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Mycoparasite secondary metabolites control fungal infections or diseases in agriculture and human health. Among genes involved in synthesizing secondary metabolites, cytochrome P450 monooxygenases (CYPs/P450s) play a key role in synthesizing and attributing diversity to the secondary metabolites. Despite the importance of P450s, a comparative analysis of P450s in mycoparasites has yet to be reported. This study is aimed at addressing this research gap. Genome-wide analysis of P450s in 43 fungi representing six fungal phyla and three distinct lifestyles, such as mycoparasitic (24 species), saprophytic (5 species), and ectomycorrhizal (14 species), revealed the expansion of P450s in Pezizomycete mycoparasites for the synthesis of secondary metabolites. The number of P450s and their families and subfamilies, the number of secondary-metabolite biosynthetic gene clusters (SMBGCs), and the number of P450s that are part of these SMBGCs were found to be highest in Pezizomycete mycoparasites compared to their counterparts of saprophytes and ectomycorrhiza, indicating P450s also play a key role in mycoparasitism. An analysis of P450 location as part of SMBGCs and the available literature on Pezizomycete P450s revealed that P450s play a key role in the synthesis of anti-fungal secondary metabolites such as trichothecene sesquiterpene, harzianum A, heptelidic acid, and gliotoxin. The mycoparasite Trichoderma virens Tv29.8 P450 CYP68Q3 is found to be a bifunctional enzyme with epoxidation and oxidation capability, and CYP5117A3 performs a Baeyer–Villiger oxidation reaction with regioselectivity. This study serves as a reference for future annotation of P450s in mycoparasites. [ABSTRACT FROM AUTHOR]

Copyright of Ecosistemas y Recursos Agropecuarios is the property of Universidad Juarez Autonoma de Tabasco and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Etlik Veteriner Mikrobiyoloji Dergisi is the property of Veteriner Kontrol Merkez Arastirma Enstitusu and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Tea garden soil extensively supports monoculture plantation of tea plant and there is comparatively little information about the distribution of spores of entomopathogenic fungi within the studied site. The entomopathogenic fungi are promising natural agents that can parasitize a wide range of insect species and most entomopathogenic fungi have several variants and each strain is adapted to various hosts, causing natural infections among insects of many different species. Hence, soil samples from selected tea gardens were qualitatively analysed to find the occurrences of entomogenous fungi in the tea plantation areas which can be used as a bio-control agent against tea pests. [ABSTRACT FROM AUTHOR]

Introduction: The fungal nail infection (onychomycosis) involves 18%-40% of all nail disorders, which, although not fatal, can cause mechanical, aesthetic, occupational, and economic problems. Drug treatments due to prolonged treatment periods, drug interactions, adverse effects, and slow progression may associate with numerous negative outcomes. This study aimed to evaluate the long-pulsed 1064-nm Nd: YAG laser effect on fungal colonies and subsequently possible change in the minimum inhibitory concentrations (MICs) of common antifungals compared with the same non-lasered colonies as a novel way to investigate laser and antifungal interaction. Methods: Sixty onychomycosis samples consisting of saprophyte (n = 20), dermatophyte (n = 20), and yeast (n = 20) duplicate colonies were isolated. A series was treated by a long-pulsed 1064-nm Nd: YAG laser. Afterward, the MIC (CLSI-M38-A2 and CLSI-M27-A3) of two series against common antifungals were compared. Results: After 1064-nm Nd: YAG laser irradiation in all 20 tested saprophytes, the MICs of terbinafine (P value < 0.035) were changed, and in all 20 tested dermatophytes, the MICs of voriconazole (P value < 0.021) were changed. Also, in all 20 tested yeasts, the MICs of caspofungin (P value < 0.037) were changed. Moreover, in saprophytes, dermatophytes, and yeasts, significant changes in the MICs of itraconazole (P value < 0.032), terbinafine (P value < 0.025), and caspofungin (P value < 0.037) were detected. Our result showed the GM MICs of the 1064-nm Nd: YAG laser in all saprophyte, dermatophyte, and yeast groups were lower than in the control group. Conclusion: The present study indicated that the long-pulsed 1064-nm Nd: YAG laser significantly changes the MICs of antifungals in onychomycosis clinical samples. [ABSTRACT FROM AUTHOR]

Isolates of Leptospira spp. were cultured from water sources at five different sites in central Iowa in the Midwestern United States and characterized by whole-genome sequencing. Isolates were helix-shaped and motile. Genome sequence analyses determined that the isolates could be clearly distinguished from other species described in the genus Leptospir a and included one species that belonged to the pathogen subclade P1, one species that belonged to the pathogen subclade P2 and three species that belonged to the saprophyte subclade S1. The names Leptospira gorisiae sp. nov. (type strain WS92.C1 T =NVSL-WS92.C1 T =KIT0303 T ), Leptospira cinconiae sp. nov. (type strain WS58.C1 T =NVSL-WS58.C1 T =KIT0304 T ), Leptospira mgodei sp. nov. (type strain WS4.C2 T =NVSL.WS4.C2 T =KIT0305 T ), Leptospira iowaensis sp. nov. (type strain WS39.C2 T =NVSL-WS39.C2 T =KIT0306 T ) and Leptospira milleri sp. nov. (type strain WS60.C2 T =NVSL-WS60.C2 T =KIT0307 T ) are proposed.

Mycoheterotrophic plants acquire nitrogen (N) directly from the soil and through their symbiotic fungi. The fungi-derived N has received considerable attention, but the contribution of soil-derived N has been largely overlooked. We investigated how the leafless, rootless, and almost mycoheterotrophic orchid Cymbidium macrorhizon obtains soil N by applying 15N-labeled ammonium nitrate in its natural habitat, and tracking metabolite accumulation and mycorrhizal fungal association after N application. The decline of N in the rhizome from flowering to fruiting indicated a transfer of N from the rhizome to fruits. At current dose of N application (0.6 g NH 4 NO 3 each plant), only 1.5% of the plant's N was derived from fertilizer, resulting in a low nitrogen use efficiency of 0.27%. The majority of those newly absorbed N (88.89%) was found sank in the rhizome. Amino acids (or their derivatives) and alkaloids were predominant differentially accumulated nitrogenous metabolites after N application, with amino acids occurring in both fruits and the rhizome, and alkaloids primarily in the fruits. The addition of N did not alter the richness of mycorrhizal fungi, but did affect their relative abundance. Our findings suggest that Cymbidium macrorhizon uses very limited soil inorganic nitrogen in its natural habitat, and the root-like rhizome primarily stores N rather than absorbs its inorganic forms, offering new insights into how mycoheterotrophic plants utilize soil N, and the influence of nutrient availability on the orchid-fungi association. [ABSTRACT FROM AUTHOR]

Non‐photosynthetic plants dependent on fungi have long fascinated botanists and mycologists. The genus Gastrodia (Orchidaceae) contains more than 100 achlorophyllous species, including some species recently discovered in Japan and Taiwan which produce only closed self‐pollinating flowers. To date, Gastrodia is probably the only genus containing species with only closed flowers, which has been verified by a decade of monitoring hundreds of individuals. Here, the unique characteristics of the genus Gastrodia have been reviewed, emphasizing the reproductive biology of these newly described species that neither photosynthesize nor bloom. Investigation of such species that scarcely resemble other plants may paradoxically enhance our understanding of plants more broadly. [ABSTRACT FROM AUTHOR]

In Colombia, Streptomyces scabiei (syn. S. scabies) is commonly believed to be the causal organism of scab disease in local potato crops. However, very little is known about this organism and about the diversity and pathogenicity of the Streptomyces species associated with potato crops in Colombia. This study, therefore, aimed to elucidate aspects regarding the diversity of these bacteria associated with potato crops in a particular region of Colombia and evaluate their pathogenicity. We obtained 33 isolates of Streptomyces from netted, superficial and deep‐pitted potato scab lesions from two main potato‐producing regions in Colombia. Of these, 17 were pathogenic based on in vitro and in planta assays. None of these isolates carried the txtA, txtB, or nec1 genes, commonly associated with pathogenicity in Streptomyces, and characteristic of the pathogenicity island (PAI). We also characterized all isolates based on phenotypic characteristics and analysed their phylogenetic relationships using the 16S rRNA, atpD, recA, rpoB, and trpB genes. The isolates were highly diverse, placed in nine clades with 15 different phenotypes. The 17 pathogenic isolates were placed into three clades, namely S. pratensis, S. xiamenensis, and unknown species. This study is a preliminary investigation towards understanding scab disease in Colombia through the study of both pathogenic and nonpathogenic species present in scab disease lesions in potatoes. Also, this is the first report of Streptomyces species associated with potato tubers in Colombia. [ABSTRACT FROM AUTHOR]

Background and Objectives: Onychomycosis is caused by dermatophyte species, non-dermatophyte moulds (NDMs), and accounts for roughly 50% of all nail diseases. As the prevalence of onychomycosis is increasing, new epidemiologic documents may help with treatment and prevention. The present investigation aims to determine the epidemiological profile of onychomycosis in 2 mycology laboratories. Materials and Methods: A cross-sectional study conducted during eight months (2019-2020) on 169 patients with positive nail mycology tests referred to two mycological laboratory centers affiliated with Tehran University of Medical Science. The nail clippings were examined by direct smear and culture. Also, molecular assays were performed if needed. Results: 10% of nail lesions referred to Razi Hospital (RH), and 30% of nail lesions referred to TUMS mycology laboratory were positive. Middle age (40-60) suffer more from onychomycosis. Aspergillus flavus, Trichophyton mentagrophytes, and Candida albicans were the most common etiologic agents in each of the three main classes of fungi causing onychomycosis. Females were more infected. NDMs were the predominant etiologic agents, and toenails were the most common site of onychomycosis. Conclusion: The pattern of etiologic agents and clinical signs of onychomycosis differs according to geographical region and age, so repeated epidemiological surveys of onychomycosis seem to be fundamental. [ABSTRACT FROM AUTHOR]

To improve our understanding of the relationship between soil higher fungi (belonging to Ascomycota and Basidiomycota) and Abies koreana, we surveyed A. koreana soil fungal communities in a forest in Mt. Halla, Jeju Island, Korea by next-generation sequencing (Illumina Miseq). To confirm the soil higher fungal communities, we collected two types of soils from a defined plot: soils with dead (AKDTs) and living A. koreana (AKLTs), respectively. Soil fungi were classified into 2 phyla, 19 classes, 64 orders, 133 families, 195 genera, and 229 OTUs (895,705 sequence reads). Nonmetric multidimensional scaling (NMDS) showed significantly different soil higher fungal communities between AKDTs and AKLTs (p

Background and Objectives: Onychomycosis is caused by dermatophyte species, non- dermatophyte moulds (NDMs), and accounts for roughly 50% of all nail diseases. As the prevalence of onychomycosis is increasing, new epidemiologic documents may help with treatment and prevention. The present investigation aims to determine the epidemiological profile of onychomycosis in 2 mycology laboratories. Materials and Methods: A cross-sectional study conducted during eight months (2019-2020) on 169 patients with positive nail mycology tests referred to two mycological laboratory centers affiliated with Tehran University of Medical Science. The nail clippings were examined by direct smear and culture. Also, molecular assays were performed if needed. Results: 10% of nail lesions referred to Razi Hospital (RH), and 30% of nail lesions referred to TUMS mycology laboratory were positive. Middle age (40-60) suffer more from onychomycosis. Aspergillus flavus, Trichophyton mentagrophytes, and Candida albicans were the most common etiologic agents in each of the three main classes of fungi causing onychomycosis. Females were more infected. NDMs were the predominant etiologic agents, and toenails were the most common site of onychomycosis. Conclusion: The pattern of etiologic agents and clinical signs of onychomycosis differs according to geographical region and age, so repeated epidemiological surveys of onychomycosis seem to be fundamental.

Listeria monocytogenes is an environmentally adapted saprophyte that can change into a human and animal bacterial pathogen with zoonotic potential through several regulatory systems. In this review, the focus is on the occurrence of Listeria sensu stricto and sensu lato in different ecological niches, the detection methods, and their analytical limitations. It also highlights the occurrence of L. monocytogenes genotypes in the environment (soil, water, and wildlife), reflects on the molecular determinants of L. monocytogenes for the saprophytic lifestyle and the potential for antibiotic resistance. In particular, the strain-specific properties with which some genotypes circulate in wastewater, surface water, soil, wildlife, and agricultural environments are of particular interest for the continuously updating risk analysis.

Listeria monocytogenes is an environmentally adapted saprophyte that can change into a human and animal bacterial pathogen with zoonotic potential through several regulatory systems. In this review, the focus is on the occurrence of Listeria sensu stricto and sensu lato in different ecological niches, the detection methods, and their analytical limitations. It also highlights the occurrence of L. monocytogenes genotypes in the environment (soil, water, and wildlife), reflects on the molecular determinants of L. monocytogenes for the saprophytic lifestyle and the potential for antibiotic resistance. In particular, the strain-specific properties with which some genotypes circulate in wastewater, surface water, soil, wildlife, and agricultural environments are of particular interest for the continuously updating risk analysis. [ABSTRACT FROM AUTHOR]

Abiotic stresses, physiological dysfunction, forest stand dynamics and primary tree attackers (native and non‐native) are all recognized as important contributors to both anomalous tree mortality and background tree mortality, and thus as important influences on biogeochemical cycling and habitat for associated terrestrial organisms. Opportunistic and latent tree pathogens and insect pests have largely been left out of this discussion, probably because they are difficult to monitor and their effects sometimes more diffuse, yet they play important roles in tree mortality scenarios.We know very little about the influence of biotic gradients, for example, forest dynamics and forest structure, on the occurrence and effects of these opportunistic biotic enemies. To better understand the influence of an important biotic gradient—forest structure as represented by tree density and competition—on the occurrence and distribution of a typical opportunistic pathogen, we analysed the relationship between tree neighbourhood competition and soil‐dwelling rhizomorphs of the fungus Armillaria gallica in regenerating (20‐year‐old) and mature (80‐ to 100‐year‐old) hardwood‐dominated forest stands in central Missouri following a severe drought.We detected A. gallica rhizomorphs in twice as many sampling sites in young (dense) plots as in mature (open) plots, and by contrast found a twofold occurrence of other saprophytic fungi in the soil of mature plots compared to young plots. Mean tree density and competition index were significantly higher in subplots where A. gallica was found than in those with no A. gallica detections, and the pattern of A. gallica occurrence tracked closely with the occurrence of dense 'hotspots' of competition in the plots.Synthesis. Early stages of forest structure and succession—potentially through initial inputs of disturbance‐produced woody biomass, increased host connectivity and competition‐influenced host tree susceptibility to fungal colonization—provide important feedbacks to A. gallica foraging, which in turn influences forest development. The recognition that tree density and competition influence A. gallica foraging suggests that, to achieve a more comprehensive understanding of forest growth, development, tree mortality and biogeochemical cycling, it may be necessary to increase life‐history studies and basic occurrence surveys for opportunistic tree pathogens and insect pests. [ABSTRACT FROM AUTHOR]

Fungi exhibit saprophytic, parasitic, and symbiotic lifestyles, and flexibly switching between them by the environmental changes and host conditions. However, only a few studies have elucidated the detailed changes in fungal DNA or morphology, including the formation of reproductive structures along with lifestyle switching. We hypothesized that Pyrenopeziza protrusa, which occurs abundantly and specifically on Magnolia obovata as a saprophyte, is also associated with living hosts and switches its lifestyles as part of its lifecycle. To elucidate this hypothesis, we periodically sampled the fresh/fallen leaves of M. obovata to observe the seasonal occurrence of reproductive structures for the isolation and detection/quantification of P. protrusa DNA with newly developed species-specific primers. The isolation frequency and amount of P. protrusa DNA drastically increased in the fresh leaves just before defoliation in autumn, but remained high in fallen leaves from autumn to spring. Abundant production of conidiomata and apothecia was also observed in the fallen leaves with increasing DNA content. These results clarified a large part of the lifecycle of P. protrusa, suggesting that the lifestyle is switched from symbiotic to saprophytic stage by significantly increasing the amount of DNA in response to host conditions according to the seasonal variations. [ABSTRACT FROM AUTHOR]

Background: Didymoplexis verrucosa is a cryptic, leafless, saprophytic ground orchid (~70 mm tall) growing on the coastal forest floors of southern Zululand and classified as Vulnerable (D2). As part of a population monitoring programme, 960 man-hours of species-specific searching over five consecutive flowering seasons were conducted, yielding only one individual plant. Objective: The aim of this study was to increase detection rate by developing a profile of environmental indicators for the accurate identification of suitable habitat. Methods: A detailed description of suitable habitat was compiled based on the Braun-Blanquet approach. Results: The results showed that key attributes shared by localities include similar topographic position in the landscape, hydrology, soils, vegetation composition and structure, forest age, leaf-litter composition of the forest floor, the co-occurrence of Isoglossa woodii, and a similar degree of protection from sunlight, wind and desiccation. Conclusion: This profile of essential habitat characteristics can be used as a surrogate in the absence of actual locality data when identifying target conservation areas and compiling management strategies for this very cryptic species. A by-product of this habitat analysis was the discovery of a long list of impacts on the long term survival of D. verrucosa. The combination of these stochastic and deterministic events will drive habitat change at rates beyond the species' ability to adapt. Managing these variables forms the crux of its successful conservation. A revision of the conservation status, based on the formal IUCN criteria, indicates that D. verrucosa should be reclassified as Critically Endangered Category B2a and D. [ABSTRACT FROM AUTHOR]

Given that the first step in performing molecular techniques such as PCR (Polymerase Chain Reaction (is having enough high quality DNA, the aim of this study was to compare five different extraction methods of genomic DNA of mycobacteria in order to introduce the best method. For this purpose, pure colonies of Mycobacterium avium paratuberculosis were used as pathogenic mycobacterium and also a saprophytic strain called Mycobacterium phelei. The quality and quantity of the obtained DNA by each method was calculated, measured and evaluated respectively; based on extracted DNA concentrations (nanograms per microliter) at a wavelength of 260 nm and also optical density (OD) ratio based on the 260/280 wavelength by using the Nanodrop technique. The highest and lowest amounts of mycobacterial genome DNA was extracted using the CTAB (Cetyltrimethylammonium bromide) and boiling methods respectively. Comparison of the purity of extracted DNA also indicated that the highest purity was obtained using the CTAB method and the lowest using the boiling method. Also no significant differences were observed regarding the quality of extracted DNA from pathogenic and saprophytic mycobacteria among the evaluated extraction methods. Thus, according to the results of this study it appears that using the CTAB method is the most suitable way to extract genomic DNA for molecular detection of mycobacteria in different samples.

Copyright of Etlik Veteriner Mikrobiyoloji Dergisi is the property of Veteriner Kontrol Merkez Arastirma Enstitusu and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Fusarium wilt of strawberry, caused by Fusarium oxysporum f. sp. fragariae, is a disease of primary concern for strawberry production in many countries. Crop rotation and anaerobic soil disinfestation (ASD) have gained recent interest for their potential to contribute to management of this disease. Both techniques involve incorporation of organic matter into soil, which may be utilized by strains of Fusarium that are competitive saprophytes. We show that F. oxysporum f. sp. fragariae can colonize strawberry, lettuce, raspberry, and broccoli leaf tissues, which are sources of organic matter generated during crop rotation. This pathogen increased in soil population density during ASD treatments that did not become anaerobic, possibly as a result of growth on the organic amendment. However, significant population decreases were observed after ASD treatment when at least 100,000 cumulative reduced mV hours occurred in a 14‐day experiment. Post‐ASD abundance of F. oxysporum f. sp. fragariae in soil was negatively correlated with cumulative reduced mV hours. The only treatment that consistently caused disinfestation was exposed to a maximum temperature of 22 °C, which indicates there is potential for developing effective ASD treatments in the cool climates where strawberries are grown. Awareness that F. oxysporum f. sp. fragariae can act as a competitive soil saprophyte should be further investigated for its potential to alter disease outcomes where organic amendments are applied. [ABSTRACT FROM AUTHOR]

The article is devoted to the study on the spatial distribution features of fungi - xylophytes and saprophytes - using the example of the oyster mushroom (Pleurotus ostreatus (Jacq.) P. Kumm.) in suburban plantations (Ukrainian Roztochya) and urbogenic conditions of the city of Lviv. The natural-climatic and forest-typological characteristics of the study region were revealed. Detailed attention was focused on the occurrence of this species in various types of plantings within suburban forest parks, parks, urban gardens and street plantings. The distribution of oyster mushroom individuals in the population was calculated according to the conventional Schwerdtfeger method. The urban-ecological conditions of the suburban and urban green plantings of the Lviv city revealed a high level of oyster mushroom (Pleurotus ostreatus (Jacq.) P. Kumm.) distribution, due to a set of favorable edaphoclimatic conditions of habitats, age and mechanical damage to trees. It was found that the distribution of the individuals in the suburban forests is half of that in the urban areas, which is confirmed by the calculation of variance (dispersion). The dispersion of oyster mushroom individuals in Lviv is 29.3 m2. With spontaneous arrangement of individuals, the value of the dispersion is approximately equal to the average value of the number of mushrooms in the population, while there is a tendency for accumulation of the studied macromycetes (S2≥ m). In urban plantings, the dispersion of individuals is twice as large as in forests, which indicates the wide possibilities for the oyster mushroom spores dispersal. [ABSTRACT FROM AUTHOR]

Abstract Background Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved. Results Combined bioinformatic and transcriptomic analyses implicated three glycoside hydrolase family 5 subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here. Conclusions Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural–functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatic predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.

Cellvibrio japonicus is a saprophytic bacterium proficient at environmental polysaccharide degradation for carbon and energy acquisition. Genetic, enzymatic, and structural characterization of C. japonicus carbohydrate active enzymes, specifically those that degrade plant and animal-derived polysaccharides, demonstrated that this bacterium is a carbohydrate-bioconversion specialist. Structural analyses of these enzymes identified highly specialized carbohydrate binding modules that facilitate activity. Steady progress has been made in developing genetic tools for C. japonicus to better understand the function and regulation of the polysaccharide-degrading enzymes it possesses, as well as to develop it as a biotechnology platform to produce renewable fuels and chemicals.

Fungi have multiple trophic behaviors, including biotrophism (parasitism on living hosts), necrotrophism (parasitism through killing host tissues), and saprotrophism (feeding on decaying organic matter). Historical classifications of plant pathogens are based on many different axes, including their trophic dependence on living and dead plants, their pathogenicity and mutualistic relationship to host plants, and their transmission pathways and infection mechanisms. Such diverse classifications sometimes conflict with each other. Clarifying the delineations among these groups would promote synthesis of fungal biology with current ecological and evolutionary concepts. To ask when biotrophic, necrotrophic, or saprotrophic fungi are maintained and favored by selection, we constructed an epidemiological model that describes the transitions between four states of host plants: susceptible living plant (S), infected living plant (I), uninfected dead plant (D), and infected dead plant, or plant residue (R). States S and D represent two kinds of resource—living and dead plant tissues—for fungal inocula (I and R). We obtained values for the basic reproductive number (R 0), which defines the persistence criteria of fungi. On the basis of our results, we propose four types of ecological groups, corresponding to the patterns of dependence on nutrient resources: (1) parasitism-dependent fungi, characterized by their critical dependence on living plants; (2) saprotrophism-dependent fungi, characterized by their critical dependence on dead plants; (3) facultatively dependent fungi, which are neither parasitism nor saprotrophism dependent; and (4) doubly dependent fungi, which are neither wholly parasitism dependent nor wholly saprotrophism dependent. This grouping can be used to suggest principles for effective pest control. Our model also reveals simple conditions for the evolution of fungal trophic behaviors. We found that, in the absence of a trade-off between virulence and other life-history parameters, milder fungal virulence in living plants is always selected for if plant-fungus population dynamics are stable. However, with sufficiently strong necrotrophic transmission, the host population densities show sustained cycles, which promote the evolution of higher virulence. Epidemiological synthesis of diverse trophism in plant-fungi relationship in our model thus opens the way to discuss the evolution of fungal lifestyles as a function of ecological conditions. [ABSTRACT FROM AUTHOR]

Some free-living Ascomycetes and white and brown rot Basidiomycetes can generate hydroxyl radicals using extracellular redox cycling. However, the mechanisms of hydroxyl radical production differ between white and brown rot Basidiomycetes, and are unknown for Ascomycetes. Here, we present a survey of extracellular hydroxyl radical production by a range of lichenized Ascomycetes. Results show that given a quinone and chelated ferric ions, many lichens can readily produce hydroxyl radicals, and this is accompanied by the reduction of Fe 3 + to Fe 2+ . In white rot fungi, extracellular redox enzymes have been proposed to be involved in hydroxyl radical generation. However, a survey of a wide range of lichens suggests that in these fungi hydroxyl radical production does not directly correlate with the activity of laccases and peroxidases. Rather, radicals are probably produced by a mechanism like that proposed for brown rot fungi. Potential roles of hydroxyl radicals produced by lichens include the breakdown of lignocellulosic residues in the soil which may allow lichens to live a partially saprotrophic existence, the breakdown of toxic soil chemicals and the formation of an ‘oxidative burst’ to deter potential pathogens. [ABSTRACT FROM AUTHOR]

Background and Objectives : Shallots are an important part of the diet of many populations and show some different pharmacological effects in different medical aspects. Some studies have been performed to evaluate the antimicrobial effects of shallots. The objective of this survey was to evaluate its antifungal activities in several fungal species. Methods: In this experimental study, after extracting shallot by soxhlet's procedure, antifungal effects of alcoholic and aqueous extracts of shallot (Allium hirtifolium) against 5 saprophyte species (Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Penicillium gryseogenum and Alternaria) and 2 dermatophyte species (Microsporum canis and Trichophyton mentagrophytes) were evaluated in vitro. Minimum Inhibitory Concentrations (MIC s ) were determined by broth macrodilution method and finally were compared with miconazole. Results: Allium hirtifolium showed antifungal effects against all the tested fungi with MIC ranged between 0.058 to 0.8 mg/ml for alcoholic extract and 0.26 to 3.84 mg/ml for aqueous extract, respectively. Minimum Fungicidal Concentrations (MFC s ) of alcoholic and aqueous extracts ranged between 0.1 to 12.8 mg/ml and 0.6 to 68.26 mg/ml, respectively. Conclusion: This study indicated that shallot crude juice has antifungal activity and looks promising to be an alternatative for chemical antifungal agents that have sometimes serious side effects.

Background: Medicinal plants synthesize a vast array of secondary metabolites that are important for human life. For medicinal purpose, antimicrobial activity of substances derived from plant extracts has been recognized for many years. Pimpinella anisum L. (Apiaceae) and Illicium verum Hook. f. (Illiciaceae) plant species, have been used for treatment of infectious diseases in Iranian traditional medicine. Objective: In this study methanol extracts of Pimpinella anisum L. (Apiaceae) and Illicium verum Hook. f. (Illiciaceae), were tested for their potential antifungal activities. Methods: Methanolic extracts were dried by freeze drying method, Minimum Inhibitory Concentration (MIC) was was determined according to agar dilution method and Minimum Fungicidal Concentration (MFC) was determined by incorporating various concentrations of extracts (2-256 mg/ml) in Sabouraud dextrose agar (SDA) in tubes against 4 dermatophyte and one saprophyte fungi. Results: The extracts of anise seeds inhibited only dermatophyte species, while extracts of star anise fruits inhibited growth of all dermatophytes and saprophytes. MIC and MFC for each extracts were different and MFC was higher than MIC for all species. Conclusion: As a result of this experiment, these plants can be candidate for further studies due to their antifungal potencies.

(Received 20 May, 2009 ; Accepted 10 August, 2009)AbstractBackground and purpose: Onychomycosis is a nail fungal infection caused by various species of dermatophytes, yeasts and non-dermatophytic molds and represents about 30% of cutaneous mycotic infections. The goal of this study was to investigate the frequency of onychomycosis and its associated factors in patients referred to Boali Sina Hospital and Toba dermatology outpatient clinics, Sari.Materials and methods: In this cross-sectional study, nail specimens were collected from 101 patients suspected of onychomycosis during a 14 month period. Nail specimens were examined by direct microscopy, using potassium hydroxide (KOH) 20%, KOH + CFW, KONCPA (KOH treated nail clipping+PAS) and also culturing on sabouraud’s dextrose agar, containing chloramphenicol (SC), and sabouraud’s dextrose agar containing cyclohexamide and chloramphenicol (SCC) mediums.Results: In this study, 79 (78%) of patients were female and 22 (22%) were male. Yeasts were isolated in 30% cases of onychomycosis, mainly from fingernails. Candida albicans, and C.krusei was the most prevalent species. Non-dermatophytic filamentous fungi were yielded at 24%, especially from toenails, with Aspergillus terreus being the most prevalent species. Dermatophytes were found in 7% of the samples, especially from toenails. Trichophyton mentagrophytes was the predominant species. Unknown filamentous fungi were identified in 19% of samples, while mixed infections were identified in 20% of samples. The highest prevalence rate of onychomycosis was identified in the patients within the 30 to 49 years of age group. Distal and lateral subfungual onychomycosis (DLSO) was the most prevalent clinical types with (88%), followed by WSO (5%), PSO (5%), TDO (1%) and DLSO + PSO (1%).Conclusion: The results of our study showed that onychomycosis is one of the most prevalent infections in patients who are suffering from nail disorders. Yeast and yeast like organisms cause these infections more than other fungus in this region. Women are more infected, as they are in daily contact with detergents and moisturJ Mazand Univ Med Sci 2009; 19(71): 33-43 (Persian)

Disease appearance on soybean can influence quality and quantity of yield. Different spieces of saprophyte and parasite fungi can be isolated from stems, pods and grain of soybean. The aim of the research was to evaluate the incidence of important disease on natural soybean grain over the period of 4 years (2004-2007) of experiment held on the location Sopot-Vinkovci and included 9 cultivars of soybean. The following plant pathogenic fungi were identified: Peronospora, Sclerotinia, Cercospora, Fusarium and Diaporthe/Phomopsis. The most frequent fungi on soybean grains were: Cladosporium, Alternaria, Penicillium, Aspergillus and Epicoccum. The health condition of the natural soybean grains over the four years period on all cultivars was good.

The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment. Fluorescence microscopy, confocal laser scanning microscopy and quantitative PCR investigated the colonization dynamics and biomass of P. liquidambari in rice in vivo. P. liquidambari formed infection structures similar to phytopathogens with infected vascular tissues that systematically spread to acrial parts. However, different from pathogenic infection, P. liquidambari colonization exhibits space restriction and quantity restriction. Direct comparison of a fungal transcriptome under three different habitats provided a better understanding of lifestyle conversion during plant-fungi interactions. The isolated total RNA of Ck (pure culture), EP (endophytic culture) and FP (saprophytic culture) was subjected to Illumina transcriptome sequencing. To the best of our knowledge, this study is the first to investigate Phomopsis sp. using RNA-seq technology to obtain whole transcriptome information. A total of 27,401,258 raw reads were generated and 22,700 unigenes were annotated. Functional annotation indicated that carbohydrate metabolism and biosynthesis of secondary metabolites played important roles. There were 2522 differentially expressed genes (DEGs) between the saprophytic and endophytic lifestyles. Quantitative PCR analysis validated the DEGs of RNA-seq. Analysis of DEGs between saprophytic and endophytic lifestyles revealed that most genes from amino acids metabolism, carbohydrate metabolism, fatty acid biosynthesis, secondary metabolism and terpenoid and steroid biosynthesis were up-regulated in EP. Secondary metabolites of these pathways may affect fungal growth and development and contribute to signaling communication with the host. Most pathways of xenobiotic biodegradation and metabolism were upregulated in FP. Cytochrome P450s play diverse vital roles in endophytism and saprophytism, as their highly specialized functions are evolutionarily adapted to various ecological niches. These results help to characterize the relationship between fungi and plants, the diversity of fungi for ecological adaptations and the application prospects for fungi in sustainable agriculture. [ABSTRACT FROM AUTHOR]

During 2000-2016, 213 entries from 29 plant species from different crop groups (cereals, legumes, industrial crops, perennial grasses, vegetables, cucurbits, aromatic and medicinal plants) from core collection of the Suceava Genebank were evaluated from phytosanitary status point of view, before the storing. The seeds testing to the micromycetes incidence in the laboratory by incubating of them on blotting paper substrate and agar medium was performed. Fungal saprophytes from genus as: Alternaria spp., Stemphylium spp., Cladosporium sp., Rhyzopus sp., Epicocum sp., Aspergillus sp., Penicillium sp., Botrytis sp. occurred frequently in seeds samples of the tested crops. Also, 12 fungal parasite were isolated: Sclerospora sp., Diplodia sp., Nigrospora sp. on maize; Drechslera spp. on wheat, barley, rye and flax; Septoria sp. on barley; Fusarium spp. on maize, barley, rye, millet, bean, pea, flax, hemp, peppers, cucumbers; Colletotrichum spp. on maize, bean and faba bean; Sclerotinia sp., Isariopsis sp. and Rhyzoctonia sp. on bean; Verticillium sp. on peppers and okra, Ascochyta sp. on pea. The obtained results were expressed as percentage of the number of fungal isolated from tested samples species, highlighting the existing microflora and need to seed health testing with major importance in maintaing of high quality germplasm avoiding the pathogens preservation and dissemination. [ABSTRACT FROM AUTHOR]

A novel species of Botrytis from Sedum sarmentosum was described based on morphology and analyses of DNA sequences of nuc rDNA ITS regions and three nuclear genes (G3PDH, HSP60, RPB2). Meanwhile pathogenicity in 32 plant species, response to temperature for growth and conidial germination for the species were determined. The Botrytis species was named Botrytis pyriformis sp. nov. It was characterized by formation of grayish mycelia, brownish conidia and melanized sclerotia on PDA. The conidia are pear-shaped, melanized and covered with abundant villiform appendages on the conidial surface. Comparison of the ITS sequences confirmed its placement in the genus Botrytis. Phylogenetic analysis based on DNA sequences of G3PDH, HSP60 and RPB2 genes indicated that B. pyriformis and other 30 Botrytis species form a monophyletic clade, which was further divided into three subclades. Subclade I comprised B. pyriformis alone, whereas subclades II and III comprised six and 24 Botrytis species, respectively. Botrytis pyriformis could not infect 32 plant species including S. sarmentosum, possibly due to deficiency in formation of infection cushions. This study presents a formal description and illustrations for B. pyriformis and provides experimental evidence, indicating that B. pyriformis might be a saprophytic species. [ABSTRACT FROM AUTHOR]

Onychomycosis is the fungal infection of the nails with worldwide occurrence, caused by various species of dermatophytes, yeasts and molds. In addition, of pain and physical effect of onychomycosis that may interfere with individual’s personal and professional life, it may also causes negative psychosocial consequences in patients. Concerning increase of onychomycosis during recent decades and effect of different climates, professional and socio-economic conditions in prevalence of onychomycosis, local investigation for defining of incidence and causative agents of onychomycosis seems necessary. In the present study, 252 patients suspected to onychomycosis were examined by direct microscopy and cultural methods. 28.3% of patients were male and the rest were female. Specimens were tested by direct microscopic examination using potassium hydroxide 20% and culturing on Sabouraud’s dextrose agar (S) and Sabouraud’s containing cyclohexamide and chloramphenicol (Scc mediums). Direct microscopy test were negative in 61.1% nail specimens and positive in rest of them. Among these positive cases, 12.3%(n=31) specimens presented branching mycelium with arthroconodia, and 21%(n=53) specimens presented blastoconidia and pseudohyphe. Beside, saprophytic mycelium has been observed in 5.6 %( n=14) of positive cases. The isolated causative agents from culture of specimens according to their frequencies were as follows: Candida albicans (13.7%), Trichophyton mentagrophytis (8.3%), Candida species (6.9%), Aspergillus flavus (2.9%), Aspergillus niger (1.5%), Scopolariopsis (1%), Trichophyton rubrum (1%) and Fusarium (0.5%). The majority of the patients were women and in both sexes, the most cases of infections were observed in the individuals who were 60-70 year old. The rate of effected fingernails and toenails were almost equal. Concerning the results of culture of specimens, Candida was the most prevalent causative agent in the fingernails such as Trichophyton (esp. Trichophyton mentagrophytis) in toenails. The most prevalent none dermatophytic moulds were Aspergillus species in particular in toe nails.

Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an a-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an a-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNα1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manα1,3Manα1,6GlαNα1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus Nacetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in themutant. The N-acetylhexosaminyltransferase activity of GntAwas substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntAwas furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol- phospholipase C as expected for GlcNAca1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis. [ABSTRACT FROM AUTHOR]

Background: Alternaria is considered one of the most common saprophytic fungal genera on the planet. It is comprised of many species that exhibit a necrotrophic phytopathogenic lifestyle. Several species are clinically associated with allergic respiratory disorders although rarely found to cause invasive infections in humans. Finally, Alternaria spp. are among the most well known producers of diverse fungal secondary metabolites, especially toxins. Description: We have recently sequenced and annotated the genomes of 25 Alternaria spp. including but not limited to many necrotrophic plant pathogens such as A. brassicicola (a pathogen of Brassicaceous crops like cabbage and canola) and A. solani (a major pathogen of Solanaceous plants like potato and tomato), and several saprophytes that cause allergy in human such as A. alternata isolates. These genomes were annotated and compared. Multiple genetic differences were found in the context of plant and human pathogenicity, notably the pro-inflammatory potential of A. alternata. The Alternaria genomes database was built to provide a public platform to access the whole genome sequences, genome annotations, and comparative genomics data of these species. Genome annotation and comparison were performed using a pipeline that integrated multiple computational and comparative genomics tools. Alternaria genome sequences together with their annotation and comparison data were ported to Ensembl database schemas using a self-developed tool (EnsImport). Collectively, data are currently hosted using a customized installation of the Ensembl genome browser platform. Conclusion: Recent efforts in fungal genome sequencing have facilitated the studies of the molecular basis of fungal pathogenicity as a whole system. The Alternaria genomes database provides a comprehensive resource of genomics and comparative data of an important saprophytic and plant/human pathogenic fungal genus. The database will be updated regularly with new genomes when they become available. The Alternaria genomes database is freely available for non-profit use at http://alternaria.vbi.vt.edu. [ABSTRACT FROM AUTHOR]

Lichens produce various oxidoreductases including heme-containing peroxidases and the copper-containing phenol oxidases tyrosinase and laccase. Our earlier findings suggested that significant oxidoreductase activity occurs mainly in lichens from the order Peltigerales. Here we show that the non-Peltigeralean lichen Usnea can display significant activities of peroxidases and laccases. Strong evidence for the involvement of peroxidases and laccases in saprotrophic activities comes from the observation that their activities are induced by “starvation” due to prolonged dark storage, and also by treatment with soluble cellulose and lignin breakdown products. We also show that, given a quinone and chelated Fe, Usnea can produce hydroxyl radicals; these radicals contribute to the break down of carbohydrates or lignin. However, hydroxyl radical production is independent of laccase and peroxidase activity. Laccases and peroxidases are involved in other aspects of lichen biology; here we show that peroxidases, but not laccases, can break down lichen substances. Reduction in the amounts of lichen substances will reduce photoprotection, which will increase the photosynthetic capacity of thalli during winter when light intensities are low. [ABSTRACT FROM AUTHOR]

The wheat grain mycobiome is only scarcely investigated and focus has been on seed-transmitted wheat pathogens of agricultural importance. In this study, we used next generation sequencing to study the mycobiome of Danish wheat grain samples at harvest. In total 228,421 sequences were obtained from 90 samples that were taken from locations across Denmark during three years. These sequences could be grouped into 173 non-singleton operational taxonomic units (OTUs) of which 21 OTUs, identified as belonging to genera such as Fusarium , Alternaria, Cladosporium. Phaeosphaeria and Microdochium, were identified as ‘core’ OTUs as they were found in all or almost all samples and accounted for almost 99 % of all sequences. The remaining OTUs were only sporadically found and only in small amounts. Cluster and factor analyses showed patterns of co-existence among the core species. Cluster analysis grouped the 21 core OTUs into three clusters: cluster 1 consisting of saprotrophs, cluster 2 consisting mainly of yeasts and saprotrophs and cluster 3 consisting of wheat pathogens. Principal component extraction showed that the Fusarium graminearum group was inversely related to OTUs of clusters 1 and 2. [ABSTRACT FROM AUTHOR]

Abstract: The genetic diversity of two agaricoid saprotroph genera, Galerina and Mycena, and their distribution across bryophyte host species, and within bryophytes'' photosynthetic and senescent tissues, was assessed using data from two pyrosequencing biodiversity inventories of bryophilous fungi. A total of 9 498 Galerina and 5 731 Mycena reads were mapped to branches broadly distributed throughout backbone trees, reflecting no obvious evolutionary specialization of particular fungal lineages to moss hosts/substrata. Although a few OTUs occurred with equal frequency across the hosts, most exhibited some degree of specialization to one or more bryophytes, indicating that the quality of different mosses as substratum varies between species. With one exception, all Galerina and Mycena OTUs were more frequent and abundant in senescent than photosynthetic tissues, likely reflecting saprotrophic nutritional modes in the fungi. A single Mycena OTU showed considerable colonization of both tissues, which may reflect an opportunistic parasitic or endophytic lifestyle. [Copyright &y& Elsevier]