Give me a sample of air and I will tell which species are found from your region: Molecular identification of fungi from airborne spore samples

Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning and are important for human health, food production and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional‐level surveys, with samples collected >100 km apart varying but samples collected <10 km apart not varying in their species composition. The data show marked phenology, and thus obtaining a representative species list requires aerial sampling that covers the entire fruiting season. In sum, aerial sampling combined with probabilistic molecular species identification offers a highly effective method for generating a species list of air‐dispersing fungi. The method presented here has the potential to revolutionize fungal surveys, as it provides a highly cost‐efficient way to include fungi as a part of large‐scale biodiversity assessments and monitoring programs.     

Purification and properties of laccase from Botrytis cinerea

The partial purification of an extracellular laccase from Botrytis cinerea is described. Specificity of the enzyme, its K_m for a number of substrates and sensitivity to some inhibitors are described. The enzyme is a typical laccase but has an exceptionally low pI and great stability to acid pH. On gel electrophoresis two isoenzymes could be detected.     

Different techniques reveal the difference of community structure and function of fungi from root and rhizosphere of Salvia miltiorrhiza Bunge

• Fungi have essential functions in plant health and performance. However, the plant-associated functions of many cultured fungi have not been established in detail.
• Here, the fungal species diversity in Salvia miltiorrhiza roots and rhizosphere was assessed for the first time using culturomics and high-throughput sequencing. We present a comprehensive functional metagenomic analysis of these fungi and verified activity of cellulase and chitinase predicted in the metagenomic analysis.
• We first collected and cultured fungi from the root and rhizosphere of S. miltiorrhiza. We found 92 species across 37 families and five phyla, with Ascomycota being dominant. Many rDNA internal transcribed spacer sequences could not be assigned to lower taxonomic levels. There were 19 genera of endophytic fungi and 37 genera of rhizosphere fungi. The culturomics approach had lower taxonomic diversity than high-throughput sequencing, but some fungi were only found in cultures. Structural analyses indicated that the dominant species differed in cultured and non-cultured samples at other levels, apart from the phylum level. Functional analysis mapped 223 carbohydrate enzyme families and 393 pathways in the CAZy and KEGG databases, respectively. The most abundant families were glycoside hydrolases and those involved in carbohydrate metabolism. As predicted by metagenomics, we experimentally verified cellulase and chitinase activity for 29 and 74 fungi, respectively.
• We provide the first evidence of biomass recycling by fungi that are associated with plants. Culturing is essential to reveal the hidden microbial community and critical functions in plant–microbe interactions.

     

Aberrant Growth and Conidiation in Wild-Type Cultures of Fusarium Species from Wheat

Fusarium avenaceum, F. graminearum, F. poae and F. tricinctum showed abnormal growth, morphology and conidiation, and a tendency to produce crystals, inclusion bodies and sclerotia when freshly isolated from wheat stem bases or kernels onto low‐carbon potato dextrose agar (PDA). Observations of alterations in conidiation and conidium morphology are particularly significant, as these are the principal morphological diagnostic characteristics for Fusarium species. The fungi had normal growth when sub‐cultured onto standard PDA, suggesting that a balance of nutrients was responsible for the effects. Specific causes are discussed in detail in relation to published information. The importance of standard media in the identification of Fusarium species is emphasized, whilst non‐standard media may be useful for specific purposes, including routine isolation of fungi from mixed communities of species with different nutrient requirements.     

Fungal endophytes from Dioscorea zingiberensis rhizomes and their antibacterial activity

AIMS: The aim of the study was to isolate and characterize the endophytic fungi from the rhizomes of the Chinese traditional medicinal plant Dioscorea zingiberensis and to detect their antibacterial activities. METHODS AND RESULTS: After strict sterile sample preparation, nine fungal endophytes were isolated from rhizomes of the Chinese traditional medicinal plant D. zingiberensis. The endophytes were classified by morphological traits and internal transcribed spacer (ITS) rRNA gene sequence analysis. Their ITS rDNA sequences were 99-100% identical to Nectria, Fusarium, Rhizopycnis, Acremonium and Penicillium spp. respectively. Of these, the most frequent genera were Fusarium and Nectria. One isolate, Dzf7, was unclassified on the basis of its low sequence similarity. The next closest species was Alternaria longissima (c. 92.4% sequence similarity). Endophyte isolate Dzf5 showed the closest sequence similarity (c. 99.5%) to an uncultured soil fungus (DQ420800) obtained from Cedar Creek, USA. Bioassays using a modified broth dilution test were used to detect the antibacterial activity of n-butanol extracts of both mycelia and culture filtrates of D. zingiberensis showed biological activity against Bacillus subtilis, Staphylococcus haemolyticus, Escherichia coli and Xanthomonas vesicatoria. Minimal inhibitory concentration (MIC) values of the extracts were between 31 x 25 microg ml(-1) and 125 microg ml(-1). CONCLUSIONS: Endophytic fungus Dzf2 (c. 99 x 8% sequence similarity to Fusarium redolens) isolated from D. zingiberensis rhizome showed the most potent antibacterial activities. SIGNIFICANCE AND IMPACT OF THE STUDY: Endophytic fungi isolated from D. zingiberensis may be used as potential producers of antibacterial natural products.     

Evidence for Fungal Infection in Cerebrospinal Fluid and Brain Tissue from Patients with Amyotrophic Lateral Sclerosis

Among neurogenerative diseases, amyotrophic lateral sclerosis (ALS) is a fatal illness characterized by a progressive motor neuron dysfunction in the motor cortex, brainstem and spinal cord. ALS is the most common form of motor neuron disease; yet, to date, the exact etiology of ALS remains unknown. In the present work, we have explored the possibility of fungal infection in cerebrospinal fluid (CSF) and in brain tissue from ALS patients. Fungal antigens, as well as DNA from several fungi, were detected in CSF from ALS patients. Additionally, examination of brain sections from the frontal cortex of ALS patients revealed the existence of immunopositive fungal antigens comprising punctate bodies in the cytoplasm of some neurons. Fungal DNA was also detected in brain tissue using PCR analysis, uncovering the presence of several fungal species. Finally, proteomic analyses of brain tissue demonstrated the occurrence of several fungal peptides. Collectively, our observations provide compelling evidence of fungal infection in the ALS patients analyzed, suggesting that this infection may play a part in the etiology of the disease or may constitute a risk factor for these patients.     

Penicillium siamensis sp. nov., from Thailand soil

Fungal flora of 20 samples of lentil seeds collected from Assiut governorate, Egypt, were studied. Seventeen genera and 13 species were isolated on glucose- (15 genera and 27 species), cellulose-(15 genera and 25 species)Czapek's agar media at 28 °C. The most common species were as follows: on glucose-Czapek's agar, Aspergillus fumigatus, A. niger, A. flavus, A. terreus, Penicillium notatum and Rhizopus oryzae and on cellulose agar, A. fumigatus, A. niger, A. flavus and P. notatum. Thin layer chromatographic (TLC) analysis and a biological test (Artemia salina) indicated the presence and the toxicity of aflatoxin in the extract of one sample (aflatoxins B₁, B₂, G₁ and G₂, at 20 mg/kg, total). This is the first report of the natural occurrence of aflatoxins in lentils.     

The fungi in Century 21. The XXI Fungal Genetics Conference, Pacific Grove, California, March 13-18, 2001

As an important opportunistic pulmonary pathogen, Pneumocystis carinii has been the focus of extensive research over the decades. The use of laboratory animal models has permitted a detailed understanding of the host-parasite interaction but an understanding of the basic biology of P. carinii has lagged due in large part to the inability of the organism to grow well in culture and to the lack of a tractable genetic system. Molecular techniques have demonstrated extensive heterogeneity among P. carinii organisms isolated from different host species. Characterization of the genes and genomes of the Pneumocystis family has supported the notion that the family comprises different species rather than strains within the genus Pneumocystis and contributed to the understanding of the pathophysiology of infection. Many of the technical obstacles in the study of the organisms have been overcome in the past decade and the pace of research into the basic biology of the organism has accelerated. Biochemical pathways have been inferred from the presence of key enzyme activities or gene sequences, and attempts to dissect cellular pathways have been initiated. The Pneumocystis genome project promises to be a rich source of information with regard to the functional activity of the organism and the presence of specific biochemical pathways. These advances in our understanding of the biology of this organism should provide for future studies leading to the control of this opportunistic pathogen.     

Isolation and properties of β-glucan synthetase from the aquatic fungus, Aphanomyces astaci

A β-glucan synthetase was isolated from a membrane fraction of the crayfish parasitic fungus Aphanomyces astaci Schikora, strain Si. [¹⁴C]-UDP-glucose was incorporated linearly for about 1 h at 30°C into an acid insoluble product. The apparent K_m for UDP-glucose was found to be approximately 4.5 m M and the apparent K_i for UDP, a competitive inhibitor of the reaction, was 1 m M . The acid insoluble product obtained after incubating this glucan synthetase with[₁₄C]-UDP-glucose was partially characterized by glucanase treatment. This product mainly consisted of β-1,3-linked glucosyl units. Synthetase activity was not stimulated by MgCl₂, but cellobiose as well as GTP and EDTA in combination or ATP alone enhanced enzyme activity. A high proportion of the A. astaci synthetase was probably already activated during preparation and not accessible to further stimulation by nucleotide additions as found for glucan synthetase of Saccharomyces cerevisiae and Candida albicans. No synthetase activity or any factors affecting this enzyme was present in the cytosol. An exudate prepared from the cuticle of the crayfish host, did not inhibit glucan synthetase activity in vitro.     

Purification and immunological characterization of a 12-kDa allergen from Epicoccum purpurascens

Exposure to Epicoccum purpurascens is implicated in respiratory allergies and asthma. Several allergens of clinical importance were identified in Epicoccum extract (EE), but only one allergen has been isolated and characterized. In the present study, a 12-kDa allergen was isolated from an Epicoccum spore-mycelial extract by concanavalin-A sepharose, reverse-phase hydrophobic and gel filtration chromatography. The purified protein was recognized as a single 12-kDa allergen on immunoblot with a serum pool of Epicoccum- sensitive patients. Of the 94 respiratory allergy patients tested intradermally, 17 showed marked positive skin reactions to EE and 12 of them reacted with the 12-kDa protein, indicating a diagnostic sensitivity of 70%. More than 80% patients' sera showed immunoglobulin E (IgE) reactivity to the purified protein in enzyme-linked immunosorbent assay and immunoblot, identifying it as a major allergen. Preincubation of pooled serum with the protein led to inhibition of IgE binding to solid-phase-bound EE (effective concentration 50%=180 ng). Twelve of the 17 serum samples showed significant basophil histamine release upon stimulation with purified protein. The protein induced significant proliferation of peripheral blood mononuclear cells of 13 patients. A high level of interleukin-4 in the culture supernatant of these cells indicated induction of a T-helper type 2 response. The purified 12-kDa protein is a clinically relevant allergen and has potential for the diagnosis and therapy of Epicoccum allergies.     

Diversity of fungal isolates from fungus-growing termite Macrotermes barneyi and characterization of bioactive compound from Xylaria escharoidea

Owing to their potential applications,as well as their structural diversity,the discovery of novel secondary metabolites from insect-associated fungi has been of interest to researchers in recent years.The aim of this study was therefore to estimate the diversity of fungi associated with fungus-growing termites and bioprospecting these for potential secondary metabolites.In total,18 fungal species were isolated and described from the gut and comb of Macrotermes barneyi based on 18S ribosomal DNA gene sequence analysis.Antimicrobial activity assays were carried out on all the known fungi,and nine isolates were recorded as active against pathogenic fungi.Xylaria escharoidea,the best performing isolate,was grown at laboratory scale and 4,8-dihydroxy-3,4-dihydronaphthalen-l(2H)was isolated and characterized.The minimum inhibitory concentration of this isolated compound against tested pathogenic organisms was found to be 6.25 fig.In addition,molecular docking studies have revealed that 4,8-dihydroxy-3,4-dihydronaphthalen-l(2H)is a prominent antibacterial agent with a marked interaction with key residues on protein A(agrAc)that regulates the accessory gene.The findings of this study support the drug discovery of antimicrobial properties in insect-associated fungi,which may lead to novel secondary metabolites.     

pH and temperature optima for growth and sporulation in some common fungi from city waste

Relationships between the growth of certain fungi isolated from city waste and pH and temperature were examined by two methods. The tested isolates showed their maximum growth and sporulation at different pHs while temperature requirements were the same (28°C), except forHumicola grisea (43°C).Cladosporium herbarum andH. grisea showed double pH optima. The ranges of pH and temperature for sporulation were more limited than those for the vegetative growth. Although all the tested isolates showed wide tolerances to pH and temperature, the degree of tolerance varied with the isolates. A considerable change from the initial pH of the liquid medium was noted at the end of the experiment.     

Two new Beauveria spp. from South America

Beauveria velata sp. nov. was found on Lepidoptera larvae in Ecuador and is characterized by ellipsoid conidia covered with a distinct mucilaginous layer. Another Beauveria species, commonly encountered on Coleoptera in Brazil proved to be identical with Isaria amorpha Höhn., originally described from a cicada in Indonesia. The new combination Beauveria amorpha is proposed. Details of the occurrence and ecology of both species are described.     

Radiosensitivity of fungi isolated from waterlogged archaeological wood

Waterlogged archaeological timbers of theMary Rose were shown to support a range of fungi, including marine soft rot fungi. These isolates, and other wood degrading fungi, were inactivated by gamma irradiation at doses of 3.1–15.0 kGy. No clear pattern of variation in radioresistance appeared between the Ascomycota, Basidiomycota and Deuteromycota. Terrestrial fungi were generally more resistant than marine fungi. Little variation in radioresistance was observed between vegetative hyphae and sporulating cultures/fruiting bodies. Sublethal doses resulted in reduced viability in some species. Gamma irradiation is suggested as a possible means of controlling fungal colonisation of waterlogged archaeological wood.     

An instrumental modification of Gerdemann and Nicolson's method for extracting VAM fungal spores from soil samples

An easily constructed apparatus for extraction of VAM fungal spores from soil samples by a modification of Gerdemann and Nicolson's wet sieving and decanting method is described. For the soils employed in this study, it proved considerably more effective and more precise than either the original wet sieving and decanting method or differential water/sucrose centrifugation. The apparatus gave results that were less subject to interference from extraneous particles than the wet sieving and decanting method. The effect of prior soil dispersion is also reported.