Molecular and Pathogenic Characterization of Fusarium Species Associated with Corm Rot Disease in Saffron from China

Molecular Identification and Pathogenicity of Fusarium Species Associated with Wood Canker, Root and Basal Rot in Turkish Grapevine Nurseries

Fusarium species are agriculturally important fungi with a broad host range and can be found as endophytic, pathogenic, or opportunistic parasites in many crop plants. This study aimed to identify Fusarium species in bare-rooted, dormant plants in Turkish grapevine nurseries using molecular identification methods and assess their pathogenicity. Asymptomatic dormant plants were sampled from grapevine nurseries (43) in different regions of the country, and fungi were isolated from plant roots and internal basal tissues. The Fusarium strains were identified by performing gene sequencing (TEF1-α, RPB2) and phylogenetic analyses. Pathogenicity tests were carried out by inoculating mycelial agar pieces of strains onto the stem or conidial suspensions into the rhizosphere of vines (1103 Paulsen rootstock). Laboratory tests revealed that Fusarium species were highly prevalent in Turkish grapevine nurseries (41 out of 43). Gene sequencing and phylogenetic analyses unraveled that 12 Fusarium species (F. annulatum, F. brachygibbosum, F. clavum, F. curvatum, F. falciforme, F. fredkrugeri, F. glycines, F. nanum, F. nematophilum, F. nirenbergiae, F. solani, and Fusarium spp.) existed in the ready-to-sale plants. Some of these species (F. annulatum, F. curvatum and F. nirenbergiae) consistently caused wood necrosis of seedling stems, rotting of the basal zone and roots, and reduced root biomass. Although the other nine species also caused some root rot and root reduction, their virulence was not as severe as the pathogenic ones, and they were considered opportunistic parasites or endophytic species. This study suggests that Fusarium species might play an important role in root-basal rot, wood canker symptoms, and young vine decline in Turkish grapevine nurseries and that these species need to be considered for healthy seedling production.

Identification and Pathogenicity of Fusarium Species Associated with Onion Basal Rot in the Moscow Region of Russian Federation

Fusarium basal rot of onions causes large losses during storage of commercial production of onion bulbs, which in turn adversely affects the food market situation in the off-season period. There are no data on the composition of Fusarium spp., which causes onion basal rot in the Russian Federation. Therefore, our research was aimed at Fusarium spp. causing onion basal rot in the Moscow Region of the Russian Federation and studying the pathogenicity of these species for the host plant. We studied 20 isolates of Fusarium spp. collected from affected mature bulbs and seed bulbs. Species identification of the isolates was carried out using analysis of the nucleotide sequences of the three genetic loci ITS, tef1 and rpb2, as well as was based on the macro- and micromorphological characteristics of these isolates. As a result, the species F. annulatum (F. fujikuroi species complex), F. oxysporum (F. oxysporum species complex), F. acuminatum (F. tricinctum species complex) and F. solani (F. solani species complex) were identified to involve in the pathogenesis of Fusarium basal rot. We have shown for the first time that the species F. annulatum and F. acuminatum are highly aggressive and capable of causing onion basal rot. The predominant species were F. annulatum and F. oxysporum. The proportion of these species in the total number of analyzed isolates was 60% and 25%, respectively. The largest proportion (33%) of highly aggressive on mature bulbs isolates was found in the species F. annulatum. The data obtained provide practical insights for developing strategies to manage Fusarium fungi responsible for onion basal rot Moscow Region of the Russian Federation. In addition, data about species composition and aggressive isolates may be used in onion breeding for resistance to Fusarium basal rot.

An evolutionary view of the Fusarium core genome

Fusarium, a member of the Ascomycota fungi, encompasses several pathogenic species significant to plants and animals. Some phytopathogenic species have received special attention due to their negative economic impact on the agricultural industry around the world. Traditionally, identification and taxonomic analysis of Fusarium have relied on morphological and phenotypic features, including the fungal host, leading to taxonomic conflicts that have been solved using molecular systematic technologies. In this work, we applied a phylogenomic approach that allowed us to resolve the evolutionary history of the species complexes of the genus and present evidence that supports the F. ventricosum species complex as the most basal lineage of the genus. Additionally, we present evidence that proposes modifications to the previous hypothesis of the evolutionary history of the F. staphyleae, F. newnesense, F. nisikadoi, F. oxysporum, and F. fujikuroi species complexes. Evolutionary analysis showed that the genome GC content tends to be lower in more modern lineages, in both, the whole-genome and core-genome coding DNA sequences. In contrast, genome size gain and losses are present during the evolution of the genus. Interestingly, core genome duplication events positively correlate with genome size. Evolutionary and genome conservation analysis supports the F3 hypothesis of Fusarium as a more compact and conserved group in terms of genome conservation. By contrast, outside of the F3 hypothesis, the most basal clades only share 8.8% of its genomic sequences with the F3 clade.

Comprehensive Investigation of Die-Back Disease Caused by Fusarium in Durian

Durian (Durio zibethinus L.) is an economically important crop in the southern and eastern parts of Thailand. The occurrence of die-back disease caused by plant pathogenic fungi poses a serious threat to the quality and quantity of durian products. However, the identification of causal agents has been a subject of mixed information and uncertainty. In this research, we conducted a comprehensive investigation of die-back disease in nine durian plantations located in Thailand. By analyzing a total of 86 Fusarium isolates obtained from infected tissues, we aimed to provide clarity and a better understanding of the fungal pathogens responsible for this economically significant disease. Through a combination of colony characteristics, microscopic morphology, and a multilocus sequence analysis (MLSA) of the internal transcribed spacer (ITS) region, translation elongation factor 1-α (TEF1-α) gene, and RNA polymerase II gene (RPB2) sequences, we were able to identify and categorize the isolates into three distinct groups, namely, Fusarium incarnatum, F. solani, and F. mangiferae. Koch's postulates demonstrated that only F. incarnatum and F. solani were capable of causing die-back symptoms. This research represents the first report of F. incarnatum as a causal agent of die-back disease in durian in Thailand. Additionally, this study uncovers the association of ambrosia beetles and F. solani, highlighting the potential involvement of E. similia in facilitating the spread of die-back disease caused by Fusarium in durian.

Identification and characterization of pathogens causing saffron corm rot in China

Corm rot is the most important disease of saffron, for which fungi from several genus such as Fusarium spp. Penicillium spp. and Botrytis spp., have been previously reported to be the pathogens. In this research, we used a combination of amplicon sequencing and traditional isolation methods to identify the causal agents, main infection source. The diversity of microbial communities in diseased saffron corms and soil decreased significantly compared with healthy corms and soil. The contents of Penicillium and Botrytis in healthy and diseased corms were similarly high, indicating that them were not directly related to the occurrence of corm rot. But the relative abundance of Fusarium, Cadophora and Fusicolla were significantly higher in the diseased corms than healthy ones. The abundance of Fusarium increased, while the abundance of Oidiodendron, Paraphaeosphaeria and the endophytic beneficial bacteria Pseudomonas decreased, which may relate to the occurrence of the disease. The co-occurrence network diagram showed that the correlation between fungal and bacterial communities was mainly positive. Plant pathogens were relatively abundant in the diseased soil, according to functional gene prediction. At the same time, we also collected 100 diseased corms from the fields in Jiande, where is known as the "hometown of saffron." All isolated pathogenic strains were identified as Fusarium oxysporum through morphological observation and phylogenetic tree analysis of ITS, Tef-1α and β-tubulin. To better clarify the biological characteristics of F. oxysporum, we cultured the isolates at different temperatures and pH values. The optimum temperature for mycelial growth and sporulation was 25°C, pH 6，carbon sources sorbitol and nitrogen sources, peptone. In short, our results suggests that F. oxysporum was the pathogen causing corm rot in Jiande and corms other than soils are the main primary infection source. These new understanding of saffron corm rot will provide the theoretical basis for its better and efficiently management.

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.

First report of Fusarium oxysporum causing stem spots on Polygonatum odoratum in China

Polygonatum odoratum (Mill.) Druce is a perennial herb in the Liliaceae family and it is one of the traditional Chinese medicinal plants. Modern pharmaceutical studies demonstrate that P. odoratum contains polysaccharides, saponins, alkaloids, flavonoids, volatile oil, and other active components (Jiang-Nan, et al., 2018). From May to June 2022, the stem spot disease was discovered on P. odoratum in the planting demonstration garden in Changsha (28°20N; 113°07E), Hunan province of China. The disease seriously retarded plant growth and was estimated to have affected approximately 40-50% of the plants, significant economic losses to growers. Plants had oval tan spots on the stems, which were light in the center and dark at the margin. The spots in the back expanded and joined together, where the disease was severe, and chlorosis was near the stem spot, while many leaves turned completely yellow and withered before falling to the ground. Finally, the whole plant faded to light green and dried up. In order to isolate pathogens, symptomatic stem samples (5×5 mm) were collected from the edges of the lesions and excised symptomatic tissues consisting of diseased and healthy parts were surface-sterilized with 2% solution of sodium hypochlorite (0.1% active ingredient of chlorine) for 1 min and 75% ethanol for 30 s. The samples were then washed thrice with sterile distilled water, air-dried on the sterile filter papers under aseptic conditions, and finally plated onto Potato Dextrose Agar (PDA) plates, which were incubated at 25 °C for 24 h to 36 h in the dark. Additionally, the emerging fungal hyphal tips were transferred to PDA and purified by the single-spore method. Next, forty plants with stem spots were isolated, and 8 cultures with the same appearance were obtained. Two strains coded hnxryzj and hnxryzj1 were randomly selected, for identification. With a mean radial growth rate of 7.5 mm/day, white and dense colonies were observed after 6 days of culture on PDA. After hnxryzj was cultured on SNA, microconidia were oval or ovate (9.25-14.8µm × 2.18-3.76µm), macroconidia were sickle-shaped and slightly curved, with 2-5 septa (21.52-23.49µm × 2.64-4.51µm (n = 50)). These morphological characteristics were consistent with the description of Fusarium oxysporum (Mirghasempour, et al., 2022) Furthermore, we amplified the partial region of the internal transcribed spacer (ITS) region, the translation elongation factors EF-1α, β-tubulin, polymerase II largest subunit (RPB1) and RNA polymerase II second largest subunit (RPB2) genes from strain hnxryzj and hnxryzj1, based on the primer pairs ITS1/ITS4, EF728F/EF986R, Bt2a/Bt2b, RPB1-F5/RPB1-R8 and fRPB2-5F2/fRPB2-7cR (Li, et al., 2013, Xie, et al., 2022), and amplicons were sequenced by Tsingke Biotechnology Co. Ltd. By sequence alignment, the ITS, EF-1α, β-tubulin , RPB1 and RPB2 of hnxryzj and hnxryzj1 were identical, respectively. The sequence alignment of hnxryzj and hnxryzj1 with the Fusarium ID database and NCBI shows the following results: the ITS region, EF-1α, RPB1 and RPB2 sequences of the strain hnxryzj (GenBank accession nos. ON872218, ON897740, OP467556 and OP467557) and hnxryzj1 (GenBank accession nos. OP071248, OP087208, OP467558 and OP467559) were 100% identical to those of F. oxysporum (GenBank accession nos. MZ890536, LC469784 , MT179509 and MW368380, respectively); whereas the β-tubulin sequences of the strain hnxryzj (GenBank accession nos. ON897741) and hnxryzj1 (GenBank accession nos. OP087207) were 96.9% identical to those of F.oxysporum (CBS144135 GenBank accession nos. MH485136). Subsequently, a phylogenetic tree was established combining EF-1α, RPB1, and RPB2. Strains hnxryzj and hnxryzj1 were F.oxysporum (JW257006 GenBank accession nos. MZ921883, MZ921657 and MZ921752)(Torres-Cruz, et al., 2022), with bootstrap values 100%. The pathogenicity test was carried out by placing mycelial discs obtained from colonies that had been actively growing on PDA for 6 days. In the pathogenicity test, two sets (5 plants in each set) of potted plants, whose stems were wounded, were taken. In one set (5 plants), the PDA cakes with F. oxysporum (d=5mm, the same below) were inoculated on the stems scratched by an inoculation needle (sterilized) (the front of the colony was close to the wound of the stem). In the other set (5 plants), potted plants inoculated with the sterile PDA cakes were served as controls. In a 25 °C greenhouse, each treatment was given a 12h/12h light/dark cycl(Nabi, et al., 2019). The symptoms were observed, and the fungus cake was removed 5 days after inoculation. Then, after 18 days, typical symptoms of oval tan spots similar to original diseased plants in the field were found on the inoculated stems, and 32 days later, the inoculated plant died, while the control stems remained asymptomatic. In addition, F. oxysporum was isolated and identified from the inoculated, symptomatic stems, verifying Koch's postulates. Based on our knowledge, this is the first report of F. oxysporum causing stem spots on P. odoratum in China. Only one other study from China that root rot of Phyllostachys officinalis also resulted from F. oxysporum (Pang, et al., 2022). Furthermore, P. odoratum is an medicinal material in Hunan province. Therefore, comprehensive prevention and control methods are required.

Morphological and Molecular Identification of Fusarium ipomoeae as the Causative Agent of Leaf Spot Disease in Tobacco from China

Tobacco (Nicotiana tabacum L.), which creates jobs for 33 million people and contributes two trillion dollars’ tax annually, is one of the most important economic plants globally. However, tobacco is seriously threatened by numerous diseases during production. Previously, the field survey of tobacco diseases was conducted in the Guizhou and Guangxi provinces, the two main tobacco-producing areas in China. A serious leaf spot disease, with a 22% to 35% incidence, was observed in farming plants. In order to determine the causal agents, we collected the disease samples and isolated the pathogenic fungi. The pathogen was identified as Fusariumipomoeae, based on the morphological characteristics and phylogenetic analysis. Pathogenicity tests showed that F. ipomoeae could induce tobacco leaf spot and blight. To our knowledge, this is the first report worldwide of F. ipomoeae causing leaf spots and stems on tobacco. Our study reveals the serious consequences of F. ipomoeae on tobacco filed production and provides information for future diagnosis and management of the Fusarium disease.