Infection cycle of maize stalk rot and ear rot caused by Fusarium verticillioides

Chemical and genetic characterization of lipopeptides from Bacillus velezensis and Paenibacillus ottowii with activity against Fusarium verticillioides

Introduction

The fungus Fusarium verticillioides significantly threatens maize crops in tropical soils. In light of this, biological control has emerged as a promising strategy to reduce fungicide costs and environmental risks. In this study, we aimed to test the antifungal activity of cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04) against F. verticillioides, thereby contributing to the development of effective biocontrol measures.

Methods

The research employed a comprehensive approach. The antifungal activity of the bacterial strains was tested using cell-free supernatant (CFS) from three Bacillus velezensis (CT02, IM14, and LIS05) and one Paenibacillus ottowii (LIS04). The UPLC-MS evaluated the CFS to identify the main bioactive molecules involved in the inhibitory effect on F. verticillioides. Scanning electron microscopy (SEM) was used to assess the impact of CFS on spores and hyphae, and genome sequencing was conducted to identify the genes involved in biological control. These robust methodologies ensure the reliability and validate our findings.

Results

The CFS of the four strains demonstrated significant inhibition of fungal growth. The UPLC-MS analysis revealed the presence of lipopeptides with antifungal activity, including surfactin and fengycins A and B expressed by the three strains of Bacillus velezensis and iturin A expressed by strains LIS05 and IM14. For Paenibacillus ottowii, fusaricidins, ABCDE, and five previously unreported lipopeptides were detected. Scanning electron microscopy (SEM) showed that treatments with CFS led to significant distortion and breakage of the F. verticillioides hyphae, in addition to the formation of cavities in the membrane. Genome mining confirmed the presence of genes coding for the lipopeptides identified by UPLC-MS, including the gene for iturin in CTO2. Genomic sequencing revealed that CT02, IM14, and LIS05 belong to different strains of Bacillus velezensis, and LIS04 belongs to Paenibacillus ottowii, a species recently described.

Discussion

The four bacterial strains, including three novel strains identified as Bacillus velezensis and one as the recently described species Paenibacillus ottowii, demonstrate significant potential as biocontrol agents for managing fungal disease. This finding underscores the novelty and potential impact of our research.

Factors influencing fumonisin B1 contamination in maize: insights from two production regions in Costa Rica

Maize (Zea mays L.) is an important cereal crop worldwide. Contaminated maize kernels pose a significant mycotoxin exposure risk for humans in Latin America. Fumonisins, the most prevalent mycotoxin in maize, typically occur during pre-harvest conditions leading to significant economic losses. Various factors, including weather conditions, may influence this contamination. This study aimed to determine the association between fumonisin B1 (FB1) contamination, prevalence of Fusarium verticillioides, weather conditions and kernel quality in the two primary maize production areas in Costa Rica (Brunca and Chorotega). All maize samples (100%) showed FB1 contamination, with higher concentrations in samples from Brunca region, consistent with the presence of F. verticilliodes. Weather conditions appeared to play an important role in this contamination, since Brunca region had the highest mean temperature and relative humidity after maize silking (R1) and the total monthly rainfall in this region was significantly higher during the last two months of maize cultivation (grain-filling and physiological maturity stages R3 to R6). Interestingly, this study found a negative correlation between grain damage and kernel contamination with FB1 and F. verticillioides. The concentration of mineral nutrients in kernels from both regions was largely similar. Most nutrients in kernels exhibited a negative correlation with FB1, particularly nitrogen. Zinc and phosphorus were the only nutrients in kernels showing a positive correlation with FB1 in samples from the Brunca region. The results highlight elevated levels of FB1 contamination in maize and contribute to a better understanding of pre-harvest factors influencing FB1 contamination in tropical conditions.

Assessment of Genetic Diversity and the Population Structure of Species from the Fusarium fujikuroi Species Complex Causing Fusarium Stalk Rot of Maize

Fusarium stalk rot (FSR), caused by the Fusarium species complex, is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium species obtained from five major maize-growing regions in India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. A phylogenetic tree showed monophyletic, polyphyletic, and paraphyletic groupings reflecting the complex evolutionary history and genetic diversity within the genus. Monophyletic groupings depicting strong bootstrap support were shown to have a single common ancestor and genetic coherence with limited genetic divergence among sequences. Polyphyletic groupings also presented significant genetic differentiation within the F. verticillioides sequences from diverse ecological niches. Nucleotide diversity of moderate level 0.02471 reflected genetic variations within populations that were attributed to factors such as mutation, genetic drift, or varying selection pressures. The Fst value of 0.98205 is particularly indicative of high genetic differentiation, implying that most of the genetic variance is due to differences between populations rather than within them. F. verticillioides, with 57 sequences, showed low genetic diversity with three segregating sites and a low haplotype diversity of 0.19486, suggesting the founder effect, where a reduced population expands from a limited genetic pool. The total data estimates across all populations for haplotype analysis showed 72 sequences, 44 segregating sites, and 9 haplotypes with a haplotype diversity of 0.48513. The evolutionary dynamics showed genetic differentiations among Fusarium species causing FSR. AMOVA indicated high within-population variations, depicting a substantial genetic diversity within individual populations. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium species causing FSR in maize in the Indian subcontinent.

Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models

KEY MESSAGE

Integrating disease screening data and genomic data for host and pathogen populations into prediction models provides breeders and pathologists with a unified framework to develop disease resistance. Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective.

Identification and genomic insights into a strain of Bacillus velezensis with phytopathogen-inhibiting and plant growth-promoting properties

The use of biological agents offers a sustainable alternative to chemical control in managing plant diseases. In this study, Bacillus velezensis IFST-221 was isolated from the rhizosphere of a healthy maize plant amidst a population showing severe disease symptoms. The investigation demonstrated a broad-spectrum antagonistic activity of IFST-221 against eight species of pathogenic ascomycetes and oomycetes, suggesting its potential utility in combating plant diseases like maize ear rot and cotton Verticillium wilt. Additionally, our study unveiled that IFST-221 has demonstrated significant plant growth-promoting properties, particularly in maize, cotton, tomato, and broccoli seedlings. This growth promotion was linked to its ability to produce indole-3-acetic acid, nitrogen fixation, phosphate and potassium solubilization, and biofilm formation in laboratory conditions. A complete genome sequencing of IFST-221 yielded a genome size of 3.858 M bp and a GC content of 46.71%. The genome analysis identified 3659 protein-coding genes, among which were nine secondary metabolite clusters with known antimicrobial properties. Additionally, three unknown compounds with potentially novel properties were also predicted from the genomic data. Genome mining also identified several key genes associated with plant growth regulation, colonization, and biofilm formation. These findings provide a compelling case for the application of B. velezensis IFST-221 in agricultural practices. The isolate's combined capabilities of plant growth promotion and antagonistic activity against common plant pathogens suggest its promise as an integrated biological agent in disease management and plant productivity enhancement.

FvMbp1-Swi6 complex regulates vegetative growth, stress tolerance, and virulence in Fusarium verticillioides

The mycotoxigenic fungus Fusarium verticillioides is a common pathogen of grain and medicine that contaminates the host with fumonisin B1 (FB1) mycotoxin, poses serious threats to human and animal health. Therefore, it is crucial to unravel the regulatory mechanisms of growth, and pathogenicity of F. verticillioides. Mbp1 is a component of the MluI cell cycle box binding factor complex and acts as an APSES-type transcription factor that regulates cell cycle progression. However, no information is available regarding its role in F. verticillioides. In this study, we demonstrate that FvMbp1 interacts with FvSwi6 that acts as the cell cycle transcription factor, to form the heteromeric transcription factor complexes in F. verticillioides. Our results show that ΔFvMbp1 and ΔFvSwi6 both cause a severe reduction of vegetative growth, conidiation, and increase tolerance to diverse environmental stresses. Moreover, ΔFvMbp1 and ΔFvSwi6 dramatically decrease the virulence of the pathogen on the stalk and ear of maize. Transcriptome profiling show that FvMbp1-Swi6 complex co-regulates the expression of genes associated with multiple stress responses. These results indicate the functional importance of the FvMbp1-Swi6 complex in the filamentous fungi F. verticillioides and reveal a potential target for the effective prevention and control of Fusarium diseases.

Antifungal effect and some properties of cell-free supernatants of two Bacillus subtilis isolates against Fusarium verticillioides

Fusarium verticillioides causes significant decrease in corn yield and quality, and produces fumonisins, which represent a serious risk to human and animal health. Bacillus species can be an effective and environmentally friendly alternative for F. verticillioides biological control. In this study, some properties of cell-free supernatants (CFSs) of two Bacillus spp. identified as Bacillus subtilis (NT1, NT2) as well as the antifungal effect against F. verticillioides 97L were evaluated. B. subtilis NT1 and NT2 were isolated from commercially available fermented whole soybeans (Nattō). Antifungal activity was observed in both CFSs of B. subtilis isolates (50-59 mm) obtained by co-culture suggesting that antifungal compound production depends on interaction between bacteria and fungi. Cell-free supernatants from the two B. subtilis isolates inhibited mycelial growth (77%-94%) and conidial germination (22%-74%) of F. verticillioides 97L. In addition, CFSs caused significant morphological changes such as distorted and collapsed hyphae with wrinkled surfaces and the presence of a large amount of extracellular material compared to the control without CFSs. Both B. subtilis isolates (NT1 and NT2) produced extracellular proteases, biosurfactants and polar low molecular weight compounds that probably act synergistically and may contribute to the antifungal activity. Antifungal compounds showed heat and pH stability and resistance to proteolytic enzymes. Furthermore, antifungal compounds showed high polarity, high affinity to water and a molecular weight less than 10 kDa. These results indicated that the two B. subtilis (NT1 and NT2) have potential as biocontrol agents for F. verticillioides.

FvKex2 is required for development, virulence, and mycotoxin production in Fusarium verticillioides

Fusarium verticillioides is one of the most important fungal pathogens causing maize ear and stalk rots, thereby undermining global food security. Infected seeds are usually unhealthy for consumption due to contamination with fumonisin B1 (FB1) mycotoxin produced by the fungus as a virulence factor. Unveiling the molecular factors that determine fungal development and pathogenesis will help in the control and management of the diseases. Kex2 is a kexin-like Golgi-resident proprotein convertase that is involved in the activation of some important proproteins. Herein, we identified and functionally characterized FvKex2 in relation to F. verticillioides development and virulence by bioinformatics and functional genomics approaches. We found that FvKex2 is required for the fungal normal vegetative growth, because the growth of the ∆Fvkex2 mutant was significantly reduced on culture media compared to the wild-type and complemented strains. The mutant also produced very few conidia with morphologically abnormal shapes when compared with those from the wild type. However, the kexin-like protein was dispensable for the male role in sexual reproduction in F. verticillioides. In contrast, pathogenicity was nearly abolished on wounded maize stalks and sugarcane leaves in the absence of FvKEX2 gene, suggesting an essential role of Fvkex2 in the virulence of F. verticillioides. Furthermore, high-performance liquid chromatography analysis revealed that the ∆Fvkex2 mutant produced a significantly lower level of FB1 mycotoxin compared to the wild-type and complemented strains, consistent with the loss of virulence observed in the mutant. Taken together, our results indicate that FvKex2 is critical for vegetative growth, FB1 biosynthesis, and virulence, but dispensable for sexual reproduction in F. verticillioides. The study presents the kexin-like protein as a potential drug target for the management of the devastating maize ear and stalk rot diseases. Further studies should aim at uncovering the link between FvKex2 activity and FB1 biosynthesis genes. KEY POINTS: •The kexin-like protein FvKex2 contributes significantly to the vegetative growth of Fusarium verticillioides. •The conserved protein is required for fungal conidiation and conidial morphology, but dispensable for sexual reproduction. •Deletion of FvKEX2 greatly attenuates the virulence and mycotoxin production potential of F. verticillioides.

Transcriptomic and Metabolomic Analyses Reveal the Role of Phenylalanine Metabolism in the Maize Response to Stalk Rot Caused by Fusarium proliferatum

Stalk rot is a prevalent disease of maize (Zea mays L.) that severely affects maize yield and quality worldwide. The ascomycete fungus Fusarium spp. is the most common pathogen of maize stalk rot. At present, the molecular mechanism of Fusarium proliferation during the maize stalk infection that causes maize stalk rot has rarely been reported. In this study, we investigated the response of maize to F. proliferatum infestation by analyzing the phenotypic, transcriptomic, and metabolomic data of inbred lines ZC17 (resistant) and CH72 (susceptible) with different levels of resistance to stalk rot. Physiological and phenotypic results showed that the infection CH72 was significantly more severe than ZC17 after inoculation. Transcriptome analysis showed that after inoculation, the number of differentially expressed genes (DEGs) was higher in CH72 than in ZC17. Nearly half of these DEGs showed the same expression trend in the two inbred lines. Functional annotation and enrichment analyses indicated that the major pathways enriched for DEGs and DEMs included the biosynthesis of plant secondary metabolites, phenylalanine metabolism, biosynthesis of plant hormones, and plant-pathogen interactions. The comprehensive analysis of transcriptome and metabolome data indicated that phenylalanine metabolism and the phenylalanine, tyrosine, and tryptophan biosynthesis pathways played a crucial role in maize resistance to F. proliferatum infection. In addition, a transcription factor (TF) analysis of the DEGs showed that several TF families, including MYB, bHLH, NAC, and WRKY, were significantly activated after inoculation, suggesting that these TFs play important roles in the molecular regulatory network of maize disease resistance. The findings of this study provide valuable insights into the molecular basis of the response of maize to Fusarium proliferatum infection and highlight the importance of combining multiple approaches, such as phenotyping, transcriptomics, and metabolomics, to gain a comprehensive understanding of plant-pathogen interactions.

Microbial diversity in soils suppressive to Fusarium diseases

Fusarium species are cosmopolitan soil phytopathogens from the division Ascomycota, which produce mycotoxins and cause significant economic losses of crop plants. However, soils suppressive to Fusarium diseases are known to occur, and recent knowledge on microbial diversity in these soils has shed new lights on phytoprotection effects. In this review, we synthesize current knowledge on soils suppressive to Fusarium diseases and the role of their rhizosphere microbiota in phytoprotection. This is an important issue, as disease does not develop significantly in suppressive soils even though pathogenic Fusarium and susceptible host plant are present, and weather conditions are suitable for disease. Soils suppressive to Fusarium diseases are documented in different regions of the world. They contain biocontrol microorganisms, which act by inducing plants' resistance to the pathogen, competing with or inhibiting the pathogen, or parasitizing the pathogen. In particular, some of the Bacillus, Pseudomonas, Paenibacillus and Streptomyces species are involved in plant protection from Fusarium diseases. Besides specific bacterial populations involved in disease suppression, next-generation sequencing and ecological networks have largely contributed to the understanding of microbial communities in soils suppressive or not to Fusarium diseases, revealing different microbial community patterns and differences for a notable number of taxa, according to the Fusarium pathosystem, the host plant and the origin of the soil. Agricultural practices can significantly influence soil suppressiveness to Fusarium diseases by influencing soil microbiota ecology. Research on microbial modes of action and diversity in suppressive soils should help guide the development of effective farming practices for Fusarium disease management in sustainable agriculture.

Genetic variation in ZmWAX2 confers maize resistance to Fusarium verticillioides

Fusarium verticillioides (F. verticillioides) is a widely distributed phytopathogen that incites multiple destructive diseases in maize, posing a grave threat to corn yields and quality worldwide. However, there are few reports of resistance genes to F. verticillioides. Here, we reveal that a combination of two single nucleotide polymorphisms (SNPs) corresponding to ZmWAX2 gene associates with quantitative resistance variations to F. verticillioides in maize through a genome-wide association study. A lack of ZmWAX2 compromises maize resistance to F. verticillioides-caused seed rot, seedling blight and stalk rot by reducing cuticular wax deposition, while the transgenic plants overexpressing ZmWAX2 show significantly increased immunity to F. verticillioides. A natural occurrence of two 7-bp deletions within the promoter increases ZmWAX2 transcription, thus enhancing maize resistance to F. verticillioides. Upon Fusarium stalk rot, ZmWAX2 greatly promotes the yield and grain quality of maize. Our studies demonstrate that ZmWAX2 confers multiple disease resistances caused by F. verticillioides and can serve as an important gene target for the development of F. verticillioides-resistant maize varieties.

Single-cell RNA sequencing profiles reveal cell type-specific transcriptional regulation networks conditioning fungal invasion in maize roots

Stalk rot caused by Fusarium verticillioides (Fv) is one of the most destructive diseases in maize production. The defence response of root system to Fv invasion is important for plant growth and development. Dissection of root cell type-specific response to Fv infection and its underlying transcription regulatory networks will aid in understanding the defence mechanism of maize roots to Fv invasion. Here, we reported the transcriptomes of 29 217 single cells derived from root tips of two maize inbred lines inoculated with Fv and mock condition, and identified seven major cell types with 21 transcriptionally distinct cell clusters. Through the weighted gene co-expression network analysis, we identified 12 Fv-responsive regulatory modules from 4049 differentially expressed genes (DEGs) that were activated or repressed by Fv infection in these seven cell types. Using a machining-learning approach, we constructed six cell type-specific immune regulatory networks by integrating Fv-induced DEGs from the cell type-specific transcriptomes, 16 known maize disease-resistant genes, five experimentally validated genes (ZmWOX5b, ZmPIN1a, ZmPAL6, ZmCCoAOMT2, and ZmCOMT), and 42 QTL or QTN predicted genes that are associated with Fv resistance. Taken together, this study provides not only a global view of maize cell fate determination during root development but also insights into the immune regulatory networks in major cell types of maize root tips at single-cell resolution, thus laying the foundation for dissecting molecular mechanisms underlying disease resistance in maize.

Cell wall-related genes and lignin accumulation contribute to the root resistance in different maize (Zea mays L.) genotypes to Fusarium verticillioides (Sacc.) Nirenberg infection

Introduction

The fungal pathogen Fusarium verticillioides (Sacc.) Nirenberg (Fv) causes considerable agricultural and economic losses and is harmful to animal and human health. Fv can infect maize throughout its long agricultural cycle, and root infection drastically affects maize growth and yield.

Methods

The root cell wall is the first physical and defensive barrier against soilborne pathogens such as Fv. This study compares two contrasting genotypes of maize (Zea mays L.) roots that are resistant (RES) or susceptible (SUS) to Fv infection by using transcriptomics, fluorescence, scanning electron microscopy analyses, and ddPCR.

Results

Seeds were infected with a highly virulent local Fv isolate. Although Fv infected both the RES and SUS genotypes, infection occurred faster in SUS, notably showing a difference of three to four days. In addition, root infections in RES were less severe in comparison to SUS infections. Comparative transcriptomics (rate +Fv/control) were performed seven days after inoculation (DAI). The analysis of differentially expressed genes (DEGs) in each rate revealed 733 and 559 unique transcripts that were significantly (P ≤0.05) up and downregulated in RES (+Fv/C) and SUS (+Fv/C), respectively. KEGG pathway enrichment analysis identified coumarin and furanocoumarin biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways as being highly enriched with specific genes involved in cell wall modifications in the RES genotype, whereas the SUS genotype mainly displayed a repressed plant-pathogen interaction pathway and did not show any enriched cell wall genes. In particular, cell wall-related gene expression showed a higher level in RES than in SUS under Fv infection. Analysis of DEG abundance made it possible to identify transcripts involved in response to abiotic and biotic stresses, biosynthetic and catabolic processes, pectin biosynthesis, phenylpropanoid metabolism, and cell wall biosynthesis and organization. Root histological analysis in RES showed an increase in lignified cells in the sclerenchymatous hypodermis zone during Fv infection.

Discussion

These differences in the cell wall and lignification could be related to an enhanced degradation of the root hairs and the epidermis cell wall in SUS, as was visualized by SEM. These findings reveal that components of the root cell wall are important against Fv infection and possibly other soilborne phytopathogens.

Fusarium verticillioides of maize plant: Potentials of propitious phytomicrobiome as biocontrol agents

Disease outbreaks have been recorded due to exposure to Fusarium verticillioides and fumonisin, a mycotoxin produced by this fungus. F. verticillioides is a fungal pathogen of maize that causes infections, such as wilting and rotting, while contact with its fumonisin derivative manifests in the form of mild to severe illnesses in humans and animals. Maize infection by F. verticillioides causes loss or reduction in expected crop yield, thereby influencing households and nations' economies. While several efforts have been made to control the pathogenic fungus and its occurrence in the environment, it remains a challenge in agriculture, particularly in maize production. Several microorganisms which are plant-associated, especially those associated with the rhizosphere niche have been noted to possess antagonistic effects against F. verticillioides. They can inhibit the pathogen and tackle its debilitating effects on plants. Hence this study reviews the use of rhizosphere-associated biocontrol agents, such as Bacillus spp., Pseudomonas, Enterobacter, and Microbacterium oleivorans which forms part of the phytomicrobiome in other to prevent and control this toxicogenic fungus. These microorganisms were found to not only be effective in controlling its occurrence on maize plants but are environmentally safe and promote crop yield.

Injury and not the pathogen is the primary cause of corm rot in Crocus sativus (saffron)

Fusarium oxysporum has been reported to be the most devastating pathogen of Crocus sativus L., a commercially significant crop that yields the saffron spice. However, most of the pathogen isolations have been done from the diseased tissue, mostly from rotten corms, but no study has been conducted on diseased saffron fields. To fill the knowledge gap, the current study was carried out with the intention of recording the diversity of cultivable fungus species from saffron fields and screening them for pathogenicity towards saffron. The three study locations in Jammu and Kashmir, Srinagar (Pampore), Kishtwar, and Ramban, yielded a total of 45 fungal isolates. The internal transcribed spacer (ITS) of rDNA was used for the molecular identification. ITS rDNA-based sequence analysis classified all the operational taxonomic units (OTUs) into two phyla-Ascomycota (88.88%) and Mucoromycota (11.11%). Moreover, Fusarium (57.77%), Geotrichum (17.77%), Mucor (11.11%), Aspergillus (4.44%), Trichoderma (4.44%), Galactomyces (2.22%), and Colletotrichum (2.22%) all had different total abundances at the genus level. It was discovered that the saffron fields in Srinagar have fewer varied fungal species than the other two selected sites. All of the fungal isolates isolated including Fusarium solani, Aspergillus flavus, Trichoderma harzianum, Fusarium neocosmosporiellum, and Mucor circinelloides were pathogenic according to the pathogenicity test; however, injury to the saffron plant was found to be a must. These fungi were pathogenic in addition to F. oxysporum, which is well documented as a major cause of saffron corm rot diseases in Srinagar, but in the present study, injury was a must for F. oxysporum as well. The percentage disease severity index for both saffron roots and corms varied for each fungal isolate.

Transcriptional differences between major Fusarium pathogens of maize, Fusarium verticillioides and Fusarium graminearum with different optimum growth temperatures

Fusarium verticillioides and Fusarium graminearum are important pathogens causing disease in maize (Zea mays) worldwide. The distributions of these fungal pathogens vary greatly in different regions and in different years, and are influenced by environmental and climatic conditions. Temperature has significant effects on the growth and mycotoxin production of Fusarium species. In this study, the effects of temperature on the growth and pathogenicity of F. verticillioides and F. graminearum were investigated. F. verticillioides grew fastest and exhibited the strongest pathogenicity to maize stems and grains at 30°C, while F. graminearum grew best at 20°C. Both species produced more toxins at 20°C than at 30°C. To explain the interspecific differences in the relationship of growth and temperature, RNA-seq was used to compare F. verticillioides and F. graminearum cultivated for 4 d at the optimum temperatures of 30°C and 20°C, respectively. Samples of F. verticillioides were also cultivated for 9 d (to maximize toxin production) at 20°C and 30°C and analyzed by RNA-seq to investigate the influence of temperature for different growth stages. The differently expressed genes (DEGs) were identified by comparison of cultures grown for the same amount of time but at different temperatures. GO enrichment analysis showed high enrichment of DEGs in categories of membrane part, catalytic activity, metabolic process, and growth at warmer temperature resulted in more down-regulated DEGs enriched in membrane components in all groups. KEGG analysis revealed enrichment of DEGs related to different temperatures in carbohydrate and amino acid metabolism pathways. For both species, there was decreased expression of many DEGs related to amino acid metabolism when cultivated at warm temperature, such as genes related to beta-alanine metabolism and arginine and proline metabolism. However, changes in genes related to glyoxylate and dicarboxylate metabolism and fatty acid degradation were more related to the growth state. The results showing different responses pattern of these pathways provides a foundation for further investigation of the molecular mechanisms underlying distinct thermal ecological niches of F. verticillioides and F. graminearum.

A novel maize microRNA negatively regulates resistance to Fusarium verticillioides

Although microRNAs (miRNAs) regulate the defence response against multiple pathogenic fungi in diverse plant species, few efforts have been devoted to deciphering the involvement of miRNA in resistance to Fusarium verticillioides, a major pathogenic fungus affecting maize production. In this study, we discovered a novel F. verticillioides-responsive miRNA designated zma-unmiR4 in maize kernels. The expression of zma-unmiR4 was significantly repressed in the resistant maize line but induced in the susceptible lines upon exposure to F. verticillioides exposure, whereas its target gene ZmGA2ox4 exhibited the opposite pattern of expression. Heterologous overexpression of zma-unmiR4 in Arabidopsis resulted in enhanced growth and compromised resistance to F. verticillioides. By contrast, transgenic plants overexpressing ZmGA2ox4 or the homologue AtGA2ox7 showed impaired growth and enhanced resistance to F. verticillioides. Moreover, zma-unmiR4-mediated suppression of AtGA2ox7 disturbed the accumulation of bioactive gibberellin (GA) in transgenic plants and perturbed the expression of a set of defence-related genes in response to F. verticillioides. Exogenous application of GA or a GA biosynthesis inhibitor modulated F. verticillioides resistance in different plants. Taken together, our results suggest that the zma-unmiR4-ZmGA2ox4 module might act as a major player in balancing growth and resistance to F. verticillioides in maize.

Distribution and Biodiversity of Seed-Borne Pathogenic and Toxigenic Fungi of Maize in Egypt and Their Correlations with Weather Variables

Studies of the biodiversity of plant pathogenic and toxigenic fungi are attracting great attention to improve the predictability of their epidemics and the development of their control programs. Two hundred maize grain samples were gathered from 25 maize-growing governorates in Egypt and 189 samples were processed for the isolation and identification of seed-borne fungal microbiome. Twenty-six fungal genera comprising 42 species were identified according to their morphological characteristics and ITS DNA sequence analysis. Occurrence and biodiversity indicators of these fungal species were calculated. Ustilago maydis, Alternaria alternata, Aspergillus flavus, A. niger, Penicillium spp., Cladosporium spp. and Fusarium verticillioides were the highly frequent (>90% for each), recording the highest relative abundance (˃50%). Al-Menia governorate showed the highest species diversity and richness, followed by Sohag, Al-Nobaria and New Valley governorates. Correlations of 18 fungal species with temperature, relative humidity, precipitation, wind speed, and solar radiation were analyzed using canonical correspondence analysis. Results showed that relative humidity, temperature, and wind speed, respectively, were the most impactful weather variables. However, the occurrence and distribution of these fungi were not clearly grouped into the distinctive climatic regions in which maize crops are grown. Monitoring the occurrence and distribution of the fungal pathogens of maize grains in Egypt will play an important role in predicting their outbreaks and developing appropriate future management strategies. The findings in this study may be useful to other maize-growing countries that have similar climatic conditions.

Evaluation and Identification of Resistance Lines and QTLs of Maize to Seedborne Fusarium verticillioides

Internal fungal contamination in cereal grains may affect plant growth and result in health concerns for humans and animals. Fusarium verticillioides is a seedborne fungus that can systemically infect maize. However, few efforts had been devoted to studying the genetics of maize resistance to seedborne F. verticillioides. In this study, we developed a disease evaluation method to identify resistance to seedborne F. verticillioides in maize, by which a set of 121 diverse maize inbred lines were evaluated. A 160 F₁₀-generation recombinant inbred line (RIL) population derived from a cross of the resistant (BT-1) and susceptible (N6) inbred line was further used to identify major quantitative trait loci (QTLs) for seedborne F. verticillioides resistance. Eighteen inbred lines with a high resistance to seedborne F. verticillioides were characterized and could be used as potential germplasm resources for genetic improvement of maize resistance. Six QTLs with high heritability across multiple environments were detected on chromosomes 3, 4, 6, and 10, among which was a major QTL, qISFR4-1. Located on chromosome 4 at the interval of 12922609-13418025, qISFR4-1 could explain 16.63% of the total phenotypic variance. Distinct expression profiles of eight candidate genes in qISFR4-1 between BT-1 and N6 inbred lines suggested their pivotal regulatory roles in seedborne F. verticillioides resistance. Taken together, these results will improve our understanding of the resistant mechanisms of seedborne F. verticillioides and would provide valuable germplasm resources for disease resistance breeding in maize.

2,4-Diacetylphloroglucinol producing Pseudomonas fluorescens JM-1 for management of ear rot disease caused by Fusarium moniliforme in Zea mays L

Maize (Zea mays L.) is a major cereal crop grown in a large number of countries. Loss in maize yield due to biotic stresses including fungal phytopathogens is a matter of immense concern. Control measures applied for eradication of fungal phytopathogens in maize are not up to the mark and more often involve harsh chemical(s)/pesticide(s) that cause deleterious effects both in humans and soil biota. Greener alternatives, such as the use of rhizosphere microbes in the form of bioinoculants, have proven to be very successful in terms of enhancing crop yield and suppressing fungal phytopathogens. In the present study, fluorescent pseudomonads were isolated from the maize rhizosphere and monitored for their plant growth-promoting (PGP) and biocontrol activities against Fusarium moniliforme. Based on various PGP traits and biocontrol potential, isolate JM-1 was found to be most effective and as per 16S rRNA gene sequencing analysis was identified as Pseudomonas fluorescens. Further experiments showed that the biocontrol potential of JM-1 against ear rot fungus involved the production of antifungal compound 2,4-diacetylphloroglucinol (DAPG). When examined for antagonistic interaction under scanning electron microscopy (SEM), structural abnormality, hyphal lysis, and deformity in fungal mycelium were observed. In the pot experiment, application of talc-based JM-1 containing bioformulation (in pot trials) showed significant enhancement in maize growth parameters (including the seed number and weight) in comparison to control even in presence of the phytopathogen. Ear fresh weight, dry weight, number of seeds per plant, and 100-grain weight were found to increase significantly by 34, 34, 52, and 18% respectively, in comparison to control. P. fluorescens JM-1 can therefore be used as a bioinoculant for ear rot disease control and sustainably enhancing maize yield.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03201-7.

Control of Fusarium verticillioides on corn with a combination of Bacillus subtilis TM3 formulation and botanical pesticides

The aim of this study was to evaluate the effectiveness of the combination of Bacillus subtilis TM3 formulation with botanical pesticides in suppressing Fusarium verticilloides infection in corn. The research was carried out at the Plant Pathology Laboratory and the Experimental Farm of Indonesian Cereals Research Institute (ICERI) from February to November 2019. The research consisted of two stages, namely an in vitro test of antagonists of botanical pesticides against F. verticilloides using 5 types of plant extracts namely betel leaf extract, turmeric, galangal, cosmos, and clove leaf. The second stage was to test the effectiveness of the combination of the formulation of B. subtilis TM3 with the best 3 types of plant extracts in vitro testing in suppressing F. verticilloides infection in plants. The results of the in vitro study showed that the plant extracts of betel leaf, clove leaf and galangal had the best inhibitory ability on the mycelia growth of F. verticilloides. Meanwhile, the field test found that the application of the B. subtilis TM3 formulation, either alone or in combination with plant extracts, was able to suppress F. verticilloides infection. The combination of B. subtilis TM3 formulation with betel leaf extract showed the best inhibition of 20% against stem rot disease and 13.33% against corn cob rot. This treatment did not affect production quantitatively, but was able to suppress the decline in seed quality due to F. verticilloides infection. Seeds grown by the Plastic Rolled Paper Test (PRPT) method were not only infected with F. verticilloides, but also infected with other seed-borne pathogens, such as Aspergillus niger and A. falvus. The presence of these two pathogens did not inhibit the growth of F. verticilloides in kernels.

Species Diversity and Chemotypes of Fusarium Species Associated With Maize Stalk Rot in Yunnan Province of Southwest China

Maize stalk rot caused by Fusarium species is one of the most important fungal diseases of maize throughout the world. The disease is responsible for considerable yield losses and has also been associated with mycotoxin contamination of the crop. In this study, a survey of maize stalk rot was performed in seven locations of Yunnan Province in China during the cropping season of 2015 and 2016. Based on morphological and molecular characteristics, 204 isolates belonging to 12 Fusarium spp. from symptomatic stalks of maize were identified. Among the isolated strains, 83 were identified as Fusarium meridionale (40.5%), 46 as Fusarium boothii (22.5%), 34 as Fusarium temperatum (16.5%), 12 as Fusarium equiseti (5.9%), 10 as Fusarium asiaticum (4.9%), six as Fusarium proliferatum (3.0%), four as Fusarium verticillioides (2.0%), four as Fusarium incarnatum (2.0%), two as Fusarium avenaceum (1.0%), one as Fusarium cerealis (0.5%), one as Fusarium graminearum (0.5%), and one as Fusarium cortaderiae (0.5%). Fusarium cortaderiae was the first report on the causal agent of maize stalk rot disease in China. These isolates were divided into five chemotypes: nivalenol (NIV), deoxynivalenol (DON), beauvericin (BEA), zearalenone (ZEN), and fumonisin (FUM). Phylogenetic analysis based on partial sequences of the translation elongation factor 1α (TEF1-α) showed a high degree of interspecific polymorphisms among the isolates. Pathogenicity analysis on maize stalks indicated that all the 12 species of Fusarium were able to cause the disease symptoms with different aggressiveness. This study on population, pathogenicity, and toxigenic chemotypes of Fusarium species associated with maize stalk rot in Yunnan Province of southwest China, will help design an effective integrated control strategy for this disease.

Plasma Technology Increases the Efficacy of Prothioconazole against Fusarium graminearum and Fusarium proliferatum Contamination of Maize (Zea mays) Seedlings

The contamination of maize by Fusarium species able to produce mycotoxins raises great concern worldwide since they can accumulate these toxic metabolites in field crop products. Furthermore, little information exists today on the ability of Fusarium proliferatum and Fusarium graminearum, two well know mycotoxigenic species, to translocate from the seeds to the plants up to the kernels. Marketing seeds coated with fungicide molecules is a common practice; however, since there is a growing need for reducing chemicals in agriculture, new eco-friendly strategies are increasingly tested. Technologies based on ionized gases, known as plasmas, have been used for decades, with newer material surfaces, products, and approaches developed continuously. In this research, we tested a plasma-generated bilayer coating for encapsulating prothioconazole at the surface of maize seeds, to protect them from F. graminearum and F. proliferatum infection. A minimum amount of chemical was used, in direct contact with the seeds, with no dispersion in the soil. The ability of F. graminearum and F. proliferatum species to translocate from seeds to seedlings of maize has been clearly proven in our in vitro experiments. As for the use of plasma technology, the combined use of the plasma-generated coating with embedded prothioconazole was the most efficient approach, with a higher reduction of the infection of the maize seminal root system and stems. The debated capability of the two Fusarium species to translocate from seeds to seedlings has been demonstrated. The plasma-generated coating with embedded prothioconazole resulted in a promising sustainable approach for the protection of maize seedlings.

Variation of rhizosphere microbial community in continuous mono-maize seed production

Soil microbe is crucial to a healthy soil, therefore its diversities and abundances under different conditions are still need fully understand.The aims of the study were to characterize the community structure and diversity of microbe in the rhizosphere soil after continuous maize seed production, and the relationship between the disease incidence of four diseases and the variation of the rhizosphere microbe. The results showed that different fungal and bacterial species were predominant in different cropping year, and long-term maize seed production had a huge impact on structure and diversity of soil microbial. Ascomycota and Mortierellomycota were the dominant fungal phyla and Mortierella and Ascomycetes represented for a large proportion of genus. A relative increase of Fusarium and Gibberella and a relative decrease of Mortierella, Chrysosporium, Podospora, and Chaetomium were observed with the increase of cropping year. Pathogenic Fusarium, Curvularia, Curvularia-lunata, Cladosporium, Gibberella-baccata, and Plectosphaerellaceae were over-presented and varied at different continuous cropping year, led to different maize disease incidence. Proteobacteria and Actinobacteria ranked in the top two of all bacterial phyla, and genus Pseudarthrobacter, Roseiflexus and RB41 dominated top 3. Haliangium and Streptomyces decreased with the continuous cropping year and mono-cropping of maize seed production increased disease incidence with the increase of cropping year, while the major disease was different. Continuous cropping of maize seed production induced the decrease of protective microbe and biocontrol genera, while pathogenic pathogen increased, and maize are in danger of pathogen invasion. Field management show great effects on soil microbial community.

Comparative Proteomic Analysis of the Defense Response to Gibberella Stalk Rot in Maize and Reveals That ZmWRKY83 Is Involved in Plant Disease Resistance

Fusarium graminearum is the causal agent of Gibberella stalk rot in maize stem, resulting in maize lodging, yield, quality, and mechanical harvesting capacity. To date, little is known about the maize stem defense mechanism in response to the invasion of F. graminearum. This study represents a global proteomic approach to document the infection by F. graminearum. A total of 1,894 differentially expressed proteins (DEPs) were identified in maize stem with F. graminearum inoculation. Functional categorization analysis indicated that proteins involved in plant-pathogen interaction were inducible at the early stages of infection. We also found that the expression of proteins involved in phenylpropanoid, flavonoid, and terpenoid biosynthesis were upregulated in response to F. graminearum infection, which may reflect that these secondary metabolism pathways were important in the protection against the fungal attack in maize stem. In continuously upregulated proteins after F. graminearum infection, we identified a WRKY transcription factor, ZmWRKY83, which could improve the resistance to plant pathogens. Together, the results show that the defense response of corn stalks against F. graminearum infection was multifaceted, involving the induction of proteins from various immune-related pathways, which had a directive significance for molecular genetic breeding of maize disease-resistant varieties.

A Survey of Mycoviral Infection in Fusarium spp. Isolated from Maize and Sorghum in Argentina Identifies the First Mycovirus from Fusarium verticillioides

Mycoviruses appear to be widespread in Fusarium species worldwide. The aim of this work was to identify mycoviral infections in Fusarium spp., isolated from maize and sorghum grown in Argentina, and to estimate their potential effects on the pathogenicity and toxigenesis of the host fungus towards maize. Mycoviruses were identified in 2 out of 105 isolates analyzed; Fusarium verticillioides strain Sec505 and Fusarium andiyazi strain 162. They were characterized as members of the genus Mitovirus by high-throughput sequencing and sequence analysis. The F. verticillioides mitovirus was a novel mycovirus whereas the F. andiyazi mitovirus was found to be a new strain of a previously identified mitovirus. We have named these mitoviruses, Fusarium verticillioides mitovirus 1 (FvMV1) and Fusarium andiyazi mitovirus 1 strain 162 (FaMV1-162). To our knowledge, FvMV1 is the first mycovirus reported as naturally infecting F. verticillioides, the major causal agent of ear rot and fumonisin producer in corn. Both mitoviruses exhibited 100% vertical transmission rate to microconidia. The Fa162 strain infected with FaMV1-162 did not show phenotypic alterations. In contract, F. verticillioides Sec505 infected with FvMV1 showed increased virulence as well as microconidia and fumonisin-B1 production, compared with two uninfected strains. These results suggest that FvMV1 could have a role in modulating F. verticillioides pathogenicity and toxin production worth further exploring.

First Demonstration of Clinical Fusarium Strains Causing Cross-Kingdom Infections from Humans to Plants

Mycotoxins from the Fusarium genus are widely known to cause economic losses in crops, as well as high mortalities rates among immunocompromised humans. However, to date, no correlation has been established for the ability of Fusarium to cause cross-kingdom infection between plants and humans. The present investigation aims to fill this gap in the literature by examining cross-kingdom infection caused by Furasium strains isolated from non-immunocompromised or non-immunosuppressed humans, which were subsequently reinfected in plants and on human tissue. The findings document for the first time cross-kingdom infective events in Fusarium species, thus enhancing our existing knowledge of how mycopathogens continue to thrive in different hosts.

High-Resolution Melting (HRM) Curve Assay for the Identification of Eight Fusarium Species Causing Ear Rot in Maize

Maize plants are often infected with fungal pathogens of the genus Fusarium. Taxonomic characterization of these species by microscopic examination of pure cultures or assignment to mating populations is time-consuming and requires specific expertise. Reliable taxonomic assignment may be strengthened by the analysis of DNA sequences. Species-specific PCR assays are available for most Fusarium pathogens, but the number of species that infect maize increases the labor and costs required for analysis. In this work, a diagnostic assay for major Fusarium pathogens of maize based on the analysis of melting curves of PCR amplicons was established. Short segments of genes RPB2 and TEF-1α, which have been widely used in molecular taxonomy of Fusarium, were amplified with universal primers in a real-time thermocycler and high-resolution melting (HRM) curves of the products were recorded. Among major Fusarium pathogens of maize ears, F. cerealis, F. culmorum, F. graminearum, F. equiseti, F. poae, F. temperatum, F. tricinctum, and F. verticillioides, all species except for the pair F. culmorum/F. graminearum could be distinguished by HRM analysis of a 304 bp segment of the RPB2 gene. The latter two species could be differentiated by HRM analysis of a 247 bp segment of the TEF-1α gene. The assay was validated with DNA extracted from pure cultures of fungal strains, successfully applied to total DNA extracted from infected maize ears and also to fungal mycelium that was added directly to the PCR master mix ("colony PCR"). HRM analysis thus offers a cost-efficient method suitable for the diagnosis of multiple fungal pathogens.

DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables

The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.

Impact of Environmental Conditions and Agronomic Practices on the Prevalence of Fusarium Species Associated with Ear- and Stalk Rot in Maize

Fusarium species are common pathogens on maize and reduce the product quality through contamination with mycotoxins thus jeopardizing safety of both animal feed and human food products. Monitoring of Fusarium infected maize ears and stalks was conducted in Germany to determine the range of Fusarium species present in the field and to assess the impact of tillage, crop rotation, and weather conditions on the frequency of Fusarium species. From 2016 till 2018, a total of 387 infected ears and 190 stalk segments from 58 locations in Germany were collected. For each sample location, site-specific agronomic data on tillage and previous crops as well as meteorological data on precipitation, air temperature, and relative humidity during the vegetation period were recorded. The most frequent Fusarium species detected in maize ears were Fusariumgraminearum, F.verticillioides and F.temperatum, whereas, F.graminearum, F.equiseti, F.culmorum, and F.temperatum were the species prevailing on maize stalks. Differences in the local species composition were found to be primarily associated with weather variations between the years and the microclimate at the different locations. The results indicate that mean temperature and precipitation in July, during flowering, has the strongest impact on the local range of Fusarium spp. on ears, whereas the incidence of Fusarium species on stalks is mostly affected by weather conditions during September. Ploughing significantly reduced the infection with F.graminearum and F.temperatum, while crop rotation exerted only minor effects.

Design and validation of a robust multiplex polymerase chain reaction assay for MAT idiomorph within the Fusarium fujikuroi species complex

We discovered that published polymerase chain reaction (PCR) assays for determining mating type (MAT) idiomorph failed to genotype some of the Fusarium fujikuroi species complex (FFSC) isolates recovered from Mangifera indica (mango), Swietenia macrophylla (big-leaf mahogany), Annona muricata (soursop), Bursera sp., and Tabebuia sp. in Mexico. Thus, the primary objective of this study was to design and validate a robust multiplex PCR-based diagnostic for typing MAT within the FFSC. To accomplish this objective, we mined the MAT1-1 or MAT1-2 locus from the genomes of 60 FFSC isolates, representing 56 phylospecies, and from four species in its sister group, the F. nisikadoi species complex (FNSC). Bioinformatic searches were facilitated by targeting DNA lyase (SLA2) and apurinic endonuclease (APN1), the genes that flank the MAT locus in Fusarium. As expected, three genes were identified within MAT1-1 (MAT1-1-1, MAT1-1-2, and MAT1-1-3) and two in MAT1-2 (MAT1-2-1 and MAT1-2-9), using the ab initio prediction tool AUGUSTUS. Of the three multiplex PCR assays we designed and tested, the one targeting MAT1-1-2 and MAT1-2-1 successfully genotyped the entire 71-isolate validation panel, which included 56 FFSC and 4 FNSC phylospecies. By contrast, the published PCR assays we tested produced positive genotypes for only 46.5-59% of the 71-isolate validation panel, but only when they were run as a uniplex assay. Although only one-fifth of the FFSC/FNSC are known to reproduce sexually, our results suggest that if they possess a sexual cycle, it is heterothallic (self-sterile).