite in soil, cysts harbor numerous bacteria whose presence can lead to cyst death and population decline. The cysts of G. rostochiensis found in two potato fields were used as a source of bacteria. The universal procedure was applied to extract DNA from bacteria which was then sequenced with 16S primers. The aims of the study were to identify bacterial microbiota associated with the PCN populations and to infer their phylogenetic relationships based on the maximum likelihood and Bayesian phylogeny of the 16S sequences. In addition, the impact of the most significant climate and edaphic factors on bacterial diversity were evaluated. Regarding the higher taxonomy, our results indicate that the prevalent bacterial classes were Bacilli, Actinobacteria and Alphaproteobacteria. Phylogenetic analyses clustered Brevibacterium frigoritolerans within the family Bacillaceae, confirming its recent reclassification. Long-term climate factors, such as air temperature, insolation hours, humidity and precipitation, as well as the content of soil organic matter, affected the bacterial diversity. The ability of cyst nematodes to persist in soil for a long time qualifies them as a significant natural source to explore the soil bacterial microbiota.

Biomanagement of rice root-knot nematode Meloidogyne graminicola using five indigenous microbial isolates under pot and field trials

AIMS

To ascertain the effectiveness of Aspergillus niger, Trichoderma harzianum, Pochonia chlamydosporia, Bacillus subtilis and Pseudomonas fluorescens against rice root-knot nematode, Meloidogyne graminicola, and to optimize their application methods.

METHODS AND RESULTS

The relative effectiveness of five indigenous biocontrol agents (BCA) against M. graminicola on rice cv. PS-5 was tested initially in pot culture. The BCAs, A. niger, P. chlamydosporia and P. fluorescens proved more effective, and significantly reduced the nematode disease. It is hypothesized that success of a biocontrol module may vary with the BCA and application methods. Hence, the effectiveness of the above three BCAs as well as seven different treatment schemes were evaluated in naturally infested farmer's fields during 2 consecutive years. In nematode-infested plots without any BCA treatments, terminal galls formed on the roots, and plants suffered a 19-31% decrease in the growth and yield. The treatments with P. chlamydosporia or A. niger through root-dip (RD) plus one soil application (SA) at 15 days after planting were found to be highly effective against the nematode.

CONCLUSIONS

Relatively greater nematode control was achieved with RD plus two SAs (15 + 30 DAP) but statistically the effect was on par with RD + one SA at 15 DAP. These treatments significantly reduced galling (22-25%), egg mass production (21-29%) and reproduction factor (63-70%) of M. graminicola, and subsequently increased the grain yield (11-21%).

SIGNIFICANCE AND IMPACT OF THE STUDY

Application methods enhanced the effectiveness of BCAs against M. graminicola. The RD plus one SA at 15 DAP proved to be most effective treatment to control root-knot disease in rice. Use of multiple treatments (root dip and SA) appears cumbersome, but in view of effectiveness and limitation of chemical control in rice paddies, farmers may adopt the above module that may lead to 11-21% yield improvement.

Organic Fertilization Assembles Fungal Communities of Wheat Rhizosphere Soil and Suppresses the Population Growth of Heterodera avenae in the Field

Heterodera avenae (cereal cyst nematode, CCN) infects wheat and other cereal crops and causes severe losses in their yield. Research has shown that CCN infestations can be mitigated by organic fertilization in wheat fields, but the mechanisms underlying this phenomenon are still largely unknown. In this study, the relationships among CCN, soil properties, and soil fungal communities with organic fertilizer (OF) or chemical fertilizer (CF) and without fertilizer (CK), were investigated for two years in a wheat field in Henan province, China. Our results showed that the concentrations of soil total N, total P, available P, available K, and organic matter were all promoted by the OF treatment at the jointing stage of wheat, coinciding with the peak in egg hatching and penetration of wheat root by CCNs. Soil total N correlated positively (R² = 0.759, p < 0.05) with wheat yields but negatively (R² = 0.663, p < 0.01) with Pf/Pi (index of cyst nematode reproduction), implying the regulated soil property contributes to suppressing CCN in the OF treatment. Furthermore, fungal community α-diversity (Shannon and Simpson) and β-diversity (PCoA) of rhizosphere soil was improved under the organic fertilizer treatment. The fungal genera negatively associated with the Pf/Pi of CCN were highly enriched, which included Mortierella and Chaetomium, two taxa already reported as being nematophagous fungi in many other studies. These two genera were heavily surrounded by much more related fungal genera in the constructs co-occurrence network. These results suggested that the OF treatment shifted soil fungal community functioning towards the suppression of CCN. Taken together, the suppressed cyst nematode reproduction with the assembly of fungal communities in the rhizosphere led to greater wheat yields under organic fertilization. These findings provide an in-depth understanding of the benefits provided by organic fertilization for developing sustainable agriculture.

Diversity of Nematode Microbial Antagonists from Algeria Shows Occurrence of Nematotoxic Trichoderma spp

Fungi and bacteria associated to phytoparasitic nematodes Globodera rostochiensis and Meloidogyne spp. in Algeria were identified and characterized. Trichoderma spp. showed the highest prevalence in the cysts of G. rostochiensis. A number of isolates were identified through PCR amplification and the sequencing of the internal transcribed spacer (ITS)1-2 and Rpb2 gene regions. The most represented species were T. harzianum and T. afroharzianum. The latter and T. hirsutum were reported for the first time in Algeria. Fusarium spp., including F. oxysporum and F. solani, comprised a second group of fungi found in cysts. Taxa associated to females of Meloidogyne spp. included T. harzianum, Fusarium spp. and other hyphomycetes. To assess the efficacy of Trichoderma spp., two assays were carried out in vitro with the culture filtrates of two T. afroharzianum and T. harzianum isolates, to check their toxicity versus the second stage juveniles of M. incognita. After 24–48 h exposure, a mortality significantly higher than the control was observed for both filtrates at 1% dilutions. The TRI genes involved in the production of trichothecenes were also amplified with the PCR from some Trichoderma spp. isolates and sequenced, supporting a putative role in nematode toxicity. Bacteria isolated from the cysts of G. rostochiensis included Brucella,Rhizobium, Stenotrophomonas and Bacillus spp., identified through 16S rRNA gene sequencing. The potential of the microbial isolates identified and their mechanisms of action are discussed, as part of a sustainable nematode management strategy.

Isolation and identification of induced systemic resistance determinants from Bacillus simplex Sneb545 against Heterodera glycines

Heterodera glycines is one of the most destructive pathogens of soybean. Soybean seeds coated with Bacillus simplex Sneb545 have shown resistance to H. glycines as a result of induced systemic resistance (ISR) in the plants. In this study, we aimed to identify the resistance-inducing determinants from this B. simplex strain. Combining the ISR bioassay, six ISR-active compounds were isolated from a culture of B. simplex Sneb545 using organic solvent gradient extraction, silica gel column chromatography, Sephadex LH-20 column chromatography, and semi-preparative high-performance liquid chromatography (HPLC), and all systems were based on activity tracking. The compounds were determined as cyclic(Pro-Tyr), cyclic(Val-Pro), cyclic(Leu-Pro), uracil, phenylalanine, and tryptophan using 1H NMR and 13C NMR. In plants from seeds coated with Bacillus simplex Sneb545, these six ISR-active compounds delayed the development of H. glycines in soybean roots. Moreover, cyclic(Pro-Tyr), cyclic(Val-Pro), and tryptophan reduced the number of nematodes in soybean roots. The expression levels of defense-related genes with cyclic(Val-Pro), tryptophan and uracil treatment soybean analysed using Quantitative real-time PCR (qRT-PCR). The results indicate cyclic(Val-Pro), tryptophan and uracil induced the expression of defense-related genes involved in the SA- and JA-pathways to against H. glycines. Our research results provide new agents for the control of H. glycines.

In vitro evaluation of Penicillium chrysogenum Snef1216 against Meloidogyne incognita (root-knot nematode)

Root-knot nematode (Meloidogyne incognita) is chief plant parasitic nematode of various crops globally. Meanwhile, the negative side effects on human health and environmental concerns associated with haphazard uses of chemical nematicides. Hence, the search for a safe and effective approach is more relevant. The present study was aimed to evaluate the nematicidal potential of Snef1216 (Penicillium chrysogenum) against M. incognita at different concentrations (5%, 10%, 25%, 50%, 75% and 100%) and with the nutritious medium. The egg hatching inhibition and mortality of second stage juveniles of M. incognita were assessed after 6, 12, 24, 48 and 72 h exposure. Results revealed that egg hatching inhibition and percent mortality of M. incognita increased with increasing concentration and exposure time. The highest mortality of juveniles was recorded at 100% conc. i.e., 24.20%, 36%, 66%, 78% and 97.8% at 6, 12, 24, 48 and 72 h, respectively. The highest ovicidal activity was recorded at 100% concentration with 5.20% of eggs hatching. The outcome suggested that Snef1216 (P. chrysogenum) resulted in the lowest LC₅₀ value was recorded as 3718.496 at 6 h exposure period followed by 10479.87, 11186.682, 14838.58 and 24001.430 at 72, 12, 48 and 24 h respectively via ovicidal assay. Whereas, in the larvicidal assay, the lowest LC₅₀ value demonstrated at 72 h being 17.628% exposure period followed by 28.345, 50.490, 215.710 and 482.595% at 48, 24, 12 and 6 h respectively. It is concluded that Snef1216 has potential being used as a biocontrol agent against M. incognita and can serve as a source of a novel nematicidal agent of fungal origin.

Exploring the key microbial changes in the rhizosphere that affect the occurrence of tobacco root-knot nematodes

Root-knot nematode (RKN) disease is a soil-borne disease. However, most studies on RKN have focused on the screening of agents and the cultivation of resistant varieties, and reports on the interaction of RKNs with soil microorganisms are few. In this study, we performed Illumina high-throughput sequencing to analyze diseased and healthy soil and the microbial-community changes in rhizosphere soil after microbial treatment (Pseudomonas flurescens, Bacillus subtilis, Paecolomyces lilacinus). Results showed significant differences in the bacterial community richness and diversity between diseased and healthy soil and the presence of different microbial species. After treatment, the richness and diversity of microbial communities in soil, as well as the number and incidence of second-stage juvenile of RKNs, decreased. Through linear discriminant analysis effect size, Pearson correlation, and Venn diagram analysis, we screened five genera that were closely related to disease occurrence, among which Pseudomonas was most related to disease inhibition. Our results suggested that the occurrence of tobacco RKN was related to changes in soil microbial communities, and that the interactions among Pseudomonas, Bryobacter, Variibacter, Coniochaeta, and Metarhizium affected the health of rhizosphere soil.

Harnessing the gut microbiome in the fight against anthelminthic drug resistance

Intestinal helminth parasites present major challenges to the welfare of humans and threaten the global food supply. While the discovery of anthelminthic drugs empowered our ability to offset these harms to society, the alarming rise of anthelminthic drug resistance mitigates contemporary efforts to treat and control intestinal helminthic infections. Fortunately, emerging research points to potential opportunities to combat anthelminthic drug resistance by harnessing the gut microbiome as a resource for discovering novel therapeutics and informing responsible drug administration. In this review, we highlight research that demonstrates this potential and provide rationale to support increased investment in efforts to uncover and translationally utilize knowledge about how the gut microbiome mediates intestinal helminthic infection and its outcomes.

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.

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

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

Cyclo(l-Pro⁻l-Leu) of Pseudomonas putida MCCC 1A00316 Isolated from Antarctic Soil: Identification and Characterization of Activity against Meloidogyne incognita

Pseudomonas putida MCCC 1A00316 was originally isolated from an Antarctic soil and has demonstrated potential nematicidal activity. Thus, it has promising applications for the biological control of Meloidogyne incognita. The larval mortality and egg-hatching inhibition rates of M. incognita will increase with the rising concentration of culture filtrates of P. putida MCCC 1A00316 and the duration of exposure. Thus, this study aimed to separate, purify, and identify nematicidal compounds from P. putida MCCC 1A00316 and to validate their anti-M. incognita activities. Compounds were purified through silica gel column chromatography and thin-layer chromatography combined with high-performance liquid chromatography (HPLC). Structural identification was conducted through liquid chromatography time-of-flight mass spectrometry, ¹H nuclear magnetic resonance (NMR) spectroscopy, ¹³C-NMR, and Marfey’s method. The isolated compounds were identified as cyclo(l-Pro–l-Leu) on the basis of the results of the above analyses and previously reported data. The effects of various concentrations of cyclo(l-Pro–l-Leu) on the mortality rates of second-stage juveniles (J2) of M. incognita were investigated. Results showed that HPLC-purified cyclo(l-Pro–l-Leu) displayed nematicidal activities. The mortality rate of M. incognita J2 reached 84.3% after 72 h of exposure to 67.5 mg/L cyclo(l-Pro–l-Leu). The lowest egg-hatching rate (9.74%) was observed after 8 days of incubation with 2000 mg/L cyclo(l-Pro–l-Leu). An egg-hatching rate of 53.11% was obtained under the control treatment (sterile distilled water). However, cyclo(l-Pro–l-Leu) did not elicit chemotaxis activity to M. incognita. This is the first work to investigate the anti-M. incognita characteristics of cyclo(l-Pro–l-Leu).

Isolation and identification of Ammodendron bifolium endophytic bacteria and the action mechanism of selected isolates-induced seed germination and their effects on host osmotic-stress tolerance

This study aimed to identify Ammodendron bifolium endophytic bacteria, and to evaluate promoting mechanism of selected isolates on seed germination and their effects on host osmotic-stress tolerance. Forty-five strains were isolated from A. bifolium and were classified into 13 different genera by 16S rDNA gene sequence analysis. AY3, AY9 and AG18, which were identified as Staphylococcus, Kocuria, Bacillus sp., promoted host seed ethylene release during germination. Ethrel and 1-aminocyclopropane-1-carboxylic acid (ACC) imitated the effect of AY3, AY9 and AG18 on seed germination. The data suggest that ethylene mediates AY3-, AY9-, AG18-induced A. bifolium seed germination. In addition, osmotic stress prevented seed germination and radicle elongation. However, the inhibitory effect of osmotic stress on seed germination and radicle elongation were rescued by AY3, AY9 and AG18. The results show that AY3, AY9 and AG18 increased osmotic-stress tolerance in A. bifolium. AY3, AY9, AG18 induced A. bifolium seed germination through promoting ethylene production during endophytic bacteria-plant interaction, and increase osmotic-stress tolerance in A. bifolium. AY3, AY9 and AG18 are potential candidates for the protection of A. bifolium.

Bacterial community assemblages in the rhizosphere soil, root endosphere and cyst of soybean cyst nematode-suppressive soil challenged with nematodes

In disease-suppressive soil, plants rely upon mutualistic associations between roots and specific microbes for nutrient acquisition and disease suppression. Notably, the transmission of suppressiveness by the cysts of sugar beet cyst nematode from suppressive to conducive soils has been previously observed in greenhouse trials. However, our current understanding of the bacterial assemblages in the cyst, root endosphere and rhizosphere soil is still limited. To obtain insights into these bacterial microbiota assemblages, the bacterial communities inhabiting the plant-associated microhabitats and cysts in soybean cyst nematode (SCN)-suppressive soil were characterized by deep sequencing, using soybean grown under growth room conditions with additional SCN challenge. Clustering analysis revealed that the cyst bacterial community was closer to the root endosphere community than to the rhizosphere and bulk soil communities. Interestingly, the cyst bacterial community was initially established by the consecutive selection of bacterial taxa from the soybean root endosphere. We found a set of potential microbial consortia, such as Pasteuria, Pseudomonas, Rhizobium, and other taxa, that were consistently enriched in the rhizocompartments under SCN challenge, and more abundant in the cysts than in the bulk soil. Our results suggest that the soybean root-associated and cyst microbiota may cause the suppressiveness of SCN in suppressive soil.

Utilization of Nematode Destroying Fungi for Management of Plant-Parasitic Nematodes-A Review

Nematode destroying fungi are potential biocontrol agent for management of plant-parasitic nematodes. They inhibit nematode population through trapping devices or by means of enzymes and metabolic products. They regulate nematode behavior by interfering plant-nematode recognition, and promote plant growth. For more effective biocontrol, thorough understanding of the biology of nematode destroying fungi, targeted nematode pest and the soil ecology and environmental condition in the field is necessary. This review highlights different types of nematode destroying fungi, their mode of action as well as commercial products based on reports published in this area of research.

Hydrogen Cyanide Produced by Pseudomonas chlororaphis O6 Exhibits Nematicidal Activity against Meloidogyne hapla

Root-knot nematodes (Meloidogyne spp.) are parasites that attack many field crops and orchard trees, and affect both the quantity and quality of the products. A root-colonizing bacterium, Pseudomonas chlororaphis O6, possesses beneficial traits including strong nematicidal activity. To determine the molecular mechanisms involved in the nematicidal activity of P. chlororaphis O6, we constructed two mutants; one lacking hydrogen cyanide production, and a second lacking an insecticidal toxin, FitD. Root drenching with wild-type P. chlororaphis O6 cells caused juvenile mortality in vitro and in planta. Efficacy was not altered in the fitD mutant compared to the wild-type but was reduced in both bioassays for the mutant lacking hydrogen cyanide production. The reduced number of galls on tomato plants caused by the wild-type strain was comparable to that of a standard chemical nematicide. These findings suggest that hydrogen cyanide-producing root colonizers, such as P. chlororaphis O6, could be formulated as "green" nematicides that are compatible with many crops and offer agricultural sustainability.

Impact of agricultural practices and environmental variables on plant-parasitic nematode communities in fields at a landscape scale

Agricultural practices shaping plant-parasitic nematode (PPN) assembly are still unclear, and this limits our understanding of the impact of anthropic disturbances on the resilience of PPN communities and the emergence of agronomic problems. Here the abundance and diversity of PPN in France’s oilseed rape production area was determined by sampling 72 fields over two consecutive years. We identified and counted PPN taxa and collected anthropic and environmental variables for the past 5 years. PPN were assigned to seven genera and one family including PPN that have not been identified to genus level. Using multiple correspondence analyses, we selected the main variables and tested their effect on the abundance of each taxon with mixed generalised linear models. We emphasise that at the landscape scale investigated, crop rotations were no longer a major factor impacting the PPN communities. However, we observed that tillage and pesticides had a significant impact on several taxa.

Possible mechanisms of control of Fusarium wilt of cut chrysanthemum by Phanerochaete chrysosporium in continuous cropping fields: A case study

Continuous cropping is a universal challenge in agriculture because it has adverse physiological effects on plants, resulting in stunting, inferior quality, and even massive loss in harvest due to diseases. In this study, Phanerochaete chrysosporium was inoculated into the field in which cut chrysanthemum had already been continuously cropped for five years to control wilt disease. After 120 days of cultivation, the addition of P. chrysosporium significantly improved the physiological status of plants and changed the bacterial and fungal community structure in the soil. The bacterial quantity in the treatment increased by 1.76 times, but the fungal quantity, especially the quantity of Fusarium oxysporum, decreased significantly in comparison with the control. The investigation into the mechanisms of control of Fusarium wilt of cut chrysanthemum by P. chrysosporium showed that P. chrysosporium in soil can inhibit the growth of F. oxysporum and decrease p-hydroxybenzoic acid (HA), which stimulates the propagation of F. oxysporum. Based on current evidence, the inhibition by P. chrysosporium and change in HA appear to be the main causes of the alleviation of wilt disease in the treatment. Other factors, such as nutrients, might also have an influence on the wilt disease of cut chrysanthemum.

An Enterotoxin-Like Binary Protein from Pseudomonas protegens with Potent Nematicidal Activity

Soil microbes are a major food source for free-living soil nematodes. It is known that certain soil bacteria have evolved systems to combat predation. We identified the nematode-antagonistic Pseudomonas protegens strain 15G2 from screening of microbes. Through protein purification we identified a binary protein, designated Pp-ANP, which is responsible for the nematicidal activity. This binary protein inhibits Caenorhabditis elegans growth and development by arresting larvae at the L1 stage and killing older-staged worms. The two subunits, Pp-ANP1a and Pp-ANP2a, are active when reconstituted from separate expression in Escherichia coli. The binary toxin also shows strong nematicidal activity against three other free-living nematodes (Pristionchus pacificus, Panagrellus redivivus, and Acrobeloides sp.), but we did not find any activity against insects and fungi under test conditions, indicating specificity for nematodes. Pp-ANP1a has no significant identity to any known proteins, while Pp-ANP2a shows ∼30% identity to E. coli heat-labile enterotoxin (LT) subunit A and cholera toxin (CT) subunit A. Protein modeling indicates that Pp-ANP2a is structurally similar to CT/LT and likely acts as an ADP-ribosyltransferase. Despite the similarity, Pp-ANP shows several characteristics distinct from CT/LT toxins. Our results indicate that Pp-ANP is a new enterotoxin-like binary toxin with potent and specific activity to nematodes. The potency and specificity of Pp-ANP suggest applications in controlling parasitic nematodes and open an avenue for further research on its mechanism of action and role in bacterium-nematode interaction.

IMPORTANCE This study reports the discovery of a new enterotoxin-like binary protein, Pp-ANP, from a Pseudomonas protegens strain. Pp-ANP shows strong nematicidal activity against Caenorhabditis elegans larvae and older-staged worms. It also shows strong activity on other free-living nematodes (Pristionchus pacificus, Panagrellus redivivus, and Acrobeloides sp.). The two subunits, Pp-ANP1a and Pp-ANP2a, can be expressed separately and reconstituted to form the active complex. Pp-ANP shows some distinct characteristics compared with other toxins, including Escherichia coli enterotoxin and cholera toxin. The present study indicates that Pp-ANP is a novel binary toxin and that it has potential applications in controlling parasitic nematodes and in studying toxin-host interaction.

The spo0A-sinI-sinR Regulatory Circuit Plays an Essential Role in Biofilm Formation, Nematicidal Activities, and Plant Protection in Bacillus cereus AR156

The rhizosphere bacterium Bacillus cereus AR156 is capable of forming biofilms, killing nematodes, and protecting plants. However, the underlying molecular mechanisms of these processes are not well understood. In this study, we found that the isogenic mutants ΔBcspo0A and ΔBcsinI have significantly reduced colonization and nematicidal activity in vitro and biological control efficacy on the tomato plant under greenhouse conditions. We further investigated the role of the spo0A-sinI-sinR regulatory circuit in biofilm formation, killing against nematodes, and biological control in AR156. Results from mutagenesis of those regulatory genes in AR156 and their heterologous expression in B. subtilis suggested that the spo0A-sinI-sinR genetic circuit is not only essential for biofilm formation and cell differentiation in AR156 but also able to functionally replace their counterparts in B. subtilis in a nearly indistinguishable fashion. Genome-wide transcriptional profiling in the wild type and the ΔBcspo0A and ΔBcsinI mutants further revealed hundreds of differentially expressed genes, likely positively regulated by both Spo0A and SinI (via SinR) in AR156. Among them, 29 genes are predicted to be directly controlled by SinR, whose counterpart in B. subtilis is a biofilm master repressor. Collectively, our studies demonstrated the essential role of the spo0A-sinI-sinR regulatory circuit in biofilm formation, cell differentiation, and bacteria-host interactions in B. cereus AR156.