The plasticity of fungal interactions

Red and far-red light improve the antagonistic ability of Trichoderma guizhouense against phytopathogenic fungi by promoting phytochrome-dependent aerial hyphal growth

Light as a source of information regulates morphological and physiological processes of fungi, including development, primary and secondary metabolism, or the circadian rhythm. Light signaling in fungi depends on photoreceptors and downstream components that amplify the signal to govern the expression of an array of genes. Here, we investigated the effects of red and far-red light in the mycoparasite Trichoderma guizhouense on its mycoparasitic potential. We show that the invasion strategy of T. guizhouense depends on the attacked species and that red and far-red light increased aerial hyphal growth and led to faster overgrowth or invasion of the colonies. Molecular experiments and transcriptome analyses revealed that red and far-red light are sensed by phytochrome FPH1 and further transmitted by the downstream MAPK HOG pathway and the bZIP transcription factor ATF1. Overexpression of the red- and far-red light-induced fluffy gene fluG in the dark resulted in abundant aerial hyphae formation and thereby improvement of its antagonistic ability against phytopathogenic fungi. Hence, light-induced fluG expression is important for the mycoparasitic interaction. The increased aggressiveness of fluG-overexpressing strains was phenocopied by four random mutants obtained after UV mutagenesis. Therefore, aerial hyphae formation appears to be a trait for the antagonistic potential of T. guizhouense.

Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.

Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth

This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The 'fungal drops' method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µl drops on a hydrophobic surface at a fixed distance. This system is akin to a two-dimensional (2D) soil-like structure in which aqueous-pockets are intermixed with air-filled pores. The fungus (spores or mycelia) is inoculated into one of the drops, from which hyphal growth and exploration take place. Hyphal structures are assessed at different scales using stereoscopic and microscopic imaging. The former allows to evaluate the local response of regions within the colony (modular behaviour), while the latter can be used for fractal dimension analyses to describe the hyphal network architecture. The method was tested with several species to underpin the transferability to multiple species. In addition, two sets of experiments were carried out to demonstrate its use in fungal biology. First, mycelial reorganization of Fusarium oxysporum was assessed as a response to patches containing different nutrient concentrations. Second, the effect of interactions with the soil bacterium Pseudomonas putida on habitat colonization by the same fungus was assessed. This method appeared as fast and accessible, allowed for a high level of replication, and complements more complex experimental platforms. Coupled with image analysis, the fungal drops method provides new insights into the study of fungal modularity both macroscopically and at a single-hypha level.

Higher white-nose syndrome fungal isolate yields from UV-guided wing biopsies compared with skin swabs and optimal culture media

BACKGROUND

North American bat populations have suffered severe declines over the last decade due to the Pseudogymnoascus destructans fungus infection. The skin disease associated with this causative agent, known as white-nose syndrome (WNS), is specific to bats hibernating in temperate regions. As cultured fungal isolates are required for epidemiological and phylogeographical studies, the purpose of the present work was to compare the efficacy and reliability of different culture approaches based on either skin swabs or wing membrane tissue biopsies for obtaining viable fungal isolates of P. destructans.

RESULTS

In total, we collected and analysed 69 fungal and 65 bacterial skin swabs and 51 wing membrane tissue biopsies from three bat species in the Czech Republic, Poland and the Republic of Armenia. From these, we obtained 12 viable P. destructans culture isolates.

CONCLUSIONS

Our results indicated that the efficacy of cultures based on wing membrane biopsies were significantly higher. Cultivable samples tended to be based on collections from bats with lower body surface temperature and higher counts of UV-visualised lesions. While cultures based on both skin swabs and wing membrane tissue biopsies can be utilised for monitoring and surveillance of P. destructans in bat populations, wing membrane biopsies guided by UV light for skin lesions proved higher efficacy. Interactions between bacteria on the host's skin also appear to play an important role.

FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species

Recently, a new annotation tool "FungalTraits" was created based on the previous FUNGuild and Fun^Fun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)-based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.

Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism

Comparative and pan-genomic analyses of the endophytic fungus Pezicula neosporulosa (Helotiales, Ascomycota) from needles of the relict fir, Abies beshanzuensis, showed expansions of carbohydrate metabolism and secondary metabolite biosynthetic genes characteristic for unrelated plant-beneficial helotialean, such as dark septate endophytes and ericoid mycorrhizal fungi. The current species within the relatively young Pliocene genus Pezicula are predominantly saprotrophic, while P. neosporulosa lacks such features. To understand the genomic background of this putatively convergent evolution, we performed population analyses of 77 P. neosporulosa isolates. This revealed a mosaic structure of a dozen non-recombining and highly genetically polymorphic subpopulations with a unique mating system structure. We found that one idiomorph of a probably duplicated mat1-2 gene was found in putatively heterothallic isolates, while the other co-occurred with mat1-1 locus suggesting homothallic reproduction for these strains. Moreover, 24 and 81 genes implicated in plant cell-wall degradation and secondary metabolite biosynthesis, respectively, showed signatures of the balancing selection. These findings highlight the evolutionary pattern of the two gene families for allowing the fungus a rapid adaptation towards endophytism and facilitating diverse symbiotic interactions.

Fungi Occurring in Norway Spruce Wood Decayed by Heterobasidion parviporum in Puszcza Borecka Stands (Northeastern Poland)

In many spruce stands, trees are frequently attacked by the pathogen Heterobasidion parviporum, albeit without visible symptoms in the crown. In the present work, the results of the presence of stem rot, assessed by PICUS Sonic Tomography, and the fungal biota on trees and stumps in eight plots in the Puszcza Borecka Forest are described. The plots were located in stands on original forest soil (4) and on post-agricultural soil (4), where around a stump with H. parviporum symptoms (signs of internal rot and basidiocarps), 30 trees were selected and examined for internal rot. Wood samples were collected from two selected trees for fungal molecular analysis. A total of 79 fungal taxa were found, including 57 taxa in plots on post-agricultural soil and 45 on forest soil. There were 395 fungal records on stumps and 22 records on trees, therein, from the inner parts of felled trunks. Significant differences in the Chao-1 diversity index indicate that the origin of the soil—post-agricultural or forest soil—influenced the alpha diversity of the fungal communities in the forests studied. The values of the Shannon and Simpson indices show that the two communities were similar in terms of species numbers. The presence of basidiomata of H. parviporum and two species of Armillaria (mainly A. cepistipes) in samples on all plots is striking, although Armillaria spp. was detected more frequently. Most of the species identified were typical saprotrophs, although rare species were also found, such as Entoloma byssisedum, Onnia tomentosa, Physisporinus vitreus, Postia ptychogaster, and Ramaria apiculata. The presence of H. parviporum in the inner woody parts was confirmed by PCR analysis, and decay was detected even up to a stem height of 6 m. Armillaria was the dominant genus in the studied stands, and H. parviporum plays a significant and underestimated role in heartwood decay of old spruce trees in Puszcza Borecka Forest.

Enzymatic Bioprospecting of Fungi Isolated from a Tropical Rainforest in Mexico

The humid tropical environment provides an ideal place for developing a high diversity of plants; this is why it is an interesting site for the enzymatic bioprospecting of fungi that are responsible for the recycling of organic matter in an efficient and accelerated way and whose enzymes could have multiple biotechnological applications. For this study, 1250 isolates of macroscopic and microscopic fungal morphotypes were collected from soil, leaf litter, and wood. One hundred and fifty strains (50 from each source) were selected for the enzymatic screening. From the first phase, 51 strains with positive activity for laccase, protease, amylase, xylanase, and lipase enzymes were evaluated, of which 20 were isolated from leaf litter, 18 from the soil, and 13 from wood. The 10 best strains were selected for the enzymatic quantification, considering the potency index and the production of at least two enzymes. High laccase activity was detected for Trametes villosa FE35 and Marasmius sp. CE25 (1179 and 710.66 U/mg, respectively), while Daedalea flavida PE47 showed laccase (521.85 U/mg) and protease activities (80.66 U/mg). Fusarium spp. PH79 and FS400 strains had amylase (14.0 U/mg, 49.23 U/mg) and xylanase activities (40.05 U/mg, 36.03 U/mg) respectively. These results confirm the enzymatic potential of fungi that inhabit little-explored tropical rainforests with applications in industry.

Biotechnology under extreme conditions: Lichens after extreme UVB radiation and extreme temperatures produce large amounts of hydrogen

The present study demonstrates biotechnological applications of the lichen Pleurosticta acetabulum, specifically the production of large amounts of hydrogen even after the lichen exposure to extreme conditions such as a) extreme UVB radiation (1.7 mW/cm² = 1000 J m^-2 min^-1) over different time periods (4, 20 & 70 h) and b) combined exposure of the lichen to high intensity UVB radiation and extreme low (-196 °C) or extreme high temperatures (+70 °C). The results highlight that the extremophilic and polyextremophilic behavior of lichens both in dehydrated and in regenerated form, under extreme conditions not necessarily recorded on earth, is compatible with their biotechnological uses. The lichen viability was measured using fluorescence induction techniques (OJIP-test), which record changes in the molecular structure and function of the photosynthetic mechanism, while its ability to produce molecular hydrogen was measured through thermal conductivity gas chromatography (GC-TCD) analysis. Hydrogen is a promising fuel for the future. The exciting result of a lichen micro-ecosystem is its ability to expel its moisture and remain in an inactive state, protecting itself from extreme conditions and maintaining its ability to high yield hydrogen production in a closed system, with the sole addition of water and without the need for additional energy. Our results expand the potential use of lichens for future biotechnological applications in extreme Earth environments, but also in environments on other planets, such as Mars, thus paving the way for astrobiotechnological applications.

Fungi inhabiting attine ant colonies: reassessment of the genus Escovopsis and description of Luteomyces and Sympodiorosea gens. nov

Escovopsis is a diverse group of fungi, which are considered specialized parasites of the fungal cultivars of fungus-growing ants. The lack of a suitable taxonomic framework and phylogenetic inconsistencies have long hampered Escovopsis research. The aim of this study is to reassess the genus Escovopsis using a taxonomic approach and a comprehensive multilocus phylogenetic analysis, in order to set the basis of the genus systematics and the stage for future Escovopsis research. Our results support the separation of Escovopsis into three distinct genera. In light of this, we redefine Escovopsis as a monophyletic clade whose main feature is to form terminal vesicles on conidiophores. Consequently, E. kreiselii and E. trichodermoides were recombined into two new genera, Sympodiorosea and Luteomyces, as S. kreiselii and L. trichodermoides, respectively. This study expands our understanding of the systematics of Escovopsis and related genera, thereby facilitating future research on the evolutionary history, taxonomic diversity, and ecological roles of these inhabitants of the attine ant colonies.

In Vitro Observations of the Interactions between Pholiota carbonaria and Polytrichum commune and Its Potential Environmental Relevance

Wildfires play a critical role in maintaining biodiversity and shaping ecosystem structure in fire-prone regions, and successional patterns involving numerous plant and fungal species in post-fire events have been elucidated. Evidence is growing to support the idea that some post-fire fungi can form endophytic/endolichenic relationships with plants and lichens. However, no direct observations of fire-associated fungal-moss interactions have been visualized to date. Therefore, physical interactions between a post-fire fungus, Pholiota carbonaria, and a moss, Polytrichum commune, were visually examined under laboratory conditions. Fungal appressoria were visualized on germinating spores and living protonemata within two weeks of inoculation in most growth chambers. Appressoria were pigmented, reddish gold to braun, and with a penetration peg. Pigmented, reddish gold to braun fungal hyphae were associated with living tissue, and numerous mature rhizoids contained fungal hyphae at six months. Inter-rhizoidal hyphae were pigmented and reddish gold to braun, but no structures were visualized on mature gametophyte leaf or stem tissues. Based on our visual evidence and previous work, we provide additional support for P. carbonaria having multiple strategies in how it obtains nutrients from the environment, and provide the first visual documentation of these structures in vitro.

Bambusicolous Fomitiporia revisited: multilocus phylogeny reveals a clade of host-exclusive species

FOMITIPORIA

is a genus of wood-inhabiting Hymenochaetaceae (Agaricomycetes) that includes pathogens and decomposers occurring on a wide array of plant substrates. Some species decay culms of woody bamboos, a poorly known biotic interaction. Four bambusicolous species of Fomitiporia are currently known. However, no studies concerning their phylogenetic relationships have been performed. In order to assess species boundaries and their relationships to each other, we conducted molecular phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuc 28S rDNA (28S), RNA polymerase II second largest subunit (RPB2), and translation elongation factor 1-α (TEF1), as well as morphological analyses. Four species that occur on culms of woody bamboos, F. bambusarum, F. spinescens, F. uncinata, and the new species F. bambusipileata, grouped together in an exclusive clade within a primarily Neotropical lineage. The new species differs from all other species in the group by the pileate basidiomata. Hypotheses regarding host-exclusivity are discussed.

Rabenchromenone and Rabenzophenone, Phytotoxic Tetrasubstituted Chromenone and Hexasubstituted Benzophenone Constituents Produced by the Oak-Decline-Associated Fungus Fimetariella rabenhorstii

A new phytotoxic tetrasubstituted chromen-4-one (1) and a new hexasubstituted benzophenone (2), named rabenchromenone and rabenzophenone, respectively, were isolated from the culture filtrates of Fimetariella rabenhorstii, an oak-decline-associated fungus in Iran. Rabenchromenone and rabenzophenone, isolated together with known moniliphenone (3) and coniochaetone A (4), were characterized as methyl 3-chloro-1,8-dihydroxy-6-methyl-9-oxo-1,9-dihydrocyclopenta[b]chromene-1-carboxylate and methyl 4-chloro-2-(2,6-dihydroxy-4-methylbenzoyl)-3-hydroxybenzoate, respectively, by spectroscopic methods (primarily nuclear magnetic resonance and high-resolution electrospray ionization mass spectrometry). The R absolute configuration at C-1 of rabenchromenone was determined by quantum chemical calculations and electronic circular dichroism experiments. All metabolites (1-4) were tested by leaf puncture on tomato and oak plants. All compounds were active in this assay by causing in both plants a necrosis diameter in the range of 0.2-0.7 cm. Specifically, rabenzophenone (2) was found to be the most phytotoxic compound in both plants.

More pieces to a huge puzzle: Two new Escovopsis species from fungus gardens of attine ants

Escovopsis (Ascomycota: Hypocreales, Hypocreaceae) is the only known parasite of the mutualistic fungi cultivated by fungus-growing ants (Formicidae: Myrmicinae: Attini: Attina, the "attines"). Despite its ecological role, the taxonomy and systematics of Escovopsis have been poorly addressed. Here, based on morphological and phylogenetic analyses with three molecular markers (internal transcribed spacer, large subunit ribosomal RNA and the translation elongation factor 1-alpha), we describe Escovopsisclavatus and E.multiformis as new species isolated from fungus gardens of Apterostigma ant species. Our analysis shows that E.clavatus and E.multiformis belong to the most derived Escovopsis clade, whose main character is the presence of conidiophores with vesicles. Nevertheless, the most outstanding feature of both new species is the presence of a swollen region in the central hypha of the conidiophore named swollen cell, which is absent in all previously described Escovopsis species. The less derived Escovopsis clades lack vesicles and their phylogenetic position within the Hypocreaceae still remains unclear. Considering the high genetic diversity in Escovopsis, the description of these new species adds barely two pieces to a huge taxonomic puzzle; however, this discovery is an important piece for building the systematics of this group of fungi.

Lichen as Micro-Ecosystem: Extremophilic Behavior with Astrobiotechnological Applications

This work demonstrates the tolerance of lichen Pleurosticta acetabulum under extreme conditions similar to those encountered in extraterrestrial environments. Specifically, the impact of three extreme Mars-like conditions-complete dehydration, extremely low temperature (-196°C/77K), and oxygen depletion-on lichens was investigated. The symbiosis of mycobiont and photobiont partners creates a micro-ecosystem that ensures viability of both symbiotic partners under prolonged desiccation and extremely low temperatures without any cultivation care. Changes in the molecular structure and function of the photosynthetic apparatus, in the level of chlorophylls, polyamines, fatty acids, carbohydrates, ergosterol, efflux of K⁺, and DNA methylation ensure the ecological integrity of the system and offer resistance of lichens to above-mentioned extreme environmental conditions. For the first time, we also demonstrate that the unprecedented polyextremophilic characteristic of lichens could be linked to biotechnological applications, following exposure to these extreme conditions, such that their ability to produce a high yield of hydrogen was unchanged. All these support that lichens are (a) ideal model systems for a space mission to inhabit other planets, supporting also the aspect that the panspermia theory could be extended to incorporate in the traveling entities not only single organisms but micro-ecosystems like lichens, and (b) ideal model systems for astrobiotechnological applications (hydrogen production), such as in the development of bioregeneration systems for extraterrestrial environments.