Bacteria isolated from the cuticle of plant-parasitic nematodes attached to and antagonized the root-knot nematode Meloidogyne hapla

Cover crop rotation suppresses root-knot nematode infection by shaping soil microbiota

Cover crop integration into grain crop rotations is a promising strategy for mitigating nematode-induced diseases in agriculture. However, the precise mechanisms underlying this phenomenon remain elusive. Here, we first assessed the impact of five commonly used cover crops on the suppression of rice root-knot nematodes (RKNs). We then chose ryegrass as a model to explore the mechanistic basis of the suppression effect. Contrary to expectations, while ryegrass rotation significantly enhances soil fertility, this increased fertility has minimal impact on RKN suppression. Furthermore, neither integrated ryegrass residues nor root exudates exhibit direct toxicity towards RKNs. We demonstrated that ryegrass rotation primarily suppresses RKNs by enriching beneficial soil microbiota. By complementing with isolated bacteria strains, we further demonstrated that ryegrass-enriched bacteria not only directly reduce RKN infectivity and preference, but also activate plant immunity via the OsLRR-RLK-MAPK-WRKY-JA cascade, thereby diminishing RKN infection. Our study highlights the crucial role of soil microbiota in plant-nematode interactions, challenging conventional views on the direct effects of cover crops in nematode suppression. It offers a mechanistic understanding of the regulation potential and action modes of cover crops in mitigating nematode diseases, providing valuable insights for sustainable agriculture.

Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes

The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.

Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism

BACKGROUND

The interplay between root-knot nematode (RKN) parasitism and the complex web of host-associated microbiota has been recognized as pivotal for effective management of the pest. However, studies assessing this relationship have focussed on the bacterial and fungal communities, neglecting the unicellular eukaryotic members. Here, we employed amplicon sequencing analysis of the bacterial 16S rRNA, fungal ITS and eukaryotic 18S rRNA genes, and comprehensively examined how the microbiome composition, diversity and networking developed with time in the rhizospheres and roots of RKN-inoculated and non-inoculated tomato plants.

RESULTS

As expected, infection with the RKN Meloidogyne incognita decreased plant growth. At individual timepoints, we found distinct bacterial, fungal and eukaryote community structures in the RKN-inoculated and non-inoculated rhizospheres and roots, and RKN inoculation affected several taxa in the root-associated microbiome differentially. Correlation analysis revealed several bacterial and fungal and few protist taxa that correlated negatively or positively with M. incognita. Moreover, network analysis using bacterial, fungal and eukaryotic data revealed more dynamic networks with higher robustness to disturbances in the RKN-inoculated than in the non-inoculated rhizospheres/roots. Hub taxa displayed a noticeable successional pattern that coincided with different phases of M. incognita parasitism. We found that fungal hubs had strong negative correlations with bacteria and eukaryotes, while positive correlations characterized hub members within individual kingdoms.

CONCLUSION

Our results reveal dynamic tomato-associated microbiomes that develop along different trajectories in plants suffering M. incognita infestation and non-infested plants. Overall, the results identify stronger associations between RKN and bacterial and fungal taxa than between eukaryotic taxa and RKN, suggesting that fungal and bacterial communities could play a larger role in the regulation of RKN. The study identifies several putative RKN-antagonistic bacterial and fungal taxa and confirms the antagonistic potential previously identified in other taxa.

Redundancy in microbiota-mediated suppression of the soybean cyst nematode

BACKGROUND

Soybean cyst nematodes (SCN) as animal parasites of plants are not usually interested in killing the host but are rather focused on completing their life cycle to increase population, resulting in substantial yield losses. Remarkably, some agricultural soils after long-term crop monoculture show a significant decline in SCN densities and suppress disease in a sustainable and viable manner. However, relatively little is known about the microbes and mechanisms operating against SCN in such disease-suppressive soils.

RESULTS

Greenhouse experiments showed that suppressive soils (S) collected from two provinces of China and transplantation soils (CS, created by mixing 10% S with 90% conducive soils) suppressed SCN. However, SCN suppressiveness was partially lost or completely abolished when S soils were treated with heat (80 °C) and formalin. Bacterial community analysis revealed that the specific suppression in S and CS was mainly associated with the bacterial phylum Bacteroidetes, specifically due to the enrichment of Chitinophaga spp. and Dyadobacter sp., in the cysts. SCN cysts colonized by Chitinophaga spp. showed dramatically reduced egg hatching, with unrecognizable internal body organization of juveniles inside the eggshell due to chitinase activity. Whereas, Dyadobacter sp. cells attached to the surface coat of J2s increased soybean resistance against SCN by triggering the expression of defence-associated genes. The disease-suppressive potential of these bacteria was validated by inoculating them into conducive soil. The Dyadobacter strain alone or in combination with Chitinophaga strains significantly decreased egg densities after one growing cycle of soybeans. In contrast, Chitinophaga strains alone required more than one growing cycle to significantly reduce SCN egg hatching and population density.

CONCLUSION

This study revealed how soybean monoculture for decades induced microbiota homeostasis, leading to the formation of SCN-suppressive soil. The high relative abundance of antagonistic bacteria in the cyst suppressed the SCN population both directly and indirectly. Because uncontrolled proliferation will likely lead to quick demise due to host population collapse, obligate parasites like SCN may have evolved to modulate virulence/proliferation to balance these conflicting needs. Video Abstract.

Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors

Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.

Metagenomic profiling of tomato rhizosphere delineates the diverse nature of uncultured microbes as influenced by Bacillus velezensis VB7 and Trichoderma koningiopsis TK towards the suppression of root-knot nematode under field conditions

The plant-parasitic Root Knot Nematodes (Meloidogyne spp.,) play a pivotal role to devastate vegetable crops across the globe. Considering the significance of plant-microbe interaction in the suppression of Root Knot Nematode, we investigated the diversity of microbiome associated with bioagents-treated and nematode-infected rhizosphere soil samples through metagenomics approach. The wide variety of organisms spread across different ecosystems showed the highest average abundance within each taxonomic level. In the rhizosphere, Proteobacteria, Firmicutes, and Actinobacteria were the dominant bacterial taxa, while Ascomycota, Basidiomycota, and Mucoromycota were prevalent among the fungal taxa. Regardless of the specific treatments, bacterial genera like Bacillus, Sphingomonas, and Pseudomonas were consistently found in high abundance. Shannon diversity index vividly ensured that, bacterial communities were maximum in B. velezensis VB7-treated soil (1.4-2.4), followed by Root Knot Nematode-associated soils (1.3-2.2), whereas richness was higher with Trichoderma konigiopsis TK drenched soils (1.3-2.0). The predominant occurrence of fungal genera such as Aspergillus Epicoccum, Choanephora, Alternaria and Thanatephorus habituate rhizosphere soils. Shannon index expressed the abundant richness of fungal species in treated samples (1.04-0.90). Further, refraction and species diversity curve also depicted a significant increase with maximum diversity of fungal species in B. velezensis VB7-treated soil than T. koningiopsis and nematode-infested soil. In field trial, bioagents-treated tomato plant (60% reduction of Meloidogyne incognita infection) had reduced gall index along with enhanced plant growth and increased fruit yield in comparison with the untreated plant. Hence, B. velezensis VB7 and T. koingiopsis can be well explored as an antinemic bioagents against RKN.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03851-1.

Nematodes: an overlooked tiny engineer of plant health

Nematodes are a crucial component of rhizosphere biodiversity, affecting plant health as the most abundant and functionally diverse soil animals. Plant-parasitic nematodes are generally considered harmful, which may overlook their potential benefits to plants when coexisting with free-living nematodes in soil. We provide new insights into nematodes as vital plant partners. Plant root damage by plant-parasitic nematodes creates opportunities for pathogens and beneficial microbiota to colonize the rhizosphere. Free-living nematodes coordinate microbiota to suppress plant diseases, but they are susceptible to mortality from plant pathogens, potentially favoring pathogen release in the root zone. We conclude that the nematode's role in regulating plant pathogens represents a missing link, constraining our ability to predict and control soil-borne diseases in healthy plants.

Investigations on Microbes Attached to the Cuticle of Phytonematodes

Nematodes form various associations with soil microbiome. Experimental studies on nematode-attached microbes can improve mechanistic understanding of these associations and lead to new discoveries relevant for the field of nematode biocontrol. Microbial attachment to the surface of phytonematodes is very specific and influenced by a multitude of factors, including the designation of nematodes and microbes, environmental and biological factors in soil, time of incubation, and the ratio and evolutionary trajectories between nematodes and microbes. Here, we describe how the classical nematological and microbiological techniques can be coupled with the advanced molecular tools to study the microbial attachment to phytonematodes in soil. We focus on the characterization of nematode-attached microbes using classical microbiological approaches and high-throughput amplicon sequencing and on the effects of nematode-attached microbes on plant defense responses.

Pathogenicity of the root lesion nematode Pratylenchus neglectus depends on pre-culture conditions

The ability of a plant parasitic nematode to infect and reproduce within a host plant depends on its genotype and the environmental conditions before and during infection. We studied the culturing conditions of the root lesion nematode Pratylenchus neglectus to produce inoculum for plant infection tests. Nematodes were either cultivated on carrot calli for different periods or directly isolated from the roots of the host plants. After infection of wheat and barley plants in the greenhouse, nematodes were quantified by RT-qPCR and by visual counting of the nematodes. We observed drastically reduced infection rates after long-term (> 96 weeks) cultivation on carrot callus. In contrast, fresh isolates from cereal roots displayed much higher pathogenicity. We recommend using root lesion nematodes cultivated on carrot calli no longer than 48 weeks to guarantee uniform infection rates.

Activity of root-knot nematodes associated with composition of a nematode-attached microbiome and the surrounding soil microbiota

We investigated if activity of the pre-infective juveniles (J2s) of root-knot nematodes is linked to the recruitment of a specific microbiome on the nematode surface and/or to the composition of the surrounding microbiota. For this, we determined the J2 activity (active vs. non-motile, which referred to dead and immobile J2s) upon a 3-day incubation in soil suspensions and studied the composition of bacteria, protists, and fungi present on the nematode surface and in the suspensions using amplicon sequencing of the 16S/18S rRNA genes, and ITS region. We also amended suspensions with Pseudomonas protegens strain CHA0 to study its effects on J2 activity and microbial composition. The J2 activity was suppressed in soil suspensions, but increased when suspensions were amended with P. protegens CHA0. The active and non-motile J2s differed in the composition of surface-attached bacteria, which was altered by the presence of P. protegens CHA0 in the soil suspensions. The bacterial genera Algoriphagus, Pedobacter, and Bdellovibrio were enriched on active J2s and may have protected the J2s against antagonists. The incubation time appeared short for attachment of fungi and protists. Altogether, our study is a step forward in disentangling the complex nematode-microbe interactions in soil for more successful nematode control.

Stress tolerance in entomopathogenic nematodes: Engineering superior nematodes for precision agriculture

Entomopathogenic nematodes (EPNs) are soil-dwelling parasitic roundworms commonly used as biocontrol agents of insect pests in agriculture. EPN dauer juveniles locate and infect a host in which they will grow and multiply until resource depletion. During their free-living stage, EPNs face a series of internal and environmental stresses. Their ability to overcome these challenges is crucial to determine their infection success and survival. In this review, we provide a comprehensive overview of EPN response to stresses associated with starvation, low/elevated temperatures, desiccation, osmotic stress, hypoxia, and ultra-violet light. We further report EPN defense strategies to cope with biotic stressors such as viruses, bacteria, fungi, and predatory insects. By comparing the genetic and biochemical basis of these strategies to the nematode model Caenorhabditis elegans, we provide new avenues and targets to select and engineer precision nematodes adapted to specific field conditions.

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.

Differential effects of rhizobacteria from uninfected and infected tomato on Meloidogyne incognita under protected cultivation

Intermingled uninfected and root-knot nematode-infected tomato plants are commonly observed under protected cultivation. To understand the role of rhizobacteria underlying the susceptibility to nematode infectivity in these tomato plants, 36 rhizobacteria (18 from each type) with morphologically distinct colony characteristics were isolated from the rhizosphere of uninfected and root-knot nematode-infected tomato plants. The in vitro nematicidal potential of rhizobacteria from the uninfected rhizosphere was significantly higher than that from the infested rhizosphere. The three most effective antagonists were identified as Microbacterium laevaniformans, Staphylococcus kloosii, Priestia aryabhattai from root-knot-nematode-infected tomato rhizosphere and Staphylococcus sciuri, Bacillus pumilus, and Priestia megaterium from the rhizosphere of uninfected tomato. Volatile organic compounds from these rhizobacteria were characterized. Except for S. kloosi, the soil drenching with other rhizobacteria significantly reduced juvenile penetration (>60%) in tomato roots. Furthermore, the application of a single or consortium of these rhizobacteria affected nematode reproduction in tomato. Four consortia of rhizobacteria (S. sciuri + B. pumilus + P. megaterium), (B. pumilus + P. megaterium), (S. sciuri + B. pumilus), and (S. sciuri + P. megaterium) from uninfested rhizosphere and two consortia (M. laevaniformans + P. aryabhattai), (M. laevaniformans + S. kloosii + P. aryabhattai) from infested rhizosphere (IRh) effectively reduced M. incognita reproduction and considerably enhanced plant growth and yield in tomato. The nematicidal efficacy, however, decreased when S. kloosii was applied in the consortium. These distinctive effects illustrate how the plant susceptibility to nematode infectivity is modulated under natural conditions.

Biocontrol efficacy of Bacillus velezensis strain YS-AT-DS1 against the root-knot nematode Meloidogyne incognita in tomato plants

Root-knot nematodes (RKNs; Meloidogyne spp.), one of the most economically important plant-parasitic nematodes (PPNs), cause severe yield and quality losses in agriculture annually. The application of biological control agents is an environmentally safe and effective approach to control RKNs. Here, we report the genomic characteristics of a Bacillus velezensis strain YS-AT-DS1 (Bv-DS1) isolated from the tidal soil, revealing that it has a 4.73 Mb circular chromosome with an average GC-content of 46.43%, 3,977 genes, 86 tRNAs, and 27 rRNAs, and contains secondary metabolite clusters for producing antimicrobial compounds. In vitro assays indicated that Bv-DS1 has not only antagonistic activities against fungal pathogens, but also shows nematicidal activity, with a mortality rate of 71.62% mortality rates in second-stage juvenile (J2s) Meloidogyne incognita. We then focused on the biocontrol efficiency of Bv-DS1 against M. incognita in pot assays. Preinoculation with Bv-DS1 enhanced tomato growth, and significantly reduced the infection rate of J2s, and the number of galls and egg masses on tomato roots. The underlying mechanism in Bv-DS1-induced resistance to M. incognita was further investigated through split-root experiments, and analysing the expression of the genes related to jasmonic acid (JA), salicylic acid (SA), and the tonoplast intrinsic protein (TIP). The results indicated that Bv-DS1 could not activate host systemic-induced resistance (ISR) in the split-root system of tomatoes. Additionally, the expression of JA- (LOX D and MC) and SA- (PAL2 and PR) responsive genes did not change in Bv-DS1-pretreated plants at 3 and 14 days after nematode inoculation. The presented data showed that JA-and SA-dependent pathways were not required for the biocontrol action of the Bv-DS1 against RKN. The TIP genes, responsible for transport of water and small substrates in plants, have previously been shown to negatively regulate the parasitism of PPNs. Surprisingly, Bv-DS1 compromised the downregulation of TIP1.1 and TIP1.3 by M. incognita. Together, our data suggest that Bv-DS1 exhibits a dual effect on plant growth promotion and protection against RKN, possibly related to the regulation of water and solute transport via TIPs. Thus, the Bv-DS1 strain could be used as a biocontrol agent for RKN control in sustainable agriculture.

The Fight against Plant-Parasitic Nematodes: Current Status of Bacterial and Fungal Biocontrol Agents

Plant-parasitic nematodes (PPNs) are among the most notorious and underrated threats to food security and plant health worldwide, compromising crop yields and causing billions of dollars of losses annually. Chemical control strategies rely heavily on synthetic chemical nematicides to reduce PPN population densities, but their use is being progressively restricted due to environmental and human health concerns, so alternative control methods are urgently needed. Here, we review the potential of bacterial and fungal agents to suppress the most important PPNs, namely Aphelenchoides besseyi, Bursaphelenchus xylophilus, Ditylenchus dipsaci, Globodera spp., Heterodera spp., Meloidogyne spp., Nacobbus aberrans, Pratylenchus spp., Radopholus similis, Rotylenchulus reniformis, and Xiphinema index.

Endophytic Paenibacillus polymyxa LMG27872 inhibits Meloidogyne incognita parasitism, promoting tomato growth through a dose-dependent effect

The root-knot nematode, Meloidogyne incognita, is a major pest in tomato production. Paenibacillus polymyxa, which is primarily found in soil and colonizing roots, is considered a successful biocontrol organism against many pathogens. To evaluate the biocontrol capacity of P. polymyxa LMG27872 against M. incognita in tomato, experiments were conducted both in vitro and in vivo. A dose-response effect [30, 50, and 100% (108 CFU/mL)] of bacterial suspensions (BSs) on growth and tomato susceptibility to M. incognita with soil drenching as a mode of application was first evaluated. The results show that the biological efficacy of P. polymyxa LMG27872 against M. incognita parasitism in tomato was dose-dependent. A significantly reduced number of galls, egg-laying females (ELF), and second-stage juveniles (J2) were observed in BS-treated plants, in a dose-dependent manner. The effect of P. polymyxa on tomato growth was also dose-dependent. A high dose of BSs had a negative effect on growth; however, this negative effect was not observed when the BS-treated plants were challenged with M. incognita, indicating tolerance or a defense priming mechanism. In subsequent in vivo experiments, the direct effect of BSs was evaluated on J2 mortality and egg hatching of M. incognita. The effect of BS on J2 mortality was observed from 12 to 24 h, whereby M. incognita J2 was significantly inhibited by the BS treatment. The effect of P. polymyxa on M. incognita egg hatching was also dependent on the BS dose. The results show a potential of P. polymyxa LMG27872 to protect plants from nematode parasitism and its implementation in integrated nematode management suitable for organic productions.

Interactions between Soil Bacterial Diversity and Plant-Parasitic Nematodes in Soybean Plants

Plant-parasitic nematodes are an important group of pests causing economic losses in agriculture worldwide. Among the plant-parasitic nematodes, the root-knot (Meloidogyne spp.) and root-lesion nematodes (Pratylenchus spp.) are considered the two most important ones affecting soybeans. In general, they damage soybean roots, causing a reduction of about one-third in productivity. The soil microbial community can exert a suppressive effect on the parasitism of plant-parasitic nematodes. Here, we investigated the effects of soil bacterial diversity on Meloidogyne javanica (Meloidogyne-assay) and Pratylenchus brachyurus (Pratylenchus-assay) suppression by manipulating microbial diversity using the dilution-to-extinction approach in two independent experiments under controlled conditions. Furthermore, we recorded the changes in the soil microbial community induced by plant-parasitic nematode infection. In Meloidogyne-assay, microbial diversity reduced the population density of M. javanica and improved plant performance. In Pratylenchus-assay, microbial diversity sustained the performance of soybean plants even at high levels of P. brachyurus parasitism. Each nematode population affected the relative abundance of different bacterial genera and altered the core microbiome of key groups within the bacterial community. Our findings provide fundamental insights into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants. IMPORTANCE Root-knot and root-lesion nematodes cause losses of billions of dollars every year to agriculture worldwide. Traditionally, they are controlled by using chemical nematicides, which in general have a negative impact on the environment and human health. Fortunately, the soil microbial community may suppress these pests, acting as an environmentally friendly alternative to control nematodes. However, the effects of soil microbial diversity on the parasitism of plant-parasitic nematodes still poorly understood. In this study, we provide fundamental insight into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants, which may be useful for the development of new strategies to control these phytopathogens.

Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion

In-depth understanding of metabolite-mediated plant-nematode interactions can guide us towards novel nematode management strategies. To improve our understanding of the effects of secondary metabolites on soil nematode communities, we grew Arabidopsis thaliana genetically altered in glucosinolate, camalexin, or flavonoid synthesis pathways, and analyzed their root-associated nematode communities using metabarcoding. To test for any modulating effects of the associated microbiota on the nematode responses, we characterized the bacterial and fungal communities. Finally, as a proxy of microbiome-modulating effects on nematode invasion, we isolated the root-associated microbiomes from the mutants and tested their effect on the ability of the plant parasitic nematode Meloidogyne incognita to penetrate tomato roots. Most mutants had altered relative abundances of several nematode taxa with stronger effects on the plant parasitic Meloidogyne hapla than on other root feeding taxa. This probably reflects that M. hapla invades and remains embedded within root tissues and is thus intimately associated with the host. When transferred to tomato, microbiomes from the flavonoid over-producing pap1-D enhanced M. incognita root-invasion, whereas microbiomes from flavonoid-deficient mutants reduced invasion. This suggests microbiome-mediated effect of flavonoids on Meloidogyne infectivity plausibly mediated by the alteration of the abundances of specific microbial taxa in the transferred microbiomes, although we could not conclusively pinpoint such causative microbial taxa.

The Difference in the Bacterial Attachment among Pratylenchus neglectus Populations and Its Effect on the Nematode Infection

Different bacterial isolates attach to the cuticle of plant-parasitic nematodes, affecting their interactions with the host plant. Nematode populations differ in their genetic and cuticle structures, causing variable interactions with host plants and natural enemies. In the current study, attachment assays were carried out to compare the attachment of soil bacteria in general and the bacterial isolate of Rothia sp. in particular among geographically diverse populations of Pratylenchus neglectus. Biological and molecular assays were further conducted to examine the effect of Rothia attachment on nematode penetration into barley roots and to sequence the fatty acid- and retinol-binding gene (Pn-far-1). The results showed that nematode populations of P. neglectus differed in their bacterial attachment. Soil bacteria and Rothia sp. attached specifically to the cuticle of P. neglectus and did so differently among the nematode populations. Rothia attachment caused a reduction in the infectivity of three nematode populations in barley roots. The sequencing of the far-1 gene revealed genetic variability within and among P. neglectus populations. In conclusion, the interaction between P. neglectus and their bacterial attachers occurs in a population-specific manner, elucidating an essential aspect of using biological agents to manage plant-parasitic nematodes. Key Message: 1. Geographically diverse populations of the root lesion nematode Pratylenchus neglectus differed in the soil bacterial communities attached to their cuticles. 2. The bacterial isolate of Rothia sp. attached to the cuticle of P. neglectus and reduced its penetration into the host plant in a population-specific manner. 3. The fatty acid- and retinol-binding gene (far-1) varied within and among P. neglectus populations with their different bacterial attachment.

Nematicidal Activity of Burkholderia arboris J211 Against Meloidogyne incognita on Tobacco

Root-knot nematode (Meloidogyne incognita) is the most widespread nematode affecting Solanaceae crops. Due to the lack of effective measures to control this nematode, its management can be achieved, using biocontrol agents. This study investigated in vitro efficacy of the antagonistic bacterial strain J211 isolated from tobacco rhizosphere soil against M. incognita, and further assessed its role in controlling nematodes, both in pot and field trials. Phylogenetic analysis of the 16S rRNA gene sequence of strain J211 assigned to Burkholderia arboris. Culture filtrates B. arboris J211 exhibited anematicidal activity against the second-stage juveniles (J2s) of M. incognita, with a 96.6% mortality after 24 h exposure. Inoculation of J211 in tobacco roots significantly reduced the root galling caused by M. incognita, both in pot and field trials. Meanwhile, plant growth-promoting (PGP) traits results showed that J211 had outstanding IAA-producing activity, and the IAA production reached 66.60 mg L⁻¹. In the field study, B. arboris J211 also promoted tobacco growth and increase flue-cured tobacco yield by 8.7–24.3%. Overall, B. arboris J211 as a high-yielding IAA nematicidal strain effectively controlled M. incognita and improved tobacco yield making it a promising alternative bionematocide.

β‐Glucan receptors on IL‐4 activated macrophages are required for hookworm larvae recognition and trapping

Recent advances in the field of host immunity against parasitic nematodes have revealed the importance of macrophages in trapping tissue migratory larvae. Protective immune mechanisms against the rodent hookworm Nippostrongylus brasiliensis (Nb) are mediated, at least in part, by IL‐4‐activated macrophages that bind and trap larvae in the lung. However, it is still not clear how host macrophages recognize the parasite. An in vitro co‐culture system of bone marrow‐derived macrophages and Nb infective larvae was utilized to screen for the possible ligand–receptor pair involved in macrophage attack of larvae. Competitive binding assays revealed an important role for β‐glucan recognition in the process. We further identified a role for CD11b and the non‐classical pattern recognition receptor ephrin‐A2 (EphA2), but not the highly expressed β‐glucan dectin‐1 receptor, in this process of recognition. This work raises the possibility that parasitic nematodes synthesize β‐glucans and it identifies CD11b and ephrin‐A2 as important pattern recognition receptors involved in the host recognition of these evolutionary old pathogens. To our knowledge, this is the first time that EphA2 has been implicated in immune responses to a helminth.

Selective Toxicity of Secondary Metabolites from the Entomopathogenic Bacterium Photorhabdus luminescens sonorensis against Selected Plant Parasitic Nematodes of the Tylenchina Suborder

Entomopathogenic Photorhabdus bacteria (Enterobacteriaceae: Gamma-proteobacteria), the natural symbionts of Heterorhabditis nematodes, are a rich source for the discovery of biologically active secondary metabolites (SMs). This study describes the isolation of three nematicidal SMs from in vitro culture supernatants of the Arizona-native Photorhabdus luminescenssonorensis strain Caborca by bioactivity-guided fractionation. Nuclear magnetic resonance spectroscopy and comparison to authentic synthetic standards identified these bioactive metabolites as trans-cinnamic acid (t-CA), (4E)-5-phenylpent-4-enoic acid (PPA), and indole. PPA and t-CA displayed potent, concentration-dependent nematicidal activities against the root-knot nematode (Meloidogyne incognita) and the citrus nematode (Tylenchulus semipenetrans), two economically and globally important plant parasitic nematodes (PPNs) that are ubiquitous in the United States. Southwest. Indole showed potent, concentration-dependent nematistatic activity by inducing the temporary rigid paralysis of the same targeted nematodes. While paralysis was persistent in the presence of indole, the nematodes recovered upon removal of the compound. All three SMs were found to be selective against the tested PPNs, exerting little effects on non-target species such as the bacteria-feeding nematode Caenorhabditis elegans or the entomopathogenic nematodes Steinernema carpocapsae, Heterorhabditis bacteriophora, and Hymenocallis sonorensis. Moreover, none of these SMs showed cytotoxicity against normal or neoplastic human cells. The combination of t-CA + PPA + indole had a synergistic nematicidal effect on both targeted PPNs. Two-component mixtures prepared from these SMs revealed complex, compound-, and nematode species-dependent interactions. These results justify further investigations into the chemical ecology of Photorhabdus SMs, and recommend t-CA, PPA and indole, alone or in combinations, as lead compounds for the development of selective and environmentally benign nematicides against the tested PPNs.

IMPORTANCE Two phenylpropanoid and one alkaloid secondary metabolites were isolated and identified from culture filtrates of Photorhabdus l. sonorensis strain Caborca. The three identified metabolites showed selective nematicidal and/or nematistatic activities against two important plant parasitic nematodes, the root-knot nematode (Meloidogyne incognita) and the citrus nematode (Tylenchulus semipenetrans). The mixture of all three metabolites had a synergistic nematicidal effect on both targeted nematodes, while other combinations showed compound- and nematode-dependent interactions.

Formalin fumigation and steaming of various composts differentially influence the nutrient release, growth and yield of muskmelon (Cucumis melo L.)

Nutrient disorder and presence of disease-causing agents in soilless media negatively influence the growth of muskmelon. To combat these issues, use of environmentally-friendly sanitation techniques is crucial for increased crop productivity. The study was conducted under greenhouse and field conditions to investigate the effect of two different sanitation techniques: steaming and formalin fumigation on various media's characteristics and their impact on muskmelon yield. Media: jantar, guar, wheat straw and rice hull and peat moss of 10% air-filled porosity and sanitized with formalin and steaming. Steaming of guar, jantar, and wheat straw increased the phosphorus (P) and potassium (K) concentrations by 13.80-14.86% and 6.22-8.45% over formalin fumigation. Likewise, P and K concentrations in muskmelon were higher under steaming. Steaming significantly inhibited the survival of Fusarium wilt sp. melonis, root knot nematode sp. meloidogyne and nitrifying bacteria in media than formalin fumigation. In conclusion, steaming decreased the prevalence of nitrifying bacteria and pathogens which thus improved the NO₃^--N:NH₄⁺-N ratios, P and K nutritional balance both in the media and muskmelon transplants. Hence, steaming as an environment-friendly approach is recommended for soilless media. Further, optimization of steaming for various composts with different crops needs to be investigated with steaming teachnique.

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.

Comparative Secretome Analyses of Toxigenic and Atoxigenic Rathayibacter Species

Phytopathogenic Rathayibacter species are unique bacterial plant pathogens because they are obligately vectored by plant parasitic anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant-associated Actinomycetes includes the neurotoxigenic plant pathogen R. toxicus, which causes annual ryegrass toxicity in grazing livestock. R. toxicus is currently endemic to Australia and is listed as a plant pathogen select agent by the U.S. Department of Agriculture-Animal and Plant Health Inspection Service. The complex Rathayibacter disease cycle requires intimate interactions with the nematode vector and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode-vectored Rathayibacter genus that compares the three agronomically damaging toxigenic and atoxigenic Rathayibacter species, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species via liquid chromatography-tandem mass spectrometry, leading to the identification of putative pathogenicity-related proteins and proteins that may mediate nematode attachment. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 and 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classic plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector attachment and host colonization and assist in the development of serological diagnostic assays.

Can microorganisms assist the survival and parasitism of plant-parasitic nematodes?

Plant-parasitic nematodes (PPNs) remain a hardly treatable problem in many crops worldwide. Low efficacy of many biocontrol agents may be due to negligence of the native microbiota that is naturally associated with nematodes in soil, and which may protect nematodes against microbial antagonists. This phenomenon is more extensively studied for other nematode parasites, so we compiled these studies and drew parallels to the existing knowledge on PPN. We describe how microbial-mediated modulation of host immune responses facilitate nematode parasitism and discuss the role of Caenorhabditis elegans-protective microbiota to get an insight into the microbial protection of PPNs in soil. Molecular mechanisms of PPN-microbial interactions are also discussed. An understanding of microbial-aided PPN performance is thus pivotal for efficient management of PPNs.

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.

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.

Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam

Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant-parasitic nematode, especially on rice. This obligate soilborne parasite induces the formation of galls that disturb the root morphology and physiology. Its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern Vietnam where we collected infected (with galls) and non-infected root tips from the same plants in three naturally infested fields. Using a metabarcoding approach, we discovered that M. graminicola infection caused modifications of the root bacterial community composition and network structure. Interestingly, we observed in infected roots a higher diversity and species richness (+24% observed ESVs) as well as a denser and more complex co-occurrence network (+44% nodes and +136% links). We identified enriched taxa that include several hubs, which could serve as potential indicators or biocontrol agents of the nematode infection. Moreover, the community of infected roots is more specific suggesting changes in the functional capabilities to survive in the gall environment. We thus describe the signature of the gall microbiome (the 'gallobiome') with shifting abundances and enrichments that lead to a strong restructuration of the root microbiome.

Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions

Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode's chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles.IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode's life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.

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.

Microbes Attaching to Endoparasitic Phytonematodes in Soil Trigger Plant Defense Upon Root Penetration by the Nematode

Root-knot nematodes (Meloidogyne spp.) are among the most aggressive phytonematodes. While moving through soil to reach the roots of their host, specific microbes attach to the cuticle of the infective second-stage juveniles (J2). Reportedly, the attached microorganisms affect nematodes and reduce their performance on the host plants. We have previously shown that some non-parasitic bacterial strains isolated from the cuticle of Meloidogyne hapla in different soils affected J2 mortality, motility, hatching, and root invasion. Here we tested whether cuticle-attached microbes trigger plant defenses upon penetration of J2. In in vitro assays, M. hapla J2-attached microbes from a suppressive soil induced pathogen-associated molecular pattern-triggered immunity (PTI) in tomato roots. All tested PTI-responsive defense genes were upregulated after root invasion of J2 with attached microbes, compared to surface-sterilized J2, particularly the jasmonic acid-mediated PTI marker genes TFT1 and GRAS4.1. The strain Microbacterium sp. K6, that was isolated from the cuticle, significantly reduced root invasion when attached to the J2. Attached K6 cells supported plant defense and counteracted suppression of plant basal defense in roots by invaded J2. The plant response to the J2-attached K6 cells was stronger in leaves than in roots, and it increased from 1 to 3 days post inoculation (dpi). At 1 dpi, the plant responded to J2-attached K6 cells by ameliorating the J2-triggered down-regulation of defense genes mostly in roots, while at 3 dpi this response was systemic and more pronounced in leaves. In a reactive oxygen species (ROS) assay, the compounds released from J2 with attached K6 cells triggered a stronger ROS burst in tomato roots than the compounds from nematodes without K6, or the metabolites released from strain K6 alone. Leaves showed a 100 times more sensitive response than roots, and the metabolites of K6 with or without J2 induced strong ROS bursts. In conclusion, our results suggest the importance of microorganisms that attach to M. hapla in suppressive soil, inducing early basal defenses in plants and suppressing nematode performance in roots.

Impacts of Root Metabolites on Soil Nematodes

Plant parasitic nematodes cause significant crop damage globally. Currently, many nematicides have been banned or are being phased out in Europe and other parts of the world because of environmental and human health concerns. Therefore, we need to focus on sustainable and alternative methods of nematode control to protect crops. Plant roots contain and release a wide range of bioactive secondary metabolites, many of which are known defense compounds. Hence, profound understanding of the root mediated interactions between plants and plant parasitic nematodes may contribute to efficient control and management of pest nematodes. In this review, we have compiled literature that documents effects of root metabolites on plant parasitic nematodes. These chemical compounds act as either nematode attractants, repellents, hatching stimulants or inhibitors. We have summarized the few studies that describe how root metabolites regulate the expression of nematode genes. As non-herbivorous nematodes contribute to decomposition, nutrient mineralization, microbial community structuring and control of herbivorous insect larvae, we also review the impact of plant metabolites on these non-target organisms.