Mycobiome of Cysts of the Soybean Cyst Nematode Under Long Term Crop Rotation

Characterization of Acid-Responsive-Release Matrine/ZIF-8@Sodium Alginate Microcapsules Prepared by Electrostatic Spray and Their Application in the Control of Soybean Cyst Nematode

Matrine (MT) is a kind of alkaloid extracted from Sophora and is a promising substitute for chemical nematicides and botanical pesticides. The present study utilized sodium alginate (SA), zeolite imidazole salt skeleton (ZIF), and MT as raw materials to prepare a pH-response-release nematicide through the electrostatic spray technique. Zinc metal-organic framework (ZIF-8) was initially synthesized, followed by the successful loading of MT. Subsequently, the electrostatic spray process was employed to encapsulate it in SA, resulting in the formation of MT/ZIF-8@SA microcapsules. The efficiency of encapsulation and drug loadings can reach 79.93 and 26.83%, respectively. Soybean cyst nematode (SCN) is one of the important pests that harm crops; acetic acid produced by plant roots and CO2 produced by root respiration causing a decrease in the pH of the surrounding environment, which is most attractive to the SCN when the pH is between 4.5 and 5.4. MT/ZIF-8@SA releases the loaded MT in response to acetic acid produced by roots and acidic oxides produced by root respiration. The rate of release was 37.67% higher at pH 5.25 compared with pH 8.60. The control efficiency can reach 89.08% under greenhouse conditions. The above results demonstrate that the prepared MT/ZIF-8@SA not only exhibited excellent efficacy but also demonstrated a pH-responsive release of the nematicide.

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.

A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield

Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.

Isolation, Identification, and Evaluation of the Predatory Activity of Chinese Arthrobotrys Species towards Economically Important Plant-Parasitic Nematodes

The current investigation aimed to isolate and identify predatory fungal strains and evaluate their efficacy in mitigating the effects of plant-parasitic nematodes. We successfully isolated three distinct nematophagous fungal strains from soil samples, identified as Arthrobotrys megalosporus, A. oligospora, and A. sinensis, using conventional and molecular identification methodologies. In vitro trials illustrated the high capture efficiency of these fungi against plant-parasitic nematodes. Over an exposure period of 48 h to Aphelenchoides besseyi, Bursaphelenchus xylophilus, and Ditylenchus destructor, A. megalosporus (GUCC220044) displayed predation rates of 99.7%, 83.0%, and 21.1%, respectively. A. oligospora (GUCC220045) demonstrated predation rates of 97.3%, 97.3%, and 54.6%, and A. sinensis (GUCC220046) showed rates of 85.1%, 68.3%, and 19.0% against the same cohort of nematodes. The experimental outcomes substantiate that all three identified fungal strains demonstrate predatory activity against the tested nematodes, albeit with varying efficiencies.

Two strains Neocosmosporastercicola (Sordariomycetes, Nectriaceae) with high nematicidal activity, isolated from the cysts of Globodera sp. (Heteroderidae) in China

Plant-parasitic nematodes (PPNs) are significant pests that result in considerable economic losses in global crop production. Due to the high toxicity of chemical nematicides, there is a need to develop new strategies for nematode control. In this context, nematophagous fungi may offer a viable option for biological control. Two fungal strains (GUCC2212 and GUCC2232) were isolated from cysts of Globodera sp., identified as Neocosmosporastercicola. The fungal filtrates of the strains were evaluated for their nematicidal activity against three species of PPNs: Aphelenchoidesbesseyi, Bursaphelenchusxylophilus and Ditylenchusdestructor. The fermentation filtrates of two strains exhibited substantial toxicity towards the evaluated nematodes, with mortality rates reaching up to 100% within 72 h. Concurrently, N.stercicola also demonstrated predatory and parasitic behavior. The eggs of Globodera sp. were parasitized by the two strains. N.stercicola represents a newly recorded species in China and a novel nematophagous species. In conclusion, the two strains of N.stercicola show promise as biocontrol agents for PPNs management.

A low-cost and open-source solution to automate imaging and analysis of cyst nematode infection assays for Arabidopsis thaliana

BACKGROUND

Cyst nematodes are one of the major groups of plant-parasitic nematode, responsible for considerable crop losses worldwide. Improving genetic resources, and therefore resistant cultivars, is an ongoing focus of many pest management strategies. One of the major bottlenecks in identifying the plant genes that impact the infection, and thus the yield, is phenotyping. The current available screening method is slow, has unidimensional quantification of infection limiting the range of scorable parameters, and does not account for phenotypic variation of the host. The ever-evolving field of computer vision may be the solution for both the above-mentioned issues. To utilise these tools, a specialised imaging platform is required to take consistent images of nematode infection in quick succession.

RESULTS

Here, we describe an open-source, easy to adopt, imaging hardware and trait analysis software method based on a pre-existing nematode infection screening method in axenic culture. A cost-effective, easy-to-build and -use, 3D-printed imaging device was developed to acquire images of the root system of Arabidopsis thaliana infected with the cyst nematode Heterodera schachtii, replacing costly microscopy equipment. Coupling the output of this device to simple analysis scripts allowed the measurement of some key traits such as nematode number and size from collected images, in a semi-automated manner. Additionally, we used this combined solution to quantify an additional trait, root area before infection, and showed both the confounding relationship of this trait on nematode infection and a method to account for it.

CONCLUSION

Taken together, this manuscript provides a low-cost and open-source method for nematode phenotyping that includes the biologically relevant nematode size as a scorable parameter, and a method to account for phenotypic variation of the host. Together these tools highlight great potential in aiding our understanding of nematode parasitism.

Soybean cyst nematode detection and management: a review

Soybeans play a key role in global food security. U.S. soybean yields, which comprise [Formula: see text] of the total soybeans planted in the world, continue to experience unprecedented grain loss due to the soybean cyst nematode (SCN) plant pathogen. SCN remains one of the primary disruptive pests despite the existence of advanced management techniques such as crop rotation and SCN-resistant varieties. SCN detection is a key step in managing this disease; however, early detection is challenging because soybeans do not show any above ground symptoms unless they  are significantly damaged. Direct soil sampling remains the most common method for SCN detection, however, this method has several problems. For example, the threshold damage methods-adopted by most of the laboratories to make recommendations-is not reliable as it does not consider soil pH, N, P, and K values and relies solely on the egg count instead of assessment of the root infection. To overcome the challenges of manual soil sampling methods, deep learning and hyperspectral imaging are important current topics in precision agriculture for plant disease detection and have been proposed as cost-effective and efficient detection methods that can work at scale. We have reviewed more than 150 research papers focusing on soybean cyst nematodes with an emphasis on deep learning techniques for detection and management. First: we describe soybean vegetation and reproduction stages, SCN life cycles, and factors influencing this disease. Second: we highlight the impact of SCN on soybean yield loss and the challenges associated with its detection. Third: we describe direct sampling methods in which the soil samples are procured and analyzed to evaluate SCN egg counts. Fourth: we highlight the advantages and limitations of these direct methods, then review computer vision- and remote sensing-based detection methods: data collection using ground, aerial, and satellite approaches followed by a review of machine learning methods for image analysis-based soybean cyst nematode detection. We highlight the evaluation approaches and the advantages of overall detection workflow in high-performance and big data environments. Lastly, we discuss various management approaches, such as crop rotation, fertilization, SCN resistant varieties such as PI 88788, and SCN's increasing resistance to these strategies. We review machine learning approaches for soybean crop yield forecasting as well as the influence of pesticides, herbicides, and fertilizers on SCN infestation reduction. We provide recommendations for soybean research using deep learning and hyperspectral imaging to accommodate the lack of the ground truth data and training and testing methodologies, such as data augmentation and transfer learning, to achieve a high level of detection accuracy while keeping costs as low as possible.

Plant growth-promoting rhizobacteria Burkholderia vietnamiensis B418 inhibits root-knot nematode on watermelon by modifying the rhizosphere microbial community

Burkholderia vietnamiensis B418 is a multifunctional plant growth-promoting rhizobacteria (PGPR) strain with nitrogen-fixing and phosphate-solubilizing capability which can be employed for root-knot nematode (RKN) management on various crops and vegetables. Here we investigated the control efficacy of B. vietnamiensis B418 inoculation against RKN on watermelon, applied either alone or combined with nematicides fosthiazate or avermectin, and their effects on bacterial and fungal microbiomes in rhizosphere soil. The results of field experiments showed individual application of B418 displayed the highest control efficacy against RKN by 71.15%. The combinations with fosthiazate and avermectin exhibited slight incompatibility with lower inhibitory effects of 62.71% and 67.87%, respectively, which were still notably higher than these nematicides applied separately. Analysis of microbiome assemblages revealed B418 inoculation resulted in a slight reduction for bacterial community and a significant increment for fungal community, suggesting that B418 could compete with other bacteria and stimulate fungal diversity in rhizosphere. The relative abundance of Xanthomonadales, Gemmatimonadales and Sphingomonadales increased while that of Actinomycetales reduced with B418 inoculation. The predominate Sordariomycetes of fungal community decreased dramatically in control treatment with B418 inoculation whereas there were increments in fosthiazate and avermectin treatments. Additionally, nitrogen (N) cycling by soil microbes was estimated by quantifying the abundance of microbial functional genes involved in N-transformation processes as B418 has the capability of N-fixation. The copy number of N-fixing gene nifH increased with B418 inoculation, and the highest increment reached 35.66% in control treatment. Our results demonstrate that B. vietnamiensis B418 is an effective biological nematicide for nematode management, which acts through the modulation of rhizosphere microbial community.

Pea-Wheat Rotation Affects Soil Microbiota Diversity, Community Structure, and Soilborne Pathogens

Intensive cultivation based on monocultures has a significant impact on ecosystem function, and sustainable agriculture must rely on alternative methods, including crop rotation. On the Canadian prairies, the use of pulse crops is a common practice, but few studies have investigated the impact on soil microorganisms. Here, we studied the effect of pea, wheat, pea–wheat rotation, and fallow in bulk soil bacterial and fungal communities. We characterized soil microbiota by high-throughput sequencing of 16S and 18S rRNA genes for bacteria and eukaryotes. Different crop rotations and fallow significantly modified soil community composition, as well as bacterial and fungal diversity. Pea alone caused a strong reduction of bacterial and fungal richness and diversity compared to wheat, pea–wheat rotation, and fallow. Notably, pea–wheat rotation increased the abundance of Fusarium graminearum compared to other management practices. The bacterial community was less responsive to crop rotation identity compared to the fungal microbiota, and we found minor differences at the phylum level, with an increase in Actinobacteria in fallow and Firmicutes in wheat. In summary, our study demonstrated that rotations alter bulk soil microbial community diversity and composition in Canadian prairies. The frequent use of pea in rotation with wheat should be carefully evaluated, balancing their ecological effects on nitrogen mineralization, water conservation, and impact on beneficial, as well as pathotrophic, fungi.

Diversity of Mycobiota Associated with the Cereal Cyst Nematode Heterodera filipjevi Originating from Some Localities of the Pannonian Plain in Serbia

Simple Summary

Heterodera filipjevi, the cereal cyst nematode, is one of the most globally recognized and economically important nematodes on wheat. As some other cyst nematodes that are plant root parasites, the cysts of H. filipjevi survive in soil for years and shelter a large number of microbes. The aims of this study were to investigate the diversity of mycobiota associated with the cereal cyst nematode H. filipjevi, to infer phylogenetic relationships of the found mycobiota, and to explore the ecological connection between fungi and the field history, including the potential of fungi in bioremediation and the production of novel bioactive compounds. The study showed that the fungal species associated with the H. filipjevi cysts belong to diverse phyla, including Ascomycota, Basidiomycota, and Mucoromycota. The members of Ascomycota (Fusarium avenaceum, Sarocladium kiliense, Setophoma terrestris) are plant parasites, indicating that crops were host plants for fungal infection of recent origin. The members of Basidiomycota (Bjerkandera adusta, Cerrena unicolor, Trametes hirsuta, etc.) are wood-decay fungi, the presence of which in agricultural soil indicates that forests were the preceding plants.

Abstract

Cereals, particularly wheat, are staple food of the people from the Balkans, dating back to the Neolithic age. In Serbia, cereals are predominantly grown in its northern part between 44° and 45.5° N of the Pannonian Plain. One of the most economically important nematodes on wheat is the cereal cyst nematode, Heterodera filipjevi. Cysts of H. filipjevi survive in soil for years and shelter a large number of microorganisms. The aims of this study were to investigate the diversity of mycobiota associated with the cereal cyst nematode H. filipjevi, to infer phylogenetic relationships of the found mycobiota, and to explore the ecological connection between fungi and the field history, including the potential of fungi in bioremediation and the production of novel bioactive compounds. Cysts were isolated from soil samples with a Spears apparatus and collected on a 150-µm sieve. The cysts were placed on potato dextrose agar, and maintained for two weeks at 27°C. Following fungal isolation and colony growing, the fungal DNA was extracted, the ITS region was amplified, and PCR products were sequenced. The study showed that the isolated fungal species belong to diverse phyla, including Ascomycota, Basidiomycota, and Mucoromycota. Ascomycota is represented by the families Clavicipitaceae, Sarocladiaceae, Nectriaceae, and Phaeosphaeriaceae. Basidiomycota is represented by the families Cerrenaceae, Polyporaceae, Phanerochaetaceae, and Meruliaceae, and the order Cantharellales. The family Mortierellaceae represents Mucoromycota. The members of Ascomycota and Basidiomycota both depict the field history. Ascomycota indicate the fungal infection is of recent origin, while Basidiomycota point toward the preceding host plants, enabling the plant field colonization history to be traced chronologically.

Robotic agricultural instrument for automated extraction of nematode cysts and eggs from soil to improve integrated pest management

Soybeans are an important crop for global food security. Every year, soybean yields are reduced by numerous soybean diseases, particularly the soybean cyst nematode (SCN). It is difficult to visually identify the presence of SCN in the field, let alone its population densities or numbers, as there are no obvious aboveground disease symptoms. The only definitive way to assess SCN population densities is to directly extract the SCN cysts from soil and then extract the eggs from cysts and count them. Extraction is typically conducted in commercial soil analysis laboratories and university plant diagnostic clinics and involves repeated steps of sieving, washing, collecting, grinding, and cleaning. Here we present a robotic instrument to reproduce and automate the functions of the conventional methods to extract nematode cysts from soil and subsequently extract eggs from the recovered nematode cysts. We incorporated mechanisms to actuate the stage system, manipulate positions of individual sieves using the gripper, recover cysts and cyst-sized objects from soil suspended in water, and grind the cysts to release their eggs. All system functions are controlled and operated by a touchscreen interface software. The performance of the robotic instrument is evaluated using soil samples infested with SCN from two farms at different locations and results were comparable to the conventional technique. Our new technology brings the benefits of automation to SCN soil diagnostics, a step towards long-term integrated pest management of this serious soybean pest.

Differential Morphological, Structural and Biological Characteristics of Cysts in Heterodera Species in Korea

Morphological (cyst shape, color, and sizes [length (L), maximum width (W), volume and "a" (L/W)]), structural (vulvar cone slope angle [VCSA], surface wrinkle [VCSW], cyst wall thickness, composition, and texture) and biological characteristics (fecundity, hatching, and emergence [number of second-stage juveniles (J2) from a cyst]) in preceding Heterodera glycines (Hg), currently-recorded H. sojae (Hs) and H. trifolii (Ht) were examined by microscopy. Cysts were lemon-shaped, indicating the genus is Heterodera except for Hs that formed frequently globular cysts with significantly flatter VCSA (102.2°) with smooth VCSW than Hg (50.6°) and Ht (82.0°), but not genus Globodera because of the presence of vulvar cone in Hs. Ht was significantly larger in all morphological characteristics than Hg and Hs, suggesting Ht may be diagnosed differentially by cyst sizes and also host plant preferences. Hs showed smaller "a" value with more globular shape and stronger structures with more thickened and strengthened collagen-like texture of cyst wall than Hg and Ht. This suggests Hs may be diagnosed differently by structural characteristics from the others, especially Hg with similar cyst sizes. There were no significant differences in emergence (inoculum potential) among cyst nematodes due to the offset of fecundity and hatching rate; however, the inoculum potential of Hs may be not so persistent as Hg and Ht in fields because of its lower fecundity and higher hatching rate (causing rapid inoculum loss) than the others. These characteristics of cysts provide information useful for simple and differential diagnoses and reliable management of cyst nematodes.

Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping

Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re-sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher (p ≤ .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p ≤ .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10-10) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p ≤ .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p ≤ .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.

Impact of Arbuscular Mycorrhizal Species on Heterodera glycines

Soybean cyst nematode (SCN, Heterodera glycines) is a widely occurring pest and the leading cause of soybean yield losses in the U.S.A. There is a need to find additional SCN management strategies as sources of SCN resistance have become less effective in managing SCN populations. Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with roots of most plants including soybean. Research has shown that AMF can reduce disease severity in plants caused by pathogens and pests, including plant parasitic nematodes. The goal of this study was to evaluate the impact of AMF on SCN cyst production, SCN juveniles in roots, and SCN egg hatching. In one experiment, all five AMF species tested (Claroideoglomus claroideum, Diversispora eburnean, Dentiscutata heterogama, Funneliformis mosseae, and Rhizophagus intraradices) reduced (P < 0.05) the number of cysts on soybean roots by 59 to 81%, compared with soybean roots not inoculated with AMF. Inoculation with F. mosseae reduced SCN J2-J3 stage juveniles in soybean roots by 60% at 7 days post inoculation. A separate experiment showed that egg hatch was reduced (P < 0.05) in the presence of F. mosseae spores and their exudates by 27% and 62%, respectively. Further research is needed to evaluate the potential usefulness of AMF in field conditions and to determine the usefulness and potential of the exudates associated with SCN hatching suppression by F. mosseae. Making AMF a more effective biological control agent would provide another management tool to reduce the negative impact of SCN on soybean production.

In Vitro Screening of a Culturable Soybean Cyst Nematode Cyst Mycobiome for Potential Biological Control Agents and Biopesticides

Fungal biological control of soybean cyst nematodes (SCN) is an important component of integrated pest management for soybean. However, very few fungal biological control agents are available in the market. In this study, we have screened fungi previously isolated from SCN cysts over 3 years from a long-term crop rotation field experiment for their ability to antagonize SCN using (i) parasitism, (ii) egg hatch inhibition, and (iii) J2 mortality. We evaluated egg parasitism using an in-vitro egg parasitism bioassays and scored parasitism using the egg parasitic index (EPI) and fluorescent microscopy. The ability of these fungi to produce metabolites causing egg hatch inhibition and J2 mortality was assessed in bioassays using filter-sterilized culture filtrates. We identified 10 high-performing isolates each for egg parasitism and toxicity toward SCN eggs and J2s and repeated the tests after storage for 1 year of cryopreservation at -80°C to validate the durability of biocontrol potential of the chosen 20 isolates. Although the parasitic ability changed slightly for the majority of strains after cryopreservation, they still scored 5/10 on EPI scales. There were no differences in the ability of fungi to produce antinemic metabolites after cryopreservation.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Corn and Soybean Host Root Endophytic Fungi with Toxicity Toward the Soybean Cyst Nematode

Although fungal endophytes are commonly investigated for their ability to deter microbial plant pathogens, few studies have examined the activity of fungal root endophytes against nematodes. The soybean cyst nematode (SCN; Heterodera glycines), the most severe yield-limiting pathogen of soybean (Glycine max), is commonly managed through rotation of soybean with corn (Zea mays), a nonhost of the SCN. A total of 626 fungal endophytes were isolated from surface-sterilized corn and soybean roots from experimental plots in which soybean and corn had been grown under annual rotation and under 1, 3, 5, and 35 years of continuous monoculture. Fungal isolates were grouped into 401 morphotypes, which were clustered into 108 operational taxonomic units (OTUs) based on 99% sequence similarity of the full internal transcribed spacer region. Morphotype representatives within each OTU were grown in malt extract broth and in a secondary metabolite-inducing medium buffered with ammonium tartrate, and their culture filtrates were tested for nematicidal activity against SCN juveniles. A majority of OTUs containing isolates with nematicidal culture filtrates were in the order Hypocreales, with the genus Fusarium being the most commonly isolated nematicidal genus from corn and soybean roots. Less commonly isolated taxa from soybean roots included the nematophagous fungi Hirsutella rhossiliensis, Metacordyceps chlamydosporia, and Arthrobotrys iridis. Root endophytic fungal diversity in soybean was positively correlated with SCN density, suggesting that the SCN plays a role in shaping the soybean root endophytic community.

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.

Fungal communities associated with Heterodera glycines and their potential in biological control: a current update

The soybean cyst nematode (SCN) is the most important pest on soybean, a major crop worldwide. The SCN is considered both parasitic and pathogenic as it derives nutrition from the host and manipulates host physiology to do so. Currently, there are no commercially available chemicals that are specific, environmentally safe and cost effective to control SCN levels. Crop rotation, use of host resistance and other cultural practices remain the main management strategies. The need for bioprospecting other methods of controlling SCN is paramount, and fungi show promise in that respect. Several studies have evaluated fungi and fungal products as biocontrol options against plant-parasitic nematodes. This review discusses fungal genera isolated from the SCN with potential for use as biocontrol agents and the effects of their secondary metabolites on various stages of SCN development. The review also summarizes efforts to control SCN using soil amendments that could potentially impact fungal communities in the soil.

The soybean cyst nematode (SCN) is the most important pest on soybean, a major crop worldwide. The SCN is considered both parasitic and pathogenic as it derives nutrition from the host and manipulates host physiology to do so. Currently, there are no commercially available chemicals that are specific, environmentally safe and cost effective to control SCN levels. Crop rotation, use of host resistance and other cultural practices remain the main management strategies. The need for bioprospecting other methods of controlling SCN is paramount, and fungi show promise in that respect. Several studies have evaluated fungi and fungal products as biocontrol options against plant-parasitic nematodes. This review discusses fungal genera isolated from the SCN with potential for use as biocontrol agents and the effects of their secondary metabolites on various stages of SCN development. The review also summarizes efforts to control SCN using soil amendments that could potentially impact fungal communities in the soil.

Seasonal Variation and Crop Sequences Shape the Structure of Bacterial Communities in Cysts of Soybean Cyst Nematode

Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is the number 1 pathogen of the important economic crop soybean. Bacteria represent potential biocontrol agents of the SCN, but few studies have characterized the dynamics of bacterial communities associated with cysts under different crop rotation sequences. The bacterial communities in SCN cysts in a long-term soybean–corn crop rotation experiment were investigated over 2 years. The crop sequences included long-term soybean monoculture (Ss), years 1–5 of soybean following 5 years corn (S1–S5), years 1 and 2 of corn following 5 years soybean (C1 and C2), and soybean–corn annual rotation (Sa and Ca). The bacterial 16S rRNA V4 region was amplified from DNA isolated from SCN cysts collected in spring at planting, midseason (2 months later), and fall at harvest and sequenced on the Illumina MiSeq platform. The SCN cyst microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidetes, and Verrucomicrobia. The bacterial community composition was influenced by both crop sequence and season. Although differences by crop sequence were not significant in the spring of each year, bacterial communities in cysts from annual rotation (Sa and Ca) or crop sequences of early years of monoculture following a 5-year rotation of the alternate crop (S1 and C1) became rapidly differentiated by crop over a single growing season. In the fall, genera of cyst bacteria associated with soybean crop sequences included Rhizobacter, Leptothrix, Cytophaga, Chitinophaga, Niastella, Streptomyces, and Halangium. The discovery of diverse bacterial taxa in SCN cysts and their dynamics across crop rotation sequences provides invaluable information for future development of biological control of the SCN.