Advanced genetic techniques in fungal pathogen research

Although fungi have been important model organisms for solving genetic, molecular, and ecological problems, recently, they are also becoming an important source of infectious disease. Despite their high medical burden, fungal pathogens are understudied, and relative to other pathogenic microbes, less is known about how their gene functions contribute to disease. This is due, in part, to a lack of powerful genetic tools to study these organisms. In turn, this has resulted in inappropriate treatments and diagnostics and poor disease management. There are a variety of reasons genetic studies were challenging in pathogenic fungi, but in recent years, most of them have been overcome or advances have been made to circumvent these barriers. In this minireview, we highlight how recent advances in genetic studies in fungal pathogens have resulted in the discovery of important biology and potential new antifungals and have created the tools to comprehensively study these important pathogens.

Wisconsin bill would restrict pathogen studies

Efforts to ban "gain-of-function" research on viruses and bacteria worry scientists.

Characteristics and potential clinical applications of the extracellular vesicles of human pathogenic Fungi

Extracellular vesicles (EVs) are a heterogeneous group of lipid membrane-enclosed compartments that contain different biomolecules and are released by almost all living cells, including fungal genera. Fungal EVs contain multiple bioactive components that perform various biological functions, such as stimulation of the host immune system, transport of virulence factors, induction of biofilm formation, and mediation of host-pathogen interactions. In this review, we summarize the current knowledge on EVs of human pathogenic fungi, mainly focusing on their biogenesis, composition, and biological effects. We also discuss the potential markers and therapeutic applications of fungal EVs.

Metallic Structures: Effective Agents to Fight Pathogenic Microorganisms

The current worldwide pandemic caused by coronavirus disease 2019 (COVID-19) had alerted the population to the risk that small microorganisms can create for humankind’s wellbeing and survival. All of us have been affected, directly or indirectly, by this situation, and scientists all over the world have been trying to find solutions to fight this virus by killing it or by stop/decrease its spread rate. Numerous kinds of microorganisms have been occasionally created panic in world history, and several solutions have been proposed to stop their spread. Among the most studied antimicrobial solutions, are metals (of different kinds and applied in different formats). In this regard, this review aims to present a recent and comprehensive demonstration of the state-of-the-art in the use of metals, as well as their mechanisms, to fight different pathogens, such as viruses, bacteria, and fungi.

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

Janus-Faced Molecules against Plant Pathogenic Fungi

The high cytotoxicity of the secondary metabolites of mycotoxins is capable of killing microbes and tumour cells alike, similarly to the genotoxic effect characteristic of Janus-faced molecules. The "double-edged sword" effect of several cytotoxins is known, and these agents have, therefore, been utilized only reluctantly against fungal infections. In this review, consideration was given to (a) toxins that could be used against plant and human pathogens, (b) animal models that measure the effect of antifungal agents, (c) known antifungal agents that have been described and efficiently prevent the growth of fungal cells, and (d) the chemical interactions that are characteristic of antifungal agents. The utilization of apoptotic effects against tumour growth by agents that, at the same time, induce mutations may raise ethical issues. Nevertheless, it deserves consideration despite the mutagenic impact of Janus-faced molecules for those patients who suffer from plant pathogenic fungal infections and are older than their fertility age, in the same way that the short-term cytotoxicity of cancer treatment is favoured over the long-term mutagenic effect.

Nosocomial Fungal Infections: Epidemiology, Infection Control, and Prevention

Invasive fungal infections are an important cause of morbidity and mortality in hospitalized patients and in the immunocompromised population. This article reviews the current epidemiology of nosocomial fungal infections in adult patients, with an emphasis on invasive candidiasis (IC) and invasive aspergillosis (IA). Included are descriptions of nosocomial infections caused by Candida auris, an emerging pathogen, and IC- and IA-associated with coronavirus disease 2019. The characteristics and availability of newer nonculture-based tests for identification of nosocomial fungal pathogens are discussed. Recently published recommendations and guidelines for the control and prevention of these nosocomial fungal infections are summarized.

Virulence of Fungi Isolated from Ambrosia Beetles to Acer amoenum Branches

In Japan, no association between the ambrosia beetle and their fungal symbionts causing branch dieback or tree mortality on maple, Acer amoenum, has been reported. However, we identified dieback of several branches and numerous holes created by three species of ambrosia beetles, Euwallacea fornicatus, Euwallacea interjectus, and Platypus calamus, on Acer amoenum trees at the University of Tokyo Tanashi Forest, Tokyo Metropolis, Japan, in 2016. The high attack density of the beetles was observed on the weakened trees; however, the contribution of the associated fungi to the branch dieback was still unknown. We isolated fungi carried by these three beetles and inoculated them to Acer amoenum cut main trunks and sapling branches to determine whether the associated fungi caused the branch dieback. Fusarium euwallaceae was isolated from all Euwallacea fornicatus and Euwallacea interjectus, whereas Arthrinium phaeospermum, Raffaelea cyclorhipidia, and Epicoccum nigrum were isolated from P. calamus, with 35, 15, and 5% isolation frequencies, respectively. Inoculation with F. euwallaceae and R. cyclorhipidia induced statistically significantly wider sapwood discoloration (six and four times wider for F. euwallaceae and R. cyclorhipidia, respectively) than the controls, and larger water-conductance loss (2 and 1.7 times larger for F. euwallaceae and R. cyclorhipidia, respectively) than the controls. However, the observed lesions were not large enough to cause discoloration, and symptoms of dieback were not observed, even 13 months after the inoculation. Therefore, we concluded that the virulence of the four investigated fungi to Acer amoenum was very low and that these fungi were likely not the primary cause of the branch dieback.

Molecular analysis of a fungal disease in the habitat-forming brown macroalga Phyllospora comosa (Fucales) along a latitudinal gradient

Infectious diseases affecting habitat-forming species can have significant impacts on population dynamics and alter the structure and functioning of marine ecosystems. Recently, a fungal infection was described as the causative agent of necrotic lesions on the stipe of the forest-forming macroalga Phyllospora comosa, a disease named "stipe rot" (SR). Here, we developed a quantitative PCR (qPCR) method for rapid detection and quantification of this pathogen, which was applied to evaluate the level of SR infection in eight P. comosa populations spanning the entire latitudinal distribution of this species along southeastern Australia. We also investigated the relationship between the abundance and prevalence of Stipe Rot Fungus (SRF) and potential host chemical defenses as well as its relationship with morphological and ecophysiological traits of P. comosa. qPCR estimates of SRF abundance reflected the levels of infection estimated by visual assessment, with higher numbers of SRF copies being observed in individuals showing high or intermediate levels of visual symptoms of SR. Concordance of conventional PCR and visual assessments was 92 and 94%, respectively, compared to qPCR detection. SRF prevalence was positively related to fucoxanthin content and herbivory, but not significant related to other traits measured (phlorotannin content, total length, thallus diameter, stipe width, number of branches, frond width, fouling, bleaching, gender, and photosynthetic efficiency). These results provide confidence for previous reports of this disease based upon visual assessments only, contribute to the development of monitoring and conservation strategies for safeguarding P. comosa forests, and generate insights into potential factors influencing host-pathogen interactions in this system.

Phytopathogenic Fungi and Toxicity

Phytopathogen fungi are responsible for serious plant diseases which might negatively affect crop productivity [...].

Advances in the biological control of phytoparasitic nematodes via the use of nematophagous fungi

Agricultural production is one of most important activities for food supply and demand, that provides a source of raw materials, and generates commercial opportunities for other industries around the world. It may be both positively and negatively affected by climatic and biological factors. Negative biological factors are those caused by viruses, bacteria, or parasites. Given the serious problems posed by phytoparasitic nematodes for farmers, causing crop losses globally every year, the agrochemical industry has developed compounds with the capacity to inhibit their development; however, they can cause the death of other beneficial organisms and their lixiviation can contaminate the water table. On the other hand, the positive biological factors are found in biotechnology, the scientific discipline that develops products, such as nematophagous fungi (of which Purpureocillium lilacinum and Pochonia chlamydosporia have the greatest potential), for the control of pests and/or diseases. The present review focuses on the importance of nematophagous fungi, particularly sedentary endoparasitic nematodes, their research on the development of biological control agents, the mass production of fungi Purpureocillium lilacinum and Pochonia chlamydosporia, and their limited commercialization due to the lack of rigorous methods that enable the anticipation of complex interactions between plant and phytopathogenic agents.

The taxonomy of two uncultivated fungal mammalian pathogens is revealed through phylogeny and population genetic analyses

Ever since the uncultivated South American fungal pathogen Lacazia loboi was first described 90 years ago, its etiology and evolutionary traits have been at the center of endless controversies. This pathogen infects the skin of humans and as long believed, dolphin skin. However, recent DNA analyses of infected dolphins placed its DNA sequences within Paracoccidioides species. This came as a surprise and suggested the human and dolphin pathogens may be different species. In this study, population genetic analyses of DNA from four infected dolphins grouped this pathogen in a monophyletic cluster sister to P. americana and to the other Paracoccidioides species. Based on the results we have emended the taxonomy of the dolphin pathogen as Paracoccidioides cetii and P. loboi the one infecting human. Our data warn that phylogenetic analysis of available taxa without the inclusion of unusual members may provide incomplete information for the accurate classification of anomalous species.

Fungal Infections in COVID-19 Intensive Care Patients

Opportunistic fungal infections increase morbidity and mortality in COVID-19 patients monitored in intensive care units (ICU). As patients' hospitalization days in the ICU and intubation period increase, opportunistic infections also increase, which prolongs hospital stay days and elevates costs. The study aimed to describe the profile of fungal infections and identify the risk factors associated with mortality in COVID-19 intensive care patients. The records of 627 patients hospitalized in ICU with the diagnosis of COVID-19 were investigated from electronic health records and hospitalization files. The demographic characteristics (age, gender), the number of ICU hospitalization days and mortality rates, APACHE II scores, accompanying diseases, antibiotic-steroid treatments taken during hospitalization, and microbiological results (blood, urine, tracheal aspirate samples) of the patients were recorded. Opportunistic fungal infection was detected in 32 patients (5.10%) of 627 patients monitored in ICU with a COVID-19 diagnosis. The average APACHE II score of the patients was 28 ± 6. While 25 of the patients (78.12%) died, seven (21.87%) were discharged from the ICU. Candida parapsilosis (43.7%) was the opportunistic fungal agent isolated from most blood samples taken from COVID-19 positive patients. The mortality rate of COVID-19 positive patients with candidemia was 80%. While two out of the three patients (66.6%) for whom fungi were grown from their tracheal aspirate died, one patient (33.3%) was transferred to the ward. Opportunistic fungal infections increase the mortality rate of COVID-19-positive patients. In addition to the risk factors that we cannot change, invasive procedures should be avoided, constant blood sugar regulation should be applied, and unnecessary antibiotics use should be avoided.

Characterization of lncRNAs and mRNAs Involved in Powdery Mildew Resistance in Cucumber

Powdery mildew (PM) is a severe fungal disease of cucumber worldwide. Identification of genetic factors resistant to PM is of great importance for marker-assisted breeding to ensure cucumber production. Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) have been shown to play important roles in plant development and immunity; however, whether they have a role in PM response in cucurbit crops remains unknown. We performed strand-specific RNA sequencing and miRNA sequencing using RNA from cucumber leaves of two near-isogenic lines (NILs), S1003 and NIL (Pm5.1) infected with PM, and systematically characterized the profiles of cucumber lncRNAs and messenger RNA (mRNAs) responsive to PM. In total, we identified 12,903 lncRNAs and 25,598 mRNAs responsive to PM. Differential expression (DE) analysis showed that 119 lncRNAs and 136 mRNAs correlated with PM resistance. Functional analysis of these DE lncRNAs and DE mRNAs revealed that they are significantly associated with phenylpropanoid biosynthesis, phenylalanine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and endocytosis. Particularly, two lncRNAs, LNC_006805 and LNC_012667, might play important roles in PM resistance. In addition, we also predicted mature miRNAs and competing endogenous RNA (ceRNA) networks of lncRNA-miRNA-mRNA involved in PM resistance. A total of 49 DE lncRNAs could potentially act as target mimics for 106 miRNAs. Taken together, our results provide an abundant resource for further exploration of cucumber lncRNAs, mRNAs, miRNAs, and ceRNAs in PM resistance, and will facilitate the molecular breeding for PM-resistant varieties to control this severe disease in cucumber.

Quassinoids with Inhibitory Activities against Plant Fungal Pathogens from Picrasma javanica

A bioactivity-guided study on the leaves of Picrasma javanica led to the isolation of 19 quassinoids, including 13 new compounds. The structures of the new compounds were elucidated by a combination of spectroscopic data analysis, X-ray crystallography studies, and electronic circular dichroism (ECD) data interpretation. Compounds 1-7 are rare examples of quassinoids with a keto carbonyl group at C-12. The biological activities of 11 of the more abundant isolates were evaluated against five phytopathogenic fungi in vitro, and several of them including 6 and 15 showed moderate inhibitory effects that were comparative to those of the positive control, carbendazim. In addition, the preliminary structure-activity relationships (SARs) of these quassinoids were also investigated.

Would it be possible to use nonpathogenic fungi to improve the turnover of crop residues?

This study was aimed to assess the suitability of four fungal species for operating in the residues of three crops in Golestan province, Iran. For this, four experiments were conducted to analyze their ability to grow on five culture media (Experiment I) and on the residues (Experiment II) and their growth responses to different pHs (Experiment III) and temperature levels (Experiment IV). Then, the possibility of establishing these fungi in the cultivated lands of studied crops was examined. Fungal growth was high on soybean and cotton residues and low on those of rice, and all the fungi produced a significant reduction in the carbon to nitrogen ratios in relation to noninoculated residues. The amount of nitrogen in fungal-treated cotton residues increased about four times compared with the control and in other studied residues increased twice as much as the control. The lowest C:N values for cotton and rice residues were found for Pleurotus ostreatus while Aspergillus niger was the most efficient for those of soybean. The results also showed that these fungi will not show the best performance in respect to temperature and pH, but will not be ineffective. The results could be the basis for further studies on the use of these fungi to improve nutrient cycling, focusing on multicriteria zoning on climatic and soil-related components.

Synthesis and Insecticidal Evaluation of Chiral Neonicotinoids Analogs: The Laurel Wilt Case

Xyleborus sp beetles are types of ambrosia beetles invasive to the United States and recently also to Mexico. The beetle can carry a fungus responsible for the Laurel Wilt, a vascular lethal disease that can host over 300 tree species, including redbay and avocado. This problem has a great economic and environmental impact. Indeed, synthetic chemists have recently attempted to develop new neonicotinoids. This is also due to severe drug resistance to “classic” insecticides. In this research, a series of neonicotinoids analogs were synthesized, characterized, and evaluated against Xyleborus sp. Most of the target compounds showed good to excellent insecticidal activity. Generally, the cyclic compounds also showed better activity in comparison with open-chain compounds. Compounds R-13, 23, S-29, and 43 showed a mortality percent of up to 73% after 12 h of exposure. These results highlight the enantioenriched compounds with absolute R configuration. The docking results correlated with experimental data which showed both cation-π interactions in relation to the aromatic ring and hydrogen bonds between the search cavity 3C79 and the novel molecules. The results suggest that these sorts of interactions are responsible for high insecticidal activity.

Transcription factor control of virulence in phytopathogenic fungi

Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.

The Emerging Role of Mast Cells in Response to Fungal Infection

Mast cells (MCs) have been considered as the core effector cells of allergic diseases. However, there are evidence suggesting that MCs are involved in the mechanisms of fungal infection. MCs are mostly located in the border between host and environment and thus may have easy contact with the external environmental pathogens. These cells express receptors which can recognize pathogen-associated molecular patterns such as Toll-like receptors (TLR2/4) and C-type Lectins receptors (Dectin-1/2). Currently, more and more data indicate that MCs can be interacted with some fungi (Candida albicans, Aspergillus fumigatus and Sporothrix schenckii). It is demonstrated that MCs can enhance immunity through triggered degranulation, secretion of cytokines and chemokines, neutrophil recruitment, or provision of extracellular DNA traps in response to the stimulation by fungi. In contrast, the involvement of MCs in some immune responses may lead to more severe symptoms, such as intestinal barrier function loss, development of allergic bronchial pulmonary aspergillosis and increased area of inflammatory in S. schenckii infection. This suggests that MCs and their relevant signaling pathways are potential treatment regimens to prevent the clinically unwanted consequences. However, it is not yet possible to make definitive statements about the role of MCs during fungal infection and/or pathomechanisms of fungal diseases. In our article, we aim to review the function of MCs in fungal infections from molecular mechanism to signaling pathways, and illustrate the role of MCs in some common host-fungi interactions.

Immunology of Fungal Infections

Complex processes mediate immunity to fungal infections. Responses vary depending on the organism, morphogenic state, and infection site. Innate immune effectors such as epithelia, phagocytes, and soluble molecules detect pathogens, kill fungi, release cytokines, and prime the adaptive response. Adaptive responses to mucocutaneous or invasive disease are markedly different but intersect at certain pathways (molecules required for IL-23 and IL-12 signaling). Many of these pathways have been elucidated from the study of inborn errors of immunity. This review explores the general aspects of antifungal immunity and delves into the mechanisms that mediate protection from frequently encountered fungi.

The airborne mycobiome and associations with mycotoxins and inflammatory markers in the Norwegian grain industry

Grain dust exposure is associated with respiratory symptoms among grain industry workers. However, the fungal assemblage that contribute to airborne grain dust has been poorly studied. We characterized the airborne fungal diversity at industrial grain- and animal feed mills, and identified differences in diversity, taxonomic compositions and community structural patterns between seasons and climatic zones. The fungal communities displayed strong variation between seasons and climatic zones, with 46% and 21% of OTUs shared between different seasons and climatic zones, respectively. The highest species richness was observed in the humid continental climate of the southeastern Norway, followed by the continental subarctic climate of the eastern inland with dryer, short summers and snowy winters, and the central coastal Norway with short growth season and lower temperature. The richness did not vary between seasons. The fungal diversity correlated with some specific mycotoxins in settled dust and with fibrinogen in the blood of exposed workers, but not with the personal exposure measurements of dust, glucans or spore counts. The study contributes to a better understanding of fungal exposures in the grain and animal feed industry. The differences in diversity suggest that the potential health effects of fungal inhalation may also be different.

Mechanisms of fungal dissemination

Fungal infections are an increasing threat to global public health. There are more than six million fungal species worldwide, but less than 1% are known to infect humans. Most of these fungal infections are superficial, affecting the hair, skin and nails, but some species are capable of causing life-threatening diseases. The most common of these include Cryptococcus neoformans, Aspergillus fumigatus and Candida albicans. These fungi are typically innocuous and even constitute a part of the human microbiome, but if these pathogens disseminate throughout the body, they can cause fatal infections which account for more than one million deaths worldwide each year. Thus, systemic dissemination of fungi is a critical step in the development of these deadly infections. In this review, we discuss our current understanding of how fungi disseminate from the initial infection sites to the bloodstream, how immune cells eliminate fungi from circulation and how fungi leave the blood and enter distant organs, highlighting some recent advances and offering some perspectives on future directions.

Microbial pathogens of freshwater crayfish: A critical review and systematization of the existing data with directions for future research

Despite important ecological role and growing commercial value of freshwater crayfish, their diseases are underresearched and many studies examining potential crayfish pathogens do not thoroughly address their epizootiology, pathology or biology. This study reviews over 100 publications on potentially pathogenic viruses, bacteria, fungi and fungal-like microorganisms reported in crayfish and systematizes them based on whether pathogenicity has been observed in an analysed species. Conclusions on pathogenicity were based on successful execution of infectivity trials. For 40.6% of examined studies, microbes were successfully systematized, while for more than a half (59.4%) no conclusion on pathogenicity could be made. Fungi and fungal-like microorganisms were the most studied group of microbes with the highest number of analysed hosts, followed by bacteria and viruses. Our analysis demonstrated the need for: (a) inclusion of higher number of potential host species in the case of viruses, (b) research of bacterial effects in tissues other than haemolymph, and (c) more research into potential fungal and fungal-like pathogens other than Aphanomyces astaci. We highlight the encountered methodological challenges and biases and call for a broad but standardized framework for execution of infectivity trials that would enable systematic data acquisition on interactions between microbes and the host.

Colonization by arbuscular mycorrhizal fungi improves salinity tolerance of eucalyptus (Eucalyptus camaldulensis) seedlings

Soil salinity affects soil quality and reduces plant performance. Arbuscular mycorrhizal fungi (AMF) can enhance the tolerance of plants under salinity stress. Cultivation of eucalyptus (Eucalyptus camaldulensis), which exhibits high water use efficiency, is possible in saline areas to produce raw materials for the pulp industry. We determined the effects of arbuscular mycorrhizal fungi (AMF) on the growth and survival of eucalyptus seedlings under saline conditions. Three different clones of eucalyptus seedlings were pre-inoculated with three salt-tolerant AMF species, namely Glomus sp.2, Gigaspora albida and G. decipiens, and without pre-inoculation. The seedlings were grown in a greenhouse for 45 days. They were then transferred to individual pots, filled with field soil and subsequently treated with NaCl solution until electro-conductivity (EC) reached 10, 15 and 20 dS m-1. They were watered for 90 days under nursery conditions. The results show that increased salinity levels reduced plant performance, fractional AMF root colonization, spore number, and eucalypt K/Na ratio. AMF significantly increased chlorophyll and decreased leaf proline concentrations by more than 50% and 20% respectively and increased the K/Na ratio three- to six-fold compared with non-inoculated plants. Pre-inoculation with AMF before outplanting also improved plant performance by more than 30% under salinity stress compared to non-inoculated plants. We conclude that AMF can alleviate the negative impacts of salinity on plant physiological and biochemical parameters.

Extraordinary Multi-Organismal Interactions Involving Bacteriophages, Bacteria, Fungi, and Rotifers: Quadruple Microbial Trophic Network in Water Droplets

Our observations of predatory fungi trapping rotifers in activated sludge and laboratory culture allowed us to discover a complicated trophic network that includes predatory fungi armed with bacteria and bacteriophages and the rotifers they prey on. Such a network seems to be common in various habitats, although it remains mostly unknown due to its microscopic size. In this study, we isolated and identified fungi and bacteria from activated sludge. We also noticed abundant, virus-like particles in the environment. The fungus developed absorptive hyphae within the prey. The bacteria showed the ability to enter and exit from the hyphae (e.g., from the traps into the caught prey). Our observations indicate that the bacteria and the fungus share nutrients obtained from the rotifer. To narrow the range of bacterial strains isolated from the mycelium, the effects of bacteria supernatants and lysed bacteria were studied. Bacteria isolated from the fungus were capable of immobilizing the rotifer. The strongest negative effect on rotifer mobility was shown by a mixture of Bacillus sp. and Stenotrophomonas maltophilia. The involvement of bacteriophages in rotifer hunting was demonstrated based on molecular analyses and was discussed. The described case seems to be an extraordinary quadruple microbiological puzzle that has not been described and is still far from being understood.

Landscape Composition and Fungicide Exposure Influence Host-Pathogen Dynamics in a Solitary Bee

Both ecosystem function and agricultural productivity depend on services provided by bees; these services are at risk from bee declines which have been linked to land use change, pesticide exposure, and pathogens. Although these stressors often co-occur in agroecosystems, a majority of pollinator health studies have focused on these factors in isolation, therefore limiting our ability to make informed policy and management decisions. Here, we investigate the combined impact of altered landscape composition and fungicide exposure on the prevalence of chalkbrood disease, caused by fungi in the genus Ascosphaera Olive and Spiltoir 1955 (Ascosphaeraceae: Onygenales), in the introduced solitary bee, Osmia cornifrons (Radoszkowski 1887) (Megachilidae: Hymenoptera). We used both field studies and laboratory assays to evaluate the potential for interactions between altered landscape composition, fungicide exposure, and Ascosphaera on O. cornifrons mortality. Chalkbrood incidence in larval O. cornifrons decreased with high open natural habitat cover, whereas Ascosphaera prevalence in adults decreased with high urban habitat cover. Conversely, high fungicide concentration and high forest cover increased chalkbrood incidence in larval O. cornifrons and decreased Ascosphaera incidence in adults. Our laboratory assay revealed an additive effect of fungicides and fungal pathogen exposure on the mortality of a common solitary bee. Additionally, we utilized phylogenetic methods and identified four species of Ascosphaera with O. cornifrons, both confirming previous reports and shedding light on new associates. Our findings highlight the impact of fungicides on bee health and underscore the importance of studying interactions among factors associated with bee decline.

Modulation of Immune Responses by Particle Size and Shape

The immune system has to cope with a wide range of irregularly shaped pathogens that can actively move (e.g., by flagella) and also dynamically remodel their shape (e.g., transition from yeast-shaped to hyphal fungi). The goal of this review is to draw general conclusions of how the size and geometry of a pathogen affect its uptake and processing by phagocytes of the immune system. We compared both theoretical and experimental studies with different cells, model particles, and pathogenic microbes (particularly fungi) showing that particle size, shape, rigidity, and surface roughness are important parameters for cellular uptake and subsequent immune responses, particularly inflammasome activation and T cell activation. Understanding how the physical properties of particles affect immune responses can aid the design of better vaccines.

Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments

Genome sequencing of fungal pathogens have documented extensive variation in genome structure and composition between species and in many cases between individuals of the same species. This type of genomic variation can be adaptive for pathogens to rapidly evolve new virulence phenotypes. Analyses of genome-wide variation in fungal pathogen genomes rely on high quality assemblies and methods to detect and quantify structural variation. Population genomic studies in fungi have addressed the underlying mechanisms whereby structural variation can be rapidly generated. Transposable elements, high mutation and recombination rates as well as incorrect chromosome segregation during mitosis and meiosis contribute to extensive variation observed in many species. We here summarize key findings in the field of fungal pathogen genomics and we discuss methods to detect and characterize structural variants including an alignment-based pipeline to study variation in population genomic data.

Measuring In Vivo Neutrophil Trafficking Responses During Fungal Infection Using Mixed Bone Marrow Chimeras

Neutrophil migration to the site of infection is an essential process for the control and clearance of microbial growth within the host. Identifying the molecular factors that mediate neutrophil chemotaxis is therefore critical for our understanding of disease pathogenesis and the mechanisms underlying protective immunity. Here, we describe a protocol that enables analysis of neutrophil recruitment from the blood into fungal-infected organs in vivo, using mixed bone marrow chimeras and flow cytometry. This method directly assesses the relative contribution of a receptor or intracellular molecule in controlling neutrophil chemotaxis during fungal infection and can be adapted to a variety of other non-fungal infection experimental settings.

Murine Models of Hematopoietic Cell Transplantation to Investigate Fungal Infections

Animal models are fundamental to unravel the complex nature of fungal infections in the host context. Here, a versatile murine model of hematopoietic cell transplantation (HCT) is described. This model can be used to investigate the establishment and progression of fungal infections after HCT and to elucidate how different transplant variables affect the recovery of host immunity.

Antifungal Activity of Some Essential Oils Emulsions Against Fungi Contaminating Ras Cheese

<b>Background and Objective:</b> Ras cheese is one of the important dairy products that are consumed in great quantities. But this cheese is vulnerable to the growth of fungi during ripening and selling until consumption. Therefore, research aimed to detect fungi contaminating Ras cheese and try to resist them. <b>Materials and Methods:</b> The effect of various concentrations (0.25, 0.5, 1, 2 and 3%) of essential oils emulsions of clove (<i>Syzygium aromaticum</i>), thyme (<i>Thymus vulgaris</i>) and peppermint (<i>Mentha piperita</i>) severally on the mycelial growth of the isolated fungi as compared to the control sample was tested <i>in vitro.</i> <b>Results:</b> The results indicated that many fungal species belonging to the genera <i>Aspergillus</i>, <i>Mucor</i>, <i>Eurotium</i> and <i>Mortierella</i> were isolated from the infected Ras cheese. Ochratoxin A was found in two samples whereas recorded the highest level in sample number 1 (2.1 μg kg<sup>1</sup>). Aflatoxin M1 was found in few levels ranged between 0.012 and 0.360 μg kg<sup>1</sup>in cheese samples, while aflatoxin B1 and B2 weren't detected in all samples. Clove essential oil emulsion completely inhibited the growth of all tested fungi at the concentration of 0.5%, followed by thyme essential oil emulsion which inhibited the fungal growth of all fungi at the concentration of 1%, while peppermint essential oil emulsion was less effective. <b>Conclusion:</b> The research recommends that clove and thyme essential oils emulsions can be used to resist the fungi of Ras cheese. Also, suggests that more research could be done on these essential oils emulsions to produce safe foods free of fungi.

CRISPR-Cas9-Mediated Gene Silencing in Cultured Human Epithelia

CRISPR/Cas9 technology enables rapid and efficient genome editing in a variety of experimental systems. Genome editing using CRISPR/Cas9 has become an increasingly popular genetic engineering tool due to (1) an extensive array of commercial ready-to-use CRIPSR/Cas9 systems, (2) improved efficiency of cell delivery, and (3) the possibility to do multigene editing. Here, we describe a method to introduce single gene disruption in lung bronchial epithelial cells. This approach can be used to study host factors important for pathogen interaction or to identify and study genetic markers determining susceptibility to fungal disease.

Recognition and defence of plant-infecting fungal pathogens

Attempted infections of plants with fungi result in diverse outcomes ranging from symptom-less resistance to severe disease and even death of infected plants. The deleterious effect on crop yield have led to intense focus on the cellular and molecular mechanisms that explain the difference between resistance and susceptibility. This research has uncovered plant resistance or susceptibility genes that explain either dominant or recessive inheritance of plant resistance with many of them coding for receptors that recognize pathogen invasion. Approaches based on cell biology and phytochemistry have contributed to identifying factors that halt an invading fungal pathogen from further invasion into or between plant cells. Plant chemical defence compounds, antifungal proteins and structural reinforcement of cell walls appear to slow down fungal growth or even prevent fungal penetration in resistant plants. Additionally, the hypersensitive response, in which a few cells undergo a strong local immune reaction, including programmed cell death at the site of infection, stops in particular biotrophic fungi from spreading into surrounding tissue. In this review, we give a general overview of plant recognition and defence of fungal parasites tracing back to the early 20th century with a special focus on Triticeae and on the progress that was made in the last 30 years.

The impact of fungal allergic sensitization on asthma

PURPOSE OF REVIEW

Fungal sensitization may contribute to the development of asthma as well as asthma severity. The purpose of this review is to summarize existing knowledge about the pathophysiology, diagnosis, and management of fungal sensitization in asthma and highlight unmet needs and target areas for future investigation.

RECENT FINDINGS

Fungal sensitization may occur by a normal or aberrant immune response. Allergic sensitization to fungi is mediated by the adaptive immune response driven by TH2 cells and the innate immune response driven by the innate lymphoid cells group 2. Diagnosis of fungal sensitization can be made by either skin prick testing or measurement of fungal-specific serum IgE. Fungal sensitization in asthma has been associated with worse disease severity, including reduced lung function, increased risk of hospitalizations, and life-threatening asthma. A spectrum of disease related to fungal sensitization has been described in asthma including allergic bronchopulmonary mycosis and severe asthma with fungal sensitization (SAFS). The role of antifungals and targeted biologic therapy in asthma with fungal sensitization need further investigation.

SUMMARY

There is increasing awareness of the contribution of fungal sensitization to asthma severity. However, there are no therapies with proven efficacy. Randomized clinical trials are needed to further investigate the role of biologics.

Sample Preparation for Culture-Independent Profiling and Isolation of Phyllosphere Bacteria to Identify Potential Biopesticides

Studying the plant phyllosphere to understand inhibition patterns to the growth of fungal foliar pathogens by using the Arabidopsis thaliana pathosystem offers unique opportunities for evaluating strategies for plant protection against foliar diseases. The wide array of bacteria inhabiting the phylloplane of plants has been researched to a much lesser extent compared to the bacteria in the rhizosphere. This difference is especially evident as bacteria derived from the aerial section of plants are rarely used in formulations of foliage sprays against pathogens and pests. In this chapter we outline easy and reliable methods for sample preparation to profile phyllosphere bacteria using high throughput amplicon sequencing and isolate/characterize potentially beneficial phyllosphere bacteria from Arabidopsis thaliana that inhibit in vitro the growth of foliar pathogens such as Alternaria brassicicola. The use of the described methods for profiling and screening phyllosphere bacteria may provide tangible progress on the discovery of new potential biological control agents against agriculturally important pathogens.

ZBP1 promotes fungi-induced inflammasome activation and pyroptosis, apoptosis, and necroptosis (PANoptosis)

Candida albicans and Aspergillus fumigatus are dangerous fungal pathogens with high morbidity and mortality, particularly in immunocompromised patients. Innate immune-mediated programmed cell death (pyroptosis, apoptosis, necroptosis) is an integral part of host defense against pathogens. Inflammasomes, which are canonically formed upstream of pyroptosis, have been characterized as key mediators of fungal sensing and drivers of proinflammatory responses. However, the specific cell death pathways and key upstream sensors activated in the context of Candida and Aspergillus infections are unknown. Here, we report that C. albicans and A. fumigatus infection induced inflammatory programmed cell death in the form of pyroptosis, apoptosis, and necroptosis (PANoptosis). Further, we identified the innate immune sensor Z-DNA binding protein 1 (ZBP1) as the apical sensor of fungal infection responsible for activating the inflammasome/pyroptosis, apoptosis, and necroptosis. The Zα2 domain of ZBP1 was required to promote this inflammasome activation and PANoptosis. Overall, our results demonstrate that C. albicans and A. fumigatus induce PANoptosis and that ZBP1 plays a vital role in inflammasome activation and PANoptosis in response to fungal pathogens.

Pathogenesis-related genes of entomopathogenic fungi

All living things on Earth experience various diseases such as those caused by viruses, bacteria, and fungi. Insects are no exception to this rule, and fungi that cause disease in insects are called entomopathogenic fungi. These fungi have been developed as microbial insecticides and are used to control various pests. Generally, the mode of action of entomopathogenic fungi is divided into the attachment of conidia, germination, penetration, growth, and generation of secondary infectious conidia. In each of these steps, that entomopathogenic fungi use genes in a complex manner (specific or diverse) has been shown by gene knock-out and RNA-sequencing analysis. In this review, the information mechanism of entomopathogenic fungi was divided into six steps: (1) attachment of conidia to host, (2) germination and appressorium, (3) penetration, (4) fungal growth in hemolymph, (5) conidia production on host, and (6) transmission and dispersal. The strategy used by the fungi in each step was described at the genetic level. In addition, an approach for studying the mode of action of the fungi is presented.

Comparative Genomics and Functional Studies of Wheat BED-NLR Loci

Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signal (NLS) in Yr7, Yr5, and the other characterized BED-NLRs. We thus propose that this is a feature of BED-NLRs that confer resistance to plant pathogens. We show that the NLS was functional in truncated versions of the Yr7 protein when expressed in N. benthamiana. We did not observe cell-death upon the overexpression of Yr7 full-length, truncated, and 'MHD' variants in N. benthamiana. This suggests that either this system is not suitable to study BED-NLR signaling or that BED-NLRs require additional components to trigger cell death. These results define novel future directions to further understand the role of BED domains in BED-NLR mediated resistance.

Antifungal immune responses in mosquitoes (Diptera: Culicidae): A review

Mosquitoes transmit many parasites and pathogens to humans that cause significant morbidity and mortality. As such, we are constantly looking for new methods to reduce mosquito populations, including the use of effective biological controls. Entomopathogenic fungi are excellent candidate biocontrol agents to control mosquitoes. Understanding the complex ecological, environmental, and molecular interactions between hosts and pathogens are essential to create novel, effective and safe biocontrol agents. Understanding how mosquitoes recognize and eliminate pathogens such as entomopathogenic fungi may allow us to create insect-order specific biocontrol agents to reduce pest populations. Here we summarize the current knowledge of fungal infection, colonization, development, and replication within mosquitoes and the innate immune responses of the mosquitoes towards the fungal pathogens, emphasizing those features required for an effective mosquito biocontrol agent.

Carrier-Mediated Drug Uptake in Fungal Pathogens

Candida, Aspergillus, and Cryptococcus species are the most frequent cause of severe human fungal infections. Clinically relevant antifungal drugs are scarce, and their effectiveness are hampered by the ability of fungal cells to develop drug resistance mechanisms. Drug effectiveness and drug resistance in human pathogens is very often affected by their “transportome”. Many studies have covered a panoply of drug resistance mechanisms that depend on drug efflux pumps belonging to the ATP-Binding Cassette and Major Facilitator Superfamily. However, the study of drug uptake mechanisms has been, to some extent, overlooked in pathogenic fungi. This review focuses on discussing current knowledge on drug uptake systems in fungal pathogens, highlighting the need for further studies on this topic of great importance. The following subjects are covered: (i) drugs imported by known transporter(s) in pathogenic fungi; and (ii) drugs imported by known transporter(s) in the model yeast Saccharomyces cerevisiae or in human parasites, aimed at the identification of their homologs in pathogenic fungi. Besides its contribution to increase the understanding of drug-pathogen interactions, the practical implications of identifying drug importers in human pathogens are discussed, particularly focusing on drug development strategies.

Fungal sphingolipids: role in the regulation of virulence and potential as targets for future antifungal therapies

INTRODUCTION

The antifungal therapy currently available includes three major classes of drugs: polyenes, azoles and echinocandins. However, the clinical use of these compounds faces several challenges: while polyenes are toxic to the host, antifungal resistance to azoles and echinocandins has been reported.

AREAS COVERED

Fungal sphingolipids (SL) play a pivotal role in growth, morphogenesis and virulence. In addition, fungi possess unique enzymes involved in SL synthesis, leading to the production of lipids which are absent or differ structurally from the mammalian counterparts. In this review, we address the enzymatic reactions involved in the SL synthesis and their relevance to the fungal pathogenesis, highlighting their potential as targets for novel drugs and the inhibitors described so far.

EXPERT OPINION

The pharmacological inhibition of fungal serine palmitoyltransferase depends on the development of specific drugs, as myriocin also targets the mammalian enzyme. Inhibitors of ceramide synthase might constitute potent antifungals, by depleting the pool of complex SL and leading to the accumulation of the toxic intermediates. Acylhydrazones and aureobasidin A, which inhibit GlcCer and IPC synthesis, are not toxic to the host and effectively treat invasive mycoses, emerging as promising new classes of antifungal drugs.

Airborne fungus-induced biosynthesis of anthocyanins in Arabidopsis thaliana via jasmonic acid and salicylic acid signaling

Anthocyanins are plant-specific pigments, the biosynthesis of which is stimulated by pathogen infection in several plant species. A. thaliana seedlings injected with airborne fungi can accumulate a high content of anthocyanins. The mechanism involved in fungus-induced anthocyanin accumulation in plants has not been fully described. In this study, the fungus Penicillium corylophilum (P. corylophilum), isolated from an Arabidopsis culture chamber, triggered jasmonic acid (JA), salicylic acid (SA), and anthocyanin accumulation in A. thaliana. Inhibitors of JA and SA biosynthesis suppressed the anthocyanin accumulation induced by P. corylophilum. The anthocyanin content was minimal in both the null mutant of JA-receptor coi1 and the null mutant of SA-receptor npr1 under P. corylophilum stimulation. The results indicate that JA and SA signaling mediated fungus-induced anthocyanin biosynthesis in A. thaliana. P. corylophilum led to different levels of anthocyanin generation in null mutants for MYB75, bHLH, EGL3, and GL3 transcription factors and WD40 protein, demonstrating that multiple MYB-bHLH-WD40 transcription factor complexes participated in fungus-induced anthocyanin accumulation in A. thaliana. The present study will help further elucidate the mechanism of plant resistance to pathogen infection.

Fungi, fungicide discovery and global food security

Securing sufficient food for a growing world population is of paramount importance for social stability and the well-being of mankind. Recently, it has become evident that fungal pathogens pose the greatest biotic challenge to our calorie crops. Moreover, the loss of commodity crops to fungal disease destabilises the economies of developing nations, thereby increasing the dimension of the threat. Our best weapon to control these pathogens is fungicides, but increasing resistance puts us in an arms race against them. New anti-fungal compounds need to be discovered, such as mono-alky lipophilic cations (MALCs) described herein. Collaborations between academia and industry are imperative to establish new and efficient ways to develop these new fungicides and to bring them to the market-place.

Measurement of Early Disease Blueberries Based on Vis/NIR Hyperspectral Imaging System

Blueberries, which are rich in nutrition, are susceptible to fungal infection during postharvest or storage. However, early detection of diseases in blueberry is challenging because of their opaque appearance and the inconspicuousness of spots in the early stage of disease. The goal of this study was to investigate the potential of hyperspectral imaging over the spectral range of 400–1000 nm to discriminate early disease in blueberries. Scanning electron microscope observation verified that fungal damage to the cellular structure takes place during the early stages. A total of 400 hyperspectral images, 200 samples each of healthy and early disease groups, were collected to obtain mean spectra of each blueberry samples. Spectral correlation analysis was performed to select an effective spectral range. Partial least square discrimination analysis (PLSDA) models were developed using two types of spectral range (i.e., full wavelength range of 400–1000 nm and effective spectral range of 685–1000 nm). The results showed that the effective spectral range made it possible to provide better classification results due to the elimination of the influence of irrelevant variables. Moreover, the effective spectral range combined with an autoscale preprocessing method was able to obtain optimal classification accuracies, with recognition rates of 100% and 99% for healthy and early disease blueberries. This study demonstrated that it is feasible to use hyperspectral imaging to measure early disease blueberries.