Fungi as mediators linking organisms and ecosystems

Early inoculation and bacterial community assembly in plants: A review

The relationship between plants and early colonizing microbes is crucial for regulating agricultural ecosystems. Recent evidence strongly suggests that by introducing beneficial microbes during the seed or seedling stages, the diversity and assembly structure of the plant-related microbial community during later plant development can be altered, recruiting beneficial bacteria to enhance plant protection. However, the mechanisms of community assembly and their effects on plant growth are still not fully understood. To deepen our understanding of the importance of early inoculation for improving plant performance, this review comprehensively summarizes recent research advancements on the effects of early introduction on plant growth and adaptability. The mechanisms and ecological significance of early inoculation in the assembly of plant-related bacterial communities are discussed, with particular emphasis on the importance of seed endophytes, plant growth-promoting rhizobacteria (PGPR), and synthetic microbial consortia as microbial inoculants in enhancing plant health and productivity. Additionally, this review proposes a new strategy: sequential inoculation during the seed and seedling stages, aiming to maximize the effects of microbes.

Theoretical conformational analysis of cross-linking bonds in fungal hydrophobin from Aspergillus fumigatus

Aspergillus fumigatus is a common saprophytic filamentous fungus that plays a crucial role in nutrient cycling but can become an opportunistic pathogen, posing a significant threat to immunocompromised individuals by causing invasive aspergillosis. A key feature of A. fumigatus is the presence of hydrophobins-small amphipathic proteins that form a protective rodlet layer on conidial surfaces, facilitating biofilm formation and immune evasion. This rodlet structure, stabilized by cross-linking disulfide bonds, provides resistance to desiccation, oxidative stress, and immune defenses, making these cross-links a compelling target for study. In this work, we employ all-atom simulations, incorporating quantum mechanics/molecular mechanics (QM/MM) calculations, to evaluate the energy and conformational effects of cross-linking disulfide bonds (CL1, CL2, CL3, and CL4) in the rodlet assembly. By integrating QM/MM approaches, we achieve a detailed representation of the electronic and structural properties of these bonds within the complex rodlet layer, gaining deeper insights into their essential role in maintaining the stability and integrity of the RodA hydrophobin protein from A. fumigatus conidial surface. We identify a group of ten residues that influence directly in the cross-linking, with Gln23 and Lys17 emerging as key candidates for experimental mutation to control rodlet assembly. Our findings shed light on the molecular mechanisms underlying rodlet formation and highlight potential targets for disrupting this protective layer, offering promising avenues for antifungal strategies.

Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening

Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realised by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the ecological group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify 60 potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterise the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.

Environmental sensitivity of amyloidogenic motifs in fungal NOD-like receptor-mediated immunity: Molecular and structural insights into amyloid assembly

This study investigates the aggregation behavior of amyloidogenic motifs associated with fungal NOD-like receptor (NLR) proteins, focusing on their sensitivity to various environmental conditions. We aimed to develop a minimal model that explains amyloid aggregation, aligning with in vivo observations and the expected role of these motifs in amyloid-based signaling. The purpose was to understand how changes in physicochemical conditions influence amyloid formation, which is crucial for fungal immune responses and has potential applications in controlling fungal infections. To achieve this, two amyloidogenic motifs, PUASM_N and PUASM_C, derived from the fungus Colletotrichum gloeosporioides, were synthesized and subjected to different conditions that simulate their natural environment. These conditions included varying pH levels, peptide concentrations, and surface adsorption properties. The aggregation kinetics, morphology, and secondary structures of the peptides were analyzed using Thioflavin T (ThT) fluorescence assay, transmission electron microscopy (TEM), and Fourier transform infrared micro-spectroscopy (micro-FTIR). The results showed that PUASM_N aggregates rapidly without a lag phase, forming long, structured fibers. In contrast, PUASM_C aggregates more slowly, with a significant lag phase, forming shorter, irregular fibers. The aggregation of PUASM_C was highly sensitive to environmental factors, such as alkaline pH and surface hydrophobicity, which accelerated its aggregation. PUASM_N, however, displayed consistent aggregation behavior under different conditions. Our findings suggest that minor environmental changes can modulate the functional roles of PUASM peptides, potentially aiding Colletotrichum gloeosporioides in regulating its antipathogenic activity in response to environmental challenges.

Discovering the dynamics of peach fruit mycobiome throughout fruit development season by high-throughput sequencing

The mycobiome is comprised of a rich array of fungal species that compete for resources, and species diversity and prevalence exhibit a dynamic structure under the influence of many factors. While the host fruit develops, the prevalence and the arrangement of fungal species in this mycobiome also change, forming a dynamic microenvironment. In this study, fungal diversity on peach fruit surfaces at different developmental stages have been determined to better understand the changes in fungal diversity and disease occurrence by using metabarcoding of the full ITS region and processing the obtained high-throughput sequencing data with various bioinformatic analyses. It has been found that fungal diversity in early developmental stages is higher, and the diversity declines as the fruit matures, likely due to more prevalent fungal species establishing themselves on the surface as the fruit develops. Additionally, this research reveals that the prevalence of pathogens does not necessarily mean that disease will develop, as pathogenic species were found to be at higher prevalence percentages when compared to non-pathogenic species in healthy fruit samples. This study also identified the Monilinia polystroma species at a molecular level for the first time in Türkiye; however, no symptomatic signals were recorded on the host. The study provides valuable data for mycobiome studies, while also highlighting its importance in optimizing sustainable disease management strategies.

Enhancing hexavalent chromium stable reduction via sodium alginate encapsulation of newly isolated fungal and bacterial consortia

Chromium [Cr(VI)]-induced soil pollution is a serious environmental threat. Bioremediation utilizes specific microbes capable of transforming Cr(VI) into the less toxic Cr(III), however, microbial efficacy can be inhibited by elevated pollutant concentrations and competition from indigenous microbial communities. Thus, this study explored the potential of single and multi-domain microbial consortia encapsulated in alginate to overcome these shortcomings. The results revealed that (i) fungal treatments demonstrated an elevated tolerance and reduction ability for Cr(VI) compared to bacterial treatments; (ii) combined application of fungi and bacteria was more effective in degrading Cr(VI) in soil compared to the individual treatments; (iii) microbial encapsulation improved microbial response to Cr(VI) toxicity thereby increasing their lifespan and Cr(VI) degrading ability; (iv) microbial consortia significantly decreased soil pH, electrical conductivity, and redox potential while simultaneously increasing soil enzyme activities (urease, sucrase, phosphatase, catalase, and laccase); and (v) The improved tolerance in the inoculated treatment resulted in increased microbial diversity and a substantial variation in microbial community structures, with 10,753 bacterial and 2697 fungal amplicon sequence variants identified across the treatment groups. This study underscores the critical importance of microbial diversity in bioremediation, emphasizing that encapsulation with the right material could improve the effectiveness of environmental remediation strategies.

Beyond Conventional Antifungals: Combating Resistance Through Novel Therapeutic Pathways

The rising burden of fungal infections presents a significant challenge to global healthcare, particularly with increasing antifungal resistance limiting treatment efficacy. Early detection and timely intervention remain critical, yet fungal pathogens employ diverse mechanisms to evade host immunity and develop resistance, undermining existing therapeutic options. Limited antifungal options and rising resistance necessitate novel treatment strategies. This review provides a comprehensive overview of conventional antifungal agents, their mechanisms of action, and emerging resistance pathways. Furthermore, it highlights recently approved and investigational antifungal compounds while evaluating innovative approaches such as nanotechnology, drug repurposing, and immunotherapy. Addressing antifungal resistance requires a multifaceted strategy that integrates novel therapeutics, enhanced diagnostic tools, and future research efforts to develop sustainable and effective treatment solutions.

Plant diversity increases diversity and network complexity rather than alters community assembly processes of leaf-associated fungi in a subtropical forest

Plant diversity significantly impacts ecosystem processes and functions, yet its influence on the community assembly of leaf fungi remains poorly understood. In this study, we investigated leaf epiphytic and endophytic fungal communities in a Chinese subtropical tree species richness experiment, ranging from 1 to 16 species, using amplicon sequencing to target the internal transcribed spacer 1 region of the rDNA. We found that the community assembly of epiphytic and endophytic fungi was predominantly governed by stochastic processes, with a higher contribution of dispersal limitation on epiphytic than on endophytic fungal communities but a higher contribution of selection on endophytic than on epiphytic fungal communities. The plant-epiphytic fungus interaction network was more complex (e.g., more highly connected and strongly nested but less specialized and modularized) than the plant-endophytic fungus interaction network. Additionally, tree species richness was positively correlated with the network complexity and diversity of epiphytic (α-, β- and γ-diversity) and endophytic (β- and γ-diversity) fungi, but was not associated with the contribution of the stochastic and deterministic processes on the community assembly of epiphytic and endophytic fungi. This study highlights that tree species diversity enhances the diversity and network complexity, rather than alters the ecological processes in community assembly of leaf-associated fungi.

Molluscicidal Screening of Hypocreales Fungi from a Brazilian Cerrado Cave Against Biomphalaria glabrata Snails

Fungi play vital roles in ecosystems through parasitism, commensalism, and mutualism. Additionally, they are widely used in industry as bioactive compound producers and biological control agents. Biomphalaria glabrata is a freshwater snail often controlled with chemical molluscicides. However, developing effective alternatives to these chemical treatments is essential. This study evaluated the molluscicidal potential of culture supernatant from Hypocreales fungi isolated from a cave in the Brazilian Cerrado against the B. glabrata. The isolates were identified based on morphological features and ITS rDNA sequences. Fifteen filtrates of Hypocreales fungi were obtained and tested both pure and in different dilutions (10% and 50%) against newly hatched snails during 96 h of exposure. The fungal isolates were identified as belonging to the genera of Clonostachys (1), Cylindrocladiella (1), Fusarium (1), Gliocladiopsis (1), Keithomyces (1), Marquandomyces (1), Ovicillium (1), Pochonia (1), Purpureocillium (1), Sarcopodium (1), Sarocladium (1), Trichoderma (3), and Volutella (1). The results showed 93.33% (14) of the fungal filtrates induced significant mortality, indicating their molluscicidal activity, with Pochonia chlamydosporia FCCUFG 100 and Volutella aeria FCCUFG 107 causing 100% mortality in all dilutions. These results reveal the potential of Hypocreales fungi from a Brazilian Cerrado cave as a promising approach for snail control.

Toward harnessing biodiversity-ecosystem function relationships in fungi

Fungi are crucial for terrestrial ecosystems, yet the role of fungal diversity in ecosystem functions remains unclear. We synthesize fungal biodiversity and ecosystem function (BEF) relationships, focusing on plant biomass production, carbon storage, decomposition, and pathogen or parasite resistance. The observed BEF relationships for these ecosystem functions vary in strength and direction, complicating generalizations. Strong positive relationships are generally observed when multiple ecosystem functions are addressed simultaneously. Often, fungal community composition outperforms species richness in predicting ecosystem functions. For more comprehensive fungal BEF research, we recommend studying natural communities, considering the simultaneous functions of a broader array of fungal guilds across spatiotemporal scales, and integrating community assembly concepts into BEF research. For this, we propose a conceptual framework and testable hypotheses.

Infection-induced host extinction: Deterministic and stochastic models for environmentally transmitted pathogens

Amphibian decline and extinction have been observed on a global scale, highlighting the urgency of identifying the underlying factors. This issue has long been recognized as a critical concern in conservation ecology and continues to receive significant attention. Pathogen infection, in particular the chytrid fungus Batrachochytrium dendrobatidis, is postulated as a key factor contributing to the decline of certain species within specific regions. In this paper, we focus on identifying the pathogen characteristics that can drive host species extinction. Both deterministic and stochastic modeling frameworks based on a susceptible-infectious-pathogen epidemic model are proposed, to assess the influence of pathogen infection on species decline and extinction. Various indices, including the reproduction numbers of the host species, the replication of the pathogen, and the transmission of the pathogen are derived. Theoretical analysis includes the stability of equilibria, the extinction and persistence of host species in the deterministic model, and the evaluation of extinction probability and average extinction time in the stochastic model. Additionally, numerical simulations are conducted to quantify the effects of various factors on host decline and extinction, as well as the probabilities of extinction. We find two crucial conditions for a pathogen to drive host extinction: (i) the pathogen's self-reproduction capacity in the environment, and (ii) the pathogen's impact on the fecundity and survival of the infected host. These findings provide insights that could aid in the design and implementation of effective conservation strategies for amphibians.

Additions to the saprobic fungi (Ascomycota) associated with macadamia trees from the Greater Mekong Subregion

Macadamia trees, the most economically important Proteaceae perennial crop, are globally renowned for their edible nuts. During our surveys of microfungi associated with macadamia in China and Thailand, we isolated three saprobic fungi from dead macadamia branches. Our multigene phylogenetic analyses (ITS, LSU, SSU, tef1-α, TUB2, and ACT loci), genealogical concordance phylogenetic species recognition (GCPSR) with a pairwise homoplasy index (PHI) test, and morphological characteristics led to the discovery of two new species, Dothiorellamacadamiae and Phaeoacremoniumchiangmaiense, and one new record, Melomastiapuerensis. We provide morphological descriptions, photo plates, phylogenetic analysis results, and PHI test results of the two new species, along with comparisons with closely related taxa. These findings have global implications for understanding the diversity of microfungi associated with macadamia trees.

Exploring the Diversity and Ecological Dynamics of Palm Leaf Spotting Fungi-A Case Study on Ornamental Palms in Portugal

Palm trees (Arecaceae) are among the most popular ornamental plants worldwide. Despite extensive research on the fungi associated with Arecaceae, the diversity and ecological dynamics of fungi affecting ornamental palms remain poorly studied, although they have significant impact on palm health and economic value. Furthermore, while research on palm fungal diversity has traditionally focused on tropical assemblages, ornamental palms in temperate climates offer a unique opportunity to explore the diversity of palm fungi in non-native habitats. The present study conducted a preliminary assessment of the diversity and ecology of potential phytopathogenic fungi associated with foliar lesions on various ornamental palm host species in Portugal, combining morphological examination, PCR-based genomic fingerprinting, and biodiversity data analysis. The examination of 134 foliar lesions sampled from 100 palm trees resulted in a collection of 2064 palm leaf spotting fungi (PLSF), representing a diverse fungal assemblage of 320 molecular operational taxonomic units (MOTUs) across 97 genera. The overall fungal community composition revealed a distinct assemblage dominated by Neosetophoma, Alternaria, Phoma, and Cladosporium, with a profusion of infrequent and rare taxa consistent with a logseries distribution. Significantly positive co-occurrence (CO) patterns among prevalent and uncommon taxa suggest potential synergistic interactions enhancing fungal colonisation, persistence, and pathogenicity. The taxonomic structures of the PLSF contrasted markedly from tropical palm fungi, especially in the prevalence of pleosporalean coelomycetes of the Didymellaceae and Phaeosphaeriaceae, including recently introduced or not previously documented genera on Arecaceae. This novel assemblage suggests that climatic constraints shape the structure of palm fungal communities, resulting in distinctive temperate and tropical assemblages. In addition, the fungal assemblages varied significantly across palm host species, with temperate-native palms hosting more diverse, coelomycete-enriched communities. The present findings highlight foliar lesions as hyperdiverse microhabitats harbouring fungal communities with intricate interactions and a complex interplay of climatic, host, and ecological factors. With climate change altering environmental conditions, the identification of fungi thriving in or inhabiting these microhabitats becomes crucial for predicting shifts in pathogen dynamics and mitigating future fungal disease outbreaks. Understanding these complex ecological dynamics is essential for identifying potential phytopathogenic threats and developing effective management strategies for the health and sustainability of ornamental plants.

Demethylation Inhibitor Fungicides Have a Significantly Detrimental Impact on Population Growth and Composition of Nectar Microbial Communities

Demethylation inhibitor (DMI) fungicides are a mainstay of modern agriculture due to their widespread use for crop protection against plant-pathogenic fungi. However, DMI residues can disperse and persist in the environment, potentially affecting non-target fungi. Previous research has demonstrated that DMIs and other fungicides inhibit yeast growth in floral nectar microbial communities and decrease fungal richness and diversity of exposed flowers with no apparent effect on bacteria. Nevertheless, the effect of DMIs on the population growth of different species of nectar inhabitants and the dynamics of these microbial communities remains understudied. To address these issues, in this study we created synthetic microbial communities including yeasts (Metschnikowia reukaufii and Metschnikowia pulcherrima) and bacteria (Rosenbergiella epipactidis and Comamonas sp.) and propagated them in culture media containing different DMIs (imazalil, propiconazole, and prothioconazole) at different doses or no fungicide. Our results showed that DMIs have a significant impact on some of the most common microbial inhabitants of floral nectar by favoring the growth of bacteria over yeasts. Furthermore, habitat generalists such as M. pulcherrima and Comamonas sp. were more impacted by the presence of fungicides than the nectar specialists M. reukaufii and R. epipactidis, especially upon dispersal across habitat patches. Future research should determine if the patterns observed in the present study hold true for other species of nectar microbes and explore the interaction between growth limitation due to fungicide presence, dispersal limitation, and other mechanisms involved in community assembly in floral nectar.

Melanized root-associated fungi: key players in plant-soil systems

Melanized root-associated fungi are a group of fungi that produce melanized structures and form root associations, including different mycorrhizal and endophytic symbioses with plants. They are pervasive across terrestrial ecosystems and play an important role in the prevailing soil carbon (C) and nutrient cycling syndromes through direct and indirect mechanisms, where they may strongly modulate plant-microbe interactions and structure root and soil microbiomes. Furthermore, melanized root-associated fungi can confer on plants an enhanced ability to tolerate abiotic and biotic stressors such as drought, extreme temperatures, heavy metals, and pathogen attacks. We propose that melanized root-associated fungi are a cohesive and ecologically relevant grouping that can be an indicator of plant-soil system functioning, and considering them will advance research on plant-soil interactions.

Pseudophylloporus Gen. nov. and Rubroleccinum Gen. nov., Two New Genera Revealed by Morphological and Phylogenetic Evidences in the Family Boletaceae from Subtropical China

Boletaceae, the largest and most diverse family of Boletales (Agaricomycetes and Basidiomycota), is both ecologically and economically important. Although many taxa have been described in China, the diversity of the family still remains incompletely understood. In the present study, Pseudophylloporus baishanzuensis gen. nov., sp. nov. and Rubroleccinum latisporus gen. nov., sp. nov. are proposed based on morphological and molecular phylogenetic analyses. These findings contribute to a deeper understanding of the diversity within the Boletaceae family.

Comparison of commonly used software pipelines for analyzing fungal metabarcoding data

BACKGROUND

Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.

RESULTS

Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n = 18), while DADA2 results for the same replicates were highly heterogeneous.

CONCLUSIONS

Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.

An overview of symbiotic and pathogenic interactions at the fungi-plant interface under environmental constraints

The complex and dynamic interactions between fungi and plants constitute a critical arena in ecological science. In this comprehensive review paper, we explore the multifaceted relationships at the fungi-plant interface, encompassing both mutualistic and antagonistic interactions, and the environmental factors influencing these associations. Mutualistic associations, notably mycorrhizal relationships, play a pivotal role in enhancing plant health and ecological balance. On the contrary, fungal diseases pose a significant threat to plant health, agriculture, and natural ecosystems, such as rusts, smuts, powdery mildews, downy mildews, and wilts, which can cause extensive damage and lead to substantial economic losses. Environmental constraints encompassing abiotic and biotic factors are elucidated to understand their role in shaping the fungi-plant interface. Temperature, moisture, and soil conditions, along with the presence of other microbes, herbivores, and competing plants, significantly influence the outcome of these interactions. The interplay between mutualism and antagonism is emphasised as a key determinant of ecosystem health and stability. The implications of these interactions extend to overall ecosystem productivity, agriculture, and conservation efforts. The potential applications of this knowledge in bioremediation, biotechnology, and biocontrol strategies emphasise the importance of adapting to climate change. However, challenges and future directions in this field include the impacts of climate change, emerging fungal pathogens, genomic insights, and the role of the fungi-plant interface in restoration ecology. Hence, this review paper provides a comprehensive overview of fungi-plant interactions, their environmental influences, and their applications in agriculture, conservation, and ecological restoration.

The postbiotic potential of Aspergillus oryzae - a narrative review

The filamentous fungus Aspergillus oryzae has a long tradition in East Asian food processing. It is therefore not surprising that in recent years fermentation products of A. oryzae have attracted attention in the emerging field of postbiotics. This review aims to provide a comprehensive summary of the potential postbiotic effects of fermentation products from A. oryzae, by discussing possible mechanisms of action against the background of the molecular composition determined so far. In particular, cell wall constituents, enzymes, extracellular polymeric substances, and various metabolites found in A. oryzae fermentation preparations are described in detail. With reference to the generally assumed key targets of postbiotics, their putative beneficial bioactivities in modulating the microbiota, improving epithelial barrier function, influencing immune responses, metabolic reactions and signaling through the nervous system are assessed. Drawing on existing literature and case studies, we highlight A. oryzae as a promising source of postbiotics, particularly in the context of animal health and nutrition. Challenges and opportunities in quality control are also addressed, with a focus on the necessity for standardized methods to fully harness the potential of fungal-based postbiotics. Overall, this article sheds light on the emerging field of A. oryzae-derived postbiotics and emphasizes the need for further research to fully realize their therapeutic potential.

Tipping the plant-microbe competition for nitrogen in agricultural soils

Nitrogen (N) is the most limiting nutrient in agroecosystems, and its indiscriminate application is at the center of the environmental challenges facing agriculture. To solve this dilemma, crops' nitrogen use efficiency (NUE) needs to increase - in other words, more of the applied nitrogen needs to reach humans. Microbes are the key to cracking this problem. Microbes use nitrogen as an energy source, an electron acceptor, or incorporate it in their biomass. These activities change the form and availability of nitrogen for crops' uptake, impacting its NUE, yields and produce quality. Plants (and microbes) have, however, evolved many mechanisms to compete for soil nitrogen. Understanding and harnessing these competitive mechanisms would enable us to tip the nitrogen balance to the advantage of crops. We will review these competitive mechanisms and highlight some approaches that were applied to reduce microbial competition for N in an agricultural context.

Diversity of African fungi, chemical constituents and biological activities

Besides plants and animals, the fungal kingdom consists of several species characterized by various forms and applications. Fungi are amazing producers of bioactive natural products with applications in medicine and agriculture. Though this kingdom has been extensively investigated worldwide, it remains relatively underexplored in Africa. To address the knowledge gaps, encourage research interest, and suggest opportunities for the discovery of more bioactive substances from African fungi, we considered it appropriate to extensively review the research work carried out on African fungi since 1988. This review summarizes the diversity and distribution of fungi throughout Africa, the secondary metabolites yet reported from studied fungi, their biological activities and, the countries where they were collected. The studied fungi originated from eleven African countries and were mainly endophytic fungi and higher fungi (macrofungi). Their investigation led to the isolation of five hundred and three (503) compounds with polyketides representing the main class of secondary metabolites. The compounds exhibited varied biological activities with antibacterial and antiproliferative properties being the most prominent.

The Zoonotic Potential of Fungal Pathogens: Another Dimension of the One Health Approach

Zoonotic diseases are caused by viruses, bacteria, fungi and parasites and they comprise about 75% of all emerging infectious diseases. These can be transmitted via the direct (scratches on skin or animal bites) or indirect mode (through environmental shedding of infectious agent by the infected animal) of transmission. Environmental changes, whether in the form of urbanization, industrialization or destruction of wildlife habitats, lead to more human invasion in wildlife areas, subsequently leading to an increased passage of animals towards human dwellings and more exposure to animals, making humans susceptible to these infections. Climate change is another major factor. Global warming and the evolving thermotolerance of fungi, adapting more to human body temperature than their saprophytic nature, is leading to the emergence of humans as new hosts for fungi. The domestication of animals, rising populations, enhanced tourism, migratory populations, intrusions into wildlife, etc., are other known factors. Zoonotic fungal infections have long been neglected and are now gaining due attention. In this review, we briefly discuss the various aspects currently known for zoonotic fungal infections and bring forth the importance of this particular issue to be addressed in a timely manner.

Fungal and bat diversities along a landscape gradient in central Mexico

Species interactions between bats and fungi are poorly known. We documented the association between fungal and bat diversities along a landscape gradient. Ten, eight, and seven bat species were captured in conserved, semi-conserved, and urban sites, respectively. Eptesicus fuscus, Myotis ciliolabrum and Corynorhinus townsendii were the most abundant in conserved and semi-conserved sites. E. fuscus, Myotis velifer, and Lasiurus cinereus were abundant in urban sites. C. townsendii was the least abundant bat. A total of 15 cultivated fungi genera included the fungal diversity in bats, of which nine fungi genera were shared along the landscape gradient. Penicillium and Aspergillus were the most abundant genera, and Aureobasidium, Bispora, Stachybotrys, and Verticillium were only documented in the conserved sites. We observed a higher fungal diversity associated with bat species along this landscape gradient. The individual site-based accumulation curves of fungal diversity showed significant decreasing values along the conserved, semi-conserved, and urban sites, respectively. In conserved and urban sites, M. californicus and M. velifer showed the highest fungal diversity, respectively. E. fuscus was associated to the fungi genera Scopulariopsis, Alternaria, Penicillium and Beauveria; L. cinereus to Cladosporium and Aspergillus, and M. velifer to Alternaria sp1, Bispora and Trichoderma. Conserved sites showed both high bat and fungal diversities [species richness and abundance] compared to semi-conserved and urban sites. More studies associating bat and fungal diversities in other ecosystems are needed to corroborate this pattern.

Identification and full-length genome characterization of a novel mitovirus hosted by the truffle species Tuber rufum

Studying the diversity of viruses found in uncultivated fungi, including those forming mycorrhizal relationships, is essential. It's equally important to explore viral communities in fungi that cause plant diseases or are economically significant. This dual approach helps us grasp the full scope of mycovirus diversity and evolution. Mycorrhizal fungi, in particular, host a wide range of viruses, shedding light on viral diversity and evolution. In this study, we present the discovery and complete genome characterization of a novel mitovirus infecting the hypogeous mycorrhizal fungus Tuber rufum. This virus, denominated "Tuber rufum mitovirus 1" (TrMV1) has a genome size of 2864 nucleotides with a G + C content of 37.53%. It contains a single open reading frame (ORF) responsible for encoding RNA dependent RNA polymerase (RdRp). Comparative analysis using BLASTp reveals that the protein encoded by TrMV1 shares significant sequence similarities with those found in the Triamitovirus genus. Specifically, TrMV1 shows the closest resemblance (43.35% identity) to Sopawar virus, a mitovirus previously detected in soil environments through metatranscriptomic analyses. Phylogenetic examination categorizes TrMV1 as a member of the Triamitovirus genus within the Mitoviridae family. This finding marks the first identification of a mitovirus within the hypogeous mycorrhizal fungus Tuber rufum. The discovery of TrMV1 expands our knowledge of Mitoviridae family diversity and evolution, contributing to the growing repository of mycovirus sequences.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00887-6.

Intrinsically disordered sequences can tune fungal growth and the cell cycle for specific temperatures

Temperature can impact every reaction essential to a cell. For organisms that cannot regulate their own temperature, adapting to temperatures that fluctuate unpredictably and on variable timescales is a major challenge. Extremes in the magnitude and frequency of temperature changes are increasing across the planet, raising questions as to how the biosphere will respond. To examine mechanisms of adaptation to temperature, we collected wild isolates from different climates of the fungus Ashbya gossypii, which has a compact genome of only ∼4,600 genes. We found control of the nuclear division cycle and polarized morphogenesis, both critical processes for fungal growth, were temperature sensitive and varied among the isolates. The phenotypes were associated with naturally varying sequences within the glutamine-rich region (QRR) IDR of an RNA-binding protein called Whi3. This protein regulates both nuclear division and polarized growth via its ability to form biomolecular condensates. In cells and in cell-free reconstitution assays, we found that temperature tunes the properties of Whi3-based condensates. Exchanging Whi3 sequences between isolates was sufficient to rescue temperature-sensitive phenotypes, and specifically, a heptad repeat sequence within the QRR confers temperature-sensitive behavior. Together, these data demonstrate that sequence variation in the size and composition of an IDR can promote cell adaptation to growth at specific temperature ranges. These data demonstrate the power of IDRs as tuning knobs for rapid adaptation to environmental fluctuations.

The fungus Aphanoascella galapagosensis affects bacterial diversity of Galapagos giant tortoise carapaces

AIMS

This study aimed to describe the bacterial microbiome associated with the carapace of three species of Galapagos giant tortoises (Chelonoidis porteri, Chelonoidis donfaustoi, and Chelonoidis vandenburghi) and determine the potential effect of the whitish lesions caused by the fungus Aphanoascella galapagosensis.

METHODS AND RESULTS

We used Oxford Nanopore's MinION to evaluate the external bacterial microbiome associated with the carapaces from the aforementioned species. Taxonomic assignment was carried out by Bugseq and the bacterial communities were compared between carapaces with and without lesions using a NMDS with Bray-Curtis as the dissimilarity index. We found four genera of bacteria that were ubiquitous throughout all individuals, suggesting the presence of shared taxa. The results also displayed a significant difference in the microbiome between carapaces with and without lesions, and for species-carapace interaction, but not among species.

CONCLUSIONS

This study establishes a baseline of the bacterial diversity of the carapace within three Galapagos giant tortoise species, showcasing the presence of a distinctive microbial community. Furthermore, our findings suggest a significant influence of the fungus Aphanoascella galapagosensis on the bacterial populations inhabiting the carapace of these reptiles.

The Impact of the Fungal Priority Pathogens List on Medical Mycology: A Northern European Perspective

Fungal diseases represent a considerable global health concern, affecting >1 billion people annually. In response to this growing challenge, the World Health Organization introduced the pivotal fungal priority pathogens list (FPPL) in late 2022. The FPPL highlights the challenges in estimating the global burden of fungal diseases and antifungal resistance (AFR), as well as limited surveillance capabilities and lack of routine AFR testing. Furthermore, training programs should incorporate sufficient information on fungal diseases, necessitating global advocacy to educate health care professionals and scientists. Established international guidelines and the FPPL are vital in strengthening local guidance on tackling fungal diseases. Future iterations of the FPPL have the potential to refine the list further, addressing its limitations and advancing our collective ability to combat fungal diseases effectively. Napp Pharmaceuticals Limited (Mundipharma UK) organized a workshop with key experts from Northern Europe to discuss the impact of the FPPL on regional clinical practice.

Ecology and evolution of algal-fungal symbioses

Ecological interactions and symbiosis between algae and fungi are ancient, widespread, and diverse with many independent origins. The heterotrophic constraint on fungal nutrition drives fungal interactions with autotrophic organisms, including algae. While ancestors of modern fungi may have evolved as parasites of algae, there remains a latent ability in algae to detect and respond to fungi through a range of symbioses that are witnessed today in the astounding diversity of lichens, associations with corticoid and polypore fungi, and endophytic associations with macroalgae. Research into algal-fungal interactions and biotechnological innovation have the potential to improve our understanding of their diversity and functions in natural systems, and to harness this knowledge to develop sustainable and novel approaches for producing food, energy, and bioproducts.

Antioxidant and Antifungal Properties of Cinnamon, Cloves, Melia azedarach L. and Ocimum gratissimum L. Extracts against Fusarium oxysporum Isolated from Infected Vegetables in Mauritius

BACKGROUND

Fusarium species, a group of economically destructive phytopathogens, are poorly studied in Mauritius where agriculture holds much significance. Furthermore, the increasing popularity of organic farming has prompted interest in alternatives to chemical fungicides.

METHODS

After gaining an overview of Fusarium prevalence in Mauritius fields through a survey, the pathogen was isolated from infected crops and identified based on morphological and molecular characteristics. Methanol and water extracts were then prepared from Melia azedarach, Ocimum gratissimum, cinnamon and cloves before determining their phytochemical profiles. Additionally, the antioxidant and antifungal effects of different concentrations of aqueous extracts were assessed.

RESULTS

The isolate was confirmed as Fusarium oxysporum, and cloves inhibited its growth by up to 100%, especially at 60 and 90 g/L, with the results being significantly higher than those of the synthetic fungicide mancozeb. Over 50% inhibition was also noted for cinnamon and Ocimum gratissimum, and these effects could be linked to the flavonoids, phenols and terpenoids in the extracts.

CONCLUSION

This study presented the aqueous extracts of cloves, cinnamon and Ocimum gratissimum as potential alternatives to chemical fungicides. It also confirmed the prevalence of Fusarium infection in Mauritius fields, thereby highlighting the need for additional studies on the pathogen.

Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences

Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.

Fungi play a crucial role in sustaining microbial networks and accelerating organic matter mineralization and humification during thermophilic phase of composting

Fungi play an important role in the mineralization and humification of refractory organic matter such as lignocellulose during composting. However, limited research on the ecological role of fungi in composting system hindered the development of efficient microbial agents. In this study, six groups of lab-scale composting experiments were conducted to reveal the role of fungal community in composting ecosystems by comparing them with bacterial community. The findings showed that the thermophilic phase was crucial for organic matter degradation and humic acid formation. The Richness index of the fungal community peaked at 1165 during this phase. PCoA analysis revealed a robust thermal stability in the fungal community. Despite temperature fluctuations, the community structure, predominantly governed by Pichia and Candida, remained largely unaltered. The stability of fungal community and the complexity of ecological networks were 1.26 times and 5.15 times higher than those observed in bacterial community, respectively. Fungi-bacteria interdomain interaction markedly enhanced network complexity, contributing to maintain microbial ecological functions. The core fungal species belonging to the family Saccharomycetaceae drove interdomain interaction during thermophilic phase. This study demonstrated the key role of fungi in the composting system, which would provide theoretical guidance for the development of high efficiency composting agents to strengthen the mineralization and humification of organic matter.

Evolution-Based Discovery of Polyketide Acylated Valine from a Cytochalasin-Like Gene Cluster in Simplicillium lamelliciola HDN13430

Utilizing a gene evolution-oriented approach for gene cluster mining, a cryptic cytochalasin-like gene cluster (sla) in Antarctic-derived Simplicillium lamelliciola HDN13430 was identified. Compared with the canonical cytochalasin biosynthetic gene clusters (BGCs), the sla gene cluster lacks the key α,β-hydrolase gene. Heterologous expression of the sla gene cluster led to the discovery of a new compound, slamysin (1), characterized by an N-acylated amino acid structure and demonstrating weak anti-Bacillus cereus activity. These findings underscore the potential of genetic evolution in uncovering novel compounds and indicating specific adaptive evolution within specialized habitats.

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.

Biomolecular condensates in fungi are tuned to function at specific temperatures

Temperature can impact every reaction and molecular interaction essential to a cell. For organisms that cannot regulate their own temperature, a major challenge is how to adapt to temperatures that fluctuate unpredictability and on variable timescales. Biomolecular condensation offers a possible mechanism for encoding temperature-responsiveness and robustness into cell biochemistry and organization. To explore this idea, we examined temperature adaptation in a filamentous-growing fungus called Ashbya gossypii that engages biomolecular condensates containing the RNA-binding protein Whi3 to regulate mitosis and morphogenesis. We collected wild isolates of Ashbya that originate in different climates and found that mitotic asynchrony and polarized growth, which are known to be controlled by the condensation of Whi3, are temperature sensitive. Sequence analysis in the wild strains revealed changes to specific domains within Whi3 known to be important in condensate formation. Using an in vitro condensate reconstitution assay we found that temperature impacts the relative abundance of protein to RNA within condensates and that this directly impacts the material properties of the droplets. Finally, we found that exchanging Whi3 genes between warm and cold isolates was sufficient to rescue some, but not all, condensate-related phenotypes. Together these data demonstrate that material properties of Whi3 condensates are temperature sensitive, that these properties are important for function, and that sequence optimizes properties for a given climate.

Soil microbiome influences human health in the context of climate change

Soil microbiomes continue to evolve and shape the human microbiota according to external anthropogenic and climate change effects. Ancient microbes are being exposed as a result of glacier melting, soil erosion and poor agricultural practices. Soil microbes subtly regulate greenhouse gas emissions and undergo profound alterations due to poor soil maintenance. This review highlights how the soil microbiome influences human digestion processes, mineral and vitamin production, mental health and mood stimulation. Although much about microbial functions remains unknown, increasing evidence suggests that beneficial soil microbes are vital for enhancing human tolerance to diseases and pathogens. Further research is essential to delineate the specific role of the soil microbiome in promoting human health, especially in light of the increasing anthropogenic pressures and changing climatic conditions.

Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.

Emergence of the fungal immune system

Investigation of fungal biology has been frequently motivated by the fact that many fungal species are important plant and animal pathogens. Such efforts have contributed significantly toward our understanding of fungal pathogenic lifestyles (virulence factors and strategies) and the interplay with host immune systems. In parallel, work on fungal allorecognition systems leading to the characterization of fungal regulated cell death determinants and pathways, has been instrumental for the emergent concept of fungal immunity. The uncovered evolutionary trans-kingdom parallels between fungal regulated cell death pathways and innate immune systems incite us to reflect further on the concept of a fungal immune system. Here, I briefly review key findings that have shaped the fungal immunity paradigm, providing a perspective on what I consider its most glaring knowledge gaps. Undertaking to fill such gaps would establish firmly the fungal immune system inside the broader field of comparative immunology.

Plant-Fungi Interactions: Where It Goes?

Fungi live different lifestyles-including pathogenic and symbiotic-by interacting with living plants. Recently, there has been a substantial increase in the study of phytopathogenic fungi and their interactions with plants. Symbiotic relationships with plants appear to be lagging behind, although progressive. Phytopathogenic fungi cause diseases in plants and put pressure on survival. Plants fight back against such pathogens through complicated self-defense mechanisms. However, phytopathogenic fungi develop virulent responses to overcome plant defense reactions, thus continuing their deteriorative impacts. Symbiotic relationships positively influence both plants and fungi. More interestingly, they also help plants protect themselves from pathogens. In light of the nonstop discovery of novel fungi and their strains, it is imperative to pay more attention to plant-fungi interactions. Both plants and fungi are responsive to environmental changes, therefore construction of their interaction effects has emerged as a new field of study. In this review, we first attempt to highlight the evolutionary aspect of plant-fungi interactions, then the mechanism of plants to avoid the negative impact of pathogenic fungi, and fungal strategies to overcome the plant defensive responses once they have been invaded, and finally the changes of such interactions under the different environmental conditions.

The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature-based solutions for mangroves

Globally, soils and sediments are affected by the bioturbation activities of benthic species. The consequences of these activities are particularly impactful in intertidal sediment, which is generally anoxic and nutrient-poor. Mangrove intertidal sediments are of particular interest because, as the most productive forests and one of the most important stores of blue carbon, they provide global-scale ecosystem services. The mangrove sediment microbiome is fundamental for ecosystem functioning, influencing the efficiency of nutrient cycling and the abundance and distribution of key biological elements. Redox reactions in bioturbated sediment can be extremely complex, with one reaction creating a cascade effect on the succession of respiration pathways. This facilitates the overlap of different respiratory metabolisms important in the element cycles of the mangrove sediment, including carbon, nitrogen, sulphur and iron cycles, among others. Considering that all ecological functions and services provided by mangrove environments involve microorganisms, this work reviews the microbial roles in nutrient cycling in relation to bioturbation by animals and plants, the main mangrove ecosystem engineers. We highlight the diversity of bioturbating organisms and explore the diversity, dynamics and functions of the sediment microbiome, considering both the impacts of bioturbation. Finally, we review the growing evidence that bioturbation, through altering the sediment microbiome and environment, determining a 'halo effect', can ameliorate conditions for plant growth, highlighting the potential of the mangrove microbiome as a nature-based solution to sustain mangrove development and support the role of this ecosystem to deliver essential ecological services.

Identification and complete genome sequencing of a novel betapartitivirus naturally infecting the mycorrhizal desert truffle Terfezia claveryi

Viruses that naturally infect fungal species and capable of establishing mycorrhizae are largely unknown. In this study, we identified and characterized a new partitivirus inhabiting the ascomycete, mycorrhizal desert truffle species Terfezia claveryi, and named it "Terfezia claveryi partitivirus 1" (TcPV1). The entire genome of TcPV1, sequenced by both high throughput sequencing of the total dsRNA extracts and by Sanger sequencing of the RLM-RACE PCR products comprised two dsRNA segments of 2404 bp and 2374 bp, respectively. Both dsRNA genome segments harbored a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. The BLASTp search of the RdRp and CP sequences revealed the highest sequence identities (41.92% and 24.13% identity, respectively) to those of Bipolaris maydis partitivirus 2 and Plasmopara viticola lesion associated partitivirus 5. Molecular phylogenetic analyses of the RdRp sequence showed that TcPV1 fall within a clade composed entirely of members of the genus Betapartitivirus, belonging to the family Partitiviridae. In light of this molecular evidence, TcPV1 is a new member of the genus Betapartitivirus. This is the first report of a new partitivirus hosted by the ascomycete, mycorrhizal fungus T. claveryi.

Altered gut bacterial-fungal interkingdom networks in children and adolescents with depression

BACKGROUND

Most studies of the gut-brain axis have focused on bacteria; little is known about commensal fungi. Children and adolescents with depression were reported to have gut bacterial microbiota dysbiosis, but the role of the mycobiota has not been evaluated.

METHODS

Faecal samples were obtained from 145 children and adolescents with depression and 110 age- and gender-matched healthy controls. We analysed the fungal microbiota, including in terms of their associations with the gut microbiota, and subjected the internal transcribed spacer 2 (ITS2) rRNA gene to mitochondrial sequencing.

RESULTS

Our findings revealed unaltered fungal diversity, but altered taxonomic composition, of the faecal fungal microbiota in the children and adolescents with depression. Key fungi such as Saccharomyces and Apiotrichum were enriched in the depressed patients, while Aspergillus and Xeromyces showed significantly decreased abundance. Interestingly, the bacterial-fungal interkingdom network was markedly altered in the children and adolescents with depression, and mycobiome profiles were associated with different bacterial microbiomes.

LIMITATION

The cross-sectional design precluded the establishment of a causal relationship between the gut mycobiota and the children and adolescents with depression.

CONCLUSIONS

The gut mycobiome is altered in the children and adolescents with depression. Our findings suggest that fungi play an important role in the balance of the gut microbiota and may help identify novel therapeutic targets for depression.

Applying molecular and genetic methods to trees and their fungal communities

Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.

Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecule mediated BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis spp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and their role in complex communities should continue to be a priority.

Diverse partitiviruses hosted by the ectomycorrhizal agaric Hebeloma mesophaeum and the natural transmission of a partitivirus between phylogenetically distant, sympatric fungi

Mycorrhizal fungi host diverse mycoviruses that contribute to our understanding of their diversity and evolution. Here we report on the identification and complete genome characterization of three novel partitiviruses naturally infecting the ectomycorrhizal fungus Hebeloma mesophaeum. During NGS derived viral sequence analyses, we identified a partitivirus that is conspecific with the previously reported partitivirus (LcPV1) described from a saprotrophic fungus Leucocybe candicans. The two distinct fungal specimens inhabited the same vicinity of a campus garden. RdRp sequences encoded by the LcPV1 isolates from both host fungi was found to be identical. Bio-tracking studies revealed that viral loads of LcPV1 drop significantly in L. candicans but not in H. mesophaeum within four years period. The physical proximity of the mycelial networks of both fungal specimens implied the occurrence of a virus transmission event with unknown mechanism. Nature of this virus transmission was discussed in relation to transient interspecific mycelial contact hypothesis.

They shall not grow mold: Soldiers of innate and adaptive immunity to fungi

Fungi are ubiquitous commensals, seasoned predators, and important agents of emerging infectious diseases [1 ]. The immune system assumes the essential responsibility for responding intelligently to the presence of known and novel fungi to maintain host health. In this Review, we describe the immune responses to pathogenic fungi and the varied array of fungal agents confronting the vertebrate host within the broader context of fungal and animal evolution. We provide an overview of the mechanistic details of innate and adaptive antifungal immune responses, as well as ways in which these basic mechanisms support the development of vaccines and immunotherapies.

Fungi Present in the Organic and Mineral Layers of Six Broad-Leaved Tree Plantations as Assessed by the Plate Dilution Method

This study examined the distribution of culturable fungi and predominant genera in the organic layer and in the upper layers of the mineral soil of six broad-leaved tree plantations in autumn, after the full fall of leaves. In total, 1335 fungal isolates were recovered from an organic layer and two mineral layers (0–4 cm and 5–8 cm) of soil. The structure of fungal genera differed in the tree plantations and in the three studied soil layers. The organic layer was the layer most populated by fungi compared to the mineral layers. In the organic layer, Penicillium and phyllosphere fungi such as Cladosporium and Phoma dominated. Deeper in the soil, the dominance of certain genera decreased with the increase in Trichoderma, Mucor, Mortierella, and entomopathogenic fungi such as Paecilomyces and Beauveria. Penicillium was one of the most abundant fungi in all soil layers studied.

The Contribution of Mycological Tourism to Well-Being, the Economy and Sustainable Development

This article analyses the scientific production related to tourism and mushrooms. The method used was a bibliometric analysis and a systematic literature review. The main results show that it is a recent area of study that predominates in Spain but that will expand and gain relevance over time. The thematic analysis has made it possible to structure the information according to the economic contribution of this tourist niche, the well-being it brings to residents and tourists, the importance of a sustainable development of the activity, and the promotion and marketing of this new tourism. Supporting mycological tourism will help the development of rural areas and bring physical, mental, social, educational, and nutritional benefits to residents and tourists. This study has allowed us to develop a future research agenda, highlighting the importance of further research to harness the benefits of mycological tourism while at the same time transferring that knowledge to stakeholders, which will be necessary.

Increased levels of cell wall degrading enzymes and peptidases are associated with aggressiveness in a virulent isolate of Pyrenophora teres f. maculata

Pyrenophora teres f. maculata (Ptm) is a fungal pathogen that causes the spot form of net blotch on barley and leads to economic losses in many of the world's barley-growing regions. Isolates of Ptm exhibit varying levels of aggressiveness that result in quantifiable changes in the severity of the disease. Previous research on plant-pathogen interactions has shown that such divergence is reflected in the proteome and secretome of the pathogen, with certain classes of proteins more prominent in aggressive isolates. Here we have made a detailed comparative analysis of the secretomes of two Ptm isolates, GPS79 and E35 (highly and mildly aggressive, respectively) using a proteomics-based approach. The secretomes were obtained in vitro using media amended with barley leaf sections. Secreted proteins therein were harvested, digested with trypsin, and fractionated offline by HPLC prior to LC-MS in a high-resolution instrument to obtain deep coverage of the proteome. The subsequent analysis used a label-free quantitative proteomics approach with relative quantification of proteins based on precursor ion intensities. A total of 1175 proteins were identified, 931 from Ptm and 244 from barley. Further analysis revealed 160 differentially abundant proteins with at least a two-fold abundance difference between the isolates, with the most enriched in the aggressive GPS79 secretome. These proteins were mainly cell-wall (carbohydrate) degrading enzymes and peptidases, with some oxidoreductases and other pathogenesis-related proteins also identified, suggesting that aggressiveness is associated with an improved ability of GPS79 to overcome cell wall barriers and neutralize host defense responses.