First Report of Fusarium proliferatum Causing Basal Rot and Dry Rot on Onion Bulbs (Allium cepa) in Spain

Spain is the second largest onion-producing country in Europe with 1,465,430 tons and an export value of 584 million € in 2021 (MAPA 2022). In summer 2022 rot bulb symptoms were observed in five commercial fields and during the storage of cultivars 'Orlenda', 'Veleta', 'Mallory', 'Citation' and 'Pantano' from La Roda in Albacete (Castilla-La Mancha, Spain). Approximately 20% of sampled bulbs (113 bulbs analyzed) were affected with dry scales showing brown to dark brown rot on the top and basal plate of the onion bulbs. Occasionally, white to light pink fungal mycelium was observed between rotten scales and the plate basal. Sections of dry scales (5-10 mm) of the apical and basal plate were cut and placed on potato dextrose agar (PDA) and Komada medium (Komada 1975). From 5-day-old cultures typical white to light pink mycelium with microconidia in chains formed on polyphialides and macroconidia resembling Fusarium proliferatum (Nelson et al. 1983). To confirm the pathogen identity, partial translation elongation factor 1-alpha (TEF1) and RNA polymerase II subunit 2 (RPB2) genes were amplified and sequenced using primers reported in O´Donnell et al. (1998) and Samuels et al. (2002) for TEF1 and Liu et al. (1999) for RPB2. In BLAST analyses, the sequences showed 100% identity to the corresponding region of F. proliferatum (KP964908 and JF740801). Sequences were submitted to GenBank, and registered accession numbers are OR061014-16 for TEF1 and OR061017-19 for RPB2. Pathogenicity tests were conducted by inoculating healthy onion bulbs (five replicates per treatment) on the apical and basal plate by placing a 7-day old mycelial plug (10 mm diameter) from PDA cultures. Two onion cultivars ('Pandero' by Nunhems USA and 'Mallory' by Bejo The Netherlands) were inoculated separately with three isolates (PRO1, PRO9, PRO12). Control bulbs were inoculated with sterile PDA. The experiment was carried out twice. All bulbs were placed in a moist chamber and incubated at 25°C in the dark. After 15 days, bulbs inoculated with mycelial plugs showed similar symptoms to those of the original diseased bulbs. Browning dry rot was observed on the apical and basal plate of bulbs. When bulbs were cut longitudinally inner progressing rot was observed. Control bulbs remained symptomless. In both experiments, F. proliferatum was successfully re-isolated and morphologically confirmed from symptomatic bulbs to fulfill Koch's postulates. These results confirmed that isolates PRO1, PRO9 and PRO12 were the pathogen causing basal and dry rot on onion bulbs. This pathogen has recently been identified in China on Allium cepa L. var. agrogatum (Liu et al. 2022) and Idaho on onion (Beck et al. 2020) and could become a serious threat to onion production in Spain, reducing the quality and yield of onion.

Biological Control of Fusarium oxysporum, the Causal Agent of Fusarium Basal Rot in Onion by Bacillus spp

Fusarium oxysporum is the main pathogen causing Fusarium basal rot in onion (Allium cepa L.), which incurs significant yield losses before and after harvest. Among management strategies, biological control is an environmentally safe and sustainable alternative to chemical control. In this study, we isolated and screened bacteria for antifungal activity against the basal rot pathogen F. oxysporum. Isolates 23-045, 23-046, 23-052, 23-055, and 23-056 significantly inhibited F. oxysporum mycelial growth and conidial germination. Isolates 23-045, 23-046, 23-052, and 23-056 suppressed the development of Fusarium basal rot in both onion seedlings and bulbs in pot and spray inoculation assays. Isolate 23-055 was effective in onion seedlings but exhibited weak inhibitory effect on onion bulbs. Based on analyses of the 16S rRNA and rpoB gene sequences together with morphological analysis, isolates 23-045, 23-046, 23-052, and 23-055 were identified as Bacillus thuringiensis, and isolate 23-056 as Bacillus toyonensis. All five bacterial isolates exhibited cellulolytic, proteolytic, and phosphate-solubilizing activity, which may contribute to their antagonistic activity against onion basal rot disease. Taken together B. thuringiensis 23-045, 23-046, 23-052, and 23-055 and B. toyonensis 23-056 have potential for the biological control of Fusarium basal rot in onion.

Identification of Fusarium Basal Rot Pathogens of Onion and Evaluation of Fungicides against the Pathogens

Onion (Allium cepa L.) is an economically important vegetable crop worldwide. However, various fungal diseases, including Fusarium basal rot (FBR), neck rot, and white rot, reduce onion production or bulb storage life. FBR caused by Fusarium species is among the most destructive onion diseases. In this study, we identified Fusarium species associated with FBR in Jeolla and Gyeongsang Provinces in South Korea and evaluated fungicides against the pathogens. Our morphological and molecular analyses showed that FBR in onions is associated with Fusarium commune, Fusarium oxysporum, and Fusarium proliferatum. We selected seven fungicides (fludioxonil, hexaconazole, mandestrobin, penthiopyrad, prochloraz-manganese, pydiflumetofen, and tebuconazole) and evaluated their inhibitory effects on mycelial growth of the pathogens at three different concentrations (0.01, 0.1, and 1 mg/mL). We found that prochloraz-manganese was highly effective, inhibiting 100% of the mycelial growth of the pathogens at all concentrations, followed by tebuconazole. Fludioxonil showed < 50% inhibition at 1 mg/mL for the tested isolates.

Population, Virulence, and Mycotoxin Profile of Fusarium spp. Associated With Basal Rot of Allium spp. in Vietnam

Fusarium basal rot (FBR) is particularly problematic to Allium producers worldwide. In Vietnam, information on the profile of FBR is scarce, even though the presence of Fusarium spp. in Allium plants has long been recorded. In this study, a total of 180 isolates of Fusarium spp. were recovered from Allium bulbs/plants showing symptoms of FBR in 34 commercial Allium fields around Da Lat, Lam Dong, Vietnam. These isolates were identified to the species level by sequencing the internal transcribed spacer region and the translation elongation factor 1α gene. F. oxysporum was most prevalent (81%) in samples from all locations and Allium varieties, followed by F. solani (15%) and F. proliferatum (4%), which were only found in onion (Allium cepa L.). Pathogenicity tests on onion seedlings (56 isolates) and mini bulbs (10 isolates) indicated that onion can be infected by all of these species but virulence varied greatly between isolates. Moreover, isolates that were virulent on seedlings were sometimes not virulent on bulbs and vice versa, which points to a specialization of isolates for the host phenology. Mycotoxin analyses showed that the highest amounts of beauvericin were detected in seedlings and bulbs infected by F. oxysporum, whereas F. proliferatum was mainly responsible for the presence of fumonisin B₁ in bulbs, suggesting a natural occurrence of beauvericin and fumonisin B₁ in onions infected by these pathogens.

Sampling and PCR method for detecting pathogenic Fusarium oxysporum strains in onion harvest

Fusarium basal rot is a worldwide disease problem in onions, and causes substantial losses in onion production, both during the growing season and in the storage. To minimize the post-harvest losses, a protocol for screening of latent infections with pathogenic Fusarium oxysporum strains from harvested onions was developed. This protocol is based on a dual PCR test with primers specific for the fungal species and new SIX3 primers specific for the onion-pathogenic F. oxysporum strains. A pooled sample containing pieces from 50 harvested symptomless onions was prepared for the dual PCR using microwave disruption of the filamentous Fusarium fungi and Whatman FTA^TM filter paper matrix technology, or as a reference protocol, by extracting DNA with a commercial kit. The two sample preparation protocols gave consistent results with the tested onion samples. Detection limit of the dual PCR protocol was 100 pg of F. oxysporum DNA, in a mixture with onion DNA, when the FTA card was applied. The new protocol reported here is simple and sensitive enough for routine testing, enabling the detection of latent infections in harvest lots even at the infection levels under 10%. SIGNIFICANCE AND IMPACT OF THE STUDY: Fusarium basal rot causes serious problems in onion production. To minimize post-harvest losses, a simple protocol based on FTA^TM technology and a dual PCR test with Fusarium oxysporum species-specific and pathogenicity-specific primers was developed. By testing pooled onion samples using this method, latent infections with F. oxysporum can be screened from a representative sample of the harvest. This screening method could be a useful tool to manage the post-harvest losses caused by latent infections with F. oxysporum and, with modification of the PCR protocol, with other Fusarium species pathogenic to onion.

Identification of pathogenicity-related genes in Fusarium oxysporum f. sp. cepae

Pathogenic isolates of Fusarium oxysporum, distinguished as formae speciales (f. spp.) on the basis of their host specificity, cause crown rots, root rots and vascular wilts on many important crops worldwide. Fusarium oxysporum f. sp. cepae (FOC) is particularly problematic to onion growers worldwide and is increasing in prevalence in the UK. We characterized 31 F. oxysporum isolates collected from UK onions using pathogenicity tests, sequencing of housekeeping genes and identification of effectors. In onion seedling and bulb tests, 21 isolates were pathogenic and 10 were non-pathogenic. The molecular characterization of these isolates, and 21 additional isolates comprising other f. spp. and different Fusarium species, was carried out by sequencing three housekeeping genes. A concatenated tree separated the F. oxysporum isolates into six clades, but did not distinguish between pathogenic and non-pathogenic isolates. Ten putative effectors were identified within FOC, including seven Secreted In Xylem (SIX) genes first reported in F. oxysporum f. sp. lycopersici. Two highly homologous proteins with signal peptides and RxLR motifs (CRX1/CRX2) and a gene with no previously characterized domains (C5) were also identified. The presence/absence of nine of these genes was strongly related to pathogenicity against onion and all were shown to be expressed in planta. Different SIX gene complements were identified in other f. spp., but none were identified in three other Fusarium species from onion. Although the FOC SIX genes had a high level of homology with other f. spp., there were clear differences in sequences which were unique to FOC, whereas CRX1 and C5 genes appear to be largely FOC specific.

Activity of Chlorine Dioxide in a Solution of Ions and pH Against Thielaviopsis basicola and Fusarium oxysporum

Chlorine dioxide (ClO₂) is a disinfestant used to control pathogens in water. To determine if interactions between inorganic ions and pH levels effect ClO₂ activity in vitro, concentrations of ClO₂ (0, 1, 3, 5, 7, 9, 22, 24, 46, 58, and 70 mg/liter) were mixed for 10 min in solutions containing a nitrogen and hard water solution with equal concentrations of ammonium, nitrate, and synthetic hard water (0 and 100 mg/liter) and a divalent metal ion solution with equal concentrations of copper, iron, manganese, and zinc (0, 1, 3, and 5 mg/liter) at pH 5 and 8. Macro- and microconidia of Fusarium oxysporum f. sp. narcissi or conidia and aleuriospores of Thielaviopsis basicola were injected into each suspension for 30 s, captured on filter paper disks that were flushed with water, and plated on 50% potato dextrose agar. Spore germination was quantified after 1 day. ClO₂ activity had a similar effect on both fungal species and all types of propagules with interactions among the divalent metal ion solution, nitrogen and hard water solution, and pH treatments. A higher concentration of ClO₂ was required at pH 8 than at pH 5 to achieve a lethal dose resulting in 50% mortality of spores (LD₅₀). The addition of the divalent metal ion solution required an increase in ClO₂ concentration to maintain a LD₅₀. When combined with the nitrogen and hard water solution, the divalent metal ion solution placed a higher demand on ClO₂ at pH 5 and a lower demand on ClO₂ at pH 8, thus requiring an increase and decrease in a ClO₂ concentration, respectively, to achieve a LD₅₀. Chlorine dioxide doses resulting in 50% mortality ranged from 0.5 to 7.0 mg/liter for conidia of F. oxysporum, 0.5 to 11.9 mg/liter for conidia of T. basicola, and 15.0 to 45.5 mg/liter for aleuriospores of T. basicola.