Rapid identification and detection of pine pathogenic fungi associated with mountain pine beetles by padlock probes

Fifteen million hectares of pine forests in western Canada have been attacked by the mountain pine beetle (Dendroctonus ponderosae; MPB), leading to devastating economic losses. Grosmannia clavigera and Leptographium longiclavatum, are two fungi intimately associated with the beetles, and are crucial components of the epidemic. To detect and discriminate these two closely related pathogens, we utilized a method based on ligase-mediated nucleotide discrimination with padlock probe technology, and signal amplification by hyperbranched rolling circle amplification (HRCA). Two padlock probes were designed to target species-specific single nucleotide polymorphisms (SNPs) located at the inter-generic spacer 2 region and large subunit of the rRNA respectively, which allows discrimination between the two species. Thirty-four strains of G. clavigera and twenty-five strains of L. longiclavatum representing a broad geographic origin were tested with this assay. The HRCA results were largely in agreement with the conventional identification based on morphology or DNA-based methods. Both probes can also efficiently distinguish the two MPB-associated fungi from other fungi in the MPB, as well as other related fungi in the order Ophiostomatales. We also tested this diagnostic method for the direct detection of these fungi from the DNA of MPB. A nested PCR approach was used to enrich amplicons for signal detection. The results confirmed the presence of these two fungi in MPB. Thus, the padlock probe assay coupled with HRCA is a rapid, sensitive and reproducible method for the identification and detection of these ophiostomatoid fungi.     

Rapid Detection of Ophiostoma piceae and O. quercus in Stained Wood by PCR

A rapid, sensitive, and simple method was developed to detect the sapstain fungi Ophiostoma piceae and O. quercus in stained wood. By using microwave heating for DNA extraction and PCR with internal transcribed spacer-derived-specific primers, detection was feasible within 4 h, even with DNA obtained from a single synnema. This method can easily be extended for the detection of other wood-inhabiting fungi.     

Mycotic biodeterioration associated with the movement and storage of commercially handled household goods

Eight mildewed shipments out of approximately 242 movements of commercially handled household goods yielded 27 species of fungi representing 19 genera. The most frequently recovered fungi included Aureobasidium pullulans, Geotrichum candidum, mycelia sterilia, Penicillium sp., P. rugulosum, Syncephalastrum racemosum and Trichoderma viride. Twelve species have been previously associated with mycotic biodeterioration of similar substrates. Of the moulded goods sampled, leather and rubber were the least colonized. All fungi recovered were associated with wooden furniture. No correlation between storage duration, method or taxa was observed.     

Investigation of keratinolytic and non-keratinolytic fungi grown above or below a 1-cm sewage sludge blanket

This study investigated the incidence of keratinolytic and non-keratinolytic fungi grown above or below a 1-cm sewage sludge blanket. The hair baiting method was used. Incubation was carried out at 23 and 37  °C. The number of keratinolytic fungi occurrences below a sludge blanket (anoxic conditions) was almost two times smaller than the number of fungal occurrences above this blanket (oxic conditions). The anoxic conditions did not significantly affect the number of non-keratinolytic fungi. Qualitative differences were also observed. Trichophyton ajelloi with its teleomorph Arthroderma uncinatum and some other fungi were found to prefer oxic conditions. In the case of non-keratinolytic fungi, the most evident differences were observed at 37  °C. Aspergillus fumigatus prevailed above a sludge blanket, while Pseudallescheria boydii was the predominating species below this blanket. The incidence of keratinolytic fungi was dependent on sludge physico-chemical characteristics: mainly on sludge organic matter stabilization (total nitrogen and ammonium nitrogen contents, proteolytic activity and C:N ratio) and hygienization (total and fecal coliforms) factors.     

Occurrence of fungi in combs of fungus-growing termites (Isoptera: Termitidae, Macrotermitinae)

Fungus-growing termites cultivate their mutualistic basidiomycete Termitomyces species on a substrate called a fungal comb. Here, the Suicide Polymerase Endonuclease Restriction (SuPER) method was adapted for the first time to a fungal study to determine the entire fungal community of fungal combs and to test whether fungi other than the symbiotic cultivar interact with termite hosts. Our molecular analyses show that although active combs are dominated by Termitomyces fungi isolated with direct Polymerase Endonuclease Restriction - Denaturing Gradient Gel Electrophoresis (PCR-DGGE), they can also harbor some filamentous fungi and yeasts only revealed by SuPER PCR-DGGE. This is the first molecular evidence of the presence of non-Termitomyces species in active combs. However, because there is no evidence for a species-specific relationship between these fungi and termites, they are mere transient guests with no specialization in the symbiosis. It is however surprising to notice that termite-associated Xylaria strains were not isolated from active combs even though they are frequently retrieved when nests are abandoned by termites. This finding highlights the implication of fungus-growing termites in the regulation of fungi occurring within the combs and also suggests that they might not have any particular evolutionary-based association with Xylaria species.     

Growth Simulation and Discrimination of Botrytis cinerea,Rhizopus stolonifer and Colletotrichum acutatum Using Hyperspectral Reflectance Imaging

This research aimed to develop a rapid and nondestructive method to model the growth and discrimination of spoilage fungi, like Botrytis cinerea, Rhizopus stolonifer and Colletotrichum acutatum, based on hyperspectral imaging system (HIS). A hyperspectral imaging system was used to measure the spectral response of fungi inoculated on potato dextrose agar plates and stored at 28°C and 85% RH. The fungi were analyzed every 12 h over two days during growth, and optimal simulation models were built based on HIS parameters. The results showed that the coefficients of determination (R²) of simulation models for testing datasets were 0.7223 to 0.9914, and the sum square error (SSE) and root mean square error (RMSE) were in a range of 2.03–53.40×10⁻⁴ and 0.011–0.756, respectively. The correlation coefficients between the HIS parameters and colony forming units of fungi were high from 0.887 to 0.957. In addition, fungi species was discriminated by partial least squares discrimination analysis (PLSDA), with the classification accuracy of 97.5% for the test dataset at 36 h. The application of this method in real food has been addressed through the analysis of Botrytis cinerea, Rhizopus stolonifer and Colletotrichum acutatum inoculated in peaches, demonstrating that the HIS technique was effective for simulation of fungal infection in real food. This paper supplied a new technique and useful information for further study into modeling the growth of fungi and detecting fruit spoilage caused by fungi based on HIS.     

Diversity of nematode destroying fungi in Taita Taveta,Kenya

The diversity of nematode destroying fungi in Taita Taveta, Wundanyi division, Coast Province, Kenya, was investigated between May 2006 and December 2007 aiming at harnessing their potential in the biological control of plant parasitic nematodes in the area. Given that the intensity of land cultivation is continually increasing in the study area, it is prudent to document the status of the nematode destroying fungi before the remaining forest habitats are ultimately disrupted. Soil samples were collected from forest, maize/bean, napier grass, shrub and vegetable fields, which represented the main land use types in the study area. The soil sprinkle technique method was used to isolate the nematode destroying fungi from the soil. The fungi were identified to species level. Eighty-five isolates, distributed in eight genera and 14 taxa were identified as nematode destroying fungi. The species identified were Arthrobotrys dactyloides, Arthrobotrys oligospora, Arthrobotrys superba, Acrostalagamus obovatus, Dactyllela lobata, Harposporium aungulilae, Harposporium liltiputanum, Harposporium spp, Haptoglosa heterospora, Monacrosporium asterospernum, Monacrosporium cianopagum, Myzocytium, spp, Nematoctonus georgenious and Nematoctonus leptosporus. Vegetable land use had the highest diversity of nematode destroying fungi. The results show that the study area is rich in nematode destroying fungi with A. oligospora being widespread and a possible candidate for biological control of plant parasitic nematodes.     

Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems

This paper describes the use of a quantitative competitive polymerase chain reaction (QC-PCR) assay; using PCR primers to the rRNA locus of rumen fungi and a standard-control DNA including design and validation. In order to test the efficiency of this method for quantifying anaerobic rumen fungi, it has been attempted to evaluate this method in in vitro conditions by comparing with an assay based on measuring cell wall chitin. The changes in fungal growth have been studied when they are grown in in vitro on either untreated (US) or sodium hydroxide treated wheat straw (TS). Results showed that rumen fungi growth was significantly higher in treated samples compared with untreated during the 12 d incubation (P < 0.05) and plotting the chitin assay's results against the competitive PCR's showed high positive correlation (R² ≥ 0.87). The low mean values of the coefficients of variance in repeatability in the QC-PCR method against the chitin assay demonstrated more reliability of this new approach. And finally, the efficiency of this method was investigated in in vivo conditions. Samples of rumen fluid were collected from four fistulated Holstein steers which were fed four different diets (basal diet, high starch, high sucrose and starch plus sucrose) in rotation. The results of QC-PCR showed that addition of these non-structural carbohydrates to the basal diets caused a significant decrease in rumen anaerobic fungi biomass. The QC-PCR method appears to be a reliable and can be used for rumen samples.     

Soursop leaves (Annona muricata L.) endophytic fungi anticancer activity against HeLa cells

Cervical cancer causes many deaths in females worldwide, including in Indonesia. Several studies have reported that soursop (Annona muricata L.) leaves can be used to treat cervical cancer. This study aims to determine the use of endophytic fungi of A. muricata leaves extract as an ingredient that inhibits cervical cancer. The isolated endophytic fungi from various soursop leave accessions were grown in culture media, then extracted using ethyl acetate. The extract was then tested against anti-yeast, cervical cancer cells, and on normal cells as control using the MTT method. Five isolated fungi were selected based on the greatest inhibition in one concentration, and the inhibitory concentration 50 (IC₅₀) value was determined. The soursop leaves endophytic fungi extracts showed cytotoxicity against cervical cancer cells by inhibiting the multiplication of HeLa cancer cells in vitro. The Sir-SM2 endophytic fungi crude ethyl acetate extract showed high cytotoxicity to cervical cancer cells (HeLa cells) but less harmful to the normal Chang cells; therefore can be a natural anticancer. Identification based on morphology shows that the isolated Sir-SM2 endophytic fungi belong to the Penicillium genus, and molecular identification based on Internal Transcribed Spacer shows high similarities with Penicillium crustosum.     

Diversity of Rhizosphere Soil Arbuscular Mycorrhizal Fungi in Various Soybean Cultivars under Different Continuous Cropping Regimes

Recent studies have shown that continuous cropping in soybean causes substantial changes to the microbial community in rhizosphere soil. In this study, we investigated the effects of continuous cropping for various time periods on the diversity of rhizosphere soil arbuscular mycorrhizal (AM) fungi in various soybean cultivars at the branching stage. The soybean cultivars Heinong 37 (an intermediate cultivar), Heinong 44 (a high-fat cultivar) and Heinong 48 (a high-protein cultivar) were seeded in a field and continuously cropped for two or three years. We analyzed the diversity of rhizosphere soil AM fungi of these soybean plants at the branching stage using morphological and denaturing gradient gel electrophoresis (DGGE) techniques. The clustering analysis of unweighted pair-group method with arithmetic averages (UPGMA) was then used to investigate the AM fungal community shifts. The results showed that increasing the number of years of continuous cropping can improve the colonization rate of AM fungi in different soybean cultivars at the branching stage. The dominant AM fungi in the experimental fields were Funneliformismosseae and Glomus spp. The number of years of continuous cropping and the soybean cultivar both had obvious effects on the diversity of AM fungi, which was consistent with the results of colonization rate analysis. This study establishes a basis for screening dominant AM fungi of soybean. In addition, the results of this study may be useful for the development of AM fungal inoculants.     

Identification of a Vesicular-Arbuscular Mycorrhizal Fungus by Using Monoclonal Antibodies in an Enzyme-Linked Immunosorbent Assay

Spore morphology is currently used to identify species of vesicular-arbuscular mycorrhizal fungi. We report the first use of a highly specific immunological method for identification of a vesicular-arbuscular mycorrhizal fungus. Two monoclonal antibodies were produced against Glomus occultum. Monoclonal antibodies reacted strongly with both spores and hyphae in an indirect enzyme-linked immunosorbent assay. All other mycorrhizal (29 species) and nonmycorrhizal (5 species) fungi tested were nonreactive with the monoclonal antibodies. A single spore of G. occultum was detectable in the presence of high numbers of spores of other vesicular-arbuscular mycorrhizal fungi. Variation in the reaction of G. occultum isolates from West Virginia, Florida, and Colombia suggests that monoclonal antibodies may differentiate strains.     

Culturable fungal endophytes in roots of Enkianthus campanulatus (Ericaceae)

Roots of plants in the genus Enkianthus, which belongs to the earliest diverging lineage in the Ericaceae, are commonly colonized by arbuscular mycorrhizal (AM) fungi. We documented the community of fungal root endophytes associated with Enkianthus species using a culture-based method for better understanding the members of root-colonizing fungi, except for AM fungi. Fungal isolates were successfully obtained from 610 out of 3,599 (16.9 %) root segments. Molecular analysis of fungal cultures based on ribosomal internal transcribed spacer (ITS) sequences yielded 63 operational taxonomical units (OTUs: 97 % sequence similarity cutoff) from 315 representative isolates. Further phylogenetic analysis showed that most (296 isolates) belonged to Ascomycota and were either members of Helotiales (Dermataceae, Hyaloscyphaceae, Phialocephala and Rhizoscyphus ericae aggregate), Oidiodendron, or other Pezizomycotina. Twenty-three out of 63 OTUs, which mainly consisted of Leotiomycetes, showed high similarities with reference sequences derived from roots of other ericaceous plants such as Rhododendron. The results indicated that Enkianthus houses variable root mycobionts including putative endophytic and mycorrhizal fungi in addition to AM fungi.     

Immunosuppression of insects by the venom of <Emphasis Type="Italic">Habrobracon hebetor</Emphasis> increases the sensitivity of bait method for the isolation of entomopathogenic fungi from soils

We evaluated the susceptibility of Galleria mellonella larvae immunosuppressed by the venom of Habrobracon hebetor to soil entomopathogenic ascomycetes with the use of bait method. It was found that the sensitivity of the modified method was significantly (by almost 200 times) increased as compared with the standard procedure, which provided the isolation of fungi when their abundance was extremely low. Envenomated larvae were more susceptible to the entomopathogenic but not saprotrophic fungi. We presented results of isolation of the entomopathogenic fungi from soils in different climatic zones (from the forest tundra to the steppe) using an improved procedure.     

The Lichen Connections of Black Fungi

Many black meristematic fungi persist on rock surfaces—hostile and exposed habitats where high doses of radiation and periods of desiccation alternate with rain and temperature extremes. To cope with these extremes, rock-inhabiting black fungi show phenotypic plasticity and produce melanin as cell wall pigments. The rather slow growth rate seems to be an additional prerequisite to oligotrophic conditions. At least some of these fungi can undergo facultative, lichen-like associations with photoautotrophs. Certain genera presenting different lifestyles are phylogenetic related among the superclass Dothideomyceta. In this paper, we focus on the genus Lichenothelia, which includes border-line lichens, that is, associations of melanised fungi with algae without forming proper lichen thalli. We provide a first phylogenetic hypothesis to show that Lichenothelia belongs to the superclass Dothideomyceta. Further, culture experiments revealed the presence of co-occurring fungi in Lichenothelia thalli. These fungi are related to plant pathogenic fungi (Mycosphaerellaceae) and to other rock-inhabiting lineages (Teratosphaeriaceae). The Lichenothelia thallus-forming fungi represent therefore consortia of different black fungal strains. Our results suggest a common link between rock-inhabiting meristematic and lichen-forming lifestyles of ascomycetous fungi.     

The annual invasive plant Impatiens glandulifera reduces hyphal biomass of soil fungi in deciduous forests

Soil fungi play a crucial role in ecosystem functioning and there is increasing evidence that exotic plants invading forests can affect soil fungal communities. We examined potential effects of the invasive plant Impatiens glandulifera on hyphal biomass of ectomycorrhizal fungi, their genetic diversity and the diversity of other soil fungi in deciduous forests in Switzerland. We compared invaded patches with patches where I. glandulifera had been removed, by establishing pairs of 3-m long transect lines at the edge of seven areas of either type. Along the transects we assessed the length of ectomycorrhizal fungal hyphae using the ‘ingrowth mesh bag method’, and used terminal restriction fragment length polymorphism (T-RFLP) analysis to examine fungal genetic diversity. The invasive plant reduced fungal hyphal biomass by 30–80%: the reduction was largest in the centre of the patch. I. glandulifera did not alter fungal richness, but affected the composition of fungal communities. This is probably the result of a decrease of mycorrhizal fungi, coupled with an increase of saprotrophic fungi. Our findings demonstrate the adverse impacts of an annual invasive plant species on both fungal hyphal biomass and the composition of soil fungal communities. This may negatively affect forest nutrient and carbon cycling, soil stability and the functionality of the fungal community, with major consequences for forest ecosystem functioning.     

Co-occurrence patterns of wood-decaying fungi and ants in dead pines of South Korea

Interaction between fungi and insects such as ants, beetles, wasps and termites inhabiting dead pine trees has significant ecological implication in the forest as they can decompose wood debris and add nutrients to the soil; however, only scarce information is available regarding the interaction between wood-decaying fungi and ants. We investigated wood-decaying fungi co-occurring with ants in dead pine trees of South Korea. A total of 57 pairs of wood-decaying fungi and ants were collected from 11 localities. 30 species of wood-decaying fungi and 14 species of ants were identified based on morphology and molecular analysis. Fungal species belonging to Trichaptum, Xylodon, Hyphodontia, and Ceriporia were dominant and co-occurred with common ant species of Lasius, Camponotus, Pristomyrmex, and Crematogaster across most of the sampling sites. This study provides a new baseline in unravelling the complex interaction between wood-decaying fungi and ants in forest ecosystems.     

Spatial Segregation and Aggregation of Ectomycorrhizal and Root-Endophytic Fungi in the Seedlings of Two Quercus Species

Diverse clades of mycorrhizal and endophytic fungi are potentially involved in competitive or facilitative interactions within host-plant roots. We investigated the potential consequences of these ecological interactions on the assembly process of root-associated fungi by examining the co-occurrence of pairs of fungi in host-plant individuals. Based on massively-parallel pyrosequencing, we analyzed the root-associated fungal community composition for each of the 249 Quercus serrata and 188 Quercus glauca seedlings sampled in a warm-temperate secondary forest in Japan. Pairs of fungi that co-occurred more or less often than expected by chance were identified based on randomization tests. The pyrosequencing analysis revealed that not only ectomycorrhizal fungi but also endophytic fungi were common in the root-associated fungal community. Intriguingly, specific pairs of these ectomycorrhizal and endophytic fungi showed spatially aggregated patterns, suggesting the existence of facilitative interactions between fungi in different functional groups. Due to the large number of fungal pairs examined, many of the observed aggregated/segregated patterns with very low P values (e.g., < 0.005) turned non-significant after the application of a multiple comparison method. However, our overall results imply that the community structures of ectomycorrhizal and endophytic fungi could influence each other through interspecific competitive/facilitative interactions in root. To test the potential of host-plants'' control of fungus–fungus ecological interactions in roots, we further examined whether the aggregated/segregated patterns could vary depending on the identity of host plant species. Potentially due to the physiological properties shared between the congeneric host plant species, the sign of hosts'' control was not detected in the present study. The pyrosequencing-based randomization analyses shown in this study provide a platform of the high-throughput investigation of fungus–fungus interactions in plant root systems.     

Taphonomy of experimental burials in Taphos-m: The role of fungi

BackgroundThe fungi present in the decaying remains enable a better understanding of the processes of decomposition after death. There are not many studies about fungi on decaying bodies and it is not known which fungal sampling methods are effective.AimsThe main objective of this study was to find the best method for sampling fungi in carcasses, prove the effectiveness of this method and identify the fungal colonies in animal carcasses from experimental burials.MethodsSamples from 13 carcasses of Sus scrofa domestica, from the experimental project Taphos-m, were taken with different materials: spatula, sterile swabs and RODAC contact plates.ResultsRODAC contact plates with the RBA culture medium showed higher proliferation of fungal colonies. Thirty genera of fungi were isolated from different substrates (bone, tissue, lime). Most of the fungi genera or groups identified have been described before in the literature, but the substrates they came from were different in some cases.ConclusionsSampling with RODAC contact plates was found to be the most effective method, as it provides a nutritional culture medium that may allow growth since the moment of sampling. Fungi colonies grew better in RBA culture medium because bacterial growth is inhibited. Most of the observed fungi are related to the environment but some others have been found related to decomposing bodies for the first time.     

Biotransformation of Phenylacetonitrile to 2-Hydroxyphenylacetic Acid by Marine Fungi

Marine fungi belonging to the genera Aspergillus, Penicillium, Cladosporium, and Bionectria catalyzed the biotransformation of phenylacetonitrile to 2-hydroxyphenylacetic acid. Eight marine fungi, selected and cultured with phenylacetonitrile in liquid mineral medium, catalyzed it quantitative biotransformation to 2-hydroxyphenylacetic acid. In this study, the nitrile group was firstly hydrolysed, and then, the aromatic ring was hydroxylated, producing 2-hydroxyphenylacetic acid with 51 % yield isolated. In addition, the 4-fluorophenylacetonitrile was exclusively biotransformed to 4-fluorophenylacetic acid by Aspergillus sydowii Ce19 (yield?=?51 %). The enzymatic biotransformation of nitriles is not trivial, and here, we describe an efficient method for production of phenylacetic acids in mild conditions.