Search

Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

Gray mold, caused by Botrytis cinerea is a major cause of post-harvest rot of fresh fruits and vegetables. The utilization of selected microorganisms as biocontrol agents is a promising alternative to effectively control gray mold on tomatoes. The current study was conducted to explore potential biocontrol mechanisms of the Pseudomonas strain to control infections on post-harvest tomatoes. Among the 8 tested bacterial isolates, Pseudomonas protegens ML15 demonstrated antagonistic activity to Botrytis cinerea. Moreover, P. protegens ML15 exhibited the production of siderophores, hydrogen cyanide, ammonia, exopolysaccharides, lipase, biosurfactant, 2,4-diacetylphloroglucinol, and several other antifungal compounds, such as 1-tetradecanol, cyclododecane, 2,4-di-tert-butylphenol, and 2-methyl-1-hexadecanol. A comprehensive genomic analysis of P. protegens ML15 unravels 18 distinct genetic regions with the potential for biosynthesizing secondary metabolites, known for their pivotal role in biocontrol responses against plant pathogens. In vivo, experiments showed that both culture suspension and cell-free supernatant of P. protegens ML15 significantly reduced fungal growth (53.0 ± 0.63%) and mitigated disease development (52.8 ± 1.5%) in cherry tomatoes at four days post-B. cinerea inoculation. During the infection, the application of P. protegens ML15 resulted in the augmentation of total antioxidant, phenolic content, and ascorbic acids content. Thus, our results suggested that P. protegens ML15’s role as a biocontrol agent against B. cinerea-induced postharvest tomato decay achieved through the secretion of antifungal substances, induction of tomato defense responses, and inhibition of mycelial growth of B. cinerea. These findings provide a significant contribution to the ongoing search for alternative, eco-friendly methods of controlling gray mold in fresh products. The utilization of P. protegens ML15 as a biocontrol agent could help to reduce the reliance on chemical fungicides and promote sustainable agriculture practices.

The first genome sequenced of a eukaryotic organism was for Saccharomyces cerevisiae, as reported in 1996, but it was more than 10 years before any of the zygomycete fungi, which are the early-diverging terrestrial fungi currently placed in the phyla Mucoromycota and Zoopagomycota, were sequenced. The genome for Rhizopus delemar was completed in 2008; currently, more than 1000 zygomycete genomes have been sequenced. Genomic data from these early-diverging terrestrial fungi revealed deep phylogenetic separation of the two major clades—primarily plant—associated saprotrophic and mycorrhizal Mucoromycota versus the primarily mycoparasitic or animal-associated parasites and commensals in the Zoopagomycota. Genomic studies provide many valuable insights into how these fungi evolved in response to the challenges of living on land, including adaptations to sensing light and gravity, development of hyphal growth, and co-existence with the first terrestrial plants. Genome sequence data have facilitated studies of genome architecture, including a history of genome duplications and horizontal gene transfer events, distribution and organization of mating type loci, rDNA genes and transposable elements, methylation processes, and genes useful for various industrial applications. Pathogenicity genes and specialized secondary metabolites have also been detected in soil saprobes and pathogenic fungi. Novel endosymbiotic bacteria and viruses have been discovered during several zygomycete genome projects. Overall, genomic information has helped to resolve a plethora of research questions, from the placement of zygomycetes on the evolutionary tree of life and in natural ecosystems, to the applied biotechnological and medical questions.

Abstract Fungi are able to switch between different lifestyles in order to adapt to environmental changes. Their ecological strategy is connected to their secretome as fungi obtain nutrients by secreting hydrolytic enzymes to their surrounding and acquiring the digested molecules. We focus on fungal serine proteases (SPs), the phylogenetic distribution of which is barely described so far. In order to collect a complete set of fungal proteases, we searched over 600 fungal proteomes. Obtained results suggest that serine proteases are more ubiquitous than expected. From 54 SP families described in MEROPS Peptidase Database, 21 are present in fungi. Interestingly, 14 of them are also present in Metazoa and Viridiplantae – this suggests that, except one (S64), all fungal SP families evolved before plants and fungi diverged. Most representatives of sequenced eukaryotic lineages encode a set of 13–16 SP families. The number of SPs from each family varies among the analysed taxa. The most abundant are S8 proteases. In order to verify hypotheses linking lifestyle and expansions of particular SP, we performed statistical analyses and revealed previously undescribed associations. Here, we present a comprehensive evolutionary history of fungal SP families in the context of fungal ecology and fungal tree of life.

There is evidence that education levels have an impact on people's attitudes toward vaccination. The recent COVID-19 pandemic has highlighted the need to maximize vaccinations - one of the most efficient ways to prevent the spread of infectious diseases. Young individuals play a major role in disease transmission due to their intense social life and frequent asymptomatic infections. In this study, a survey of upper secondary school students in Poland was conducted to assess their microbiological awareness depending on subjects that they studied on the extended level and COVID-19 vaccination willingness. Participants learning biology and chemistry on the extended level had significantly higher microbiological awareness. Clear proof of microbiological awareness's influence on vaccination willingness was not found. Although studying biology did not significantly influence students' willingness to be vaccinated, their place of residence did. Students from bigger cities were more willing to get vaccinated. These results show that while science education raises microbiological awareness among upper secondary school students, place of residence, likely through social pressure, is a more important factor influencing vaccination willingness. It is suggested that more effort should be put into educating society as a whole and encouraging vaccination particularly.

Abstract Many social insect species build nests, which differ from the surrounding environment and are often occupied by specific organismal communities. These organisms may interact mutualistically or parasitically with the nest‐builders, or simply co‐occur, being able to survive in these microenvironments. In temperate forests, red wood ants (e.g. Formica polyctena) are known to create distinct, highly developed nests, which consist of large, above‐ground mounds, built primarily out of plant matter collected from the forest litter. The microorganismal communities of such mounds remain understudied. As representatives of Mucoromycota fungi commonly engage in the decomposition process of the forest litter, they would be expected to occur in the mounds. However, it is still not known whether the Mucoromycota community of these ants' nests differ from the one of the surrounding forest litter. In order to distinguish mound‐associated taxa, we characterized Mucoromycota communities of Formica polyctena mounds and the surrounding forest litter. We sampled four sites, twice in a season. Sampled material was plated on agar media and emerging Mucoromycota colonies were identified based on their morphology. Fungal identification was further confirmed using DNA barcoding. In order to compare described communities, PERMANOVA test and non‐metric multidimensional scaling ordinations were used. To distinguish taxa associated with the mounds, multilevel pattern analysis was performed. Our results show that the Mucoromycota community of Formica polyctena's mound differs from the community of the surrounding forest litter. While representatives of Entomortierella lignicola and Absidia cylindrospora clade were found to be associated with the mound environment, representatives of Umbelopsis curvata and Podila verticillata‐humilis clade were associated with forest litter, and were rarely present in the mounds. Our findings strongly suggest that the red wood ants' nest is a specific microenvironment in the temperate forest floor, which is a preferred microhabitat for the mound‐associated Mucoromycota, possibly adapted to live in proximity to ants.

In this study, we decided to test the hypothesis that the fungal biostarter M. flavus used during a 21-day beef dry-aging process significantly impacts the composition of other microorganisms, the profile of volatile compounds, meat hardness characteristics, and, consequently, the sensory quality. The experiments were performed on samples derived from animals crossbred between Holstein–Fresian cows and meat breed bulls. Two groups of samples were studied, including the control group, without biostarter, and a group inoculated with the M. flavus biostarter. Both sample groups were seasoned for 21 days in the dry-aging fridge. The physicochemical parameters (pH, color parameters), the chemical composition of muscle, the determination of the shear force, the profile of volatile compounds (VOCs), and the sensory quality were evaluated after aging. During this study, classical microbiological methods were used to investigate the influence of fungal biostarters on the growth and survival of bacteria and other fungi (e.g., yeasts) during the dry-aging process of beef (DAB). The M. flavus biostarter improved the sensory quality of DAB, allowing high sensory quality to be achieved after just 21 days. This is likely due to the diverse VOCs produced by the fungus, including 1-tetradecanol, 2-nonenal, trans-2-undecenoic acid, and the following esters: formic acid hexyl ester, 10-undecenoic acid methyl ester, and 4-methylpentanoic acid methyl ester. The presence of the biostarter had no significant effect on the number of the bacteria or the survivability of the L. monocytogenes on the meat’s surface in laboratory conditions.

Abstract Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.

Meat aging is a process consisting of its storage in specific conditions which leads to an increase in its organoleptic qualities. The most common method of meat aging is the wet vacuum-bag based method, whereas the traditional method, called dry-aging, involves keeping meat at a low temperature for an extended time. However, this process is characterized by low repeatability of the results. Therefore, different approaches to stabilize the process are tested. The aim of this study was to analyze the influence of the Mucor flavus biostarter on the physicochemical characteristics and sensory quality of dry-aged beef (DAB). We hypothesized that a fungal biostarter positively influences the quality of DAB and stabilizes the dry-aging process. Meat control samples (N = 7) and samples inoculated with the Mucor flavus biostarter (N = 7), originating from 14 individuals crossbred from Holstein-Friesian cows with bulls of meat breeds, were put into the dry-aging fridge (DryAger, Bad Saulgau, Germany) for 28 days. The physicochemical parameters (pH, color parameters, WHC, GP (glycolytic potential), chemical composition of muscle, the content of malondialdehyde, shear force), muscular protein proteolysis (SDS-PAGE), sensory quality, and microbial composition of DAB were assessed after aging. The results showed a significant effect of the fungal biostarter on pH increase (0.25 units), and light myosin chain proteolysis (approximately 16%) as well as improvement of sensory quality (e.g., acceptability was improved by one unit in an applied scale 1–9). All together, the M. flavus-based biostarter was shown to increase the quality of DAB.

A total of 561 records of 233 species of fungi are reported from the Polish part of Białowieża Forest as a result of a short-term inventory that was conducted during the 18th Congress of European Mycologists (September 18–29, 2019). Four species new to Poland (Bryocentria brongniartii, Tremella coppinsii, T. hypocenomycis, and Zevadia peroccidentalis), and eight species new to Białowieża Primeval Forest (Hypomyces chrysostomus, Hypomyces rosellus, Lachnellula resinaria, Peniophora lycii, Phellinus viticola, Phlebia subochracea, Pronectria anisospora, and Typhula quisquiliaris) were recorded.

Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.

Aureoboletus projectellus is a bolete species native to eastern North America, which has been introduced to Central Europe. Here we present summarized data about occurrence of the fungus in both disjunctive ranges based on (1) de novo georeferencing of herbarium specimens and occurrence reports; (2) information from peer-reviewed articles, mycological forums and websites; (3) personal observations and (4) from queries sent to Forest Districts and National Parks in Poland. Corresponding background data were acquired from public databases and include range of genus Pinus – obligatory mycorrhizal partner of A. projectellus – and WorldClim bioclimatic data. Both datasets were fit for purpose of range modelling, i.e. were represented as spatially compatible equal-area raster grids encompassing temperate forest biom in eastern North America and Europe. Additionally, maps of habitat suitability, reflecting association between occurrence and background data, were obtained using maximum entropy approach implemented in MaxEnt.

Early-diverging fungi harbour unprecedented diversity in terms of living forms, biological traits and genome architecture. Before the sequencing era, non-Dikarya fungi were considered unable to produce secondary metabolites (SM); however, this perspective is changing. The main classes of secondary metabolites in fungi include polyketides, nonribosomal peptides, terpenoids and siderophores that serve different biological roles, including iron chelation and plant growth promotion. The same classes of SM are reported for representatives of early-diverging fungal lineages. Encouraged by the advancement in the field, we carried out a systematic survey of SM in Mucoromycotina and corroborated the presence of various SM clusters (SMCs) within the phylum. Among the core findings, considerable representation of terpene and nonribosomal peptide synthetase (NRPS)-like candidate SMCs was found. Terpene clusters with diverse domain composition and potentially highly variable products dominated the landscape of candidate SMCs. A uniform low-copy distribution of siderophore clusters was observed among most assemblies. Mortierellomycotina are highlighted as the most potent SMC producers among the Mucoromycota and as a source of novel peptide products. SMC identification is dependent on gene model quality and can be successfully performed on a batch scale with genomes of different quality and completeness.

During research carried on peatlands in northeastern Poland, small leaf-litter ascomycete identified as Wentiomyces sp. was found on decaying litter of Sphagnum sp. and Vaccinium oxycoccos. The taxonomy of this genus remains obscure, and there are still few and incidental published records in the mycological literature. This taxon is therefore described in the present paper in more detail and a short overview on the current knowledge regarding ecology and systematics of Wentiomyces spp. is provided.

The purpose of this study was to initially evaluate the species diversity of microfungi growing on litter of 15 plant species occurring on the poor fen and neighbouring area of the Torfy Lake, Masovian voivodeship, Poland. The lake is located near the planned road investment (construction of the Warsaw southern express ring road S2). The place is biologically valuable as there are rare plant communities from Rhynchosporion albae alliance protected under the Habitats Directive adopted by the European Union. On the examined plant debris 73 taxa of fungi were recorded (3 basidiomycetes, 13 ascomycetes, 2 zygomycetes, 43 anamorphic ascomycetes, 12 unidentified). Two of them, Dicranidion sp. and Wentiomyces sp. are presented here as new to Poland. Among the plant species examined, the litter of Rhododendron tomentosum harbored the highest number of fungal taxa (16). The highest percents of substrate-specific microfungi (i.e. recorded only on one plant species) was noted on R. tomentosum (81.3 %), and Pteridium aquilinum (75%). It is emphasized that the lake area should be protected not only because of rare plant community but also because of the uniqueness and diversity of mycobiota.

Hesperomyces virescens Thaxt. is a fungal parasite of coccinellid beetles. One of its hosts is the invasive harlequin ladybird Harmonia axyridis (Pallas). We present the first records of this combination from Poland.

Ecological information concerning 292 fungal taxa is reported as a result of two surverys in the Biebrza National Park. Most data presented come from the 5-day all-fungi inventory of the Polish Mycological Society in 2013, and 47 species were recorded during studies in the Biele Suchowolskie fen in 2008/2009. In total, 27 species of zygomycetes, 232 ascomycetes (including anamorphs) and 27 basidiomycetes (mainly Pucciniales). Additionaly some representatives of fungi-like organisms from Stramenopiles (4 species) and Dictyostelia (2) were identified. Fungal groups included were the same as in the previous survey in 2012: 190 taxa associated with plants, 15 with animals, 8 with fungi and 71 isolated from soil, plant debris and animal excrements. The most numerous were anamorphic ascomycetes (159 species). Nineteen species have not been previously known from Poland and 31 species are rare (1–3 localities). For the Biebrza National Park 197 species (67.5%) are new.