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Applied and environmental microbiology (2023). doi:10.1128/aem.00078-23, Published by American Society for Microbiology, Washington, DC [u.a.]

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.

There is a gradual shift from representing a species' genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The "intronless" mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the "host" gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.

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 (

novel fungal species systematics

Eumycetoma is a chronic fungal infection characterised by large subcutaneous masses and the presence of sinuses discharging coloured grains. The causative agents of black-grain eumycetoma mostly belong to the orders Sordariales and Pleosporales. The aim of the present study was to clarify the phylogeny and taxonomy of pleosporalean agents, viz. Madurella grisea, Medicopsis romeroi (syn.: Pyrenochaeta romeroi), Nigrograna mackinnonii (syn. Pyrenochaeta mackinnonii), Leptosphaeria senegalensis, L. tompkinsii, and Pseudochaetosphaeronema larense. A phylogenetic analysis based on five loci was performed: the Internal Transcribed Spacer (ITS), large (LSU) and small (SSU) subunit ribosomal RNA, the second largest RNA polymerase subunit (RPB2), and translation elongation factor 1-alpha (TEF1) gene. In addition, the morphological and physiological characteristics were determined. Three species were well-resolved at the family and genus level. Madurella grisea, L. senegalensis, and L. tompkinsii were found to belong to the family Trematospheriaceae and are reclassified as Trematosphaeria grisea comb. nov., Falciformispora senegalensis comb. nov., and F. tompkinsii comb. nov. Medicopsis romeroi and Pseudochaetosphaeronema larense were phylogenetically distant and both names are accepted. The genus Nigrograna is reduced to synonymy of Biatriospora and therefore N. mackinnonii is reclassified as B. mackinnonii comb. nov. Mycetoma agents in Pleosporales were phylogenetically quite diverse despite their morphological similarity in the formation of pycnidia, except for the ascosporulating genus Falciformispora (formerly in Leptosphaeria). Most of the species diagnosed from human mycetoma were found to be related to waterborne or marine fungi, suggesting an association of the virulence factors with oligotrophism or halotolerance.

In the present study, we studied the effect of cattle diet on the survival of E. coli O157:H7 in manure from dairy cattle subjected to 6 different feeding regimes consisting of 3 different roughage types and 2 levels of crude protein concentrates. In addition, the rate of survival of E. coli O157:H7 in manure-amended soil as a function of manure type (manure vs. slurry) and dairy farm management (organic vs. conventional) was determined. The roughage type affected significantly the decline rate of E. coli O157:H7: decline was faster in manures with relative higher pH and fiber content. Decline was faster in slurry compared to manure and in organic slurry compared to conventional slurry.