Dominik Begerow

Fungi represent the largest group of plant pathogens, causing significant economic losses in agriculture and forestry worldwide. Species of the genus Exobasidium ( Exobasidiales , Basidiomycota ) are considered pathogens of plants from the order Ericales . While Exobasidium species notably impact tea and fruit production, their complete life cycles remain poorly understood, which hampers their management. These species are characterized by a dikaryotic parasitic stage tightly associated with living host tissues and a haploid, yeast-like saprotrophic stage. The prevalence, ecological significance, and potential contribution of this saprotrophic stage to the persistence of Exobasidium outside living host plants remain understudied. In this study, we confirmed the presence of several Exobasidium species in the leaf phyllosphere of five broad-leaved tree species in Central Europe using both cultivation and environmental DNA ITS2-based approaches. Additionally, we describe a new species without a known parasitic phase, E. phylloplanum sp. nov ., along with its physiological description and annotated genome. Environmental DNA surveys, using the GlobalFungi database, revealed that E. phylloplanum is not only common locally but also the most frequently detected Exobasidium lineage worldwide. This broad ecological amplitude contrasts with the narrow host specificity typical of parasitic congeners, suggesting that E. phylloplanum has adapted to a generalist saprotrophic life-history strategy. Our findings demonstrate that Exobasidium species can persist saprotrophically on diverse hosts, suggesting a broader ecological role and higher diversity than previously recognized. This research elucidates the diverse ecological roles of Exobasidium species and suggests that further genomic studies could reveal the genetic factors that underpin the different life strategies within this genus.

A rare smut fungus, Anthracoidea pseudofoetidae, is reported for the first time from Russia, based on a specimen from the Altai Republic. Carex enervis is a new host record for A. pseudofoetidae. Two new records for Greece, Microbotryum duriaeanum and M. moenchiae-manticae, and a new record for Morocco, Microbotryum moehringiae, are also presented. Microbotryum moehringiae is recorded for the first time from Africa. Cerastium brachypetalum subsp. roeseri is a new host record for Microbotryum duriaeanum. New molecular data are provided for these smut fungi. Updated phylogenetic trees for Anthracoidea and Microbotryum are also given.

Convergent evolution is the phenomenon of similar traits evolving independently in different lineages of the tree of life. Studying convergent evolution provides an excellent opportunity to understand natural selection for specific traits and physiological constraints to evolution that allow a broadened view on evolutionary mechanisms as a whole. Smut fungi, a polyphyletic group of plant-parasitic fungi with a specific infection and life cycle pattern, are a prime example of convergent evolution. Most notably, smut fungi in the genus Microbotryum that belongs to the subdivision Pucciniomycotina and smut fungi from the subdivision Ustilaginomycotina show strong similarities despite millions of years of independent evolution. However, the conceptual connections drawn between the two groups are scarce, thereby limiting the opportunities for exploring convergent evolution between these taxa. To facilitate knowledge exchange within the research community, we provide a summary of databases, molecular and biological tools and a brief introduction to the structure of populations and the characteristics of host specificity in both groups. Furthermore, we compare the life cycles and research emphases between the two groups. The comparisons are supplemented with an analysis of genome composition and gene function, which aims to advance research on the convergent evolution of smut fungi using existing data.

Background: The Ustilaginales comprise hundreds of plant-parasitic fungi with a characteristic life cycle that directly links sexual reproduction and parasitism: One of the two mating-type loci codes for a transcription factor that not only facilitates mating, but also initiates the infection process. However, several species within the Ustilaginales have no described parasitic stage and were historically assigned to the genus Pseudozyma. Molecular studies have shown that the group is polyphyletic, with members being scattered in various lineages of the Ustilaginales. Together with recent findings of conserved fungal effectors in these non-parasitic species, this raises the question if parasitism has been lost recently and in multiple independent events or if there are hitherto undescribed parasitic stages of these fungi. Results: In this study, we sequenced genomes of five Pseudozyma species together with six parasitic species from the Ustilaginales to compare their genomic capability to perform two central functions in sexual reproduction: mating and meiosis. While the loss of sexual capability is assumed in certain lineages and asexual species are common in Asco- and Basidiomycota, we were able to successfully annotate potentially functional mating and meiosis genes that are conserved throughout the whole group. Conclusion: Our data suggest that at least the key functions of a sexual lifestyle are maintained in the analyzed genomes, challenging the current understanding of the so-called asexual species with respect to their evolution and ecological role.

Anthracoidea species are highly host-specific smut fungi. Their host range is restricted to a single sedge species or sedge species belonging to the same or closely related sections. The species on Carex obtusata was referred to as Anthracoidea caryophylleae. However, the hosts of A. caryophylleae were reduced to carices in Carex sect. Mitratae, in its traditional circumscription. In the most recently proposed classification of Carex, C. obtusata has been placed within the Capitata Clade of C. subgen. Euthyceras. In order to clarify the taxonomic status of the Anthracoidea species on C. obtusata, we conducted a molecular study of specimens on C. obtusata and C. caryophyllea, using LSU rDNA sequences. It was found that the Anthracoidea species on C. obtusata is distinct from A. caryophylleae. A new species, Anthracoidea obtusatae on C. obtusata, is described and illustrated from Russia, based on a specimen from the Altay Mts. Its phylogenetic placement and affinities in Anthracoidea are analyzed. Anthracoidea obtusatae is distributed in Central Asia—the Northern Tian Shan Range (Zailiysky Alatau Range and Ketmen Ridge) and the Russian and Mongolian Altay Mts. A morphological examination of a specimen of Anthracoidea on C. obtusata from Canada found that its spore morphology did not match that of A. obtusatae. Additional collections and molecular study are required to clarify the taxonomic status of the North American Anthracoidea species on C. obtusata.

Heat resistance is the ability to survive short, extreme temperature stresses, exceeding the own growth temperature by far. Despite their occurrence in natural substrates and their relevance for the food and healthcare industry, the diversity of fungi with heat resistance abilities is poorly studied. Sampling of boreal forest soils in Canada in combination with a heat-shock treatment (75 °C, 30 min) yielded, among others, four heat resistant, mesophilic fungal isolates. Based on rDNA barcode sequences, the novel isolates were assigned to Basidiomycota. In this study, we use macromorphological and micromorphological observations, cultivation assays and comparative genomics for physiological characterization, interspecific differentiation, and phylogenetic placement of these isolates. A phylogeny of 38 single-copy orthologous genes, an orthology analysis, and septal pore type analysis revealed the isolates as representatives of two new basidiomycetous species of the novel class Peribolosporomycetes, a sister lineage to all other members of Ustilaginomycotina. Further genomic and phenotypic data support two different species (Peribolospora kevripleyi, Peribolospora baueri), which are heat resistant and osmotolerant.

In forest ecosystems, decomposition is essential for carbon and nutrient cycling and therefore a key process for ecosystem functioning. During the decomposition process, litter chemistry, involved decomposer organisms, and enzymatic activity change interdependently. Chemical composition of the litter is the most complex and dynamic component in the decomposition process and therefore challenging to assess holistically. In this study, we aimed to characterize chemical shifts during decomposition and link them to changes in decomposer fungal activity. We characterized the chemical composition of freshly fallen autumn leaves of European beech (Fagus sylvatica) and the corresponding leaf litter after 1 year of decomposition by proton nuclear magnetic resonance spectroscopy. We further tested the applicability of spiking experiments for qualitative and quantitative characterization of leaves and litter chemistry. The composition and transcriptional activity of fungal communities was assessed by high-throughput Illumina sequencing in the same litter samples. We were able to distinguish freshly fallen leaves from 1-year-old litter based on their chemical composition. Chemical composition of leaves converged among regions with progressing decomposition. Fungal litter communities differed in composition among regions, but they were functionally redundant according to the expression of genes encoding litter degrading enzymes (CAZymes). Fungi of the saprotrophic genera Mycena and Chalara correlated with transcription of litter-degrading CAZymes in 1-year-old litter. Forestry measures influenced the diversity and transcription rate of the detected CAZymes transcripts in litter. Their expression was primarily predicted by composition of the soluble chemical fraction of the litter. Environmental NMR fingerprints thus proved valuable for inferring ecological contexts. We propose and discuss a holistic framework to link fungal activity, enzyme expression, and chemical composition.