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Medical Mycology Case Reports Jun 2015Opportunistic subcutaneous fungal infections are increasing in present times due to increasing incidence of many medical conditions causing immunosupression like...
Opportunistic subcutaneous fungal infections are increasing in present times due to increasing incidence of many medical conditions causing immunosupression like diabetes, AIDS, organ transplant recipients and anticancer therapy. Pyrenochaeta romeroi, a fungus from the dematiaceae group, first described by Borelli in 1959, is saprophyte to soil and plants.We present a rare case of subcutaneous phaeohyphomycotic cyst in a diabetic female caused by P. romeroi.
PubMed: 25941632
DOI: 10.1016/j.mmcr.2015.04.001 -
Journal of Clinical Microbiology May 2009We report a new fungus as an agent of fungal keratitis in a diabetic woman. The fungal etiology was established by classic microbiology and PCR following 3 months of...
We report a new fungus as an agent of fungal keratitis in a diabetic woman. The fungal etiology was established by classic microbiology and PCR following 3 months of antibacterial therapy. The morphological features of the isolate and sequence analysis of the internal transcribed spacer region indicate a new species of Pyrenochaeta (Coelomycetes).
Topics: Aged; Ascomycota; Cornea; DNA, Fungal; DNA, Ribosomal Spacer; Diabetes Complications; Eye; Female; Humans; Keratitis; Molecular Sequence Data; Mycological Typing Techniques; Mycoses; Sequence Analysis, DNA
PubMed: 19297598
DOI: 10.1128/JCM.01912-08 -
Database : the Journal of Biological... 2016Many species of dematiaceous fungi are associated with allergic reactions and potentially fatal diseases in human, especially in tropical climates. Over the past 10...
Many species of dematiaceous fungi are associated with allergic reactions and potentially fatal diseases in human, especially in tropical climates. Over the past 10 years, we have isolated more than 400 dematiaceous fungi from various clinical samples. In this study, DemaDb, an integrated database was designed to support the integration and analysis of dematiaceous fungal genomes. A total of 92 072 putative genes and 6527 pathways that identified in eight dematiaceous fungi (Bipolaris papendorfii UM 226, Daldinia eschscholtzii UM 1400, D. eschscholtzii UM 1020, Pyrenochaeta unguis-hominis UM 256, Ochroconis mirabilis UM 578, Cladosporium sphaerospermum UM 843, Herpotrichiellaceae sp. UM 238 and Pleosporales sp. UM 1110) were deposited in DemaDb. DemaDb includes functional annotations for all predicted gene models in all genomes, such as Gene Ontology, EuKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes (KEGG), Pfam and InterProScan. All predicted protein models were further functionally annotated to Carbohydrate-Active enzymes, peptidases, secondary metabolites and virulence factors. DemaDb Genome Browser enables users to browse and visualize entire genomes with annotation data including gene prediction, structure, orientation and custom feature tracks. The Pathway Browser based on the KEGG pathway database allows users to look into molecular interaction and reaction networks for all KEGG annotated genes. The availability of downloadable files containing assembly, nucleic acid, as well as protein data allows the direct retrieval for further downstream works. DemaDb is a useful resource for fungal research community especially those involved in genome-scale analysis, functional genomics, genetics and disease studies of dematiaceous fungi. Database URL: http://fungaldb.um.edu.my.
Topics: Databases, Genetic; Genes, Fungal; Genome, Fungal; Humans; Internet; Models, Genetic; Molecular Sequence Annotation
PubMed: 26980516
DOI: 10.1093/database/baw008 -
Studies in Mycology Jun 2018The taxonomy of the coelomycetes has undergone dramatic changes in recent years, but remains controversial due to the high number of taxa involved, their poor...
The taxonomy of the coelomycetes has undergone dramatic changes in recent years, but remains controversial due to the high number of taxa involved, their poor morphological differentiation, the rare occurrence of the sexual morphs, and rapid loss of fertility . In the present study, we revisited the families and (), which include numerous plant pathogens, endophytic species associated with a wide host range, and saprobes. The taxonomy of two of the most relevant genera, i.e. and , remains ambiguous after several phylogenetic studies, and needs further revision. We have studied a total of 143 strains of coelomycetes from clinical or environmental origin, by combining the LSU, ITS, 2 and 2 sequences for a multi-locus analysis and a detailed morphological comparison. The resulting phylogenetic tree revealed that some fungi previously considered as members of represented five different families, and four of them, , , and , are proposed here as new. Furthermore, 13 new genera, 28 new species, and 20 new combinations are proposed within the . Moreover, four new typifications are introduced to stabilise the taxonomy of these fungi.
PubMed: 29255336
DOI: 10.1016/j.simyco.2017.11.003 -
BMC Genomics Apr 2014Pyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing...
BACKGROUND
Pyrenochaeta lycopersici is a soil-dwelling ascomycete pathogen that causes corky root rot disease in tomato (Solanum lycopersicum) and other Solanaceous crops, reducing fruit yields by up to 75%. Fungal pathogens that infect roots receive less attention than those infecting the aerial parts of crops despite their significant impact on plant growth and fruit production.
RESULTS
We assembled a 54.9Mb P. lycopersici draft genome sequence based on Illumina short reads, and annotated approximately 17,000 genes. The P. lycopersici genome is closely related to hemibiotrophs and necrotrophs, in agreement with the phenotypic characteristics of the fungus and its lifestyle. Several gene families related to host-pathogen interactions are strongly represented, including those responsible for nutrient absorption, the detoxification of fungicides and plant cell wall degradation, the latter confirming that much of the genome is devoted to the pathogenic activity of the fungus. We did not find a MAT gene, which is consistent with the classification of P. lycopersici as an imperfect fungus, but we observed a significant expansion of the gene families associated with heterokaryon incompatibility (HI).
CONCLUSIONS
The P. lycopersici draft genome sequence provided insight into the molecular and genetic basis of the fungal lifestyle, characterizing previously unknown pathogenic behaviors and defining strategies that allow this asexual fungus to increase genetic diversity and to acquire new pathogenic traits.
Topics: Ascomycota; Genome, Fungal; Solanum lycopersicum; Soil Microbiology
PubMed: 24767544
DOI: 10.1186/1471-2164-15-313 -
The Journal of Antibiotics Dec 1979Cynodontin, emodin, endocrocin and secalonic acids A, E and G have been isolated from five strains of Pyrenochaeta terrestis. Aspergillus aculeatus produces emodin,...
Cynodontin, emodin, endocrocin and secalonic acids A, E and G have been isolated from five strains of Pyrenochaeta terrestis. Aspergillus aculeatus produces emodin, endocrocin and secalonic acids B, D and F. No cynodontin was detected. Isolation of emodin in small amounts supports previous evidence that it is an intermediate in secalonic acid biosynthesis. Isolation of cynodontin and endocrocin, which are co-produced with secalonic acids in other organisms, suggests that these compounds are formed by a common branching pathway. A natural isolate of P. terrestris contained variant strains which produced different relative amounts of secalonic acids A, E and G. From the combinations of secalonic acids produced in organisms so far examined it is concluded that precursor tetrahydroxanthone units or formed in pairs differing in stereo-chemistry only at C-5 or at the trans-invariant C-6 : C-10a positions. A possible biosynthetic pathway is discussed.
Topics: Acetylation; Anthracenes; Anthraquinones; Anti-Bacterial Agents; Aspergillus; Culture Media; Emodin; Fermentation; Mitosporic Fungi; Xanthenes; Xanthones
PubMed: 541252
DOI: 10.7164/antibiotics.32.1256 -
Frontiers in Microbiology 2020Intensive greenhouse vegetable cultivation aggravates continuous cropping, resulting in the disturbance of the microbial community structure and the diversity of the...
Intensive greenhouse vegetable cultivation aggravates continuous cropping, resulting in the disturbance of the microbial community structure and the diversity of the soil matrix. In this study, we evaluated the diversity of the rhizosphere matrix fungi in rotation and continuous cropping systems by using high-throughput sequencing analysis of substrates under 6-years of continuous tomato cropping and rotation with cabbage, bean, or celery in greenhouse pots. The results showed that fungal richness in the Chinese cabbage rotation treatment (B) was significantly lower than that of other treatments, and fungal diversities of treatment B and the bean rotation treatment (D) were significantly lower than that of continuous tomato cropping (CK). Contrastingly, the celery rotation treatment (Q) increased the fungal diversity and richness. Furthermore, a principal coordinate analysis showed that the fungal soil community structure of each rotation treatment was different from that of CK. The relative abundances of several harmful fungi (such as , , and ) in control CK were significantly higher than those in rotation treatments. In addition, the matrix electrical conductivity, organic matter, total K, and available P in treatments B and D were significantly higher than those in control CK. Moreover, pH and total N of treatment Q were significantly higher than those of control CK. Most fungi were positively correlated with organic matter and available P and negatively correlated with pH. Therefore, rotation with celery could improve the abundance and diversity of fungi in continuous tomato cropping substrates and reduce the relative abundance of harmful fungi. These results indicated that the rotation of celery and tomato could effectively maintain the ecological balance of the substrate microenvironment and provide a more effective way to prevent the problems of continuous tomato cropping in greenhouse.
PubMed: 32508762
DOI: 10.3389/fmicb.2020.00829 -
Journal of Fungi (Basel, Switzerland) Jun 2022Moso bamboo () has an extremely fast growth rate and major carbon sequestration potential. However, little information is available on the dynamics of soil C...
Moso bamboo () has an extremely fast growth rate and major carbon sequestration potential. However, little information is available on the dynamics of soil C accumulation and fungi communities related to different management practices. Here, we investigated changes in the soil organic carbon (SOC) fractions and fungal communities of a Moso bamboo plantation under three different management practices (M0: undisturbed; M1: extensively managed; and M2: intensively managed). Compared with M0, SOC levels were reduced by 41.2% and 71.5% in M1 and M2, respectively; furthermore, four SOC fractions (C1: very labile; C2: labile; C3: less labile; and C4: nonlabile) and the carbon management index (CMI) were also significantly reduced by plantation management. These practices further altered fungal communities, for example, by increasing and , and by decreasing and . , , , and were identified as keystone taxa. Soil fungal communities were significantly related to the pH, NH-N, AP, C3, and the C4 fractions of SOC. Random forest modeling identified soil C3 and as the most important predictors of the CMI. Our results suggest that reducing human interference would be beneficial for fungal community improvement and C sequestration in Moso bamboo plantations.
PubMed: 35736123
DOI: 10.3390/jof8060640 -
PloS One 2016Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes,...
Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
Topics: Ascomycota; Biodegradation, Environmental; Carbon; Cations, Divalent; Cellulases; Computational Biology; Glycoside Hydrolases; Hydroxyl Radical; Lignin; Manganese; Molecular Sequence Annotation; Oxidation-Reduction; Polygalacturonase; Soil Microbiology; Species Specificity
PubMed: 27434633
DOI: 10.1371/journal.pone.0157844 -
Studies in Mycology Jun 2013The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and...
UNLABELLED
The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), β-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, Pleurophoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively.
TAXONOMIC NOVELTIES
New genera: Medicopsis Gruyter, Verkley & Crous, Nigrograna Gruyter, Verkley & Crous, Paraleptosphaeria Gruyter, Verkley & Crous, Subplenodomus Gruyter, Verkley & Crous. New species: Aposphaeria corallinolutea Gruyter, Aveskamp & Verkley, Paraconiothyrium maculicutis Verkley & Gruyter. New combinations: Coniothyrium carteri (Gruyter & Boerema) Verkley & Gruyter, C. dolichi (Mohanty) Verkley & Gruyter, C. glycines (R.B. Stewart) Verkley & Gruyter, C. multiporum (V.H. Pawar, P.N. Mathur & Thirum.) Verkley & Gruyter, C. telephii (Allesch.) Verkley & Gruyter, Heterospora (Boerema, Gruyter & Noordel.) Gruyter, Verkley & Crous, H. chenopodii (Westend.) Gruyter, Aveskamp & Verkley, H. dimorphospora (Speg.) Gruyter, Aveskamp & Verkley, Leptosphaeria errabunda (Desm.) Gruyter, Aveskamp & Verkley, L. etheridgei (L.J. Hutchison & Y. Hirats.) Gruyter, Aveskamp & Verkley, L. macrocapsa (Trail) Gruyter, Aveskamp & Verkley, L. pedicularis (Fuckel) Gruyter, Aveskamp & Verkley, L. rubefaciens (Togliani) Gruyter, Aveskamp & Verkley, L. sclerotioides (Sacc.) Gruyter, Aveskamp & Verkley, L. sydowii (Boerema, Kesteren & Loer.) Gruyter, Aveskamp & Verkley, L. veronicae (Hollós) Gruyter, Aveskamp & Verkley, Medicopsis romeroi (Borelli) Gruyter, Verkley & Crous, Nigrograna mackinnonii (Borelli) Gruyter, Verkley & Crous, Paraconiothyrium flavescens (Gruyter, Noordel. & Boerema) Verkley & Gruyter, Paracon. fuckelii (Sacc.) Verkley & Gruyter, Paracon. fusco-maculans (Sacc.) Verkley & Gruyter, Paracon. lini (Pass.) Verkley & Gruyter, Paracon. tiliae (F. Rudolphi) Verkley & Gruyter, Paraleptosphaeria dryadis (Johanson) Gruyter, Aveskamp & Verkley, Paralept. macrospora (Thüm.) Gruyter, Aveskamp & Verkley, Paralept. nitschkei (Rehm ex G. Winter) Gruyter, Aveskamp & Verkley, Paralept. orobanches (Schweinitz: Fr.) Gruyter, Aveskamp & Verkley, Paralept. praetermissa (P. Karst.) Gruyter, Aveskamp & Verkley, Plenodomus agnitus (Desm.) Gruyter, Aveskamp & Verkley, Plen. biglobosus (Shoemaker & H. Brun) Gruyter, Aveskamp & Verkley, Plen. chrysanthemi (Zachos, Constantinou & Panag.) Gruyter, Aveskamp & Verkley, Plen. collinsoniae (Dearn. & House) Gruyter, Aveskamp & Verkley, Plen. confertus (Niessl ex Sacc.) Gruyter, Aveskamp & Verkley, Plen. congestus (M.T. Lucas) Gruyter, Aveskamp & Verkley, Plen. enteroleucus (Sacc.) Gruyter, Aveskamp & Verkley, Plen. fallaciosus (Berl.) Gruyter, Aveskamp & Verkley, Plen. hendersoniae (Fuckel) Gruyter, Aveskamp & Verkley, Plen. influorescens (Boerema & Loer.) Gruyter, Aveskamp & Verkley, Plen. libanotidis (Fuckel) Gruyter, Aveskamp & Verkley, Plen. lindquistii (Frezzi) Gruyter, Aveskamp & Verkley, Plen. lupini (Ellis & Everh.) Gruyter, Aveskamp & Verkley, Plen. pimpinellae (Lowen & Sivan.) Gruyter, Aveskamp & Verkley, Plen. tracheiphilus (Petri) Gruyter, Aveskamp & Verkley, Plen. visci (Moesz) Gruyter, Aveskamp & Verkley, Pleospora fallens (Sacc.) Gruyter & Verkley, Pleo. flavigena (Constantinou & Aa) Gruyter & Verkley, Pleo. incompta (Sacc. & Martelli) Gruyter & Verkley, Pyrenochaetopsis pratorum (P.R. Johnst. & Boerema) Gruyter, Aveskamp & Verkley, Subplenodomus apiicola (Kleb.) Gruyter, Aveskamp & Verkley, Subplen. drobnjacensis (Bubák) Gruyter, Aveskamp & Verkley, Subplen. valerianae (Henn.) Gruyter, Aveskamp & Verkley, Subplen. violicola (P. Syd.) Gruyter, Aveskamp & Verkley, Westerdykella capitulum (V.H. Pawar, P.N. Mathur & Thirum.) de Gruyter, Aveskamp & Verkley, W. minutispora (P.N. Mathur ex Gruyter & Noordel.) Gruyter, Aveskamp & Verkley. New names: Pleospora angustis Gruyter & Verkley, Pleospora halimiones Gruyter & Verkley.
PubMed: 24014897
DOI: 10.3114/sim0004