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Microbes and Environments Jul 2018A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate...
A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures. A model temperate crop, loose leaf lettuce, was grown on eutrophic soil under soil cooling and a number of parameters, such as fresh weight, height, the number of leaves, and root length, were evaluated upon harvest. Under soil cooling, significant differences were observed in the average fresh weight (P<0.05) and positive development of the roots, shoots, and leaves of lettuce. Janthinobacterium (8.142%), Rhodoplanes (1.991%), Arthrospira (1.138%), Flavobacterium (0.857%), Sphingomonas (0.790%), Mycoplana (0.726%), and Pseudomonas (0.688%) were the dominant bacterial genera present in cooled soil. Key soil fungal communities, including Pseudaleuria (18.307%), Phoma (9.968%), Eocronartium (3.527%), Trichosporon (1.791%), and Pyrenochaeta (0.171%), were also recovered from cooled soil. The present results demonstrate that the growth of temperate crops is dependent on soil temperature, which subsequently affects the abundance and diversity of soil microbial communities that maintain the growth of temperate crops at low soil temperatures.
Topics: Bacteria; Biodiversity; Crops, Agricultural; Fungi; Lactuca; Malaysia; Soil; Soil Microbiology; Temperature; Tropical Climate
PubMed: 29709895
DOI: 10.1264/jsme2.ME17181 -
Mycoses Oct 2018The taxonomy of the fungi that produce human infections and that develop asexual fruiting bodies in culture has become very complex. Recent molecular studies have... (Review)
Review
The taxonomy of the fungi that produce human infections and that develop asexual fruiting bodies in culture has become very complex. Recent molecular studies have produced dramatic changes in their classification. Currently, the coelomycetes traditionally included in Sphaeropsidales and Melanconiales are in fact distributed across at least three different classes of the Phylum Ascomycota. Approximately 1000 genera and 7000 species have been grouped in the classes Dothideomycetes, Leotiomycetes and Sordariomycetes and their proper identification can only be made by analysing their DNA sequences and comparing them with those corresponding to type strains available in the adequate databases. To facilitate this task for scientists and clinicians involved in the study of these complex, and every day more numerous taxa, we have updated the knowledge about the taxonomy of the commonest coelomycetes of clinical interest with the aim of improving their identification and antifungal treatment.
Topics: Ascomycota; DNA, Fungal; Humans; Molecular Diagnostic Techniques; Mycoses; Sequence Analysis, DNA
PubMed: 29693732
DOI: 10.1111/myc.12785 -
Studies in Mycology Jun 2018Fresh collections, type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, , and sequences were used to evaluate the...
Fresh collections, type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-ITS-LSU rDNA, , and sequences were used to evaluate the boundaries of in a strict sense and of several related genera of the . Two species are recognised in and 19 in . The monotypic genera , , , , and are described as new. is here included as its generic type (= ), which is lecto- and epitypified. and are combined in . Asexual morphs of , where known, are all pyrenochaeta- or phoma-like. Comparison of the phylogenetic analyses of the ITS-LSU and combined matrices demonstrate that at least sequences should be added whenever possible to improve phylogenetic resolution of the tree backbone; in addition, the introns should be added as well to improve delimitation of closely related species.
PubMed: 29276320
DOI: 10.1016/j.simyco.2017.11.002 -
Journal of Clinical Microbiology Mar 2018Mycetoma, a chronic and mutilating subcutaneous infection recognized by the WHO as a neglected tropical disease, has been reported in >25 countries in Africa, Asia, and...
Mycetoma, a chronic and mutilating subcutaneous infection recognized by the WHO as a neglected tropical disease, has been reported in >25 countries in Africa, Asia, and South America. In Latin America, is assumed to be the prevalent fungal agent. Recent molecular studies have shown that this is an environmental saprobe in Europe, where it is rarely implicated in human diseases. The aim of the present paper is to establish the identity of Latin American cases ascribed to Three cases analyzed were caused by Data on an additional 21 strains in the literature revealed that rather than is responsible for most cases of black grain eumycetoma in Latin America.
Topics: Adult; Antifungal Agents; Ascomycota; DNA, Fungal; DNA, Ribosomal; Female; Humans; Itraconazole; Latin America; Madurella; Male; Mexico; Middle Aged; Mycetoma; Phylogeny; Sequence Analysis, DNA; Treatment Outcome
PubMed: 29263207
DOI: 10.1128/JCM.01723-17 -
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 -
Fungal Genetics and Biology : FG & B Sep 2017Fungi generate a wide range of extracellular hydrolytic and oxidative enzymes and reactive metabolites, collectively known as the secretome, that synergistically drive... (Comparative Study)
Comparative Study
Fungi generate a wide range of extracellular hydrolytic and oxidative enzymes and reactive metabolites, collectively known as the secretome, that synergistically drive plant litter decomposition in the environment. While secretome studies of model organisms have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates, particularly filamentous Ascomycetes, or directly compared temporal patterns of enzyme utilization among diverse species. Thus, the mechanisms of carbon (C) degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of iTRAQ proteomics and extracellular enzyme activity assays to compare the protein composition of the secretomes of four manganese(II)-oxidizing Ascomycete fungi over a three-week time course. We demonstrate that the fungi exhibit striking differences in the regulation of extracellular lignocellulose-degrading enzymes among species and over time, revealing species-specific and temporal shifts in C utilization strategies as they degrade the same substrate. Specifically, our findings suggest that Alternaria alternata SRC1lrK2f and Paraconiothyrium sporulosum AP3s5-JAC2a employ sequential enzyme secretion patterns concomitant with decreasing resource availability. Stagonospora sp. SRC1lsM3a preferentially degrades proteinaceous substrate before switching to carbohydrates, and Pyrenochaeta sp. DS3sAY3a utilizes primarily peptidases to aggressively attack carbon sources in a concentrated burst. This work highlights the diversity of operative metabolic strategies among understudied yet ubiquitous cellulose-degrading Ascomycetes, enhancing our understanding of their contribution to C turnover in the environment.
Topics: Analysis of Variance; Ascomycota; Carbon; Fungal Proteins; Hydrolysis; Lignin; Manganese; Plants; Proteomics; Species Specificity
PubMed: 28676260
DOI: 10.1016/j.fgb.2017.06.004 -
Persoonia Dec 2016Novel species of fungi described in this study include those from various countries as follows: : on sp., on , (incl. gen. nov.) on , on , on , on , on sp.,...
Novel species of fungi described in this study include those from various countries as follows: : on sp., on , (incl. gen. nov.) on , on , on , on , on sp., on , on , on , on , on , on , (incl. gen. nov.) on the cocoon of an unidentified microlepidoptera, (incl. gen. nov.) on , on , (incl. gen. nov.) on sp., on dead ant, on sp., on sp., on , on , on sp., on , on , on , on , on , on , on , on sp., on , on sp., and on : (incl gen. nov.) on , (incl. gen. nov.) on , (endophyte from ), on sandy soil, on soil, on dead leaves and sticks, on decayed angiosperm trunk, on , and on . : on : from submerged wood, and from fluids of a wastewater treatment plant. : , , , and (all on ): on dead semi-woody stems, and from soil. : from hypersaline soil. : from leaves of sp. : on × , (incl. gen. nov.) on , on , (incl. gen. nov.) on , on sp., (incl. gen. nov.) as hyperparasite on on leaves of , (incl. gen. nov.) on , and on : from soil. : on , on sp., (incl. gen. nov.) on , on , on , on , and on : from needle litter of cf. . : on leaves of sp., (incl. gen. nov.) on , (incl. gen. nov.) on sp., and (incl. gen. nov.) on : on bare ground in field, on small fallen branches of , in humus of , and (incl. gen. nov.) from soil. : on , and on . : from dead stromata of on bark of . : from house dust. : (incl. gen. nov.) on sp, on leaf litter, from human toenail, from knee wound of a soldier, and from sp Morphological and culture characteristics along with DNA barcodes are provided.
PubMed: 28232766
DOI: 10.3767/003158516X694499 -
Journal of Clinical Microbiology Feb 2017Human infections by coelomycetous fungi are becoming more frequent and range from superficial to systemic dissemination. Traumatic implantation of contaminated plant...
Human infections by coelomycetous fungi are becoming more frequent and range from superficial to systemic dissemination. Traumatic implantation of contaminated plant material is the most common cause. The typical morphological feature of these fungi is the production of asexual spores (conidia) within fruiting bodies called conidiomata. This study aimed to determine the distribution of the coelomycetes in clinical samples by a phenotypic and molecular study of a large set of isolates received from a U.S. reference mycological institution and by obtaining the in vitro antifungal susceptibility pattern of nine antifungals against a selected group of isolates. A total of 230 isolates were identified by sequencing the D1 and D2 domains of the large subunit (LSU) nuclear ribosomal RNA (nrRNA) gene and by morphological characterization. Eleven orders of the phylum Ascomycota were identified: Pleosporales (the largest group; 66.1%), Botryosphaeriales (19.57%), Glomerellales (4.35%), Diaporthales (3.48%), Xylariales (2.17%), Hysteriales and Valsariales (0.87%), and Capnodiales, Helotiales, Hypocreales and Magnaporthales (0.43% each). The most prevalent species were Neoscytalidium dimidiatum, Paraconiothyrium spp., Phoma herbarum, Didymella heteroderae, and Epicoccum sorghinum The most common anatomical site of isolation was superficial tissue (66.5%), followed by the respiratory tract (17.4%). Most of the isolates tested were susceptible to the majority of antifungals, and only flucytosine showed poor antifungal activity.
Topics: Antifungal Agents; Ascomycota; Cluster Analysis; DNA, Fungal; DNA, Ribosomal; Genes, rRNA; Humans; Microbial Sensitivity Tests; Mycoses; Phylogeny; RNA, Fungal; RNA, Ribosomal; Sequence Analysis, DNA; United States; Wounds and Injuries
PubMed: 27927918
DOI: 10.1128/JCM.02221-16 -
Plant Diversity Feb 2017var. s is an important medicinal plant with abundant saponins that are widely used in the pharmaceuticals industry. It is unclear why the levels of active ingredients...
var. s is an important medicinal plant with abundant saponins that are widely used in the pharmaceuticals industry. It is unclear why the levels of active ingredients increase as these plants age. We speculated that the concentrations of those components in the rhizomes are mediated by fungal endophytes. To test this hypothesis, we took both culture-dependent and -independent (metagenomics) approaches to analyze the communities of endophytic fungi that inhabit those rhizomes in plants of different age classes (four, six, and eight years old). In all, 147 isolates representing 18 fungal taxa were obtained from 270 segments (90 per age class). Based on morphological and genetic characteristics, (46.55% frequency of occurrence) was the predominant endophyte, followed by sp. (8.66%) and (6.81%). Colonization of endophytic fungi was maximized in the eight-year-old rhizomes (33.33%) when compared with four-year-old (21.21%) and six-year-old (15.15%) rhizomes. Certain fungal species were present only at particular ages. For example, sp., sp., sp., , sp., , , and were found only in the oldest plants. Analysis of (metagenomics) community DNA extracted from different-aged samples revealed that, at the class level, the majority of fungi had the highest sequence similarity to members of Sordariomycetes, followed by Eurotiomycetes and Saccharomycetes. These results were mostly in accord with those we obtained using culture methods. Fungal diversity and richness also changed over time. Our investigation is the first to show that the diversity of fungi in rhizomes of var. is altered as plants age, and our findings provide a foundation for future examinations of useful compounds.
PubMed: 30159492
DOI: 10.1016/j.pld.2016.11.006 -
Frontiers in Microbiology 2016Opportunistic subcutaneous fungal infections are increasing nowadays due to the growing number of medical conditions causing immunosuppression, especially organ...
Opportunistic subcutaneous fungal infections are increasing nowadays due to the growing number of medical conditions causing immunosuppression, especially organ transplant. The incidence rate of subcutaneous phaeohyphomycosis is very low. Most studies found are case reports. They showed a wide variation of clinical presentations. Pyrenochaeta romeroi, a fungus from the Dematiaceae group is a saprophyte found in soil and plants and a possible causative agent of phaeohyphomycosis. We present a rare case of subcutaneous phaeohyphomycosis caused by P. romeroi mimicking a synovial cyst in a diabetic patient.
PubMed: 27630637
DOI: 10.3389/fmicb.2016.01405