Epitypification of Fusarium oxysporum - clearing the taxonomic chaos

Fusarium and allied genera from China: species diversity and distribution

The genus Fusarium includes numerous important plant and human pathogens, as well as many industrially and commercially important species. During our investigation of fungal diversity in China, a total of 356 fusarioid isolates were obtained and identified from diverse diseased and healthy plants, or different environmental habitats, i.e., air, carbonatite, compost, faeces, soil and water, representing hitherto one of the most intensive sampling and identification efforts of fusarioid taxa in China. Combining morphology, multi-locus phylogeny and ecological preference, these isolates were identified as 72 species of Fusarium and allied genera, i.e., Bisifusarium (1), Fusarium (60), and Neocosmospora (11). A seven-locus dataset, comprising the 5.8S nuclear ribosomal RNA gene with the two flanking internal transcribed spacer (ITS) regions, the intergenic spacer region of the rDNA (IGS), partial translation elongation factor 1-alpha (tef1), partial calmodulin (cam), partial RNA polymerase largest subunit (rpb1), partial RNA polymerase second largest subunit (rpb2) gene regions, and partial β-tubulin (tub2), were sequenced and employed in phylogenetic analyses. A genus-level phylogenetic tree was constructed using combined tef1, rpb1, and rpb2 sequences, which confirmed the presence of four fusarioid genera among the isolates studied. Further phylogenetic analyses of two allied genera (Bisifusarium and Neocosmospora) and nine species complexes of Fusarium were separately conducted employing different multi-locus datasets, to determine relationships among closely related species. Twelve novel species were identified and described in this paper. The F. babinda species complex is herein renamed as the F. falsibabinda species complex, including descriptions of new species. Sixteen species were reported as new records from China.

First Report of Seedling Stem Rot on Jinxianlian (Anoectochilus roxburghii) Caused by Fusarium oxysporum in China

Anoectochilus roxburghii is an important Chinese herbal medicine plant belonging to Orchidaceae and known as Jinxianlian. This orchid is cultivated and mostly adopted to treat diabetes and hepatitis. About 2 billion artificially cultivated seedlings of Jinxianlian are required each year and approximately $600 million in fresh A. roxburghii seedlings is produced in China. From 2011, sporadic occurrence of stem rot on Jinxianlian have been observed in greenhouses in Jinhua City (N29°05', E119°38'), Zhejiang Province. In 2018, nearly 30% of seedlings of Jinxianlian grown in greenhouse conditions were affected by stem rot in Jinhua City. Symptoms initially occurred in the stem at the soil line causing dark discoloration lesions, rotted tissues, wilting, and eventually leading to the death of the plants. A total of 23 diseased seedlings collected from seven different greenhouses were surface sterilized with 1.5% sodium hypochlorite for 3 min, then rinsed in water. Pieces of tissues disinfected from each sample were plated on 2% potato dextrose agar (PDA), and incubated at 25°C in the dark for 5 days (Kirk et al. 2008). A total of 19 isolates were recovered. They developed colonies with purple mycelia and beige or orange colors after 7 days of incubation under 25°C on PDA and carnation leaf agar (CLA) media (Kirk et al. 2008; Zhang et al. 2016). Colonies on PDA had an average radial growth rate of 3.1 to 4.0 mm /d at 25°C. Colony surface was pale vinaceous, floccose with abundant aerial mycelium. On CLA, aerial mycelium was sparse with abundant bright orange sporodochia forming on the carnation leaves. Microconidia were hyaline and oval-ellipsoid to cylindrical (3.7 to 9.3 × 1.3 to 2.9 μm) (n=19). Macroconidia were 3 to 5 septate and fusoid-subulate with a pedicellate base (27.4 to 35.6 × 3.2 to 4.2 μm) (n=19). These morphological features were consistent with Fusarium oxysporum (Sun et al. 2008; Lombard et al., 2019). To confirm the identification based on these morphological features, the internal transcribed spacer region (ITS) and translation elongation factor1 (TEF) were amplified from the DNA of 3 out of 19 isolates chosen at random respectively using the set primer ITS1/ITS4 and EF1/ EF2 (Sun, S., et al. 2018; Lombard et al., 2019). BLAST analysis revealed that the ITS sequences (OK147619, OK147620, OK147621) had 99% identity to that of F. oxysporum isolate JJF2 (GenBank MN626452) and TEF sequence (OK155999, OK156000, OK156001) had 100% identity to that of F. oxysporum isolate gss100 (GenBank MH341210). A multilocus phylogenetic analysis by Bayesian inference (BI) and maximum likelihood (ML) trees based on ITS and TEF indicated that the pathogen grouped consistently with F. oxysporum. Three out of 19 isolates chosen at random were selected to evaluate pathogenicity. Uninfected healthy A. roxburghii seedlings about 40 day-old planted in sterilized substrates were sprayed with distilled water containing 2 x 106 conidia per ml suspensions as inoculums, and plants sprayed with distilled water alone served as controls. Plants were then incubated at 25°C and 85% relative humidity. Ten plants were inoculated for each isolate. After 10 days, all plants inoculated developed stem rot symptoms, while control plants remained healthy. Cultures of Fusarium spp. were re-isolated only from inoculated plants with the frequency of 100% and re-identified by morphological characteristics as F. oxysporum, fulfilling Koch's postulates. To the best of our knowledge, this is the first report of F. oxysporum causing stem rot on A. roxburghii seedlings. As F. oxysporum is a devastating pathogenic fungus with a broad host range, measures should be taken in advance to manage stem rot of A. roxburghii.

Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Leaf spot of Hosta ventricosa caused by Fusarium oxysporum in China

Leaf spot of Hosta ventricosa is a new disease in China. This disease seriously affects the ornamental value and greening function of H. ventricosa. Identification of the causal agent can prevent and control leaf spot in H. ventricosa and promote the healthy development of the H. ventricosa industry. Known incidents of leaf spot of H. ventricosa occurred in three places, and samples were collected. After the fungus were isolated, its pathogenicity was tested according to Koch's postulates. Isolates ZE-1b and ZE-2b were identified as Fusarium oxysporum based on morphological features and multigene phylogenetic analyses of calmodulin (CMDA), RNA polymerase II subunit A (RPB1), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1). These results provide a theoretical basis for the control of this disease of H. ventricosa.

Taxonomic Revision of the Banana Fusarium Wilt TR4 Pathogen Is Premature

Taxonomic revisions for pathogens of crops should be based on robust underpinning evidence. Recently, a substantial revision was proposed for the taxonomy of the causative agent of Fusarium wilt on banana. We reanalyzed the data on which this revision was based and discovered that the data do not robustly support the proposals. Several apparent discrepancies and errors in the published phylogenies cast further doubt on the conclusions drawn from them. Although we do not assert that the authors' conclusions are incorrect, we posit that the taxonomic changes are premature, given the data currently in the public domain.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Morphological and molecular characteristics of fungal species associated with crown rot of strawberry in South Korea

BACKGROUND

Crown and root rot is the most important and destructive strawberry diseases in Korea as it causes substantial economic loss. In August 2020, a severe outbreak of crown and root rot on strawberries (Fragaria × ananassa Duch.) was observed in the greenhouse at Sangju, South Korea. Infected plantlets displayed browning rot within the crown and root, stunted growth, and poor rooting.

METHODS AND RESULTS

Thirty fungal isolates were obtained from the affected plantlet. Isolates were identified based on morphological characteristics and pathogenicity test as well as sequence data obtained from internal transcribed spacer, large subunit ribosomal ribonucleic acid, translation elongation factor, and RNA polymerase II-second largest subunit. Results showed that the crown and root rot of strawberry in Korea was caused by three distinct fungal species: Fusarium oxysporum f. sp. fragariae, F. solani, and Plectosphaerella cucumerina. To the best of our knowledge, F. solani, and P. cucumerina are reported for the first time as the causal agents of the crown and root rot of strawberry in South Korea. Pathogenicity tests confirmed that these isolates are pathogenic to strawberry.

CONCLUSIONS

Understanding the composition and biology of the pathogen population will be helpful to provide effective control strategies for the disease.

Detection and Characterization of Fusarium Wilt (Fusarium oxysporum f. sp. vasinfectum) Race 4 Causing Fusarium Wilt of Cotton Seedlings in New Mexico

Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. vasinfectum (Atk.) W.C. Snyder & H.N. Hans (FOV), is one of the most destructive diseases of cotton (Gossypium spp.) worldwide. FOV race 4 (FOV4) is a highly virulent nominal race of this pathogen and a significant threat to cotton production in the western and southwestern USA and, potentially, the entire Cotton Belt. A field survey to identify FOV4 was performed in three southern counties of New Mexico in 619 cotton fields from 2018 to 2020. From 132 samples of cotton plants that exhibited wilt symptoms, Fusarium spp. were the most frequently isolated group of fungal species, with an isolation frequency of 57.4%. Eighty-four Fusarium spp. isolates were subsequently characterized by a DNA sequence analysis of three genes, EF-1α, PHO, and BT, encoding for translation elongation factor, phosphate permease, and β-tubulin, respectively. Forty-two isolates from 10 cotton fields were identified as FOV4 and confirmed with a positive 500-bp fragment diagnostic for FOV4. Twenty-six (62%) of the 42 FOV4 isolates were T type and the remainder (38%) were null type with and without a Tfo1 insertion in PHO, respectively. Each FOV4-infested field contained the same FOV4 genotype. Ten representative FOV4 isolates (one each from the 10 FOV4-infested fields) were evaluated for their pathogenicity on resistant Pima PHY 841 RF and susceptible Upland PHY 725 RF at 7, 14, 21, and 28 days after inoculation under temperature-controlled conditions at 21 to 22°C. Based on the disease severity rating, mortality rate, and area under the disease progress curve value, all 10 isolates were pathogenic to both cotton cultivars and differed in virulence; four isolates of the T genotype as a whole were more virulent than the six isolates of the N genotype. PHY 841 RF had significantly higher levels of resistance than PHY 725 RF to all FOV4 isolates. The results provide the first comprehensive account of the occurrence, distribution, and virulence of FOV4 in cotton production in New Mexico and will be useful for developing an effective strategy to manage FW in the state of New Mexico and the entire western and southwestern Cotton Belt.

Fusarium elaeidis Causes Stem and Root Rot on Alocasia longiloba in South China

Alocasia longiloba is a popular ornamental plant in China, however pests and diseases associated with A. longiloba reduce the ornamental value of this plant. From 2016 to 2021, stem and root rot has been observed on A. longiloba in Guangdong Province, China. Once the disease became severe, plants wilted and died. A fungus was isolated from the diseased stem and identified as Fusarium elaeidis using both morphological characteristics and molecular analysis of DNA-directed RNA polymerase II subunit (rpb2), translation elongation factor-1α (tef1) gene and β-tubulin (tub2) sequence data. The pathogenicity test showed the fungus was able to produce typical symptoms on A. longiloba similar to those observed in the field. The original pathogen was reisolated from inoculated plants fulfilling Koch’s postulates. This is the first report of Fusarium elaeidis causing stem rot on A. longiloba. These results will provide a baseline to identify and control diseases associated with A. longiloba.

Isolation, Identification, and Antibacterial Mechanisms of Bacillus amyloliquefaciens QSB-6 and Its Effect on Plant Roots

Apple replant disease (ARD) is a common problem in major apple planting areas, and biological factors play a leading role in its etiology. Here, we isolated the bacterial strain QSB-6 from the rhizosphere soil of healthy apple trees in a replanted orchard using the serial dilution method. Strain QSB-6 was provisionally identified as Bacillus amyloliquefaciens based on its morphology, physiological and biochemical characteristics, carbon source utilization, and chemical sensitivity. Maximum likelihood analysis based on four gene sequences [16S ribosomal RNA gene (16S rDNA), DNA gyrase subunit A (gyrA), DNA gyrase subunit B (gyrB), and RNA polymerase subunit B (rpoB)] from QSB-6 and other strains indicated that it had 100% homology with B. amyloliquefaciens, thereby confirming its identification. Flat standoff tests showed that strain QSB-6 had a strong inhibitory effect on Fusarium proliferatum, Fusarium solani, Fusarium verticillioides, Fusarium oxysporum, Alternaria alternata, Aspergillus flavus, Phoma sp., Valsa mali, Rhizoctonia solani, Penicillium brasilianum, and Albifimbria verrucaria, and it had broad-spectrum antibacterial characteristics. Extracellular metabolites from strain QSB-6 showed a strong inhibitory effect on Fusarium hyphal growth and spore germination, causing irregular swelling, atrophy, rupture, and cytoplasmic leakage of fungal hyphae. Analysis of its metabolites showed that 1,2-benzenedicarboxylic acid and benzeneacetic acid, 3- hydroxy-, methyl ester had good inhibitory effects on Fusarium, and increased the length of primary roots and the number of lateral roots of Arabidopsis thaliana plantlet. Pot experiments demonstrated that a QSB-6 bacterial fertilizer treatment (T2) significantly improved the growth of Malus hupehensis Rehd. seedlings. It increased root length, surface area, tips, and forks, respiration rate, protective enzyme activities, and the number of soil bacteria while reducing the number of soil fungi. Fermentation broth from strain QSB-6 effectively prevented root damage from Fusarium. terminal restriction fragment length polymorphism (T-RFLP) and quantitative PCR (qPCR) assays showed that the T2 treatment significantly reduced the abundance of Fusarium in the soil and altered the soil fungal community structure. In summary, B. amyloliquefaciens QSB-6 has a good inhibitory effect on Fusarium in the soil and can significantly promote plant root growth. It has great potential as a biological control agent against ARD.

Fusarium nirenbergiae (Fusarium oxysporum Species Complex) Causing the Wilting of Passion Fruit in Italy

Passion fruit (Passiflora edulis Sims.) is an ever-increasing interest crop in Italy because it is mainly cultivated for its edible fruit and, secondly, as an ornamental evergreen climber. During the summer of 2020, two-year-old plants of purple passion fruit in one of the most important expanding production areas of Sicily (southern Italy) showed symptoms of yellowing, wilting, and vascular discoloration. Fusarium-like fungal colonies were consistently yielded from symptomatic crown and stem tissues. Five representative isolates were characterized by a morphological and molecular analysis based on a multilocus phylogeny using RNA polymerase’s second largest subunit (RPB2) and translation elongation factor 1-alpha (EF-1α) genes, as Fusarium nirenbergiae (Fusarium oxysporum species complex). Pathogenicity tests conducted on healthy 1-year-old passion fruit cuttings revealed symptoms similar to those observed in the field. To our knowledge, this is the first report of Fusarium wilt on passion fruit caused by Fusarium nirenbergiae. This report focuses on the phytopathological implications of this fungal pathogen, which may represent a future significant threat for the expanding passion fruit production in Italy and Europe.

Names of Phytopathogenic Fungi: A Practical Guide

Using the correct name for phytopathogenic fungi and oomycetes is essential for communicating knowledge about species and their biology, control, and quarantine as well as for trade and research purposes. However, many plant pathogenic fungi are pleomorphic, meaning they produce different asexual (anamorph) and sexual (teleomorph) morphs in their life cycles. Therefore, more than one name has been applied to different morphs of the same species, which has confused users. The onset of DNA technologies makes it possible to connect different morphs of the same species, resulting in a move to a more natural classification system for fungi in which a single name for a genus and species can now be used. This move to a single nomenclature, coupled with the advent of molecular systematics and the introduction of polythetic taxonomic approaches, has been the main driving force for a reclassification of fungi, including pathogens. Nonetheless, finding the correct name for species remains challenging. In this article we outline a series of steps or considerations to greatly simplify this process and provide links to various online databases and resources to aid in determining the correct name. Additionally, a list of accurate names is provided for the most common genera and species of phytopathogenic fungi.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genetic Diversity of the Fusarium oxysporum Complex Isolated from the Grassland Biome of South Africa

The genetic diversity of pathogenic members of the Fusarium oxysporum species complex (FOSC) has been intensively studied worldwide, yet strains occurring in native soils with low anthropogenic disturbance remain poorly understood. This study focused on 355 F. oxysporum isolates from soils with low anthropogenic activity obtained from the grassland biome of South Africa. Analysis of the translation elongation factor 1-alpha (tef-1α) gene revealed high levels of sequence type diversity within the soil population in comparison with the global dataset. Phylogenetic relationships of the South African isolates revealed that four nested within FOSC clade 1. This is the first report of members of the basal clade recovered from ecosystems with low anthropogenic disturbance from Sub-Saharan Africa. The remaining strains nested within clades 2 to 5. This study contributes significantly to our understanding of the distribution of the FOSC in natural systems as we show that FOSC populations in the South African grassland biome are genetically diverse. This fills in our knowledge gap because previous studies reported only on the occurrence and diversity of the FOSC isolated from plant debris in South Africa. This is the first comprehensive survey of fusaria from grassland soils with low anthropogenic disturbance in South Africa.

Identification of molds with MALDI-TOF mass spectrometry: performance of the newly developed MSI-2 application in comparison with the Bruker filamentous fungi database and MSI-1

Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) represents a promising tool for the rapid and efficient identification of molds, but improvements are still necessary to achieve satisfactory results when identifying cryptic species. Here, we aimed to validate a new web application, MSI-2, which replaces MSI-1, an application that was built and deployed online in 2017. For the evaluation, we gathered 633 challenging isolates obtained from daily hospital practice that were first identified with DNA-based methods, and we submitted their corresponding mass spectra to three identification programs (Bruker, MSI-1 and MSI-2). The MSI-2 application had a better identification performance at the species level than MSI-1 and Bruker, reaching 83.25% correct identifications compared with 63.19% (MSI-1), 38.07% (Bruker with 1.7 threshold) and 21.8% (Bruker with 2.0 threshold). The MSI-2 application performed especially well for Aspergillus and Fusarium species, including for many cryptic species, reaching 90% correct identifications for Aspergillus species and 78% for Fusarium species compared to 69% and 43% with MSI-1. Such improvement may have a positive impact on patient management by facilitating the identification of cryptic species potentially associated with a specific antifungal resistance profile.

Structure and Abundance of Fusarium Communities Inhabiting the Litter of Beech Forests in Central Europe

Members of the genus Fusarium and related genera are important components of many ecosystems worldwide and are responsible for many plant diseases. However, the structure of beech litter-inhabiting Fusarium communities and their potential role in reducing the natural regeneration of European beech are not well understood. To address this issue, we examined Fusarium communities in the litter of uneven-aged, old-growth beech-dominated forests in the Carpathians (Poland) and in the Alps (Austria), and in a managed beech stand (Poland). The fungi inhabiting beech litter were investigated using beechnuts and pine seedlings as bait. The pathogenicity of the most common species was investigated by inoculating beech germinants. Fusarium spp. were identified based on morphology and DNA sequence comparisons of RPB2 and TEF1-α genes, combined with phylogenetic analyses. Twelve fungal species were identified from 402 isolates, including nine known and three currently undescribed species. The isolates resided in three species complexes within the genus Fusarium. These were the F. oxysporum (one taxon), F. sambucinum (three taxa), and F. tricinctum (six taxa) species complexes. In addition, one isolate was assigned to the genus Neocosmospora, and one isolate could be placed within the genus Fusicolla. The most frequently isolated fungi from beechnuts and beech germinants were F. avenaceum (Fr.) Sacc., F. sporotrichioides Sherb. and Fusarium sp. B. The structure and abundance of species within Fusarium communities varied by beech forest type. The species richness of Fusarium spp. was greatest in old-growth beech-dominated stands, while abundances of Fusarium spp. were higher in managed beech-dominated stands. Pathogenicity tests showed that all four Fusarium species isolated from beechnuts and beech germinants could cause germinants to rot beech, suggesting that these fungi may play a negative role in the natural beech regeneration.

Bedding Plant Production and the Challenge of Fungal Diseases

Bedding plants are a major group of ornamentals produced in greenhouses or nurseries worldwide and planted outdoors. Their economic importance has increased continuously in the last four decades in both the United States and the European Union. These plants are subject to a broad number of diseases that can negatively impact their production and cultivation. The initial steps of production strongly influence the health status of these plants and, consequently, their aesthetic appeal, which is a strong requisite for consumers. Seeds, cuttings, and other forms of propagative material, along with production systems and growing media, can influence the phytosanitary status of the final product. In this article, case studies of soilborne and foliar diseases are presented together with preventive measures to achieve innovative disease management strategies. Quarantine restrictions and eradication measures are also discussed, in consideration of the high likelihood for ornamental plants to be long-distance vectors of new pathogens and pests.

Fusarium: more than a node or a foot-shaped basal cell

Recent publications have argued that there are potentially serious consequences for researchers in recognising distinct genera in the terminal fusarioid clade of the family Nectriaceae. Thus, an alternate hypothesis, namely a very broad concept of the genus Fusarium was proposed. In doing so, however, a significant body of data that supports distinct genera in Nectriaceae based on morphology, biology, and phylogeny is disregarded. A DNA phylogeny based on 19 orthologous protein-coding genes was presented to support a very broad concept of Fusarium at the F1 node in Nectriaceae. Here, we demonstrate that re-analyses of this dataset show that all 19 genes support the F3 node that represents Fusarium sensu stricto as defined by F. sambucinum (sexual morph synonym Gibberella pulicaris). The backbone of the phylogeny is resolved by the concatenated alignment, but only six of the 19 genes fully support the F1 node, representing the broad circumscription of Fusarium. Furthermore, a re-analysis of the concatenated dataset revealed alternate topologies in different phylogenetic algorithms, highlighting the deep divergence and unresolved placement of various Nectriaceae lineages proposed as members of Fusarium. Species of Fusarium s. str. are characterised by Gibberella sexual morphs, asexual morphs with thin- or thick-walled macroconidia that have variously shaped apical and basal cells, and trichothecene mycotoxin production, which separates them from other fusarioid genera. Here we show that the Wollenweber concept of Fusarium presently accounts for 20 segregate genera with clear-cut synapomorphic traits, and that fusarioid macroconidia represent a character that has been gained or lost multiple times throughout Nectriaceae. Thus, the very broad circumscription of Fusarium is blurry and without apparent synapomorphies, and does not include all genera with fusarium-like macroconidia, which are spread throughout Nectriaceae (e.g., Cosmosporella, Macroconia, Microcera). In this study four new genera are introduced, along with 18 new species and 16 new combinations. These names convey information about relationships, morphology, and ecological preference that would otherwise be lost in a broader definition of Fusarium. To assist users to correctly identify fusarioid genera and species, we introduce a new online identification database, Fusarioid-ID, accessible at www.fusarium.org. The database comprises partial sequences from multiple genes commonly used to identify fusarioid taxa (act1, CaM, his3, rpb1, rpb2, tef1, tub2, ITS, and LSU). In this paper, we also present a nomenclator of names that have been introduced in Fusarium up to January 2021 as well as their current status, types, and diagnostic DNA barcode data. In this study, researchers from 46 countries, representing taxonomists, plant pathologists, medical mycologists, quarantine officials, regulatory agencies, and students, strongly support the application and use of a more precisely delimited Fusarium (= Gibberella) concept to accommodate taxa from the robust monophyletic node F3 on the basis of a well-defined and unique combination of morphological and biochemical features. This F3 node includes, among others, species of the F. fujikuroi, F. incarnatum-equiseti, F. oxysporum, and F. sambucinum species complexes, but not species of Bisifusarium [F. dimerum species complex (SC)], Cyanonectria (F. buxicola SC), Geejayessia (F. staphyleae SC), Neocosmospora (F. solani SC) or Rectifusarium (F. ventricosum SC). The present study represents the first step to generating a new online monograph of Fusarium and allied fusarioid genera (www.fusarium.org).

Clinical Origin and Species Distribution of Fusarium spp. Isolates Identified by Molecular Sequencing and Mass Spectrometry: A European Multicenter Hospital Prospective Study

Fusarium spp. are widespread environmental fungi as well as pathogens that can affect plants, animals and humans. Yet the epidemiology of human fusariosis is still cloudy due to the rapidly evolving taxonomy. The Mass Spectrometry Identification database (MSI) has been developed since 2017 in order to allow a fast, accurate and free-access identification of fungi by matrix-assisted laser desorption ionization—time of flight (MALDI-TOF) mass spectrometry. Taking advantage of the MSI database user network, we aim to study the species distribution of Fusarium spp. isolates in an international multicenter prospective study. This study also allowed the assessment of the abilities of miscellaneous techniques to identify Fusarium isolates at the species level. The identification was performed by PCR-sequencing and phylogenic-tree approach. Both methods are used as gold standard for the evaluation of mass spectrometry. Identification at the species complex was satisfactory for all the tested methods. However, identification at the species level was more challenging and only 32% of the isolates were correctly identified with the National Center for Biotechnology Information (NCBI) DNA database, 20% with the Bruker MS database and 43% with the two MSI databases. Improvement of the mass spectrometry database is still needed to enable precise identification at the species level of any Fusarium isolates encountered either in human pathology or in the environment.

Effect of in Planta Treatment of 'Cavendish' Banana with Herbicides and Fungicides on the Colonisation and Sporulation by Fusarium oxysporum f.sp. cubense Subtropical Race 4

Fusarium wilt caused by the soil-borne fungus Fusarium oxysporum f.sp. cubense (Foc) is a significant constraint to banana production worldwide, with the recent expansion of banana growing regions impacted by Foc Tropical Race 4 (TR4). The lack of commercially acceptable Cavendish cultivars with Foc resistance means the only current means of effective control is through strict quarantine and inoculum management. One method of control that is currently advocated includes the removal of infected plants which have been killed using herbicide injections. The aim of this work was to examine the effect of herbicide and fungicide treatments on sporulation of the fungus. In glasshouse studies using a green fluorescent transformed Foc Subtropical Race 4 isolate, we found treatments with herbicide hastened colonisation of the banana tissue and the production of micro- and macroconidia. The use of a fungicide did not prevent sporulation of the fungus in such tissue. This study demonstrates that herbicide treated plants are a source of potential inoculum for infection of nearby plants.

Severe outbreak of Fusarium wilt on common beans (Phaseolus vulgaris) caused by Fusarium oxysporum in the Maule Region, central Chile

Common bean (Phaseolus vulgaris L.) is an important grain legume cultivated worldwide as food for humans and livestock (Schwartz et al., 2005). Common beans in central Chile reach up to 3,893 ha from which 1,069 ha are located in the Maule region. Common bean is produced by small farmers who have limited access to fertilization, technical irrigation, and crop protection. In spring 2018, bean plants initially showed a slight yellowing and premature senescence 50 days after sowing (das) until showing wilting symptoms (70 -100 das) in Curepto fields (35 05'S; 72 01'W), Maule region. The basal part of affected plants displayed internal reddish-brown discoloration of the vascular tissues. Based on the plant external symptoms, we estimated an incidence between 15% and 45% in bean fields. Nine symptomatic plants were collected, and surface washed with sterile water and disinfested with 75% ethanol (v/v). Then small fragments (5-mm) from damage vascular tissue from each plant were cut and placed on Petri dishes containing PDA acidified with 0.5 ml/l of 92% lactic acid (APDA, 2%). The isolations were incubated for seven days at 25°C. Nine Fusarium-like isolates from single-spore on APDA (2%) became pale vinaceous, floccose with abundant aerial mycelium and dark vinaceous reverse colony, with a growing rate of 10.8 to 11.6 mm/d at 25°C (Lombard et al., 2019). Phialides were short, singular growing laterally on the mycelium. Macroconidia were hyaline, fusiform with basal foot cells shaped to pointed and apical cells tapered, 2-5 septate, and 28.6 to 47.6 (av. 38.1) μm long x 2.2 to 3.6 (av. 3.1) μm wide. Microconidia were hyaline, oval to ellipsoid, one-celled, and 4.5 to 10.9 (av. 6.1) μm long and 2.2 to 3.3 (av. 2.7) μm wide (n=50 spore). For molecular identification, three isolates (Curi-3.1, Be-8.1, and Be-11.3) were sequenced using PCR amplification of the partial sequences of beta-tubulin (BT) and translation elongation factor 1-α gene (TEF) (Lombard et al., 2019). NCBI BLAST analysis showed 99 to 100% similarity with sequences (TEF; BT) of strain CPC 25822 of Fusarium oxysporum. The maximum-likelihood phylogenetic analysis placed the Chilean isolates in the F. oxysporum complex clade. Chilean sequences were deposited into GenBank under accession numbers MW419125, MW419126, MW419127 (TEF) and MW419128, MW419129, MW419130 (BT). Pathogenicity tests (isolates Curi-3.1, Be-8.1, and Be-11.3) were conducted under greenhouse (15-28°C, 85%RH) on healthy bean plants (n=30) cv. Blanco Español INIA cultivated in pots (sand/peat moss/soil) at the University of Talca. Plants that are 30 days-old were inoculated using 200 μl of conidial suspension (106 conidia/ml) on wounded roots (crown). Control plants (n=10) were similarly inoculated with sterile distilled water. After 45 days, all inoculated plants with F. oxysporum isolates developed necrotic lesions on vascular tissue, and chlorosis, and wilting while control plants remained healthy. This experiment was conducted twice. The pathogen was reisolated (100%) from diseased plants and molecularly identified as F. oxysporum. To our knowledge, this is the report of a severe outbreak of F. oxysporum causing Fusarium yellows in P. vulgaris in the Maule region, Chile. Previously, F. oxysporum has been reported affecting tomato (Sepúlveda-Chavera et al., 2014) and blueberry in Chile (Moya-Elizondo et al., 2019).

Effector Profiles of Endophytic Fusarium Associated with Asymptomatic Banana (Musa sp.) Hosts

During the infection of a host, plant pathogenic fungi secrete small proteins called effectors, which then modulate the defence response of the host. In the Fusarium oxysporum species complex (FOSC), the secreted in xylem (SIX) gene effectors are important for host-specific pathogenicity, and are also useful markers for identifying the various host-specific lineages. While the presence and diversity of the SIX genes has been explored in many of the pathogenic lineages of F. oxysporum, there is a limited understanding of these genes in non-pathogenic, endophytic isolates of F. oxysporum. In this study, universal primers for each of the known SIX genes are designed and used to screen a panel of endophytically-associated Fusarium species isolated from healthy, asymptomatic banana tissue. SIX gene orthologues are identified in the majority of the Fusarium isolates screened in this study. Furthermore, the SIX gene profiles of these endophytic isolates do not overlap with the SIX genes present in the pathogenic lineages of F. oxysporum that are assessed in this study. SIX gene orthologues have not been commonly identified in Fusarium species outside of the FOSC nor in non-pathogenic isolates of F. oxysporum. The results of this study indicate that the SIX gene effectors may be more broadly distributed throughout the Fusarium genus than previously thought. This has important implications for understanding the evolution of pathogenicity in the FOSC.

A light life together: photosensing in the plant microbiota

Bacteria and fungi of the plant microbiota can be phytopathogens, parasites or symbionts that establish mutually advantageous relationships with plants. They are often rich in photoreceptors for UVA-Visible light, and in many cases, they exhibit light regulation of growth patterns, infectivity or virulence, reproductive traits, and production of pigments and of metabolites. In addition to the light-driven effects, often demonstrated via the generation of photoreceptor gene knock-outs, microbial photoreceptors can exert effects also in the dark. Interestingly, some fungi switch their attitude towards plants in dependence of illumination or dark conditions in as much as they may be symbiotic or pathogenic. This review summarizes the current knowledge about the roles of light and photoreceptors in plant-associated bacteria and fungi aiming at the identification of common traits and general working ideas. Still, reports on light-driven infection of plants are often restricted to the description of macroscopically observable phenomena, whereas detailed information on the molecular level, e.g., protein-protein interaction during signal transduction or induction mechanisms of infectivity/virulence initiation remains sparse. As it becomes apparent from still only few molecular studies, photoreceptors, often from the red- and the blue light sensitive groups interact and mutually modulate their individual effects. The topic is of great relevance, even in economic terms, referring to plant-pathogen or plant-symbionts interactions, considering the increasing usage of artificial illumination in greenhouses, the possible light-regulation of the synthesis of plant-growth stimulating substances or herbicides by certain symbionts, and the biocontrol of pests by selected fungi and bacteria in a sustainable agriculture.

Putative Effector Genes Distinguish Two Pathogenicity Groups of Fusarium oxysporum f. sp. spinaciae

Fusarium wilt of spinach, caused by Fusarium oxysporum f. sp. spinaciae, is an important disease during warm conditions in production regions with acid soils, yet little is known about what confers pathogenicity to spinach in F. oxysporum f. sp. spinaciae genetically. To identify candidate fungal genes that contribute to spinach Fusarium wilt, each of 69 geographically diverse F. oxysporum isolates was tested for pathogenicity on each of three spinach inbreds. Thirty-nine isolates identified as F. oxysporum f. sp. spinaciae caused quantitative differences in disease severity among the inbreds that revealed two distinct pathogenicity groups of F. oxysporum f. sp. spinaciae. Putative effector gene profiles, predicted from whole-genome sequences generated for nine F. oxysporum f. sp. spinaciae isolates and five nonpathogenic, spinach-associated F. oxysporum (NPS) isolates, distinguished the F. oxysporum f. sp. spinaciae isolates from the NPS isolates, and separated the F. oxysporum f. sp. spinaciae isolates into two groups. Five of the putative effector genes appeared to be unique to F. oxysporum f. sp. spinaciae, as they were not found in 222 other publicly available genome assemblies of F. oxysporum, implicating potential involvement of these genes in pathogenicity to spinach. In addition, two combinations of the 14 known Secreted in Xylem (SIX) genes that have been affiliated with host pathogenicity in other formae speciales of F. oxysporum were identified in genome assemblies of the nine F. oxysporum f. sp. spinaciae isolates, either SIX8 and SIX9 or SIX4, SIX8, and SIX14. Characterization of these putative effector genes should aid in understanding mechanisms of pathogenicity in F. oxysporum f. sp. spinaciae, developing molecular tools for rapid detection and quantification of F. oxysporum f. sp. spinaciae, and breeding for resistance to Fusarium wilt in spinach.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Ungual hyalohyphomycosis caused by Fusarium cugenangense

Fusarium onychomycosis is uncommon in the temperate climate zone of Japan. Based on the morphological characteristics and a gene analysis, we diagnosed a patient with ungual hyalohyphomycosis caused by Fusarium cugenangense belonging to the F oxysporum complex. This intractable disease was cured by 6-month treatment with efinaconazole 10% solution.

Reconsideration of species boundaries and proposed DNA barcodes for Calonectria

Calonectria represents a genus of phytopathogenic ascomycetous fungi with a worldwide distribution. In recent years, there has been an increase in the number of taxonomic studies on these fungi. Currently, there are 169 described species of Calonectria based on comparisons of DNA sequence data, combined with morphological characteristics. However, for some of these species, the sequence data utilised at the time of their description were relatively limited. This has justified an urgent need to reconsider the species boundaries for Calonectria based on robust genus-wide phylogenetic analyses. In this study, we utilised 240 available isolates including the ex-types of 128 Calonectria species, and re-sequenced eight gene regions (act, cmdA, his3, ITS, LSU, rpb2, tef1 and tub2) for them. Sequences for 44 Calonectria species, for which cultures could not be obtained, were downloaded from GenBank. DNA sequence data of all the 169 Calonectria species were then used to determine their phylogenetic relationships. As a consequence, 51 species were reduced to synonymy, two new species were identified, and the name Ca. lauri was validated. This resulted in the acceptance of 120 clearly defined Calonectria spp. The overall data revealed that the genus includes 11 species complexes, distributed across the Prolate and Sphaero-Naviculate Groups known to divide Calonectria. The results also made it possible to develop a robust set of DNA barcodes for Calonectria spp. To accomplish this goal, we evaluated the outcomes of each of the eight candidate DNA barcodes for the genus, as well as for each of the 11 species complexes. No single gene region provided a clear identity for all Calonectria species. Sequences of the tef1 and tub2 genes were the most reliable markers; those for the cmdA, his3, rpb2 and act gene regions also provided a relatively effective resolution for Calonectria spp., while the ITS and LSU failed to produce useful barcodes for species discrimination. At the species complex level, results showed that the most informative barcodes were inconsistent, but that a combination of six candidate barcodes (tef1, tub2, cmdA, his3, rpb2 and act) provided stable and reliable resolution for all 11 species complexes. A six-gene combined phylogeny resolved all 120 Calonectria species, and revealed that tef1, tub2, cmdA, his3, rpb2 and act gene regions are effective DNA barcodes for Calonectria.

Fusarium Species and Fusarium oxysporum Species Complex Genotypes Associated With Yam Wilt in South-Central China

Chinese yam (Dioscorea polystachya Thunb.) is an important root crop. Wilt caused by Fusarium is among the most important emerging diseases on yams. However, there is currently limited information on the molecular epidemiology of Fusarium causing yam wilt. Here, we investigated wilted yam samples from six regions in South-Central China. A total of 117 Fusarium isolates were obtained from diseased tissues of 37 wilted yam plants. These yam plants belonged to two varieties characterized by white and purple fleshy tubers, respectively. Analyses of ef1-α sequences identified that these 117 Fusarium isolates belonged to 11 putative species, with F. aff. commune being the most common (31.6%), followed by F. aff. cugenangense (29.1%), a potential undescribed species Fusarium aff. sp. (11.1%), F. aff. gossypinum (9.4%), F. aff. fujikuroi (8.5%), F. aff. nirenbergiae (6%), and one isolate each (0.85%) of F. aff. asiaticum, F. aff. curvatum, F. aff. odoratissimum, F. aff. solani, and F. aff. verticillioides. Six of these species were recently described as new species within the Fusarium oxysporum species complex (FOSC). Interestingly, 18 of the 37 yam plants were infected by two or more Fusarium species each and there was evidence for differential Fusarium species distributions based on geographic location and/or yam host variety. Multilocus microsatellite genotyping of the 67 FOSC isolates revealed that isolates of the same species from the same diseased plants often belonged to different genotypes. Interestingly, several FOSC microsatellite genotypes were shared among distinct geographic regions, consistent with long-distance dispersal. However, population genetic analyses revealed significant contributions of geographic separation to the overall genetic variation of FOSC with several pairs of geographic populations showing significant genetic differentiations, consistent with differential geographic distribution of the species within FOSC. The implications of our results to the managements of Fusarium wilt in yams were discussed.

Phylogenetic Analysis of Clinically Relevant Fusarium Species in Iran

Fungi of the genus Fusarium are well known as major plant pathogens but also cause a broad spectrum of human infections. Sixty-three clinical isolates, collected during 2014-2017, were identified using a part of the TEF1 gene as barcoding marker. Fusarium fujikuroi species complex (FFSC, n = 41, 65%) showed to be the dominant etiological agent, followed by F. solani species complex (FSSC, n = 14, 22%) and F. oxysporum species complex (FOSC, n = 7, 11%). There was one strain belonging to F. lateritium species complex (FLSC, n = 1, 1.5%). For final identification, a phylogenetic tree was constructed including the type strains of each species complex. Most cases of fusariosis were due to nail infection (n = 38, 60.3%), followed by keratitis (n = 22, 34%). Fusarium infections are difficult to be treated due to their intrinsic resistance to different azoles; however, accurate and fast identification of etiological agents may enhance management of the infection. We present the first phylogenetic study on clinical Fusarium spp. from Iran.

A novel metabarcoding approach to investigate Fusarium species composition in soil and plant samples

The genus Fusarium contains more than 300 species, most of which are plant pathogens. Appropriate molecular tools for accurately and rapidly describing temporal and spatial shifts in Fusarium communities would be useful for the development of control strategies. Here, we present a new Fusarium-specific primer pair targeting the translation elongation factor 1-α (EF1α) gene with amplicons of ~430 bp, suitable for MiSeq metabarcoding sequencing. Mock Fusarium communities were used to evaluate its resolution and to optimize read filtering and downstream analyses. The use of the DADA2 pipeline coupled with operational taxonomic unit (OTU) picking at 98% similarity cut-off significantly increased the accuracy of read filtering. Building a phylogenetic tree using a manually curated database as a reference allowed taxonomic assignment at the species or species-complex level. This methodology was tested on soil and maize residue samples collected from crop fields. Up to 18 Fusarium OTUs, belonging to 17 species and 8 species complexes, were obtained, with F. oxysporum being the most abundant species in soil samples, while F. graminearum and F. avenaceum were the most abundant in maize residues. We demonstrated the high performance of this workflow which could be further used for profiling Fusarium species composition and dynamics during the cultivation cycle.

Phylogenetic relationship between Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model

BACKGROUND

The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic relatedness within the complex has been studied by sequencing either the genes or the barcoding gene regions within those genes. Phylogenetic analyses have demonstrated a great deal of diversity which is reflected in the differing number of clades identified: three, five and eight. Genetic limitation within the species in the complex has been studied through Genealogical Concordance Phylogenetic Species Recognition (GCPSR) analyses with varying number of phylogenetic 'species' identified ranging from two to 21. Such differing views have continued to confuse users of these taxonomies.

RESULTS

The phylogenetic relationships between Australian F. oxysporum isolates from both natural and agricultural ecosystems were determined using three datasets: whole genome, nuclear genes, and mitochondrial genome sequences. The phylogenies were concordant except for three isolates. There were three concordant clades from all the phylogenies suggesting similar evolutionary history for mitochondrial genome and nuclear genes for the isolates in these three clades. Applying a multispecies coalescent (MSC) model on the eight single copy nuclear protein coding genes from the nuclear gene dataset concluded that the three concordant clades correspond to three phylogenetic species within the FOSC. There was 100% posterior probability support for the formation of three species within the FOSC. This is the first report of using the MSC model to estimate species within the F. oxysporum species complex. The findings from this study were compared with previously published phylogenetics and species delimitation studies.

CONCLUSION

Phylogenetic analyses using three different gene datasets from Australian F. oxysporum isolates have all supported the formation of three major clades which delineated into three species. Species 2 (Clade 3) may be called F. oxysporum as it contains the neotype for F. oxysporum.

Neotypification of Fusarium chlamydosporum - a reappraisal of a clinically important species complex

Fusarium chlamydosporum represents a well-defined morpho-species of both phytopathological and clinical importance. Presently, five phylo-species lacking Latin binomials have been resolved in the F. chlamydosporum species complex (FCSC). Naming these phylo-species is complicated due to the lack of type material for F. chlamydosporum. Over the years a number of F. chlamydosporum isolates (which were formerly identified based on morphology only) have been accessioned in the culture collection of the Westerdijk Fungal Biodiversity Institute. The present study was undertaken to correctly identify these 'F. chlamydosporum' isolates based on multilocus phylogenetic inference supported by morphological characteristics. Closer scrutiny of the metadata associated with one of these isolates allowed us to propose a neotype for F. chlamydosporum. Phylogenetic inference revealed the presence of nine phylo-species within the FCSC in this study. Of these, eight could be provided with names supported by subtle morphological characters. In addition, a new species, as F. nodosum, is introduced in the F. sambucinum species complex and F. chlamydosporum var. fuscum is raised to species level, as F. coffeatum, in the F. incarnatum-equiseti species complex (FIESC).