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Through partitioning of ecological niches, several fungi are able to coexist on the same host crop. In (partial) absence of niche partitioning, competitive exclusion among fungi can occur. Competitive exclusion is one of the bases for biocontrol. We investigated fungal correlations, in terms of relative abundance of the fungi, in pre-harvest maize, as a natural ecosystem model. Internal mycobiome fungal relative abundance of maize was used to establish correlations. The maize had been harvested from dry and wet agro-ecological zones of Zambia. The relative abundances of the fungal genera were determined using DNA amplicon sequencing. For this study, positive or absence of correlations between fungal genera signified good niche partitioning (co-existence), whereas negative correlations signified poor niche partitioning and potential for competitive exclusion. When species compete within one niche (competitive exclusion), we may expect to detect higher levels of mycotoxins—since mycotoxins are considered antagonistic agents aimed at defending or invading an ecological niche. To estimate the importance of mycotoxins in competitive exclusion, we measured the influence of the fungal correlations on levels of fumonisin-B1 (FB1) in the maize. FB1 data were derived from a previous study on the maize, determined by HPLC. Results showed that Sarocladium and Stenocarpella had the strongest significant negative correlation with Fusarium, suggesting poor niche partitioning and potential for antagonism of these genera with Fusarium. Furthermore, higher levels of Stenocarpella resonated with lower levels of FB1 and vice versa. It was also observed that, when Sarocladium was in low abundance (< 10%), the frequency of detection of higher levels of FB1 (> 100 µg kg−1) in the pre-harvest maize was highest.

In this project, the infection process of Fusarium oxysporum in gerbera was studied using plant pathogenic Fusarium oxysporum marked with green fluorescent protein (GFP). This method has also been used to investigate the effect of beneficial microorganisms from biopesticides on the speed of Fusarium infection in gerbera. Experiments in gerbera greenhouses with control of Fusarium/Verticillium during gerbera cultivation with five different biopesticides have also been carried out at two companies producing gerbera flowers. Research shows that antagonistic microorganisms can delay the spread of Fusarium oxysporum in gerbera plant., In dit project is het infectieproces van Fusarium oxysporum in gerbera bestudeerd met behulp van plantpathogene Fusarium oxysporum gemarkeerd met groen fluorescent eiwit (GFP). Met deze methode is er ook onderzoek gedaan naar het effect van nuttige micro-organismen uit biopesticiden op snelheid van de Fusarium infectie in gerbera. Ook zijn er praktijkproeven uitgevoerd bij twee bedrijven met beheersing van Fusarium/ Verticillium gedurende de teelt van gerbera met vijf verschillende biopesticiden. Uit onderzoek blijkt dat antagonistische micro-organismen de infectie van Fusarium oxysporum in gerbera planten kunnen vertragen.

Aspergillus section Flavi (Flavi) is a diverse group of fungal species whose common members include A. flavus and A. parasiticus. These are well-known for the production of aflatoxin (AF) B and G and other toxic metabolites, like cyclopiazonic acid (CPA). They are saprophytic soil dwellers and also become crop opportunistic epiphytes. The consequence is contamination of the crop with mycotoxins, such as carcinogenic AF. We investigated the Flavi community structure of maize and that of their surrounding soil, including their mycotoxigenicity. Furthermore, we investigated the link of the maize Flavi diversity with preharvest maize AF levels. The study was carried out in four selected districts of Zambia, in a low rainfall zone. The Flavi characterisation was triphasic, involving morphological (colony colour and sclerotia formation), metabolic (AF and CPA production) and genetic (calmodulin gene polymorphism) analyses. Flavi abundance was determined by dilution plate technique on modified rose Bengal agar. Results showed that Flavi communities on maize and in soil differed. Maize had a higher Flavi species diversity than soil. A. parasiticus dominated the soil community by frequency of field appearance (85%), while maize was dominated by A. minisclerotigenes (45%). CPA-producers with or without AF production dominated the maize (65%) while producers of only AF (B/G) dominated the soil (88%). The ratio between maize A. parasiticus and A. minisclerotigenes abundance seemed to have had a bearing on the levels of AF in maize, with a ratio close to 1:1 having higher levels than a pure community of either A. parasiticus or A. minisclerotigenes.

Exploiting wheat cultivars with stable resistance to Fusarium Head blight (FHB) and toxin accumulation is a cost-effective and environmentally friendly strategy to reduce the risk of yield losses and contamination with mycotoxins. To facilitate the deployment of stable cultivar resistance, we evaluated FHB resistance and resistance to mycotoxin accumulation in 410 wheat lines bred by local breeders from four major wheat growing regions in China after natural infection at three distinct locations (Hefei, Yangzhou and Nanping). Significant differences in disease index were observed among the three locations. The disease indexes (DI’s) in Nanping were the highest, followed by Yangzhou and Hefei. The distribution of DI’s in Yangzhou showed the best discrimination of FHB resistance in cultivars. Growing region and cultivar had significant effect on DI and mycotoxins. Among the climate factors, relative humidity and rainfall were the key factors resulting in the severe disease. Even though most cultivars were still susceptible to FHB under the strongly conducive conditions applied, the ratio of resistant lines increased in the Upper region of the Yangtze River (UYR) and the Middle and Lower Region of the Yangtze River (MLYR) between 2015 and 2019. Deoxynivalenol (DON) was the dominant mycotoxin found in Hefei and Yangzhou, while NIV was predominant in Nanping. Disease indexes were significantly correlated with DON content in wheat grain.

Binnen het Uireka werkpakket Fusarium zijn in 2020 en 2021 de volgende stappen gezet: • Met een biotoets op uienbollen zijn in Uireka (1) verzamelde isolaten van Fusariumoxysporum, F. solani en F. proliferatum getest op pathogeniteit: F. oxysporum formaspeciales cepae blijkt het sterkste pathogeen, maar ook niet pathogene F. oxysporumkomen voor. • Vergelijkingen van de genomen van F. oxysporum f.sp. cepae en niet ui-pathogenen heeftlaten zien welke gen- en allelsequenties in het DNA uniek en verantwoordelijk zijn voor de pathogeniteit van een schimmel-isolaat. Op deze specifieke sequenties is een kwantitatieve op TaqMan gebaseerde diagnostische toets ontwikkeld waarmee het risico op fusarium rot gekwantificeerd kan worden. Door de test te combineren met een kweekstap op selectief medium, ontstaat een kwantitatieve Bio-TaqMan die de Fusarium dichtheid vanaf enkele sporen per gram kan vaststellen. • De Bio-TaqMan diagnostische toets is geschikt voor de detectie van F. oxysporum forma speciales cepae in plantmateriaal en in grond. In het overgrote deel van de in 2020 en 2021 verzamelde uien blijkt F. oxysporum f.sp. cepae aanwezig. In de grond bleek tijdens seizoen2021 in de uienteelt het pathogeen gemiddeld in 50-voud toe te nemen in de periode van planten tot aan de oogst. • Voor reststromen: Tijdens vergisting duurt het 3 weken om circa 99.99% van F. oxysporumf.sp. cepae te doden, maar bij continue doorstroom van materiaal in de vergister is er dus een behoorlijke kans dat levend materiaal de vergister verlaat. Bij compostering is na 1cyclus (8 a 10 dagen)meer dan 99.99% van de schimmel afgedood, na twee composteringscycli is er geen levend Fusarium materiaal meer aanwezig.

As the honey bee and bumble bee may suffer from the same or related microbial pathogens, cross contamination from commercially reared Bombus spp. to honey bees and wild bumble bees and vice versa is a major concern. Honey bee-collected pollen to feed commercially reared Bombus spp. is a potential risk. Nosema spp. is a fungal pathogen in bees. In this study, we developed new quantitative detection tools based on the detection of RNA using a TaqMan-based RT-qPCR for Nosema ceranae and Nosema apis, with extraction controls based on the actin gene of honey bees and bumble bees, respectively. These tools were subsequently applied to study the epidemiology of N. ceranae, a main disease in honey bees. We screened gamma radiation and cold treatment sterilisation for their efficacy to kill N. ceranae spores fed in sugar water and in pollen to honey bees and bumble bees, respectively. N. ceranae infection in adult bumble bees was checked. Spores passing the inter-alimentary track were found but no infection was observed. N. ceranae spores were fed to honey bees. Their presence and multiplication were demonstrated, showing the spores were both viable and infectious. Our results indicate that N. ceranae found in honey bees cannot infect commercially reared bumble bees (Bombus terrestris) and, that gamma radiation effectively kills N. ceranae. The highly specific and sensitive molecular assays developed, were exploited to detect N. ceranae in pollen and faeces, which would allow more comprehensive epidemiological studies on this important pathogen.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

The Fusarium fujikuroi species complex (FFSC) and F. oxysporum species complex (FOSC) are two related groups of plant pathogens causing a wide diversity of diseases in agricultural crops world wide. The aims of this study are (1) to clarify the phylogeny of the FFSC, (2) to identify potential deviation from tree-like evolution, (3) to explore the value of using mitogenomes for these kinds of analyses, and (4) to better understand mitogenome evolution. In total, we have sequenced 24 species from the FFSC and a representative set of recently analyzed FOSC strains was chosen, while F. redolens was used as outgroup for the two species complexes. A species tree was constructed based on the concatenated alignment of seven nuclear genes and the mitogenome, which was contrasted to individual gene trees to identify potential conflicts. These comparisons indicated conflicts especially within the previously described African clade of the FFSC. Furthermore, the analysis of the mitogenomes revealed the presence of a variant of the large variable (LV) region in FFSC which was previously only reported for FOSC. The distribution of this variant and the results of sequence comparisons indicate horizontal genetic transfer between members of the two species complexes, most probably through introgression. In addition, a duplication of atp9 was found inside an intron of cob, which suggests that even highly conserved mitochondrial genes can have paralogs. Paralogization in turn may lead to inaccurate single gene phylogenies. In conclusion, mitochondrial genomes provide a robust basis for phylogeny. Comparative phylogenetic analysis indicated that gene flow among and between members of FFSC and FOSC has played an important role in the evolutionary history of these two groups. Since mitogenomes show greater levels of conservation and synteny than nuclear regions, they are more likely to be compatible for recombination than nuclear regions. Therefore, mitogenomes can be used as indicators t

Background: Cucumber Fusarium wilt, caused by Fusarium oxysporum f. Sp. Cucumerinum (Foc), is one of the most notorious diseases in cucumber production. Our previous research showed the virulence of Foc significantly increases over consecutive rounds of infection in a resistant cultivar. To understand the virulence variation of Foc under host pressure, the mildly virulent strain foc-3b (WT) and its virulence-enhanced variant Ra-4 (InVir) were selected and their transcriptome profiles in infected cucumber roots were analyzed at 24 h after inoculation (hai) and 120 hai. Results: A series of differentially expressed genes (DEGs) potentially involved in fungal pathogenicity and pathogenicity variation were identified and prove mainly involved in metabolic, transport, oxidation-reduction, cell wall degradation, macromolecules modification, and stress and defense. Among these DEGs, 190 up- and 360 down-regulated genes were expressed in both strains, indicating their importance in Foc infection. Besides, 286 and 366 DEGs showed up-regulated expression, while 492 and 214 showed down-regulated expression in InVir at 24 and 120 hai, respectively. These DEGs may be involved in increased virulence. Notably, transposases were more active in InVir than WT, indicating transposons may contribute to adaptive evolution. Conclusions: By a comparative transcriptome analysis of the mildly and highly virulent strains of Foc during infection of cucumber, a series of DEGs were identified that may be associated with virulence. Hence, this study provides new insight into the transcriptomic profile underlying pathogenicity and virulence differentiation of Foc.

The Fusarium solani species complex (FSSC) is the most common group of fusaria associated with superficial and life-threatening infections in humans. Here we formally introduce Fusarium metavorans sp. nov., widely known as FSSC6 (Fusarium solani species complex lineage 6), one of the most frequent agents of human opportunistic infections. The species is described with multilocus molecular data including sequences of internal transcribed spacer region (ITS), portions of the translation elongation factor 1-a gene (TEF1), and the partial RNA polymerase II gene (rPB2). A phylogenetic approach was used to evaluate species delimitation. Topologies of the trees were concordant. Phylogenetic analyses suggest that the FSSC consists of three major clades encompassing a large number of phylogenetic species; Fusarium metavorans corresponds to phylogenetic species 6 within FSSC clade 3. The species has a global distribution and a wide ecological amplitude, also including strains from soil and agents of opportunistic plant disease; it was also isolated from the gut of the wood-boring cerambycid beetle Anoplophora glabripennis.

Mycopathologia was founded in 1938 to 'diffuse the understanding of fungal diseases in man and animals among mycologists.' This was an important mission considering that pathogenic fungi for humans and animals represent a tiny minority of the estimated 1.5-5 million fungal inhabitants on Earth. These pathogens have diverged from the usual saprotrophic lifestyles of most fungi to colonize and infect humans and animals. Medical and veterinary mycology is the subdiscipline of microbiology that dwells into the mysteries of parasitic, fungal lifestyles. Among the oldest continuing scientific publications on the subject, Mycopathologia had its share of 'classic papers' since the first issue was published in 1938. An analysis of the eight decades of notable contributions reveals many facets of host-pathogen interactions among 183 volumes comprising about 6885 articles. We have analyzed the impact and relevance of this body of work using a combination of citation tools (Google Scholar and Scopus) since no single citation metric gives an inclusive perspective. Among the highly cited Mycopathologia publications, those on experimental mycology accounted for the major part of the articles (36%), followed by diagnostic mycology (16%), ecology and epidemiology (15%), clinical mycology (14%), taxonomy and classification (10%), and veterinary mycology (9%). The first classic publication, collecting nearly 200 citations, appeared in 1957, while two articles published in 2010 received nearly 150 citations each, which is notable for a journal covering a highly specialized field of study. An empirical analysis of the publication trends suggests continuing interests in novel diagnostics, fungal pathogenesis, review of clinical diseases especially with relevance to the laboratory scientists, taxonomy and classification of fungal pathogens, fungal infections and carriage in pets and wildlife, and changing ecology and epidemiology of fungal diseases around the globe. We anticipate that

The density of fungal contamination and the fungal diversity in an indoor swimming pool facility were assessed. A total of 16 surface samples and 6 water samples were analysed by using a combination of different (semi-) selective culture media. Isolated fungal colonies were identified to the genus or species level by sequencing of the internal transcribed spacer (ITS). The highest fungal counts in water and on surfaces were in the recreational pool (17CFU/100mL) and on a flexibeam (5.8CFU/cm2), respectively as compared with low counts (<0.1CFU/cm2) on the diving platform, bench tops and walls. The 357 obtained isolates belonged to 79 species and species complexes, 42 of which known as clinically relevant. Phialophora oxyspora (13.7%) and Phoma spp. (12.3%) were the most frequently identified groups. We demonstrated that despite chlorine treatment and regular cleaning of surfaces both water and surfaces were commonly infested with fungi, including many clinically relevant species.

Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype's determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the fr

Background: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties. Results: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species. Conclusions: The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

Recent studies on a field population of F. graminearum sensu stricto from Argentina revealed an atypical panel of strains identified through PCR genotyping as 15ADON genotypes, but producing high levels of 3ADON. Based on representative strain CBS 139514, we asked if the discrepancy between the trichothecene genotype and chemotype might result from an inter-chemotype recombination of the chemotype-determining genes. To answer this, we sequenced the complete core Tri gene cluster (around 30,200 bp) from this strain and compared its sequence to sequence data of typical type B trichothecene genotypes/chemotypes. Sequence alignment showed that CBS 139514 has an identical sequence within the entire core Tri cluster to the 15ADON genotype. The revealed discrepancy underlines the need for using both molecular and chemical methods for reliable characterization of toxigenic strains of Fusarium.

This study aimed to elucidate the genetic relatedness and epidemiology of 127 clinical and environmental Candida glabrata isolates from Europe and Africa using multilocus microsatellite analysis. Each isolate was first identified using phenotypic and molecular methods and subsequently, six unlinked microsatellite loci were analyzed using automated fluorescent genotyping. Genetic relationships were estimated using the minimum-spanning tree (MStree) method. Microsatellite analyses revealed the existence of 47 different genotypes. The fungal population showed an irregular distribution owing to the over-representation of genetically different infectious haplotypes. The most common genotype was MG-9, which was frequently found in both European and African isolates. In conclusion, the data reported here emphasize the role of specific C. glabrata genotypes in human infections for at least some decades and highlight the widespread distribution of some isolates, which seem to be more able to cause disease than others.

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

The two most common filamentous fungi causing mycotic keratitis are Aspergillus and Fusarium spp. Around 70 Fusarium spp. are involved in causing human infections. In this study, four cases of keratitis in sugarcane farmers in India are being reported, caused by the sugar cane pathogen Fusarium sacchari, a species of the Fusarium fujikuroi species complex. Fusarial keratitis was established by potassium hydroxide/Calcofluor white wet mounts and fungal culture of corneal scrapings on conventional media. Final identification was done by genetic sequencing at CBS-KNAW, Utrecht, The Netherlands. The antifungal susceptibility testing was done using broth microdilution method as per CLSI document M38-A2. Four cases of F. sacchari keratitis were identified. Three of them had trauma with sugarcane leaves, whereas one sugarcane farmer reported trauma by vegetative matter. The morphological similarities among various Fusarium species warrant use of molecular methods for identification of cryptic species. A wide distribution of sugarcane farming could be the possible explanation for emergence of F. sacchari keratitis in India.