Population Subdivision of Fusarium graminearum from Barley and Wheat in the Upper Midwestern United States at the Turn of the Century

The Emerging Fusarium graminearum NA3 Population Produces High Levels of Mycotoxins in Wheat and Barley

Fusarium graminearum (Fg) is the primary causal agent of Fusarium head blight (FHB) in wheat, barley, and other small grains in North America and worldwide. FHB results in yield reduction and contaminates grain with mycotoxins that pose threats to human and livestock health. Three genetically distinct North American (NA) populations of Fg have been characterized, which are generally associated with differences in their predominant trichothecene chemotype: NA1/15-acetyl-deoxynivalenol (15-ADON), NA2/3-acetyl-deoxynivalenol (3-ADON), and NA3/3α-acetoxy, 7,15-dihydroxy-12,13-epoxytrichothec-9-ene (NX-2). Recent studies found that the NA3 population had significantly less spread on point-inoculated wheat spikes than the NA1 and NA2 populations, and NX toxins are important for Fg spread and initial infection in wheat. In this follow-up study, to compare the effect of the three populations on initial infection and mycotoxin production on different hosts, we dip-inoculated spikes of the moderately resistant wheat cultivar Alsen and the susceptible barley cultivar Voyager using five strains from each population to evaluate disease, trichothecene mycotoxin accumulation, and trichothecene production per unit of fungal biomass. In dip-inoculated wheat spikes, the NA3 population produced significantly more trichothecene per unit of fungal biomass and accumulated higher levels of trichothecene per plant biomass than the NA1 and NA2 populations, regardless of the disease levels caused by the three populations. In contrast to its critical role during wheat infection, NX toxins had no effect on barley infection. In dip-inoculated barley, the NA1 population was more infectious and caused more severe FHB symptoms than the NA2 and NA3 populations; however, the NA3 population produced significantly higher toxin per unit of fungal biomass in infected barley tissues than the NA1 population. This study provides critical information on the emerging NA3 population, which produces high levels of NX toxin and poses a potential food safety concern.

Population genomics of Fusarium graminearum isolates from the Americas

Fusarium head blight (FHB) is a major disease of wheat and barley worldwide and is caused by different species in the genus Fusarium, Fusarium graminearum being the most important. We conducted population genomics analyses using SNPs obtained through genotyping by sequencing of over 500 isolates of F. graminearum from the US Upper Midwest, New York, Louisiana, and Uruguay. PCA and STRUCTURE analyses group our isolates into four previously described populations: NA1, NA2, Southern Louisiana (SLA) and Gulf Coast (GC). Some isolates were not assigned to populations because of mixed ancestry. Population structure was associated with toxin genotype and geographic origin. The NA1, NA2, and SLA populations are differentiated (FST 0.385 - 0.551) but the presence of admixed isolates indicates that the populations are not reproductively isolated. Patterns of linkage disequilibrium (LD) decay suggest frequent recombination within populations. Fusarium graminearum populations from the US have great evolutionary potential given the high recombination rate and a large proportion of admixed isolates. The NA1, NA2, and Southern Louisiana (SLA) populations separated from their common ancestral population roughly at the same time in the past and are evolving with moderate levels of subsequent gene flow between them. Genome-wide selection scans in all three populations revealed outlier regions with the strongest signatures of recent positive natural selection. These outlier regions include many genes with unknown function and some genes with known roles in plant-microbe interaction, fungicide/drug resistance, cellular transport and genes that are related to cellular organelles. Only a very small proportion of outlier regions are shared as outliers among the three populations, suggesting unique host-pathogen interactions and environmental adaptation.

New insights into mycotoxin risk management through fungal population genetics and genomics

Mycotoxin contamination of food and feed is a major global concern. Chronic or acute dietary exposure to contaminated food and feed can negatively affect both human and animal health. Contamination occurs through plant infection by toxigenic fungi, primarily Aspergillus and Fusarium spp., either before or after harvest. Despite the application of various management strategies, controlling these pathogens remains a major challenge primarily because of their ability to adapt to environmental changes and selection pressures. Understanding the genetic structure of plant pathogen populations is pivotal for gaining new insights into their biology and epidemiology, as well as for understanding the mechanisms behind their adaptability. Such deeper understanding is crucial for developing effective and preemptive management strategies tailored to the evolving nature of pathogenic populations. This review focuses on the population-level variations within the two most economically significant toxigenic fungal genera according to space, host, and pathogenicity. Outcomes in terms of migration patterns, gene flow within populations, mating abilities, and the potential for host jumps are examined. We also discuss effective yet often underutilized applications of population genetics and genomics to address practical challenges in the epidemiology and disease control of toxigenic fungi.

Insights into the Aggressiveness of the Emerging North American Population 3 (NA3) of Fusarium graminearum

In the United States and Canada, Fusarium graminearum (Fg) is the predominant etiological agent of Fusarium head blight (FHB), an economically devastating fungal disease of wheat and other small grains. Besides yield losses, FHB leads to grain contamination with trichothecene mycotoxins that are harmful to plant, human, and livestock health. Three genetic North American populations of Fg, differing in their predominant trichothecene chemotype (i.e., NA1/15ADON, NA2/3ADON, and NA3/NX-2), have been identified. To improve our understanding of the newly discovered population NA3 and how population-level diversity influences FHB outcomes, we inoculated heads of the moderately resistant wheat cultivar Alsen with 15 representative strains from each population and evaluated disease progression, mycotoxin accumulation, and mycotoxin production per unit Fg biomass. Additionally, we evaluated population-specific differences in induced host defense responses. The NA3 population was significantly less aggressive than the NA1 and NA2 populations but posed a similar mycotoxigenic potential. Multiomics analyses revealed patterns in mycotoxin production per unit Fg biomass, expression of Fg aggressiveness-associated genes, and host defense responses that did not always correlate with the NA3-specific severity difference. Our comparative disease assay of NA3/NX-2 and admixed NA1/NX-2 strains indicated that the reduced NA3 aggressiveness is not due solely to the NX-2 chemotype. Notably, the NA1 and NA2 populations did not show a significant advantage over NA3 in perithecia production, a fitness-related trait. Together, our data highlight that the disease outcomes were not due to mycotoxin production or host defense alone, indicating that other virulence factors and/or host defense mechanisms are likely involved.

Biological characterization and in vitro fungicide screenings of a new causal agent of wheat Fusarium head blight in Tibet, China

Wheat (Triticum aestivum L.) is an important cereal crop, widely grown throughout the temperate zones, and also suitable for cultivation at higher elevations. Fusarium head blight (FHB) is a highly destructive disease of wheat throughout the globe. In July 2020, serious wheat FHB symptoms were observed in open fields located in Linzhi City, southeast of Tibet, China. The causal agent was identified as Fusarium avenaceum (Fr.) Sacc. by amplification and sequencing of the internal transcribed spacer (ITS) region, translation elongation factor 1-alpha (EF-1α) gene, and RNA polymerase II subunit (RPB-2) gene, as well as by morphological characterization. Koch’s postulates were confirmed by a pathogenicity test on healthy spikes, including re-isolation and identification. To our knowledge, this is the first report of F. avenaceum causing FHB on wheat in Tibet, China. Moreover, to determine pathogen characteristics that may be useful for future disease management, the utilization of different carbon and nitrogen resources, temperature, light, and ultraviolet (UV) irradiation on mycelium growth and conidia germination were studied. Soluble starch and peptone were the best carbon, and nitrogen source for the pathogen respectively. The optimal temperatures for the pathogen’s mycelium growth and conidia germination were 15–20°C, matching the average temperature during the growing season in Linzhi (Tibet). Meanwhile, alternating 8-h light and 16-h dark was shown to be conducive to mycelia growth, and complete darkness facilitated conidia germination. In addition, UV Irradiation of 48 MJ/cm², approximately 100 times of the local condition, did not inhibit the germination of conidia. Furthermore, in vitro screening of effective fungicides was conducted. Among the seven tested pesticides, carbendazim showed the best inhibition rate, with an EC₅₀ (concentration for 50% of maximal effect) value of 2.1 mg/L. Propiconazole also showed sufficient inhibitory effects against F. avenaceum, with an EC₅₀ value of 2.6 mg/L. The study provides insights into the newly identified causal agent of wheat FHB in Tibet, China, as well as first pathogen characteristics and promising candidate substances for its management.

Genetic Diversity and Aggressiveness of Fusarium virguliforme Isolates Across the Midwestern United States

Sudden death syndrome (SDS) of soybean is a damaging disease caused by the fungus Fusarium virguliforme. Since this pathogen was first reported in the southern U.S. state of Arkansas in 1971, it has spread throughout the midwestern United States. The SDS pathogen primarily colonizes roots but also produces toxins that translocate to and damage leaves. Previous studies have detected little to no genetic differentiation among isolates, suggesting F. virguliforme in North America has limited genetic diversity and a clonal population structure. Yet, isolates vary in virulence to roots and leaves. We characterized a set of F. virguliforme isolates from the midwestern United States, representing a south to north latitudinal gradient from Arkansas to Minnesota. Ten previously tested microsatellite loci were used to genotype isolates, and plant assays were conducted to assess virulence. Three distinct population clusters were differentiated across isolates. Although isolates ranged in virulence classes from low to very high, little correlation was found between virulence phenotype and cluster membership. Similarly, population structure and geographic location were not highly correlated. However, the earliest diverging cluster had the lowest genetic diversity and was detected only in southern states, whereas the two other clusters were distributed across the Midwest and were predominant in Minnesota. One of the midwestern clusters had the greatest genetic diversity and was found along the northern edge of the known distribution. The results support three genetically distinct population clusters of F. virguliforme in the United States, with two clusters contributing most to spread of this fungus across the Midwest.

Effects of Atmospheric CO2 and Temperature on Wheat and Corn Susceptibility to Fusarium graminearum and Deoxynivalenol Contamination

This work details the impact of atmospheric CO2 and temperature conditions on two strains of Fusarium graminearum, their disease damage, pathogen growth, mycotoxin accumulation, and production per unit fungal biomass in wheat and corn. An elevated atmospheric CO2 concentration, 1000 ppm CO2, significantly increased the accumulation of deoxynivalenol in infected plants. Furthermore, growth in cool growing conditions, 20 °C/18 °C, day and night, respectively, resulted in the highest amounts of pathogen biomass and toxin accumulation in both inoculated wheat and corn. Warm temperatures, 25 °C/23 °C, day and night, respectively, suppressed pathogen growth and toxin accumulation, with reductions as great as 99% in corn. In wheat, despite reduced pathogen biomass and toxin accumulation at warm temperatures, the fungal pathogen was more aggressive with greater disease damage and toxin production per unit biomass. Disease outcomes were also pathogen strain specific, with complex interactions between host, strain, and growth conditions. However, we found that atmospheric CO2 and temperature had essentially no significant interactions, except for greatly increased deoxynivalenol accumulation in corn at cool temperatures and elevated CO2. Plants were most susceptible to disease damage at warm and cold temperatures for wheat and corn, respectively. This work helps elucidate the complex interaction between the abiotic stresses and biotic susceptibility of wheat and corn to Fusarium graminearum infection to better understand the potential impact global climate change poses to future food security.

Intrapopulation Antagonism Can Reduce the Growth and Aggressiveness of the Wheat Head Blight Pathogen Fusarium graminearum

Fusarium graminearum is a causal agent of Fusarium head blight (FHB), a disease that reduces yield and quality of cereal crops and contaminates grain with mycotoxins that pose health risks to humans and livestock. Interpopulation antagonistic interactions between isolates that produce different trichothecene mycotoxins can reduce FHB in wheat, but it is not known if interactions between isolates with a shared population identity that produce the same trichothecenes have a similar effect. Using isolates from the predominant F. graminearum populations in North America (NA1 and NA2), we examined intrapopulation interactions by comparing growth, disease progression, and toxin production of individual isolates with multi-isolate mixes. In vitro, mycelial growth was significantly greater when most NA1 and NA2 isolates were cultured individually versus when cultured as a mixture of isolates from the same population. In susceptible wheat Norm, FHB generally progressed faster in heads inoculated with an individual isolate versus a multi-isolate mixture, but the antagonistic effect of intrapopulation interactions was more pronounced for NA1 than NA2 isolates. By contrast, in moderately resistant wheat Alsen, mixtures of isolates from either population caused obvious reductions in FHB development. Mycotoxin contamination was not consistently affected by intrapopulation interactions and varied depending on the interacting isolates from either population. Our results indicate that antagonistic intrapopulation interactions can influence FHB in controlled environmental conditions. Understanding if the regional composition of pathogen populations similarly influences FHB in the field could improve disease forecasting and management practices.

Spike culture derived wheat (Triticum aestivum L.) variants exhibit improved resistance to multiple chemotypes of Fusarium graminearum

Fusarium head blight (FHB) in wheat (Triticum aestivum L.), predominantly caused by Fusarium graminearum, has been categorized into three chemotypes depending on the major mycotoxin produced. The three mycotoxins, namely, 3-acetyldeoxynivalenol (3-ADON), 15-acetyldeoxynivalenol (15-ADON) and nivalenol (NIV) also determine their aggressiveness and response to fungicides. Furthermore, prevalence of these chemotypes changes over time and dynamic changes in chemotypes population in the field have been observed. The objective of this study was to identify spike culture derived variants (SCDV) exhibiting resistance to multiple chemotypes of F. graminearum. First, the optimal volume of inoculum for point inoculation of the spikelets was determined using the susceptible AC Nanda wheat genotype. Fifteen μL of 10⁵ macroconidia/mL was deemed optimal based on FHB disease severity assessment with four chemotypes. Following optimal inoculum volume determination, five chemotypes (Carman-NIV, Carman-705-2-3-ADON, M9-07-1-3-ADON, M1-07-2-15-ADON and China-Fg809-15-ADON) were used to point inoculate AC Nanda spikelets to confirm the mycotoxin produced and FHB severity during infection. Upon confirmation of the mycotoxins produced by the chemotypes, 55 SCDV were utilized to evaluate FHB severity and mycotoxin concentrations. Of the 55 SCDV, five (213.4, 244.1, 245.6, 250.2 and 252.3) resistant lines were identified with resistance to multiple chemotypes and are currently being utilized in a breeding program to develop wheat varieties with improved FHB resistance.

Population Genetics of Fusarium graminearum at the Interface of Wheat and Wild Grass Communities in New York

Fusarium graminearum is primarily understood as an agricultural pathogen affecting cereal crops, but its host range also includes diverse, noncultivated grasses ubiquitous across agricultural and natural environments. Wild grasses may select for the production of diverse toxin variants (chemotypes) and serve as reservoirs of genetic diversity or sources of disease-inciting inoculum. Populations at the intersection of wheat and wild grass communities were described using 909 isolates collected from wheat spikes, wild grass spikes, and overwintered wild grass stems found at natural and agricultural sites in regions of high and low crop production. Trichothecene (TRI) genotypes correlated to pathogen chemotype were predicted from two loci, and multilocus genotypes (MLGs) were determined using eight microsatellite loci. The genetic diversity of wild grass and wheat-derived populations was comparable, and their differentiation was low. Duplicate MLGs were rare even in samples collected from a single square meter, although they could be found in multiple hosts, environments, regions, and years. TRI genotype frequencies differed between region and land use. Admixture between TRI genotype-defined populations, which correspond to three previously described sympatric North American populations, was detected and was highest in a region with remote host communities and little agricultural production. Nonagricultural environments may maintain different pathogen TRI genotypes than wheat fields and provide an opportunity for recombination between isolates from different F. graminearum populations. A lack of structural barriers suggests that pathogen gene flow is uninhibited between wheat and wild grass communities, and the recovery of putative clones from multiple hosts and environments provides initial evidence that noncultivated grasses are a source of local and regional inoculum.

Trichothecenes in Cereal Grains - An Update

Trichothecenes are sesquiterpenoid mycotoxins produced by fungi from the order Hypocreales, including members of the Fusarium genus that infect cereal grain crops. Different trichothecene-producing Fusarium species and strains have different trichothecene chemotypes belonging to the Type A and B class. These fungi cause a disease of small grain cereals, called Fusarium head blight, and their toxins contaminate host tissues. As potent inhibitors of eukaryotic protein synthesis, trichothecenes pose a health risk to human and animal consumers of infected cereal grains. In 2009, Foroud and Eudes published a review of trichothecenes in cereal grains for human consumption. As an update to this review, the work herein provides a comprehensive and multi-disciplinary review of the Fusarium trichothecenes covering topics in chemistry and biochemistry, pathogen biology, trichothecene toxicity, molecular mechanisms of resistance or detoxification, genetics of resistance and breeding strategies to reduce their contamination of wheat and barley.

Pyrrolnitrin is more essential than phenazines for Pseudomonas chlororaphis G05 in its suppression of Fusarium graminearum

Fusarium graminearum is the major causal agent of Fusarium head blight (FHB) disease in cereal crops worldwide. Infection with this fungal phytopathogen can regularly cause severe yield and quality losses and mycotoxin contamination in grains. In previous other studies, one research group reported that pyrrolnitrin had an ability to suppress of mycelial growth of F. graminearum. Other groups revealed that phenazine-1-carboxamide, a derivative of phenazine-1-carboxylic acid, could also inhibit the growth of F. graminearum and showed great potentials in the bioprotection of crops from FHB disease. In our recent work with Pseudomonas chlororaphis strain G05, however, we found that although the phz operon (phenazine biosynthetic gene cluster) was knocked out, the phenazine-deficient mutant G05Δphz still exhibited effective inhibition of the mycelial growth of some fungal phytopathogens in pathogen inhibition assay, especially including F. graminearum, Colletotrichum gloeosporioides, Botrytis cinerea. With our further investigations, including deletion and complementation of the prn operon (pyrrolnitrin biosynthetic gene cluster), purification and identification of fungal compounds, we first verified that not phenazines but pyrrolnitrin biosynthesized in P. chlororaphis G05 plays an essential role in growth suppression of F. graminearum and the bioprotection of cereal crops against FHB disease.

Population genomics of Fusarium graminearum reveals signatures of divergent evolution within a major cereal pathogen

The cereal pathogen Fusarium graminearum is the primary cause of Fusarium head blight (FHB) and a significant threat to food safety and crop production. To elucidate population structure and identify genomic targets of selection within major FHB pathogen populations in North America we sequenced the genomes of 60 diverse F. graminearum isolates. We also assembled the first pan-genome for F. graminearum to clarify population-level differences in gene content potentially contributing to pathogen diversity. Bayesian and phylogenomic analyses revealed genetic structure associated with isolates that produce the novel NX-2 mycotoxin, suggesting a North American population that has remained genetically distinct from other endemic and introduced cereal-infecting populations. Genome scans uncovered distinct signatures of selection within populations, focused in high diversity, frequently recombining regions. These patterns suggested selection for genomic divergence at the trichothecene toxin gene cluster and thirteen additional regions containing genes potentially involved in pathogen specialization. Gene content differences further distinguished populations, in that 121 genes showed population-specific patterns of conservation. Genes that differentiated populations had predicted functions related to pathogenesis, secondary metabolism and antagonistic interactions, though a subset had unique roles in temperature and light sensitivity. Our results indicated that F. graminearum populations are distinguished by dozens of genes with signatures of selection and an array of dispensable accessory genes, suggesting that FHB pathogen populations may be equipped with different traits to exploit the agroecosystem. These findings provide insights into the evolutionary processes and genomic features contributing to population divergence in plant pathogens, and highlight candidate genes for future functional studies of pathogen specialization across evolutionarily and ecologically diverse fungi.

Fusarium graminearum: pathogen or endophyte of North American grasses?

Mycotoxin-producing Fusarium graminearum and related species cause Fusarium head blight on cultivated grasses, such as wheat and barley. However, these Fusarium species may have had a longer evolutionary history with North American grasses than with cultivated crops and may interact with the ancestral hosts in ways which are biochemically distinct. We assayed 25 species of asymptomatic native grasses for the presence of Fusarium species and confirmed infected grasses as hosts using re-inoculation tests. We examined seed from native grasses for the presence of mycotoxin-producing Fusarium species and evaluated the ability of these fungi to produce mycotoxins in both native grass and wheat hosts using biochemical analysis. Mycotoxin-producing Fusarium species were shown to be prevalent in phylogenetically diverse native grasses, colonizing multiple tissue types, including seeds, leaves and inflorescence structures. Artificially inoculated grasses accumulated trichothecenes to a much lesser extent than wheat, and naturally infected grasses showed little to no accumulation. Native North American grasses are commonly inhabited by Fusarium species, but appear to accommodate these toxigenic fungi differently from cultivated crops. This finding highlights how host identity and evolutionary history may influence the outcome of plant-fungal interactions and may inform future efforts in crop improvement.

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum

BACKGROUND

The Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies.

RESULTS

A comparison of genome structure and gene content revealed a 93-99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection.

CONCLUSIONS

The genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.

The geographic distribution and complex evolutionary history of the NX-2 trichothecene chemotype from Fusarium graminearum

Fusarium graminearum and 21 related species comprising the F. sambucinum species complex lineage 1 (FSAMSC-1) are the most important Fusarium Head Blight pathogens of cereal crops world-wide. FSAMSC-1 species typically produce type B trichothecenes. However, some F. graminearum strains were recently found to produce a novel type A trichothecene (NX-2) resulting from functional variation in the trichothecene biosynthetic enzyme Tri1. We used a PCR-RFLP assay targeting the TRI1 gene to identify the NX-2 allele among a global collection of 2515 F. graminearum. NX-2 isolates were only found in southern Canada and the northern U.S., where they were observed at low frequency (1.8%), but over a broader geographic range and set of cereal hosts than previously recognized. Phylogenetic analyses of TRI1 and adjacent genes produced gene trees that were incongruent with the history of species divergence within FSAMSC-1, indicating trans-species evolution of ancestral polymorphism. In addition, placement of NX-2 strains in the TRI1 gene tree was influenced by the accumulation of nonsynonymous substitutions associated with the evolution of the NX-2 chemotype, and a significant (P<0.001) change in selection pressure was observed along the NX-2 branch (ω=1.16) in comparison to other branches (ω=0.17) in the TRI1 phylogeny. Parameter estimates were consistent with positive selection for specific amino-acid changes during the evolution of NX-2, but direct tests of positive selection were not significant. Phylogenetic analyses of fourfold degenerate sites and intron sequences in TRI1 indicated the NX-2 chemotype had a single evolutionary origin and evolved recently from a type B ancestor. Our results indicate the NX-2 chemotype may be indigenous, and possibly endemic, to southern Canada and the northern U.S. In addition, we demonstrate that the evolution of TRI1 within FSAMSC-1 has been complex, with evidence of trans-species evolution and chemotype-specific shifts in selective constraint.