11 Application of Genomics to the Study of Pathogenicity and Development in Fusarium

Fusarium species are major fungal pathogens causing root rot in Lonicera macranthoides and other agriculturally and medicinally important plants. They exhibit a broad host range and high pathogenicity, leading to yield losses, reduced quality, and plant mortality. Current control measures rely primarily on chemical pesticides, with few sustainable biological options available. This study compared rhizosphere microbial diversity between healthy and diseased Lonicera macranthoides, revealing increased pathogenic fungi abundance (Fusarium, Plectosphaerella, p < 0.01) and reduced beneficial fungi abundance (Trichoderma) along with significantly lower Chao1 and Shannon diversity indices (p < 0.05). An endophytic Bacillus velezensis strain, NS13, was isolated from healthy roots. Plate confrontation assays showed strong inhibition of Fusarium oxysporum from L. macranthoides and other Fusarium species (Fusarium solani, Fusarium graminearum, Fusarium fujikuroi). The 3.95 Mb genome encoded 4,060 proteins, including 96 biocontrol-related genes. AntiSMASH identified 15 biosynthetic gene clusters, including antifungal (fengycin, surfactin), antibacterial (bacillaene, difficidin), and other bioactive metabolites (bacilysin, bacillibactin), alongside seven potentially novel clusters. The presence of these BGCs was further corroborated by LC-MS/MS metabolomic profiling, which detected multiple corresponding antifungal metabolites, including cyclic dipeptides, fatty acid amides (e.g., erucamide), and oleanolic acid. These results demonstrate soil microbial dysbiosis in L. macranthoides affected by root rot and confirm the broad-spectrum anti-Fusarium potential of NS13, highlighting its promise as a biocontrol resource against Fusarium pathogens in medicinal plants. The findings provide both theoretical insights and practical guidance for developing sustainable biocontrol strategies against Fusarium and other soil-borne pathogens, benefiting both the scientific community and agricultural practitioners.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12866-025-04551-x.

Interactions between cultivated and wild plants with their fungal pathogens have strong ecological, evolutionary and economic implications. Antagonistic interactions, however, have been scantily studied in an applied context by using ecological networks, phylogeny and spatial ecology concurrently. In this study, we describe for the first time, the topological structure of plant-fungi networks involving species of the genusFusariumand their native and introduced (exotic) cultivated host plants in Mexico. For this, we based our study on a recent database describing the attack on 75 native and introduced plant species, including 35 species of the genusFusarium. Host plant species varied in their degree of phylogenetical relatedness (Monocots and Dicots) and spatial geographical distribution. Therefore, we also tested whether or not plant-Fusariumnetworks are phylogenetically structured and highlighted the spatial correlation between pathogens and their host plants across the country. In general, the pathogen-plant network is more specialized and compartmentalized in closely related taxa. Closely related hosts are more likely to share the same pathogenicFusariumspecies. Host plants are present in different ecosystems and climates, with regions having more cultivated plant species presenting the highest number of fusaria pathogens. From an economic standpoint, different species of the same taxonomic family may be more susceptible to being attacked by the same species ofFusarium, whereas from an ecological standpoint the movement of pathogens may expose wild and cultivated plants to new diseases. Our study highlights the relevance of interaction intimacy in structuring trophic relationships between plants and fusaria species in native and introduced species. Furthermore, we show that the analytical tools regarding host distribution and phylogeny could permit a rapid assessment of which plant species in a region are most likely to be attacked by a given fusaria.

Fusarium species are common plant and animal pathogens. For humans, there are two dominant species complexes, F. solani species complex (FSSC) and F. oxysporum species complex (FOSC), which both infect immunocompromised individuals. However, there are few reports related to elasmobranchs infected by Fusarium species. In this study, we report a case of a rough-tail stingray from an ocean park infected by FSSC diagnosed using histopathology and microscopic observation, with morphological characteristics and molecular techniques used to identify the pathogen. Histopathology showed fungal hyphae invading stingray tissues, while micro/macroconidia were found under the microscope. We identified this pathogen as FSSC 12 through phylogenetic analysis using internal transcribed spacer (ITS) and elongation factor 1-alpha (EF1-α) sequences. Furthermore, we report that application of voriconazole (orally) and terbinafine (topically) constituted an effective therapy, curing the stingray.

Hyalohyphomycoses refer to human infections caused by soil-dwelling and plant saprophytic moulds (Ajello, 1986). Hyalohyphomycosis encompasses a loose artificial classification system since it does not refer to a specific taxonomic classification (Rippon, 1988a). Agents of hyalohyphomycosis include nonmelanin-producing, nondematiaceous moulds (Anaissie et al, 1989) whose typical appearance in histopathologic sections consists of colorless, hyaline, or light-colored septate hyphae. These hyphae are either branched or unbranched, and occasionally they are toruloid (Ajello, 1986; Anaissie et al, 1989; Liu et al, 1998). Table 16–1 lists the fungal species reported to cause hyalohyphomycosis. Important human pathogens included in this group are Aspergillus, Fusarium, Scopulariopsis, Pseudallescheria, and Scedosporium (Ajello, 1986; Anaissie et al, 1989). The fungi are identified at the genus and species levels largely on the basis of morphology of their reproductive structures, including phialides (fertile cells), and conidia (spores) (Liu et al, 1998). The general characteristics of the heterogeneous group of fungi-causing hyalohyphomycosis are shown in Table 16–2. Although several nondematiaceous moulds can cause opportunistic fungal infections in humans, this chapter focuses only on those that have been recognized as emerging pathogens. More common causes of hyalohyphomycosis, such as aspergillosis and penicilliosis, are discussed in Chapters 14 and 23, respectively. Epidemiology. Fusarium derives its name from its fusiform conidia (Young et al, 1978). Long been known as plant pathogens, these ubiquitous moulds are common in decomposing organic matter and soil (Anaissie et al, 1988; Walsh and Groll, 1999). Fusarium species cause fusariosis, an increasingly recognized life-threatening mycotic infection worldwide (Boutati and Anaissie, 1997; Walsh and Groll, 1999; Marr et al, 2002). Of note, the epidemiological distribution of fusariosis is not homogeneous, since 50% to 85% of the cases have been reported in the United States (Martino et al, 1994; Girmenia et al, 2000). It is unclear whether this reflects a unique ecological niche for these fungi or is at least partially due to the increased recognition of this infection in the United States. Outside the United States, most cases of fusariosis have been reported in the Mediterranean (e.g., France, Italy) or in tropical countries (e.g., Brazil) (Guarro and Gene, 1995; Girmenia et al, 2000). Similarly, a heterogeneous distribution of cases of fusariosis have been described in different cancer centers, with most cases reported from only a few centers within the United States (Girmenia et al, 2000). In fact, Fusarium species have emerged in some tertiary care cancer centers as the second most common filamentous fungal pathogen after Aspergillus (Walsh and Groll, 1999). Indeed, in a recent small study from a Brazilian cancer center, Fusarium species were identified as the most common mould associated with true fungemia in bone marrow transplant (BMT) recipients (Trabasso et al, 2001). The portals of entry for Fusarium infection include the aerodigestive tract and the skin (via vascular catheters, periungual regions, or burns) (Richardson et al, 1988; Merz et al, 1988; Anaissie et al, 1989; Martino et al, 1994; Walsh and Groll 1999). The predominant mode of infection is inhalation into the lungs or upper airways (Fridkin and Jarvis, 1996). Therefore, not surprisingly, most cases of fusariosis are considered community acquired. However, Fusarium species can also cause nosocomial infections, such as postoperative endophthalmitis or peritonitis associated with dialysis catheters (Young et al, 1984; Fridkin and Jarvis, 1996). The water distribution system has been implicated recently as a reservoir of Fusarium species (Squier et al, 2000; Anaissie et al, 2001). In contrast, others have reported that the most likely source of Fusarium infection is the external environment rather than a nosocomial source (Raad et al, 2002). More research is needed in this controversial area.

Mycotoxins are naturally occurring substances produced by fungi as secondary metabolites (Ingle et al. 2009). Many of these toxins are pathogenic to human beings and animals. It is estimated that more than 300 mycotoxins are produced by 350 species of fungi (Ingle et al. 2009). The trichothecene mycotoxins are a chemically related family of compounds that are produced by different species of Fusarium. Species of the genus Fusarium are common plant pathogens occurring worldwide, mainly associated with cereal crops. Fusarium species can produce over 100 secondary metabolites, some of which can unfavorably affect human and animal health due to their immunosuppressive effects (Rabodonirina et al. 1994). The most important Fusarium mycotoxins, which can frequently occur at biologically significant concentrations in cereals, are fumonisins, zearalenone and trichothecenes [deoxynivalenol (DON), nivalenol (NIV) and T-2 toxin]. These compounds can occur naturally in cereals (Girish and Goyal 1986), either individually or as specific clusters of two or more of them, depending on the producing fungal species (or strain); of these, T-2 toxin and DON are of special importance, because these are causative agents in a variety of animal diseases and have been associated with human diseases. Wheat and barley are mainly subjected to contamination of T-2 toxin and related trichothecenes. The major Fusarium species producing these mycotoxins are F. culmorum, F. graminearum, F. avenaceum, F. acuminatum, F. poae, F. solani, F. sporotrichioides, F. tricinctum and F. scripi, etc. F. sporotrichioides and F. graminearum are known to produce T-2 toxin and DON respectively (Ueno et al. 1975; Edwards 2004).

Three laboratory experiments were done in order to assess the efiéctiveness of both most commonly used fungicides and Trichoderma Isolates against pathogenic Fusarium spp., as well as the interaction between fungicides and Trichoderma isolates. In the first one: Eighteen of commonly used fungicides as chemical control for Fusarium diseases (thiabendazoie, thiophanate-methyl, imazalil, monceren, carboxin. vitavax-200, vitavax-300, captan, tolclofos-methyl, iriadimefon, penconazole, propconazole, hexaconazole, mancozeb, ridomil MZ, ridomil plus, iprodione and homal) were evaluated against eight species of Fusarium which cause Fusarium diseases of different legumes (Fusarium oxysporum f.sp. phaseoli, E solani f.sp.phaseoli from bean seeds "F 1, F2"; F. oxysporum f.sp lupini, E. solani f.sp.lupini from luprne seeds "F3, F4"; F oxysporum f.sp cicens, F. solani f.sp ciceris from chickpea seeds "F5, F6" and E monliforme, F. solani from cowpea seeds "F7, F8"). The results in this part showed that Imamlil was extremely highly effective fungicide since the EC50 values for all tested Fusarium species were ranged from less than 0.1 µg ml-1 to 0.22 µg ml-1 Thiabendazole, homai, and thiophanate-methyl were highly effective fungicides with EC50 values less than 10 µg ml-1 (0.03 µg ml-1 for thiabendazole against F2 and 6.05 µg ml-I for homai against F7), and generally we can arrange the eight species of Fusarium according to their sensitivity to the tested fungicides in ascending order as follows: Fl, F8, F4. F2, F6, F5, F3, and F7. In the second part of work: efficacy of biological antagonists was studied by using twenty four isolates of Trichoderma against the eight species of Fusarium, and we found that most cf the Trichoderma isolates had antagonistic effect against most of the tested Fusarium species. Finally we examined the most effective tested fungicides against the most antagonists of Trichoderma against Fusarium species, The data revealed that most of Trichoderma isolates are Insensitive (tolerant) han tungi of Fusarium sop, to the tested fungicides. Imazalil was the most suitable fungicide because it was highly effective fungicide against Fusarium species (pathogenic fungi), while the Trichoderma (non pathogenic fungi) are insensitive to it without any exceptions, followed by thiabendazole with only one exception.

Fusarium head blight is a destructive disease caused by Fusarium species. Little is known about the pathogenic molecular weapons of Fusarium graminearum. The gene encoding a small secreted protein, Fg02685, in F.graminearum was found to be upregulated during wheat head infection. Knockout mutation of Fg02685 reducedthe growth and development of Fusarium in wheat spikes. Transient expression of Fg02685 or recombinant protein led to plant cell death in a BAK1- and SOBIR1-independent system. Fg02685 was found to trigger plant basal immunity by increasing the deposition of callose, the accumulation of reactive oxygen species (ROS), and the expression of defence-related genes. The Fg02685 signal peptide was required for the plant's apoplast accumulation and induces cell death, indicating Fg02685 is a novel conserved pathogen-associated molecular pattern. Moreover, its homologues are widely distributed in oomycetes and fungal pathogens and induced cell death in tobacco. The conserved α-helical motif at the N-terminus was necessary for the induction of cell death. Moreover, a 32-amino-acid peptide, Fg02685 N-terminus peptide 32 (FgNP32), was essential for the induction of oxidative burst, callose deposition, and mitogen-activated protein kinase signal activation in plants. Prolonged exposure to FgNP32 enhanced the plant's resistance to Fusarium and Phytophthora. This study provides new approaches for an environment-friendly control strategy for crop diseases by applying plant immune inducers to strengthen broad-spectrum disease resistance in crops.

Fusarium species are common hyaline soil saprophytes and plant pathogens that are opportunistic fungal pathogens of immunocompromised patients. The treatment for fusariosis remains uncertain with an unfavourable prognosis; new possibilities for treatment, such as various synergistic drug interactions, must be uncovered. In this study, we evaluated the in vitro interactions of amphotericin B with caspofungin, ketoconazole, 5-flucytosine, itraconazole, miconazole, rifampin, fluconazole, terbinafine and voriconazole against isolates of Fusarium spp. using the chequerboard method with interactions evaluated by fractional inhibitory concentration indices. The highest percentages of synergistic interactions were observed for the combinations of amphotericin B and caspofungin (68.7%), amphotericin B and rifampin (68.7%), amphotericin B plus 5-flucytosine (59.3%) and amphotericin B with voriconazole (37.5%). The pattern of susceptibility to antifungal agents among Fusarium species and their consequence on the effects of drug combinations are also discussed.

Species of the necrotrophic fungal pathogen Fusarium that cause head blight and crown rot of cereals including wheat also infect a number of alternative host plants. This raises the prospect of more damaging pathogen strains originating and persisting as highly successful saprophytes on hosts other than wheat. The immediate impact on pathogenic (aggressiveness) and saprophytic (growth rate and fecundity) behaviour of six isolates with low, moderate or high initial aggressiveness was examined in two species of Fusarium after their passage through 10 alternative plant hosts. One passage through alternative hosts significantly reduced the pathogenic fitness of most isolates, but this change was not associated with a concomitant change in their overall saprophytic behaviour. The overall weak association between aggressiveness, fecundity and growth rate both before and after passage through the alternative hosts indicate that pathogenic and saprophytic fitness traits may be independently controlled in both Fusarium species. Thus, there was no trade-off between pathogenic and saprophytic fitness in these necrotrophic plant pathogens.

Fusarium species are important pathogens that affect many vegetable, cereal, and pulse crops in Canada. These pathogens also infect a diverse range of horticultural crops, including cannabis (Cannabis sativa L.). A range of disease symptoms have been reported on cannabis plants upon infection by several Fusarium species, which include root rot, wilting, stem rot, and bud rot. In this study, we report the genome sequences of five Fusarium species that were recovered from symptomatic greenhouse-grown cannabis plants in British Columbia: F. graminearum, F. sporotrichioides, F. culmorum, F. proliferatum, and F. oxysporum. Comparative genomic analysis revealed that the isolates from cannabis displayed a high percentage genome alignment to currently recognized pathogenic Fusarium species infecting other crops. This may suggest that horizontal transmission of the pathogens has occurred between these crops, potentially through air, soil, or seed-borne inoculum. In addition, analysis of secondary metabolites and toxin production in the Fusarium species affecting cannabis indicated they have the potential to produce several mycotoxins, including trichothecenes, fumonisin, zearalenone, beauvericin and culmorin. Further epidemiological and in planta studies are needed to establish the extent to which horizontal spread of Fusarium species from horticultural and field crops to cannabis plants is occurring and the impact this can have on post-harvest quality and mycotoxin production. Studies on genetic changes that may be occurring in the Fusarium species as they adapt to cannabis as a host would provide evolutionary insights into the pathogenicity of this complex, versatile and important group of plant pathogens.

Crown and root rot are among the most important wheat diseases caused by Fusarium species. The aim of this study was the identification of Fusarium spp. isolates obtained from wheat with crown and root rot symptoms in Yazd province of Iran, based on morphological and molecular characteristics. The ef1/ef2 and ITS4/ITS5 primers were used for molecular identification of the isolates. The results of morphological and molecular investigations revealed that among 40 isolates, 11 isolates were identified as F. equiseti, six isolates as F. pseudograminearum, five isolates as F. culmorum, five isolates as F. flocciferum, four isolates as F. acuminatum, four isolates as F. oxysporum, three isolates as F. solani and two isolates as F. proliferatum. Pathogenicity of the isolates was evaluated on wheat cultivar Falat. Comparing pathogenicity of different Fusarium spp. isolates on wheat seedlings revealed that the highest level of disease index was observed for F. pseudograminearum, F. culmorum, F. flocciferum and F. solani and the lowest disease severity was observed for F. equiseti. This is the first report on the identification of Fusarium spp., causing wheat crown and root rot in Yazd province of Iran, and on pathogenicity of F. flocciferum on wheat.

Fusarium genus comprises important saprophytic and phytopathogenic fungi and is widespread in nature. The present study reports the occurrence of Fusarium spp. in soils from two mangrove forests in northern Peninsular Malaysia and analyzed physico-chemical properties of the mangrove soil. Based on TEF-1α sequences, nine Fusarium species were identified: Fusarium solani species complex (FSSC) (n = 77), Fusarium verticillioides (n = 20), Fusarium incarnatum (n = 10), Fusarium proliferatum (n = 7), Fusarium lateritium (n = 4), Fusarium oxysporum (n = 3), Fusarium rigidiuscula (n = 2), Fusarium chlamydosporum (n = 1), and Fusarium camptoceras (n = 1); FSSC isolates were the most prevalent. Phylogenetic analysis of the combined TEF-1α and ITS sequences revealed diverse phylogenetic affinities among the FSSC isolates and potentially new phylogenetic clades of FSSC. Soil analysis showed varied carbon content, pH, soil moisture, and salinity, but not nitrogen content, between sampling locations. Regardless of the physico-chemical properties, various Fusarium species were recovered from the mangrove soils. These were likely saprophytes; however, some were well-known plant pathogens and opportunistic human pathogens. Thus, mangrove soils might serve as inoculum sources for plant and human pathogenic Fusarium species. The present study demonstrates the occurrence of various Fusarium species in the extreme environment of mangrove soil, thereby contributing to the knowledge on species diversity in Fusarium.

HIGHLIGHTS Isolation two species of pathogens Fusarium from sugarcane. Identification the difference in morphological characterization between two species of Fusarium. Determination the ability of pathogens Fusarium to produce mycotoxin Beauvericin. Determination of the toxicity Beauvericin on the brine shrimp.

Whole-Genome Sequence Resource of <i>Fusarium oxysporum</i> Strain TH15, a Plant Growth Promoting Endophytic Fungus Isolated from <i>Tetrastigma hemsleyanum</i>

Fusarium head blight (FHB) is a devastating wheat disease, mainly caused by Fusarium graminearum (FG)—a deoxynivalenol (DON)-producing species. However, Fusarium avenaceum (FA), able to biosynthesize enniatins (ENNs), has recently increased its relevance worldwide, often in co-occurrence with FG. While DON is a well-known mycotoxin, ENN activity, also in association with DON, is poorly understood. This study aims to explore enniatin B (ENB) activity, alone or combined with DON, on bread wheat and on Fusarium development. Pure ENB, DON, and ENB+DON (10 mg kg−1) were used to assess the impacts on seed germination, seedling growth, cell death induction (trypan blue staining), chlorophyll content, and oxidative stress induction (malondialdehyde quantification). The effect on FG and FA growth was tested using ENB, DON, and ENB+DON (10, 50, and 100 mg kg−1). Synergistic activity in the reduction of seed germination, growth, and chlorophyll degradation was observed. Conversely, antagonistic interaction in cell death and oxidative stress induction was found, with DON counteracting cellular stress produced by ENB. Fusarium species responded to mycotoxins in opposite directions. ENB inhibited FG development, while DON promoted FA growth. These results highlight the potential role of ENB in cell death control, as well as in fungal competition.