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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Hirsutellaminnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genomewas de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. [ABSTRACT FROM AUTHOR]

The cyst of the soya bean cyst nematode (SCN; Heterodera glycines), an economically important pathogen of soya beans worldwide, represents a unique microhabitat in soil. The fungi inhabiting cysts may include natural antagonists of the SCN as well as saprotrophs and other opportunists. This study aimed to characterise the entire culturable mycobiome of SCN cysts obtained from a long-term soya bean-corn rotation experiment using ITS fungal barcoding. Fusarium was consistently the most frequently isolated taxon across all sampling time points and crop sequences, followed by Ilyonectria. Among fourteen genera frequently isolated from SCN cysts, five fell within the single family Nectriaceae (Sordariomycetes) and five within the order Pleosporales (Dothideomycetes), suggesting independent evolutionary origins and shared adaptations in these groups towards colonisation of SCN cysts. Six genera (Pochonia , Clonostachys , Fusarium, Neonectria, Alternaria , and Leptosphaeria) varied significantly by crop sequence in at least one year. [ABSTRACT FROM AUTHOR]

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 invitro 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. [ABSTRACT FROM AUTHOR]

The soybean cyst nematode ( Heterodera glycines ) is a plant parasitic nematode that is a major plant pest worldwide and causes severe economic and yield losses. Piriformospora indica , a plant growth promoting fungus isolated from the Thar Deserts of western India, has been shown to protect a wide range of plants from various biotic and abiotic stresses. To evaluate the potential of P. indica to protect soybean ( Glycine max ) seedlings from damage by the soybean cyst nematode (SCN), we amended soil with two different concentrations of P. indica (2.5% and 5% w/w) and inoculated with second-stage juveniles (J2s) of SCN in each treatment. After 60 days, abundance of nematode eggs was measured by calculating SCN egg population densities. We found that egg density/100 cc soil was significantly decreased by 29.7% and 36.7% respectively in the soil amended with 2.5% and 5% P. indica compared to a control. Amendment with P. indica also had a strong growth and yield promoting effect in Soybean. Although root biomass was significantly decreased by 27.9% and 33.5% in the two treatments compared to the control, shoot biomass (dry weight) increased by 30.8% and 8.2% in the 2.5% and 5% P. indica treatments compared to the control. Additionally, plant development was accelerated and a 75% increase in flowering was observed between the 2.5% P. indica treatment and the control. We conclude that P. indica used as a soil amendment decreases abundance of the SCN in soil and has plant-growth promoting properties that may help offset yield losses due to plant parasitic nematodes. [ABSTRACT FROM AUTHOR]

• Twenty fungi screened in planta against SCN. • Three isolates showed high biocontrol efficacy. • One Purpureocillium sp. controlled performed as well as commercial biologicals at lower dosage. The soybean cyst nematode (SCN; Heterodera glycines) is the most economically consequential pathogen of soybeans worldwide. Although biological control of SCN was proposed decades ago, only a few products are available on the market. Mining for new fungal biological control organisms and evaluating their potential to enhance integrated management of SCN is crucial. In this study, we evaluated 20 candidate biological control organisms in vivo that were selected out of a culturable mycobiome of over 5000 isolates based on their performance in in vitro assays. Of these isolates, labelled A through T, we identified three isolates, one Ilyonectria sp. (D), and two Purpureocillium sp. isolates (E and T), that significantly reduced SCN reproduction on a susceptible soybean variety (Sturdy) inoculated with both high and low levels of SCN eggs, compared to an untreated control, in a growth chamber cone-tainer assay. In a greenhouse pot assay, Purpureocillium isolates E and T also controlled nematode reproduction better than an untreated control and performed on par with the commercial fungal biological control agent, MeloCon® WG, which was applied at 41-fold higher concentration. In a second greenhouse assay, with higher nematode numbers, only isolate E performed as well as MeloCon® WG. This research identified promising candidate biological control agents of SCN that are as or more effective than existing products at much lower spore inoculation levels. [ABSTRACT FROM AUTHOR]