Molecular systematics and phylogeography of theGibberella fujikuroispecies complex

Green-Synthesized Silver Nanoparticles in the Prevention of Multidrug-Resistant Proteus mirabilis Infection and Incrustation of Urinary Catheters BioAgNPs Against P. mirabilis Infection

This study aimed to assess the activity of AgNPs biosynthesized by Fusarium oxysporum (bio-AgNPs) against multidrug-resistant uropathogenic Proteus mirabilis, and to assess the antibacterial activity of catheters coated with bio-AgNPs. Broth microdilution and time-kill kinetics assays were used to determine the antibacterial activity of bio-AgNPs. Catheters were coated with two (2C) and three (3C) bio-AgNPs layers using polydopamine as crosslinker. Catheters were challenged with urine inoculated with P. mirabilis to assess the anti-incrustation activity. MIC was found to be 62.5 µmol l-1, causing total loss of viability after 4 h and bio-AgNPs inhibited biofilm formation by 76.4%. Catheters 2C and 3C avoided incrustation for 13 and 20 days, respectively, and reduced biofilm formation by more than 98%, while the pristine catheter was encrusted on the first day. These results provide evidence for the use of bio-AgNPs as a potential alternative to combat of multidrug-resistant P. mirabilis infections.

Identification and Aggressiveness of Fusarium Species Associated with Onion Bulb (Allium cepa L.) during Storage

Plant pathogens present a major challenge to crop production, leading to decreased yield and quality during growth and storage. During long-term storage, healthy onions can develop diseases from latent pathogen infections. This poses a challenge for onion growers because infected bulbs without visible symptoms can lead to significant crop losses during the growing season. In this study, we aimed to isolate and identify Fusarium species from yellow onion bulbs (Allium cepa L.) that developed disease symptoms during storage. The aggressiveness of these strains against onion bulbs and seedlings was also evaluated. The isolated strains were further subjected to morphological and molecular differentiation. The results revealed that all 16 isolated strains belonged to the Fusarium complex species incarnatum-equiseti and Fusarium fujikuroi, namely, F. proliferatum (98%), F. oxysporum (1%), and Fusarium sp. (1%). Koch's postulate analysis of isolated strains revealed varying aggressiveness on onion bulbs and plants depending on fungal species. Disease symptoms developed more slowly on plants than on onion bulb plants according to Koch's postulates. Moreover, the results revealed that Fusarium strains that can infect onion plants were less pathogenic to onion bulbs and vice versa. In addition, three isolates were found to be non-pathogenic to onions. Furthermore, the in vitro control of Fusarium species through Bacillus velezensis KS04-AU and Streptomyces albidoflavus MGMM6 showed high potential for controlling the growth of these pathogenic fungi. These results may contribute to the development of environmentally friendly approaches for controlling onion spoilage caused by pathogens during storage.

Fungal Species and Mycotoxins Associated with Maize Ear Rots Collected from the Eastern Cape in South Africa

Maize production in South Africa is concentrated in its central provinces. The Eastern Cape contributes less than 1% of total production, but is steadily increasing its production and has been identified as a priority region for future growth. In this study, we surveyed ear rots at maize farms in the Eastern Cape, and mycotoxins were determined to be present in collected samples. Fungal isolations were made from mouldy ears and species identified using morphology and DNA sequences. Cladosporium, Diplodia, Fusarium and Gibberella ear rots were observed during field work, and of these, we collected 78 samples and isolated 83 fungal strains. Fusarium was identified from Fusarium ear rot (FER) and Gibberella ear rot (GER) and Stenocarpella from Diplodia ear rot (DER) samples, respectively. Using LC-MS/MS multi-mycotoxin analysis, it was revealed that 83% of the collected samples contained mycotoxins, and 17% contained no mycotoxins. Fifty percent of samples contained multiple mycotoxins (deoxynivalenol, 15-acetyl-deoxynivalenol, diplodiatoxin and zearalenone) and 33% contained a single mycotoxin. Fusarium verticillioides was not isolated and fumonisins not detected during this survey. This study revealed that ear rots in the Eastern Cape are caused by a wide range of species that may produce various mycotoxins.

Chromosome-Level Assemblies for the Pine Pitch Canker Pathogen Fusarium circinatum

The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome's distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.

Diversity and Pathogenicity of Fusarium Species Associated with Stalk and Crown Rot in Maize in Northern Italy

The genus Fusarium includes several agronomically important and toxin-producing species that are distributed worldwide and can cause a wide range of diseases. Crown and stalk rot and grain infections are among the most severe symptoms that Fusarium spp. can cause in maize. Disease development usually occurs during germination, but it may also affect the later phases of plant growth. The purpose of this study was to investigate the diversity and pathogenicity of 41 isolates recovered from symptomatic seedlings collected in Northern Italy and seeds of five different geographical origins in 2019 and 2020. The pathogenicity was tested and confirmed in 23 isolates causing rotting in maize seedlings, with disease indexes from 20% to 90%. A multilocus phylogeny analysis based on four genomic loci (tef1-α, rpb2, calm and tub2) was performed on 23 representative isolates. Representative isolates were identified as species belonging to three species complexes (SC), including Fusarium verticillioides and F. annulatum in the F. fujikuroi SC. Fusarium commune was identified in the F. nisikadoi SC, and three different lineages were found in the Fusarium oxysporum SC. This study reports F. annulatum and two lineages of the Fusarium oxysporum SC as maize pathogens for the first time in Italy.

A LAMP Assay for Rapid Detection of the Pitch Canker Pathogen Fusarium circinatum

The pine pitch canker pathogen Fusarium circinatum is endemic in the southeastern United States and Central America and represents an invasive threat globally. This ecologically adaptable fungus readily infects all parts of its pine hosts, leading to widespread mortality of nursery seedlings and decline in the health and productivity of forest stands. Because trees infected by F. circinatum can remain asymptomatic for long periods of time, accurate and rapid tools are needed for real-time diagnostics and surveillance at ports, in nurseries, and in plantations. To meet this need and to limit the spread and impact of the pathogen, we developed a molecular test using loop-mediated isothermal amplification (LAMP), a technology that allows for the rapid detection of pathogen DNA on portable, field-capable devices. LAMP primers were designed and validated to amplify a gene region unique to F. circinatum. Using a globally representative collection of F. circinatum isolates and other closely related species, we have demonstrated that the assay can be used to identify F. circinatum across its genetic diversity and that it is sensitive to as few as 10 cells from purified DNA extracts. The assay can also be used with a simple, pipette-free DNA extraction method and is compatible with testing symptomatic pine tissues in the field. This assay has the potential to facilitate diagnostic and surveillance efforts both in the laboratory and in the field and, thus, to reduce the spread and impact of pitch canker worldwide.

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 pathogenicity analysis of Fusarium spp. on peach in China

BACKGROUND

Vascular system is affected by diseases that can seriously damage plant health by inducing browning and death of branches. This study aimed to identify and analyze the pathogenicity of Fusarium spp. isolates obtained from diseased peach branches in several peach-producing areas of China.

RESULTS

We obtained and confirmed nine Fusarium isolates based on morphological and molecular characteristics. Phylogenetic relationships using a combination of rDNA-internal transcribed spacer (ITS), elongation factor (EF)-1α, and mitochondrial small subunit (mtSSU) gene sequences were analyzed. GJH-Z1, GJH-6, and GJH-1 were identified as F. avenaceum; HYR-Z3, and ZLZT-6 as F. concentricum, HH-2020-G2, and HYTZ-4 as F. solani, GG-2020-1 as F. asiaticum, SYGZ-1 as F. equiseti. Through acupuncture comparison, the pathogenicity of F. equiseti (SYGZ-1) was highest amongst nine strains. Meanwhile, F. concentricum (HYR-Z3 and ZLZT-6), and F. solaini (HYTZ-4) had a higher level of pathogenicity as revealed by impregnation.

CONCLUSIONS

Our study shed light on the findings that Fusarium spp. can inflict vascular bundle browning of peach plants. Our results will extend the understanding of pathogenic diseases in China's peach industry.

Fusarium Species and Mycotoxins Associated with Sorghum Grains in Uruguay

Grain mold and stalk rot are among the fungal diseases that cause significant losses in sorghum worldwide and are caused by different Fusarium spp. The presence of Fusarium species in sorghum grains causes yield losses and mycotoxin contamination, which represents a risk to consumers. In this study, Fusarium graminearum species complex (FGSC) had a high incidence, followed by Fusarium fujikuroi species complex (FFSC) and F. incarnatum-equiseti species complex. Within FFSC, F. proliferatum, F. andiyazi, F. fujikuroi, F. thapsinum, F. verticillioides and F. subglutinans were identified, and this was the first report of F. fujikuroi in sorghum. The most frequent toxins found in sorghum samples were deoxynivalenol (DON) and zearalenone (ZEN). The presence of fumonisins and nivalenol (NIV) was detected at low levels. This study adds new knowledge about the occurrence of Fusarium species and mycotoxins in sorghum grains. Furthermore, this is the first report in Uruguay on fungicide sensitivity for Fusarium isolates from sorghum, which constitutes an important starting point for defining management practices to minimize fungal infection and mycotoxin contamination.

Molecular Identification and Characterization of Fusarium Associated with Walnut Branch Blight Disease in China

In October 2020, samples of walnut branch blight were collected from Longnan. Pathogens were isolated and identified based on morphological and molecular features, and their characteristics were analyzed by pathogenicity. Pathogenicity testing revealed that seven strains (LN-1, LN-3, LN-6, LN-19, LN-27, QY3-1, and QY9-1) induced symptoms of walnut branch blight that were consistent with those observed in the field after inoculation. Furthermore, some Fusarium-type conidia and spherical chlamydospores were visible indicating that they were Fusarium spp. A molecular characterization including sequence and phylogenetic analysis of the ITS, TEF-1α, βTUB, Fu, and LSU gene regions revealed that LN-1 and LN-19 belonged to F. avenaceum, LN-3 and LN-6 to F. acuminatum, LN-27 to F. sporotrichioides, and QY3-1 and QY9-1 to F. tricinctum. This is the first time that F. acuminatum-, F. sporotrichioides-, and F. tricinctum-caused walnut branch blight has been reported in China.

New Species of Neocosmospora (Ascomycota) from China as Evidenced by Morphological and Molecular Data

Species of Neocosmospora are commonly found in soil, plant debris, and living woody or herbaceous substrates and occasionally found in water and air. Some species are reported as saprobes, endophytes, opportunistic pathogens of plants and animals, or producers of bioactive natural products, cytotoxic compounds, and industrial enzymes. To reveal the species diversity of Neocosmospora, specimens from different provinces of China were investigated. Five new species, Neocosmospora anhuiensis, N. aurantia, N. dimorpha, N. galbana, and N. maoershanica, were introduced based on morphological characteristics and DNA sequence analyses of combined calmodulin (CAM), the internal transcribed spacer (ITS), the second largest subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α (TEF1) regions. Differences between these new species and their close relatives are compared in detail.

Different diagnostic approaches for the characterization of the fungal community and Fusarium species complex composition of Italian durum wheat grain and correlation with secondary metabolite accumulation

BACKGROUND

The evolution of the fungal communities associated with durum wheat was assessed using different diagnostic approaches. Durum wheat grain samples were collected in three different Italian cultivation macro-areas (north, center and south). Fungal isolation was realized by potato dextrose agar (PDA) and by deep-freezing blotter (DFB). Identification of Fusarium isolates obtained from PDA was achieved by partial tef1α sequencing (PDA + tef1α), while those obtained from DFB were identified from their morphological characteristics (DFB + mc). The fungal biomass of eight Fusarium species was quantified in grains by quantitative polymerase chain reaction (qPCR). Fungal secondary metabolites were analyzed in grains by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Correlations between Fusarium detection techniques (PDA + tef1α; DFB + mc and qPCR) and mycotoxins in grains were assessed.

RESULTS

Alternaria and Fusarium showed the highest incidence among the fungal genera developed from grains. Within the Fusarium community, PDA + tef1α highlighted that F. avenaceum and F. graminearum were the most represented members, while, DFB + mc detected a high presence of F. proliferatum. Alternaria and Fusarium mycotoxins, principally enniatins, were particularly present in the grain harvested in central Italy. Deoxynivalenol was mainly detected in northern-central Italy.

CONCLUSIONS

The adoption of the different diagnostic techniques of Fusarium detection highlighted that, for some species, qPCR was the best method of predicting their mycotoxin contamination in grains. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genetic Diversity and Pathogenicity of Fusarium fujikuroi Species Complex (FFSC) Causing Sugarcane Pokkah Boeng Disease (PBD) in China

Pokkah boeng disease (PBD), a sugarcane foliar disease, is caused by various Fusarium spp. within the Fusarium fujikuroi species complex (FFSC). In the current study, we investigated the diversity of Fusarium spp. associated with PBD in China. In total, 320 leaf samples displaying PBD symptoms were collected over 10 consecutive years (2012 to 2021), during winter and summer, from six various sugarcane-growing regions (Guangxi, Yunnan, Guangdong, Zhejiang, Hainan, and Fujian) in China. Phylogenetic analysis of Fusarium spp. was reconstructed using translation elongation factor 1-α, and DNA-directed RNA polymerase II largest subunit and second-largest subunit multigene sequences. Evolutionary studies of these regions categorized the isolates into four FFSC species (F. sacchari, F. proliferatum, F. verticillioides, and F. andiyazi). The identified isolates, which developed irregular necrotic patches and rotting symptoms on the sugarcane plant after approximately 30 days were tested for their pathogenicity. Symptoms that appeared during pathogenicity testing were consistent with those observed under field conditions. Each strain of the pathogenic Fusarium spp. belonged to different vegetative compatibility groups (VCGs), and there was no affinity between VCGs. Our results contribute to understanding FFSC and accurately identifying Fusarium spp. associated with the sugarcane crop.

Multigene Phylogeny and Pathogenicity Trials Revealed Alternaria alternata as the Causal Agent of Black Spot Disease and Seedling Wilt of Pecan (Carya illinoinensis) in South Africa

The pecan (Carya illinoinensis) industry in South Africa is growing rapidly, and it is becoming increasingly crucial to understand the risks posed to pecans by fungal pathogens. Black spots on leaves, shoots, and nuts in shucks caused by Alternaria species have been observed since 2014 in the Hartswater region of the Northern Cape Province of South Africa. Species of Alternaria include some of the most ubiquitous plant pathogens on earth. The aim of this study was to use molecular techniques to identify the causative agents of Alternaria black spot and seedling wilt isolated from major South African pecan-production areas. Symptomatic and non-symptomatic pecan plant organs (leaves, shoots, and nuts-in-shucks) were collected from pecan orchards, representing the six major production regions in South Africa. Thirty Alternaria isolates were retrieved from the sampled tissues using Potato Dextrose Agar (PDA) culture media and molecular identification was conducted. The phylogeny of multi-locus DNA sequences of Gapdh, Rpb2, Tef1, and Alt a 1 genes revealed that the isolates were all members of Alternaria alternata sensu stricto, forming part of the Alternaria alternata species complex. The virulence of six A. alternata isolates were tested on detached nuts of Wichita and Ukulinga cultivars, respectively, as well as detached leaves of Wichita. The A. alternata isolates were also evaluated for their ability to cause seedling wilt in Wichita. The results differed significantly between wounded and unwounded nuts of both cultivars, but not between the cultivars. Similarly, the disease lesions on the wounded detached leaves were significantly different in size from the unwounded leaves. The seedling tests confirmed that A. alternata is pathogenic and that A. alternata causes black spot disease and seedling wilt of pecans. This study is one of the first documentations of Alternaria black spot disease of pecan trees and its widespread occurrence in South Africa.

Attraction, mobility, and preference by Lasioderma serricorne (Coleoptera: Ptinidae) to microbially-mediated volatile emissions by two species of fungi in stored grain

Insects and microbes are known to interact in a variety of ways at food facilities, compounding damage. However, little research has explicated how specific common fungal species affect the behavior of the cosmopolitan secondary stored product pest, Lasioderma serricorne. Enhanced knowledge about attraction to microbially-produced volatile organic compounds (MVOCs) may be used to manipulate insect behavior. Aspergillus flavus and Fusarium verticillioides are two common, widespread pre- and postharvest fungi on small cereals that produce aflatoxins and fumonisins, respectively, while directly competing with each other for nutrients. Our goals were to (1) characterize the volatile emissions from grain inoculated by A. flavus or F. verticillioides derived from the cuticle of L. serricorne compared to uninoculated and sanitized grain, and (2) understand how MVOCs from each fungal species affects mobility, attraction, and preference by L. serricorne. Headspace collection revealed that the F. verticillioides- and A. flavus-inoculated grain produced significantly different volatiles compared to sanitized grain or the positive control. Changes in MVOC emissions affected close-range foraging during an Ethovision movement assay, with a greater frequency of entering and spending time in a small zone with kernels inoculated with A. flavus compared to other treatments. In the release-recapture assay, MVOCs were found to be attractive to L. serricorne at longer distances in commercial pitfall traps. There was no preference shown among semiochemical stimuli in a still-air, four-way olfactometer. Overall, our study suggests that MVOCs are important for close- and long-range orientation of L. serricorne during foraging, and that MVOCs may have the potential for inclusion in behaviorally-based tactics for this species.

Fusarium mindanaoense sp. nov., a New Fusarium Wilt Pathogen of Cavendish Banana from the Philippines Belonging to the F. fujikuroi Species Complex

The pathogen causing Fusarium wilt in banana is reported to be Fusarium oxysporum f. sp. cubense (FOC). In 2019, wilt symptoms in banana plants (cultivar: Cavendish) in the Philippines were detected, i.e., the yellowing of the leaves and discoloration of the pseudostem and vascular tissue. The fungus isolated from the vascular tissue was found to be pathogenic to Cavendish bananas and was identified as a new species, F. mindanaoense, belonging to the F. fujikuroi species complex (FFSC); species classification was assessed using molecular phylogenetic analyses based on the tef1, tub2, cmdA, rpb1, and rpb2 genes and morphological analyses. A reciprocal blast search using genomic data revealed that this fungus exclusively included the Secreted in Xylem 6 (SIX6) gene among the SIX homologs related to pathogenicity; it exhibited a highly conserved amino acid sequence compared with that of species in the FFSC, but not with that of FOC. This was the first report of Fusarium wilt in Cavendish bananas caused by a species of the genus Fusarium other than those in the F. oxysporum species complex.

Identifying phytopathogenic fungi in Al-Baha province, Saudi Arabia through their molecular and morphological features: An overview

Fungi are major pathogens of plants. They are responsible for most of the spoilage that occurs to plants in fields or in storage conditions. In addition to the direct impacts of fungi upon the plant's fruiting body, such as leaf spot, wilt, rust, dieback and rot, fungi can contaminate plants with mycotoxins. Twenty isolates were molecularly identified in this study representing eight genera and twelve species. The most common species identified in this work belongs to Aspergillus (33.3%), Penicillium (16.6%) and Fusarium (16.6%) genera, which are well known to have mycotoxigenic species. Environmental factors have a significant influence on the biological activity of fungi, including growth, sporulation and mycotoxin production. Temperature and water activity affect fungal virulence factors, such as growth, colonisation, spread and mycotoxin production. This work found the optimal temperature for the growth of isolates, was 30 °C for 75 % of isolates and at 25 °C for 25 % of isolates. This information is useful, as it helps to identify the phytopathogenic and mycotoxigenic species, and determining optimal growth temperatures is important to control them and reduce their threats.

Fungal Pathogens Associated with Crown and Root Rot in Wheat-Growing Areas of Northern Kyrgyzstan

Fungal species associated with crown and root rot diseases in wheat have been extensively studied in many parts of the world. However, no reports on the relative importance and distribution of pathogens associated with wheat crown and root rot in Kyrgyzstan have been published. Hence, fungal species associated with wheat crown/root rot were surveyed in three main wheat production regions in northern Kyrgyzstan. Fungal species were isolated on 1/5 strength potato-dextrose agar amended with streptomycin (0.1 g/L) and chloramphenicol (0.05 g/L). A total of 598 fungal isolates from symptomatic tissues were identified using morphological features of the cultures and conidia, as well as sequence analysis of the nuclear ribosomal internal transcribed spacer (ITS) region, the translation elongation factor 1α (TEF1), and the RNA polymerase II beta subunit (RPB2) genes. The percentage of fields from which each fungus was isolated and their relative percentage isolation levels were determined. Bipolaris sorokiniana, the causal agent of common root rot, was the most prevalent pathogenic species isolated, being isolated from 86.67% of the fields surveyed at a frequency of isolation of 40.64%. Fusarium spp. accounted for 53.01% of all isolates and consisted of 12 different species. The most common Fusarium species identified was Fusarium acuminatum, which was isolated from 70% of the sites surveyed with an isolation frequency of 21.57%, followed by Fusarium culmorum, Fusarium nygamai, Fusarium oxysporum, and Fusarium equiseti, all of which had a field incidence of more than 23%. Inoculation tests with 44 isolates representing 17 species on the susceptible Triticum aestivum cv. Seri 82 revealed that Fusarium pseudograminearum and F. culmorum isolates were equally the most virulent pathogens. The widespread distribution of moderately virulent B. sorokiniana appears to be a serious threat to wheat culture, limiting yield and quality. With the exception of F. culmorum, the remaining Fusarium species did not pose a significant threat to wheat production in the surveyed areas because common species, such as F. acuminatum, F. nygamai, F. oxysporum, and F. equiseti, were non-pathogenic but infrequent species, such as Fusarium redolens, Fusarium algeriense, and F. pseudograminearum, were highly or moderately virulent. Curvularia inaequalis, which was found in three different fields, was mildly virulent. The remaining Fusarium species, Fusarium solani, Fusarium proliferatum, Fusarium burgessii, and Fusarium tricinctum, as well as Microdochium bolleyi, Microdochium nivale, and Macrophomina phaseolina, were non-pathogenic and considered to be secondary colonizers. The implications of these findings are discussed.

Polymorphisms of rDNA genes in Cyberlindnera yeast suggest birth-and-death evolution events

In eukaryotes, the ribosome machinery is encoded by repeats of the ribosomal RNA genes: 26/28S, 18S, 5.8S, and 5S, structured in tandem arrays and frequently homogenized within a genome. This homogenization is thought to be driven by concerted evolution, evolving as a unit, which contributes to its target as the species barcode in modern taxonomy. However, high heterogeneity of rDNA genes has been reported, including in Saccharomycotina yeasts. Here, we describe the polymorphisms and heterogeneity of D1/D2 domains (26S rRNA) and the intergenic transcribed spacer of a new yeast species with affinities to the genus Cyberlindnera and their evolution. Both regions are not homogenized, failing the prediction of concerted evolution. Phylogenetic network analysis of cloned sequences revealed that Cyberlindnera sp. rDNAs are diverse and evolved by reticulation rather than by bifurcating tree evolution model. Predicted rRNA secondary structures also confirmed structural differences, except for some conserved hairpin loops. We hypothesize that some rDNA is inactive within this species and evolves by birth-and-death rather than concerted evolution. Our findings propel further investigation into the evolution of rDNA genes in yeasts.

Multilocus molecular phylogenetic-led discovery and formal recognition of four novel root-colonizing Fusarium species from northern Kazakhstan and the phylogenetically divergent Fusarium steppicola lineage

In this study, DNA sequence data were used to characterize 290 Fusarium strains isolated during a survey of root-colonizing endophytic fungi of agricultural and nonagricultural plants in northern Kazakhstan. The Fusarium collection was screened for species identity using partial translation elongation factor 1-α (TEF1) gene sequences. Altogether, 16 different Fusarium species were identified, including eight known and four novel species, as well as the discovery of the phylogenetically divergent F. steppicola lineage. Isolates of the four putatively novel fusaria were further analyzed phylogenetically with a multilocus data set comprising partial sequences of TEF1, RNA polymerase II largest (RPB1) and second-largest (RPB2) subunits, and calmodulin (CaM) to assess their genealogical exclusivity. Based on the molecular phylogenetic and comprehensive morphological analyses, four new species are formally described herein: F. campestre, F. kazakhstanicum, F. rhizicola, and F. steppicola.

Utilizing volatile organic compounds for early detection of Fusarium circinatum

Fusarium circinatum, a fungal pathogen deadly to many Pinus species, can cause significant economic and ecological losses, especially if it were to become more widely established in Europe. Early detection tools with high-throughput capacity can increase our readiness to implement mitigation actions against new incursions. This study sought to develop a disease detection method based on volatile organic compound (VOC) emissions to detect F. circinatum on different Pinus species. The complete pipeline applied here, entailing gas chromatography-mass spectrometry of VOCs, automated data analysis and machine learning, distinguished diseased from healthy seedlings of Pinus sylvestris and Pinus radiata. In P. radiata, this distinction was possible even before the seedlings became visibly symptomatic, suggesting the possibility for this method to identify latently infected, yet healthy looking plants. Pinus pinea, which is known to be relatively resistant to F. circinatum, remained asymptomatic and showed no changes in VOCs over 28 days. In a separate analysis of in vitro VOCs collected from different species of Fusarium, we showed that even closely related Fusarium spp. can be readily distinguished based on their VOC profiles. The results further substantiate the potential for volatilomics to be used for early disease detection and diagnostic recognition.

Evaluation of Pathogenic Fusarium spp. Associated with Soybean Seed (Glycine max) in Hubei Province, China

Soybean (Glycine max L.) seeds showing serious symptoms from rotted pods were collected from fields during the harvesting period (July to August 2020) in Taihu Farm, Jingzhou City, Hubei Province, China. Fusarium strains were frequently encountered during fungal isolation. According to the morphology and prepathogenicity tests, six strains showing variable effects on the seeds were selected for identification based on morphology and multilocus phylogenetic analysis of the internal transcribed spacer (ITS) region of the ribosomal DNA, translation elongation factor (EF-1α), calmodulin (CAM), β-tubulin (TUB), and partial RNA polymerase second largest subunit (RPB2), and to evaluate the pathogenic abilities on seed, root, and pod. The results indicated that the strains contained two species (Fusarium fujikuroi and F. proliferatum) in the Fusarium fujikuroi species complex (FFSC) and two species (F. luffae and F. sulawense) from the Fusarium incarnatum-equiseti species complex (FIESC). The two species of FFSC were more aggressive than those of FIESC on soybean seed, root, and pod. Among the strains, F. proliferatum YZU 201408 exhibited the most pathogenicity on all tests, with 72.2 to 90% disease severity.

Physiological and metabolic analyses provide insight into soybean seed resistance to fusarium fujikuroi causing seed decay

Seed-borne pathogens cause diverse diseases at the growth, pre- and post-harvest stage of soybean resulting in a large reduction in yield and quality. The physiological and metabolic aspects of seeds are closely related to their defense against pathogens. Recently, Fusarium fujikuroi has been identified as the dominant seed-borne fungi of soybean seed decay, but little information on the responses of soybean seeds induced by F. fujikuroi is available. In this study, a time-course symptom development of seed decay was observed after F. fujikuroi inoculation through spore suspension soaking. The germination rate and the contents of soluble sugar and soluble protein were significantly altered over time. Both chitinase and β-1,3-glucanase as important fungal cell wall-degrading enzymes of soybean seeds were also rapidly and transiently activated upon the early infection of F. fujikuroi. Metabolic profile analysis showed that the metabolites in glycine, serine, and threonine metabolism and tryptophan metabolism were clearly induced by F. fujikuroi, but different metabolites were mostly enriched in isoflavone biosynthesis, flavone biosynthesis, and galactose pathways. Interestingly, glycitein and glycitin were dramatically upregulated while daidzein, genistein, genistin, and daidzin were largely downregulated. These results indicate a combination of physiological responses, cell wall-related defense, and the complicated metabolites of soybean seeds contributes to soybean seed resistance against F. fujikuroi, which are useful for soybean resistance breeding.

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.

Survey of Natural Enemies of the Invasive Boxwood Moth Cydalima perspectalis in Southwestern Mediterranean Europe and Biocontrol Potential of a Native Beauveria bassiana (Bals.-Criv.) Vuill. Strain

Cydalima perspectalis (Lepidoptera: Crambidae), a species native to East Asia, has been especially devastating in the Mediterranean region and Catalonia, northeast Spain, where Buxus sempervirens is an essential component of the natural forest. As an invasive species, the lack of biotic mortality factors in the arrival region has been one of the main factors allowing its expansion. Therefore, this study aimed to collect and identify possible indigenous natural enemies adapting to the new species in the boxwood of the southwest Mediterranean region. Later, the efficacy of some of the collected species for controlling C. perspectalis larvae was tested in laboratory conditions. The larval collection was carried out in successive years in the boxwood of the region. Several collected larvae were infected with an entomopathogen, Beauveria bassiana, or parasitized by Compsilura concinnata, both common in native Lepidoptera caterpillars. The B. bassiana strain was found to be highly virulent against the developed larvae of C. perspectalis, which suggests that B. bassiana may be an effective treatment in parks and gardens when the first overwintering larvae are detected. The biology of the parasitoid identified is not very well known in Europe, which suggests the necessity of studying its biology and alternative hosts in the region in order to improve its population.

Diversity of Fusarium Species Isolated from Symptomatic Plants Belonging to a Wide Range of Agri-Food and Ornamental Crops in Lebanon

Lebanon is a small Mediterranean country with different pedoclimatic conditions that allow the growth of both temperate and tropical plants. Currently, few studies are available on the occurrence and diversity of Fusarium species on Lebanese crops. A wide population of Fusarium strains was isolated from different symptomatic plants in the last 10 years. In the present investigation, a set of 134 representative strains were molecularly identified by sequencing the translation elongation factor, used in Fusarium as a barcoding gene. Great variability was observed, since the strains were grouped into nine different Fusarium Species Complexes (SCs). Fusarium oxysporum SC and Fusarium solani SC were the most frequent (53% and 24%, respectively). Members of important mycotoxigenic SCs were also detected: F. fujikuroi SC (7%), F. sambucinum SC (5%), F. incarnatum-equiseti SC (3%), and F. tricinctum SC (4%). Two strains belonging to F. lateritium SC, a single strain belonging to F. burgessii SC, and a single strain belonging to F. redolens SC were also detected. This paper reports, for the first time, the occurrence of several Fusarium species on Lebanese host plants. The clear picture of the Fusarium species distribution provided in this study can pose a basis for both a better understanding of the potential phytopathological and toxicological risks and planning future Fusarium management strategies in Lebanon.

Identification of Fusarium andiyazi Associated with the Bakanae Disease of Rice in Turkey

Rice is an important nutrient staple for much of the Turkish population. In this study, field surveys were carried out to collect isolates of Fusarium andiyazi, a member of the Fusarium fujikuroi species complex (FFSC) associated with Bakanae disease. As part of the study, morphological and microscopic features of Fusarium andiyazi isolates recovered from infected rice plants were determined. The molecular detection of F. andiyazi was carried out through PCR analysis of partial translation elongation factor 1-alpha (TEF-1α) gene and the internal transcribed spacer (ITS) region. Gib2 and Fgc primers were used for specific detection of strain of FFSC. In the phylogenetic analysis, using the sequences of the partial TEF-1α gene, F. andiyazi were clustered in the same branch with the reference isolates. The pathogenicity tests revealed that the isolates of F. andiyazi were pathogen on susceptible Baldo cultivar under room climate conditions. The disease severity ranged from 3.27% to 86.30%. The pathogen causes typical disease symptoms associated with Bakanae and mostly inhibited seed germination, while most of the isolates caused abnormal elongation compared to the control plants. This is the first report of presence of F. andiyazi causing Bakanae disease on rice in Turkey.

Bioactivity of mefentrifluconazole against different Fusarium spp

Emergence and development of resistance to 14α-demethylase inhibitors (DMIs) have become a critical issue in both agriculture and medical fields. Mefentrifluconazole, the first isopropanol triazole fungicide belonging to a new subclass of DMIs, has been proposed to show high activity, minimal adverse side effects, and inconsistent cross resistance with other DMIs due to its high structural flexibility. In this study, mefentrifluconazole showed disparate inhibitory activity against the mycelium growth of seven tested Fusarium species. The most sensitive species included F. oxysporum, F. proliferatum, F. commuae, and F. fujikuroi, followed by F. equiseti and F. graminearum, while F. solani was most insensitive. Consistently, mefentrifluconazole presented the strongest inhibiting effects on conidium germination, cell membrane integrity, and ergosterol biosynthesis in F. fujikuroi, followed by F. graminearum, while F. solani ranked last. Further results indicated that all F. fujikuroi isolates causing rice bakanae disease (RBD) were sensitive to mefentrifluconazole regardless of their resistance to prochloraz, tebuconazole, carbendazim, and phenamacril. Additionally, the inoculation tests found that mefentrifluconazole presented a better protective efficacy on rice seedlings when applied 12 h before the F. fujikuroi inoculation, compared to applied 12 h post the inoculation. Overall, this study demonstrated the various bioactivity of mefentrifluconazole combating Fusarium spp. and put new insights into RBD management as well as the applications of DMIs.

Characterization of Host-Specific Genes from Pine- and Grass-Associated Species of the Fusarium fujikuroi Species Complex

The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of their respective plant hosts. We characterized the identity, possible functions, evolutionary origins, and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi. The 72 and 47 genes identified as unique to the respective genome groups were potentially involved in diverse processes, ranging from transcription, regulation, and substrate transport through to virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were only subsequently retained in some lineages, while some had origins outside Fusarium. Although differences in the densities of these genes were especially noticeable on the conditionally dispensable chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the pine-associates), the host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted the diversity of the molecular processes potentially underlying niche-specificity in these and other Fusarium species.

First Report of Chestnut Blight Caused by Cryphonectria parasitica on Chestnut (Castanea seguinii) in Gansu Province, China

In China, chestnut blight usually causes insignificant damage to fruit production of Chinese chestnut (Castanea mollissima Blume) and no serious disease epidemics occur, due to the high resistance to Cryphonectria parasitica (Huang et al. 1998). According to recent surveys, chestnut blight was mainly found in sixteen provinces including Shandong, Hebei, Anhui, Hunan, Jiangxi, Beijing, and Fujian, with severe cases occurring occasionally (Guo et al. 2005). The disease incidence has been aggravated with increasing monoculture of newly improved chestnut cultivars in chestnut-producing areas (Yan et al. 2007), though it was not detected in Gansu Province. In September 2021, some chestnut trees (Castanea seguinii) showing symptoms of crown dieback and diffuse sunken cankers on the trunk with swelled margins and subsequent cracking of the outer bark, were collected in mountains of Hui County in Longnan City, Gansu Province (E 104° 15' 5.76″ ，N 35° 11' 30.84″). Symptomatic branches were washed using tap water and dried on sterilized tissue paper. The Junction between diseased and healthy tissue was cut from the bark and sterilized with NaClO (2.5 %) for 2 minutes, then plated on potato dextrose agar (PDA) and incubated at 25 ℃ for 3 to 4 days. After fungal colonies formed, mycelia were transferred and subcultured onto new PDA media and then purified using single spore culture. After 7 days, colonies turned yellow white. Uninucleate conidia were formed in orange pycnidia and the orange pigments could turn purple if in 2% KOH. Conidia were straight or slightly curved, hyaline, with 2.5-3.5 × 1.2-1.5 μm in size. The characteristics of the culture and morphology were similar with those of C. parasitica (Tziros et al. 2016). Perithecia were not found on culture medium. In accordance with previous findings, the sexual stage of C. parasitica appears on diseased trees in late October. For molecular identification, genomic DNA was extracted from mycelium using a Fungal Genomic DNA Extraction Kit (Tsingke Biotech Co. Ltd, Xi'an, China), the ITS region was amplified with primers ITS1/ITS4 (Sorrentino et al. 2019), and the TEF1-α region was amplified with primers TEF-1H/TEF-2T (O'Donnel et al. 1998). Cloning and sequencing of PCR products were carried out by Tsingke Biotech Co. Ltd, Xi'an, China. The resulting sequences were deposited in GenBank (ITS sequence accession number: OM033734, TEF sequence accession number: OM12254). BLAST results revealed that the sequences of ITS and TEF shared identity over 99% with those of C. parasitica strains (GenBank accession number: AY308953, KP524763, KP824756 and KF220299). Based on morphological and molecular characteristic, the fungal isolates were identified as C. parasitica. To verify pathogenicity, thirty 3-year-old chestnut seeding (70 cm high, 1 cm diameter) of Castanea seguinii were used for inoculation. Chestnut branches were wounded (five wounds per sapling) using a hole punch and inoculated with a mycelial plug (5 mm in diameter) from the edge of 7-day-old, actively growing colonies. Pathogen-free PDA plugs were used as controls. To prevent desiccation, inoculated wounds were sealed with parafilm, and saplings were incubated in a greenhouse at 25℃. Each treatment consisted of 5 seedling and the pathogenicity tests were repeated three times. After inoculation for 5 weeks, symptoms of bark cankers were observed on branches similar to those of diseased chestnut trees in the field. Control saplings with sterile PDA discs did not display symptoms. C. parasitica was reisolated from inoculated branches. To our knowledge, this is the first report of C. parasitica causing chestnut blight in Gansu Province, one of the few areas in the China thought to be free of the disease. The specimens were found in the westernmost part of the natural distribution of chestnuts in China. There are more than 2.6 million chestnut trees, which constitute one of the most important economic forests in Hui County Gansu Province (Yang et al. 2005). The occurrence of chestnut blight could be a restricting factor for chestnut forests.

Fusarium abutilonis and F. guadeloupense, two novel species in the Fusarium buharicum clade supported by multilocus molecular phylogenetic analyses

This study was conducted to elucidate evolutionary relationships and species diversity within the Fusarium buharicum species complex (FBSC). We also evaluate the potential of these species to produce mycotoxins and other bioactive secondary metabolites. Maximum likelihood and maximum parsimony analyses of sequences from portions of four marker loci (ITS rDNA, TEF1, RPB1, and RPB2) and the combined 4495 bp data set support recognition of seven genealogically exclusive species within the FBSC. Two of the three newly discovered species are formally described as F. abutilonis and F. guadeloupense based on concordance of gene genealogies and morphological data. Fusarium abutilonis induces leaf, stem, and root lesions on several weedy Malvaceae (Abution theophrasti, Anoda cristata, Sida spinosa) and a fabaceous host (Senna obtusifolia) in North America and also was recovered from soil in New Caledonia. Fusarium abutilonis, together with its unnamed sister, Fusarium sp. ex common marsh mallow (Hibiscus moscheutos) from Washington state, and F. buharicum pathogenic to cotton and kenaf in Russia and Iran, respectively, were strongly supported as a clade of malvaceous pathogens. The four other species of the FBSC are not known to be phytopathogenic; however, F. guadeloupense was isolated from human blood in Texas and soil in Guadeloupe. The former isolate is unique because it represents the only known case of a fusarial infection disseminated hematogenously by a species lacking microconidia and the only documented fusariosis caused by a member of the FBSC. Whole genome sequence data and extracts of cracked maize kernel cultures were analyzed to assess the potential of FBSC isolates to produce mycotoxins, pigments, and phytohormones.

Co-infection of Fusarium aglaonematis sp. nov. and Fusarium elaeidis Causing Stem Rot in Aglaonema modestum in China

Aglaonema modestum (A. modestum) (Araceae) is an evergreen herbage, which is intensively grown as an ornamental plant in South China. A new disease was observed in A. modestum from 2020 to 2021 in Guangdong province, China. The disease symptoms associated with plants were initial leaf wilt, stem rot, and resulting plant death, leading to severe economic losses. In total, six Fusarium isolates were obtained from diseased plants. The putative pathogen was identified using both morphological characteristics and molecular phylogenetic analysis of calmodulin A (cmdA), RNA polymerase largest subunit 1 (rpb1), RNA polymerase II (rpb2), translation elongation factor-1α (tef1-α), and beta-tubulin (β-tubulin) sequences. Two Fusarium species were identified, namely, one new species, Fusarium aglaonematis (F. aglaonematis) belonging to Fusarium fujikuroi species complex. In addition, Fusarium elaeidis (F. elaeidis) belonging to the Fusarium oxysporum (F. oxysporum) species complex was also identified. Pathogenicity assays were conducted by inoculating each species into potted A. modestum plants and co-inoculating two species. The results showed that two Fusarium species could infect plants independently and can infect them together. Co-infection of these two species enhanced the disease severity of A. modestum. Compared to single inoculation of F. elaeidis, severity was higher and disease development was quicker when plants were only inoculated with F. aglaonematis. In addition, these two Fusarium species could infect Aglaonema plants without wounds, while inoculation with a physical injury increased disease severity. This is the first report of co-infection by F. aglaonematis and F. elaeidis causing stem rot on A. modestum worldwide. This study will be an addition to the knowledge of Fusarium diseases in ornamental plants. These results will provide a baseline to identify and control diseases associated with A. modestum.

Multigene Phylogeny, Beauvericin Production and Bioactive Potential of Fusarium Strains Isolated in India

The taxonomy of the genus Fusarium has been in a flux because of ambiguous circumscription of species-level identification based on morphotaxonomic criteria. In this study, multigene phylogeny was conducted to resolve the evolutionary relationships of 88 Indian Fusarium isolates based on the internal transcribed spacer region, 28S large subunit, translation elongation factor 1-alpha, RNA polymerase second largest subunit, beta-tubulin and calmodulin gene regions. Fusarium species are well known to produce metabolites such as beauvericin (BEA) and enniatins. These identified isolates were subjected to fermentation in Fusarium-defined media for BEA production and tested using TLC, HPLC and HRMS. Among 88 isolates studied, 50 were capable of producing BEA, which varied from 0.01 to 15.82 mg/g of biomass. Fusarium tardicrescens NFCCI 5201 showed maximum BEA production (15.82 mg/g of biomass). The extract of F. tardicrescens NFCCI 5201 showed promising antibacterial activity against Staphylococcus aureusMLS16 MTCC 2940 and Micrococcus luteus MTCC 2470 with MIC of 62.5 and 15.63 µg/mL, respectively. Similarly, the F. tardicrescens NFCCI 5201 extract in potato dextrose agar (40 µg/mL) exhibited antifungal activity in the food poison technique against plant pathogenic and other fungi, Rhizoctonia solani NFCCI 4327, Sclerotium rolfsii NFCCI 4263, Geotrichum candidum NFCCI 3744 and Pythium sp. NFCCI 3482, showing % inhibition of 84.31, 49.76, 38.22 and 35.13, respectively. The antibiotic effect was found to synergize when Fusarium extract and amphotericin B (20 µg/mL each in potato dextrose agar) were used in combination against Rhizopus sp. NFCCI 2108, Sclerotium rolfsii NFCCI 4263, Bipolaris sorokiniana NFCCI 4690 and Absidia sp. NFCCI 2716, showing % inhibition of 50.35, 79.37, 48.07 and 76.72, respectively. The extract also showed satisfactory dose-dependent DPPH radical scavenging activity with an IC50 value of 0.675 mg/mL. This study reveals the correct identity of the Indian Fusarium isolates based on multigene phylogeny and also throws light on BEA production potential, suggesting their possible applicability in the medicine, agriculture and industry.

Diaporthe citri: A Fungal Pathogen Causing Melanose Disease

Citrus melanose is a fungal disease caused by Diaporthe citri F.A. Wolf. It is found in various citrus-growing locations across the world. The host range of D. citri is limited to plants of the Citrus genus. The most economically important hosts are Citrus reticulata (mandarin), C. sinensis (sweet orange), C. grandis or C. maxima (pumelo), and C. paradisi (grapefruit). In the life cycle of D. citri throughout the citrus growing season, pycnidia can be seen in abundance on dead branches, especially after rain, with conidia appearing as slimy masses discharged from the dead twigs. Raindrops can transmit conidia to leaves, twigs, and fruits, resulting in disease dispersion throughout small distances. Persistent rains and warm climatic conditions generally favor disease onset and development. The melanose disease causes a decline in fruit quality, which lowers the value of fruits during marketing and exportation. High rainfall areas should avoid planting susceptible varieties. In this article, information about the disease symptoms, history, geographic distribution, epidemiology, impact, and integrated management practices, as well as the pathogen morphology and identification, was reviewed and discussed.

FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/blast.php) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

DNA Sequence-Based Identification of Fusarium: A Work in Progress

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent's identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue (Torres-Cruz et al. 2022), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

Deciphering β-tubulin gene of carbendazim resistant Fusarium solani isolate and its comparison with other Fusarium species

Exploration of molecular structure of β-tubulin is key to understand mechanism of action of carbendazim since its activity depends on strong binding to β-tubulin. Resistance against the fungicide is often associated with mutation in β-tubulin gene. A full-length (1619 bp) β-tubulin gene has been cloned and sequenced from a carbendazim resistant and a sensitive isolates of F. solani isolated from agricultural fields of Murshidabad (24.23 °N, 88.25 °E), West Bengal, India. Phylogenetic position of the isolates was confirmed using internal transcribed spacer and β-tubulin gene sequences. In the β-tubulin based phylogenetic tree, Fusarium species with available data were clustered in nine species complexes and members of both F. solani species complex and F. fujikuroi species complex were distributed into three clades each. The β-tubulin gene of F. solani was found to be shortest due to least number of non-coding sequences indicating its primitiveness among the Fusarium species. The coding region (G + C 58.54%) was organized into five exons. The protein has 446 amino acid, 49.834 KD molecular weight and 4.64 isoelectric point. Amino acid sequence of the resistant and the sensitive isolates were identical, suggesting that the mechanism of carbendazim resistance in the F. solani isolate was not due to point mutation in β-tubulin gene. The secondary and tertiary structure of β-tubulin were similar in all the species except F. oxysporum f.sp. cubense. The identification of binding sites for GDP, carbendazim and α-tubulin would resolve how carbendazim prevents tubulin polymerization. All the data are useful to design tubulin-targeted fungicide with better performance.

Fusarium species isolated from post-hatchling loggerhead sea turtles (Caretta caretta) in South Africa

Species in the Fusarium solani species complex are fast growing, environmental saprophytic fungi. Members of this genus are filamentous fungi with a wide geographical distribution. Fusarium keratoplasticum and F. falciforme have previously been isolated from sea turtle nests and have been associated with high egg mortality rates. Skin lesions were observed in a number of stranded, post-hatchling loggerhead sea turtles (Caretta caretta) in a rehabilitation facility in South Africa. Fungal hyphae were observed in epidermal scrapes of affected turtles and were isolated. The aim of this study was to characterise the Fusarium species that were isolated from these post-hatchling loggerhead sea turtles (Caretta caretta) that washed up on beaches along the South African coastline. Three gene regions were amplified and sequenced, namely the internal transcribed spacer region (ITS), a part of the nuclear large subunit (LSU), and part of the translation elongation factor 1 α (tef1) gene region. Molecular characteristics of strains isolated during this study showed high similarity with Fusarium isolates, which have previously been associated with high egg mortality rates in loggerhead sea turtles. This is the first record of F. keratoplasticum, F. falciforme and F. crassum isolated from stranded post-hatchling loggerhead sea turtles in South Africa.

A-to-I mRNA editing controls spore death induced by a fungal meiotic drive gene in homologous and heterologous expression systems

Spore killers are meiotic drive elements that can block development of sexual spores in fungi. In the maize ear rot and mycotoxin-producing fungus Fusarium verticillioides, a spore killer called SkK has been mapped to a 102-kb interval of chromosome V. Here, we show that a gene within this interval, SKC1, is required for SkK-mediated spore killing and meiotic drive. We also demonstrate that SKC1 is associated with at least four transcripts, two sense (sense-SKC1a and sense-SKC1b) and two antisense (antisense-SKC1a and antisense-SKC1b). Both antisense SKC1 transcripts lack obvious protein-coding sequences and thus appear to be non-coding RNAs. In contrast, sense-SKC1a is a protein-coding transcript that undergoes A-to-I editing to sense-SKC1b in sexual tissue. Translation of sense-SKC1a produces a 70 amino acid protein (Skc1a), whereas translation of sense-SKC1b produces an 84 amino acid protein (Skc1b). Heterologous expression analysis of SKC1 transcripts shows that sense-SKC1a also undergoes A-to-I editing to sense-SKC1b during the Neurospora crassa sexual cycle. Site directed mutagenesis studies indicate that Skc1b is responsible for spore killing in F. verticillioides and that it induces most meiotic cells to die in N. crassa. Finally, we report that SKC1 homologs are present in over 20 Fusarium species. Overall, our results demonstrate that fungal meiotic drive elements like SKC1 can influence the outcome of meiosis by hijacking a cell's A-to-I editing machinery and that the involvement of A-to-I editing in a fungal meiotic drive system does not preclude its horizontal transfer to a distantly related species.

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.

Fusarium chaquense, sp. nov, a novel type A trichothecene-producing species from native grasses in a wetland ecosystem in Argentina

The Chaco wetland is among the most biologically diverse regions in Argentina. In collections of fungi from asymptomatic native grasses (Poaceae) from the wetlands, we identified isolates of Fusarium that were morphologically similar to F. armeniacum, but distinct from it by their production of abundant microconidia. All the isolates had identical, or nearly identical, partial sequences of TEF1 and RPB2. But they were distinct from reference sequences from F. armeniacum and Fusarium species closely related to it. Phylogenetic analysis of 34 full-length housekeeping gene sequences retrieved from whole genome sequences of three Chaco wetland isolates, 29 genes resolved the isolates as an exclusive clade within the F. sambucinum species complex. Based on results of the morphological and phylogenetic analysis, we concluded that the Chaco wetland isolates are a distinct and novel species, herein described as Fusarium chaquense, sp. nov., which is closely related to F. armeniacum. F. chaquense in culture can produce the trichothecenes T-2 and HT-2 toxin, neosolaniol, diacetoxyscirpenol, and monoacetoxyscirpenol, as well as beauvericin and the pigment aurofusarin. Genome sequence analysis also revealed the presence of three previously described loci required for trichothecene biosynthesis. This research represents the first study of Fusarium in a natural ecosystem in Argentina.

Activity of a SDHI fungicide penflufen and the characterization of natural-resistance in Fusarium fujikuroi

The occurrence of bakanae disease of rice caused by the fungus Fusarium fujikuroi in Zhejiang Province has become increasingly aggravated in recent years, concomitant with the development of resistance to the widely applied fungicides, prochloraz and phenamacril. In this study, the activity of a novel succinate dehydrogenase inhibitor (SDHI) fungicide, penflufen, against different fungi was evaluated in addition to the potential of penflufen in controlling F. fujikuroi infections. Penflufen exhibited good bioactivity against F. fujikuroi, but weak activity against Fusarium spp. and other investigated plant-pathogenic fungi including Colletotrichum spp. In addition to inhibiting mycelial growth, penflufen effectively inhibited F. fujikuroi conidium production. For germination, penflufen could effectively inhibit that of small conidia, but only delay the germination of large conidia. In addition, the sensitivity to penflufen among 100 F. fujikuroi isolates that were collected in areas that were never exposed to SDHIs was determined based on mycelium growth. Sensitivities surprisingly exhibited bimodal distributions, indicating the presence of natural resistance. Cross-resistance was not observed between penflufen in F. fujikuroi and two fungicides that have been extensively applied in field including prochloraz (a DMI) and phenamacril (a 2-cyanoacrylate fungicide), nor with the three SDHIs, fluopyram, benzovindiflupyr, and pydiflumetofen. Additional analysis identified five different point mutations in SDH-A (i.e., at residues 46, 225, 283, 430, and 586) of naturally resistant isolates. These results inform the potential application of the new SDHI fungicide penflufen for managing crop diseases and understanding possible resistance mechanisms among pathogens.

Identification and First Report of Fusarium andiyazi Causing Sheath Rot of Zizania latifolia in China

Zizania latifolia is a perennial plant native to East Asia. The swollen culm of Z. latifolia is a popular vegetable and traditional herbal medicine consumed in China and some other Asian countries. From 2019 to 2021, a sheath rot disease was found in Zhejiang Province of China. Symptoms mainly occurred in the leaf sheath showing as brown necrotic lesions surrounded by yellow halos. The pathogen fungal isolates were isolated from the affected sheaths. Ten representative isolates were selected for morphological and molecular identification by phylogenetic analyses of the translation elongation factor 1-α (TEF1) and the RNA polymerase II subunit beta (RPB2) gene regions. Based on the combined datasets, the fungal isolates were identified as Fusarium andiyazi. Koch’s postulates were confirmed by pathogenicity test, re-isolation and re-identification of the fungal isolates. To the best of our knowledge, this is the first report of sheath rot caused by F. andiyazi in Z. latifolia in China.

Genetic structure of Fusarium verticillioides populations from maize in Iran

Fusarium verticillioides is one of the most important fungal pathogens of maize since it causes severe yield losses and produces the mycotoxins fumonisins that represent a major concern for human and animal health. Information about genetic diversity and population structure of fungal pathogens is essential for developing disease management strategies. The aim of this research was to investigate the genetic structure of F. verticillioides isolated from different provinces of Iran through determination of mating type idiomorphs, phylogenetic analyses based on translation elongation factor-1 alpha (EF-1α), RNA Polymerase II Subunit (RPB2), beta-tubulin (tub2) and Calmodulin (cmdA) genes and genetic diversity analyses based on 6 simple-sequence repeats (SSRs). Both mating types were detected in Iranian populations of F. verticillioides, particularly in Qazvin and Khuzestan, with equal frequency, which highlighted that sexual reproduction is favorable under field conditions. However, the linkage disequilibrium indices did not support the hypothesis of random mating in Khuzestan and Fars. Although assessment of nucleotide diversity based on housekeeping genes showed low level of variation among strains, genotype diversity based on SSRs revealed a high level of genetic diversity within Iranian populations. AMOVA analysis highlighted that the genetic variation of F. verticillioides in Iran was mainly distributed within population of a single area (97%), while a small proportion of genetic variation (3%) resided among populations. These patterns of variation are likely explained by the continuous gene flow among populations isolated from different areas. On the other hand, principal coordinate analysis indicated that the distribution of genetic variation among populations could be explained by the geographical distances. Consequently, to reduce pathogen gene flow among regions, the quarantine processes in Iran should be intensified.

A second capsidless hadakavirus strain with 10 positive-sense single-stranded RNA genomic segments from Fusarium nygamai

A unique capsidless virus with a positive-sense, single-stranded RNA genome (hadakavirus 1, HadV1), a member of the extended picorna-like supergroup, was isolated previously from the phytopathogenic fungus Fusarium oxysporum. Here, we describe the molecular and biological characterisation of a second hadakavirus strain from Fusarium nygamai, which has not been investigated in detail previously as a virus host. This virus, hadakavirus 1 strain 1NL (HadV1-1NL), has features similar to the first hadakavirus, HadV1-7n, despite having a different number of segments (10 for HadV1-1NL vs. 11 for HadV1-7n). The 10 genomic RNA segments of HadV1-1NL range in size from 0.9 kb to 2.5 kb. All HadV1-1NL segments show 67% to 86% local nucleotide sequence identity to their HadV1-7n counterparts, whereas HadV1-1NL has no homolog of HadV1-7n RNA8, which encodes a zinc-finger motif. Another interesting feature is the possible coding incapability of HadV1-1NL RNA10. HadV1-1NL was predicted to be capsidless based on the RNase A susceptibility of its replicative form dsRNA. Phenotypic comparison of multiple virus-infected and virus-free single-spore isolates indicated asymptomatic infection by HadV1-1NL. Less-efficient vertical transmission via spores was observed as the infected fungal colonies from which the spores were derived became older, as was observed for HadV1-7n. This study shows a second example of a hadakavirus that appears to have unusual features.

Phylogeny and Mycotoxin Profile of Pathogenic Fusarium Species Isolated from Sudden Decline Syndrome and Leaf Wilt Symptoms on Date Palms (Phoenix dactylifera) in Tunisia

In 2017–2018, extensive symptoms of sudden decline and fruit rot were observed on date palms in southern Tunisia. Samples of diseased plants were randomly collected in six localities. Based on morphological identification, Fusarium was the most frequent fungal genus detected. A sequencing of translation elongation factor, calmodulin, and second largest subunit of RNA polymerase II genes was used to identify 63 representative Fusarium strains at species level and investigate their phylogenetic relationships. The main species detected was Fusarium proliferatum, and at a much lesser extent, Fusarium brachygibbosum, Fusarium caatingaense, Fusarium clavum, Fusarium incarnatum, and Fusarium solani. Pathogenicity on the Deglet Nour variety plantlets and the capability to produce mycotoxins were also assessed. All Fusarium species were pathogenic complying Koch’s postulates. Fusarium proliferatum strains produced mainly fumonisins (FBs), beauvericin (BEA), and, to a lesser extent, enniatins (ENNs) and moniliformin (MON). All F. brachygibbosum strains produced low levels of BEA, diacetoxyscirpenol, and neosolaniol; two strains produced also T-2 toxin, and a single strain produced HT-2 toxin. Fusarium caatingaense, F. clavum, F. incarnatum produced only BEA. Fusarium solani strains produced MON, BEA, and ENNs. This work reports for the first time a comprehensive multidisciplinary study of Fusarium species on date palms, concerning both phytopathological and food safety issues.

Water distribution systems in Sardinian hospitals host invasive clonal lineages of the Fusarium oxysporum and Fusarium solani species complexes

Several Fusarium species cause disease on human hosts, including commonly fatal infections in immunocompromised individuals. Recently, cases of hospitalized patients affected by fusaria were reported in the Tyrrhenian Island of Sardinia, Italy. To precisely characterize the Fusarium species and haplotypes present in hospitals of the region, a multilocus DNA sequence typing (MLST) approach was applied. Water distribution systems in four departments belonging to four Sardinian hospitals were sampled. Fusarium species and sequence types (STs) were identified using MLST based on sequences of the elongation factor 1-alpha (EF-1α) gene, the nuclear ribosomal DNA intergenic spacer region (IGS rDNA), and/or a portion of the second-largest subunit of RNA polymerase (RPB2) gene. The majority of isolates obtained from Sardinian hospitals (90.7%) were identified as representatives of the Fusarium oxysporum species complex (FOSC), followed by those of the F. solani species complex (FSSC) (8.2%), and F. dimerum (1.1% of all isolates). Ten STs were found among the FOSC and FSSC, with more than 60% of the isolates identified as either FOSC ST 33 or FSSC 1 (F. petroliphilum). More than half of the FOSC isolates obtained from the water systems in all four hospitals belonged to the worldwide distributed clonal lineage ST 33. This haplotype is the most prevalent among the FOSC in different countries, being responsible for the vast majority of cases of human fusariosis.